From 79336d46c5f7575619992e5d004d561166751c36 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 4 Apr 2022 15:52:31 +0200 Subject: [PATCH 001/214] [Clean Context] first naive implementation of a functionality to clean not wanted contextes from one result. This implementation simply verifies the main title of the results start with a given string --- .../oa/graph/clean/CleanContextSparkJob.java | 113 +++++++++++++ .../graph/input_clean_context_parameters.json | 37 ++++ .../dhp/oa/graph/clean/CleanContextTest.java | 159 ++++++++++++++++++ .../clean/publication_clean_context.json | 7 + 4 files changed, 316 insertions(+) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_context_parameters.json create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/publication_clean_context.json diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java new file mode 100644 index 000000000..b20dcb67b --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java @@ -0,0 +1,113 @@ +package eu.dnetlib.dhp.oa.graph.clean; + +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.Context; +import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.schema.oaf.OafEntity; +import eu.dnetlib.dhp.schema.oaf.Result; +import eu.dnetlib.dhp.utils.ISLookupClientFactory; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.Serializable; +import java.util.List; +import java.util.Optional; +import java.util.stream.Collectors; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +public class CleanContextSparkJob implements Serializable { + private static final Logger log = LoggerFactory.getLogger(CleanContextSparkJob.class); + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + public static void main(String[] args) throws Exception { + + String jsonConfiguration = IOUtils + .toString( + CleanContextSparkJob.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/input_clean_context_parameters.json")); + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + String inputPath = parser.get("inputPath"); + log.info("inputPath: {}", inputPath); + + String workingPath = parser.get("workingPath"); + log.info("workingPath: {}", workingPath); + + String contextId = parser.get("contextId"); + log.info("contextId: {}", contextId); + + String verifyParam = parser.get("verifyParam"); + log.info("verifyParam: {}", verifyParam); + + + String graphTableClassName = parser.get("graphTableClassName"); + log.info("graphTableClassName: {}", graphTableClassName); + + Class entityClazz = (Class) Class.forName(graphTableClassName); + + + SparkConf conf = new SparkConf(); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + + cleanContext(spark, contextId, verifyParam, inputPath, entityClazz, workingPath); + }); + } + + private static void cleanContext(SparkSession spark, String contextId, String verifyParam, String inputPath, Class entityClazz, String workingPath) { + Dataset res = spark + .read() + .textFile(inputPath) + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, entityClazz), + Encoders.bean(entityClazz)); + + res.map((MapFunction) r -> { + if(!r.getTitle() + .stream() + .filter(t -> t.getQualifier().getClassid() + .equalsIgnoreCase(ModelConstants.MAIN_TITLE_QUALIFIER.getClassid())) + .anyMatch(t -> t.getValue().toLowerCase().startsWith(verifyParam.toLowerCase()))){ + return r; + } + r.setContext(r.getContext().stream().filter(c -> !c.getId().split("::")[0] + .equalsIgnoreCase(contextId)).collect(Collectors.toList())); + return r; + } ,Encoders.bean(entityClazz)) + .write() + .mode(SaveMode.Overwrite) + .option("compression","gzip") + .json(workingPath); + + spark.read().textFile(workingPath).map((MapFunction) value -> OBJECT_MAPPER.readValue(value, entityClazz), + Encoders.bean(entityClazz)) + .write() + .mode(SaveMode.Overwrite) + .option("compression","gzip") + .json(inputPath); + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_context_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_context_parameters.json new file mode 100644 index 000000000..9b1588283 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_context_parameters.json @@ -0,0 +1,37 @@ +[ + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "when true will stop SparkSession after job execution", + "paramRequired": false + }, + { + "paramName": "in", + "paramLongName": "inputPath", + "paramDescription": "the path to the graph data dump to read", + "paramRequired": true + }, + { + "paramName": "wp", + "paramLongName": "workingPath", + "paramDescription": "the path to store the output graph", + "paramRequired": true + }, + { + "paramName": "ci", + "paramLongName": "contextId", + "paramDescription": "url to the ISLookup Service", + "paramRequired": true + }, + { + "paramName": "class", + "paramLongName": "graphTableClassName", + "paramDescription": "class name moelling the graph table", + "paramRequired": true + },{ + "paramName": "vf", + "paramLongName": "verifyParam", + "paramDescription": "url to the ISLookup Service", + "paramRequired": true +} +] diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java new file mode 100644 index 000000000..bba814346 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java @@ -0,0 +1,159 @@ +package eu.dnetlib.dhp.oa.graph.clean; + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.oa.graph.dump.Constants; +import eu.dnetlib.dhp.oa.graph.dump.DumpJobTest; +import eu.dnetlib.dhp.oa.graph.dump.DumpProducts; +import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.dump.oaf.Instance; +import eu.dnetlib.dhp.schema.dump.oaf.OpenAccessRoute; +import eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Software; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import org.apache.commons.io.FileUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.List; +import java.util.Locale; + +public class CleanContextTest { + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path workingDir; + + private static final Logger log = LoggerFactory.getLogger(CleanContextTest.class); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files.createTempDirectory(DumpJobTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(DumpJobTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(DumpJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + public void testResultClean() throws Exception { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/clean/publication_clean_context.json") + .getPath(); + final String prefix = "gcube "; + + + spark.read().textFile(sourcePath).map((MapFunction) r -> OBJECT_MAPPER.readValue(r, Publication.class), Encoders.bean(Publication.class)) + .write().json(workingDir.toString() + "/publication"); + + + CleanContextSparkJob.main(new String[] { + "--isSparkSessionManaged", Boolean.FALSE.toString(), + "--inputPath", workingDir.toString() + "/publication", + "-graphTableClassName", Publication.class.getCanonicalName(), + "-workingPath", workingDir.toString() + "/working", + "-contextId","sobigdata", + "-verifyParam","gCube " + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/publication") + .map(item -> OBJECT_MAPPER.readValue(item, Publication.class)); + + Assertions.assertEquals(7, tmp.count()); + + //original result with sobigdata context and gcube as starting string in the main title for the publication + Assertions.assertEquals(0, + tmp.filter(p->p.getId().equals("50|DansKnawCris::0224aae28af558f21768dbc6439c7a95")).collect().get(0).getContext().size()); + + //original result with sobigdata context without gcube as starting string in the main title for the publication + Assertions.assertEquals(1, + tmp.filter(p->p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")).collect().get(0).getContext().size()); + Assertions.assertEquals("sobigdata::projects::2",tmp.filter(p->p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")).collect().get(0).getContext().get(0).getId() ); + + //original result with sobigdata context with gcube as starting string in the subtitle + Assertions.assertEquals(1, + tmp.filter(p->p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")).collect().get(0).getContext().size()); + Assertions.assertEquals("sobigdata::projects::2",tmp.filter(p->p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")).collect().get(0).getContext().get(0).getId() ); + List titles = tmp.filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")).collect().get(0).getTitle(); + Assertions.assertEquals(1, titles.size()); + Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix) ); + Assertions.assertEquals("subtitle", titles.get(0).getQualifier().getClassid()); + + //original result with sobigdata context with gcube not as starting string in the main title + Assertions.assertEquals(1, + tmp.filter(p->p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")).collect().get(0).getContext().size()); + Assertions.assertEquals("sobigdata::projects::1",tmp.filter(p->p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")).collect().get(0).getContext().get(0).getId() ); + titles = tmp.filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")).collect().get(0).getTitle(); + Assertions.assertEquals(1, titles.size()); + Assertions.assertFalse(titles.get(0).getValue().toLowerCase().startsWith(prefix) ); + Assertions.assertTrue(titles.get(0).getValue().toLowerCase().contains(prefix.trim()) ); + Assertions.assertEquals("main title", titles.get(0).getQualifier().getClassid()); + + //original result with sobigdata in context and also other contexts with gcube as starting string for the main title + Assertions.assertEquals(1, + tmp.filter(p->p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")).collect().get(0).getContext().size()); + Assertions.assertEquals("dh-ch",tmp.filter(p->p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")).collect().get(0).getContext().get(0).getId() ); + titles = tmp.filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")).collect().get(0).getTitle(); + Assertions.assertEquals(1, titles.size()); + Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix) ); + Assertions.assertEquals("main title", titles.get(0).getQualifier().getClassid()); + + //original result with multiple main title one of which whith gcube as starting string and with 2 contextes + Assertions.assertEquals(1, + tmp.filter(p->p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")).collect().get(0).getContext().size()); + Assertions.assertEquals("dh-ch",tmp.filter(p->p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")).collect().get(0).getContext().get(0).getId() ); + titles = tmp.filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")).collect().get(0).getTitle(); + Assertions.assertEquals(2, titles.size()); + Assertions.assertTrue(titles.stream().anyMatch(t -> t.getQualifier().getClassid().equals("main title") && t.getValue().toLowerCase().startsWith(prefix)) ); + + + //original result without sobigdata in context with gcube as starting string for the main title + Assertions.assertEquals(1, + tmp.filter(p->p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")).collect().get(0).getContext().size()); + Assertions.assertEquals("dh-ch",tmp.filter(p->p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")).collect().get(0).getContext().get(0).getId() ); + titles = tmp.filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")).collect().get(0).getTitle(); + Assertions.assertEquals(2, titles.size()); + + Assertions.assertTrue(titles.stream().anyMatch(t -> t.getQualifier().getClassid().equals("main title") && t.getValue().toLowerCase().startsWith(prefix))); + + + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/publication_clean_context.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/publication_clean_context.json new file mode 100644 index 000000000..b7c51d810 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/publication_clean_context.json @@ -0,0 +1,7 @@ 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Nach Pausanias"},{"dataInfo":null,"qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"value":"gcube xiv die worter άγαλμα eίχών ξόανον ανδρuις und verwandte in ihren verschiedenen beziehungen nach pausanias"}],"journal":{"conferencedate":null,"conferenceplace":null,"dataInfo":null,"edition":null,"ep":null,"iss":null,"issnLinking":null,"issnOnline":"2196-7008","issnPrinted":"0031-7985","name":"Philologus","sp":null,"vol":"24"}} \ No newline at end of file From e6124896709ab5087bf69c6905df96f641d0c8ab Mon Sep 17 00:00:00 2001 From: Serafeim Chatzopoulos Date: Wed, 6 Apr 2022 19:12:44 +0300 Subject: [PATCH 002/214] Add fileGZip collector plugin and respective test --- .../dhp/collection/CollectorWorker.java | 3 + .../collection/plugin/CollectorPlugin.java | 2 +- .../fileGZip/FileGZipCollectorPlugin.java | 49 ++++++++++++++++ .../fileGZip/FileGZipCollectorPluginTest.java | 55 ++++++++++++++++++ .../plugin/fileGZip/opendoar.xml.gz | Bin 0 -> 372515 bytes 5 files changed, 108 insertions(+), 1 deletion(-) create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/fileGZip/FileGZipCollectorPlugin.java create mode 100644 dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/fileGZip/FileGZipCollectorPluginTest.java create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/plugin/fileGZip/opendoar.xml.gz diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java index 2ea3f35cc..03f592169 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java @@ -7,6 +7,7 @@ import java.io.IOException; import java.util.Optional; import java.util.concurrent.atomic.AtomicInteger; +import eu.dnetlib.dhp.collection.plugin.fileGZip.FileGZipCollectorPlugin; import org.apache.hadoop.fs.FileSystem; import org.apache.hadoop.fs.Path; import org.apache.hadoop.io.IntWritable; @@ -114,6 +115,8 @@ public class CollectorWorker extends ReportingJob { return new OaiCollectorPlugin(clientParams); case rest_json2xml: return new RestCollectorPlugin(clientParams); + case fileGZip: + return new FileGZipCollectorPlugin(); case other: final CollectorPlugin.NAME.OTHER_NAME plugin = Optional .ofNullable(api.getParams().get("other_plugin_type")) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java index 841d42fea..7d6aaaff8 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java @@ -10,7 +10,7 @@ import eu.dnetlib.dhp.common.collection.CollectorException; public interface CollectorPlugin { enum NAME { - oai, other, rest_json2xml; + oai, other, rest_json2xml, fileGZip; public enum OTHER_NAME { mdstore_mongodb_dump, mdstore_mongodb diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/fileGZip/FileGZipCollectorPlugin.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/fileGZip/FileGZipCollectorPlugin.java new file mode 100644 index 000000000..38f328890 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/fileGZip/FileGZipCollectorPlugin.java @@ -0,0 +1,49 @@ +package eu.dnetlib.dhp.collection.plugin.fileGZip; + +import eu.dnetlib.dhp.collection.ApiDescriptor; +import eu.dnetlib.dhp.collection.plugin.CollectorPlugin; +import eu.dnetlib.dhp.common.aggregation.AggregatorReport; +import eu.dnetlib.dhp.common.collection.CollectorException; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.*; +import java.net.URL; +import java.util.Optional; +import java.util.stream.Stream; +import java.util.zip.GZIPInputStream; + +public class FileGZipCollectorPlugin implements CollectorPlugin { + + private static final Logger log = LoggerFactory.getLogger(FileGZipCollectorPlugin.class); + + public static final String ENCODING = "encoding"; + + @Override + public Stream collect(ApiDescriptor api, AggregatorReport report) throws CollectorException { + + final String baseUrl = Optional + .ofNullable(api.getBaseUrl()) + .orElseThrow( () -> new CollectorException("missing baseUrl, required by the fileGZip collector plugin")); + + log.info("fileGZip.baseUrl: {}", baseUrl); + + final String encoding = Optional + .ofNullable(api.getParams().get(ENCODING)) + .orElseThrow(() -> new CollectorException(String.format("missing parameter '%s', required by the fileGZip collector plugin", ENCODING))); + + log.info("fileGZip.encoding: {}", encoding); + + try { + + InputStream gzipStream = new GZIPInputStream(new FileInputStream(baseUrl)); + Reader decoder = new InputStreamReader(gzipStream, encoding); + BufferedReader reader = new BufferedReader(decoder); + + return reader.lines(); + + } catch (Exception e) { + throw new CollectorException(e); + } + } +} diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/fileGZip/FileGZipCollectorPluginTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/fileGZip/FileGZipCollectorPluginTest.java new file mode 100644 index 000000000..793a5b04c --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/fileGZip/FileGZipCollectorPluginTest.java @@ -0,0 +1,55 @@ +package eu.dnetlib.dhp.collection.plugin.fileGZip; + +import eu.dnetlib.dhp.collection.ApiDescriptor; +import eu.dnetlib.dhp.common.aggregation.AggregatorReport; +import eu.dnetlib.dhp.common.collection.CollectorException; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.util.HashMap; +import java.util.stream.Stream; + +public class FileGZipCollectorPluginTest { + + private static final Logger log = LoggerFactory.getLogger(FileGZipCollectorPluginTest.class); + + private final ApiDescriptor api = new ApiDescriptor(); + private FileGZipCollectorPlugin plugin; + + private static final String SPLIT_ON_ELEMENT = "repository"; + private static final String ENCODING = "UTF-8"; + + @BeforeEach + public void setUp() { + + final String gzipFile = this + .getClass() + .getResource("/eu/dnetlib/dhp/collection/plugin/fileGZip/opendoar.xml.gz") + .getFile(); + + System.out.println(gzipFile); + api.setBaseUrl(gzipFile); + + HashMap params = new HashMap<>(); + params.put("splitOnElement", SPLIT_ON_ELEMENT); + params.put("encoding", ENCODING); + + api.setParams(params); + + plugin = new FileGZipCollectorPlugin(); + } + + @Test + void test() throws CollectorException { + + final Stream stream = plugin.collect(api, new AggregatorReport()); + + stream.limit(10).forEach(s -> { + Assertions.assertTrue(s.length() > 0); + log.info(s); + }); + } +} diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/plugin/fileGZip/opendoar.xml.gz b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/plugin/fileGZip/opendoar.xml.gz new file mode 100644 index 0000000000000000000000000000000000000000..f783b69e7ba5339a691817fb012566c5c3e95dca GIT binary patch literal 372515 zcmV)hK%>7OiwFqZ<@Q?u18;C;Ze(v^axQpnYyj-NTa)8hb}sg=i1`mY>Oox4~6u_83{Ajdgj z%i(jRBR!PnwWswL^h> z_4PAVsXZgi(ztF|{jZ;WxPDdbJR`r{`^BGpbv|a+@%h0ep=0Bl=>Ent_>qvWG(Ntw 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set"}],"version":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"1"}} \ No newline at end of file From 8a72de401167f522e1f825a7b9c31d3e2ecb4179 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 4 May 2022 10:10:56 +0200 Subject: [PATCH 049/214] [EOSCTag] modified workflow to execute all the steps and not only the last one --- .../resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml index 4c34886e6..f34c5110f 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml @@ -29,7 +29,7 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] From 846975c8866d341112d3b6f10c1f533a75abf8cc Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 5 May 2022 11:37:58 +0200 Subject: [PATCH 050/214] [eosc_services] using the correct 'keyword' subject type, as declared in the dnet:subject_classification_typologies vocabulary --- .../resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql index 81eab8163..c4096f90d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql @@ -47,7 +47,7 @@ SELECT d.namespaceprefix AS namespaceprefix, NULL AS odnumberofitems, NULL AS odnumberofitemsdate, - (SELECT array_agg(s|| '###keywords@@@dnet:subject_classification_typologies') + (SELECT array_agg(s|| '###keyword@@@dnet:subject_classification_typologies') FROM UNNEST( ARRAY( SELECT trim(s) From cfbbcaf7c42c85f8bd9095ecd97c5adadf049bdf Mon Sep 17 00:00:00 2001 From: Antonis Lempesis Date: Fri, 6 May 2022 12:49:36 +0300 Subject: [PATCH 051/214] commented out indi_result_org_country_collab --- .../scripts/step16-createIndicatorsTables.sql | 24 +++++++++---------- 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql index 24e6bff7e..09b24f741 100755 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql @@ -82,18 +82,18 @@ on r.id= tmp.id; compute stats indi_funded_result_with_fundref; -create table indi_result_org_country_collab stored as parquet as -with tmp as -(select o.id as id, o.country , ro.id as result,r.type from organization o -join result_organization ro on o.id=ro.organization -join result r on r.id=ro.id where o.country <> 'UNKNOWN') -select o1.id org1,o2.country country2, o1.type, count(distinct o1.result) as collaborations -from tmp as o1 -join tmp as o2 on o1.result=o2.result -where o1.id<>o2.id and o1.country<>o2.country -group by o1.id, o1.type,o2.country; - -compute stats indi_result_org_country_collab; +-- create table indi_result_org_country_collab stored as parquet as +-- with tmp as +-- (select o.id as id, o.country , ro.id as result,r.type from organization o +-- join result_organization ro on o.id=ro.organization +-- join result r on r.id=ro.id where o.country <> 'UNKNOWN') +-- select o1.id org1,o2.country country2, o1.type, count(distinct o1.result) as collaborations +-- from tmp as o1 +-- join tmp as o2 on o1.result=o2.result +-- where o1.id<>o2.id and o1.country<>o2.country +-- group by o1.id, o1.type,o2.country; +-- +-- compute stats indi_result_org_country_collab; create table indi_result_org_collab stored as parquet as with tmp as From 61b4c19e6554b7b9ed53d1d1966240ce956c1211 Mon Sep 17 00:00:00 2001 From: Antonis Lempesis Date: Fri, 6 May 2022 12:52:10 +0300 Subject: [PATCH 052/214] restored indi_result_org_country_collab, removed indi_result_org_collab --- .../scripts/step16-createIndicatorsTables.sql | 40 +++++++++---------- 1 file changed, 20 insertions(+), 20 deletions(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql index 09b24f741..c40618510 100755 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql @@ -82,31 +82,31 @@ on r.id= tmp.id; compute stats indi_funded_result_with_fundref; --- create table indi_result_org_country_collab stored as parquet as --- with tmp as --- (select o.id as id, o.country , ro.id as result,r.type from organization o --- join result_organization ro on o.id=ro.organization --- join result r on r.id=ro.id where o.country <> 'UNKNOWN') --- select o1.id org1,o2.country country2, o1.type, count(distinct o1.result) as collaborations --- from tmp as o1 --- join tmp as o2 on o1.result=o2.result --- where o1.id<>o2.id and o1.country<>o2.country --- group by o1.id, o1.type,o2.country; --- --- compute stats indi_result_org_country_collab; - -create table indi_result_org_collab stored as parquet as +create table indi_result_org_country_collab stored as parquet as with tmp as -(select o.id, ro.id as result,r.type from organization o +(select o.id as id, o.country , ro.id as result,r.type from organization o join result_organization ro on o.id=ro.organization -join result r on r.id=ro.id) -select o1.id org1,o2.id org2, o1.type, count(distinct o1.result) as collaborations +join result r on r.id=ro.id where o.country <> 'UNKNOWN') +select o1.id org1,o2.country country2, o1.type, count(distinct o1.result) as collaborations from tmp as o1 join tmp as o2 on o1.result=o2.result -where o1.id<>o2.id -group by o1.id, o2.id, o1.type; +where o1.id<>o2.id and o1.country<>o2.country +group by o1.id, o1.type,o2.country; -compute stats indi_result_org_collab; +compute stats indi_result_org_country_collab; + +-- create table indi_result_org_collab stored as parquet as +-- with tmp as +-- (select o.id, ro.id as result,r.type from organization o +-- join result_organization ro on o.id=ro.organization +-- join result r on r.id=ro.id) +-- select o1.id org1,o2.id org2, o1.type, count(distinct o1.result) as collaborations +-- from tmp as o1 +-- join tmp as o2 on o1.result=o2.result +-- where o1.id<>o2.id +-- group by o1.id, o2.id, o1.type; +-- +-- compute stats indi_result_org_collab; create table indi_funder_country_collab stored as parquet as with tmp as (select funder, project, country from organization_projects op From a056f59c6e3839986120ecbb4847f96851c73f78 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 9 May 2022 12:51:35 +0200 Subject: [PATCH 053/214] [UsageCount] make it as an action set as it should be, plus changed the test to make them work as well now --- .../usagestats/SparkAtomicActionUsageJob.java | 19 +++++++++++++------ .../SparkAtomicActionCountJobTest.java | 19 ++++++++----------- 2 files changed, 21 insertions(+), 17 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java index c284ad8bd..9428f5c59 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java @@ -9,7 +9,10 @@ import java.util.Arrays; import java.util.List; import java.util.Optional; +import eu.dnetlib.dhp.schema.action.AtomicAction; import org.apache.commons.io.IOUtils; +import org.apache.hadoop.io.Text; +import org.apache.hadoop.mapred.SequenceFileOutputFormat; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.MapGroupsFunction; @@ -29,6 +32,7 @@ import eu.dnetlib.dhp.schema.oaf.DataInfo; import eu.dnetlib.dhp.schema.oaf.Measure; import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; +import scala.Tuple2; /** * created the Atomic Action for each type of results @@ -73,7 +77,7 @@ public class SparkAtomicActionUsageJob implements Serializable { spark -> { removeOutputDir(spark, outputPath); prepareResults(dbname, spark, workingPath); - prepareActionSet(spark, workingPath, outputPath); + writeActionSet(spark, workingPath, outputPath); }); } @@ -89,7 +93,7 @@ public class SparkAtomicActionUsageJob implements Serializable { .json(workingPath); } - public static void prepareActionSet(SparkSession spark, String inputPath, String outputPath) { + public static void writeActionSet(SparkSession spark, String inputPath, String outputPath) { readPath(spark, inputPath, UsageStatsModel.class) .groupByKey((MapFunction) us -> us.getResult_id(), Encoders.STRING()) .mapGroups((MapGroupsFunction) (k, it) -> { @@ -105,10 +109,13 @@ public class SparkAtomicActionUsageJob implements Serializable { res.setMeasures(getMeasure(first.getDownloads(), first.getViews())); return res; }, Encoders.bean(Result.class)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); + .toJavaRDD() + .map(p -> new AtomicAction(p.getClass(), p)) + .mapToPair( + aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), + new Text(OBJECT_MAPPER.writeValueAsString(aa)))) + .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class); + } private static List getMeasure(Long downloads, Long views) { diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionCountJobTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionCountJobTest.java index 7cc9eb326..1af408629 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionCountJobTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionCountJobTest.java @@ -8,14 +8,12 @@ import java.nio.file.Files; import java.nio.file.Path; import java.util.stream.Collectors; +import eu.dnetlib.dhp.schema.action.AtomicAction; import org.apache.commons.io.FileUtils; import org.apache.hadoop.io.Text; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.Row; import org.apache.spark.sql.SparkSession; import org.junit.jupiter.api.AfterAll; import org.junit.jupiter.api.Assertions; @@ -26,8 +24,6 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob; -import eu.dnetlib.dhp.schema.action.AtomicAction; import eu.dnetlib.dhp.schema.oaf.Result; public class SparkAtomicActionCountJobTest { @@ -72,19 +68,20 @@ public class SparkAtomicActionCountJobTest { @Test void testMatch() { String usageScoresPath = getClass() - .getResource("/eu/dnetlib/dhp/actionmanager/usagestats/usagestatsdb") - .getPath(); + .getResource("/eu/dnetlib/dhp/actionmanager/usagestats/usagestatsdb") + .getPath(); - SparkAtomicActionUsageJob.prepareActionSet(spark, usageScoresPath, workingDir.toString() + "/actionSet"); + SparkAtomicActionUsageJob.writeActionSet(spark, usageScoresPath, workingDir.toString() + "/actionSet"); final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/actionSet") - .map(usm -> OBJECT_MAPPER.readValue(usm, Result.class)); + JavaRDD tmp = sc.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class) + .map(usm -> OBJECT_MAPPER.readValue(usm._2.getBytes(), AtomicAction.class)) + .map(aa -> (Result) aa.getPayload()); Assertions.assertEquals(9, tmp.count()); + tmp.foreach(r -> Assertions.assertEquals(2, r.getMeasures().size())); tmp .foreach( From 89657a0b78d214017e11613ee4e34b0af805330f Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 9 May 2022 14:43:27 +0200 Subject: [PATCH 054/214] [UsageCount] refactoring --- .../usagestats/SparkAtomicActionUsageJob.java | 14 +++++++------- .../usagestats/SparkAtomicActionCountJobTest.java | 14 +++++++------- 2 files changed, 14 insertions(+), 14 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java index 9428f5c59..5f099b8f2 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java @@ -9,7 +9,6 @@ import java.util.Arrays; import java.util.List; import java.util.Optional; -import eu.dnetlib.dhp.schema.action.AtomicAction; import org.apache.commons.io.IOUtils; import org.apache.hadoop.io.Text; import org.apache.hadoop.mapred.SequenceFileOutputFormat; @@ -27,6 +26,7 @@ import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.schema.action.AtomicAction; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.DataInfo; import eu.dnetlib.dhp.schema.oaf.Measure; @@ -109,12 +109,12 @@ public class SparkAtomicActionUsageJob implements Serializable { res.setMeasures(getMeasure(first.getDownloads(), first.getViews())); return res; }, Encoders.bean(Result.class)) - .toJavaRDD() - .map(p -> new AtomicAction(p.getClass(), p)) - .mapToPair( - aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), - new Text(OBJECT_MAPPER.writeValueAsString(aa)))) - .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class); + .toJavaRDD() + .map(p -> new AtomicAction(p.getClass(), p)) + .mapToPair( + aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), + new Text(OBJECT_MAPPER.writeValueAsString(aa)))) + .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class); } diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionCountJobTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionCountJobTest.java index 1af408629..8aa718bae 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionCountJobTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionCountJobTest.java @@ -8,7 +8,6 @@ import java.nio.file.Files; import java.nio.file.Path; import java.util.stream.Collectors; -import eu.dnetlib.dhp.schema.action.AtomicAction; import org.apache.commons.io.FileUtils; import org.apache.hadoop.io.Text; import org.apache.spark.SparkConf; @@ -24,6 +23,7 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.schema.action.AtomicAction; import eu.dnetlib.dhp.schema.oaf.Result; public class SparkAtomicActionCountJobTest { @@ -68,20 +68,20 @@ public class SparkAtomicActionCountJobTest { @Test void testMatch() { String usageScoresPath = getClass() - .getResource("/eu/dnetlib/dhp/actionmanager/usagestats/usagestatsdb") - .getPath(); + .getResource("/eu/dnetlib/dhp/actionmanager/usagestats/usagestatsdb") + .getPath(); SparkAtomicActionUsageJob.writeActionSet(spark, usageScoresPath, workingDir.toString() + "/actionSet"); final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); - JavaRDD tmp = sc.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class) - .map(usm -> OBJECT_MAPPER.readValue(usm._2.getBytes(), AtomicAction.class)) - .map(aa -> (Result) aa.getPayload()); + JavaRDD tmp = sc + .sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class) + .map(usm -> OBJECT_MAPPER.readValue(usm._2.getBytes(), AtomicAction.class)) + .map(aa -> (Result) aa.getPayload()); Assertions.assertEquals(9, tmp.count()); - tmp.foreach(r -> Assertions.assertEquals(2, r.getMeasures().size())); tmp .foreach( From 378020e30af91206126377b0d7716452f0fb6f22 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 9 May 2022 16:05:06 +0200 Subject: [PATCH 055/214] [eosc_services] unit test adaptation --- .../raw/MigrateDbEntitiesApplicationTest.java | 4 ++-- .../dhp/oa/graph/hostedbymap/datasource.json | 2 +- ...atasourceorganization_resultset_entry.json | 2 +- .../graph/raw/services_resultset_entry.json | 14 +------------- .../sample/datasource/datasource_10.json.gz | Bin 2227 -> 2211 bytes 5 files changed, 5 insertions(+), 17 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java index 948dbfa50..9048a22ea 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java @@ -136,8 +136,8 @@ public class MigrateDbEntitiesApplicationTest { assertEquals(getValueAsString("releaseenddate", fields), ds.getReleasestartdate()); assertEquals(getValueAsString("missionstatementurl", fields), ds.getMissionstatementurl()); - assertEquals(false, ds.getDataprovider().getValue()); - assertEquals(false, ds.getServiceprovider().getValue()); + assertEquals(null, ds.getDataprovider()); + assertEquals(null, ds.getServiceprovider()); assertEquals(getValueAsString("databaseaccesstype", fields), ds.getDatabaseaccesstype()); assertEquals(getValueAsString("datauploadtype", fields), ds.getDatauploadtype()); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/datasource.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/datasource.json index 5eb41bff5..3bf560135 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/datasource.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/datasource.json @@ -7,4 +7,4 @@ 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Geography)"}],"versioning":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":true},"websiteurl":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"http://www.snsb.info/dwb_biocase.html"}} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/datasourceorganization_resultset_entry.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/datasourceorganization_resultset_entry.json index 06b0d483b..a41fac8b8 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/datasourceorganization_resultset_entry.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/datasourceorganization_resultset_entry.json @@ -1,6 +1,6 @@ [ { - "field": "datasource", + "field": "service", "type": "string", "value": "openaire____::revistasunicauca" }, diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/services_resultset_entry.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/services_resultset_entry.json index 445334de5..3614c5266 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/services_resultset_entry.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/services_resultset_entry.json @@ -1,6 +1,6 @@ [ { - "field": "datasourceid", + "field": "id", "type": "string", "value": "274269ac6f3b::2579-5449" }, @@ 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zz>H7dv$rwh&!f@M+^Rcsqjz}?!FF@(5C$`T^@C!gQDrD-PS<=|ahBv(ZB)c_zDGz5 zx!;2dXCGspS&NTgmA-SB!dhIPiZGmz6j#u^EF4*k?$8%F@;LMajs%W8XFuL+>u@1~ zY0OQ77EG`ZyMxcp9gtp-Uib&nd-|Tejr4wD+OYY(l3(seJCNS(=7;;>Sg+=FL3&Sx z^wQv{{6urQ+m!k@70*NAPw+$fJ@Z|NeAvCd$-FN7w4Q_wG9;Np>2m3=7D@c?g{AP5 zMpxs>Mt%stf5cl1>(Cd7_c-(f;sxS8XFuKx@w(7jNM~rJL@RX};2UE=zUS-?kS~xg z`~&hmeb3&8e6vo`l5hD&hw(*=Gj`c(a<41e{ebr_JN=;3?l&)*or_EV8|1s)d^8nb zq*C#mrq6Pz?`6$vmrs3@bZlHcWTcJtVlYV66WyG8;qX7xap(rM+des5*M2t|>}&VK z|L-B-pO}%n^25)=+t0rYE1#}^d`}ciDZTRitNF13W2`BzQ>^_urILhIs1VZ4PX?2MS?}bzawLj{{=-lef9_000885 Bh;RS^ From 77bc9863e95ac55fcd5f12039e623d8686ae65b9 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 9 May 2022 16:06:04 +0200 Subject: [PATCH 056/214] [openorgs] mapping parent/child relations without massaging the semantic labels --- .../dhp/oa/graph/raw/MigrateDbEntitiesApplication.java | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java index 552125307..63fa8b7e0 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java @@ -741,10 +741,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i final Relation r = new Relation(); r.setRelType(ORG_ORG_RELTYPE); r.setSubRelType(ModelConstants.RELATIONSHIP); - r - .setRelClass( - rs.getString("type").equalsIgnoreCase("parent") ? ModelConstants.IS_PARENT_OF - : ModelConstants.IS_CHILD_OF); + r.setRelClass(rs.getString("type")); r.setSource(orgId1); r.setTarget(orgId2); r.setCollectedfrom(collectedFrom); From 2a8e0fb72f10ca5a1ae4496e24649e9e86d9f1e7 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 9 May 2022 16:06:04 +0200 Subject: [PATCH 057/214] [openorgs] mapping parent/child relations without massaging the semantic labels --- .../dhp/oa/graph/raw/MigrateDbEntitiesApplication.java | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java index b5801ca5c..3e23e3493 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java @@ -711,10 +711,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i final Relation r = new Relation(); r.setRelType(ORG_ORG_RELTYPE); r.setSubRelType(ModelConstants.RELATIONSHIP); - r - .setRelClass( - rs.getString("type").equalsIgnoreCase("parent") ? ModelConstants.IS_PARENT_OF - : ModelConstants.IS_CHILD_OF); + r.setRelClass(rs.getString("type")); r.setSource(orgId1); r.setTarget(orgId2); r.setCollectedfrom(collectedFrom); From 23334479bb7e5219ae14541e41abd7ee3903a3e2 Mon Sep 17 00:00:00 2001 From: Antonis Lempesis Date: Wed, 11 May 2022 13:05:52 +0300 Subject: [PATCH 058/214] removed yet another collab, added more orgs in monitor --- .../scripts/step16-createIndicatorsTables.sql | 24 ++++++------- .../scripts/step20-createMonitorDB.sql | 35 +++++++++++-------- 2 files changed, 33 insertions(+), 26 deletions(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql index c40618510..db40cf973 100755 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql @@ -82,18 +82,18 @@ on r.id= tmp.id; compute stats indi_funded_result_with_fundref; -create table indi_result_org_country_collab stored as parquet as -with tmp as -(select o.id as id, o.country , ro.id as result,r.type from organization o -join result_organization ro on o.id=ro.organization -join result r on r.id=ro.id where o.country <> 'UNKNOWN') -select o1.id org1,o2.country country2, o1.type, count(distinct o1.result) as collaborations -from tmp as o1 -join tmp as o2 on o1.result=o2.result -where o1.id<>o2.id and o1.country<>o2.country -group by o1.id, o1.type,o2.country; - -compute stats indi_result_org_country_collab; +-- create table indi_result_org_country_collab stored as parquet as +-- with tmp as +-- (select o.id as id, o.country , ro.id as result,r.type from organization o +-- join result_organization ro on o.id=ro.organization +-- join result r on r.id=ro.id where o.country <> 'UNKNOWN') +-- select o1.id org1,o2.country country2, o1.type, count(distinct o1.result) as collaborations +-- from tmp as o1 +-- join tmp as o2 on o1.result=o2.result +-- where o1.id<>o2.id and o1.country<>o2.country +-- group by o1.id, o1.type,o2.country; +-- +-- compute stats indi_result_org_country_collab; -- create table indi_result_org_collab stored as parquet as -- with tmp as diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql index bcc9f0b5d..4dd434101 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql @@ -18,20 +18,27 @@ create table TARGET.result stored as parquet as select * from SOURCE.result r where exists (select 1 from SOURCE.result_concepts rc where rc.id=r.id) union all select * from SOURCE.result r where exists (select 1 from SOURCE.result_organization ro where ro.id=r.id and ro.organization in ( - 'openorgs____::759d59f05d77188faee99b7493b46805', - 'openorgs____::b84450f9864182c67b8611b5593f4250', - 'openorgs____::d41cf6bd4ab1b1362a44397e0b95c975', - 'openorgs____::eadc8da90a546e98c03f896661a2e4d4', - 'openorgs____::d2a09b9d5eabb10c95f9470e172d05d2', - 'openorgs____::d169c7407dd417152596908d48c11460', - 'openorgs____::1ec924b1759bb16d0a02f2dad8689b21', - 'openorgs____::2fb1e47b4612688d9de9169d579939a7', - 'openorgs____::759d59f05d77188faee99b7493b46805', - 'openorgs____::cad284878801b9465fa51a95b1d779db', - 'openorgs____::eadc8da90a546e98c03f896661a2e4d4', - 'openorgs____::c0286313e36479eff8676dba9b724b40' - -- ,'openorgs____::c80a8243a5e5c620d7931c88d93bf17a' -- Paris Diderot - ) )) foo; + 'openorgs____::b84450f9864182c67b8611b5593f4250', --"Athena Research and Innovation Center In Information Communication & Knowledge Technologies', --ARC" + 'openorgs____::d41cf6bd4ab1b1362a44397e0b95c975', --National Research Council + 'openorgs____::d2a09b9d5eabb10c95f9470e172d05d2', --??? Not exists ?? + 'openorgs____::d169c7407dd417152596908d48c11460', --Masaryk University + 'openorgs____::1ec924b1759bb16d0a02f2dad8689b21', --University of Belgrade + 'openorgs____::2fb1e47b4612688d9de9169d579939a7', --University of Helsinki + 'openorgs____::759d59f05d77188faee99b7493b46805', --University of Minho + 'openorgs____::cad284878801b9465fa51a95b1d779db', --Universidad Politécnica de Madrid + 'openorgs____::eadc8da90a546e98c03f896661a2e4d4', --University of Göttingen + 'openorgs____::c0286313e36479eff8676dba9b724b40', --National and Kapodistrian University of Athens + -- 'openorgs____::c80a8243a5e5c620d7931c88d93bf17a', --Université Paris Diderot + 'openorgs____::c08634f0a6b0081c3dc6e6c93a4314f3', --Bielefeld University + 'openorgs____::6fc85e4a8f7ecaf4b0c738d010e967ea', --University of Southern Denmark + 'openorgs____::3d6122f87f9a97a99d8f6e3d73313720', --Humboldt-Universität zu Berlin + 'openorgs____::16720ada63d0fa8ca41601feae7d1aa5', --TU Darmstadt + 'openorgs____::ccc0a066b56d2cfaf90c2ae369df16f5', --KU Leuven + 'openorgs____::4c6f119632adf789746f0a057ed73e90', --University of the Western Cape + 'openorgs____::ec3665affa01aeafa28b7852c4176dbd', --Rudjer Boskovic Institute + 'openorgs____::5f31346d444a7f06a28c880fb170b0f6', --Ghent University + 'openorgs____::2dbe47117fd5409f9c61620813456632', --University of Luxembourg + 'openorgs____::6445d7758d3a40c4d997953b6632a368', --National Institute of Informatics (NII) ) )) foo; compute stats TARGET.result; create table TARGET.result_citations stored as parquet as select * from SOURCE.result_citations orig where exists (select 1 from TARGET.result r where r.id=orig.id); From 5d3b4a9c2529b12b2be1d62f137eff83e6accc0d Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 11 May 2022 14:13:06 +0200 Subject: [PATCH 059/214] [graph merge beta] merge datasource originalid, collectedfrom, and pid lists --- .../graph/merge/MergeGraphTableSparkJob.java | 31 ++++++++++++++++++- .../merge/MergeGraphTableSparkJobTest.java | 19 +++++++++++- .../dhp/oa/graph/merge/datasource_cris.json | 6 +++- .../graph/merge/datasource_openaire2.0.json | 5 ++- 4 files changed, 57 insertions(+), 4 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/merge/MergeGraphTableSparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/merge/MergeGraphTableSparkJob.java index 474944260..5f2cd6808 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/merge/MergeGraphTableSparkJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/merge/MergeGraphTableSparkJob.java @@ -5,6 +5,7 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.util.*; import java.util.stream.Collectors; +import java.util.stream.Stream; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; @@ -136,7 +137,7 @@ public class MergeGraphTableSparkJob { /** * Datasources involved in the merge operation doesn't obey to the infra precedence policy, but relies on a custom * behaviour that, given two datasources from beta and prod returns the one from prod with the highest - * compatibility among the two. + * compatibility among the two. Furthermore, the procedure merges the collectedfrom, originalId, and pid lists. * * @param p datasource from PROD * @param b datasource from BETA @@ -160,9 +161,37 @@ public class MergeGraphTableSparkJob { List list = Arrays.asList(dp.getOpenairecompatibility(), db.getOpenairecompatibility()); dp.setOpenairecompatibility(Collections.min(list, new DatasourceCompatibilityComparator())); + dp + .setCollectedfrom( + Stream + .concat( + Optional + .ofNullable(dp.getCollectedfrom()) + .map(Collection::stream) + .orElse(Stream.empty()), + Optional + .ofNullable(db.getCollectedfrom()) + .map(Collection::stream) + .orElse(Stream.empty())) + .distinct() // relies on KeyValue.equals + .collect(Collectors.toList())); + + dp.setOriginalId(mergeLists(dp.getOriginalId(), db.getOriginalId())); + dp.setPid(mergeLists(dp.getPid(), db.getPid())); + return (P) dp; } + private static final List mergeLists(final List... lists) { + return Arrays + .stream(lists) + .filter(Objects::nonNull) + .flatMap(List::stream) + .filter(Objects::nonNull) + .distinct() + .collect(Collectors.toList()); + } + private static

P mergeWithPriorityToPROD(Optional

p, Optional b) { if (b.isPresent() & !p.isPresent()) { return (P) b.get(); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/merge/MergeGraphTableSparkJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/merge/MergeGraphTableSparkJobTest.java index 2d28ee305..7dcb4bca4 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/merge/MergeGraphTableSparkJobTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/merge/MergeGraphTableSparkJobTest.java @@ -2,6 +2,7 @@ package eu.dnetlib.dhp.oa.graph.merge; import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertNotNull; import java.io.IOException; import java.util.Optional; @@ -25,7 +26,23 @@ class MergeGraphTableSparkJobTest { } @Test - void testMergeDatasources() throws IOException { + void testMerge() throws IOException { + Datasource d = MergeGraphTableSparkJob + .mergeDatasource( + d("datasource_cris.json"), + d("datasource_openaire2.0.json")); + + assertEquals("10|274269ac6f3b::2a2e2793b500f3f7b47ef24b1a9277b7", d.getId()); + assertNotNull(d.getOriginalId()); + assertEquals(2, d.getOriginalId().size()); + assertNotNull(d.getCollectedfrom()); + assertEquals(2, d.getCollectedfrom().size()); + assertNotNull(d.getPid()); + assertEquals(1, d.getPid().size()); + } + + @Test + void testMergeCompatibility() throws IOException { assertEquals( "openaire-cris_1.1", MergeGraphTableSparkJob diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/merge/datasource_cris.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/merge/datasource_cris.json index 6f2b7aa7d..64627dd2b 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/merge/datasource_cris.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/merge/datasource_cris.json @@ -1 +1,5 @@ -{ "id": "10|274269ac6f3b::2a2e2793b500f3f7b47ef24b1a9277b7", "openairecompatibility": { "classid": "openaire-cris_1.1" }} \ No newline at end of file +{ "id": "10|274269ac6f3b::2a2e2793b500f3f7b47ef24b1a9277b7", "openairecompatibility": { "classid": "openaire-cris_1.1" }, + "originalId": ["eurocrisdris::1234"], + "collectedfrom": [{"key": "eurocrisdris::2b29d08e383ff4cd8a2b6b226ce37e38", "value": "Directory of Research Information System (DRIS)"}], + "pid": [{"value": "10.1010.xyx", "qualifier": {"classid": "doi"}}] +} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/merge/datasource_openaire2.0.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/merge/datasource_openaire2.0.json index e2db47943..cb2916a27 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/merge/datasource_openaire2.0.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/merge/datasource_openaire2.0.json @@ -1 +1,4 @@ -{ "id": "10|274269ac6f3b::2a2e2793b500f3f7b47ef24b1a9277b7", "openairecompatibility": { "classid": "openaire2.0" }} \ No newline at end of file +{ "id": "10|274269ac6f3b::2a2e2793b500f3f7b47ef24b1a9277b7", "openairecompatibility": { "classid": "openaire2.0" }, + "originalId": ["opendoar____::1234"], + "collectedfrom": [{"key": "openaire____::47ce9e9f4fad46e732cff06419ecaabb", "value": "OpenDOAR"}] +} \ No newline at end of file From ca8d26bcb49e7eca531fffff1d05338be411b9b2 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Wed, 11 May 2022 15:29:57 +0200 Subject: [PATCH 060/214] added better filter for openCitations --- .../sx/graph/SparkConvertRDDtoDataset.scala | 13 +- .../dhp/sx/graph/pangaea/PangaeaUtils.scala | 136 ------------------ .../SparkGeneratePanagaeaDataset.scala | 58 -------- .../dhp/sx/pangaea/PangaeaTransformTest.scala | 29 ---- 4 files changed, 11 insertions(+), 225 deletions(-) delete mode 100644 dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/pangaea/PangaeaUtils.scala delete mode 100644 dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/pangaea/SparkGeneratePanagaeaDataset.scala delete mode 100644 dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/pangaea/PangaeaTransformTest.scala diff --git a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala index f13c14da5..7c3a212ac 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala @@ -7,6 +7,7 @@ import org.apache.commons.io.IOUtils import org.apache.spark.SparkConf import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession} import org.slf4j.{Logger, LoggerFactory} +import scala.collection.JavaConverters._ object SparkConvertRDDtoDataset { @@ -94,21 +95,29 @@ object SparkConvertRDDtoDataset { log.info("Converting Relation") val relationSemanticFilter = List( - "cites", - "iscitedby", +// "cites", +// "iscitedby", "merges", "ismergedin", "HasAmongTopNSimilarDocuments", "IsAmongTopNSimilarDocuments" ) + val rddRelation = spark.sparkContext .textFile(s"$sourcePath/relation") .map(s => mapper.readValue(s, classOf[Relation])) .filter(r => r.getDataInfo != null && r.getDataInfo.getDeletedbyinference == false) .filter(r => r.getSource.startsWith("50") && r.getTarget.startsWith("50")) + //filter OpenCitations relations + .filter(r => r.getCollectedfrom!= null && r.getCollectedfrom.size()>0 && !r.getCollectedfrom.asScala.exists(k => "opencitations".equalsIgnoreCase(k.getValue))) .filter(r => !relationSemanticFilter.exists(k => k.equalsIgnoreCase(r.getRelClass))) spark.createDataset(rddRelation).as[Relation].write.mode(SaveMode.Overwrite).save(s"$relPath") + + + + + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/pangaea/PangaeaUtils.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/pangaea/PangaeaUtils.scala deleted file mode 100644 index 23f4da6c7..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/pangaea/PangaeaUtils.scala +++ /dev/null @@ -1,136 +0,0 @@ -package eu.dnetlib.dhp.sx.graph.pangaea - -import org.apache.spark.sql.expressions.Aggregator -import org.apache.spark.sql.{Encoder, Encoders} -import org.json4s -import org.json4s.DefaultFormats -import org.json4s.jackson.JsonMethods.parse - -import java.util.regex.Pattern -import scala.language.postfixOps -import scala.xml.{Elem, Node, XML} - -case class PangaeaDataModel( - identifier: String, - title: List[String], - objectType: List[String], - creator: List[String], - publisher: List[String], - dataCenter: List[String], - subject: List[String], - language: String, - rights: String, - parent: String, - relation: List[String], - linkage: List[(String, String)] -) {} - -object PangaeaUtils { - - def toDataset(input: String): PangaeaDataModel = { - implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats - lazy val json: json4s.JValue = parse(input) - val xml = (json \ "xml").extract[String] - parseXml(xml) - } - - def findDOIInRelation(input: List[String]): List[String] = { - val pattern = Pattern.compile("\\b(10[.][0-9]{4,}(?:[.][0-9]+)*\\/(?:(?![\"&\\'<>])\\S)+)\\b") - input - .map(i => { - val matcher = pattern.matcher(i) - if (matcher.find()) - matcher.group(0) - else - null - }) - .filter(i => i != null) - } - - def attributeOpt(attribute: String, node: Node): Option[String] = - node.attribute(attribute) flatMap (_.headOption) map (_.text) - - def extractLinkage(node: Elem): List[(String, String)] = { - (node \ "linkage") - .map(n => (attributeOpt("type", n), n.text)) - .filter(t => t._1.isDefined) - .map(t => (t._1.get, t._2))(collection.breakOut) - } - - def parseXml(input: String): PangaeaDataModel = { - val xml = XML.loadString(input) - - val identifier = (xml \ "identifier").text - val title: List[String] = (xml \ "title").map(n => n.text)(collection.breakOut) - val pType: List[String] = (xml \ "type").map(n => n.text)(collection.breakOut) - val creators: List[String] = (xml \ "creator").map(n => n.text)(collection.breakOut) - val publisher: List[String] = (xml \ "publisher").map(n => n.text)(collection.breakOut) - val dataCenter: List[String] = (xml \ "dataCenter").map(n => n.text)(collection.breakOut) - val subject: List[String] = (xml \ "subject").map(n => n.text)(collection.breakOut) - val language = (xml \ "language").text - val rights = (xml \ "rights").text - val parentIdentifier = (xml \ "parentIdentifier").text - val relation: List[String] = (xml \ "relation").map(n => n.text)(collection.breakOut) - val relationFiltered = findDOIInRelation(relation) - val linkage: List[(String, String)] = extractLinkage(xml) - - PangaeaDataModel( - identifier, - title, - pType, - creators, - publisher, - dataCenter, - subject, - language, - rights, - parentIdentifier, - relationFiltered, - linkage - ) - } - - def getDatasetAggregator(): Aggregator[(String, PangaeaDataModel), PangaeaDataModel, PangaeaDataModel] = - new Aggregator[(String, PangaeaDataModel), PangaeaDataModel, PangaeaDataModel] { - - override def zero: PangaeaDataModel = null - - override def reduce(b: PangaeaDataModel, a: (String, PangaeaDataModel)): PangaeaDataModel = { - if (b == null) - a._2 - else { - if (a == null) - b - else { - if (b.title != null && b.title.nonEmpty) - b - else - a._2 - - } - } - } - - override def merge(b1: PangaeaDataModel, b2: PangaeaDataModel): PangaeaDataModel = { - if (b1 == null) - b2 - else { - if (b2 == null) - b1 - else { - if (b1.title != null && b1.title.nonEmpty) - b1 - else - b2 - - } - } - } - override def finish(reduction: PangaeaDataModel): PangaeaDataModel = reduction - - override def bufferEncoder: Encoder[PangaeaDataModel] = Encoders.kryo[PangaeaDataModel] - - override def outputEncoder: Encoder[PangaeaDataModel] = Encoders.kryo[PangaeaDataModel] - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/pangaea/SparkGeneratePanagaeaDataset.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/pangaea/SparkGeneratePanagaeaDataset.scala deleted file mode 100644 index 8ff8a8b1a..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/pangaea/SparkGeneratePanagaeaDataset.scala +++ /dev/null @@ -1,58 +0,0 @@ -package eu.dnetlib.dhp.sx.graph.pangaea - -import eu.dnetlib.dhp.application.ArgumentApplicationParser -import org.apache.spark.rdd.RDD -import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession} -import org.apache.spark.{SparkConf, SparkContext} -import org.slf4j.{Logger, LoggerFactory} -import scala.collection.JavaConverters._ - -import scala.io.Source - -object SparkGeneratePanagaeaDataset { - - def main(args: Array[String]): Unit = { - val logger: Logger = LoggerFactory.getLogger(getClass) - val conf: SparkConf = new SparkConf() - val parser = new ArgumentApplicationParser( - Source - .fromInputStream( - getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/pangaea/pangaea_to_dataset.json") - ) - .mkString - ) - parser.parseArgument(args) - - val spark: SparkSession = - SparkSession - .builder() - .config(conf) - .appName(SparkGeneratePanagaeaDataset.getClass.getSimpleName) - .master(parser.get("master")) - .getOrCreate() - - parser.getObjectMap.asScala.foreach(s => logger.info(s"${s._1} -> ${s._2}")) - logger.info("Converting sequential file into Dataset") - val sc: SparkContext = spark.sparkContext - - val workingPath: String = parser.get("workingPath") - - implicit val pangaeaEncoders: Encoder[PangaeaDataModel] = Encoders.kryo[PangaeaDataModel] - - val inputRDD: RDD[PangaeaDataModel] = - sc.textFile(s"$workingPath/update").map(s => PangaeaUtils.toDataset(s)) - - spark - .createDataset(inputRDD) - .as[PangaeaDataModel] - .map(s => (s.identifier, s))(Encoders.tuple(Encoders.STRING, pangaeaEncoders)) - .groupByKey(_._1)(Encoders.STRING) - .agg(PangaeaUtils.getDatasetAggregator().toColumn) - .map(s => s._2) - .write - .mode(SaveMode.Overwrite) - .save(s"$workingPath/dataset") - - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/pangaea/PangaeaTransformTest.scala b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/pangaea/PangaeaTransformTest.scala deleted file mode 100644 index b90827e81..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/pangaea/PangaeaTransformTest.scala +++ /dev/null @@ -1,29 +0,0 @@ -package eu.dnetlib.dhp.sx.pangaea - -import eu.dnetlib.dhp.sx.graph.pangaea.PangaeaUtils -import org.junit.jupiter.api.Test - -import java.util.TimeZone -import java.text.SimpleDateFormat -import java.util.Date -import scala.io.Source -class PangaeaTransformTest { - - - - @Test - def test_dateStamp() :Unit ={ - - - - val d = new Date() - - val s:String = s"${new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss.SSS")format d}Z" - println(s) - - - val xml = Source.fromInputStream(getClass.getResourceAsStream("input.xml")).mkString - println(PangaeaUtils.parseXml(xml)) - } - -} From c25134f28d8586591284a1740f8bd89b7cc0b0d5 Mon Sep 17 00:00:00 2001 From: antleb Date: Thu, 12 May 2022 14:55:47 +0300 Subject: [PATCH 061/214] fixed typo --- .../graph/stats/oozie_app/scripts/step20-createMonitorDB.sql | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql index 4dd434101..2dde7171f 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql @@ -38,7 +38,8 @@ create table TARGET.result stored as parquet as 'openorgs____::ec3665affa01aeafa28b7852c4176dbd', --Rudjer Boskovic Institute 'openorgs____::5f31346d444a7f06a28c880fb170b0f6', --Ghent University 'openorgs____::2dbe47117fd5409f9c61620813456632', --University of Luxembourg - 'openorgs____::6445d7758d3a40c4d997953b6632a368', --National Institute of Informatics (NII) ) )) foo; + 'openorgs____::6445d7758d3a40c4d997953b6632a368', --National Institute of Informatics (NII) + ) )) foo; compute stats TARGET.result; create table TARGET.result_citations stored as parquet as select * from SOURCE.result_citations orig where exists (select 1 from TARGET.result r where r.id=orig.id); From e4eac1d20bd8981939fe4efbbd94c26d680d6999 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 13 May 2022 11:01:33 +0200 Subject: [PATCH 062/214] [EOSC TAG] added code to remove EOSC Jupyter Notebook from subjects and put EOSC as classid in the qualifier --- .../java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java | 11 +++++++++-- .../dhp/sx/graph/SparkConvertRDDtoDataset.scala | 12 +++++------- 2 files changed, 14 insertions(+), 9 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java index 561e1d57e..e8c79e11d 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java @@ -30,7 +30,7 @@ public class SparkEoscTag { public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); public static final Qualifier EOSC_QUALIFIER = OafMapperUtils .qualifier( - "eosc", + "EOSC", "European Open Science Cloud", ModelConstants.DNET_SUBJECT_TYPOLOGIES, ModelConstants.DNET_SUBJECT_TYPOLOGIES); public static final DataInfo EOSC_DATAINFO = OafMapperUtils @@ -95,7 +95,14 @@ public class SparkEoscTag { if (containsCriteriaNotebook(s)) { sbject.add(EOSC_NOTEBOOK); - + if (sbject.stream().anyMatch(sb -> sb.getValue().equals("EOSC Jupyter Notebook"))){ + sbject = sbject.stream().map(sb -> { + if (sb.getValue().equals("EOSC Jupyter Notebook")){ + return null; + } + return sb; + }).filter(Objects::nonNull).collect(Collectors.toList()); + } } if (containsCriteriaGalaxy(s)) { sbject.add(EOSC_GALAXY); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala index 7c3a212ac..bd970a5cf 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala @@ -103,21 +103,19 @@ object SparkConvertRDDtoDataset { "IsAmongTopNSimilarDocuments" ) - val rddRelation = spark.sparkContext .textFile(s"$sourcePath/relation") .map(s => mapper.readValue(s, classOf[Relation])) .filter(r => r.getDataInfo != null && r.getDataInfo.getDeletedbyinference == false) .filter(r => r.getSource.startsWith("50") && r.getTarget.startsWith("50")) //filter OpenCitations relations - .filter(r => r.getCollectedfrom!= null && r.getCollectedfrom.size()>0 && !r.getCollectedfrom.asScala.exists(k => "opencitations".equalsIgnoreCase(k.getValue))) + .filter(r => + r.getCollectedfrom != null && r.getCollectedfrom.size() > 0 && !r.getCollectedfrom.asScala.exists(k => + "opencitations".equalsIgnoreCase(k.getValue) + ) + ) .filter(r => !relationSemanticFilter.exists(k => k.equalsIgnoreCase(r.getRelClass))) spark.createDataset(rddRelation).as[Relation].write.mode(SaveMode.Overwrite).save(s"$relPath") - - - - - } } From 3fc9efeab6559edc2fd0ad839473a6bbc03c89f5 Mon Sep 17 00:00:00 2001 From: Antonis Lempesis Date: Fri, 13 May 2022 14:28:13 +0300 Subject: [PATCH 063/214] fixed typo, addded open citations and apcs in monitor --- .../oozie_app/scripts/step20-createMonitorDB.sql | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql index 4dd434101..3cf155869 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql @@ -38,15 +38,25 @@ create table TARGET.result stored as parquet as 'openorgs____::ec3665affa01aeafa28b7852c4176dbd', --Rudjer Boskovic Institute 'openorgs____::5f31346d444a7f06a28c880fb170b0f6', --Ghent University 'openorgs____::2dbe47117fd5409f9c61620813456632', --University of Luxembourg - 'openorgs____::6445d7758d3a40c4d997953b6632a368', --National Institute of Informatics (NII) ) )) foo; + 'openorgs____::6445d7758d3a40c4d997953b6632a368' --National Institute of Informatics (NII) + ) )) foo; compute stats TARGET.result; create table TARGET.result_citations stored as parquet as select * from SOURCE.result_citations orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.result_citations; +create table TARGET.result_references_oc stored as parquet as select * from SOURCE.result_references_oc orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.result_references_oc; + +create table TARGET.result_citations_oc stored as parquet as select * from SOURCE.result_citations_oc orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.result_citations_oc; + create table TARGET.result_classifications stored as parquet as select * from SOURCE.result_classifications orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.result_classifications; +create table TARGET.result_apc stored as parquet as select * from SOURCE.result_apc orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.result_apc; + create table TARGET.result_concepts stored as parquet as select * from SOURCE.result_concepts orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.result_concepts; From 0dc33ea391f033578e890a8335dc28d36b8128d8 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 16 May 2022 09:20:30 +0200 Subject: [PATCH 064/214] [openorgs] fixed parent/child query, using the correct semantic labels --- .../dnetlib/dhp/oa/graph/sql/queryParentChildRelsOpenOrgs.sql | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryParentChildRelsOpenOrgs.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryParentChildRelsOpenOrgs.sql index 388fee3f5..0ac843401 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryParentChildRelsOpenOrgs.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryParentChildRelsOpenOrgs.sql @@ -10,4 +10,4 @@ SELECT 'OpenOrgs Database' AS collectedfromname, 'sysimport:crosswalk:entityregistry@@@dnet:provenance_actions' AS provenanceaction FROM relationships -WHERE reltype = 'Child' OR reltype = 'Parent' \ No newline at end of file +WHERE reltype = 'IsChildOf' OR reltype = 'IsParentOf' \ No newline at end of file From 6031acb2e3a0a268ac2a837183d35a54999c5c91 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 16 May 2022 09:20:30 +0200 Subject: [PATCH 065/214] [openorgs] fixed parent/child query, using the correct semantic labels --- .../dnetlib/dhp/oa/graph/sql/queryParentChildRelsOpenOrgs.sql | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryParentChildRelsOpenOrgs.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryParentChildRelsOpenOrgs.sql index 388fee3f5..0ac843401 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryParentChildRelsOpenOrgs.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryParentChildRelsOpenOrgs.sql @@ -10,4 +10,4 @@ SELECT 'OpenOrgs Database' AS collectedfromname, 'sysimport:crosswalk:entityregistry@@@dnet:provenance_actions' AS provenanceaction FROM relationships -WHERE reltype = 'Child' OR reltype = 'Parent' \ No newline at end of file +WHERE reltype = 'IsChildOf' OR reltype = 'IsParentOf' \ No newline at end of file From 46c07e0724f655d8cc86e6af1a4ec34fd19d7d21 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Mon, 16 May 2022 09:39:54 +0200 Subject: [PATCH 066/214] deleted hierarchical rels from ror action set --- .../ror/GenerateRorActionSetJob.java | 62 ++++--------------- 1 file changed, 11 insertions(+), 51 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java index e4d458780..6c76f8a4d 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java @@ -3,7 +3,6 @@ package eu.dnetlib.dhp.actionmanager.ror; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import static eu.dnetlib.dhp.schema.common.ModelConstants.ENTITYREGISTRY_PROVENANCE_ACTION; -import static eu.dnetlib.dhp.schema.common.ModelConstants.ORG_ORG_RELTYPE; import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.dataInfo; import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.field; import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.listKeyValues; @@ -39,7 +38,6 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.actionmanager.ror.model.ExternalIdType; -import eu.dnetlib.dhp.actionmanager.ror.model.Relationship; import eu.dnetlib.dhp.actionmanager.ror.model.RorOrganization; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; @@ -51,7 +49,6 @@ import eu.dnetlib.dhp.schema.oaf.KeyValue; import eu.dnetlib.dhp.schema.oaf.Oaf; import eu.dnetlib.dhp.schema.oaf.Organization; import eu.dnetlib.dhp.schema.oaf.Qualifier; -import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.StructuredProperty; import eu.dnetlib.dhp.utils.DHPUtils; import scala.Tuple2; @@ -64,21 +61,17 @@ public class GenerateRorActionSetJob { private static final String ROR_NS_PREFIX = "ror_________"; - private static final List ROR_COLLECTED_FROM = listKeyValues( - "10|openaire____::993a7ae7a863813cf95028b50708e222", "ROR"); + private static final List ROR_COLLECTED_FROM = listKeyValues("10|openaire____::993a7ae7a863813cf95028b50708e222", "ROR"); - private static final DataInfo ROR_DATA_INFO = dataInfo( - false, "", false, false, ENTITYREGISTRY_PROVENANCE_ACTION, "0.92"); + private static final DataInfo ROR_DATA_INFO = dataInfo(false, "", false, false, ENTITYREGISTRY_PROVENANCE_ACTION, "0.92"); - private static final Qualifier ROR_PID_TYPE = qualifier( - "ROR", "ROR", ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES); + private static final Qualifier ROR_PID_TYPE = qualifier("ROR", "ROR", ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES); public static void main(final String[] args) throws Exception { final String jsonConfiguration = IOUtils - .toString( - GenerateRorActionSetJob.class - .getResourceAsStream("/eu/dnetlib/dhp/actionmanager/ror/action_set_parameters.json")); + .toString(GenerateRorActionSetJob.class + .getResourceAsStream("/eu/dnetlib/dhp/actionmanager/ror/action_set_parameters.json")); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); @@ -116,9 +109,8 @@ public class GenerateRorActionSetJob { readInputPath(spark, inputPath) .map(GenerateRorActionSetJob::convertRorOrg) .flatMap(List::iterator) - .mapToPair( - aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), - new Text(OBJECT_MAPPER.writeValueAsString(aa)))) + .mapToPair(aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), + new Text(OBJECT_MAPPER.writeValueAsString(aa)))) .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class); } @@ -153,12 +145,9 @@ public class GenerateRorActionSetJob { o.setEcnutscode(null); if (r.getCountry() != null) { o - .setCountry( - qualifier( - r.getCountry().getCountryCode(), r - .getCountry() - .getCountryName(), - ModelConstants.DNET_COUNTRY_TYPE, ModelConstants.DNET_COUNTRY_TYPE)); + .setCountry(qualifier(r.getCountry().getCountryCode(), r + .getCountry() + .getCountryName(), ModelConstants.DNET_COUNTRY_TYPE, ModelConstants.DNET_COUNTRY_TYPE)); } else { o.setCountry(null); } @@ -168,38 +157,10 @@ public class GenerateRorActionSetJob { final List> res = new ArrayList<>(); res.add(new AtomicAction<>(Organization.class, o)); - for (final Relationship rorRel : r.getRelationships()) { - if (rorRel.getType().equalsIgnoreCase("parent")) { - final String orgId1 = calculateOpenaireId(r.getId()); - final String orgId2 = calculateOpenaireId(rorRel.getId()); - res - .add( - new AtomicAction<>(Relation.class, - calculateHierarchyRel(orgId1, orgId2, ModelConstants.IS_PARENT_OF))); - res - .add( - new AtomicAction<>(Relation.class, - calculateHierarchyRel(orgId2, orgId1, ModelConstants.IS_CHILD_OF))); - } - } - return res; } - private static Relation calculateHierarchyRel(final String source, final String target, final String relClass) { - final Relation rel = new Relation(); - rel.setSource(source); - rel.setTarget(target); - rel.setRelType(ORG_ORG_RELTYPE); - rel.setSubRelType(ModelConstants.RELATIONSHIP); - rel.setRelClass(relClass); - rel.setCollectedfrom(ROR_COLLECTED_FROM); - rel.setDataInfo(ROR_DATA_INFO); - rel.setLastupdatetimestamp(System.currentTimeMillis()); - return rel; - } - private static String calculateOpenaireId(final String rorId) { return String.format("20|%s::%s", ROR_NS_PREFIX, DHPUtils.md5(rorId)); } @@ -212,8 +173,7 @@ public class GenerateRorActionSetJob { final String type = e.getKey(); final List all = e.getValue().getAll(); if (all != null) { - final Qualifier qualifier = qualifier( - type, type, ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES); + final Qualifier qualifier = qualifier(type, type, ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES); for (final String pid : all) { pids .add(structuredProperty(pid, qualifier, ROR_DATA_INFO)); From 4c50f35c8bc41530f9f2dec095a11f3b3b2eaf9b Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Mon, 16 May 2022 10:29:36 +0200 Subject: [PATCH 067/214] update publication Date format --- .../resources/eu/dnetlib/dhp/sx/provision/scholix_index.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/sx/provision/scholix_index.json b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/sx/provision/scholix_index.json index 93032712a..86e80206f 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/sx/provision/scholix_index.json +++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/sx/provision/scholix_index.json @@ -41,7 +41,8 @@ } }, "publicationDate": { - "type": "keyword" + "type": "date", + "format": "yyyy-MM-dd" }, "relationship": { "properties": { From 997c50078e01e3d64897661cd40fb96421c5e466 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 16 May 2022 12:07:40 +0200 Subject: [PATCH 068/214] [graph grouping] drop relation target path before copying from source --- .../dnetlib/dhp/oa/graph/group/oozie_app/workflow.xml | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/group/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/group/oozie_app/workflow.xml index f77b46105..888a873c5 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/group/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/group/oozie_app/workflow.xml @@ -283,7 +283,15 @@ - + + + + + + + + + From 52cb086506161dfdbd98a331b4ff004e5fb8f2bd Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 16 May 2022 12:07:40 +0200 Subject: [PATCH 069/214] [graph grouping] drop relation target path before copying from source --- .../dnetlib/dhp/oa/graph/group/oozie_app/workflow.xml | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/group/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/group/oozie_app/workflow.xml index f77b46105..888a873c5 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/group/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/group/oozie_app/workflow.xml @@ -283,7 +283,15 @@ - + + + + + + + + + From 8dd5517548d1224e5067c4f48c68bda5817431ca Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 16 May 2022 14:35:24 +0200 Subject: [PATCH 070/214] code formatting --- .../ror/GenerateRorActionSetJob.java | 31 +++++++---- .../doiboost/SparkGenerateDoiBoost.scala | 52 ++++++++----------- 2 files changed, 43 insertions(+), 40 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java index 6c76f8a4d..6b5bed5b8 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java @@ -61,17 +61,21 @@ public class GenerateRorActionSetJob { private static final String ROR_NS_PREFIX = "ror_________"; - private static final List ROR_COLLECTED_FROM = listKeyValues("10|openaire____::993a7ae7a863813cf95028b50708e222", "ROR"); + private static final List ROR_COLLECTED_FROM = listKeyValues( + "10|openaire____::993a7ae7a863813cf95028b50708e222", "ROR"); - private static final DataInfo ROR_DATA_INFO = dataInfo(false, "", false, false, ENTITYREGISTRY_PROVENANCE_ACTION, "0.92"); + private static final DataInfo ROR_DATA_INFO = dataInfo( + false, "", false, false, ENTITYREGISTRY_PROVENANCE_ACTION, "0.92"); - private static final Qualifier ROR_PID_TYPE = qualifier("ROR", "ROR", ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES); + private static final Qualifier ROR_PID_TYPE = qualifier( + "ROR", "ROR", ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES); public static void main(final String[] args) throws Exception { final String jsonConfiguration = IOUtils - .toString(GenerateRorActionSetJob.class - .getResourceAsStream("/eu/dnetlib/dhp/actionmanager/ror/action_set_parameters.json")); + .toString( + GenerateRorActionSetJob.class + .getResourceAsStream("/eu/dnetlib/dhp/actionmanager/ror/action_set_parameters.json")); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); @@ -109,8 +113,9 @@ public class GenerateRorActionSetJob { readInputPath(spark, inputPath) .map(GenerateRorActionSetJob::convertRorOrg) .flatMap(List::iterator) - .mapToPair(aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), - new Text(OBJECT_MAPPER.writeValueAsString(aa)))) + .mapToPair( + aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), + new Text(OBJECT_MAPPER.writeValueAsString(aa)))) .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class); } @@ -145,9 +150,12 @@ public class GenerateRorActionSetJob { o.setEcnutscode(null); if (r.getCountry() != null) { o - .setCountry(qualifier(r.getCountry().getCountryCode(), r - .getCountry() - .getCountryName(), ModelConstants.DNET_COUNTRY_TYPE, ModelConstants.DNET_COUNTRY_TYPE)); + .setCountry( + qualifier( + r.getCountry().getCountryCode(), r + .getCountry() + .getCountryName(), + ModelConstants.DNET_COUNTRY_TYPE, ModelConstants.DNET_COUNTRY_TYPE)); } else { o.setCountry(null); } @@ -173,7 +181,8 @@ public class GenerateRorActionSetJob { final String type = e.getKey(); final List all = e.getValue().getAll(); if (all != null) { - final Qualifier qualifier = qualifier(type, type, ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES); + final Qualifier qualifier = qualifier( + type, type, ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES); for (final String pid : all) { pids .add(structuredProperty(pid, qualifier, ROR_DATA_INFO)); diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala index fbe42ef7c..72b93749b 100644 --- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala +++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala @@ -177,43 +177,37 @@ object SparkGenerateDoiBoost { .map(DoiBoostMappingUtil.fixPublication) .map(p => (p.getId, p)) .groupByKey(_._1) - .reduceGroups((left, right) => - { - //Check left is not null - if (left != null && left._1 != null) - { - //If right is null then return left - if (right == null || right._2 == null) - left - else { - // Here Left and Right are not null - // So we have to merge - val b1 = left._2 - val b2 = right._2 - b1.mergeFrom(b2) - b1.mergeOAFDataInfo(b2) - val authors = AuthorMerger.mergeAuthor(b1.getAuthor, b2.getAuthor) - b1.setAuthor(authors) - if (b2.getId != null && b2.getId.nonEmpty) - b1.setId(b2.getId) - //Return publication Merged - (b1.getId, b1) - } - } + .reduceGroups((left, right) => { + //Check left is not null + if (left != null && left._1 != null) { + //If right is null then return left + if (right == null || right._2 == null) + left else { - // Left is Null so we return right - right + // Here Left and Right are not null + // So we have to merge + val b1 = left._2 + val b2 = right._2 + b1.mergeFrom(b2) + b1.mergeOAFDataInfo(b2) + val authors = AuthorMerger.mergeAuthor(b1.getAuthor, b2.getAuthor) + b1.setAuthor(authors) + if (b2.getId != null && b2.getId.nonEmpty) + b1.setId(b2.getId) + //Return publication Merged + (b1.getId, b1) } + } else { + // Left is Null so we return right + right } - - ) - .filter(s => s!= null && s._2!=null) + }) + .filter(s => s != null && s._2 != null) .map(s => s._2._2) .write .mode(SaveMode.Overwrite) .save(s"$workingDirPath/doiBoostPublicationFiltered") - val affiliationPath = parser.get("affiliationPath") val paperAffiliationPath = parser.get("paperAffiliationPath") From 1dda11e0319eebe5ec3a772b1fafd6c75912ff56 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 16 May 2022 15:53:27 +0200 Subject: [PATCH 071/214] [hb patch] updated map --- .../eu/dnetlib/dhp/datacite/hostedBy_map.json | 15 ++++++++++----- 1 file changed, 10 insertions(+), 5 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/hostedBy_map.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/hostedBy_map.json index 947a9a255..ecae6811a 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/hostedBy_map.json +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/hostedBy_map.json @@ -15,7 +15,7 @@ "official_name": "Aperta TÜBİTAK Open Archive" }, "BL.CAM": { - "openaire_id": "re3data_____::r3d100010620", + "openaire_id": "opendoar____::109", "datacite_name": "Apollo", "official_name": "Apollo" }, @@ -196,7 +196,7 @@ }, "CSIC.DIGITAL": { "openaire_id": "re3data_____::r3d100011076", - "datacite_name": "DIGITAL.CSIC", + "datacite_name": "Digital CSIC", "official_name": "DIGITAL.CSIC" }, "BL.DRI": { @@ -644,6 +644,11 @@ "datacite_name": "PANGAEA", "official_name": "PANGAEA" }, + "TIB.PANGAEA": { + "openaire_id": "re3data_____::r3d100010134", + "datacite_name": "PANGAEA", + "official_name": "PANGAEA" + }, "NASAPDS.NASAPDS": { "openaire_id": "re3data_____::r3d100010121", "datacite_name": "PDS", @@ -896,7 +901,7 @@ }, "FIGSHARE.UCT": { "openaire_id": "re3data_____::r3d100012633", - "datacite_name": "ZivaHub", + "datacite_name": "University of Cape Town (UCT)", "official_name": "ZivaHub" }, "BL.UCLAN": { @@ -1030,9 +1035,9 @@ "official_name": "ZBW Journal Data Archive" }, "CERN.ZENODO": { - "openaire_id": "re3data_____::r3d100010468", + "openaire_id": "opendoar____::2659", "datacite_name": "Zenodo", - "official_name": "Zenodo" + "official_name": "ZENODO" }, "ZBW.ZEW": { "openaire_id": "re3data_____::r3d100010399", From d098ad0d9357e40dff1e0e2d8b07777dca5057a5 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 16 May 2022 15:53:27 +0200 Subject: [PATCH 072/214] [hb patch] updated map --- .../eu/dnetlib/dhp/datacite/hostedBy_map.json | 15 ++++++++++----- 1 file changed, 10 insertions(+), 5 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/hostedBy_map.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/hostedBy_map.json index 947a9a255..ecae6811a 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/hostedBy_map.json +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/hostedBy_map.json @@ -15,7 +15,7 @@ "official_name": "Aperta TÜBİTAK Open Archive" }, "BL.CAM": { - "openaire_id": "re3data_____::r3d100010620", + "openaire_id": "opendoar____::109", "datacite_name": "Apollo", "official_name": "Apollo" }, @@ -196,7 +196,7 @@ }, "CSIC.DIGITAL": { "openaire_id": "re3data_____::r3d100011076", - "datacite_name": "DIGITAL.CSIC", + "datacite_name": "Digital CSIC", "official_name": "DIGITAL.CSIC" }, "BL.DRI": { @@ -644,6 +644,11 @@ "datacite_name": "PANGAEA", "official_name": "PANGAEA" }, + "TIB.PANGAEA": { + "openaire_id": "re3data_____::r3d100010134", + "datacite_name": "PANGAEA", + "official_name": "PANGAEA" + }, "NASAPDS.NASAPDS": { "openaire_id": "re3data_____::r3d100010121", "datacite_name": "PDS", @@ -896,7 +901,7 @@ }, "FIGSHARE.UCT": { "openaire_id": "re3data_____::r3d100012633", - "datacite_name": "ZivaHub", + "datacite_name": "University of Cape Town (UCT)", "official_name": "ZivaHub" }, "BL.UCLAN": { @@ -1030,9 +1035,9 @@ "official_name": "ZBW Journal Data Archive" }, "CERN.ZENODO": { - "openaire_id": "re3data_____::r3d100010468", + "openaire_id": "opendoar____::2659", "datacite_name": "Zenodo", - "official_name": "Zenodo" + "official_name": "ZENODO" }, "ZBW.ZEW": { "openaire_id": "re3data_____::r3d100010399", From f5207885e371e8e538069d2b301094bb0af185b0 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 17 May 2022 15:09:22 +0200 Subject: [PATCH 073/214] [EOSCTag] changed code to remove EOSC Jupyter Notebook and modified test to exclude galaxy + software from the tagging for Galaxy --- .../eu/dnetlib/dhp/bulktag/SparkEoscTag.java | 5 +++-- .../dnetlib/dhp/bulktag/EOSCTagJobTest.java | 21 ++++++------------- .../eosctag/jupyter/software/software_10.json | 2 +- 3 files changed, 10 insertions(+), 18 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java index e8c79e11d..b9de5dd11 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java @@ -95,13 +95,14 @@ public class SparkEoscTag { if (containsCriteriaNotebook(s)) { sbject.add(EOSC_NOTEBOOK); - if (sbject.stream().anyMatch(sb -> sb.getValue().equals("EOSC Jupyter Notebook"))){ + if (sbject.stream().anyMatch(sb -> sb.getValue().equals("EOSC Jupyter Notebook"))) { sbject = sbject.stream().map(sb -> { - if (sb.getValue().equals("EOSC Jupyter Notebook")){ + if (sb.getValue().equals("EOSC Jupyter Notebook")) { return null; } return sb; }).filter(Objects::nonNull).collect(Collectors.toList()); + s.setSubject(sbject); } } if (containsCriteriaGalaxy(s)) { diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java index 55d3939e1..1ea254157 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java @@ -132,7 +132,7 @@ public class EOSCTagJobTest { Assertions .assertEquals( - 2, tmp + 1, tmp .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) .collect() .get(0) @@ -326,7 +326,7 @@ public class EOSCTagJobTest { Assertions .assertEquals( - 2, + 1, tmp .filter( s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Galaxy Workflow"))) @@ -352,21 +352,12 @@ public class EOSCTagJobTest { Assertions .assertEquals( - 6, tmp + 5, tmp .filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11")) .collect() .get(0) .getSubject() .size()); - Assertions - .assertTrue( - tmp - .filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11")) - .collect() - .get(0) - .getSubject() - .stream() - .anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); Assertions .assertEquals( @@ -394,7 +385,7 @@ public class EOSCTagJobTest { Assertions .assertEquals( - 2, + 1, orp .filter( s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Galaxy Workflow"))) @@ -438,14 +429,14 @@ public class EOSCTagJobTest { Assertions .assertEquals( - 3, orp + 2, orp .filter(sw -> sw.getId().equals("50|od______2017::1e400f1747487fd15998735c41a55c72")) .collect() .get(0) .getSubject() .size()); Assertions - .assertTrue( + .assertFalse( orp .filter(sw -> sw.getId().equals("50|od______2017::1e400f1747487fd15998735c41a55c72")) .collect() diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/jupyter/software/software_10.json b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/jupyter/software/software_10.json index 2439dc1b6..2acc856a4 100644 --- a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/jupyter/software/software_10.json +++ b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/jupyter/software/software_10.json @@ -1,4 +1,4 @@ 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This contribution is splitted in two components: one due to the diversity of the population, the other due to its differentiation from the remaining populations. The program may also be used to obtain allelic richness after rarefaction (to a sample size chosen by the investigator) for a set of populations. It can be used in conjunction with the program haplodiv, based on the paper by Pons & Petit 1995, TAG 90, 462-470, which will provide standard errors for the diversity and differentiation parameters. The input file is a text file (see example: rartest.txt), where the first line indicates the number of haplotypes (here it is 18), the number of populations (here it is 4), and the rarefaction size (it should not be larger than the smallest population sample size; here the rarefaction size is 10, and the smallest sample size is 20). Then follows the data for each population (line), with the number of each haplotype in each population (don't use relative frequencies): 18 4 10 1 0 1 0 0 0 1 1 ...(18 columns) 0 1 2 1 1 0 13 0 ... 0 0 8 0 0 3 6 0 ... 1 0 9 0 0 3 7 1 Results can be seen in the output file (rartest.out here; to be printed horizontally). General measures are given first: within population diversity (Hs), total diversity (Ht), and Gst are given, followed by similar measures based on allelic richness. Then you get the results for each population : H, its standard error, allelic richness after rarefaction, the divergence from the other populations (DHs, DHt, DGst, see the paper in Conservation Biology), and the contributions Ct, Cs, Cd followed by the contributions for allelic richness measures. The program is written for an haploid gene but may be used for nuclear genes, assuming Hardy-Weinberg equilibrium. How to proceed when there are several loci? Do not take the mean across Gst or across Contributions. They are ratios, so you should take the mean of the numerator and the mean of the denominator separately. For the denominator: take the mean of hT and Rt-1 across loci. For the numerator: multiply the contributions by hT or Rt-1 (respectively for contributions to diversity or to allelic richness) and take the mean of these products across loci. Then compute the ratio of the two 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into account the distances between haplotypes (ie, that consider all haplotypes equally divergent).[br/] The source file should be an ASCII file (its name should have 8 characters maximum: 12345678.txt) and should include the following information:[br/] First line :[br/] Number of cytotypes Number of populations Number of characters distinguishing the variants (for instance number of polymorphic fragments, or of polymorphic nucleotide sites). The program asks for the number of permutations to be made.[br/] see the example (\\ExamplePermut\\input.txt and \\ExamplePermut\\output.out).[br/] Then follows the number of individuals having a given cytotype (column) in a given population (row). Finally, and without interruption, provide the table of character states for all haplotypes, where each line corresponds to one haplotype, and each column to a character. No column should be empty (no missing haplotype) and each population (row) should be composed of AT LEAST 3 individuals![br/] The output file provides permutated values of Nst in a single row, and the value of the last 5% and last 1%. The mean of the permutated values is also given and should be close to the Gst value (by construction). To test if the observed Nst value is larger than the Gst, we count how many permutated values are larger than the observed Nst. If you have 5% of the permutated values greater than the observed value of Nst, then your test is not significant, otherwise it is and you know the P-value. This is akin to testing if Gst = Nst.[br/] [br/] README CpSSR :[br/] It computes measures of diversity and differenciation from haploid population genetic data, when the difference in number of repeats between alleles is available, and tests whether the differentiation and diversity measures differ from the equivalent measures when the distances between haplotypes is not considered (ie, when all haplotypes are considered equally divergent). The source file should be an ASCII file (its name should have 8 characters maximum: 12345678.txt) and should include the following information:[br/] First line :[br/] Number of cytotypes Number of populations Number of cpSSR loci. The program asks for the number of permutations to be made. See the example (\\ExampleCpSSR\\input.txt and \\ExamplePermut\\CpSSR.out).[br/] Then follows the number of individuals having a given haplotype (column) in a given population (row). Finally, and without interruption, provide the table of length variant states for all haplotypes, where each line corresponds to one haplotype, and each column to a character. No column should be empty (no missing haplotype) and each population (row) should be composed of AT LEAST 3 individuals![br/] The output file provides permutated values of Rst in a single row, and the value of the last 5% and last 1%. The mean of the permutated values is also given and should be close to the Gst value (by construction). To test if the observed Rst value is larger than the Gst, you count how many permutated values are larger than the observed Rst. If you have 5% of the permutated values greater than the observed value of Rst, then your test is not significant, otherwise it is and you know the P-value. 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Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"instancetype":{"classid":"0029","classname":"Software","schemeid":"dnet:publication_resource","schemename":"dnet:publication_resource"},"hostedby":{"key":"opendoar____::1582","value":"ProdInra","dataInfo":null},"url":["http://prodinra.inra.fr/record/402973"],"distributionlocation":"","collectedfrom":{"key":"opendoar____::1582","value":"ProdInra","dataInfo":null},"dateofacceptance":{"value":"2017-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"processingchargeamount":null,"processingchargecurrency":null,"refereed":null}],"documentationUrl":[],"license":[],"codeRepositoryUrl":null,"programmingLanguage":null} From c298c148cb285e73fab8079d63f6bbef4670f653 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 20 May 2022 09:11:46 +0200 Subject: [PATCH 074/214] [CountryPropagation] fix NPE issue --- .../SparkCountryPropagationJob.java | 18 ++++++++++++------ 1 file changed, 12 insertions(+), 6 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/SparkCountryPropagationJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/SparkCountryPropagationJob.java index 56aa953b4..25cd82248 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/SparkCountryPropagationJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/SparkCountryPropagationJob.java @@ -102,21 +102,27 @@ public class SparkCountryPropagationJob { private static MapFunction, R> getCountryMergeFn() { return t -> { Optional.ofNullable(t._2()).ifPresent(r -> { - t._1().getCountry().addAll(merge(t._1().getCountry(), r.getCountrySet())); + if(Optional.ofNullable(t._1().getCountry()).isPresent()) + t._1().getCountry().addAll(merge(t._1().getCountry(), r.getCountrySet())); + else + t._1().setCountry(merge(null, t._2().getCountrySet())); }); return t._1(); }; } private static List merge(List c1, List c2) { - HashSet countries = c1 - .stream() - .map(Qualifier::getClassid) - .collect(Collectors.toCollection(HashSet::new)); + HashSet countries = new HashSet<>(); + if(Optional.ofNullable(c1).isPresent()){ + countries = c1.stream().map(Qualifier::getClassid) + .collect(Collectors.toCollection(HashSet::new)); + } + + HashSet finalCountries = countries; return c2 .stream() - .filter(c -> !countries.contains(c.getClassid())) + .filter(c -> !finalCountries.contains(c.getClassid())) .map(c -> getCountry(c.getClassid(), c.getClassname())) .collect(Collectors.toList()); } From 5e0b8f9b5fa27dc7e595c65753a682b12ec3e553 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 20 May 2022 09:15:53 +0200 Subject: [PATCH 075/214] [CountryPropagation] refactoring --- .../SparkCountryPropagationJob.java | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/SparkCountryPropagationJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/SparkCountryPropagationJob.java index 25cd82248..d9f6433a0 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/SparkCountryPropagationJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/SparkCountryPropagationJob.java @@ -102,7 +102,7 @@ public class SparkCountryPropagationJob { private static MapFunction, R> getCountryMergeFn() { return t -> { Optional.ofNullable(t._2()).ifPresent(r -> { - if(Optional.ofNullable(t._1().getCountry()).isPresent()) + if (Optional.ofNullable(t._1().getCountry()).isPresent()) t._1().getCountry().addAll(merge(t._1().getCountry(), r.getCountrySet())); else t._1().setCountry(merge(null, t._2().getCountrySet())); @@ -113,11 +113,12 @@ public class SparkCountryPropagationJob { private static List merge(List c1, List c2) { HashSet countries = new HashSet<>(); - if(Optional.ofNullable(c1).isPresent()){ - countries = c1.stream().map(Qualifier::getClassid) - .collect(Collectors.toCollection(HashSet::new)); - } - + if (Optional.ofNullable(c1).isPresent()) { + countries = c1 + .stream() + .map(Qualifier::getClassid) + .collect(Collectors.toCollection(HashSet::new)); + } HashSet finalCountries = countries; return c2 From db088cc69c6878e5242e5edb8b8d1ebb894a3136 Mon Sep 17 00:00:00 2001 From: antleb Date: Tue, 7 Jun 2022 04:04:28 +0300 Subject: [PATCH 076/214] fixed *_organization tables --- .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql | 1 + .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql index e1c36cbc0..b5eba6111 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql @@ -127,6 +127,7 @@ CREATE TABLE ${stats_db_name}.result_organization STORED AS PARQUET AS SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS organization FROM ${openaire_db_name}.relation r WHERE r.reltype = 'resultOrganization' + and r.target like '50|%' and r.datainfo.deletedbyinference = false and r.datainfo.invisible=false; CREATE TABLE ${stats_db_name}.result_projects STORED AS PARQUET AS diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql index fa3eca1a9..6fa0e6fdf 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql @@ -93,7 +93,7 @@ where d.datainfo.deletedbyinference=false and d.datainfo.invisible=false; CREATE TABLE ${stats_db_name}.datasource_organizations STORED AS PARQUET AS SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS organization FROM ${openaire_db_name}.relation r -WHERE r.reltype = 'datasourceOrganization' and r.datainfo.deletedbyinference = false and r.datainfo.invisible=false; +WHERE r.reltype = 'datasourceOrganization' and r.datainfo.deletedbyinference = false and r.target like '20|%' and r.datainfo.invisible=false; -- datasource sources: -- where the datasource info have been collected from. From 4b6913787bb48b92c9ae8b6f4cab0b59392798f9 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 8 Jun 2022 14:55:19 +0200 Subject: [PATCH 077/214] [DOI-BOOST] added one method in test of crossref mapping to aof and one resource. Related to ticket 7807 --- .../doiboost/crossref/article_nojournal.json | 368 ++++++++++++++++++ .../crossref/CrossrefMappingTest.scala | 28 ++ 2 files changed, 396 insertions(+) create mode 100644 dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/article_nojournal.json diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/article_nojournal.json b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/article_nojournal.json new file mode 100644 index 000000000..48a3777b7 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/article_nojournal.json @@ -0,0 +1,368 @@ + +{ + + "indexed": { + "date-parts": [ + [ + 2022, + 4, + 22 + ] + ], + "date-time": "2022-04-22T15:30:54Z", + "timestamp": 1650641454218 + }, + "reference-count": 31, + "publisher": "Cambridge University Press (CUP)", + "issue": "2", + "license": [ + { + "start": { + "date-parts": [ + [ + 2017, + 8, + 22 + ] + ], + "date-time": "2017-08-22T00:00:00Z", + "timestamp": 1503360000000 + }, + "content-version": "unspecified", + "delay-in-days": 21, + "URL": "https://www.cambridge.org/core/terms" + } + ], + "content-domain": { + "domain": [ + + ], + "crossmark-restriction": false + }, + "short-container-title": [ + "Dance Res. J." + ], + "published-print": { + "date-parts": [ + [ + 2017, + 8 + ] + ] + }, + "abstract": "Gaga, a practice developed by Israeli choreographer Ohad Naharin, is one of the most popular training methods on the global dance market. Structured as a metatechnique, or a system for negotiating techniques within one's body, Gaga teaches students to both draw on and reject multiple movement techniques to create their own movement. I consider how the paradigms of choreography, technique, and improvisation are blurred together in the pedagogical model of a metatechnique and how training dancers to shift between choreographer, dancer, and improviser has significant ramifications for understanding their agency. The metatechnique model of Gaga falls in line with neoliberal values of efficiency and a wide range of skills and knowledge; this analysis provides an understanding of recent trends in dance training in relation to contemporary political and socioeconomic structures.", + "DOI": "10.1017/s0149767717000183", + "type": "journal-article", + "created": { + "date-parts": [ + [ + 2017, + 8, + 22 + ] + ], + "date-time": "2017-08-22T13:32:38Z", + "timestamp": 1503408758000 + }, + "page": "26-43", + "source": "Crossref", + "is-referenced-by-count": 10, + "title": [ + "Gaga as Metatechnique: Negotiating Choreography, Improvisation, and Technique in a Neoliberal Dance Market" + ], + "prefix": "10.1017", + "volume": "49", + "author": [ + { + "given": "Meghan", + "family": "Quinlan", + "sequence": "first", + "affiliation": [ + + ] + } + ], + "member": "56", + "published-online": { + "date-parts": [ + [ + 2017, + 8, + 22 + ] + ] + }, + "reference": [ + { + "key": "S0149767717000183_ref22", + "first-page": "38", + "article-title": "‘I Don't Want to do African … What About My Technique?’: Transforming Dancing Places into Spaces in the Academy", + "volume": "4", + "author": "Monroe", + "year": "2011", + "journal-title": "The Journal of Pan African Studies" + }, + { + "key": "S0149767717000183_ref8", + "volume-title": "Discipline and Punish: The Birth of the Prison", + "author": "Foucault", + "year": "1995" + }, + { + "key": "S0149767717000183_ref24", + "volume-title": "Sharing the Dance: Contact Improvisation and American Culture", + "author": "Novack", + "year": "1990" + }, + { + "key": "S0149767717000183_ref26", + "doi-asserted-by": "publisher", + "DOI": "10.1215/9780822387879" + }, + { + "key": "S0149767717000183_ref10", + "doi-asserted-by": "publisher", + "DOI": "10.1080/01472526.2015.1085759" + }, + { + "key": "S0149767717000183_ref4", + "doi-asserted-by": "crossref", + "first-page": "235", + "volume-title": "Meaning in Motion", + "author": "Foster", + "year": "1997", + "DOI": "10.1215/9780822397281-013" + }, + { + "key": "S0149767717000183_ref17", + "doi-asserted-by": "publisher", + "DOI": "10.1093/acprof:oso/9780199360369.001.0001" + }, + { + "key": "S0149767717000183_ref30", + "volume-title": "The Precariat: The New Dangerous Class", + "author": "Standing", + "year": "2011" + }, + { + "key": "S0149767717000183_ref7", + "volume-title": "Choreographing Empathy: Kinesthesia in Performance", + "author": "Foster", + "year": "2011" + }, + { + "key": "S0149767717000183_ref14", + "volume-title": "A Brief History of Neoliberalism", + "author": "Harvey", + "year": "2007" + }, + { + "key": "S0149767717000183_ref27", + "unstructured": "Quinlan Meghan . 2016. “Gaga as Politics: A Case Study of Contemporary Dance Training.” PhD diss., University of California, Riverside." + }, + { + "key": "S0149767717000183_ref11", + "first-page": "xiii", + "volume-title": "Taken by Surprise: A Dance Improvisation Reader", + "author": "Gere", + "year": "2003" + }, + { + "key": "S0149767717000183_ref13", + "volume-title": "Declaration", + "author": "Hardt", + "year": "2012" + }, + { + "key": "S0149767717000183_ref29", + "doi-asserted-by": "publisher", + "DOI": "10.1057/9780230236844_9" + }, + { + "key": "S0149767717000183_ref5", + "doi-asserted-by": "publisher", + "DOI": "10.1057/9780230236844_6" + }, + { + "key": "S0149767717000183_ref28", + "doi-asserted-by": "publisher", + "DOI": "10.1017/S0149767700000528" + }, + { + "key": "S0149767717000183_ref12", + "doi-asserted-by": "publisher", + "DOI": "10.3998/mpub.287881" + }, + { + "key": "S0149767717000183_ref18", + "first-page": "135", + "volume-title": "Taken by Surprise: A Dance Improvisation Reader", + "author": "Marks", + "year": "2003" + }, + { + "key": "S0149767717000183_ref3", + "doi-asserted-by": "crossref", + "volume-title": "Bodies That Matter: On the Discursive Limits of Sex", + "author": "Butler", + "year": "2011", + "DOI": "10.4324/9780203828274" + }, + { + "key": "S0149767717000183_ref32", + "volume-title": "Choreographing Difference: The Body and Identity in Contemporary Dance", + "author": "Albright", + "year": "1997" + }, + { + "key": "S0149767717000183_ref16", + "doi-asserted-by": "publisher", + "DOI": "10.1017/S0149767714000163" + }, + { + "key": "S0149767717000183_ref15", + "doi-asserted-by": "publisher", + "DOI": "10.2307/1477803" + }, + { + "key": "S0149767717000183_ref21", + "first-page": "455", + "volume-title": "Incorporations", + "author": "Mauss", + "year": "1992" + }, + { + "key": "S0149767717000183_ref1", + "volume-title": "The Body Eclectic: Evolving Practices in Dance Training", + "author": "Bales", + "year": "2008" + }, + { + "key": "S0149767717000183_ref9", + "unstructured": "Gaga Movement Ltd. 2016. Gaga People. Dancers. Accessed June 28, 2016. http://gagapeople.com/english/." + }, + { + "key": "S0149767717000183_ref19", + "volume-title": "Critical Moves: Dance Studies in Theory and Politics", + "author": "Martin", + "year": "1998" + }, + { + "key": "S0149767717000183_ref2", + "volume-title": "Undoing the Demos: Neoliberalism's Stealth Revolution", + "author": "Brown", + "year": "2015" + }, + { + "key": "S0149767717000183_ref20", + "doi-asserted-by": "publisher", + "DOI": "10.1162/DRAM_a_00214" + }, + { + "key": "S0149767717000183_ref6", + "doi-asserted-by": "publisher", + "DOI": "10.1215/01610775-2009-016" + }, + { + "key": "S0149767717000183_ref23", + "doi-asserted-by": "publisher", + "DOI": "10.1093/acprof:oso/9780190201661.001.0001" + }, + { + "key": "S0149767717000183_ref25", + "volume-title": "Flexible Citizenship: The Cultural Logics of Transnationality", + "author": "Ong", + "year": "1999" + } + ], + "container-title": [ + "Dance Research Journal" + ], + "original-title": [ + + ], + "language": "en", + "link": [ + { + "URL": "https://www.cambridge.org/core/services/aop-cambridge-core/content/view/S0149767717000183", + "content-type": "unspecified", + "content-version": "vor", + "intended-application": "similarity-checking" + } + ], + "deposited": { + "date-parts": [ + [ + 2020, + 10, + 16 + ] + ], + "date-time": "2020-10-16T01:00:32Z", + "timestamp": 1602810032000 + }, + "score": 1, + "resource": { + "primary": { + "URL": "https://www.cambridge.org/core/product/identifier/S0149767717000183/type/journal_article" + } + }, + "subtitle": [ + + ], + "short-title": [ + + ], + "issued": { + "date-parts": [ + [ + 2017, + 8 + ] + ] + }, + "references-count": 31, + "journal-issue": { + "issue": "2", + "published-print": { + "date-parts": [ + [ + 2017, + 8 + ] + ] + } + }, + "alternative-id": [ + "S0149767717000183" + ], + "URL": "http://dx.doi.org/10.1017/s0149767717000183", + "relation": { + + }, + "ISSN": [ + "0149-7677", + "1940-509X" + ], + "issn-type": [ + { + "value": "0149-7677", + "type": "print" + }, + { + "value": "1940-509X", + "type": "electronic" + } + ], + "subject": [ + "Visual Arts and Performing Arts" + ], + "published": { + "date-parts": [ + [ + 2017, + 8 + ] + ] + } + } diff --git a/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala b/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala index 78ed375c6..30928fdd0 100644 --- a/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala +++ b/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala @@ -473,6 +473,34 @@ class CrossrefMappingTest { }) + } + + @Test + def testConvertFromCrossRef2OafIssue(): Unit = { + val json = Source + .fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/article_nojournal.json")) + .mkString + assertNotNull(json) + + assertFalse(json.isEmpty); + + val resultList: List[Oaf] = Crossref2Oaf.convert(json) + + assertTrue(resultList.nonEmpty) + + val items = resultList.filter(p => p.isInstanceOf[Publication]) + + assert(items.nonEmpty) + assert(items.size == 1) + val pub: Publication = items.head.asInstanceOf[Publication] + + assertNotNull(pub.getJournal.getIssnPrinted) + assertNotNull(pub.getJournal.getIssnOnline) + assertNotNull(pub.getJournal.getName) + + + + } @Test From ab8868bd3a5b170efc1d2fdc62812a6b308c589f Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 8 Jun 2022 17:03:15 +0200 Subject: [PATCH 078/214] [ZENODO-API] changed to iterate in all the deposited products and not just the last ten --- .../dhp/common/api/ZenodoAPIClient.java | 29 ++++++++++++------- 1 file changed, 18 insertions(+), 11 deletions(-) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/ZenodoAPIClient.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/ZenodoAPIClient.java index 3f5c6ad4a..56366bc72 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/ZenodoAPIClient.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/ZenodoAPIClient.java @@ -191,7 +191,7 @@ public class ZenodoAPIClient implements Serializable { * @throws MissingConceptDoiException */ public int newVersion(String concept_rec_id) throws IOException, MissingConceptDoiException { - setDepositionId(concept_rec_id); + setDepositionId(concept_rec_id, 1); String json = "{}"; OkHttpClient httpClient = new OkHttpClient.Builder().connectTimeout(600, TimeUnit.SECONDS).build(); @@ -253,9 +253,9 @@ public class ZenodoAPIClient implements Serializable { } - private void setDepositionId(String concept_rec_id) throws IOException, MissingConceptDoiException { + private void setDepositionId(String concept_rec_id, Integer page) throws IOException, MissingConceptDoiException { - ZenodoModelList zenodoModelList = new Gson().fromJson(getPrevDepositions(), ZenodoModelList.class); + ZenodoModelList zenodoModelList = new Gson().fromJson(getPrevDepositions(String.valueOf(page)), ZenodoModelList.class); for (ZenodoModel zm : zenodoModelList) { if (zm.getConceptrecid().equals(concept_rec_id)) { @@ -263,20 +263,26 @@ public class ZenodoAPIClient implements Serializable { return; } } - - throw new MissingConceptDoiException("The concept record id specified was missing in the list of depositions"); + if(zenodoModelList.size() == 0) + throw new MissingConceptDoiException("The concept record id specified was missing in the list of depositions"); + setDepositionId(concept_rec_id, page + 1); } - private String getPrevDepositions() throws IOException { + private String getPrevDepositions(String page) throws IOException { + OkHttpClient httpClient = new OkHttpClient.Builder().connectTimeout(600, TimeUnit.SECONDS).build(); + HttpUrl.Builder urlBuilder = HttpUrl.parse(urlString).newBuilder(); + urlBuilder.addQueryParameter("page", page); + String url = urlBuilder.build().toString(); + Request request = new Request.Builder() - .url(urlString) - .addHeader(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString()) // add request headers - .addHeader(HttpHeaders.AUTHORIZATION, "Bearer " + access_token) - .get() - .build(); + .url(url) + .addHeader(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString()) // add request headers + .addHeader(HttpHeaders.AUTHORIZATION, "Bearer " + access_token) + .get() + .build(); try (Response response = httpClient.newCall(request).execute()) { @@ -289,6 +295,7 @@ public class ZenodoAPIClient implements Serializable { } + private String getBucket(String url) throws IOException { OkHttpClient httpClient = new OkHttpClient.Builder() .connectTimeout(600, TimeUnit.SECONDS) From b94a791bc5fe023aaeb43453c1fe4042e9441d24 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Thu, 9 Jun 2022 12:25:34 +0200 Subject: [PATCH 079/214] unit tests to transform cnr explora --- .../transformation/TransformationJobTest.java | 49 +++- .../dnetlib/dhp/transform/cnr_explora_tr.xslt | 214 ++++++++++++++ .../dhp/transform/input_cnr_explora.xml | 57 ++++ .../eu/dnetlib/dhp/transform/synonyms.txt | 266 +++++++++++++++++- .../eu/dnetlib/dhp/transform/terms.txt | 135 ++++++++- 5 files changed, 704 insertions(+), 17 deletions(-) create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/cnr_explora_tr.xslt create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/input_cnr_explora.xml diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java index 7bd7baaea..fea7b53ac 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java @@ -19,7 +19,9 @@ import org.apache.spark.sql.Encoder; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; import org.apache.spark.util.LongAccumulator; -import org.junit.jupiter.api.*; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.DisplayName; +import org.junit.jupiter.api.Test; import org.junit.jupiter.api.extension.ExtendWith; import org.junit.jupiter.api.io.TempDir; import org.mockito.junit.jupiter.MockitoExtension; @@ -50,7 +52,7 @@ class TransformationJobTest extends AbstractVocabularyTest { @Test @DisplayName("Test Date cleaner") void testDateCleaner() throws Exception { - DateCleaner dc = new DateCleaner(); + final DateCleaner dc = new DateCleaner(); assertEquals("1982-09-20", dc.clean("20/09/1982")); assertEquals("2002-09-20", dc.clean("20-09-2002")); assertEquals("2002-09-20", dc.clean("2002-09-20")); @@ -68,9 +70,9 @@ class TransformationJobTest extends AbstractVocabularyTest { mr.setProvenance(new Provenance("DSID", "DSNAME", "PREFIX")); mr.setBody(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/transform/input_zenodo.xml"))); // We Load the XSLT transformation Rule from the classpath - XSLTTransformationFunction tr = loadTransformationRule("/eu/dnetlib/dhp/transform/zenodo_tr.xslt"); + final XSLTTransformationFunction tr = loadTransformationRule("/eu/dnetlib/dhp/transform/zenodo_tr.xslt"); - MetadataRecord result = tr.call(mr); + final MetadataRecord result = tr.call(mr); // Print the record System.out.println(result.getBody()); @@ -86,9 +88,9 @@ class TransformationJobTest extends AbstractVocabularyTest { mr.setProvenance(new Provenance("DSID", "DSNAME", "PREFIX")); mr.setBody(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/transform/input_itgv4.xml"))); // We Load the XSLT transformation Rule from the classpath - XSLTTransformationFunction tr = loadTransformationRule("/eu/dnetlib/dhp/transform/zenodo_tr.xslt"); + final XSLTTransformationFunction tr = loadTransformationRule("/eu/dnetlib/dhp/transform/zenodo_tr.xslt"); - MetadataRecord result = tr.call(mr); + final MetadataRecord result = tr.call(mr); // Print the record System.out.println(result.getBody()); @@ -108,9 +110,9 @@ class TransformationJobTest extends AbstractVocabularyTest { mr.setProvenance(new Provenance("DSID", "DSNAME", "PREFIX")); mr.setBody(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/transform/input_itgv4.xml"))); // We Load the XSLT transformation Rule from the classpath - XSLTTransformationFunction tr = loadTransformationRule(xslTransformationScript); + final XSLTTransformationFunction tr = loadTransformationRule(xslTransformationScript); - MetadataRecord result = tr.call(mr); + final MetadataRecord result = tr.call(mr); // Print the record System.out.println(result.getBody()); @@ -129,9 +131,9 @@ class TransformationJobTest extends AbstractVocabularyTest { mr.setProvenance(new Provenance("DSID", "DSNAME", "PREFIX")); mr.setBody(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/transform/input_omicsdi.xml"))); // We Load the XSLT transformation Rule from the classpath - XSLTTransformationFunction tr = loadTransformationRule(xslTransformationScript); + final XSLTTransformationFunction tr = loadTransformationRule(xslTransformationScript); - MetadataRecord result = tr.call(mr); + final MetadataRecord result = tr.call(mr); // Print the record System.out.println(result.getBody()); @@ -140,7 +142,7 @@ class TransformationJobTest extends AbstractVocabularyTest { @Test @DisplayName("Test TransformSparkJobNode.main with oaiOpenaire_datacite (v4)") - void transformTestITGv4OAIdatacite(@TempDir Path testDir) throws Exception { + void transformTestITGv4OAIdatacite(@TempDir final Path testDir) throws Exception { try (SparkSession spark = SparkSession.builder().config(sparkConf).getOrCreate()) { @@ -150,9 +152,7 @@ class TransformationJobTest extends AbstractVocabularyTest { .getFile(); final String mdstore_output = testDir.toString() + "/version"; - mockupTrasformationRule( - "simpleTRule", - "/eu/dnetlib/dhp/transform/scripts/xslt_cleaning_oaiOpenaire_datacite_ExchangeLandingpagePid.xsl"); + mockupTrasformationRule("simpleTRule", "/eu/dnetlib/dhp/transform/scripts/xslt_cleaning_oaiOpenaire_datacite_ExchangeLandingpagePid.xsl"); final Map parameters = Stream.of(new String[][] { { @@ -203,7 +203,7 @@ class TransformationJobTest extends AbstractVocabularyTest { @Test @DisplayName("Test TransformSparkJobNode.main") - void transformTest(@TempDir Path testDir) throws Exception { + void transformTest(@TempDir final Path testDir) throws Exception { try (SparkSession spark = SparkSession.builder().config(sparkConf).getOrCreate()) { @@ -256,6 +256,25 @@ class TransformationJobTest extends AbstractVocabularyTest { } } + @Test + @DisplayName("Test Transform Single XML using cnr_explora_tr XSLTTransformator") + void testCnrExploraTransformSaxonHE() throws Exception { + + // We Set the input Record getting the XML from the classpath + final MetadataRecord mr = new MetadataRecord(); + + mr.setProvenance(new Provenance("openaire____::cnr_explora", "CNR ExploRA", "cnr_________")); + mr.setBody(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/transform/input_cnr_explora.xml"))); + // We Load the XSLT transformation Rule from the classpath + final XSLTTransformationFunction tr = loadTransformationRule("/eu/dnetlib/dhp/transform/cnr_explora_tr.xslt"); + + final MetadataRecord result = tr.call(mr); + + // Print the record + System.out.println(result.getBody()); + // TODO Create significant Assert + } + private XSLTTransformationFunction loadTransformationRule(final String path) throws Exception { final String trValue = IOUtils.toString(this.getClass().getResourceAsStream(path)); final LongAccumulator la = new LongAccumulator(); diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/cnr_explora_tr.xslt b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/cnr_explora_tr.xslt new file mode 100644 index 000000000..78b167fde --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/cnr_explora_tr.xslt @@ -0,0 +1,214 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/input_cnr_explora.xml b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/input_cnr_explora.xml new file mode 100644 index 000000000..220c4ddbe --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/input_cnr_explora.xml @@ -0,0 +1,57 @@ + + +

+ + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/synonyms.txt b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/synonyms.txt index 4fd95554a..74a75e46a 100644 --- a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/synonyms.txt +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/synonyms.txt @@ -1232,4 +1232,268 @@ dnet:review_levels @=@ 0001 @=@ 印刷物/電子媒体-学術雑誌論文（査 dnet:review_levels @=@ 0001 @=@ 印刷物/電子媒体-紀要論文（査読有り） dnet:review_levels @=@ 0001 @=@ 印刷物/電子媒体-雑誌記事（査読有り） dnet:review_levels @=@ 0001 @=@ 原著論文（査読有り） -dnet:review_levels @=@ 0001 @=@ 査読論文 \ No newline at end of file +dnet:review_levels @=@ 0001 @=@ 査読論文 +cnr:institutes @=@ https://ror.org/00brf2d87 @=@ CDS001 +cnr:institutes @=@ https://ror.org/00brf2d87 @=@ IDASC - Istituto di Acustica e Sensoristica \"Orso Mario Corbino\" +cnr:institutes @=@ https://ror.org/006qkqr45 @=@ CDS002 +cnr:institutes @=@ https://ror.org/006qkqr45 @=@ IAMC - Istituto per l'ambiente marino costiero +cnr:institutes @=@ https://ror.org/054ye0e45 @=@ CDS003 +cnr:institutes @=@ https://ror.org/054ye0e45 @=@ IASI - Istituto di analisi dei sistemi ed informatica \"Antonio Ruberti\" +cnr:institutes @=@ https://ror.org/00ygy3d85 @=@ CDS004 +cnr:institutes @=@ https://ror.org/00ygy3d85 @=@ IAC - Istituto per le applicazioni del calcolo \"Mauro Picone\" +cnr:institutes @=@ https://ror.org/000sy1f36 @=@ CDS005 +cnr:institutes @=@ https://ror.org/000sy1f36 @=@ IASF - Istituto di astrofisica spaziale e fisica cosmica +cnr:institutes @=@ https://ror.org/00x5wpm25 @=@ CDS006 +cnr:institutes @=@ https://ror.org/00x5wpm25 @=@ IBAM - Istituto per i beni archeologici e monumentali +cnr:institutes @=@ https://ror.org/03eqeqg74 @=@ CDS007 +cnr:institutes @=@ https://ror.org/03eqeqg74 @=@ IBP - Istituto di biochimica delle proteine +cnr:institutes @=@ https://ror.org/041xzk838 @=@ CDS008 +cnr:institutes @=@ https://ror.org/041xzk838 @=@ IBF - Istituto di biofisica +cnr:institutes @=@ https://ror.org/00s2j5046 @=@ CDS009 +cnr:institutes @=@ https://ror.org/00s2j5046 @=@ IBFM - Istituto di bioimmagini e fisiologia molecolare +cnr:institutes @=@ __CDS010__ @=@ CDS010 +cnr:institutes @=@ __CDS010__ @=@ IBAF - Istituto di biologia agro-ambientale e forestale +cnr:institutes @=@ __CDS011__ @=@ CDS011 +cnr:institutes @=@ __CDS011__ @=@ IBC - Istituto di biologia cellulare +cnr:institutes @=@ https://ror.org/02e5sbe24 @=@ CDS012 +cnr:institutes @=@ https://ror.org/02e5sbe24 @=@ IBBA - Istituto di biologia e biotecnologia agraria +cnr:institutes @=@ https://ror.org/01nyatq71 @=@ CDS013 +cnr:institutes @=@ https://ror.org/01nyatq71 @=@ IBPM - Istituto di biologia e patologia molecolari +cnr:institutes @=@ https://ror.org/01dy2q607 @=@ CDS014 +cnr:institutes @=@ https://ror.org/01dy2q607 @=@ IBIM - Istituto di biomedicina e di immunologia molecolare \"Alberto Monroy\" +cnr:institutes @=@ https://ror.org/05nzf7q96 @=@ CDS015 +cnr:institutes @=@ https://ror.org/05nzf7q96 @=@ IBIOM - Istituto di Biomembrane, Bioenergetica e Biotecnologie Molecolari +cnr:institutes @=@ https://ror.org/05m1yqp60 @=@ CDS016 +cnr:institutes @=@ https://ror.org/05m1yqp60 @=@ IBIMET - Istituto di biometeorologia +cnr:institutes @=@ https://ror.org/03rqtqb02 @=@ CDS017 +cnr:institutes @=@ https://ror.org/03rqtqb02 @=@ IBB - Istituto di biostrutture e bioimmagini +cnr:institutes @=@ https://ror.org/04r5fge26 @=@ CDS018 +cnr:institutes @=@ https://ror.org/04r5fge26 @=@ ICAR - Istituto di calcolo e reti ad alte prestazioni +cnr:institutes @=@ https://ror.org/03wyf0g15 @=@ CDS019 +cnr:institutes @=@ https://ror.org/03wyf0g15 @=@ ICB - Istituto di chimica biomolecolare +cnr:institutes @=@ https://ror.org/02fkw1114 @=@ CDS020 +cnr:institutes @=@ https://ror.org/02fkw1114 @=@ ICCOM - Istituto di chimica dei composti organo metallici +cnr:institutes @=@ https://ror.org/0141vn777 @=@ CDS021 +cnr:institutes @=@ https://ror.org/0141vn777 @=@ ICRM - Istituto di chimica del riconoscimento molecolare +cnr:institutes @=@ __CDS022__ @=@ CDS022 +cnr:institutes @=@ __CDS022__ @=@ ICTP - Istituto di chimica e tecnologia dei polimeri +cnr:institutes @=@ __CDS023__ @=@ CDS023 +cnr:institutes @=@ __CDS023__ @=@ ICIS - Istituto di chimica inorganica e delle superfici +cnr:institutes @=@ https://ror.org/00be3zh53 @=@ CDS024 +cnr:institutes @=@ https://ror.org/00be3zh53 @=@ ISASI - Istituto di Scienze Applicate e Sistemi Intelligenti \"Eduardo Caianiello\" +cnr:institutes @=@ __CDS025__ @=@ CDS025 +cnr:institutes @=@ __CDS025__ @=@ ICEVO - Istituto di Studi sulle Civiltà dell'Egeo e del Vicino Oriente +cnr:institutes @=@ https://ror.org/02ynrme92 @=@ CDS026 +cnr:institutes @=@ https://ror.org/02ynrme92 @=@ ICVBC - Istituto per la conservazione e valorizzazione dei beni culturali +cnr:institutes @=@ https://ror.org/05wba8r86 @=@ CDS027 +cnr:institutes @=@ https://ror.org/05wba8r86 @=@ IC - Istituto di cristallografia +cnr:institutes @=@ https://ror.org/03z58xd74 @=@ CDS028 +cnr:institutes @=@ https://ror.org/03z58xd74 @=@ IDPA - Istituto per la dinamica dei processi ambientali +cnr:institutes @=@ https://ror.org/00n4jbh84 @=@ CDS029 +cnr:institutes @=@ https://ror.org/00n4jbh84 @=@ IEIIT - Istituto di elettronica e di ingegneria dell'informazione e delle telecomunicazioni +cnr:institutes @=@ https://ror.org/04sn06036 @=@ CDS030 +cnr:institutes @=@ https://ror.org/04sn06036 @=@ IEOS - Istituto per l'endocrinologia e l'oncologia \"Gaetano Salvatore\" +cnr:institutes @=@ https://ror.org/01rg40y89 @=@ CDS031 +cnr:institutes @=@ https://ror.org/01rg40y89 @=@ ICMATE - Istituto di Chimica della Materia Condensata e di Tecnologie per l'Energia +cnr:institutes @=@ https://ror.org/00dqega85 @=@ CDS032 +cnr:institutes @=@ https://ror.org/00dqega85 @=@ IFAC - Istituto di fisica applicata \"Nello Carrara\" +cnr:institutes @=@ https://ror.org/02n2bgz18 @=@ CDS033 +cnr:institutes @=@ https://ror.org/02n2bgz18 @=@ IFP - Istituto di fisica del plasma \"Piero Caldirola\" +cnr:institutes @=@ __CDS034__ @=@ CDS034 +cnr:institutes @=@ __CDS034__ @=@ IFSI - Istituto di fisica dello spazio interplanetario +cnr:institutes @=@ https://ror.org/01kdj2848 @=@ CDS035 +cnr:institutes @=@ https://ror.org/01kdj2848 @=@ IFC - Istituto di fisiologia clinica +cnr:institutes @=@ https://ror.org/049ebw417 @=@ CDS036 +cnr:institutes @=@ https://ror.org/049ebw417 @=@ IFN - Istituto di fotonica e nanotecnologie +cnr:institutes @=@ https://ror.org/01f5tnx94 @=@ CDS037 +cnr:institutes @=@ https://ror.org/01f5tnx94 @=@ IGI - Istituto gas ionizzati +cnr:institutes @=@ __CDS038__ @=@ CDS038 +cnr:institutes @=@ __CDS038__ @=@ IGP - Istituto di genetica delle popolazioni +cnr:institutes @=@ https://ror.org/04hadk112 @=@ CDS039 +cnr:institutes @=@ https://ror.org/04hadk112 @=@ IGB - Istituto di genetica e biofisica \"Adriano Buzzati Traverso\" +cnr:institutes @=@ https://ror.org/03qpd8w66 @=@ CDS040 +cnr:institutes @=@ https://ror.org/03qpd8w66 @=@ IGM - Istituto di genetica molecolare \"Luigi Luca Cavalli Sforza\" +cnr:institutes @=@ https://ror.org/01gtsa866 @=@ CDS041 +cnr:institutes @=@ https://ror.org/01gtsa866 @=@ IBBR - Istituto di Bioscienze e Biorisorse +cnr:institutes @=@ https://ror.org/00ytw6m58 @=@ CDS042 +cnr:institutes @=@ https://ror.org/00ytw6m58 @=@ IGAG - Istituto di geologia ambientale e geoingegneria +cnr:institutes @=@ https://ror.org/015bmra78 @=@ CDS043 +cnr:institutes @=@ https://ror.org/015bmra78 @=@ IGG - Istituto di geoscienze e georisorse +cnr:institutes @=@ https://ror.org/02gdcn153 @=@ CDS044 +cnr:institutes @=@ https://ror.org/02gdcn153 @=@ IIT - Istituto di informatica e telematica +cnr:institutes @=@ __CDS045__ @=@ CDS045 +cnr:institutes @=@ __CDS045__ @=@ ISIB - Istituto di ingegneria biomedica +cnr:institutes @=@ https://ror.org/05hky6p02 @=@ CDS046 +cnr:institutes @=@ https://ror.org/05hky6p02 @=@ IIA - Istituto sull'inquinamento atmosferico +cnr:institutes @=@ https://ror.org/011n2hw53 @=@ CDS047 +cnr:institutes @=@ https://ror.org/011n2hw53 @=@ ILIESI - Istituto per il lessico intellettuale europeo e storia delle idee +cnr:institutes @=@ https://ror.org/028g3pe33 @=@ CDS048 +cnr:institutes @=@ https://ror.org/028g3pe33 @=@ ILC - Istituto di linguistica computazionale \"Antonio Zampolli\" +cnr:institutes @=@ __CDS049__ @=@ CDS049 +cnr:institutes @=@ __CDS049__ @=@ IMAMOTER - Istituto per le macchine agricole e movimento terra +cnr:institutes @=@ https://ror.org/03m0n3c07 @=@ CDS050 +cnr:institutes @=@ https://ror.org/03m0n3c07 @=@ IMATI - Istituto di matematica applicata e tecnologie informatiche \"Enrico Magenes\" +cnr:institutes @=@ __CDS051__ @=@ CDS051 +cnr:institutes @=@ __CDS051__ @=@ IMCB - Istituto per i materiali compositi e biomedici +cnr:institutes @=@ https://ror.org/00z8ws214 @=@ CDS052 +cnr:institutes @=@ https://ror.org/00z8ws214 @=@ IMEM - Istituto dei materiali per l'elettronica ed il magnetismo +cnr:institutes @=@ __CDS053__ @=@ CDS053 +cnr:institutes @=@ __CDS053__ @=@ ISB - Istituto per i Sistemi Biologici +cnr:institutes @=@ https://ror.org/00bc51d88 @=@ CDS054 +cnr:institutes @=@ https://ror.org/00bc51d88 @=@ NANOTEC - Istituto di Nanotecnologia +cnr:institutes @=@ https://ror.org/024ye7w89 @=@ CDS055 +cnr:institutes @=@ https://ror.org/024ye7w89 @=@ IMAA - Istituto di metodologie per l'analisi ambientale +cnr:institutes @=@ __CDS056__ @=@ CDS056 +cnr:institutes @=@ __CDS056__ @=@ IMGC - Istituto di metrologia \"Gustavo Colonnetti\" +cnr:institutes @=@ https://ror.org/05vk2g845 @=@ CDS057 +cnr:institutes @=@ https://ror.org/05vk2g845 @=@ IMM - Istituto per la microelettronica e microsistemi +cnr:institutes @=@ https://ror.org/02qwy8e97 @=@ CDS058 +cnr:institutes @=@ https://ror.org/02qwy8e97 @=@ IM - Istituto motori +cnr:institutes @=@ __CDS059__ @=@ CDS059 +cnr:institutes @=@ __CDS059__ @=@ INMM - Istituto di neurobiologia e medicina molecolare +cnr:institutes @=@ https://ror.org/02dr63s31 @=@ CDS060 +cnr:institutes @=@ https://ror.org/02dr63s31 @=@ IRGB - Istituto di Ricerca Genetica e Biomedica +cnr:institutes @=@ https://ror.org/0240rwx68 @=@ CDS061 +cnr:institutes @=@ https://ror.org/0240rwx68 @=@ IN - Istituto di neuroscienze +cnr:institutes @=@ https://ror.org/02rzxrg25 @=@ CDS062 +cnr:institutes @=@ https://ror.org/02rzxrg25 @=@ OVI - Istituto opera del vocabolario italiano +cnr:institutes @=@ https://ror.org/05patmk97 @=@ CDS063 +cnr:institutes @=@ https://ror.org/05patmk97 @=@ IPCF - Istituto per i processi chimico-fisici +cnr:institutes @=@ __CDS064__ @=@ CDS064 +cnr:institutes @=@ __CDS064__ @=@ IPP - Istituto per la protezione delle piante +cnr:institutes @=@ https://ror.org/029st3z03 @=@ CDS065 +cnr:institutes @=@ https://ror.org/029st3z03 @=@ IRA - Istituto di radioastronomia +cnr:institutes @=@ https://ror.org/0040zx077 @=@ CDS066 +cnr:institutes @=@ https://ror.org/0040zx077 @=@ IRPI - Istituto di ricerca per la protezione idrogeologica +cnr:institutes @=@ https://ror.org/044bfsy89 @=@ CDS067 +cnr:institutes @=@ https://ror.org/044bfsy89 @=@ IRCRES - Istituto di Ricerca sulla Crescita Economica Sostenibile +cnr:institutes @=@ https://ror.org/01n1ayq61 @=@ CDS068 +cnr:institutes @=@ https://ror.org/01n1ayq61 @=@ IRPPS - Istituto di ricerche sulla popolazione e le politiche sociali +cnr:institutes @=@ https://ror.org/02db0kh50 @=@ CDS069 +cnr:institutes @=@ https://ror.org/02db0kh50 @=@ IRSA - Istituto di ricerca sulle acque +cnr:institutes @=@ https://ror.org/05813wx75 @=@ CDS070 +cnr:institutes @=@ https://ror.org/05813wx75 @=@ IRC - Istituto di ricerche sulla combustione +cnr:institutes @=@ https://ror.org/04vnwke91 @=@ CDS071 +cnr:institutes @=@ https://ror.org/04vnwke91 @=@ IRISS - Istituto di Ricerca su Innovazione e Servizi per lo Sviluppo +cnr:institutes @=@ https://ror.org/02wxw4x45 @=@ CDS072 +cnr:institutes @=@ https://ror.org/02wxw4x45 @=@ IREA - Istituto per il rilevamento elettromagnetico dell'ambiente +cnr:institutes @=@ https://ror.org/01j6drw72 @=@ CDS073 +cnr:institutes @=@ https://ror.org/01j6drw72 @=@ ISTEC - Istituto di scienza e tecnologia dei materiali ceramici +cnr:institutes @=@ https://ror.org/05kacka20 @=@ CDS074 +cnr:institutes @=@ https://ror.org/05kacka20 @=@ ISTI - Istituto di scienza e tecnologie dell'informazione \"Alessandro Faedo\" +cnr:institutes @=@ https://ror.org/00n8ttd98 @=@ CDS075 +cnr:institutes @=@ https://ror.org/00n8ttd98 @=@ ISAC - Istituto di scienze dell'atmosfera e del clima +cnr:institutes @=@ https://ror.org/0013zhk30 @=@ CDS076 +cnr:institutes @=@ https://ror.org/0013zhk30 @=@ ISA - Istituto di Scienze dell'Alimentazione +cnr:institutes @=@ https://ror.org/03x7xkr71 @=@ CDS077 +cnr:institutes @=@ https://ror.org/03x7xkr71 @=@ ISPA - Istituto di scienze delle produzioni alimentari +cnr:institutes @=@ https://ror.org/05w9g2j85 @=@ CDS078 +cnr:institutes @=@ https://ror.org/05w9g2j85 @=@ ISTC - Istituto di scienze e tecnologie della cognizione +cnr:institutes @=@ https://ror.org/032tyv240 @=@ CDS079 +cnr:institutes @=@ https://ror.org/032tyv240 @=@ ISTM - Istituto di scienze e tecnologie molecolari +cnr:institutes @=@ https://ror.org/02hdf6119 @=@ CDS080 +cnr:institutes @=@ https://ror.org/02hdf6119 @=@ ISMAR - Istituto di scienze marine +cnr:institutes @=@ https://ror.org/01yg57d71 @=@ CDS081 +cnr:institutes @=@ https://ror.org/01yg57d71 @=@ ISN - Istituto di scienze neurologiche +cnr:institutes @=@ https://ror.org/021z1mz76 @=@ CDS082 +cnr:institutes @=@ https://ror.org/021z1mz76 @=@ ISOF - Istituto per la sintesi organica e la fotoreattività +cnr:institutes @=@ https://ror.org/01wqae691 @=@ CDS083 +cnr:institutes @=@ https://ror.org/01wqae691 @=@ ISPAAM - Istituto per il sistema produzione animale in ambiente Mediterraneo +cnr:institutes @=@ __CDS084__ @=@ CDS084 +cnr:institutes @=@ __CDS084__ @=@ ISAFoM - Istituto per i sistemi agricoli e forestali del mediterraneo +cnr:institutes @=@ https://ror.org/00awwz417 @=@ CDS085 +cnr:institutes @=@ https://ror.org/00awwz417 @=@ ISPF - Istituto per la storia del pensiero filosofico e scientifico moderno +cnr:institutes @=@ https://ror.org/03a111314 @=@ CDS086 +cnr:institutes @=@ https://ror.org/03a111314 @=@ ISEM - Istituto di storia dell'Europa mediterranea +cnr:institutes @=@ https://ror.org/01zz9wh30 @=@ CDS087 +cnr:institutes @=@ https://ror.org/01zz9wh30 @=@ ISM - Istituto di struttura della materia +cnr:institutes @=@ https://ror.org/035y5td47 @=@ CDS088 +cnr:institutes @=@ https://ror.org/035y5td47 @=@ ISGI - Istituto di studi giuridici internazionali +cnr:institutes @=@ __CDS089__ @=@ CDS089 +cnr:institutes @=@ __CDS089__ @=@ ISPRI - Istituto sperimentale di studi socio - economici sull'innovazione e le politiche della ricerca +cnr:institutes @=@ https://ror.org/051t1q308 @=@ CDS090 +cnr:institutes @=@ https://ror.org/051t1q308 @=@ ISSIA - Istituto di studi sui sistemi intelligenti per l'automazione +cnr:institutes @=@ https://ror.org/05k3cs357 @=@ CDS091 +cnr:institutes @=@ https://ror.org/05k3cs357 @=@ ISSIRFA - Istituto di studi sui sistemi regionali federali e sulle autonomie \"Massimo Severo Giannini\" +cnr:institutes @=@ https://ror.org/02gcxw165 @=@ CDS092 +cnr:institutes @=@ https://ror.org/02gcxw165 @=@ ISMA - Istituto di Studi sul Mediterraneo Antico +cnr:institutes @=@ https://ror.org/05db0es39 @=@ CDS093 +cnr:institutes @=@ https://ror.org/05db0es39 @=@ ISMed - Istituto di studi sul Mediterraneo +cnr:institutes @=@ https://ror.org/029k6t707 @=@ CDS094 +cnr:institutes @=@ https://ror.org/029k6t707 @=@ ISE - Istituto per lo studio degli ecosistemi +cnr:institutes @=@ https://ror.org/00w6r1881 @=@ CDS095 +cnr:institutes @=@ https://ror.org/00w6r1881 @=@ ISMN - Istituto per lo studio dei materiali nanostrutturati +cnr:institutes @=@ https://ror.org/01mfmr054 @=@ CDS096 +cnr:institutes @=@ https://ror.org/01mfmr054 @=@ ISMAC - Istituto per lo studio delle macromolecole +cnr:institutes @=@ https://ror.org/058nrs650 @=@ CDS097 +cnr:institutes @=@ https://ror.org/058nrs650 @=@ ITM - Istituto per la tecnologia delle membrane +cnr:institutes @=@ https://ror.org/0331xj092 @=@ CDS098 +cnr:institutes @=@ https://ror.org/0331xj092 @=@ ITABC - Istituto per le tecnologie applicate ai beni culturali +cnr:institutes @=@ https://ror.org/052q58629 @=@ CDS099 +cnr:institutes @=@ https://ror.org/052q58629 @=@ ITAE - Istituto di tecnologie avanzate per l'energia \"Nicola Giordano\" +cnr:institutes @=@ https://ror.org/04ehykb85 @=@ CDS100 +cnr:institutes @=@ https://ror.org/04ehykb85 @=@ ITB - Istituto di tecnologie biomediche +cnr:institutes @=@ https://ror.org/0221agg28 @=@ CDS101 +cnr:institutes @=@ https://ror.org/0221agg28 @=@ ITC - Istituto per le tecnologie della costruzione +cnr:institutes @=@ https://ror.org/02xz4xc25 @=@ CDS102 +cnr:institutes @=@ https://ror.org/02xz4xc25 @=@ ITD - Istituto per le tecnologie didattiche +cnr:institutes @=@ __CDS103__ @=@ CDS103 +cnr:institutes @=@ __CDS103__ @=@ STIIMA - Istituto di Sistemi e Tecnologie Industriali Intelligenti per il Manifatturiero Avanzato +cnr:institutes @=@ https://ror.org/01as2bh37 @=@ CDS104 +cnr:institutes @=@ https://ror.org/01as2bh37 @=@ ITTIG - Istituto di teoria e tecniche dell'informazione giuridica +cnr:institutes @=@ https://ror.org/01y5w6t76 @=@ CDS105 +cnr:institutes @=@ https://ror.org/01y5w6t76 @=@ ITOI - Istituto per i trapianti d'organo e immunocitologia +cnr:institutes @=@ https://ror.org/04xy2mq71 @=@ CDS106 +cnr:institutes @=@ https://ror.org/04xy2mq71 @=@ IVALSA - Istituto per la valorizzazione del legno e delle specie arboree +cnr:institutes @=@ __CDS107__ @=@ CDS107 +cnr:institutes @=@ __CDS107__ @=@ IVV - Istituto di virologia vegetale +cnr:institutes @=@ https://ror.org/013nxtf56 @=@ CDS108 +cnr:institutes @=@ https://ror.org/013nxtf56 @=@ IRSIG - Istituto di ricerca sui sistemi giudiziari +cnr:institutes @=@ https://ror.org/05rcgef49 @=@ CDS109 +cnr:institutes @=@ https://ror.org/05rcgef49 @=@ ISC - Istituto dei sistemi complessi +cnr:institutes @=@ __CDS110__ @=@ CDS110 +cnr:institutes @=@ __CDS110__ @=@ INFM - Centro di responsabilità scientifica INFM +cnr:institutes @=@ https://ror.org/02dp3a879 @=@ CDS111 +cnr:institutes @=@ https://ror.org/02dp3a879 @=@ INO - Istituto nazionale di ottica +cnr:institutes @=@ __CDS112__ @=@ CDS112 +cnr:institutes @=@ __CDS112__ @=@ IDAIC - Centro di responsabilità di attività scientifica IDAIC +cnr:institutes @=@ https://ror.org/00p03yg71 @=@ CDS113 +cnr:institutes @=@ https://ror.org/00p03yg71 @=@ SPIN - Istituto superconduttori, materiali innovativi e dispositivi +cnr:institutes @=@ https://ror.org/00yfw2296 @=@ CDS114 +cnr:institutes @=@ https://ror.org/00yfw2296 @=@ IOM - Istituto officina dei materiali +cnr:institutes @=@ https://ror.org/0042e5975 @=@ CDS115 +cnr:institutes @=@ https://ror.org/0042e5975 @=@ NANO - Istituto Nanoscienze +cnr:institutes @=@ https://ror.org/03ta8pf33 @=@ CDS116 +cnr:institutes @=@ https://ror.org/03ta8pf33 @=@ IFT - Istituto di Farmacologia Traslazionale +cnr:institutes @=@ https://ror.org/040xhth73 @=@ CDS117 +cnr:institutes @=@ https://ror.org/040xhth73 @=@ IBCN - Istituto di Biologia Cellulare e Neurobiologia +cnr:institutes @=@ https://ror.org/02qnx8e75 @=@ CDS118 +cnr:institutes @=@ https://ror.org/02qnx8e75 @=@ INM - Istituto di iNgegneria del Mare +cnr:institutes @=@ https://ror.org/05nr7xa08 @=@ CDS119 +cnr:institutes @=@ https://ror.org/05nr7xa08 @=@ IPCB - Istituto per i Polimeri, Compositi e Biomateriali +cnr:institutes @=@ https://ror.org/008fjbg42 @=@ CDS121 +cnr:institutes @=@ https://ror.org/008fjbg42 @=@ IPSP - Istituto per la Protezione Sostenibile delle Piante +cnr:institutes @=@ __CDS122__ @=@ CDS122 +cnr:institutes @=@ __CDS122__ @=@ IRBIM - Istituto per le Risorse Biologiche e le Biotecnologie Marine +cnr:institutes @=@ __CDS123__ @=@ CDS123 +cnr:institutes @=@ __CDS123__ @=@ ISPC - Istituto di Scienze del Patrimonio Culturale +cnr:institutes @=@ __CDS124__ @=@ CDS124 +cnr:institutes @=@ __CDS124__ @=@ IAS - Istituto per lo studio degli impatti Antropici e Sostenibilità in ambiente marino +cnr:institutes @=@ __CDS125__ @=@ CDS125 +cnr:institutes @=@ __CDS125__ @=@ IRET - Istituto di Ricerca sugli Ecosistemi Terrestri +cnr:institutes @=@ https://ror.org/03a0vt050 @=@ CDS126 +cnr:institutes @=@ https://ror.org/03a0vt050 @=@ ISTP - Istituto per la Scienza e Tecnologia dei Plasmi +cnr:institutes @=@ __CDS127__ @=@ CDS127 +cnr:institutes @=@ __CDS127__ @=@ ISP - Istituto di Scienze Polari +cnr:institutes @=@ https://ror.org/03byxpq91 @=@ CDS128 +cnr:institutes @=@ https://ror.org/03byxpq91 @=@ IRIB - Istituto per la Ricerca e l'Innovazione Biomedica +cnr:institutes @=@ __CDS129__ @=@ CDS129 +cnr:institutes @=@ __CDS129__ @=@ IGSG - Istituto di Informatica Giuridica e Sistemi Giudiziari +cnr:institutes @=@ __CDS130__ @=@ CDS130 +cnr:institutes @=@ __CDS130__ @=@ IBBC - Istituto di Biochimica e Biologia Cellulare +cnr:institutes @=@ __CDS131__ @=@ CDS131 +cnr:institutes @=@ __CDS131__ @=@ IBE - Istituto per la BioEconomia +cnr:institutes @=@ https://ror.org/0263zy895 @=@ CDS132 +cnr:institutes @=@ https://ror.org/0263zy895 @=@ SCITEC - Istituto di Scienze e Tecnologie Chimiche \"Giulio Natta\" +cnr:institutes @=@ __CDS133__ @=@ CDS133 +cnr:institutes @=@ __CDS133__ @=@ STEMS - Istituto di Scienze e Tecnologie per l'Energia e la Mobilità Sostenibili \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/terms.txt b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/terms.txt index 93cc00eca..0f0ebaad4 100644 --- a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/terms.txt +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/terms.txt @@ -1077,4 +1077,137 @@ dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/DATASET/IS_SUPPLEMENTED dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/AUTHOR/ORCID @=@ An Open Researcher and Contributor ID (ORCID) that can be associated to an author of your publications dnet:review_levels @=@ dnet:review_levels @=@ 0000 @=@ Unknown dnet:review_levels @=@ dnet:review_levels @=@ 0002 @=@ nonPeerReviewed -dnet:review_levels @=@ dnet:review_levels @=@ 0001 @=@ peerReviewed \ No newline at end of file +dnet:review_levels @=@ dnet:review_levels @=@ 0001 @=@ peerReviewed +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/00brf2d87 @=@ https://ror.org/00brf2d87 +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/006qkqr45 @=@ https://ror.org/006qkqr45 +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/054ye0e45 @=@ https://ror.org/054ye0e45 +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/00ygy3d85 @=@ https://ror.org/00ygy3d85 +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/000sy1f36 @=@ https://ror.org/000sy1f36 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https://ror.org/01wqae691 @=@ https://ror.org/01wqae691 +cnr:institutes @=@ cnr:institutes @=@ __CDS084__ @=@ __CDS084__ +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/00awwz417 @=@ https://ror.org/00awwz417 +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/03a111314 @=@ https://ror.org/03a111314 +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/01zz9wh30 @=@ https://ror.org/01zz9wh30 +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/035y5td47 @=@ https://ror.org/035y5td47 +cnr:institutes @=@ cnr:institutes @=@ __CDS089__ @=@ __CDS089__ +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/051t1q308 @=@ https://ror.org/051t1q308 +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/05k3cs357 @=@ https://ror.org/05k3cs357 +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/02gcxw165 @=@ https://ror.org/02gcxw165 +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/05db0es39 @=@ https://ror.org/05db0es39 +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/029k6t707 @=@ https://ror.org/029k6t707 +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/00w6r1881 @=@ https://ror.org/00w6r1881 +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/01mfmr054 @=@ https://ror.org/01mfmr054 +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/058nrs650 @=@ https://ror.org/058nrs650 +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/0331xj092 @=@ https://ror.org/0331xj092 +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/052q58629 @=@ https://ror.org/052q58629 +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/04ehykb85 @=@ https://ror.org/04ehykb85 +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/0221agg28 @=@ https://ror.org/0221agg28 +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/02xz4xc25 @=@ https://ror.org/02xz4xc25 +cnr:institutes @=@ cnr:institutes @=@ __CDS103__ @=@ __CDS103__ +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/01as2bh37 @=@ https://ror.org/01as2bh37 +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/01y5w6t76 @=@ https://ror.org/01y5w6t76 +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/04xy2mq71 @=@ https://ror.org/04xy2mq71 +cnr:institutes @=@ cnr:institutes @=@ __CDS107__ @=@ __CDS107__ +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/013nxtf56 @=@ https://ror.org/013nxtf56 +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/05rcgef49 @=@ https://ror.org/05rcgef49 +cnr:institutes @=@ cnr:institutes @=@ __CDS110__ @=@ __CDS110__ +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/02dp3a879 @=@ https://ror.org/02dp3a879 +cnr:institutes @=@ cnr:institutes @=@ __CDS112__ @=@ __CDS112__ +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/00p03yg71 @=@ https://ror.org/00p03yg71 +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/00yfw2296 @=@ https://ror.org/00yfw2296 +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/0042e5975 @=@ https://ror.org/0042e5975 +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/03ta8pf33 @=@ https://ror.org/03ta8pf33 +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/040xhth73 @=@ https://ror.org/040xhth73 +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/02qnx8e75 @=@ https://ror.org/02qnx8e75 +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/05nr7xa08 @=@ https://ror.org/05nr7xa08 +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/008fjbg42 @=@ https://ror.org/008fjbg42 +cnr:institutes @=@ cnr:institutes @=@ __CDS122__ @=@ __CDS122__ +cnr:institutes @=@ cnr:institutes @=@ __CDS123__ @=@ __CDS123__ +cnr:institutes @=@ cnr:institutes @=@ __CDS124__ @=@ __CDS124__ +cnr:institutes @=@ cnr:institutes @=@ __CDS125__ @=@ __CDS125__ +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/03a0vt050 @=@ https://ror.org/03a0vt050 +cnr:institutes @=@ cnr:institutes @=@ __CDS127__ @=@ __CDS127__ +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/03byxpq91 @=@ https://ror.org/03byxpq91 +cnr:institutes @=@ cnr:institutes @=@ __CDS129__ @=@ __CDS129__ +cnr:institutes @=@ cnr:institutes @=@ __CDS130__ @=@ __CDS130__ +cnr:institutes @=@ cnr:institutes @=@ __CDS131__ @=@ __CDS131__ +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/0263zy895 @=@ https://ror.org/0263zy895 +cnr:institutes @=@ cnr:institutes @=@ __CDS133__ @=@ __CDS133__ + From 574492c659ea7a6d8e54f4332ba76a6ad45555fd Mon Sep 17 00:00:00 2001 From: Antonis Lempesis Date: Thu, 9 Jun 2022 15:48:13 +0300 Subject: [PATCH 080/214] removed double result_apc table creation from monitor --- .../graph/stats/oozie_app/scripts/step20-createMonitorDB.sql | 5 ----- 1 file changed, 5 deletions(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql index 3cf155869..7412910a9 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql @@ -107,11 +107,6 @@ compute stats TARGET.result_sources; create table TARGET.result_topics stored as parquet as select * from SOURCE.result_topics orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.result_topics; -create table TARGET.result_apc stored as parquet as select * from SOURCE.result_apc orig where exists (select 1 from TARGET.result r where r.id=orig.id); -compute stats TARGET.result_apc; - - - create view TARGET.foo1 as select * from SOURCE.result_result rr where rr.source in (select id from TARGET.result); create view TARGET.foo2 as select * from SOURCE.result_result rr where rr.target in (select id from TARGET.result); create table TARGET.result_result STORED AS PARQUET as select distinct * from (select * from TARGET.foo1 union all select * from TARGET.foo2) foufou; From 68bd58d6a46c3ffc1c4ddafcb5b25bf065edde31 Mon Sep 17 00:00:00 2001 From: Alessia Bardi Date: Fri, 10 Jun 2022 17:29:11 +0200 Subject: [PATCH 081/214] tests for ROHub --- .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 14 +++ .../dnetlib/dhp/oa/graph/clean/synonyms.txt | 1 + .../eu/dnetlib/dhp/oa/graph/clean/terms.txt | 1 + .../eu/dnetlib/dhp/oa/graph/raw/rohub.xml | 103 ++++++++++++++++++ 4 files changed, 119 insertions(+) create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/rohub.xml diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index bdb73abf5..7bc2c6e7c 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -835,6 +835,20 @@ class MappersTest { assertEquals("EUR", p.getProcessingchargecurrency().getValue()); } + @Test + void testROHub() throws IOException, DocumentException { + final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("rohub.xml"))); + final List list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml); + System.out.println("***************"); + System.out.println(new ObjectMapper().writeValueAsString(list)); + System.out.println("***************"); +// final Dataset p = (Dataset) list.get(0); +// assertValidId(p.getId()); +// assertValidId(p.getCollectedfrom().get(0).getKey()); +// System.out.println(p.getTitle().get(0).getValue()); +// assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue())); + } + private void assertValidId(final String id) { // System.out.println(id); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt index 09bd58aeb..39ed0cef1 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt @@ -497,6 +497,7 @@ dnet:publication_resource @=@ 0044 @=@ Graduate diploma dnet:publication_resource @=@ 0044 @=@ Undergraduate diploma dnet:publication_resource @=@ 0000 @=@ UNKNOWN dnet:publication_resource @=@ 0042 @=@ EGI Virtual Appliance +dnet:publication_resource @=@ 0048 @=@ RO-crate dnet:languages @=@ abk @=@ ab dnet:languages @=@ aar @=@ aa dnet:languages @=@ afr @=@ af diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt index bb1e5fbf9..59311d5a7 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt @@ -164,6 +164,7 @@ dnet:publication_resource @=@ dnet:publication_resource @=@ 0030 @=@ Sound dnet:publication_resource @=@ dnet:publication_resource @=@ 0044 @=@ Thesis dnet:publication_resource @=@ dnet:publication_resource @=@ 0000 @=@ Unknown dnet:publication_resource @=@ dnet:publication_resource @=@ 0042 @=@ Virtual Appliance +dnet:publication_resource @=@ dnet:publication_resource @=@ 0048 @=@ Research Object ec:funding_typologies @=@ ec:funding_typologies @=@ ec:frameworkprogram @=@ frameworkprogram ec:funding_typologies @=@ ec:funding_typologies @=@ ec:program @=@ program ec:funding_typologies @=@ ec:funding_typologies @=@ ec:specificprogram @=@ specificprogram diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/rohub.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/rohub.xml new file mode 100644 index 000000000..ca3ebe6c2 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/rohub.xml @@ -0,0 +1,103 @@ + + +
+ eosca5322f5f::4dd1aaf93ae136b65dc9ee4e6f76eac9 + 53aa90bf-c593-4e6d-923f-d4711ac4b0e1 + 2022-05-25T15:35:48.262Z + eosca5322f5f + 53aa90bf-c593-4e6d-923f-d4711ac4b0e1 + 2022-05-25T15:35:38Z + rohub_data + ro-crate_data + 2022-05-25T15:36:11.094Z +
+ + + https://w3id.org/ro-id/53aa90bf-c593-4e6d-923f-d4711ac4b0e1 + + http://api.rohub.org/api/ros/53aa90bf-c593-4e6d-923f-d4711ac4b0e1/ + + + + https://github.com/NordicESMhub/RELIANCE/blob/main/content/science/notebooks/air_quality_lockdown.ipynb + + https://github.com/NordicESMhub/RELIANCE/blob/main/content/science/notebooks/air_quality_lockdown.ipynb + + https://nordicesmhub.github.io/RELIANCE/science/notebooks/air_quality_lockdown.html + + https://nordicesmhub.github.io/RELIANCE/science/notebooks/air_quality_lockdown.html + + + + + Anne Fouilloux + + + + + 2021-12-19T21:18:33Z + + + The COVID-19 pandemic has led to significant reductions in economic activity, especially during lockdowns. Several studies has shown that the concentration of nitrogen dioxyde and particulate matter levels have reduced during lockdown events. Reductions in transportation sector emissions are most likely largely responsible for the NO2 anomalies. In this study, we analyze the impact of lockdown events on the air quality using data from Copernicus Atmosphere Monitoring Service over Europe and at selected locations. + + + + European Commission + 10.13039/501100000781 + 101017502 + Research Lifecycle Management for Earth Science Communities and Copernicus Users + + + MIT License + University of Oslo + 2021 + RO-crate + + open access + + + 11.971 MB + + + Applied sciences + Meteorology + EOSC::RO-crate + + + Impact of the Covid-19 Lockdown on Air quality over Europe + + + https://w3id.org/ro-id/53aa90bf-c593-4e6d-923f-d4711ac4b0e1 + 0048 + + OPEN + https://opensource.org/licenses/MIT + und + + + + + + + https%3A%2F%2Fapi.rohub.org%2Fapi%2Foai2d%2F + 53aa90bf-c593-4e6d-923f-d4711ac4b0e1 + 2022-05-25T15:35:38Z + + + + + false + false + 0.9 + + + + + \ No newline at end of file From 634869ce95611156d6e8e5b2412241b535c339ae Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Mon, 16 May 2022 09:39:54 +0200 Subject: [PATCH 082/214] deleted hierarchical rels from ror action set --- .../ror/GenerateRorActionSetJob.java | 62 ++++--------------- 1 file changed, 11 insertions(+), 51 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java index e4d458780..6c76f8a4d 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java @@ -3,7 +3,6 @@ package eu.dnetlib.dhp.actionmanager.ror; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import static eu.dnetlib.dhp.schema.common.ModelConstants.ENTITYREGISTRY_PROVENANCE_ACTION; -import static eu.dnetlib.dhp.schema.common.ModelConstants.ORG_ORG_RELTYPE; import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.dataInfo; import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.field; import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.listKeyValues; @@ -39,7 +38,6 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.actionmanager.ror.model.ExternalIdType; -import eu.dnetlib.dhp.actionmanager.ror.model.Relationship; import eu.dnetlib.dhp.actionmanager.ror.model.RorOrganization; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; @@ -51,7 +49,6 @@ import eu.dnetlib.dhp.schema.oaf.KeyValue; import eu.dnetlib.dhp.schema.oaf.Oaf; import eu.dnetlib.dhp.schema.oaf.Organization; import eu.dnetlib.dhp.schema.oaf.Qualifier; -import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.StructuredProperty; import eu.dnetlib.dhp.utils.DHPUtils; import scala.Tuple2; @@ -64,21 +61,17 @@ public class GenerateRorActionSetJob { private static final String ROR_NS_PREFIX = "ror_________"; - private static final List ROR_COLLECTED_FROM = listKeyValues( - "10|openaire____::993a7ae7a863813cf95028b50708e222", "ROR"); + private static final List ROR_COLLECTED_FROM = listKeyValues("10|openaire____::993a7ae7a863813cf95028b50708e222", "ROR"); - private static final DataInfo ROR_DATA_INFO = dataInfo( - false, "", false, false, ENTITYREGISTRY_PROVENANCE_ACTION, "0.92"); + private static final DataInfo ROR_DATA_INFO = dataInfo(false, "", false, false, ENTITYREGISTRY_PROVENANCE_ACTION, "0.92"); - private static final Qualifier ROR_PID_TYPE = qualifier( - "ROR", "ROR", ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES); + private static final Qualifier ROR_PID_TYPE = qualifier("ROR", "ROR", ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES); public static void main(final String[] args) throws Exception { final String jsonConfiguration = IOUtils - .toString( - GenerateRorActionSetJob.class - .getResourceAsStream("/eu/dnetlib/dhp/actionmanager/ror/action_set_parameters.json")); + .toString(GenerateRorActionSetJob.class + .getResourceAsStream("/eu/dnetlib/dhp/actionmanager/ror/action_set_parameters.json")); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); @@ -116,9 +109,8 @@ public class GenerateRorActionSetJob { readInputPath(spark, inputPath) .map(GenerateRorActionSetJob::convertRorOrg) .flatMap(List::iterator) - .mapToPair( - aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), - new Text(OBJECT_MAPPER.writeValueAsString(aa)))) + .mapToPair(aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), + new Text(OBJECT_MAPPER.writeValueAsString(aa)))) .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class); } @@ -153,12 +145,9 @@ public class GenerateRorActionSetJob { o.setEcnutscode(null); if (r.getCountry() != null) { o - .setCountry( - qualifier( - r.getCountry().getCountryCode(), r - .getCountry() - .getCountryName(), - ModelConstants.DNET_COUNTRY_TYPE, ModelConstants.DNET_COUNTRY_TYPE)); + .setCountry(qualifier(r.getCountry().getCountryCode(), r + .getCountry() + .getCountryName(), ModelConstants.DNET_COUNTRY_TYPE, ModelConstants.DNET_COUNTRY_TYPE)); } else { o.setCountry(null); } @@ -168,38 +157,10 @@ public class GenerateRorActionSetJob { final List> res = new ArrayList<>(); res.add(new AtomicAction<>(Organization.class, o)); - for (final Relationship rorRel : r.getRelationships()) { - if (rorRel.getType().equalsIgnoreCase("parent")) { - final String orgId1 = calculateOpenaireId(r.getId()); - final String orgId2 = calculateOpenaireId(rorRel.getId()); - res - .add( - new AtomicAction<>(Relation.class, - calculateHierarchyRel(orgId1, orgId2, ModelConstants.IS_PARENT_OF))); - res - .add( - new AtomicAction<>(Relation.class, - calculateHierarchyRel(orgId2, orgId1, ModelConstants.IS_CHILD_OF))); - } - } - return res; } - private static Relation calculateHierarchyRel(final String source, final String target, final String relClass) { - final Relation rel = new Relation(); - rel.setSource(source); - rel.setTarget(target); - rel.setRelType(ORG_ORG_RELTYPE); - rel.setSubRelType(ModelConstants.RELATIONSHIP); - rel.setRelClass(relClass); - rel.setCollectedfrom(ROR_COLLECTED_FROM); - rel.setDataInfo(ROR_DATA_INFO); - rel.setLastupdatetimestamp(System.currentTimeMillis()); - return rel; - } - private static String calculateOpenaireId(final String rorId) { return String.format("20|%s::%s", ROR_NS_PREFIX, DHPUtils.md5(rorId)); } @@ -212,8 +173,7 @@ public class GenerateRorActionSetJob { final String type = e.getKey(); final List all = e.getValue().getAll(); if (all != null) { - final Qualifier qualifier = qualifier( - type, type, ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES); + final Qualifier qualifier = qualifier(type, type, ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES); for (final String pid : all) { pids .add(structuredProperty(pid, qualifier, ROR_DATA_INFO)); From b8cda654872507e4ad622e05705c6d950186c355 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 13 Jun 2022 09:20:03 +0200 Subject: [PATCH 083/214] code formatting --- .../ror/GenerateRorActionSetJob.java | 31 ++++++++++++------- 1 file changed, 20 insertions(+), 11 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java index 6c76f8a4d..6b5bed5b8 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java @@ -61,17 +61,21 @@ public class GenerateRorActionSetJob { private static final String ROR_NS_PREFIX = "ror_________"; - private static final List ROR_COLLECTED_FROM = listKeyValues("10|openaire____::993a7ae7a863813cf95028b50708e222", "ROR"); + private static final List ROR_COLLECTED_FROM = listKeyValues( + "10|openaire____::993a7ae7a863813cf95028b50708e222", "ROR"); - private static final DataInfo ROR_DATA_INFO = dataInfo(false, "", false, false, ENTITYREGISTRY_PROVENANCE_ACTION, "0.92"); + private static final DataInfo ROR_DATA_INFO = dataInfo( + false, "", false, false, ENTITYREGISTRY_PROVENANCE_ACTION, "0.92"); - private static final Qualifier ROR_PID_TYPE = qualifier("ROR", "ROR", ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES); + private static final Qualifier ROR_PID_TYPE = qualifier( + "ROR", "ROR", ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES); public static void main(final String[] args) throws Exception { final String jsonConfiguration = IOUtils - .toString(GenerateRorActionSetJob.class - .getResourceAsStream("/eu/dnetlib/dhp/actionmanager/ror/action_set_parameters.json")); + .toString( + GenerateRorActionSetJob.class + .getResourceAsStream("/eu/dnetlib/dhp/actionmanager/ror/action_set_parameters.json")); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); @@ -109,8 +113,9 @@ public class GenerateRorActionSetJob { readInputPath(spark, inputPath) .map(GenerateRorActionSetJob::convertRorOrg) .flatMap(List::iterator) - .mapToPair(aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), - new Text(OBJECT_MAPPER.writeValueAsString(aa)))) + .mapToPair( + aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), + new Text(OBJECT_MAPPER.writeValueAsString(aa)))) .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class); } @@ -145,9 +150,12 @@ public class GenerateRorActionSetJob { o.setEcnutscode(null); if (r.getCountry() != null) { o - .setCountry(qualifier(r.getCountry().getCountryCode(), r - .getCountry() - .getCountryName(), ModelConstants.DNET_COUNTRY_TYPE, ModelConstants.DNET_COUNTRY_TYPE)); + .setCountry( + qualifier( + r.getCountry().getCountryCode(), r + .getCountry() + .getCountryName(), + ModelConstants.DNET_COUNTRY_TYPE, ModelConstants.DNET_COUNTRY_TYPE)); } else { o.setCountry(null); } @@ -173,7 +181,8 @@ public class GenerateRorActionSetJob { final String type = e.getKey(); final List all = e.getValue().getAll(); if (all != null) { - final Qualifier qualifier = qualifier(type, type, ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES); + final Qualifier qualifier = qualifier( + type, type, ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES); for (final String pid : all) { pids .add(structuredProperty(pid, qualifier, ROR_DATA_INFO)); From 116902c028c5c498be74b5bbe55b78f50c99fb78 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 13 Jun 2022 14:31:48 +0200 Subject: [PATCH 084/214] mapping relationship from trasformed records based on oaf:relation --- .../raw/AbstractMdRecordToOafMapper.java | 65 ++++++++++++--- .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 82 +++++++++++++------ .../dnetlib/dhp/oa/graph/raw/oaf_record.xml | 7 ++ 3 files changed, 117 insertions(+), 37 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index 3e8ca1763..bf337e6c9 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -18,14 +18,7 @@ import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.oaiIProvenance; import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.qualifier; import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.structuredProperty; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Date; -import java.util.HashMap; -import java.util.List; -import java.util.Map; -import java.util.Optional; -import java.util.Set; +import java.util.*; import org.apache.commons.lang3.StringUtils; import org.dom4j.*; @@ -35,6 +28,7 @@ import com.google.common.collect.Sets; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.AccessRight; import eu.dnetlib.dhp.schema.oaf.Author; import eu.dnetlib.dhp.schema.oaf.Context; @@ -199,8 +193,13 @@ public abstract class AbstractMdRecordToOafMapper { final List oafs = Lists.newArrayList(entity); if (!oafs.isEmpty()) { - oafs.addAll(addProjectRels(doc, entity)); - oafs.addAll(addOtherResultRels(doc, entity)); + Set rels = Sets.newHashSet(); + + rels.addAll(addProjectRels(doc, entity)); + rels.addAll(addOtherResultRels(doc, entity)); + rels.addAll(addRelations(doc, entity)); + + oafs.addAll(rels); } return oafs; @@ -278,6 +277,52 @@ public abstract class AbstractMdRecordToOafMapper { return res; } + private List addRelations(Document doc, OafEntity entity) { + + final List rels = Lists.newArrayList(); + + for (Object o : doc.selectNodes("//oaf:relation")) { + Element element = (Element) o; + + final Relation rel = new Relation(); + rel.setCollectedfrom(entity.getCollectedfrom()); + rel.setDataInfo(entity.getDataInfo()); + rel.setLastupdatetimestamp(entity.getLastupdatetimestamp()); + + String relType = element.attributeValue("relType"); + String subRelType = element.attributeValue("subRelType"); + String relClass = element.attributeValue("relClass"); + String relClassInverse = ModelSupport + .findInverse(ModelSupport.rel(relType, subRelType, relClass)) + .getInverseRelClass(); + + rel.setSource(entity.getId()); + String target = StringUtils.trim(element.getText()); + + final String validationdDate = ((Node) o).valueOf("@validationDate"); + + if (StringUtils.isNotBlank(target)) { + + // TODO discover the target entity type with a dedicated attribute, e.g. @targetType. + final String[] parts = relType.split("(?=\\p{Upper})"); + final String targetType = parts[1].toLowerCase(); + final String targetId = createOpenaireId(targetType, target, true); + + rels + .add( + getRelation( + entity.getId(), targetId, relType, subRelType, relClass, entity, validationdDate)); + rels + .add( + getRelation( + targetId, entity.getId(), relType, subRelType, relClassInverse, entity, validationdDate)); + } + + } + + return rels; + } + protected Relation getRelation(final String source, final String target, final String relType, diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index 7bc2c6e7c..dd69bae85 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -57,14 +57,10 @@ class MappersTest { final List list = new OafToOafMapper(vocs, false, true).processMdRecord(xml); - assertEquals(3, list.size()); - assertTrue(list.get(0) instanceof Publication); - assertTrue(list.get(1) instanceof Relation); - assertTrue(list.get(2) instanceof Relation); + assertEquals(1, list.stream().filter(o -> o instanceof Publication).count()); + assertEquals(4, list.stream().filter(o -> o instanceof Relation).count()); - final Publication p = (Publication) list.get(0); - final Relation r1 = (Relation) list.get(1); - final Relation r2 = (Relation) list.get(2); + Publication p = (Publication) list.stream().filter(o -> o instanceof Publication).findFirst().get(); assertValidId(p.getId()); @@ -125,26 +121,58 @@ class MappersTest { assertNotNull(p.getBestaccessright()); assertEquals("OPEN", p.getBestaccessright().getClassid()); - assertValidId(r1.getSource()); - assertValidId(r1.getTarget()); - assertValidId(r2.getSource()); - assertValidId(r2.getTarget()); - assertValidId(r1.getCollectedfrom().get(0).getKey()); - assertValidId(r2.getCollectedfrom().get(0).getKey()); - assertNotNull(r1.getDataInfo()); - assertNotNull(r2.getDataInfo()); - assertNotNull(r1.getDataInfo().getTrust()); - assertNotNull(r2.getDataInfo().getTrust()); - assertEquals(r1.getSource(), r2.getTarget()); - assertEquals(r2.getSource(), r1.getTarget()); - assertTrue(StringUtils.isNotBlank(r1.getRelClass())); - assertTrue(StringUtils.isNotBlank(r2.getRelClass())); - assertTrue(StringUtils.isNotBlank(r1.getRelType())); - assertTrue(StringUtils.isNotBlank(r2.getRelType())); - assertTrue(r1.getValidated()); - assertTrue(r2.getValidated()); - assertEquals("2020-01-01", r1.getValidationDate()); - assertEquals("2020-01-01", r2.getValidationDate()); + + // RESULT PROJECT + List resultProject = list + .stream() + .filter(o -> o instanceof Relation) + .map(o -> (Relation) o) + .filter(r -> ModelConstants.RESULT_PROJECT.equals(r.getRelType())) + .collect(Collectors.toList()); + + assertEquals(2, resultProject.size()); + final Relation rp1 = resultProject.get(0); + final Relation rp2 = resultProject.get(1); + + verifyRelation(rp1); + verifyRelation(rp2); + + assertTrue(rp1.getValidated()); + assertTrue(rp2.getValidated()); + assertEquals("2020-01-01", rp1.getValidationDate()); + assertEquals("2020-01-01", rp2.getValidationDate()); + + assertEquals(rp1.getSource(), rp2.getTarget()); + assertEquals(rp2.getSource(), rp1.getTarget()); + + // AFFILIATIONS + List affiliation = list + .stream() + .filter(o -> o instanceof Relation) + .map(o -> (Relation) o) + .filter(r -> ModelConstants.RESULT_ORGANIZATION.equals(r.getRelType())) + .collect(Collectors.toList()); + + assertEquals(2, affiliation.size()); + final Relation aff1 = affiliation.get(0); + final Relation aff2 = affiliation.get(1); + + verifyRelation(aff1); + verifyRelation(aff2); + + assertEquals(aff1.getSource(), aff2.getTarget()); + assertEquals(aff2.getSource(), aff1.getTarget()); + } + + private void verifyRelation(Relation r) { + assertValidId(r.getSource()); + assertValidId(r.getTarget()); + assertValidId(r.getCollectedfrom().get(0).getKey()); + assertNotNull(r.getDataInfo()); + assertNotNull(r.getDataInfo().getTrust()); + assertTrue(StringUtils.isNotBlank(r.getRelClass())); + assertTrue(StringUtils.isNotBlank(r.getRelType())); + } @Test diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_record.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_record.xml index f4b0c477f..2946ba0b5 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_record.xml +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_record.xml @@ -60,6 +60,13 @@ https://oneecosystem.pensoft.net/article/13718/ One Ecosystem 0001 + ror_________::https://ror.org/02gdcn153 + corda_______::226852 From 88d531dc91294236fca929f13b1bf5ab00ef4c72 Mon Sep 17 00:00:00 2001 From: Alessia Bardi Date: Mon, 13 Jun 2022 16:17:17 +0200 Subject: [PATCH 085/214] exclude FAIRsharing records from Datacite --- .../datacite/DataciteToOAFTransformation.scala | 18 ++++++++++++------ .../datacite/record_fairsharing.json | 1 + .../dhp/datacite/DataciteToOAFTest.scala | 15 +++++++++++++++ 3 files changed, 28 insertions(+), 6 deletions(-) create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/datacite/record_fairsharing.json diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala index 48d0f1497..ff966aaea 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala @@ -47,13 +47,18 @@ object DataciteToOAFTransformation { } /** This method should skip record if json contains invalid text - * defined in gile datacite_filter + * defined in file datacite_filter * - * @param json + * @param record : unparsed datacite record + * @param json : parsed record * @return True if the record should be skipped */ - def skip_record(json: String): Boolean = { - datacite_filter.exists(f => json.contains(f)) + def skip_record(record: String, json: org.json4s.JValue): Boolean = { + implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats + datacite_filter.exists(f => record.contains(f)) || (json \\ "publisher") + .extractOrElse[String]("") + .equalsIgnoreCase("FAIRsharing") + } @deprecated("this method will be removed", "dhp") @@ -304,12 +309,13 @@ object DataciteToOAFTransformation { vocabularies: VocabularyGroup, exportLinks: Boolean ): List[Oaf] = { - if (skip_record(input)) - return List() implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats lazy val json = parse(input) + if (skip_record(input, json)) + return List() + val resourceType = (json \ "attributes" \ "types" \ "resourceType").extractOrElse[String](null) val resourceTypeGeneral = (json \ "attributes" \ "types" \ "resourceTypeGeneral").extractOrElse[String](null) diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/datacite/record_fairsharing.json b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/datacite/record_fairsharing.json new file mode 100644 index 000000000..08e80b33b --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/datacite/record_fairsharing.json @@ -0,0 +1 @@ +{"id":"10.5517/ccdc.csd.cc25rpzm","type":"dois","attributes":{"doi":"10.5517/ccdc.csd.cc25rpzm","prefix":"10.5517","suffix":"ccdc.csd.cc25rpzm","identifiers":[{"identifier":"2018781","identifierType":"CCDC"}],"alternateIdentifiers":[{"alternateIdentifierType":"CCDC","alternateIdentifier":"2018781"}],"creators":[{"name":"Ling, Irene","affiliation":[],"nameIdentifiers":[]},{"name":"Sobolev, Alexandre N.","affiliation":[],"nameIdentifiers":[]},{"name":"Raston, Colin L.","affiliation":[],"nameIdentifiers":[]}],"titles":[{"title":"CCDC 2018781: Experimental Crystal Structure Determination"}],"publisher":"fairsharing","container":{},"publicationYear":2021,"subjects":[{"subject":"Crystal Structure"},{"subject":"Experimental 3D Coordinates"},{"subject":"Crystal System"},{"subject":"Space Group"},{"subject":"Cell Parameters"},{"subject":"Crystallography"},{"subject":"bis[penta-aqua-copper(ii)] bis(mu-5,11,17,23-tetra-sulfonato-25,26,27,28-tetrahydroxycalix(4)arene)-dodeca-aqua-tri-copper(ii) bis(nitrate) heptahydrate"}],"contributors":[],"dates":[],"language":"en","types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[{"relationType":"IsSupplementTo","relatedIdentifier":"10.1080/00958972.2020.1849642","relatedIdentifierType":"DOI"}],"sizes":[],"formats":["CIF"],"version":null,"rightsList":[],"descriptions":[{"description":"Related Article: Irene Ling, Alexandre N. Sobolev, Colin L. Raston|2021|J.Coord.Chem.|74|40|doi:10.1080/00958972.2020.1849642","descriptionType":"Other"}],"geoLocations":[],"fundingReferences":[],"xml":"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","url":"http://www.ccdc.cam.ac.uk/services/structure_request?id=doi:10.5517/ccdc.csd.cc25rpzm&sid=DataCite","contentUrl":null,"metadataVersion":3,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"api","isActive":true,"state":"findable","reason":null,"viewCount":0,"viewsOverTime":[],"downloadCount":0,"downloadsOverTime":[],"referenceCount":0,"citationCount":0,"citationsOverTime":[],"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":0,"created":"2021-03-09T13:25:35.000Z","registered":"2021-03-09T13:25:36.000Z","published":"2021","updated":"2021-03-31T21:49:56.000Z"},"relationships":{"client":{"data":{"id":"ccdc.csd","type":"clients"}},"provider":{"data":{"id":"ccdc","type":"providers"}},"media":{"data":{"id":"10.5517/ccdc.csd.cc25rpzm","type":"media"}},"references":{"data":[]},"citations":{"data":[]},"parts":{"data":[]},"partOf":{"data":[]},"versions":{"data":[]},"versionOf":{"data":[]}}} \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala index 8e41de83c..31784c7e9 100644 --- a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala +++ b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala @@ -107,4 +107,19 @@ class DataciteToOAFTest extends AbstractVocabularyTest { } + @Test + def testFilter(): Unit = { + val record = Source + .fromInputStream( + getClass.getResourceAsStream("/eu/dnetlib/dhp/actionmanager/datacite/record_fairsharing.json") + ) + .mkString + + val mapper = new ObjectMapper().enable(SerializationFeature.INDENT_OUTPUT) + val res: List[Oaf] = DataciteToOAFTransformation.generateOAF(record, 0L, 0L, vocabularies, true) + + assertTrue(res.isEmpty) + + } + } From 4c8e820ff0af53cb2b86d6553281afb2839d1699 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 14 Jun 2022 08:49:02 +0200 Subject: [PATCH 086/214] mapping relationship from trasformed records based on oaf:relation --- .../raw/AbstractMdRecordToOafMapper.java | 56 +++++++++---------- .../dnetlib/dhp/oa/graph/raw/oaf_record.xml | 4 +- 2 files changed, 28 insertions(+), 32 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index bf337e6c9..739be3df4 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -284,42 +284,36 @@ public abstract class AbstractMdRecordToOafMapper { for (Object o : doc.selectNodes("//oaf:relation")) { Element element = (Element) o; - final Relation rel = new Relation(); - rel.setCollectedfrom(entity.getCollectedfrom()); - rel.setDataInfo(entity.getDataInfo()); - rel.setLastupdatetimestamp(entity.getLastupdatetimestamp()); + final String target = StringUtils.trim(element.getText()); + final String relType = element.attributeValue("relType"); + final String subRelType = element.attributeValue("subRelType"); + final String relClass = element.attributeValue("relClass"); - String relType = element.attributeValue("relType"); - String subRelType = element.attributeValue("subRelType"); - String relClass = element.attributeValue("relClass"); - String relClassInverse = ModelSupport - .findInverse(ModelSupport.rel(relType, subRelType, relClass)) - .getInverseRelClass(); + if (StringUtils.isNotBlank(target) && StringUtils.isNotBlank(relType) && StringUtils.isNotBlank(subRelType) + && StringUtils.isNotBlank(relClass)) { - rel.setSource(entity.getId()); - String target = StringUtils.trim(element.getText()); + final String relClassInverse = ModelSupport + .findInverse(ModelSupport.rel(relType, subRelType, relClass)) + .getInverseRelClass(); + final String validationdDate = ((Node) o).valueOf("@validationDate"); - final String validationdDate = ((Node) o).valueOf("@validationDate"); - - if (StringUtils.isNotBlank(target)) { - - // TODO discover the target entity type with a dedicated attribute, e.g. @targetType. - final String[] parts = relType.split("(?=\\p{Upper})"); - final String targetType = parts[1].toLowerCase(); - final String targetId = createOpenaireId(targetType, target, true); - - rels - .add( - getRelation( - entity.getId(), targetId, relType, subRelType, relClass, entity, validationdDate)); - rels - .add( - getRelation( - targetId, entity.getId(), relType, subRelType, relClassInverse, entity, validationdDate)); + if (StringUtils.isNotBlank(target)) { + final String targetType = element.attributeValue("targetType"); + if (StringUtils.isNotBlank(targetType)) { + final String targetId = createOpenaireId(targetType, target, true); + rels + .add( + getRelation( + entity.getId(), targetId, relType, subRelType, relClass, entity, validationdDate)); + rels + .add( + getRelation( + targetId, entity.getId(), relType, subRelType, relClassInverse, entity, + validationdDate)); + } + } } - } - return rels; } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_record.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_record.xml index 2946ba0b5..277578185 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_record.xml +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_record.xml @@ -62,10 +62,12 @@ 0001 ror_________::https://ror.org/02gdcn153 + subRelType="affiliation" + targetType="organization">ror_________::https://ror.org/02gdcn153 corda_______::226852 From b295a40d9cd88ad8c88c4a387eb10baa58502f64 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 16 Jun 2022 12:20:43 +0200 Subject: [PATCH 087/214] restored use of name_particles when parsing author names --- .../eu/dnetlib/dhp/common/PacePerson.java | 74 ++++++++++++------- .../eu/dnetlib/dhp/common}/name_particles.txt | 2 +- .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 45 +++++++++++ .../dnetlib/dhp/oa/graph/raw/odf_zenodo.xml | 69 +++++++++++++++++ 4 files changed, 161 insertions(+), 29 deletions(-) rename {dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/pace => dhp-common/src/main/resources/eu/dnetlib/dhp/common}/name_particles.txt (85%) create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_zenodo.xml diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/PacePerson.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/PacePerson.java index 91c6c1825..fac9a7565 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/PacePerson.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/PacePerson.java @@ -1,18 +1,18 @@ package eu.dnetlib.dhp.common; +import java.io.IOException; import java.nio.charset.StandardCharsets; import java.text.Normalizer; -import java.util.HashSet; -import java.util.List; -import java.util.Set; +import java.util.*; +import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.text.WordUtils; +import com.ctc.wstx.dtd.LargePrefixedNameSet; import com.google.common.base.Joiner; import com.google.common.base.Splitter; -import com.google.common.collect.Iterables; import com.google.common.collect.Lists; import com.google.common.hash.Hashing; @@ -29,7 +29,19 @@ public class PacePerson { private List fullname = Lists.newArrayList(); private final String original; - private static Set particles = null; + private static Set particles; + + static { + try { + particles = new HashSet<>(IOUtils + .readLines( + PacePerson.class + .getResourceAsStream( + "/eu/dnetlib/dhp/common/name_particles.txt"))); + } catch (IOException e) { + throw new RuntimeException(e); + } + } /** * Capitalizes a string @@ -37,29 +49,20 @@ public class PacePerson { * @param s the string to capitalize * @return the input string with capital letter */ - public static final String capitalize(final String s) { + public static String capitalize(final String s) { + if (particles.contains(s)) { + return s; + } return WordUtils.capitalize(s.toLowerCase(), ' ', '-'); } /** * Adds a dot to a string with length equals to 1 */ - public static final String dotAbbreviations(final String s) { + public static String dotAbbreviations(final String s) { return s.length() == 1 ? s + "." : s; } - public static Set loadFromClasspath(final String classpath) { - final Set h = new HashSet<>(); - try { - for (final String s : IOUtils.readLines(PacePerson.class.getResourceAsStream(classpath))) { - h.add(s); - } - } catch (final Throwable e) { - return new HashSet<>(); - } - return h; - } - /** * The constructor of the class. It fills the fields of the class basing on the input fullname. * @@ -128,10 +131,6 @@ public class PacePerson { } private List splitTerms(final String s) { - if (particles == null) { - particles = loadFromClasspath("/eu/dnetlib/dhp/oa/graph/pace/name_particles.txt"); - } - final List list = Lists.newArrayList(); for (final String part : Splitter.on(" ").omitEmptyStrings().split(s)) { if (!particles.contains(part.toLowerCase())) { @@ -187,17 +186,36 @@ public class PacePerson { } public List getCapitalFirstnames() { - return Lists - .newArrayList( - Iterables.transform(getNameWithAbbreviations(), PacePerson::capitalize)); + return Optional + .ofNullable(getNameWithAbbreviations()) + .map( + name -> name + .stream() + .map(PacePerson::capitalize) + .collect(Collectors.toList())) + .orElse(new ArrayList<>()); } public List getCapitalSurname() { - return Lists.newArrayList(Iterables.transform(surname, PacePerson::capitalize)); + return Optional + .ofNullable(getSurname()) + .map( + surname -> surname + .stream() + .map(PacePerson::capitalize) + .collect(Collectors.toList())) + .orElse(new ArrayList<>()); } public List getNameWithAbbreviations() { - return Lists.newArrayList(Iterables.transform(name, PacePerson::dotAbbreviations)); + return Optional + .ofNullable(getName()) + .map( + name -> name + .stream() + .map(PacePerson::dotAbbreviations) + .collect(Collectors.toList())) + .orElse(new ArrayList<>()); } public boolean isAccurate() { diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/pace/name_particles.txt b/dhp-common/src/main/resources/eu/dnetlib/dhp/common/name_particles.txt similarity index 85% rename from dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/pace/name_particles.txt rename to dhp-common/src/main/resources/eu/dnetlib/dhp/common/name_particles.txt index dae37c9dc..d21610522 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/pace/name_particles.txt +++ b/dhp-common/src/main/resources/eu/dnetlib/dhp/common/name_particles.txt @@ -4,4 +4,4 @@ de dell sig mr -mrs +mrs \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index dd69bae85..f5cb86bfd 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -762,6 +762,51 @@ class MappersTest { assertFalse(p_cleaned.getTitle().isEmpty()); } + @Test + void testZenodo() throws IOException, DocumentException { + final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_zenodo.xml"))); + final List list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml); + + System.out.println("***************"); + System.out.println(new ObjectMapper().writeValueAsString(list)); + System.out.println("***************"); + + final Publication p = (Publication) list.get(0); + assertValidId(p.getId()); + assertValidId(p.getCollectedfrom().get(0).getKey()); + + assertNotNull(p.getTitle()); + assertFalse(p.getTitle().isEmpty()); + assertEquals(1, p.getTitle().size()); + assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue())); + + assertNotNull(p.getAuthor()); + assertEquals(2, p.getAuthor().size()); + + Author author = p + .getAuthor() + .stream() + .filter(a -> a.getPid().stream().anyMatch(pi -> pi.getValue().equals("0000-0003-3272-8007"))) + .findFirst() + .get(); + assertNotNull(author); + assertTrue(StringUtils.isBlank(author.getSurname())); + assertTrue(StringUtils.isBlank(author.getName())); + assertEquals("Anne van Weerden", author.getFullname()); + + author = p + .getAuthor() + .stream() + .filter(a -> a.getPid().stream().anyMatch(pi -> pi.getValue().equals("0000-0003-3272-8008"))) + .findFirst() + .get(); + assertNotNull(author); + assertFalse(StringUtils.isBlank(author.getSurname())); + assertFalse(StringUtils.isBlank(author.getName())); + assertFalse(StringUtils.isBlank(author.getFullname())); + + } + @Test void testOdfFromHdfs() throws IOException, DocumentException { final String xml = IOUtils diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_zenodo.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_zenodo.xml new file mode 100644 index 000000000..0fc568e56 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_zenodo.xml @@ -0,0 +1,69 @@ + +> +
+ oai:zenodo.org:3406824 + 2020-01-20T16:45:20Z + openaire + 2022-06-07T10:21:24.06Z + test________::92fe3efa47883b2f3401e6a4bd92e9d7 + 2020-05-21T05:26:15.93Z + 2020-08-01T11:06:26.977Z +
+ + + 10.5281/zenodo.3406824 + + http://dx.doi.org/10.5281/zenodo.3406824 + + + + Anne van Weerden + 0000-0003-3272-8007 + Utrecht University Library + + + Anne van, Weerden + 0000-0003-3272-8008 + Utrecht University Library + + + + Helen Bayly and Catherine Disney as influences in the life of Sir William Rowan Hamilton + + Zenodo + 2018 + + Sir William Rowan Hamilton, Lady Helena Maria Hamilton Bayly, Catherine Disney, Ireland, history, biography, nineteenth century + + + 2018-12-28 + + en + + + 10.5281/zenodo.3406823 + + + Creative Commons Attribution 4.0 International + Open Access + + +

In the 1880s Robert Graves published a biography about Sir William Rowan Hamilton (1805-1865), to which in a 1980 biography Thomas Hankins added further information. From these biographies a picture emerged of a man who was unhappily married because he had lost the love of his life, which raised the question how such an unhappy man could produce so much beautiful mathematics. In this article it is stated that a main cause for the unhappy picture is that Graves ignored the influence on one another of Hamilton and his wife Helen Bayly, and Hankins that of Hamilton and his first and lost love Catherine Disney. It is then shown that if these influences are taken into account a very different view on Hamilton;s private life arises, in which he was happily married to a wife who enabled him to work as he needed to.

 + + + 10.5281/zenodo.3406824 + 0001 + 2018-12-28 + OPEN + https://creativecommons.org/licenses/by/4.0/legalcode + eng + + + + \ No newline at end of file From 7423577a082318d6d7648945243e237c9f847029 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 21 Jun 2022 14:51:38 +0200 Subject: [PATCH 088/214] [Graph DUMP] add code to produce the delta of new projects with respect to the previous delta/dump --- .../ProjectsSubsetSparkJob.java | 80 ++++++++ .../graph/dump/project_subset_parameters.json | 27 +++ .../oozie_app/config-default.xml | 30 +++ .../dump/projectsubset/oozie_app/workflow.xml | 171 ++++++++++++++++++ 4 files changed, 308 insertions(+) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/project_subset_parameters.json create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/oozie_app/config-default.xml create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/oozie_app/workflow.xml diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java new file mode 100644 index 000000000..67da24185 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java @@ -0,0 +1,80 @@ +package eu.dnetlib.dhp.oa.graph.dump.projectssubset; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; +import java.io.Serializable; +import java.util.List; +import java.util.Objects; +import java.util.Optional; +import java.util.stream.Collectors; +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.FilterFunction; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.jetbrains.annotations.NotNull; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.oa.graph.dump.Utils; +import eu.dnetlib.dhp.schema.dump.oaf.community.Funder; +import eu.dnetlib.dhp.schema.dump.oaf.graph.Project; +import scala.Tuple2; +public class ProjectsSubsetSparkJob implements Serializable { + private static final Logger log = LoggerFactory.getLogger(ProjectsSubsetSparkJob.class); + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + ProjectsSubsetSparkJob.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump/project_subset_parameters.json")); + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + final String inputPath = parser.get("sourcePath"); + log.info("inputPath: {}", inputPath); + final String outputPath = parser.get("outputPath"); + log.info("outputPath: {}", outputPath); + final String projectListPath = parser.get("projectListPath"); + log.info("projectListPath: {}", projectListPath); + SparkConf conf = new SparkConf(); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath); + getNewProjectList(spark, inputPath, outputPath, projectListPath); + }); + } + private static void getNewProjectList(SparkSession spark, String inputPath, String outputPath, + String projectListPath) { + Dataset projectList = spark.read().textFile(projectListPath); + // projectList.show(false); + Dataset projects; + projects = Utils.readPath(spark, inputPath, Project.class); + projects + .joinWith(projectList, projects.col("id").equalTo(projectList.col("value")), "left") + .map((MapFunction, Project>) t2 -> { + if (Optional.ofNullable(t2._2()).isPresent()) + return null; + return t2._1(); + }, Encoders.bean(Project.class)) + .filter(Objects::nonNull) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath); + Utils + .readPath(spark, outputPath, Project.class) + .map((MapFunction) p -> p.getId(), Encoders.STRING()) + .write() + .mode(SaveMode.Append) + .option("compression", "gzip") + .text(projectListPath); + } +} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/project_subset_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/project_subset_parameters.json new file mode 100644 index 000000000..ed2313680 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/project_subset_parameters.json @@ -0,0 +1,27 @@ +[ + { + "paramName":"s", + "paramLongName":"sourcePath", + "paramDescription": "the path of the sequencial file to read", + "paramRequired": true + }, + { + "paramName": "out", + "paramLongName": "outputPath", + "paramDescription": "the path used to store temporary output files", + "paramRequired": true + }, + { + "paramName": "ssm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "true if the spark session is managed, false otherwise", + "paramRequired": false + }, + { + "paramName": "pl", + "paramLongName": "projectListPath", + "paramDescription": "the path of the association result projectlist", + "paramRequired": true + } +] + diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/oozie_app/config-default.xml new file mode 100644 index 000000000..d262cb6e0 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/oozie_app/config-default.xml @@ -0,0 +1,30 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + hiveMetastoreUris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + hiveJdbcUrl + jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000 + + + hiveDbName + openaire + + + oozie.launcher.mapreduce.user.classpath.first + true + + diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/oozie_app/workflow.xml new file mode 100644 index 000000000..619e3aa20 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/oozie_app/workflow.xml @@ -0,0 +1,171 @@ + + + + sourcePath + the source path + + + projectListPath + the path to the project list + + + outputPath + the output path + + + accessToken + the access token used for the deposition in Zenodo + + + connectionUrl + the connection url for Zenodo + + + metadata + the metadata associated to the deposition + + + depositionType + the type of deposition we want to perform. "new" for brand new deposition, "version" for a new version of a published deposition (in this case the concept record id must be provided), "upload" to upload content to an open deposition for which we already have the deposition id (in this case the deposition id should be provided) + + + conceptRecordId + for new version, the id of the record for the old deposition + + + depositionId + the depositionId of a deposition open that has to be added content + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + + + spark2YarnHistoryServerAddress + spark 2.* yarn history server address + + + spark2EventLogDir + spark 2.* event log dir location + + + + ${jobTracker} + ${nameNode} + + + mapreduce.job.queuename + ${queueName} + + + oozie.launcher.mapred.job.queue.name + ${oozieLauncherQueueName} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + yarn + cluster + Dump table project + eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/project + --resultTableNameeu.dnetlib.dhp.schema.oaf.Project + --outputPath${workingDir}/project + --communityMapPathnoneed + + + + + + + yarn + cluster + Dump table project + eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectsSubsetSparkJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/project + --outputPath${workingDir}/tar/project + --projectListPath${projectListPath} + + + + + + + eu.dnetlib.dhp.oa.graph.dump.MakeTar + --hdfsPath${outputPath} + --nameNode${nameNode} + --sourcePath${workingDir}/tar + + + + + + + eu.dnetlib.dhp.oa.graph.dump.SendToZenodoHDFS + --hdfsPath${outputPath} + --nameNode${nameNode} + --accessToken${accessToken} + --connectionUrl${connectionUrl} + --metadata${metadata} + --conceptRecordId${conceptRecordId} + --depositionType${depositionType} + --depositionId${depositionId} + + + + + + \ No newline at end of file From b98f904d48a2923b13225a656510da850c07d533 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 21 Jun 2022 17:52:27 +0200 Subject: [PATCH 089/214] [Funder Products Dump] new way to avoid using hive --- .../community/SparkPrepareResultProject.java | 6 +- .../funderresults/SparkDumpFunderResults.java | 171 ++++----- .../SparkResultLinkedToProject.java | 102 ++--- .../graph/dump/funder_result_parameters.json | 12 +- .../dump/input_parameter_select_relation.json | 20 + .../graph/dump/input_parameters_link_prj.json | 6 + .../oozie_app/config-default.xml | 30 -- .../oozie_app/workflow.xml | 347 ------------------ .../community/oozie_app/import.txt | 2 - .../community/oozie_app/workflow.xml | 273 ++++++++++++-- .../complete/oozie_app/workflow.xml | 1 + .../subworkflows/funder/oozie_app/import.txt | 2 - .../funder/oozie_app/workflow.xml | 71 ++-- .../dump/PrepareResultProjectJobTest.java | 281 +++++++------- .../ResultLinkedToProjectTest.java | 85 +++-- .../dump/funderresult/SplitPerFunderTest.java | 74 ++-- .../communityMapPath/communityMap | 1 + .../{extendeddump/orp => ext/dataset} | 0 .../funderresource/ext/otherresearchproduct | 0 .../oa/graph/dump/funderresource/ext/project | 12 + .../graph/dump/funderresource/ext/publication | 13 + .../oa/graph/dump/funderresource/ext/software | 0 .../extendeddump/otherresearchproduct | 32 ++ .../dump/funderresource/fundersList/list | 8 + .../funderresource/preparedInfo/resultProject | 1 + 25 files changed, 744 insertions(+), 806 deletions(-) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameter_select_relation.json delete mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/config-default.xml delete mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/workflow.xml delete mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/import.txt delete mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/import.txt create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/communityMapPath/communityMap rename dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/{extendeddump/orp => ext/dataset} (100%) create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext/otherresearchproduct create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext/project create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext/publication create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext/software create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/otherresearchproduct create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/fundersList/list create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo/resultProject diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java index 87ac20948..410feea02 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java @@ -10,6 +10,7 @@ import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.MapGroupsFunction; import org.apache.spark.sql.Dataset; @@ -81,8 +82,9 @@ public class SparkPrepareResultProject implements Serializable { Dataset relation = Utils .readPath(spark, inputPath + "/relation", Relation.class) .filter( - "dataInfo.deletedbyinference = false and lower(relClass) = '" - + ModelConstants.IS_PRODUCED_BY.toLowerCase() + "'"); + (FilterFunction) r -> !r.getDataInfo().getDeletedbyinference() && + r.getRelClass().equalsIgnoreCase(ModelConstants.IS_PRODUCED_BY)); + Dataset projects = Utils .readPath(spark, inputPath + "/project", eu.dnetlib.dhp.schema.oaf.Project.class); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java index 6aed9d7a8..cfe47f29f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java @@ -1,140 +1,119 @@ - package eu.dnetlib.dhp.oa.graph.dump.funderresults; - import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - import java.io.Serializable; import java.util.List; import java.util.Objects; import java.util.Optional; - +import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.FlatMapFunction; +import org.apache.spark.api.java.function.ForeachFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.*; +import org.jetbrains.annotations.NotNull; import org.slf4j.Logger; import org.slf4j.LoggerFactory; - import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; +import eu.dnetlib.dhp.schema.dump.oaf.community.Funder; import eu.dnetlib.dhp.schema.dump.oaf.community.Project; - /** * Splits the dumped results by funder and stores them in a folder named as the funder nsp (for all the funders, but the EC * for the EC it specifies also the fundingStream (FP7 or H2020) */ public class SparkDumpFunderResults implements Serializable { private static final Logger log = LoggerFactory.getLogger(SparkDumpFunderResults.class); - public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils - .toString( - SparkDumpFunderResults.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json")); - + .toString( + SparkDumpFunderResults.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json")); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); parser.parseArgument(args); - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String inputPath = parser.get("sourcePath"); log.info("inputPath: {}", inputPath); - final String outputPath = parser.get("outputPath"); log.info("outputPath: {}", outputPath); - - final String graphPath = parser.get("graphPath"); - log.info("relationPath: {}", graphPath); - SparkConf conf = new SparkConf(); - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - writeResultProjectList(spark, inputPath, outputPath, graphPath); - }); + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath); + writeResultProjectList(spark, inputPath, outputPath); + }); } - - private static void writeResultProjectList(SparkSession spark, String inputPath, String outputPath, - String graphPath) { - - Dataset project = Utils - .readPath(spark, graphPath + "/project", eu.dnetlib.dhp.schema.oaf.Project.class); - + private static void writeResultProjectList(SparkSession spark, String inputPath, String outputPath) { Dataset result = Utils - .readPath(spark, inputPath + "/publication", CommunityResult.class) - .union(Utils.readPath(spark, inputPath + "/dataset", CommunityResult.class)) - .union(Utils.readPath(spark, inputPath + "/orp", CommunityResult.class)) - .union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class)); - - List funderList = project - .select("id") - .map((MapFunction) value -> value.getString(0).substring(0, 15), Encoders.STRING()) - .distinct() - .collectAsList(); - + .readPath(spark, inputPath + "/publication", CommunityResult.class) + .union(Utils.readPath(spark, inputPath + "/dataset", CommunityResult.class)) + .union(Utils.readPath(spark, inputPath + "/otherresearchproduct", CommunityResult.class)) + .union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class)); + log.info("Number of result {}", result.count()); + Dataset tmp = result + .flatMap((FlatMapFunction) cr -> cr.getProjects().stream().map(p -> { + return getFunderName(p); + }).collect(Collectors.toList()).iterator(), Encoders.STRING()) + .distinct(); + List funderList = tmp.collectAsList(); funderList.forEach(funder -> { - String fundernsp = funder.substring(3); - String funderdump; - if (fundernsp.startsWith("corda")) { - funderdump = "EC_"; - if (fundernsp.endsWith("h2020")) { - funderdump += "H2020"; - } else { - funderdump += "FP7"; - } - } else { - funderdump = fundernsp.substring(0, fundernsp.indexOf("_")).toUpperCase(); - } - writeFunderResult(funder, result, outputPath, funderdump); + dumpResults(funder, result, outputPath); }); - } - - private static void dumpResults(String nsp, Dataset results, String outputPath, - String funderName) { - - results.map((MapFunction) r -> { - if (!Optional.ofNullable(r.getProjects()).isPresent()) { - return null; + @NotNull + private static String getFunderName(Project p) { + Optional ofunder = Optional.ofNullable(p.getFunder()); + if (ofunder.isPresent()) { + String fName = ofunder.get().getShortName(); + if (fName.equalsIgnoreCase("ec")) { + fName += "_" + ofunder.get().getFundingStream(); } - for (Project p : r.getProjects()) { - if (p.getId().startsWith(nsp)) { - if (nsp.startsWith("40|irb")) { - if (p.getFunder().getShortName().equals(funderName)) - return r; - else - return null; - } - return r; + return fName; + } else { + String fName = p.getId().substring(3, p.getId().indexOf("_")).toUpperCase(); + if (fName.equalsIgnoreCase("ec")) { + if (p.getId().contains("h2020")) { + fName += "_H2020"; + } else { + fName += "_FP7"; } + } else if (fName.equalsIgnoreCase("conicytf")) { + fName = "CONICYT"; + } else if (fName.equalsIgnoreCase("dfgf")) { + fName = "DFG"; + } else if (fName.equalsIgnoreCase("tubitakf")) { + fName = "TUBITAK"; + } else if (fName.equalsIgnoreCase("euenvagency")) { + fName = "EEA"; } - return null; - }, Encoders.bean(CommunityResult.class)) - .filter(Objects::nonNull) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath + "/" + funderName); + return fName; + } } - - private static void writeFunderResult(String funder, Dataset results, String outputPath, - String funderDump) { - - if (funder.startsWith("40|irb")) { - dumpResults(funder, results, outputPath, "HRZZ"); - dumpResults(funder, results, outputPath, "MZOS"); - } else - dumpResults(funder, results, outputPath, funderDump); - + private static void dumpResults(String funder, Dataset results, String outputPath) { + results.map((MapFunction) r -> { + if (!Optional.ofNullable(r.getProjects()).isPresent()) { + return null; + } + for (Project p : r.getProjects()) { + String fName = getFunderName(p); + if (fName.equalsIgnoreCase(funder)) { + return r; + } + } + return null; + }, Encoders.bean(CommunityResult.class)) + .filter(Objects::nonNull) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath + "/" + funder); } - -} +} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java index d89b9e86d..5eed64e89 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java @@ -5,9 +5,12 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.io.Serializable; import java.util.Optional; +import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.FilterFunction; +import org.apache.spark.api.java.function.FlatMapFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.MapGroupsFunction; import org.apache.spark.sql.Dataset; @@ -18,11 +21,18 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.oa.graph.dump.Constants; +import eu.dnetlib.dhp.oa.graph.dump.DumpProducts; +import eu.dnetlib.dhp.oa.graph.dump.ResultMapper; import eu.dnetlib.dhp.oa.graph.dump.Utils; +import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; +import eu.dnetlib.dhp.oa.graph.dump.community.ResultProject; import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; import eu.dnetlib.dhp.schema.oaf.Project; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Result; +import scala.Tuple2; /** * Selects the results linked to projects. Only for these results the dump will be performed. @@ -35,18 +45,18 @@ public class SparkResultLinkedToProject implements Serializable { public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils - .toString( - SparkResultLinkedToProject.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json")); + .toString( + SparkResultLinkedToProject.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json")); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); parser.parseArgument(args); Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); final String inputPath = parser.get("sourcePath"); @@ -58,59 +68,51 @@ public class SparkResultLinkedToProject implements Serializable { final String resultClassName = parser.get("resultTableName"); log.info("resultTableName: {}", resultClassName); - final String graphPath = parser.get("graphPath"); - log.info("graphPath: {}", graphPath); + final String resultProjectsPath = parser.get("graphPath"); + log.info("graphPath: {}", resultProjectsPath); + + String communityMapPath = parser.get("communityMapPath"); @SuppressWarnings("unchecked") Class inputClazz = (Class) Class.forName(resultClassName); SparkConf conf = new SparkConf(); runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - writeResultsLinkedToProjects(spark, inputClazz, inputPath, outputPath, graphPath); - }); + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath); + writeResultsLinkedToProjects( + communityMapPath, spark, inputClazz, inputPath, outputPath, resultProjectsPath); + }); } - private static void writeResultsLinkedToProjects(SparkSession spark, Class inputClazz, - String inputPath, String outputPath, String graphPath) { + private static void writeResultsLinkedToProjects(String communityMapPath, SparkSession spark, + Class inputClazz, + String inputPath, String outputPath, String resultProjectsPath) { Dataset results = Utils - .readPath(spark, inputPath, inputClazz) - .filter("dataInfo.deletedbyinference = false and datainfo.invisible = false"); - Dataset relations = Utils - .readPath(spark, graphPath + "/relation", Relation.class) - .filter( - "dataInfo.deletedbyinference = false and lower(relClass) = '" - + ModelConstants.IS_PRODUCED_BY.toLowerCase() + "'"); - Dataset project = Utils.readPath(spark, graphPath + "/project", Project.class); - - results.createOrReplaceTempView("result"); - relations.createOrReplaceTempView("relation"); - project.createOrReplaceTempView("project"); - - Dataset tmp = spark - .sql( - "Select res.* " + - "from relation rel " + - "join result res " + - "on rel.source = res.id " + - "join project p " + - "on rel.target = p.id " + - "") - .as(Encoders.bean(inputClazz)); - tmp - .groupByKey( - (MapFunction) value -> value - .getId(), - Encoders.STRING()) - .mapGroups((MapGroupsFunction) (k, it) -> it.next(), Encoders.bean(inputClazz)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); + .readPath(spark, inputPath, inputClazz) + .filter( + (FilterFunction) r -> !r.getDataInfo().getDeletedbyinference() && + !r.getDataInfo().getInvisible()); + Dataset resultProjectDataset = Utils + .readPath(spark, resultProjectsPath, ResultProject.class); + CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath); + results + .joinWith(resultProjectDataset, results.col("id").equalTo(resultProjectDataset.col("resultId"))) + .map((MapFunction, CommunityResult>) t2 -> { + CommunityResult cr = (CommunityResult) ResultMapper + .map( + t2._1(), + communityMap, Constants.DUMPTYPE.FUNDER.getType()); + cr.setProjects(t2._2().getProjectsList()); + return cr; + }, Encoders.bean(CommunityResult.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json index 5dc8e8910..5669dca37 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json @@ -17,10 +17,10 @@ "paramDescription": "true if the spark session is managed, false otherwise", "paramRequired": false }, -{ - "paramName": "gp", - "paramLongName": "graphPath", - "paramDescription": "the relationPath", - "paramRequired": true -} + { + "paramName": "gp", + "paramLongName": "graphPath", + "paramDescription": "the relationPath", + "paramRequired": false + } ] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameter_select_relation.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameter_select_relation.json new file mode 100644 index 000000000..1a67134a6 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameter_select_relation.json @@ -0,0 +1,20 @@ +[ + { + "paramName":"s", + "paramLongName":"sourcePath", + "paramDescription": "the path of the sequencial file to read", + "paramRequired": true + }, + { + "paramName": "out", + "paramLongName": "outputPath", + "paramDescription": "the path used to store temporary output files", + "paramRequired": true + }, + { + "paramName": "ssm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "true if the spark session is managed, false otherwise", + "paramRequired": false + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json index f5641bc45..6c45538cf 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json @@ -28,6 +28,12 @@ "paramLongName":"graphPath", "paramDescription": "the path to the relations", "paramRequired": true + }, + { + "paramName":"cmp", + "paramLongName":"communityMapPath", + "paramDescription": "the path to the relations", + "paramRequired": true } ] diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/config-default.xml deleted file mode 100644 index e5ec3d0ae..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/config-default.xml +++ /dev/null @@ -1,30 +0,0 @@ - - - jobTracker - yarnRM - - - nameNode - hdfs://nameservice1 - - - oozie.use.system.libpath - true - - - hiveMetastoreUris - thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 - - - hiveJdbcUrl - jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000 - - - hiveDbName - openaire - - - oozie.launcher.mapreduce.user.classpath.first - true - - \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/workflow.xml deleted file mode 100644 index 5f954ff38..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/workflow.xml +++ /dev/null @@ -1,347 +0,0 @@ - - - - - sourcePath - the source path - - - outputPath - the output path - - - communityMapPath - the path to the community map - - - selectedResults - the path the the possible subset ot results to be dumped - - - hiveDbName - the target hive database name - - - hiveJdbcUrl - hive server jdbc url - - - hiveMetastoreUris - hive server metastore URIs - - - sparkDriverMemory - memory for driver process - - - sparkExecutorMemory - memory for individual executor - - - sparkExecutorCores - number of cores used by single executor - - - oozieActionShareLibForSpark2 - oozie action sharelib for spark 2.* - - - spark2ExtraListeners - com.cloudera.spark.lineage.NavigatorAppListener - spark 2.* extra listeners classname - - - spark2SqlQueryExecutionListeners - com.cloudera.spark.lineage.NavigatorQueryListener - spark 2.* sql query execution listeners classname - - - spark2YarnHistoryServerAddress - spark 2.* yarn history server address - - - spark2EventLogDir - spark 2.* event log dir location - - - - - ${jobTracker} - ${nameNode} - - - mapreduce.job.queuename - ${queueName} - - - oozie.launcher.mapred.job.queue.name - ${oozieLauncherQueueName} - - - oozie.action.sharelib.for.spark - ${oozieActionShareLibForSpark2} - - - - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - - - - - - - - - - - yarn - cluster - Dump table publication for community/funder related products - eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${selectedResults}/publication - --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication - --outputPath${workingDir}/dump/publication - --communityMapPath${communityMapPath} - --dumpType${dumpType} - - - - - - - - yarn - cluster - Dump table dataset for community/funder related products - eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${selectedResults}/dataset - --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset - --outputPath${workingDir}/dump/dataset - --communityMapPath${communityMapPath} - - - - - - - - yarn - cluster - Dump table ORP for community related products - eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${selectedResults}/otherresearchproduct - --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct - --outputPath${workingDir}/dump/otherresearchproduct - --communityMapPath${communityMapPath} - - - - - - - - yarn - cluster - Dump table software for community related products - eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${selectedResults}/software - --resultTableNameeu.dnetlib.dhp.schema.oaf.Software - --outputPath${workingDir}/dump/software - --communityMapPath${communityMapPath} - - - - - - - - - - yarn - cluster - Prepare association result subset of project info - eu.dnetlib.dhp.oa.graph.dump.community.SparkPrepareResultProject - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath} - --outputPath${workingDir}/preparedInfo - - - - - - - - - - - - - - - yarn - cluster - Extend dumped publications with information about project - eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${workingDir}/dump/publication - --outputPath${outputPath}/ext/publication - --preparedInfoPath${workingDir}/preparedInfo - - - - - - - - yarn - cluster - Extend dumped dataset with information about project - eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${workingDir}/dump/dataset - --outputPath${outputPath}/ext/dataset - --preparedInfoPath${workingDir}/preparedInfo - - - - - - - - yarn - cluster - Extend dumped ORP with information about project - eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${workingDir}/dump/otherresearchproduct - --outputPath${outputPath}/ext/orp - --preparedInfoPath${workingDir}/preparedInfo - - - - - - - - yarn - cluster - Extend dumped software with information about project - eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${workingDir}/dump/software - --outputPath${outputPath}/ext/software - --preparedInfoPath${workingDir}/preparedInfo - - - - - - - - - - - diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/import.txt b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/import.txt deleted file mode 100644 index 15387e988..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/import.txt +++ /dev/null @@ -1,2 +0,0 @@ -## This is a classpath-based import file (this header is required) -dump_common classpath eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml index 319517026..b559a25dc 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml @@ -77,42 +77,259 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - ${wf:appPath()}/dump_common - - - - - sourcePath - ${sourcePath} - - - selectedResults - ${sourcePath} - - - communityMapPath - ${workingDir}/communityMap - - - outputPath - ${workingDir} - - - - - + + + + + + + + + + yarn + cluster + Dump table publication for community/funder related products + eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${selectedResults}/publication + --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication + --outputPath${workingDir}/dump/publication + --communityMapPath${communityMapPath} + --dumpType${dumpType} + + + + + + + + yarn + cluster + Dump table dataset for community/funder related products + eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${selectedResults}/dataset + --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset + --outputPath${workingDir}/dump/dataset + --communityMapPath${communityMapPath} + + + + + + + + yarn + cluster + Dump table ORP for community related products + eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${selectedResults}/otherresearchproduct + --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct + --outputPath${workingDir}/dump/otherresearchproduct + --communityMapPath${communityMapPath} + + + + + + + + yarn + cluster + Dump table software for community related products + eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${selectedResults}/software + --resultTableNameeu.dnetlib.dhp.schema.oaf.Software + --outputPath${workingDir}/dump/software + --communityMapPath${communityMapPath} + + + + + + + + + + yarn + cluster + Prepare association result subset of project info + eu.dnetlib.dhp.oa.graph.dump.community.SparkPrepareResultProject + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath} + --outputPath${workingDir}/preparedInfo + + + + + + + + + + + + + + + yarn + cluster + Extend dumped publications with information about project + eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/dump/publication + --outputPath${outputPath}/ext/publication + --preparedInfoPath${workingDir}/preparedInfo + + + + + + + + yarn + cluster + Extend dumped dataset with information about project + eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/dump/dataset + --outputPath${outputPath}/ext/dataset + --preparedInfoPath${workingDir}/preparedInfo + + + + + + + + yarn + cluster + Extend dumped ORP with information about project + eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/dump/otherresearchproduct + --outputPath${outputPath}/ext/orp + --preparedInfoPath${workingDir}/preparedInfo + + + + + + + + yarn + cluster + Extend dumped software with information about project + eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/dump/software + --outputPath${outputPath}/ext/software + --preparedInfoPath${workingDir}/preparedInfo + + + - + yarn diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/workflow.xml index 8eab56992..7cc133323 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/workflow.xml @@ -298,6 +298,7 @@ --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + --conf spark.sql.shuffle.partitions=3840 --sourcePath${sourcePath} --outputPath${workingDir}/validrelation diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/import.txt b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/import.txt deleted file mode 100644 index 15387e988..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/import.txt +++ /dev/null @@ -1,2 +0,0 @@ -## This is a classpath-based import file (this header is required) -dump_common classpath eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/workflow.xml index b990f4e49..2c05256cf 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/workflow.xml @@ -77,12 +77,36 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + yarn + cluster + Prepare association result subset of project info + eu.dnetlib.dhp.oa.graph.dump.community.SparkPrepareResultProject + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath} + --outputPath${workingDir}/preparedInfo + + + + + @@ -111,7 +135,8 @@ --sourcePath${sourcePath}/publication --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication --outputPath${workingDir}/result/publication - --graphPath${sourcePath} + --graphPath${workingDir}/preparedInfo + --communityMapPath${communityMapPath} @@ -137,7 +162,8 @@ --sourcePath${sourcePath}/dataset --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset --outputPath${workingDir}/result/dataset - --graphPath${sourcePath} + --graphPath${workingDir}/preparedInfo + --communityMapPath${communityMapPath} @@ -163,7 +189,8 @@ --sourcePath${sourcePath}/otherresearchproduct --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct --outputPath${workingDir}/result/otherresearchproduct - --graphPath${sourcePath} + --graphPath${workingDir}/preparedInfo + --communityMapPath${communityMapPath} @@ -189,41 +216,14 @@ --sourcePath${sourcePath}/software --resultTableNameeu.dnetlib.dhp.schema.oaf.Software --outputPath${workingDir}/result/software - --graphPath${sourcePath} + --graphPath${workingDir}/preparedInfo + --communityMapPath${communityMapPath} - - - - - ${wf:appPath()}/dump_common - - - - - sourcePath - ${sourcePath} - - - selectedResults - ${workingDir}/result - - - communityMapPath - ${workingDir}/communityMap - - - outputPath - ${workingDir} - - - - - - + @@ -242,9 +242,8 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - --sourcePath${workingDir}/ext + --sourcePath${workingDir}/result --outputPath${outputPath} - --graphPath${sourcePath} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java index 86d2f93c9..c6798ac58 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java @@ -35,12 +35,12 @@ public class PrepareResultProjectJobTest { private static Path workingDir; private static final Logger log = LoggerFactory - .getLogger(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class); + .getLogger(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class); @BeforeAll public static void beforeAll() throws IOException { workingDir = Files - .createTempDirectory(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class.getSimpleName()); + .createTempDirectory(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class.getSimpleName()); log.info("using work dir {}", workingDir); SparkConf conf = new SparkConf(); @@ -54,10 +54,10 @@ public class PrepareResultProjectJobTest { conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); spark = SparkSession - .builder() - .appName(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); + .builder() + .appName(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); } @AfterAll @@ -70,23 +70,23 @@ public class PrepareResultProjectJobTest { void testNoMatch() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/no_match") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/no_match") + .getPath(); SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); + .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); assertEquals(0, verificationDataset.count()); @@ -96,37 +96,37 @@ public class PrepareResultProjectJobTest { void testMatchOne() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_one") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_one") + .getPath(); SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); + .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); assertEquals(1, verificationDataset.count()); assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); verificationDataset.createOrReplaceTempView("table"); Dataset check = spark - .sql( - "Select projList.provenance.provenance " + - "from table " + - "lateral view explode (projectsList) pl as projList"); + .sql( + "Select projList.provenance.provenance " + + "from table " + + "lateral view explode (projectsList) pl as projList"); assertEquals(1, check.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); @@ -138,88 +138,88 @@ public class PrepareResultProjectJobTest { void testMatch() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match") + .getPath(); SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); + .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); assertEquals(2, verificationDataset.count()); assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); verificationDataset.createOrReplaceTempView("dataset"); String query = "select resultId, MyT.id project , MyT.title title, MyT.acronym acronym , MyT.provenance.provenance provenance " - + "from dataset " - + "lateral view explode(projectsList) p as MyT "; + + "from dataset " + + "lateral view explode(projectsList) p as MyT "; org.apache.spark.sql.Dataset resultExplodedProvenance = spark.sql(query); assertEquals(3, resultExplodedProvenance.count()); assertEquals( - 2, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") - .count()); + 2, + resultExplodedProvenance + .filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") - .count()); + 1, + resultExplodedProvenance + .filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") + .count()); assertEquals( - 2, - resultExplodedProvenance - .filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'") - .count()); + 2, + resultExplodedProvenance + .filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'") - .count()); + 1, + resultExplodedProvenance + .filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::03376222b28a3aebf2730ac514818d04' and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::03376222b28a3aebf2730ac514818d04' and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") + .count()); assertEquals( - 3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); + 3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); } @@ -227,98 +227,121 @@ public class PrepareResultProjectJobTest { public void testMatchValidated() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_validatedRels") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_validatedRels") + .getPath(); SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); + .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); assertEquals(2, verificationDataset.count()); assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); verificationDataset.createOrReplaceTempView("dataset"); String query = "select resultId, MyT.id project , MyT.title title, MyT.acronym acronym , MyT.provenance.provenance provenance, " - + - "MyT.validated.validatedByFunder, MyT.validated.validationDate " - + "from dataset " - + "lateral view explode(projectsList) p as MyT "; + + + "MyT.validated.validatedByFunder, MyT.validated.validationDate " + + "from dataset " + + "lateral view explode(projectsList) p as MyT "; org.apache.spark.sql.Dataset resultExplodedProvenance = spark.sql(query); assertEquals(3, resultExplodedProvenance.count()); assertEquals(3, resultExplodedProvenance.filter("validatedByFunder = true").count()); assertEquals( - 2, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") - .count()); + 2, + resultExplodedProvenance + .filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") - .count()); + 1, + resultExplodedProvenance + .filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") + .count()); assertEquals( - 2, - resultExplodedProvenance - .filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'") - .count()); + 2, + resultExplodedProvenance + .filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + - "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + - "and validatedByFunder = true " + - "and validationDate = '2021-08-06'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + + "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + + "and validatedByFunder = true " + + "and validationDate = '2021-08-06'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + - "and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80' " + - "and validatedByFunder = true and validationDate = '2021-08-04'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + + "and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80' " + + "and validatedByFunder = true and validationDate = '2021-08-04'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'") - .count()); + 1, + resultExplodedProvenance + .filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::03376222b28a3aebf2730ac514818d04' " + - "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + - "and validatedByFunder = true and validationDate = '2021-08-05'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::03376222b28a3aebf2730ac514818d04' " + + "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + + "and validatedByFunder = true and validationDate = '2021-08-05'") + .count()); assertEquals( - 3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); + 3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); } + + @Test + void testMatchx() throws Exception { + + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match") + .getPath(); + + SparkPrepareResultProject.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); + + tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r))); + } + } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java index 4967ae5a5..579958a62 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java @@ -22,6 +22,7 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject; +import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; import eu.dnetlib.dhp.schema.oaf.Publication; import eu.dnetlib.dhp.schema.oaf.Result; @@ -34,15 +35,15 @@ public class ResultLinkedToProjectTest { private static Path workingDir; private static final Logger log = LoggerFactory - .getLogger(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class); + .getLogger(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class); private static final HashMap map = new HashMap<>(); @BeforeAll public static void beforeAll() throws IOException { workingDir = Files - .createTempDirectory( - eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()); + .createTempDirectory( + eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()); log.info("using work dir {}", workingDir); SparkConf conf = new SparkConf(); @@ -56,10 +57,10 @@ public class ResultLinkedToProjectTest { conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); spark = SparkSession - .builder() - .appName(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); + .builder() + .appName(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); } @AfterAll @@ -72,32 +73,34 @@ public class ResultLinkedToProjectTest { void testNoMatch() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json") + .getPath(); final String graphPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo") + .getPath(); + + final String communityMapPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/communityMapPath") + .getPath(); SparkResultLinkedToProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-graphPath", graphPath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath, + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", + "-graphPath", graphPath, + "-communityMapPath", communityMapPath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, Result.class)); + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Result.class)); - - Assertions.assertEquals(0, verificationDataset.count()); + Assertions.assertEquals(0, tmp.count()); } @@ -105,32 +108,34 @@ public class ResultLinkedToProjectTest { void testMatchOne() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/papers.json") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/papers.json") + .getPath(); - final String relationPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match") - .getPath(); + final String graphPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo") + .getPath(); + + final String communityMapPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/communityMapPath") + .getPath(); SparkResultLinkedToProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-graphPath", relationPath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath, + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", + "-graphPath", graphPath, + "-communityMapPath", communityMapPath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, Publication.class)); + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Publication.class)); - - Assertions.assertEquals(1, verificationDataset.count()); + Assertions.assertEquals(1, tmp.count()); } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java index 477481c08..5bb5a1178 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java @@ -5,10 +5,14 @@ import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; +// import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkDumpFunderResults2; +// import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkGetFunderList; import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.ForeachFunction; +import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; import org.junit.jupiter.api.AfterAll; @@ -52,10 +56,10 @@ public class SplitPerFunderTest { conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); spark = SparkSession - .builder() - .appName(SplitPerFunderTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); + .builder() + .appName(SplitPerFunderTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); } @AfterAll @@ -68,86 +72,80 @@ public class SplitPerFunderTest { void test1() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext") + .getPath(); SparkDumpFunderResults.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/split", - "-sourcePath", sourcePath, - "-graphPath", sourcePath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/split", + "-sourcePath", sourcePath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - // FP7 3 + // FP7 3 and H2020 3 JavaRDD tmp = sc - .textFile(workingDir.toString() + "/split/EC_FP7") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/EC_FP7") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); + .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); Assertions.assertEquals(3, verificationDataset.count()); Assertions - .assertEquals( - 1, verificationDataset.filter("id = '50|dedup_wf_001::0d16b1714ab3077df73893a8ea57d776'").count()); + .assertEquals( + 1, verificationDataset.filter("id = '50|dedup_wf_001::0d16b1714ab3077df73893a8ea57d776'").count()); // CIHR 2 tmp = sc - .textFile(workingDir.toString() + "/split/CIHR") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/CIHR") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(2, tmp.count()); // NWO 1 tmp = sc - .textFile(workingDir.toString() + "/split/NWO") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/NWO") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(1, tmp.count()); // NIH 3 tmp = sc - .textFile(workingDir.toString() + "/split/NIH") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/NIH") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(2, tmp.count()); // NSF 1 tmp = sc - .textFile(workingDir.toString() + "/split/NSF") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/NSF") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(1, tmp.count()); // SNSF 1 tmp = sc - .textFile(workingDir.toString() + "/split/SNSF") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/SNSF") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(1, tmp.count()); // NHMRC 1 tmp = sc - .textFile(workingDir.toString() + "/split/NHMRC") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/NHMRC") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(1, tmp.count()); // H2020 3 tmp = sc - .textFile(workingDir.toString() + "/split/EC_H2020") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/EC_H2020") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(3, tmp.count()); // MZOS 1 tmp = sc - .textFile(workingDir.toString() + "/split/MZOS") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/MZOS") + .map(item -> 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Departamento de Ciencias Ambientales y Recursos Naturales","Universidad de Alicante. Centro Iberoamericano de la Biodiversidad","Biodiversidad y Biotecnología aplicadas a la Biología de la Conservación","Terrestrial Ecology (TE)"],"country":[{"code":"NL","label":"Netherlands","provenance":{"provenance":"Propagation of country to result collected from datasources of type institutional repositories","trust":"0.85"}},{"code":"ES","label":"Spain","provenance":{"provenance":"Propagation of country to result collected from datasources of type institutional repositories","trust":"0.85"}}],"coverage":[],"dateofcollection":"2018-10-03T06:57:46.116Z","description":["Herbivory affects subsequent herbivores, mainly regulated by the phytohormones jasmonic (JA) and salicylic acid (SA). Additionally, organisms such as soil microbes belowground or parasitoids that develop inside their herbivorous hosts aboveground, can change plant responses to herbivory. However, it is not yet well known how organisms of trophic levels other than herbivores, below- and above-ground, alter the interactions between insect species sharing a host plant. Here, we investigated whether the parasitoid Aphidius colemani and different soil microbial communities (created through plant-soil feedbacks) affect the JA and SA signalling pathways in response to the aphid Myzus persicae and the thrips Frankliniella occidentalis, as well as subsequent thrips performance. Our results show that the expression of the JA-responsive gene CaPINII in sweet pepper was more suppressed by aphids than by parasitised aphids. However, parasitism did not affect the expression of CaPAL1, a biosynthetic gene of SA. Furthermore, aphid feeding enhanced thrips performance compared with uninfested plants, but this was not observed when aphids were parasitised. Soils where different plant species were previously grown, did not affect plant responses or the interaction between herbivores. Our study shows that members of the third trophic level can modify herbivore interactions by altering plant physiology.\nThis work and T.V.’s activities were supported by Spanish Ministry of Science and Innovation, (CGL2016-79054), the Open Technology Program of NWO (TTW-13848), and the STSM Cost Action FA1405 funded by the European Union. A.P. research activities were supported by the Netherlands Organisation for Scientific Research (NWO, project no. 870.15.080)."],"format":["application/pdf","application/octet-stream"],"id":"50|dedup_wf_001::01644aebfe64e809f593492e515bc070","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::e820a45f1dfc7b95282d10b6087e11c0","value":"Repositorio Institucional de la Universidad de Alicante"},"hostedby":{"key":"10|opendoar____::e820a45f1dfc7b95282d10b6087e11c0","value":"Repositorio Institucional de la Universidad de Alicante"},"license":"Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.","publicationdate":"2018-09-26","refereed":"UNKNOWN","type":"Article","url":["http://hdl.handle.net/10045/80968"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"},"hostedby":{"key":"10|doajarticles::70703810b20723fe33cba6ffd7128212","value":"Scientific 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(NWO)","shortName":"NWO"},"id":"40|nwo_________::dc69ada721bf21ed51055b6421850d73","provenance":{"provenance":"Harvested","trust":"0.900000000000000022"},"title":"Exploring and exploiting phytochemicals to lure hyperparasitoids away from beneficial biocontrol agents"},{"code":"2300189714","funder":{"jurisdiction":"NL","name":"Netherlands Organisation for Scientific Research (NWO)","shortName":"NWO"},"id":"40|nwo_________::39d892199c3b3d3b5ae9869a79e5bba8","provenance":{"provenance":"Harvested","trust":"0.900000000000000022"},"title":"Linking aboveground-belowground interactions and plant-soil feedback to improve pest control and sustainability in greenhouse cut-flowers"}],"publicationdate":"2018-09-26","publisher":"Springer Nature","subjects":[{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Plant-mediated interactions"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Herbivores"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Feeding guilds"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Parasitism"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Belowground interactions"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Zoología"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Medicine"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"R"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Science"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Q"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"international"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Laboratorium voor Entomologie"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"PE&RC"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Laboratory of Entomology"}},{"subject":{"scheme":"keywords","value":"Multidisciplinary"}}],"type":"publication"} +{"author":[{"fullname":"Bonnie Berger","name":"Bonnie","pid":{"id":{"scheme":"orcid","value":"0000-0002-2724-7228"}},"rank":1,"surname":"Berger"}],"bestaccessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":[{"key":"10|opendoar____::958adb57686c2fdec5796398de5f317a","value":"MPG.PuRe"},{"key":"10|share_______::bbd802baad85d1fd440f32a7a3a2c2b1","value":"bioRxiv"},{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"},{"key":"10|openaire____::8ac8380272269217cb09a928c8caa993","value":"UnpayWall"},{"key":"10|openaire____::806360c771262b4d6770e7cdf04b5c5a","value":"ORCID"},{"key":"10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a","value":"Microsoft Academic Graph"},{"key":"10|opendoar____::89f0fd5c927d466d6ec9a21b9ac34ffa","value":"eScholarship - University of 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Computer Science and Artificial Intelligence Laboratory","Massachusetts Institute of Technology. Department of Mathematics","Lipson, Mark","Loh, Po-Ru","Berger, Bonnie"],"country":[{"code":"DZ","label":"Algeria","provenance":{"provenance":"Propagation of country to result collected from datasources of type institutional repositories","trust":"0.85"}},{"code":"US","label":"United States","provenance":{"provenance":"Propagation of country to result collected from datasources of type institutional repositories","trust":"0.85"}}],"coverage":[],"dateofcollection":"2020-09-12T07:56:34.334Z","description":["Austronesian languages are spread across half the globe, from Easter Island to Madagascar. Evidence from linguistics and archaeology indicates that the ‘Austronesian expansion,’ which began 4,000–5,000 years ago, likely had roots in Taiwan, but the ancestry of present-day Austronesian-speaking populations remains controversial. Here, we analyse genome-wide data from 56 populations using new methods for tracing ancestral gene flow, focusing primarily on Island Southeast Asia. We show that all sampled Austronesian groups harbour ancestry that is more closely related to aboriginal Taiwanese than to any present-day mainland population. Surprisingly, western Island Southeast Asian populations have also inherited ancestry from a source nested within the variation of present-day populations speaking Austro-Asiatic languages, which have historically been nearly exclusive to the mainland. Thus, either there was once a substantial Austro-Asiatic presence in Island Southeast Asia, or Austronesian speakers migrated to and through the mainland, admixing there before continuing to western Indonesia.","National Science Foundation (U.S.). Graduate Research Fellowship Program","Simons Foundation","National Institutes of Health (U.S.) (Grant R01GM108348)","National Institutes of Health (U.S.) (Training Grant 5T32HG004947-04)"],"format":["application/pdf"],"id":"50|dedup_wf_001::025dff86cc73c1c865ed35e5b7646e73","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::958adb57686c2fdec5796398de5f317a","value":"MPG.PuRe"},"hostedby":{"key":"10|opendoar____::958adb57686c2fdec5796398de5f317a","value":"MPG.PuRe"},"license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","publicationdate":"2014-01-01","refereed":"UNKNOWN","type":"Article","url":["http://hdl.handle.net/11858/00-001M-0000-0024-1F46-B","http://hdl.handle.net/11858/00-001M-0000-0024-1F8F-7","http://hdl.handle.net/11858/00-001M-0000-0024-1F90-1"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|share_______::bbd802baad85d1fd440f32a7a3a2c2b1","value":"bioRxiv"},"hostedby":{"key":"10|share_______::bbd802baad85d1fd440f32a7a3a2c2b1","value":"bioRxiv"},"publicationdate":"2014-05-27","refereed":"nonPeerReviewed","type":"Preprint","url":["http://dx.doi.org/10.1101/005603"]},{"accessright":{"code":"c_16ec","label":"RESTRICTED","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"},"hostedby":{"key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c","value":"Unknown 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Due to the portability and relative inexpensiveness of electroencephalography, the N400 event-related potential component has been proposed as a clinically valid means to identify preserved linguistic function in non-communicative patients. Across three experiments, we show that changes in both stimuli and task demands significantly influence the probability of detecting statistically significant N400 effects — that is, the difference in N400 amplitudes caused by the experimental manipulation. In terms of task demands, passively heard linguistic stimuli were significantly less likely to elicit N400 effects than task-relevant stimuli. Due to the inability of the majority of patients with disorders of consciousness to follow task commands, the insensitivity of passive listening would impede the identification of residual language abilities even when such abilities exist. In terms of stimuli, passively heard normatively associated word pairs produced the highest detection rate of N400 effects (50% of the participants), compared with semantically-similar word pairs (0%) and high-cloze sentences (17%). This result is consistent with a prediction error account of N400 magnitude, with highly predictable targets leading to smaller N400 waves, and therefore larger N400 effects. Overall, our data indicate that non-repeating normatively associated word pairs provide the highest probability of detecting single-subject N400s during passive listening, and may thereby provide a clinically viable means of assessing residual linguistic function. 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New polyethers, such as iubol (2), 22-hydroxy-15(28)- dehydrovenustatriol (3), 1,2-dehydropseudodehydrothyrsiferol (4), and secodehydrothyrsiferol (5) have been isolated and characterized from this alga. The structures were determined through the interpretation of NMR spectroscopic data and the relative configuration was proposed on the basis of NOESY spectrum and biogenetic considerations. All new compounds exhibited significant cytotoxic activity against a panel of cancer cell lines. © 2011 by the authors.","Financial support was provided by the grants MAREX (FP 7; KBBE-3-245137) (EU), CTQ2008-06754-C04-01 and SAF2008-02251 (MICINN); C2008000145 and EXMAR (ACISII); RD06/0020/1037 from Red Temática de Investigación Cooperativa en Cáncer, Instituto de Salud Carlos III, co-funded by the Fondo Europeo de Desarrollo Regional of the European Union, and Junta de Castilla y León (CSI052A11-2, and GR15-Experimental Therapeutics and Translational Oncology Program). 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The validity and utility of standard measures of childhood maltreatment requires clarification in order to inform the design of future studies investigating the mental health consequences of maltreatment. The present study assessed agreement between prospective informant-reports and retrospective self-reports of childhood maltreatment, as well as the comparative utility of both reports for predicting a range of psychiatric problems at age 18. Data were obtained from the Environmental Risk (E-Risk) Longitudinal Twin Study, a nationally-representative birth cohort of 2232 children followed to 18 years of age (with 93% retention). Childhood maltreatment was assessed in two ways: (i) prospective informant-reports from caregivers, researchers, and clinicians when children were aged 5, 7, 10 and 12; and (ii) retrospective self-reports of maltreatment experiences occurring up to age 12, obtained at age 18 using the Childhood Trauma Questionnaire. Participants were privately interviewed at age 18 concerning several psychiatric problems including depression, anxiety, self-injury, alcohol/cannabis dependence, and conduct disorder. There was only slight to fair agreement between prospective and retrospective reports of childhood maltreatment (all Kappa's ≤ 0.31). Both prospective and retrospective reports of maltreatment were associated with age-18 psychiatric problems, though the strongest associations were found when maltreatment was retrospectively self-reported. These findings indicate that prospective and retrospective reports of childhood maltreatment capture largely non-overlapping groups of individuals. Young adults who recall being maltreated have a particularly elevated risk for psychopathology."],"format":["application/pdf","text"],"id":"50|dedup_wf_001::085f9efc74e1192abca87031fb573d70","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::566a9968b43628588e76be5a85a0f9e8","value":"King's Research Portal"},"hostedby":{"key":"10|opendoar____::566a9968b43628588e76be5a85a0f9e8","value":"King's Research 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Plants inoculated with the fungal pathogen showed reduced disease symptoms in the resistant genotype in both soils, but the susceptible genotype was partially protected from the pathogen only when grown on the suppressive soil.\r\nThe ‘state of alert’ detected in tomatoes reveals novel mechanisms operating in plants in native soils and the soil microbiota appears to be one of the drivers of these plant responses."],"format":[],"id":"50|dedup_wf_001::09e54cbad6670d8f40a7de2704e2d2a4","instance":[{"accessright":{"code":"c_16ec","label":"RESTRICTED","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"},"hostedby":{"key":"10|issn___print::35ee75a5ad42581d604be113a8f56427","value":"New Phytologist"},"license":"http://doi.wiley.com/10.1002/tdm_license_1.1","publicationdate":"2018-02-09","refereed":"UNKNOWN","type":"Article","url":["https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2Fnph.15014","http://onlinelibrary.wiley.com/wol1/doi/10.1111/nph.15014/fullpdf","http://dx.doi.org/10.1111/nph.15014"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::8ac8380272269217cb09a928c8caa993","value":"UnpayWall"},"hostedby":{"key":"10|issn___print::35ee75a5ad42581d604be113a8f56427","value":"New Phytologist"},"refereed":"UNKNOWN","type":"Article","url":["https://nph.onlinelibrary.wiley.com/doi/pdfdirect/10.1111/nph.15014"]},{"collectedfrom":{"key":"10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a","value":"Microsoft Academic Graph"},"hostedby":{"key":"10|issn___print::35ee75a5ad42581d604be113a8f56427","value":"New Phytologist"},"refereed":"UNKNOWN","type":"Article","url":["https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.15014","https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.15014","http://onlinelibrary.wiley.com/doi/10.1111/nph.15014/abstract","https://aperto.unito.it/handle/2318/1660820","https://academic.microsoft.com/#/detail/2793208206"]},{"accessright":{"code":"c_16ec","label":"RESTRICTED","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::89fcd07f20b6785b92134bd6c1d0fa42","value":"Archivio Istituzionale"},"hostedby":{"key":"10|opendoar____::89fcd07f20b6785b92134bd6c1d0fa42","value":"Archivio Istituzionale"},"publicationdate":"2018-01-01","refereed":"UNKNOWN","type":"Article","url":["http://hdl.handle.net/2318/1660820"]},{"collectedfrom":{"key":"10|openaire____::9e3be59865b2c1c335d32dae2fe7b254","value":"Datacite"},"hostedby":{"key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c","value":"Unknown Repository"},"publicationdate":"2018-12-01","refereed":"UNKNOWN","type":"Other literature type","url":["http://dx.doi.org/10.1111/nph.15014"]}],"language":{"code":"und","label":"Undetermined"},"lastupdatetimestamp":1603727328518,"maintitle":"Native soils with their microbiotas elicit a state of alert in tomato plants","originalId":["10.1111/nph.15014","2793208206","oai:iris.unito.it:2318/1660820"],"pid":[{"scheme":"doi","value":"10.1111/nph.15014"},{"scheme":"pmid","value":"29424928"}],"projects":[{"acronym":"TomRes","code":"727929","funder":{"fundingStream":"H2020","jurisdiction":"EU","name":"European Commission","shortName":"EC"},"id":"40|corda__h2020::94c4a066401e22002c4811a301bb4655","provenance":{"provenance":"Harvested","trust":"0.900000000000000022"},"title":"A NOVEL AND INTEGRATED APPROACH TO INCREASE MULTIPLE AND COMBINED STRESS TOLERANCE IN PLANTS USING TOMATO AS A MODEL"}],"publicationdate":"2018-12-01","publisher":"Wiley","subjects":[{"subject":{"scheme":"keywords","value":"Plant Science"}},{"subject":{"scheme":"keywords","value":"Physiology"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Arbuscular mycorrhizal fungi; Defence responses; Lignin biosynthesis; Microbiota; Suppressive and conducive soils; Susceptible and resistant genotypes; Tomato; Physiology; Plant Science"}},{"provenance":{"provenance":"Inferred by OpenAIRE","trust":"0.891"},"subject":{"scheme":"mesheuropmc","value":"food and beverages"}},{"provenance":{"provenance":"Inferred by OpenAIRE","trust":"0.891"},"subject":{"scheme":"mesheuropmc","value":"fungi"}},{"provenance":{"provenance":"Inferred by OpenAIRE","trust":"0.8739"},"subject":{"scheme":"mesheuropmc","value":"complex mixtures"}}],"type":"publication"} +{"author":[{"fullname":"K.P. 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This study focuses on estimating the evapotranspiration and crop coefficients of table grapes vineyards trained on overhead “tendone” systems in the Apulia region (Italy). Maximum vineyard transpiration was estimated by adopting the “direct” methodology for ETp proposed by the Food and Agriculture Organization in Irrigation and Drainage Paper No. 56, with crop parameters estimated from Landsat 8 and RapidEye satellite data in combination with ground-based meteorological data. The modeling results of two growing seasons (2013 and 2014) indicated that canopy growth, seasonal and 10-day sums evapotranspiration values were strictly related to thermal requirements and rainfall events. The estimated values of mean seasonal daily evapotranspiration ranged between 4.2 and 4.1 mm·d−1, while midseason estimated values of crop coefficients ranged from 0.88 to 0.93 in 2013, and 1.02 to 1.04 in 2014, respectively. The experimental evapotranspiration values calculated represent the maximum value in absence of stress, so the resulting crop coefficients should be used with some caution. It is concluded that the retrieval of crop parameters and evapotranspiration derived from remotely-sensed data could be helpful for downscaling to the field the local weather conditions and agronomic practices and thus may be the basis for supporting grape growers and irrigation managers."],"format":["application/pdf"],"id":"50|dedup_wf_001::0bc332de35b4eb0cc3d0c54b3ff22dd3","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::a8db6f6b2ce4fe72e8b2314a9a93e7d9","value":"Sygma"},"hostedby":{"key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c","value":"Unknown Repository"},"license":"https://creativecommons.org/licenses/by/4.0/","refereed":"UNKNOWN","type":"Article","url":["http://dx.doi.org/10.3390/rs71114708"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"},"hostedby":{"key":"10|doajarticles::f7180a75ef642fcf5309759e0d2c431a","value":"Remote Sensing"},"license":"https://creativecommons.org/licenses/by/4.0/","publicationdate":"2015-11-05","refereed":"UNKNOWN","type":"Article","url":["http://www.mdpi.com/2072-4292/7/11/14708/pdf","http://dx.doi.org/10.3390/rs71114708"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::8ac8380272269217cb09a928c8caa993","value":"UnpayWall"},"hostedby":{"key":"10|doajarticles::f7180a75ef642fcf5309759e0d2c431a","value":"Remote Sensing"},"license":"cc-by","refereed":"UNKNOWN","type":"Article","url":["https://www.mdpi.com/2072-4292/7/11/14708/pdf"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a","value":"Microsoft Academic Graph"},"hostedby":{"key":"10|doajarticles::f7180a75ef642fcf5309759e0d2c431a","value":"Remote Sensing"},"refereed":"UNKNOWN","type":"Article","url":["https://dblp.uni-trier.de/db/journals/remotesensing/remotesensing7.html#VaninoPNMBD15","https://doi.org/10.3390/rs71114708","https://core.ac.uk/display/55147144","http://doi.org/10.3390/rs71114708","https://academic.microsoft.com/#/detail/2149946514"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::c2cdfa5866e03cdd07d313cbc8fb8311","value":"Multidisciplinary Digital Publishing Institute"},"hostedby":{"key":"10|doajarticles::f7180a75ef642fcf5309759e0d2c431a","value":"Remote Sensing"},"license":"http://creativecommons.org/licenses/by/3.0/","publicationdate":"2015-11-05","refereed":"UNKNOWN","type":"Other literature type","url":["http://dx.doi.org/10.3390/rs71114708"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"},"hostedby":{"key":"10|doajarticles::f7180a75ef642fcf5309759e0d2c431a","value":"Remote Sensing"},"publicationdate":"2015-11-01","refereed":"UNKNOWN","type":"Article","url":["http://www.mdpi.com/2072-4292/7/11/14708","https://doaj.org/toc/2072-4292"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::d8c24ca8f23c562a5600876ca2a550ce","value":"Archivio della ricerca - 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Vertical velocities can be estimated indirectly from in situ observations by theoretical frameworks like the-equation. Direct measures of vertical exchanges are challenging due to their typically ephemeral spatiotemporal scales. In this study we address this problem with an adaptive sampling strategy coupling various biophysical instruments. We analyze the 3-D organization of a cyclonic mesoscale structure finely sampled during the Observing Submesoscale Coupling At High Resolution cruise in the Ligurian Sea during fall 2015. The observations, acquired with a moving vessel profiler, highlight a subsurface low-salinity layer (≃50 m), as well as rising isopycnals, generated by geostrophic cyclonic circulation, in the structure's center. Reconstructed 3-D fields of density and horizontal velocities are used to estimate the vertical velocity field down to 250 m by applying the adiabatic QG-equation, for the first time in this region. The vertical motions are characterized by multipolar patterns of downward and upward velocities on the edges of the structure and significantly smaller vertical velocities in its center. Both the 3-D distribution of particles (size ≥100 μm), measured with a laser optical plankton counter, and the Synechococcus and Prochlorococcus abundances (cell per cubic meter) measured by flow cytometry are consistent with the 3-D velocity field. In particular, a secondary vertical recirculation is identified that upwells particles (from 250 to 100 m) along isohalines to the structure's center. Besides demonstrating the effect of vertical patterns on biogeochemical distributions, this case study suggests to use particle matter as a tracer to assess physical dynamics."],"format":["application/pdf"],"id":"50|dedup_wf_001::0d16b1714ab3077df73893a8ea57d776","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::7e7757b1e12abcb736ab9a754ffb617a","value":"Hyper Article en Ligne"},"hostedby":{"key":"10|opendoar____::7e7757b1e12abcb736ab9a754ffb617a","value":"Hyper Article en 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Personality traits, affective status and stress are some of the relevant factors contributing to lower quality of life and symptom exacerbation in IBS patients. In order to examine the role of stress in IBS symptom exacerbation, the aims of this study were to explore the relationship of daily stressful events and symptom severity in a prospective manner and to explore the roles of neuroticism, anxiety, depression and stress in the vicious circle of symptom perpetuation. A total of 49 patients with IBS reported their symptom severity and daily stressful events intensity each day for 14 consecutive days. They also completed the Big five personality inventory, the Beck Depression Inventory and the State-trait anxiety inventory. Cross-correlation analyses were performed on the time series data for daily stress and symptom severity for each participant separately. Four different patterns of relationships were found in different subgroups of participants: positive cross-correlations of symptom severity and stress intensity on the same day; higher symptom severity on days following stressful days; lower symptom severity on days following stressful days; and lower stress intensity on days following severe symptoms. Using average scores for daily stress and symptom severity, as well as scores for neuroticism, anxiety and depression, we performed a path analysis to test a model of symptom exacerbation. It showed that, on the group level, average stress intensity predicts average symptom severity. Neuroticism and anxiety were not significant predictors of symptom severity, while depression showed a marginally significant relationship with symptom severity, mediated by stress intensity. In conclusion, depression and daily stress seem to be important contributors to the vicious circle of IBS symptom perpetuation.","Síndrome del intestino irritable se considera un trastorno biopsicosocial, el resultado de la combinación compleja de factores predisponentes, precipitantes y perpetuos. Rasgos de personalidad, estado afectivo y estrés son algunos de los factores relevantes que contribuyen a la calidad de vida más baja y la exacerbación sintomática de los pacientes con SII. Para examinar el papel del estrés en la exacerbación sintomática de SII, el objetivo de este estudio era explorar la relación entre los acontecimientos cotidianos estresantes y la intensidad de los síntomas de forma prospectiva, tanto como explorar los papeles del neuroticismo, ansiedad, depresión y estrés en el círculo vicioso de perpetuación de los síntomas. Todos los 49 pacientes con SII informaron sobre la intensidad de los síntomas y la intensidad de los acontecimientos cotidianos estresantes cada día durante 14 días consecutivos. Además, completaron el Test de personalidad de los cinco grandes, Inventario de depresión de Beck e Inventario de ansiedad estado-rasgo. En los datos de series temporales se hizo el análisis de correlación cruzada para la intensidad del estrés diario y de los síntomas para cada participante por separado. Se encontraron cuatro patrones de relación diferentes en diferentes subgrupos de participantes: correlación cruzada positiva de la intensidad de los síntomas y del estrés el mismo día; intensidad de los síntomas más alta en los días después de los días estresantes; intensidad de los síntomas más baja en los días después de los días estresantes e intensidad del estrés más baja en los días después de los síntomas graves. Usando resultados promedios para el estrés diario y la intensidad de los síntomas, tanto como resultados para el neuroticismo, ansiedad y depresión, realizamos un análisis del camino para examinar el modelo de la exacerbación de los síntomas. Mostró que, al nivel de grupo, la intensidad del estrés promedia predice la intensidad de los síntomas promedia. Neuroticismo y ansiedad no eran predictores significativos de la intensidad de los síntomas, mientras que la depresión demostró una relación marginalmente significante con la intensidad de los síntomas, mediada por la intensidad del estrés. En conclusión, la depresión y el estrés diario parecen ser contribuidores importantes al círculo vicioso de la perpetuación de los síntomas SII."],"format":["application/pdf"],"id":"50|dedup_wf_001::054ea3bc3ccc386d150d900776e1070d","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::2e3d2c4f33a7a1f58bc6c81cacd21e9c","value":"Repository of the University of Rijeka, Faculty of Humanities and Social Sciences"},"hostedby":{"key":"10|opendoar____::2e3d2c4f33a7a1f58bc6c81cacd21e9c","value":"Repository of the University of Rijeka, Faculty of Humanities and Social Sciences"},"license":"http://creativecommons.org/licenses/by/4.0/","publicationdate":"2016-04-01","refereed":"UNKNOWN","type":"Article","url":["https://repository.ffri.uniri.hr/islandora/object/ffri:1182","https://urn.nsk.hr/urn:nbn:hr:186:701987","https://repository.ffri.uniri.hr/islandora/object/ffri:1182/datastream/FILE0"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::1c1d4df596d01da60385f0bb17a4a9e0","value":"HRČAK - Portal of scientific journals of Croatia"},"hostedby":{"key":"10|opendoar____::1c1d4df596d01da60385f0bb17a4a9e0","value":"HRČAK - Portal of scientific journals of Croatia"},"publicationdate":"2016-01-01","refereed":"UNKNOWN","type":"Other literature type","url":["https://hrcak.srce.hr/156331","https://hrcak.srce.hr/file/230444"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"},"hostedby":{"key":"10|doajarticles::23738aeeb586d9f9b652c75aaff54dd4","value":"Psychological Topics"},"publicationdate":"2016-04-01","refereed":"UNKNOWN","type":"Article","url":["http://pt.ffri.hr/index.php/pt/article/view/317","https://doaj.org/toc/1332-0742"]}],"language":{"code":"eng","label":"English"},"lastupdatetimestamp":1603727328518,"maintitle":"The role of stress in IBS symptom severity","originalId":["oai:repository.ffri.uniri.hr:ffri_1182","oai:hrcak.srce.hr:156331","oai:doaj.org/article:4394c5a4f62849ffac7ea485a91540a3"],"pid":[],"projects":[{"code":"009-0092660-2655","funder":{"jurisdiction":"HR","name":"Ministry of Science, Education and Sports of the Republic of Croatia (MSES)","shortName":"MZOS"},"id":"40|irb_hr______::ad496254144c27606e4058841e060fa0","provenance":{"provenance":"Harvested","trust":"0.900000000000000022"},"title":"Psychosomatic aspects of chronic functional and inflammatory bowel diseases"}],"publicationdate":"2016-04-01","subjects":[{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"irritable bowel syndrome"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"symptom severity"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"daily stress"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"depression"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"DRUŠTVENE ZNANOSTI. 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A set of model alloys with low nickel content, lower than 0.2 mass%, was used for the study. Copper and phosphorus contents were varied in a wide range: 0.005–0.99 and 0.002–0.039 mass%, respectively. Recovery efficiency has been estimated by the value of residual embrittlement after annealing, measured in terms of a shift in transition temperature (ΔTKres). A comparison of the results obtained on model alloys with data for VVER-440 RPV materials has also been carried out. Comparative analysis has confirmed the conclusion that ΔTKres is independent of phosphorus content while the effect of copper on ΔTKres is not significant for typical VVER-440 RPV materials with a typical range of Cu contents between 0.10 and 0.24 mass%. 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central problem for the function and manufacture of materials where performance relies on nanoscale structure is to control the compatibility and interactions of the building blocks. In natural materials, such as nacre, there are examples of multifunctional macromolecules that have combined binding affinities for different materials within the same molecule, thereby bridging these materials and acting as a molecular glue. Here, we describe the use of a designed multifunctional protein that is used for self-assembly of nanofibrillar cellulose. Recent advances in the production of cellulose nanofibrils have given inspiration for new uses of cellulosic materials. Cellulose nanofibrils have mechanical and structural features that open new possibilities for performance in composites and other nanoscale materials. Functionalisation was realised through a bi-functional fusion protein having both an ability to bind to cellulose and a second functionality of surface activity. The cellulose-binding function was obtained using cellulose-binding domains from cellulolytic enzymes and the surface activity through the use of a surface active protein called hydrophobin. Using the bi-functional protein, cellulose nanofibrils could be assembled into tightly packed thin films at the air/water interface and at the oil/water interface. It was shown that the combination of protein and cellulose nanofibrils resulted in a synergistic improvement in the formation and stability of oil-in-water emulsions resulting in emulsions that were stable for several months. The bi-functionality of the protein also allowed the binding of hydrophobic solid drug nanoparticles to cellulose nanofibrils and thereby improving their long-term stability under physiological conditions."}],"externalReference":[],"extraInfo":[],"format":[],"fulltext":[],"id":"50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb","instance":[{"accessright":{"classid":"CLOSED","classname":"Closed Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"collectedfrom":{"key":"10|openaire____::4692342f0992d91f9e705c26959f09e0","value":"VTT Research Information 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Ce qui nous frappe en premier lieu dans le roman de Melchior Mbonimpa, Le Totem des Baranda, c'est l'efficacité de sa fonction didactique. Le livre est porteur d'un message, d'une vision sur l'histoire de l'Afrique des Grands Lacs qu'on rencontre rarement dans l'actualité ou l'histoire immédiate que nous livrent les médias.

Cette thèse se penchera sur un aspect de ce roman qui a particulièrement attiré notre attention: la représentation de la résistance à travers l'affirmation identitaire des personnages féminins. Dans notre analyse de ce thème, nous accordons une grande importance au contexte socioculturel et à l'imaginaire collectif qui nourrissent l'auteur et dans lesquels s'inscrivent ses personnages. L'étude soulignera la fonction sociale de l'écrivain et relèvera la contribution de la fiction à la culture africaine. Nous mettrons en évidence les positions idéologiques de l'auteur et le message de sensibilisation qu'il adresse à diverses catégories de lecteurs: ceux qui se trouvent en Afrique, les Africains de la diaspora, et les lecteurs non-Africains qui s'intéressent à son œuvre. Cette orientation idéologique affecte évidemment la manière dont s'exprime la résistance des pnncIpaux personnages féminins du roman. Elle détermine la place que cette fiction accorde à la femme, et qui correspond sans doute à la place que, selon les souhaits de l'auteur, la femme devrait occuper dans le contexte culturel africain. Notre étude insiste aussi sur le fait que dans ce roman, la modernité se nourrit de la culture traditionnelle et ne renie pas les valeurs du passé.

Ainsi, le parcours narratif montre que dans leur résistance, les héroïnes de la généalogie vivent à leur époque, mais chacune porte plus loin une mission transmise par les précédentes.

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The superconducting transition in the magnetic resistance of members of the family of bismuth based high temperature superconductors was investigated. Measurements were performed in magnetic fields up to 1.7 T. Small current densities ranging from 0.03 A/cm² to 3.0 A/cm² were applied. The resistivity of Bi₂Sr₂CaCu₂Ox single crystals was analyzed in terms of the thermally activated flux flow expression, ρ =ρ₀U/T exp(-U/T) where T is the temperature. It was found that the activation energy was given by Uα(Hsinθ)^(⁻α) where α≈1/3 and that the prefactor had the form, ρ₀Hsinθ, where H was the applied field and θ the angle of the field with respect to the CuO₂ planes. Results demonstrated that dissipation could be accounted for by the motion of two-dimensional vortices whose density is given by the field, Hsinθ, projected on the CuO₂ planes. Measurements of the resistivity and current dependent resistivity were performed with two Sn-doped and two Sb-doped polycrystalline Bi(1.7)Pb(0.3)Sr₂Ca₂Cu₃O(y) samples. Features in the temperature derivative of the resistivity curves were associated with the presence of a superconducting transition between superconducting grains, coupled by weak links with a distribution of critical currents and critical temperatures, and the superconducting transition within grains. The transition between grains was more strongly suppressed in temperature with the application of a magnetic field in samples with weaker coupling between grains. The presence of a transition in a magnetic field due to weak links between grains was verified at 77 K by the observation of a current dependent resistivity in a magnetic field. Measurements of a Bi₂Sr₂CaCu₂Ox diffusion grown thick film ring were done. The transverse voltage, the voltage at the centre of a 120 μm thick branch with respect to the centre of a 76 μm thick branch, was measured. A higher critical temperature from the presence of more texturing in the 76 μm branch as determined by separate resistivity, x-ray and scanning electron microscopy measurements was consistent with the measurement of a crossover from a negative to positive transverse voltage as the temperature of the sample went through its superconducting transition.

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This study examines Leonard Cohen's novel Beautiful Losers through the lenses of allegorical and authorial theories to appreciate how the novel uses allegorical techniques to code into symbolic terms an exploration of the polysemous nature of the word ''translation.'' The first chapter studies the stylistic and conceptual dimensions of allegory as a literary genre - as critics like Northrop Frye, Angus Fletchet, and Maureen Quilligan help to define it - while arguing that Cohen's novel is consciously allegorical, challenging readers to interpret what it \"means,\" or may mean. The second chapter performs an intensive re-reading of Beautiful Losers, examining how the novel uses complex systems of verbal play (particularly puns) to coordinate a reunification of various dichotomies historical \"reality\"/imaginative myth, secularity/spirituality, enslavement/sanctification, among others - employed throughout the text. The thesis concludes that the novel is perpetually playing with various types of translation (spiritual, linguistic, physical, and so forth), affirming the need for emotionally-charged, devotional forms of expression (like song and prayer) over more clinical attempts to reorder or recreate the world and its inhabitants. Ultimately, this discussion argues that an understanding of the allegorical dimensions of Beautiful Losers may illuminate how Cohen's other works (particularly his songs) may be studied as attempts to associate word with voice, to emphasize the process of expression (translation) rather than just the finished product.

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00:00:00 2001 From: "miriam.baglioni" Date: Tue, 21 Jun 2022 18:02:51 +0200 Subject: [PATCH 090/214] [DUMP NEW FUNDED PRODUCTS] change in resources --- .../dhp/oa/graph/dump/funderresource/nomatch/papers.json | 2 +- .../dhp/oa/graph/dump/funderresource/preparedInfo/resultProject | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json index fda631c2f..dd6026980 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json @@ -12,7 +12,7 @@ {"author":[{"fullname":"Sharp, 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This study examines Leonard Cohen's novel Beautiful Losers through the lenses of allegorical and authorial theories to appreciate how the novel uses allegorical techniques to code into symbolic terms an exploration of the polysemous nature of the word ''translation.'' The first chapter studies the stylistic and conceptual dimensions of allegory as a literary genre - as critics like Northrop Frye, Angus Fletchet, and Maureen Quilligan help to define it - while arguing that Cohen's novel is consciously allegorical, challenging readers to interpret what it \"means,\" or may mean. The second chapter performs an intensive re-reading of Beautiful Losers, examining how the novel uses complex systems of verbal play (particularly puns) to coordinate a reunification of various dichotomies historical \"reality\"/imaginative myth, secularity/spirituality, enslavement/sanctification, among others - employed throughout the text. The thesis concludes that the novel is perpetually playing with various types of translation (spiritual, linguistic, physical, and so forth), affirming the need for emotionally-charged, devotional forms of expression (like song and prayer) over more clinical attempts to reorder or recreate the world and its inhabitants. Ultimately, this discussion argues that an understanding of the allegorical dimensions of Beautiful Losers may illuminate how Cohen's other works (particularly his songs) may be studied as attempts to associate word with voice, to emphasize the process of expression (translation) rather than just the finished product.

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osallisuuden vahvistaminen sekä oikeus tulla kuulluksi ovat keskeisiä lasten palveluja ohjaavia periaatteita. Osallisuuden toteutumisessa on kuitenkin edelleen puutteita. Tämän tutkimuksen tarkoituksena oli selvittää päihdepalvelujen esimiesten käsityksiä siitä, miten päihdepalvelujen piirissä olevien vanhempien osallisuutta tuetaan. Osallisuuden tukemista arvioitiin työntekijöille modifiodulla Family Empowerment Scale -mittarilla (FES). Aineisto kerättiin päihdepalveluissa toimivilta esimiehiltä (n=372). Vastausprosentti oli 36. Taustamuuttujien perusteella määräytyvien vastaajaryhmien väliset erot analysoitiin riippumattomien otosten t-testillä sekä yksisuuntaisella varianssianalyysillä. Vanhempien osallisuuden tukeminen toteutui kohtuullisesti kaikissa toimipisteissä. Merkittävimmät kehittämiskohteet liittyivät perheiden riittämättömään tiedonsaantiin, heikkoihin palautteen antomahdollisuuksin, perheen ja henkilöstön välisen yhteistyön sekä vanhempien yhteiskunnallisten vaikutusmahdollisuuksien lisäämiseen. 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a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo/resultProject b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo/resultProject index 515d1c9a6..5749f731d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo/resultProject +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo/resultProject @@ -1 +1 @@ -{"resultId":"50|a89337edbe55::43e8b61e5e8d682545cb867be8118585","projectsList":[{"id":"40|aka_________::01bb7b48e29d732a1c7bc5150b9195c4","code":"135027","acronym":null,"title":"Dynamic 3D resolution-enhanced low-coherence interferometric imaging / Consortium: Hi-Lo","funder":{"shortName":"AKA","name":"Academy of 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Finland","jurisdiction":"FI","fundingStream":null},"provenance":{"provenance":"Harvested","trust":"0.900000000000000022"},"validated":null},{"id":"40|aka_________::9d1af21dbd0f5bc719f71553d19a6b3a","code":"316061","acronym":null,"title":"Finnish Imaging of Degenerative Shoulder Study (FIMAGE): A study on the prevalence of degenerative imaging changes of the shoulder and their relevance to clinical symptoms in the general population.","funder":{"shortName":"AKA","name":"Academy of Finland","jurisdiction":"FI","fundingStream":null},"provenance":{"provenance":"Harvested","trust":"0.900000000000000022"},"validated":null}]} \ No newline at end of file From f561f13dd9d9796613198c1cdb54f8f74b166d5a Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 21 Jun 2022 18:18:17 +0200 Subject: [PATCH 091/214] [Funder Products Dump] fixed names of parameters in workflow --- .../community/oozie_app/workflow.xml | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml index b559a25dc..dfbe93b67 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml @@ -107,7 +107,7 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - --sourcePath${selectedResults}/publication + --sourcePath${sourcePath}/publication --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication --outputPath${workingDir}/dump/publication --communityMapPath${communityMapPath} @@ -134,7 +134,7 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - --sourcePath${selectedResults}/dataset + --sourcePath${sourcePath}/dataset --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset --outputPath${workingDir}/dump/dataset --communityMapPath${communityMapPath} @@ -160,7 +160,7 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - --sourcePath${selectedResults}/otherresearchproduct + --sourcePath${sourcePath}/otherresearchproduct --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct --outputPath${workingDir}/dump/otherresearchproduct --communityMapPath${communityMapPath} @@ -186,7 +186,7 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - --sourcePath${selectedResults}/software + --sourcePath${sourcePath}/software --resultTableNameeu.dnetlib.dhp.schema.oaf.Software --outputPath${workingDir}/dump/software --communityMapPath${communityMapPath} @@ -246,7 +246,7 @@ --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} --sourcePath${workingDir}/dump/publication - --outputPath${outputPath}/ext/publication + --outputPath${workingDir}/ext/publication --preparedInfoPath${workingDir}/preparedInfo @@ -271,7 +271,7 @@ --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} --sourcePath${workingDir}/dump/dataset - --outputPath${outputPath}/ext/dataset + --outputPath${workingDir}/ext/dataset --preparedInfoPath${workingDir}/preparedInfo @@ -296,7 +296,7 @@ --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} --sourcePath${workingDir}/dump/otherresearchproduct - --outputPath${outputPath}/ext/orp + --outputPath${workingDir}/ext/orp --preparedInfoPath${workingDir}/preparedInfo @@ -321,7 +321,7 @@ --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} --sourcePath${workingDir}/dump/software - --outputPath${outputPath}/ext/software + --outputPath${workingDir}/ext/software --preparedInfoPath${workingDir}/preparedInfo From edddfc6c637d601823681c190305aa1105ee5834 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 21 Jun 2022 18:28:53 +0200 Subject: [PATCH 092/214] [DUMP DELTA PROJECTS] adding test and resource --- .../projectssubset/ProjectSubsetTest.java | 118 ++++++++++++++++++ .../graph/dump/projectsubset/allnew/projects | 12 ++ .../dump/projectsubset/matchOne/projects | 12 ++ .../dhp/oa/graph/dump/projectsubset/projectId | 28 +++++ 4 files changed, 170 insertions(+) create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/allnew/projects create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/matchOne/projects create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/projectId diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java new file mode 100644 index 000000000..d5b1ce776 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java @@ -0,0 +1,118 @@ +package eu.dnetlib.dhp.oa.graph.dump.projectssubset; +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.HashMap; +import org.apache.commons.io.FileUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject; +import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; +import eu.dnetlib.dhp.schema.dump.oaf.graph.Project; +public class ProjectSubsetTest { + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static SparkSession spark; + private static Path workingDir; + private static final Logger log = LoggerFactory + .getLogger(eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class); + private static final HashMap map = new HashMap<>(); + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files + .createTempDirectory( + eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + SparkConf conf = new SparkConf(); + conf.setAppName(eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class.getSimpleName()); + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + spark = SparkSession + .builder() + .appName(eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + @Test + void testAllNew() throws Exception { + final String projectListPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/projectId") + .getPath(); + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/allnew/projects") + .getPath(); + spark + .read() + .textFile(projectListPath) + .write() + .mode(SaveMode.Overwrite) + .text(workingDir.toString() + "/projectIds"); + ProjectsSubsetSparkJob.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/projects", + "-sourcePath", sourcePath, + "-projectListPath", workingDir.toString() + "/projectIds" + }); + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/projects") + .map(item -> OBJECT_MAPPER.readValue(item, Project.class)); + Assertions.assertEquals(12, tmp.count()); + Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("aka_________")).count()); + Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("anr_________")).count()); + Assertions.assertEquals(4, tmp.filter(p -> p.getId().substring(3, 15).equals("arc_________")).count()); + Assertions.assertEquals(3, tmp.filter(p -> p.getId().substring(3, 15).equals("conicytf____")).count()); + Assertions.assertEquals(1, tmp.filter(p -> p.getId().substring(3, 15).equals("corda_______")).count()); + Assertions.assertEquals(40, sc.textFile(workingDir.toString() + "/projectIds").count()); + } + @Test + void testMatchOne() throws Exception { + final String projectListPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/projectId") + .getPath(); + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/matchOne/projects") + .getPath(); + spark + .read() + .textFile(projectListPath) + .write() + .mode(SaveMode.Overwrite) + .text(workingDir.toString() + "/projectIds"); + ProjectsSubsetSparkJob.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/projects", + "-sourcePath", sourcePath, + "-projectListPath", workingDir.toString() + "/projectIds" + }); + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/projects") + .map(item -> OBJECT_MAPPER.readValue(item, Project.class)); + Assertions.assertEquals(11, tmp.count()); + Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("aka_________")).count()); + Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("anr_________")).count()); + Assertions.assertEquals(4, tmp.filter(p -> p.getId().substring(3, 15).equals("arc_________")).count()); + Assertions.assertEquals(3, tmp.filter(p -> p.getId().substring(3, 15).equals("conicytf____")).count()); + Assertions.assertEquals(0, tmp.filter(p -> p.getId().substring(3, 15).equals("corda__h2020")).count()); + Assertions.assertEquals(39, sc.textFile(workingDir.toString() + "/projectIds").count()); + } +} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/allnew/projects b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/allnew/projects new file mode 100644 index 000000000..82d9bef76 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/allnew/projects @@ -0,0 +1,12 @@ +{"id":"40|aka_________::01bb7b48e29d732a1c7bc5150b9195c4","websiteurl":null,"code":"135027","acronym":null,"title":"Dynamic 3D resolution-enhanced low-coherence interferometric imaging / Consortium: Hi-Lo","startdate":null,"enddate":null,"callidentifier":"Fotoniikka ja modernit kuvantamismenetelmät LT","keywords":null,"openaccessmandateforpublications":false,"openaccessmandatefordataset":false,"subject":[],"funding":[{"shortName":"AKA","name":"Academy of Finland","jurisdiction":"FI","funding_stream":null}],"summary":null,"granted":null,"h2020programme":[]} +{"id":"40|aka_________::9d1af21dbd0f5bc719f71553d19a6b3a","websiteurl":null,"code":"316061","acronym":null,"title":"Finnish Imaging of Degenerative Shoulder Study (FIMAGE): A study on the prevalence of degenerative imaging changes of the shoulder and their relevance to clinical symptoms in the general population.","startdate":null,"enddate":null,"callidentifier":"Academy Project Funding TT","keywords":null,"openaccessmandateforpublications":false,"openaccessmandatefordataset":false,"subject":[],"funding":[{"shortName":"AKA","name":"Academy of Finland","jurisdiction":"FI","funding_stream":null}],"summary":null,"granted":null,"h2020programme":[]} +{"id":"40|anr_________::1f21edc5c902be305ee47148955c6e50","websiteurl":null,"code":"ANR-17-CE05-0033","acronym":"MOISE","title":"METAL OXIDES AS LOW LOADED NANO-IRIDIUM SUPPORT FOR COMPETITIVE WATER 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+{"id":"40|arc_________::838e781a8d479e27a11101421fd8b296","websiteurl":"http://purl.org/au-research/grants/arc/LE0347462","code":"LE0347462","acronym":null,"title":"Femtosecond laser micromachining facility","startdate":"2003-01-01","enddate":"2003-12-31","callidentifier":null,"keywords":"biomedical nanostructures,femtosecond laser machining,laser manufacturing,laser micromachining,microphotonics,photonic bandgap structures","openaccessmandateforpublications":false,"openaccessmandatefordataset":false,"subject":[],"funding":[{"shortName":"ARC","name":"Australian Research Council (ARC)","jurisdiction":"AU","funding_stream":{"id":"ARC::Linkage Infrastructure, Equipment and Facilities","description":"Linkage Infrastructure, Equipment and Facilities"}}],"summary":null,"granted":null,"h2020programme":[]} +{"id":"40|arc_________::a461f180f7b6700c0499d4d3d53e58c7","websiteurl":"http://purl.org/au-research/grants/arc/LP140100567","code":"LP140100567","acronym":null,"title":"Linkage Projects - 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Commission","jurisdiction":"EU","funding_stream":{"id":"EC::FP7::SP3::PEOPLE","description":"SEVENTH FRAMEWORK PROGRAMME - SP3-People - Marie-Curie Actions"}}],"summary":null,"granted":null,"h2020programme":[]} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/projectId b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/projectId new file mode 100644 index 000000000..9a7ea9085 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/projectId @@ -0,0 +1,28 @@ +40|nih_________::4c32cdbc4c9949853f02219fc4780a30 +40|nih_________::b485512ef116af73bee79d50c8f9ca01 +40|nih_________::b44d9bc8e99d9a0477ac06897e3e9c19 +40|nih_________::7d2d2b7d1644a722a6bbcb031d82fec6 +40|nsf_________::6b2674b0341e07b818a56c6f0daa2633 +40|nih_________::96bb39aecc8f7b9f3b02ed36ef09538b +40|nsf_________::88d92bdf20ec2fac3ed9740f962b4fad +40|nih_________::4bb8c14729a0082378bb04db8321ce14 +40|nih_________::08a8eed6c17c6d8e427afcfd29f87c7b +40|nsf_________::c314f3d35af1990121bf5b803937e112 +40|nih_________::3ad6a2e6ebd561206f0da69468337f50 +40|nih_________::d02c60c65a59629e69a30abcf2ceaed1 +40|nih_________::d5a241cc94253feb72181cde15f51e96 +40|nih_________::b5df718bbca69af50d4b7213e26af3f0 +40|nih_________::bc90893c1be80503578e48f6ef6b7061 +40|rcuk________::2c39b38c26c260b14a9816b88c91c132 +40|nih_________::ab103ad117cd0579df66f7592a7d4adf +40|nih_________::147aa6ad8bd201e2a02c7b6cc3f68348 +40|corda__h2020::bf5d35ec8d24ae4abfb4a1c6a0af3856 +40|nih_________::b8083208156f2764d07c736ba9b49dd2 +40|nih_________::f4d1e0aece0e6a9eff8d054c28e082db +40|nsf_________::56297da8b472a4be8ac3f09af813c9f6 +40|nsf_________::6b6dc3398eeebb3de1ab66e6eb8c5cb3 +40|nih_________::93289a36ebffb0bee3d6b01c6fc0a3d6 +40|nih_________::6c3b00dd4ae9d43d6630ff18f189ebae +40|nih_________::1d983a87768f13bc8377b1b7d17290a2 +40|nih_________::c3b56e91859b114644c1403e892eb80f +40|rcuk________::c1e15330fc7956063652f9c06e584548 \ No newline at end of file From 929b145130a99f60de6dde4ed740fbbf8c73983b Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 21 Jun 2022 23:07:06 +0200 Subject: [PATCH 093/214] code formatting --- .../dhp/collection/CollectorWorker.java | 4 +- .../file/AbstractSplittedRecordPlugin.java | 91 +++---- .../plugin/file/FileCollectorPlugin.java | 36 +-- .../plugin/file/FileGZipCollectorPlugin.java | 38 +-- .../collection/plugin/utils/XMLIterator.java | 243 +++++++++--------- .../plugin/file/FileCollectorPluginTest.java | 67 ++--- .../file/FileGZipCollectorPluginTest.java | 73 +++--- 7 files changed, 285 insertions(+), 267 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java index f6cba6fb8..9d9400068 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java @@ -7,8 +7,6 @@ import java.io.IOException; import java.util.Optional; import java.util.concurrent.atomic.AtomicInteger; -import eu.dnetlib.dhp.collection.plugin.file.FileCollectorPlugin; -import eu.dnetlib.dhp.collection.plugin.file.FileGZipCollectorPlugin; import org.apache.hadoop.fs.FileSystem; import org.apache.hadoop.fs.Path; import org.apache.hadoop.io.IntWritable; @@ -21,6 +19,8 @@ import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.aggregation.common.ReporterCallback; import eu.dnetlib.dhp.aggregation.common.ReportingJob; import eu.dnetlib.dhp.collection.plugin.CollectorPlugin; +import eu.dnetlib.dhp.collection.plugin.file.FileCollectorPlugin; +import eu.dnetlib.dhp.collection.plugin.file.FileGZipCollectorPlugin; import eu.dnetlib.dhp.collection.plugin.mongodb.MDStoreCollectorPlugin; import eu.dnetlib.dhp.collection.plugin.mongodb.MongoDbDumpCollectorPlugin; import eu.dnetlib.dhp.collection.plugin.oai.OaiCollectorPlugin; diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/file/AbstractSplittedRecordPlugin.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/file/AbstractSplittedRecordPlugin.java index 97f61980a..f2fa3d2bb 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/file/AbstractSplittedRecordPlugin.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/file/AbstractSplittedRecordPlugin.java @@ -1,3 +1,4 @@ + package eu.dnetlib.dhp.collection.plugin.file; import java.io.BufferedInputStream; @@ -9,69 +10,71 @@ import java.util.Spliterators; import java.util.stream.Stream; import java.util.stream.StreamSupport; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + import eu.dnetlib.dhp.collection.ApiDescriptor; import eu.dnetlib.dhp.collection.plugin.CollectorPlugin; import eu.dnetlib.dhp.collection.plugin.utils.XMLIterator; import eu.dnetlib.dhp.common.aggregation.AggregatorReport; import eu.dnetlib.dhp.common.collection.CollectorException; -import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.fs.Path; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - public abstract class AbstractSplittedRecordPlugin implements CollectorPlugin { - private static final Logger log = LoggerFactory.getLogger(AbstractSplittedRecordPlugin.class); + private static final Logger log = LoggerFactory.getLogger(AbstractSplittedRecordPlugin.class); - public static final String SPLIT_ON_ELEMENT = "splitOnElement"; + public static final String SPLIT_ON_ELEMENT = "splitOnElement"; - private final FileSystem fileSystem; + private final FileSystem fileSystem; - public AbstractSplittedRecordPlugin(FileSystem fileSystem) { - this.fileSystem = fileSystem; - } + public AbstractSplittedRecordPlugin(FileSystem fileSystem) { + this.fileSystem = fileSystem; + } - @Override - public Stream collect(ApiDescriptor api, AggregatorReport report) throws CollectorException { + @Override + public Stream collect(ApiDescriptor api, AggregatorReport report) throws CollectorException { - // get path to file - final Path filePath = Optional - .ofNullable(api.getBaseUrl()) - .map(Path::new) - .orElseThrow( () -> new CollectorException("missing baseUrl")); + // get path to file + final Path filePath = Optional + .ofNullable(api.getBaseUrl()) + .map(Path::new) + .orElseThrow(() -> new CollectorException("missing baseUrl")); - log.info("baseUrl: {}", filePath); + log.info("baseUrl: {}", filePath); - // check that path to file exists - try { - if (!fileSystem.exists(filePath)) { - throw new CollectorException("path does not exist: " + filePath); - } - } catch (IOException e) { - throw new CollectorException(e); - } + // check that path to file exists + try { + if (!fileSystem.exists(filePath)) { + throw new CollectorException("path does not exist: " + filePath); + } + } catch (IOException e) { + throw new CollectorException(e); + } - // get split element - final String splitOnElement = Optional - .ofNullable(api.getParams().get(SPLIT_ON_ELEMENT)) - .orElseThrow(() -> new CollectorException(String.format("missing parameter '%s', required by the AbstractSplittedRecordPlugin", SPLIT_ON_ELEMENT))); + // get split element + final String splitOnElement = Optional + .ofNullable(api.getParams().get(SPLIT_ON_ELEMENT)) + .orElseThrow( + () -> new CollectorException(String + .format("missing parameter '%s', required by the AbstractSplittedRecordPlugin", SPLIT_ON_ELEMENT))); - log.info("splitOnElement: {}", splitOnElement); + log.info("splitOnElement: {}", splitOnElement); - final BufferedInputStream bis = getBufferedInputStream(filePath); + final BufferedInputStream bis = getBufferedInputStream(filePath); - Iterator xmlIterator = new XMLIterator(splitOnElement, bis); + Iterator xmlIterator = new XMLIterator(splitOnElement, bis); - return StreamSupport.stream( - Spliterators.spliteratorUnknownSize(xmlIterator, Spliterator.ORDERED), - false - ); - } + return StreamSupport + .stream( + Spliterators.spliteratorUnknownSize(xmlIterator, Spliterator.ORDERED), + false); + } - abstract protected BufferedInputStream getBufferedInputStream(final Path filePath) throws CollectorException; + abstract protected BufferedInputStream getBufferedInputStream(final Path filePath) throws CollectorException; - public FileSystem getFileSystem() { - return fileSystem; - } -} \ No newline at end of file + public FileSystem getFileSystem() { + return fileSystem; + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/file/FileCollectorPlugin.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/file/FileCollectorPlugin.java index d7a992038..f771def93 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/file/FileCollectorPlugin.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/file/FileCollectorPlugin.java @@ -1,31 +1,33 @@ + package eu.dnetlib.dhp.collection.plugin.file; -import eu.dnetlib.dhp.common.collection.CollectorException; +import java.io.BufferedInputStream; + import org.apache.hadoop.fs.FileSystem; import org.apache.hadoop.fs.Path; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import java.io.BufferedInputStream; +import eu.dnetlib.dhp.common.collection.CollectorException; public class FileCollectorPlugin extends AbstractSplittedRecordPlugin { - private static final Logger log = LoggerFactory.getLogger(FileCollectorPlugin.class); + private static final Logger log = LoggerFactory.getLogger(FileCollectorPlugin.class); - public FileCollectorPlugin(FileSystem fileSystem) { - super(fileSystem); - } + public FileCollectorPlugin(FileSystem fileSystem) { + super(fileSystem); + } - @Override - protected BufferedInputStream getBufferedInputStream(final Path filePath) throws CollectorException { + @Override + protected BufferedInputStream getBufferedInputStream(final Path filePath) throws CollectorException { - log.info("filePath: {}", filePath); + log.info("filePath: {}", filePath); - try { - FileSystem fs = super.getFileSystem(); - return new BufferedInputStream(fs.open(filePath)); - } catch (Exception e) { - throw new CollectorException("Error reading file " + filePath, e); - } - } -} \ No newline at end of file + try { + FileSystem fs = super.getFileSystem(); + return new BufferedInputStream(fs.open(filePath)); + } catch (Exception e) { + throw new CollectorException("Error reading file " + filePath, e); + } + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/file/FileGZipCollectorPlugin.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/file/FileGZipCollectorPlugin.java index b724cfefd..91a6e9f16 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/file/FileGZipCollectorPlugin.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/file/FileGZipCollectorPlugin.java @@ -1,33 +1,35 @@ + package eu.dnetlib.dhp.collection.plugin.file; -import eu.dnetlib.dhp.common.collection.CollectorException; +import java.io.BufferedInputStream; +import java.util.zip.GZIPInputStream; + import org.apache.hadoop.fs.FileSystem; import org.apache.hadoop.fs.Path; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import java.io.BufferedInputStream; -import java.util.zip.GZIPInputStream; +import eu.dnetlib.dhp.common.collection.CollectorException; public class FileGZipCollectorPlugin extends AbstractSplittedRecordPlugin { - private static final Logger log = LoggerFactory.getLogger(FileGZipCollectorPlugin.class); + private static final Logger log = LoggerFactory.getLogger(FileGZipCollectorPlugin.class); - public FileGZipCollectorPlugin(FileSystem fileSystem) { - super(fileSystem); - } + public FileGZipCollectorPlugin(FileSystem fileSystem) { + super(fileSystem); + } - @Override - protected BufferedInputStream getBufferedInputStream(final Path filePath) throws CollectorException { + @Override + protected BufferedInputStream getBufferedInputStream(final Path filePath) throws CollectorException { - log.info("filePath: {}", filePath); + log.info("filePath: {}", filePath); - try { - FileSystem fs = super.getFileSystem(); - GZIPInputStream stream = new GZIPInputStream(fs.open(filePath)); - return new BufferedInputStream(stream); - } catch (Exception e) { - throw new CollectorException("Error reading file " + filePath, e); - } - } + try { + FileSystem fs = super.getFileSystem(); + GZIPInputStream stream = new GZIPInputStream(fs.open(filePath)); + return new BufferedInputStream(stream); + } catch (Exception e) { + throw new CollectorException("Error reading file " + filePath, e); + } + } } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/utils/XMLIterator.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/utils/XMLIterator.java index 853973ebb..e05fe263a 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/utils/XMLIterator.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/utils/XMLIterator.java @@ -1,3 +1,4 @@ + package eu.dnetlib.dhp.collection.plugin.utils; import java.io.InputStream; @@ -23,148 +24,154 @@ import org.apache.commons.logging.LogFactory; public class XMLIterator implements Iterator { - private static final Log log = LogFactory.getLog(XMLIterator.class); + private static final Log log = LogFactory.getLog(XMLIterator.class); - private ThreadLocal inputFactory = new ThreadLocal() { + private ThreadLocal inputFactory = new ThreadLocal() { - @Override - protected XMLInputFactory initialValue() { - return XMLInputFactory.newInstance(); - } - }; + @Override + protected XMLInputFactory initialValue() { + return XMLInputFactory.newInstance(); + } + }; - private ThreadLocal outputFactory = new ThreadLocal() { + private ThreadLocal outputFactory = new ThreadLocal() { - @Override - protected XMLOutputFactory initialValue() { - return XMLOutputFactory.newInstance(); - } - }; + @Override + protected XMLOutputFactory initialValue() { + return XMLOutputFactory.newInstance(); + } + }; - private ThreadLocal eventFactory = new ThreadLocal() { + private ThreadLocal eventFactory = new ThreadLocal() { - @Override - protected XMLEventFactory initialValue() { - return XMLEventFactory.newInstance(); - } - }; + @Override + protected XMLEventFactory initialValue() { + return XMLEventFactory.newInstance(); + } + }; - public static final String UTF_8 = "UTF-8"; + public static final String UTF_8 = "UTF-8"; - final XMLEventReader parser; + final XMLEventReader parser; - private XMLEvent current = null; + private XMLEvent current = null; - private String element; + private String element; - private InputStream inputStream; + private InputStream inputStream; - public XMLIterator(final String element, final InputStream inputStream) { - super(); - this.element = element; - this.inputStream = inputStream; - this.parser = getParser(); - try { - this.current = findElement(parser); - } catch (XMLStreamException e) { - log.warn("cannot init parser position. No element found: " + element); - current = null; - } - } + public XMLIterator(final String element, final InputStream inputStream) { + super(); + this.element = element; + this.inputStream = inputStream; + this.parser = getParser(); + try { + this.current = findElement(parser); + } catch (XMLStreamException e) { + log.warn("cannot init parser position. No element found: " + element); + current = null; + } + } - @Override - public boolean hasNext() { - return current != null; - } + @Override + public boolean hasNext() { + return current != null; + } - @Override - public String next() { - String result = null; - try { - result = copy(parser); - current = findElement(parser); - return result; - } catch (XMLStreamException e) { - throw new RuntimeException(String.format("error copying xml, built so far: '%s'", result), e); - } - } + @Override + public String next() { + String result = null; + try { + result = copy(parser); + current = findElement(parser); + return result; + } catch (XMLStreamException e) { + throw new RuntimeException(String.format("error copying xml, built so far: '%s'", result), e); + } + } - @Override - public void remove() { - throw new UnsupportedOperationException(); - } + @Override + public void remove() { + throw new UnsupportedOperationException(); + } - @SuppressWarnings("finally") - private String copy(final XMLEventReader parser) throws XMLStreamException { - final StringWriter result = new StringWriter(); - try { - final XMLEventWriter writer = outputFactory.get().createXMLEventWriter(result); - final StartElement start = current.asStartElement(); - final StartElement newRecord = eventFactory.get().createStartElement(start.getName(), start.getAttributes(), start.getNamespaces()); + @SuppressWarnings("finally") + private String copy(final XMLEventReader parser) throws XMLStreamException { + final StringWriter result = new StringWriter(); + try { + final XMLEventWriter writer = outputFactory.get().createXMLEventWriter(result); + final StartElement start = current.asStartElement(); + final StartElement newRecord = eventFactory + .get() + .createStartElement(start.getName(), start.getAttributes(), start.getNamespaces()); - // new root record - writer.add(newRecord); + // new root record + writer.add(newRecord); - // copy the rest as it is - while (parser.hasNext()) { - final XMLEvent event = parser.nextEvent(); + // copy the rest as it is + while (parser.hasNext()) { + final XMLEvent event = parser.nextEvent(); - // TODO: replace with depth tracking instead of close tag tracking. - if (event.isEndElement() && event.asEndElement().getName().getLocalPart().equals(element)) { - writer.add(event); - break; - } + // TODO: replace with depth tracking instead of close tag tracking. + if (event.isEndElement() && event.asEndElement().getName().getLocalPart().equals(element)) { + writer.add(event); + break; + } - writer.add(event); - } - writer.close(); - } finally { - return result.toString(); - } - } + writer.add(event); + } + writer.close(); + } finally { + return result.toString(); + } + } - /** - * Looks for the next occurrence of the splitter element. - * - * @param parser - * @return - * @throws XMLStreamException - */ - private XMLEvent findElement(final XMLEventReader parser) throws XMLStreamException { + /** + * Looks for the next occurrence of the splitter element. + * + * @param parser + * @return + * @throws XMLStreamException + */ + private XMLEvent findElement(final XMLEventReader parser) throws XMLStreamException { - /* - * if (current != null && element.equals(current.asStartElement().getName().getLocalPart())) { return current; } - */ + /* + * if (current != null && element.equals(current.asStartElement().getName().getLocalPart())) { return current; } + */ - XMLEvent peek = parser.peek(); - if (peek != null && peek.isStartElement()) { - String name = peek.asStartElement().getName().getLocalPart(); - if (element.equals(name)) { return peek; } - } + XMLEvent peek = parser.peek(); + if (peek != null && peek.isStartElement()) { + String name = peek.asStartElement().getName().getLocalPart(); + if (element.equals(name)) { + return peek; + } + } - while (parser.hasNext()) { - final XMLEvent event = parser.nextEvent(); - if (event != null && event.isStartElement()) { - String name = event.asStartElement().getName().getLocalPart(); - if (element.equals(name)) { return event; } - } - } - return null; - } + while (parser.hasNext()) { + final XMLEvent event = parser.nextEvent(); + if (event != null && event.isStartElement()) { + String name = event.asStartElement().getName().getLocalPart(); + if (element.equals(name)) { + return event; + } + } + } + return null; + } - private XMLEventReader getParser() { - try { - return inputFactory.get().createXMLEventReader(sanitize(inputStream)); - } catch (XMLStreamException e) { - throw new RuntimeException(e); - } - } + private XMLEventReader getParser() { + try { + return inputFactory.get().createXMLEventReader(sanitize(inputStream)); + } catch (XMLStreamException e) { + throw new RuntimeException(e); + } + } - private Reader sanitize(final InputStream in) { - final CharsetDecoder charsetDecoder = Charset.forName(UTF_8).newDecoder(); - charsetDecoder.onMalformedInput(CodingErrorAction.REPLACE); - charsetDecoder.onUnmappableCharacter(CodingErrorAction.REPLACE); - return new InputStreamReader(in, charsetDecoder); - } + private Reader sanitize(final InputStream in) { + final CharsetDecoder charsetDecoder = Charset.forName(UTF_8).newDecoder(); + charsetDecoder.onMalformedInput(CodingErrorAction.REPLACE); + charsetDecoder.onUnmappableCharacter(CodingErrorAction.REPLACE); + return new InputStreamReader(in, charsetDecoder); + } -} \ No newline at end of file +} diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/file/FileCollectorPluginTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/file/FileCollectorPluginTest.java index ed0578059..6fd101634 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/file/FileCollectorPluginTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/file/FileCollectorPluginTest.java @@ -1,9 +1,10 @@ + package eu.dnetlib.dhp.collection.plugin.file; -import eu.dnetlib.dhp.collection.ApiDescriptor; -import eu.dnetlib.dhp.common.aggregation.AggregatorReport; -import eu.dnetlib.dhp.common.collection.CollectorException; -import net.bytebuddy.asm.Advice; +import java.io.IOException; +import java.util.HashMap; +import java.util.stream.Stream; + import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.fs.FileSystem; import org.apache.hadoop.fs.LocalFileSystem; @@ -13,48 +14,48 @@ import org.junit.jupiter.api.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import java.io.IOException; -import java.util.HashMap; -import java.util.stream.Stream; +import eu.dnetlib.dhp.collection.ApiDescriptor; +import eu.dnetlib.dhp.common.aggregation.AggregatorReport; +import eu.dnetlib.dhp.common.collection.CollectorException; +import net.bytebuddy.asm.Advice; public class FileCollectorPluginTest { - private static final Logger log = LoggerFactory.getLogger(FileGZipCollectorPluginTest.class); + private static final Logger log = LoggerFactory.getLogger(FileGZipCollectorPluginTest.class); - private final ApiDescriptor api = new ApiDescriptor(); + private final ApiDescriptor api = new ApiDescriptor(); - private FileCollectorPlugin plugin; + private FileCollectorPlugin plugin; - private static final String SPLIT_ON_ELEMENT = "repository"; + private static final String SPLIT_ON_ELEMENT = "repository"; - @BeforeEach - public void setUp() throws IOException { + @BeforeEach + public void setUp() throws IOException { - final String gzipFile = this - .getClass() - .getResource("/eu/dnetlib/dhp/collection/plugin/file/opendoar.xml") - .getFile(); + final String gzipFile = this + .getClass() + .getResource("/eu/dnetlib/dhp/collection/plugin/file/opendoar.xml") + .getFile(); - api.setBaseUrl(gzipFile); + api.setBaseUrl(gzipFile); - HashMap params = new HashMap<>(); - params.put("splitOnElement", SPLIT_ON_ELEMENT); + HashMap params = new HashMap<>(); + params.put("splitOnElement", SPLIT_ON_ELEMENT); - api.setParams(params); + api.setParams(params); - FileSystem fs = FileSystem.get(new Configuration()); - plugin = new FileCollectorPlugin(fs); - } + FileSystem fs = FileSystem.get(new Configuration()); + plugin = new FileCollectorPlugin(fs); + } - @Test - void test() throws CollectorException { + @Test + void test() throws CollectorException { - final Stream stream = plugin.collect(api, new AggregatorReport()); + final Stream stream = plugin.collect(api, new AggregatorReport()); - stream.limit(10).forEach(s -> { - Assertions.assertTrue(s.length() > 0); - log.info(s); - }); - } + stream.limit(10).forEach(s -> { + Assertions.assertTrue(s.length() > 0); + log.info(s); + }); + } } - diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/file/FileGZipCollectorPluginTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/file/FileGZipCollectorPluginTest.java index 23f08e6ea..dc24d6f13 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/file/FileGZipCollectorPluginTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/file/FileGZipCollectorPluginTest.java @@ -1,8 +1,13 @@ + package eu.dnetlib.dhp.collection.plugin.file; -import eu.dnetlib.dhp.collection.ApiDescriptor; -import eu.dnetlib.dhp.common.aggregation.AggregatorReport; -import eu.dnetlib.dhp.common.collection.CollectorException; +import java.io.File; +import java.io.IOException; +import java.nio.file.Files; +import java.util.HashMap; +import java.util.Objects; +import java.util.stream.Stream; + import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.fs.FileSystem; import org.apache.hadoop.fs.LocalFileSystem; @@ -13,53 +18,51 @@ import org.mockito.junit.jupiter.MockitoExtension; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import java.io.File; -import java.io.IOException; -import java.nio.file.Files; -import java.util.HashMap; -import java.util.Objects; -import java.util.stream.Stream; - +import eu.dnetlib.dhp.collection.ApiDescriptor; +import eu.dnetlib.dhp.common.aggregation.AggregatorReport; +import eu.dnetlib.dhp.common.collection.CollectorException; @TestMethodOrder(MethodOrderer.OrderAnnotation.class) @ExtendWith(MockitoExtension.class) public class FileGZipCollectorPluginTest { - private static final Logger log = LoggerFactory.getLogger(FileGZipCollectorPluginTest.class); + private static final Logger log = LoggerFactory.getLogger(FileGZipCollectorPluginTest.class); - private final ApiDescriptor api = new ApiDescriptor(); + private final ApiDescriptor api = new ApiDescriptor(); - private FileGZipCollectorPlugin plugin; + private FileGZipCollectorPlugin plugin; - private static final String SPLIT_ON_ELEMENT = "repository"; + private static final String SPLIT_ON_ELEMENT = "repository"; - @BeforeEach - public void setUp() throws IOException { + @BeforeEach + public void setUp() throws IOException { - final String gzipFile = Objects.requireNonNull(this - .getClass() - .getResource("/eu/dnetlib/dhp/collection/plugin/file/opendoar.xml.gz")) - .getFile(); + final String gzipFile = Objects + .requireNonNull( + this + .getClass() + .getResource("/eu/dnetlib/dhp/collection/plugin/file/opendoar.xml.gz")) + .getFile(); - api.setBaseUrl(gzipFile); + api.setBaseUrl(gzipFile); - HashMap params = new HashMap<>(); - params.put("splitOnElement", SPLIT_ON_ELEMENT); + HashMap params = new HashMap<>(); + params.put("splitOnElement", SPLIT_ON_ELEMENT); - api.setParams(params); + api.setParams(params); - FileSystem fs = FileSystem.get(new Configuration()); - plugin = new FileGZipCollectorPlugin(fs); - } + FileSystem fs = FileSystem.get(new Configuration()); + plugin = new FileGZipCollectorPlugin(fs); + } - @Test - void test() throws CollectorException { + @Test + void test() throws CollectorException { - final Stream stream = plugin.collect(api, new AggregatorReport()); + final Stream stream = plugin.collect(api, new AggregatorReport()); - stream.limit(10).forEach(s -> { - Assertions.assertTrue(s.length() > 0); - log.info(s); - }); - } + stream.limit(10).forEach(s -> { + Assertions.assertTrue(s.length() > 0); + log.info(s); + }); + } } From 5130eac24747237213a80ce552c891128adf6366 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 24 Jun 2022 17:16:42 +0200 Subject: [PATCH 094/214] mapping by participant project contribution --- .../dhp/schema/oaf/utils/OafMapperUtils.java | 58 +++++++ .../raw/AbstractMdRecordToOafMapper.java | 52 ++---- .../raw/MigrateDbEntitiesApplication.java | 155 +++++------------- .../oa/graph/sql/queryProjectOrganization.sql | 1 + 4 files changed, 114 insertions(+), 152 deletions(-) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java index ac9cfe330..6f452e846 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java @@ -419,4 +419,62 @@ public class OafMapperUtils { m.setUnit(Arrays.asList(newKeyValueInstance(key, value, dataInfo))); return m; } + + public static Relation getRelation(final String source, + final String target, + final String relType, + final String subRelType, + final String relClass, + final OafEntity entity) { + return getRelation(source, target, relType, subRelType, relClass, entity, null); + } + + public static Relation getRelation(final String source, + final String target, + final String relType, + final String subRelType, + final String relClass, + final OafEntity entity, + final String validationDate) { + return getRelation( + source, target, relType, subRelType, relClass, entity.getCollectedfrom(), entity.getDataInfo(), + entity.getLastupdatetimestamp(), validationDate, null); + } + + public static Relation getRelation(final String source, + final String target, + final String relType, + final String subRelType, + final String relClass, + final List collectedfrom, + final DataInfo dataInfo, + final Long lastupdatetimestamp) { + return getRelation( + source, target, relType, subRelType, relClass, collectedfrom, dataInfo, lastupdatetimestamp, null, null); + } + + public static Relation getRelation(final String source, + final String target, + final String relType, + final String subRelType, + final String relClass, + final List collectedfrom, + final DataInfo dataInfo, + final Long lastupdatetimestamp, + final String validationDate, + final List properties) { + final Relation rel = new Relation(); + rel.setRelType(relType); + rel.setSubRelType(subRelType); + rel.setRelClass(relClass); + rel.setSource(source); + rel.setTarget(target); + rel.setCollectedfrom(collectedfrom); + rel.setDataInfo(dataInfo); + rel.setLastupdatetimestamp(lastupdatetimestamp); + rel.setValidated(StringUtils.isNotBlank(validationDate)); + rel.setValidationDate(StringUtils.isNotBlank(validationDate) ? validationDate : null); + rel.setProperties(properties); + return rel; + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index 739be3df4..846440a69 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -267,10 +267,13 @@ public abstract class AbstractMdRecordToOafMapper { res .add( - getRelation( - docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, entity, validationdDate)); + OafMapperUtils + .getRelation( + docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, entity, validationdDate)); res - .add(getRelation(projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, entity, validationdDate)); + .add( + OafMapperUtils + .getRelation(projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, entity, validationdDate)); } } @@ -303,13 +306,16 @@ public abstract class AbstractMdRecordToOafMapper { final String targetId = createOpenaireId(targetType, target, true); rels .add( - getRelation( - entity.getId(), targetId, relType, subRelType, relClass, entity, validationdDate)); + OafMapperUtils + .getRelation( + entity.getId(), targetId, relType, subRelType, relClass, entity, + validationdDate)); rels .add( - getRelation( - targetId, entity.getId(), relType, subRelType, relClassInverse, entity, - validationdDate)); + OafMapperUtils + .getRelation( + targetId, entity.getId(), relType, subRelType, relClassInverse, entity, + validationdDate)); } } } @@ -317,36 +323,6 @@ public abstract class AbstractMdRecordToOafMapper { return rels; } - protected Relation getRelation(final String source, - final String target, - final String relType, - final String subRelType, - final String relClass, - final OafEntity entity) { - return getRelation(source, target, relType, subRelType, relClass, entity, null); - } - - protected Relation getRelation(final String source, - final String target, - final String relType, - final String subRelType, - final String relClass, - final OafEntity entity, - final String validationDate) { - final Relation rel = new Relation(); - rel.setRelType(relType); - rel.setSubRelType(subRelType); - rel.setRelClass(relClass); - rel.setSource(source); - rel.setTarget(target); - rel.setCollectedfrom(entity.getCollectedfrom()); - rel.setDataInfo(entity.getDataInfo()); - rel.setLastupdatetimestamp(entity.getLastupdatetimestamp()); - rel.setValidated(StringUtils.isNotBlank(validationDate)); - rel.setValidationDate(StringUtils.isNotBlank(validationDate) ? validationDate : null); - return rel; - } - protected abstract List addOtherResultRels( final Document doc, final OafEntity entity); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java index 63fa8b7e0..8296e99cd 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java @@ -1,32 +1,7 @@ package eu.dnetlib.dhp.oa.graph.raw; -import static eu.dnetlib.dhp.schema.common.ModelConstants.DATASET_DEFAULT_RESULTTYPE; -import static eu.dnetlib.dhp.schema.common.ModelConstants.DATASOURCE_ORGANIZATION; -import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PROVENANCE_ACTIONS; -import static eu.dnetlib.dhp.schema.common.ModelConstants.ENTITYREGISTRY_PROVENANCE_ACTION; -import static eu.dnetlib.dhp.schema.common.ModelConstants.HAS_PARTICIPANT; -import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_MERGED_IN; -import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_PARTICIPANT; -import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_PRODUCED_BY; -import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_PROVIDED_BY; -import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_RELATED_TO; -import static eu.dnetlib.dhp.schema.common.ModelConstants.MERGES; -import static eu.dnetlib.dhp.schema.common.ModelConstants.ORG_ORG_RELTYPE; -import static eu.dnetlib.dhp.schema.common.ModelConstants.ORP_DEFAULT_RESULTTYPE; -import static eu.dnetlib.dhp.schema.common.ModelConstants.OUTCOME; -import static eu.dnetlib.dhp.schema.common.ModelConstants.PARTICIPATION; -import static eu.dnetlib.dhp.schema.common.ModelConstants.PRODUCES; -import static eu.dnetlib.dhp.schema.common.ModelConstants.PROJECT_ORGANIZATION; -import static eu.dnetlib.dhp.schema.common.ModelConstants.PROVIDES; -import static eu.dnetlib.dhp.schema.common.ModelConstants.PROVISION; -import static eu.dnetlib.dhp.schema.common.ModelConstants.PUBLICATION_DATASET; -import static eu.dnetlib.dhp.schema.common.ModelConstants.PUBLICATION_DEFAULT_RESULTTYPE; -import static eu.dnetlib.dhp.schema.common.ModelConstants.RELATIONSHIP; -import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_PROJECT; -import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_RESULT; -import static eu.dnetlib.dhp.schema.common.ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE; -import static eu.dnetlib.dhp.schema.common.ModelConstants.USER_CLAIM; +import static eu.dnetlib.dhp.schema.common.ModelConstants.*; import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.*; import java.io.Closeable; @@ -45,6 +20,8 @@ import org.apache.commons.lang3.StringUtils; import org.slf4j.Logger; import org.slf4j.LoggerFactory; +import com.google.common.collect.Lists; + import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.DbClient; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; @@ -68,6 +45,7 @@ import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.Software; import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; import eu.dnetlib.dhp.utils.ISLookupClientFactory; public class MigrateDbEntitiesApplication extends AbstractMigrationApplication implements Closeable { @@ -437,25 +415,14 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i final List collectedFrom = listKeyValues( createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname")); - final Relation r1 = new Relation(); - r1.setRelType(DATASOURCE_ORGANIZATION); - r1.setSubRelType(PROVISION); - r1.setRelClass(IS_PROVIDED_BY); - r1.setSource(dsId); - r1.setTarget(orgId); - r1.setCollectedfrom(collectedFrom); - r1.setDataInfo(info); - r1.setLastupdatetimestamp(lastUpdateTimestamp); + final Relation r1 = OafMapperUtils + .getRelation( + dsId, orgId, DATASOURCE_ORGANIZATION, PRODUCES, IS_PROVIDED_BY, collectedFrom, info, + lastUpdateTimestamp); - final Relation r2 = new Relation(); - r2.setRelType(DATASOURCE_ORGANIZATION); - r2.setSubRelType(PROVISION); - r2.setRelClass(PROVIDES); - r2.setSource(orgId); - r2.setTarget(dsId); - r2.setCollectedfrom(collectedFrom); - r2.setDataInfo(info); - r2.setLastupdatetimestamp(lastUpdateTimestamp); + final Relation r2 = OafMapperUtils + .getRelation( + orgId, dsId, DATASOURCE_ORGANIZATION, PRODUCES, PROVIDES, collectedFrom, info, lastUpdateTimestamp); return Arrays.asList(r1, r2); } catch (final Exception e) { @@ -471,25 +438,20 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i final List collectedFrom = listKeyValues( createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname")); - final Relation r1 = new Relation(); - r1.setRelType(PROJECT_ORGANIZATION); - r1.setSubRelType(PARTICIPATION); - r1.setRelClass(HAS_PARTICIPANT); - r1.setSource(projectId); - r1.setTarget(orgId); - r1.setCollectedfrom(collectedFrom); - r1.setDataInfo(info); - r1.setLastupdatetimestamp(lastUpdateTimestamp); + final List properties = Lists + .newArrayList( + keyValue("contribution", String.valueOf(rs.getDouble("totalcost"))), + keyValue("currency", rs.getString("currency"))); - final Relation r2 = new Relation(); - r2.setRelType(PROJECT_ORGANIZATION); - r2.setSubRelType(PARTICIPATION); - r2.setRelClass(IS_PARTICIPANT); - r2.setSource(orgId); - r2.setTarget(projectId); - r2.setCollectedfrom(collectedFrom); - r2.setDataInfo(info); - r2.setLastupdatetimestamp(lastUpdateTimestamp); + final Relation r1 = OafMapperUtils + .getRelation( + projectId, orgId, PROJECT_ORGANIZATION, PARTICIPATION, HAS_PARTICIPANT, collectedFrom, info, + lastUpdateTimestamp, null, properties); + + final Relation r2 = OafMapperUtils + .getRelation( + orgId, projectId, PROJECT_ORGANIZATION, PARTICIPATION, IS_PARTICIPANT, collectedFrom, info, + lastUpdateTimestamp, null, properties); return Arrays.asList(r1, r2); } catch (final Exception e) { @@ -703,25 +665,12 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i final List collectedFrom = listKeyValues( createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname")); - final Relation r1 = new Relation(); - r1.setRelType(ORG_ORG_RELTYPE); - r1.setSubRelType(ModelConstants.DEDUP); - r1.setRelClass(MERGES); - r1.setSource(orgId1); - r1.setTarget(orgId2); - r1.setCollectedfrom(collectedFrom); - r1.setDataInfo(info); - r1.setLastupdatetimestamp(lastUpdateTimestamp); + final Relation r1 = OafMapperUtils + .getRelation(orgId1, orgId2, ORG_ORG_RELTYPE, DEDUP, MERGES, collectedFrom, info, lastUpdateTimestamp); - final Relation r2 = new Relation(); - r2.setRelType(ORG_ORG_RELTYPE); - r2.setSubRelType(ModelConstants.DEDUP); - r2.setRelClass(IS_MERGED_IN); - r2.setSource(orgId2); - r2.setTarget(orgId1); - r2.setCollectedfrom(collectedFrom); - r2.setDataInfo(info); - r2.setLastupdatetimestamp(lastUpdateTimestamp); + final Relation r2 = OafMapperUtils + .getRelation( + orgId2, orgId1, ORG_ORG_RELTYPE, DEDUP, IS_MERGED_IN, collectedFrom, info, lastUpdateTimestamp); return Arrays.asList(r1, r2); } catch (final Exception e) { throw new RuntimeException(e); @@ -738,17 +687,12 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i final List collectedFrom = listKeyValues( createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname")); - final Relation r = new Relation(); - r.setRelType(ORG_ORG_RELTYPE); - r.setSubRelType(ModelConstants.RELATIONSHIP); - r.setRelClass(rs.getString("type")); - r.setSource(orgId1); - r.setTarget(orgId2); - r.setCollectedfrom(collectedFrom); - r.setDataInfo(info); - r.setLastupdatetimestamp(lastUpdateTimestamp); - - return Arrays.asList(r); + return Arrays + .asList( + OafMapperUtils + .getRelation( + orgId1, orgId2, ORG_ORG_RELTYPE, RELATIONSHIP, rs.getString("type"), collectedFrom, info, + lastUpdateTimestamp)); } catch (final Exception e) { throw new RuntimeException(e); } @@ -765,29 +709,12 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i final List collectedFrom = listKeyValues( createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname")); - final Relation r1 = new Relation(); - r1.setRelType(ORG_ORG_RELTYPE); - r1.setSubRelType(ModelConstants.DEDUP); - r1.setRelClass(relClass); - r1.setSource(orgId1); - r1.setTarget(orgId2); - r1.setCollectedfrom(collectedFrom); - r1.setDataInfo(info); - r1.setLastupdatetimestamp(lastUpdateTimestamp); - - // removed because there's no difference between two sides //TODO - // final Relation r2 = new Relation(); - // r2.setRelType(ORG_ORG_RELTYPE); - // r2.setSubRelType(ORG_ORG_SUBRELTYPE); - // r2.setRelClass(relClass); - // r2.setSource(orgId2); - // r2.setTarget(orgId1); - // r2.setCollectedfrom(collectedFrom); - // r2.setDataInfo(info); - // r2.setLastupdatetimestamp(lastUpdateTimestamp); - // return Arrays.asList(r1, r2); - - return Arrays.asList(r1); + return Arrays + .asList( + OafMapperUtils + .getRelation( + orgId1, orgId2, ORG_ORG_RELTYPE, DEDUP, relClass, collectedFrom, info, + lastUpdateTimestamp)); } catch (final Exception e) { throw new RuntimeException(e); } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjectOrganization.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjectOrganization.sql index d9a77427d..9a5133e4b 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjectOrganization.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjectOrganization.sql @@ -3,6 +3,7 @@ SELECT po.resporganization AS resporganization, po.participantnumber AS participantnumber, po.contribution AS contribution, + po.currency AS currency, NULL AS startdate, NULL AS enddate, false AS inferred, From 316b0fd73c9b71cbde067b1d0d4a62b64da2d76e Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 27 Jun 2022 09:36:51 +0200 Subject: [PATCH 095/214] added 'von' to the name particles file --- .../src/main/resources/eu/dnetlib/dhp/common/name_particles.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/dhp-common/src/main/resources/eu/dnetlib/dhp/common/name_particles.txt b/dhp-common/src/main/resources/eu/dnetlib/dhp/common/name_particles.txt index d21610522..07cf06a98 100644 --- a/dhp-common/src/main/resources/eu/dnetlib/dhp/common/name_particles.txt +++ b/dhp-common/src/main/resources/eu/dnetlib/dhp/common/name_particles.txt @@ -1,4 +1,5 @@ van +von der de dell From 1d1fe3b151646e52a60d4c5f9fd70d313c506b2a Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 27 Jun 2022 18:04:59 +0200 Subject: [PATCH 096/214] [DUMP DELTA PROJECTS] refactoring --- .../projectssubset/ProjectSubsetTest.java | 204 +++++++++--------- 1 file changed, 106 insertions(+), 98 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java index d5b1ce776..4ff1e1b96 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java @@ -1,8 +1,11 @@ + package eu.dnetlib.dhp.oa.graph.dump.projectssubset; + import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; import java.util.HashMap; + import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; @@ -15,104 +18,109 @@ import org.junit.jupiter.api.BeforeAll; import org.junit.jupiter.api.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; + import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject; -import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; + import eu.dnetlib.dhp.schema.dump.oaf.graph.Project; + public class ProjectSubsetTest { - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - private static SparkSession spark; - private static Path workingDir; - private static final Logger log = LoggerFactory - .getLogger(eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class); - private static final HashMap map = new HashMap<>(); - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory( - eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - SparkConf conf = new SparkConf(); - conf.setAppName(eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class.getSimpleName()); - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - spark = SparkSession - .builder() - .appName(eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - @Test - void testAllNew() throws Exception { - final String projectListPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/projectId") - .getPath(); - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/allnew/projects") - .getPath(); - spark - .read() - .textFile(projectListPath) - .write() - .mode(SaveMode.Overwrite) - .text(workingDir.toString() + "/projectIds"); - ProjectsSubsetSparkJob.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/projects", - "-sourcePath", sourcePath, - "-projectListPath", workingDir.toString() + "/projectIds" - }); - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/projects") - .map(item -> OBJECT_MAPPER.readValue(item, Project.class)); - Assertions.assertEquals(12, tmp.count()); - Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("aka_________")).count()); - Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("anr_________")).count()); - Assertions.assertEquals(4, tmp.filter(p -> p.getId().substring(3, 15).equals("arc_________")).count()); - Assertions.assertEquals(3, tmp.filter(p -> p.getId().substring(3, 15).equals("conicytf____")).count()); - Assertions.assertEquals(1, tmp.filter(p -> p.getId().substring(3, 15).equals("corda_______")).count()); - Assertions.assertEquals(40, sc.textFile(workingDir.toString() + "/projectIds").count()); - } - @Test - void testMatchOne() throws Exception { - final String projectListPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/projectId") - .getPath(); - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/matchOne/projects") - .getPath(); - spark - .read() - .textFile(projectListPath) - .write() - .mode(SaveMode.Overwrite) - .text(workingDir.toString() + "/projectIds"); - ProjectsSubsetSparkJob.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/projects", - "-sourcePath", sourcePath, - "-projectListPath", workingDir.toString() + "/projectIds" - }); - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/projects") - .map(item -> OBJECT_MAPPER.readValue(item, Project.class)); - Assertions.assertEquals(11, tmp.count()); - Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("aka_________")).count()); - Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("anr_________")).count()); - Assertions.assertEquals(4, tmp.filter(p -> p.getId().substring(3, 15).equals("arc_________")).count()); - Assertions.assertEquals(3, tmp.filter(p -> p.getId().substring(3, 15).equals("conicytf____")).count()); - Assertions.assertEquals(0, tmp.filter(p -> p.getId().substring(3, 15).equals("corda__h2020")).count()); - Assertions.assertEquals(39, sc.textFile(workingDir.toString() + "/projectIds").count()); - } -} \ No newline at end of file + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static SparkSession spark; + private static Path workingDir; + private static final Logger log = LoggerFactory + .getLogger(eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class); + + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files + .createTempDirectory( + eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + SparkConf conf = new SparkConf(); + conf.setAppName(eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class.getSimpleName()); + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + spark = SparkSession + .builder() + .appName(eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + void testAllNew() throws Exception { + final String projectListPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/projectId") + .getPath(); + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/allnew/projects") + .getPath(); + spark + .read() + .textFile(projectListPath) + .write() + .mode(SaveMode.Overwrite) + .text(workingDir.toString() + "/projectIds"); + ProjectsSubsetSparkJob.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/projects", + "-sourcePath", sourcePath, + "-projectListPath", workingDir.toString() + "/projectIds" + }); + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/projects") + .map(item -> OBJECT_MAPPER.readValue(item, Project.class)); + Assertions.assertEquals(12, tmp.count()); + Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("aka_________")).count()); + Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("anr_________")).count()); + Assertions.assertEquals(4, tmp.filter(p -> p.getId().substring(3, 15).equals("arc_________")).count()); + Assertions.assertEquals(3, tmp.filter(p -> p.getId().substring(3, 15).equals("conicytf____")).count()); + Assertions.assertEquals(1, tmp.filter(p -> p.getId().substring(3, 15).equals("corda_______")).count()); + Assertions.assertEquals(40, sc.textFile(workingDir.toString() + "/projectIds").count()); + } + + @Test + void testMatchOne() throws Exception { + final String projectListPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/projectId") + .getPath(); + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/matchOne/projects") + .getPath(); + spark + .read() + .textFile(projectListPath) + .write() + .mode(SaveMode.Overwrite) + .text(workingDir.toString() + "/projectIds"); + ProjectsSubsetSparkJob.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/projects", + "-sourcePath", sourcePath, + "-projectListPath", workingDir.toString() + "/projectIds" + }); + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/projects") + .map(item -> OBJECT_MAPPER.readValue(item, Project.class)); + Assertions.assertEquals(11, tmp.count()); + Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("aka_________")).count()); + Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("anr_________")).count()); + Assertions.assertEquals(4, tmp.filter(p -> p.getId().substring(3, 15).equals("arc_________")).count()); + Assertions.assertEquals(3, tmp.filter(p -> p.getId().substring(3, 15).equals("conicytf____")).count()); + Assertions.assertEquals(0, tmp.filter(p -> p.getId().substring(3, 15).equals("corda__h2020")).count()); + Assertions.assertEquals(39, sc.textFile(workingDir.toString() + "/projectIds").count()); + } +} From 71744a1f5274957a48e761a95c14370ec8f488a1 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 27 Jun 2022 18:07:58 +0200 Subject: [PATCH 097/214] [DUMP DELTA PROJECTS] refactoring --- .../ProjectsSubsetSparkJob.java | 121 +++++++++--------- 1 file changed, 60 insertions(+), 61 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java index 67da24185..83a9f3464 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java @@ -1,80 +1,79 @@ + package eu.dnetlib.dhp.oa.graph.dump.projectssubset; + import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.io.Serializable; -import java.util.List; import java.util.Objects; import java.util.Optional; -import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; -import org.jetbrains.annotations.NotNull; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.schema.dump.oaf.community.Funder; import eu.dnetlib.dhp.schema.dump.oaf.graph.Project; import scala.Tuple2; + public class ProjectsSubsetSparkJob implements Serializable { - private static final Logger log = LoggerFactory.getLogger(ProjectsSubsetSparkJob.class); - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - ProjectsSubsetSparkJob.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/project_subset_parameters.json")); - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - final String projectListPath = parser.get("projectListPath"); - log.info("projectListPath: {}", projectListPath); - SparkConf conf = new SparkConf(); - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - getNewProjectList(spark, inputPath, outputPath, projectListPath); - }); - } - private static void getNewProjectList(SparkSession spark, String inputPath, String outputPath, - String projectListPath) { - Dataset projectList = spark.read().textFile(projectListPath); - // projectList.show(false); - Dataset projects; - projects = Utils.readPath(spark, inputPath, Project.class); - projects - .joinWith(projectList, projects.col("id").equalTo(projectList.col("value")), "left") - .map((MapFunction, Project>) t2 -> { - if (Optional.ofNullable(t2._2()).isPresent()) - return null; - return t2._1(); - }, Encoders.bean(Project.class)) - .filter(Objects::nonNull) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); - Utils - .readPath(spark, outputPath, Project.class) - .map((MapFunction) p -> p.getId(), Encoders.STRING()) - .write() - .mode(SaveMode.Append) - .option("compression", "gzip") - .text(projectListPath); - } -} \ No newline at end of file + private static final Logger log = LoggerFactory.getLogger(ProjectsSubsetSparkJob.class); + + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + ProjectsSubsetSparkJob.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump/project_subset_parameters.json")); + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + final String inputPath = parser.get("sourcePath"); + log.info("inputPath: {}", inputPath); + final String outputPath = parser.get("outputPath"); + log.info("outputPath: {}", outputPath); + final String projectListPath = parser.get("projectListPath"); + log.info("projectListPath: {}", projectListPath); + SparkConf conf = new SparkConf(); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath); + getNewProjectList(spark, inputPath, outputPath, projectListPath); + }); + } + + private static void getNewProjectList(SparkSession spark, String inputPath, String outputPath, + String projectListPath) { + Dataset projectList = spark.read().textFile(projectListPath); + Dataset projects; + projects = Utils.readPath(spark, inputPath, Project.class); + projects + .joinWith(projectList, projects.col("id").equalTo(projectList.col("value")), "left") + .map((MapFunction, Project>) t2 -> { + if (Optional.ofNullable(t2._2()).isPresent()) + return null; + return t2._1(); + }, Encoders.bean(Project.class)) + .filter(Objects::nonNull) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath); + Utils + .readPath(spark, outputPath, Project.class) + .map((MapFunction) p -> p.getId(), Encoders.STRING()) + .write() + .mode(SaveMode.Append) + .option("compression", "gzip") + .text(projectListPath); + } +} From 7da24c1dec2e942b85aa821f2140094fd8886dcf Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 28 Jun 2022 13:47:49 +0200 Subject: [PATCH 098/214] added more logging --- .../src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java | 5 +++++ .../oa/graph/raw/MigrateHdfsMdstoresApplication.java | 10 ++++++++++ 2 files changed, 15 insertions(+) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java index 5a59bc0df..e10d0c500 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java @@ -75,9 +75,14 @@ public class DHPUtils { final HttpGet req = new HttpGet(url); + log.info("MDStoreManager request: {}", req); + try (final CloseableHttpClient client = HttpClients.createDefault()) { try (final CloseableHttpResponse response = client.execute(req)) { final String json = IOUtils.toString(response.getEntity().getContent()); + + log.info("MDStoreManager response: {}", json); + final MDStoreWithInfo[] mdstores = objectMapper.readValue(json, MDStoreWithInfo[].class); return Arrays .stream(mdstores) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateHdfsMdstoresApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateHdfsMdstoresApplication.java index 6c72e4dfc..ab6f54b92 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateHdfsMdstoresApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateHdfsMdstoresApplication.java @@ -65,11 +65,19 @@ public class MigrateHdfsMdstoresApplication extends AbstractMigrationApplication log.info("isSparkSessionManaged: {}", isSparkSessionManaged); final String mdstoreManagerUrl = parser.get("mdstoreManagerUrl"); + log.info("mdstoreManagerUrl: {}", mdstoreManagerUrl); + final String mdFormat = parser.get("mdFormat"); + log.info("mdFormat: {}", mdFormat); + final String mdLayout = parser.get("mdLayout"); + log.info("mdLayout: {}", mdLayout); + final String mdInterpretation = parser.get("mdInterpretation"); + log.info("mdInterpretation: {}", mdInterpretation); final String hdfsPath = parser.get("hdfsPath"); + log.info("hdfsPath: {}", hdfsPath); final Set paths = mdstorePaths(mdstoreManagerUrl, mdFormat, mdLayout, mdInterpretation); @@ -95,6 +103,8 @@ public class MigrateHdfsMdstoresApplication extends AbstractMigrationApplication .filter(p -> HdfsSupport.exists(p, sc.hadoopConfiguration())) .toArray(size -> new String[size]); + log.info("Processing existing paths {}", Arrays.asList(validPaths)); + if (validPaths.length > 0) { spark .read() From a88103bcf940b323d6950ebbc80dea04fd115f44 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 1 Jul 2022 09:06:59 +0200 Subject: [PATCH 099/214] [action manager] added more testing --- ...moteActionPayloadForGraphTableJobTest.java | 55 +++++++++++++++++++ .../publication_table/result.json | 3 +- 2 files changed, 57 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJobTest.java b/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJobTest.java index 99ce961aa..df9202ed8 100644 --- a/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJobTest.java +++ b/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJobTest.java @@ -172,6 +172,61 @@ public class PromoteActionPayloadForGraphTableJobTest { } } + @Test + void shouldPromoteActionPayload_custom() throws Exception { + + Class rowClazz = Publication.class; + Class actionPayloadClazz = Result.class; + MergeAndGet.Strategy strategy = MergeAndGet.Strategy.MERGE_FROM_AND_GET; + + // given + Path inputGraphTableDir = createGraphTable(inputGraphRootDir, rowClazz); + Path inputActionPayloadDir = createActionPayload(inputActionPayloadRootDir, rowClazz, actionPayloadClazz); + Path outputGraphTableDir = outputDir.resolve("graph").resolve(rowClazz.getSimpleName().toLowerCase()); + + // when + PromoteActionPayloadForGraphTableJob + .main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-inputGraphTablePath", + inputGraphTableDir.toString(), + "-graphTableClassName", + rowClazz.getCanonicalName(), + "-inputActionPayloadPath", + inputActionPayloadDir.toString(), + "-actionPayloadClassName", + actionPayloadClazz.getCanonicalName(), + "-outputGraphTablePath", + outputGraphTableDir.toString(), + "-mergeAndGetStrategy", + strategy.name(), + "--shouldGroupById", + "true" + }); + + // then + assertTrue(Files.exists(outputGraphTableDir)); + + List actualOutputRows = readGraphTableFromJobOutput(outputGraphTableDir.toString(), rowClazz) + .collectAsList() + .stream() + .sorted(Comparator.comparingInt(Object::hashCode)) + .collect(Collectors.toList()); + + Publication p = actualOutputRows + .stream() + .map(o -> (Publication) o) + .filter(o -> "50|4ScienceCRIS::6a67ed3daba1c380bf9de3c13ed9c879".equals(o.getId())) + .findFirst() + .get(); + + assertNotNull(p.getMeasures()); + assertTrue(p.getMeasures().size() > 0); + + } + public static Stream promoteJobTestParams() { return Stream .of( diff --git a/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/input/action_payload/publication_table/result.json b/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/input/action_payload/publication_table/result.json index f98ee4b78..d98bfe98f 100644 --- a/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/input/action_payload/publication_table/result.json +++ b/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/input/action_payload/publication_table/result.json @@ -17,4 +17,5 @@ {"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"","inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}},"lastupdatetimestamp":1572018243405,"id":"50|CSC_________::00019460865d6cc381b36076131a5bc1","originalId":[],"collectedfrom":[],"pid":[],"dateofcollection":"","dateoftransformation":"","extraInfo":[],"oaiprovenance":null,"author":[],"resulttype":{"classid":"","classname":"","schemeid":"","schemename":""},"language":{"classid":"","classname":"","schemeid":"","schemename":""},"country":[],"subject":[{"value":"Computer Science::Networking and Internet Architecture","qualifier":{"classid":"arxiv","classname":"arxiv","schemeid":"dnet:subject_classification_typologies","schemename":"dnet:subject_classification_typologies"},"dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"0.7416","inferenceprovenance":"iis::document_classes","provenanceaction":{"classid":"iis","classname":"iis","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[],"relevantdate":[],"description":[],"dateofacceptance":{"value":"","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"","inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}},"publisher":{"value":"","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"","inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}},"embargoenddate":{"value":"","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"","inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}},"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":{"classid":"","classname":"","schemeid":"","schemename":""},"coverage":[],"bestaccessright":{"classid":"UNKNOWN","classname":"not available","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"context":[],"externalReference":null,"instance":[]} {"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"","inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}},"lastupdatetimestamp":1572018243405,"id":"50|CSC_________::00019460865d6cc381b36076131a5bc1","originalId":[],"collectedfrom":[],"pid":[],"dateofcollection":"","dateoftransformation":"","extraInfo":[],"oaiprovenance":null,"author":[],"resulttype":{"classid":"","classname":"","schemeid":"","schemename":""},"language":{"classid":"","classname":"","schemeid":"","schemename":""},"country":[],"subject":[{"value":"Computer Science::Networking and Internet 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available","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"context":[],"externalReference":null,"instance":[]} +{"collectedfrom":null,"dataInfo":null,"lastupdatetimestamp":null,"id":"50|4ScienceCRIS::6a67ed3daba1c380bf9de3c13ed9c879","originalId":null,"pid":null,"dateofcollection":null,"dateoftransformation":null,"extraInfo":null,"oaiprovenance":null,"processingchargeamount":null,"processingchargecurrency":null,"measures":[{"id":"influence","unit":[{"key":"score","value":"1.64385446761e-08","dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"","inferenceprovenance":"update","provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}]},{"id":"popularity_alt","unit":[{"key":"score","value":"18.9590813696","dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"","inferenceprovenance":"update","provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}]},{"id":"popularity","unit":[{"key":"score","value":"6.00577981643e-08","dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"","inferenceprovenance":"update","provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}]}],"author":null,"resulttype":null,"language":null,"country":null,"subject":null,"title":null,"relevantdate":null,"description":null,"dateofacceptance":null,"publisher":null,"embargoenddate":null,"source":null,"fulltext":null,"format":null,"contributor":null,"resourcetype":null,"coverage":null,"bestaccessright":null,"context":null,"externalReference":null,"instance":null} \ No newline at end of file From 072f19285387fa3df2a8fcd0dfd2acbf448bdcb5 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 1 Jul 2022 09:54:56 +0200 Subject: [PATCH 100/214] include the class information in the measure XML serialization --- .../oa/provision/utils/XmlRecordFactory.java | 16 +- .../oa/provision/XmlRecordFactoryTest.java | 15 +- .../dnetlib/dhp/oa/provision/publication.json | 174 +++++++++++++++++- 3 files changed, 188 insertions(+), 17 deletions(-) diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java index 27128138c..b34ec9693 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java @@ -999,17 +999,11 @@ public class XmlRecordFactory implements Serializable { private List measuresAsXml(List measures) { return measures .stream() - .flatMap( - m -> m - .getUnit() - .stream() - .map( - u -> Lists - .newArrayList( - new Tuple2<>("id", m.getId()), - new Tuple2<>("key", u.getKey()), - new Tuple2<>("value", u.getValue()))) - .map(l -> XmlSerializationUtils.asXmlElement("measure", l))) + .map(m -> { + List> l = Lists.newArrayList(new Tuple2<>("id", m.getId())); + m.getUnit().forEach(kv -> l.add(new Tuple2<>(kv.getKey(), kv.getValue()))); + return XmlSerializationUtils.asXmlElement("measure", l); + }) .collect(Collectors.toList()); } diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java index f4763618b..92d9f497f 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java @@ -73,11 +73,20 @@ public class XmlRecordFactoryTest { assertEquals("EUR", doc.valueOf("//processingchargecurrency/text()")); assertEquals( - "1.00889953098e-08", doc.valueOf("//*[local-name() = 'result']/measure[./@id = 'influence']/@value")); + "5.06690394631e-09", doc.valueOf("//*[local-name() = 'result']/measure[./@id = 'influence']/@score")); assertEquals( - "30.6576853333", doc.valueOf("//*[local-name() = 'result']/measure[./@id = 'popularity_alt']/@value")); + "C", doc.valueOf("//*[local-name() = 'result']/measure[./@id = 'influence']/@class")); + assertEquals( - "4.62970429725e-08", doc.valueOf("//*[local-name() = 'result']/measure[./@id = 'popularity']/@value")); + "0.0", doc.valueOf("//*[local-name() = 'result']/measure[./@id = 'popularity_alt']/@score")); + assertEquals( + "C", doc.valueOf("//*[local-name() = 'result']/measure[./@id = 'popularity_alt']/@class")); + + assertEquals( + "3.11855618382e-09", doc.valueOf("//*[local-name() = 'result']/measure[./@id = 'popularity']/@score")); + assertEquals( + "C", doc.valueOf("//*[local-name() = 'result']/measure[./@id = 'popularity']/@class")); + } @Test diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json index 2c52ce269..41ced45ae 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json @@ -5,7 +5,37 @@ "unit": [ { "key": "score", - "value": "1.00889953098e-08" + "value": "5.06690394631e-09", + "dataInfo": { + "invisible": false, + "inferred": true, + "deletedbyinference": false, + "trust": "", + "inferenceprovenance": "update", + "provenanceaction": { + "classid": "measure:bip", + "classname": "Inferred by OpenAIRE", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + { + "key": "class", + "value": "C", + "dataInfo": { + "invisible": false, + "inferred": true, + "deletedbyinference": false, + "trust": "", + "inferenceprovenance": "update", + "provenanceaction": { + "classid": "measure:bip", + "classname": "Inferred by OpenAIRE", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } } ] }, @@ -14,7 +44,37 @@ "unit": [ { "key": "score", - "value": "30.6576853333" + "value": "0.0", + "dataInfo": { + "invisible": false, + "inferred": true, + "deletedbyinference": false, + "trust": "", + "inferenceprovenance": "update", + "provenanceaction": { + "classid": "measure:bip", + "classname": "Inferred by OpenAIRE", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + { + "key": "class", + "value": "C", + "dataInfo": { + "invisible": false, + "inferred": true, + "deletedbyinference": false, + "trust": "", + "inferenceprovenance": "update", + "provenanceaction": { + "classid": "measure:bip", + "classname": "Inferred by OpenAIRE", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } } ] }, @@ -23,7 +83,115 @@ "unit": [ { "key": "score", - "value": "4.62970429725e-08" + "value": "3.11855618382e-09", + "dataInfo": { + "invisible": false, + "inferred": true, + "deletedbyinference": false, + "trust": "", + "inferenceprovenance": "update", + "provenanceaction": { + "classid": "measure:bip", + "classname": "Inferred by OpenAIRE", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + { + "key": "class", + "value": "C", + "dataInfo": { + "invisible": false, + "inferred": true, + "deletedbyinference": false, + "trust": "", + "inferenceprovenance": "update", + "provenanceaction": { + "classid": "measure:bip", + "classname": "Inferred by OpenAIRE", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + } + ] + }, + { + "id": "influence_alt", + "unit": [ + { + "key": "score", + "value": "0.0", + "dataInfo": { + "invisible": false, + "inferred": true, + "deletedbyinference": false, + "trust": "", + "inferenceprovenance": "update", + "provenanceaction": { + "classid": "measure:bip", + "classname": "Inferred by OpenAIRE", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + { + "key": "class", + "value": "C", + "dataInfo": { + "invisible": false, + "inferred": true, + "deletedbyinference": false, + "trust": "", + "inferenceprovenance": "update", + "provenanceaction": { + "classid": "measure:bip", + "classname": "Inferred by OpenAIRE", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + } + ] + }, + { + "id": "impulse", + "unit": [ + { + "key": "score", + "value": "0.0", + "dataInfo": { + "invisible": false, + "inferred": true, + "deletedbyinference": false, + "trust": "", + "inferenceprovenance": "update", + "provenanceaction": { + "classid": "measure:bip", + "classname": "Inferred by OpenAIRE", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + { + "key": "class", + "value": "C", + "dataInfo": { + "invisible": false, + "inferred": true, + "deletedbyinference": false, + "trust": "", + "inferenceprovenance": "update", + "provenanceaction": { + "classid": "measure:bip", + "classname": "Inferred by OpenAIRE", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } } ] } From 0cb1c7078826ceca91a652ab8e23931728621a97 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 1 Jul 2022 10:44:08 +0200 Subject: [PATCH 101/214] code formatting --- .../dhp/common/api/ZenodoAPIClient.java | 19 +- .../transformation/TransformationJobTest.java | 10 +- .../dnetlib/dhp/bulktag/SparkBulkTagJob.java | 2 +- .../funderresults/SparkDumpFunderResults.java | 86 +++--- .../SparkResultLinkedToProject.java | 68 ++--- .../ProjectsSubsetSparkJob.java | 3 + .../dump/PrepareResultProjectJobTest.java | 272 +++++++++--------- .../ResultLinkedToProjectTest.java | 70 ++--- .../dump/funderresult/SplitPerFunderTest.java | 60 ++-- .../projectssubset/ProjectSubsetTest.java | 1 - 10 files changed, 304 insertions(+), 287 deletions(-) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/ZenodoAPIClient.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/ZenodoAPIClient.java index 56366bc72..63f890a10 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/ZenodoAPIClient.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/ZenodoAPIClient.java @@ -255,7 +255,8 @@ public class ZenodoAPIClient implements Serializable { private void setDepositionId(String concept_rec_id, Integer page) throws IOException, MissingConceptDoiException { - ZenodoModelList zenodoModelList = new Gson().fromJson(getPrevDepositions(String.valueOf(page)), ZenodoModelList.class); + ZenodoModelList zenodoModelList = new Gson() + .fromJson(getPrevDepositions(String.valueOf(page)), ZenodoModelList.class); for (ZenodoModel zm : zenodoModelList) { if (zm.getConceptrecid().equals(concept_rec_id)) { @@ -263,8 +264,9 @@ public class ZenodoAPIClient implements Serializable { return; } } - if(zenodoModelList.size() == 0) - throw new MissingConceptDoiException("The concept record id specified was missing in the list of depositions"); + if (zenodoModelList.size() == 0) + throw new MissingConceptDoiException( + "The concept record id specified was missing in the list of depositions"); setDepositionId(concept_rec_id, page + 1); } @@ -278,11 +280,11 @@ public class ZenodoAPIClient implements Serializable { String url = urlBuilder.build().toString(); Request request = new Request.Builder() - .url(url) - .addHeader(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString()) // add request headers - .addHeader(HttpHeaders.AUTHORIZATION, "Bearer " + access_token) - .get() - .build(); + .url(url) + .addHeader(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString()) // add request headers + .addHeader(HttpHeaders.AUTHORIZATION, "Bearer " + access_token) + .get() + .build(); try (Response response = httpClient.newCall(request).execute()) { @@ -295,7 +297,6 @@ public class ZenodoAPIClient implements Serializable { } - private String getBucket(String url) throws IOException { OkHttpClient httpClient = new OkHttpClient.Builder() .connectTimeout(600, TimeUnit.SECONDS) diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java index fea7b53ac..7fc80d168 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java @@ -142,7 +142,8 @@ class TransformationJobTest extends AbstractVocabularyTest { @Test @DisplayName("Test TransformSparkJobNode.main with oaiOpenaire_datacite (v4)") - void transformTestITGv4OAIdatacite(@TempDir final Path testDir) throws Exception { + void transformTestITGv4OAIdatacite(@TempDir + final Path testDir) throws Exception { try (SparkSession spark = SparkSession.builder().config(sparkConf).getOrCreate()) { @@ -152,7 +153,9 @@ class TransformationJobTest extends AbstractVocabularyTest { .getFile(); final String mdstore_output = testDir.toString() + "/version"; - mockupTrasformationRule("simpleTRule", "/eu/dnetlib/dhp/transform/scripts/xslt_cleaning_oaiOpenaire_datacite_ExchangeLandingpagePid.xsl"); + mockupTrasformationRule( + "simpleTRule", + "/eu/dnetlib/dhp/transform/scripts/xslt_cleaning_oaiOpenaire_datacite_ExchangeLandingpagePid.xsl"); final Map parameters = Stream.of(new String[][] { { @@ -203,7 +206,8 @@ class TransformationJobTest extends AbstractVocabularyTest { @Test @DisplayName("Test TransformSparkJobNode.main") - void transformTest(@TempDir final Path testDir) throws Exception { + void transformTest(@TempDir + final Path testDir) throws Exception { try (SparkSession spark = SparkSession.builder().config(sparkConf).getOrCreate()) { diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java index ad1e8721a..982e8ea75 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java @@ -103,7 +103,7 @@ public class SparkBulkTagJob { ResultTagger resultTagger = new ResultTagger(); readPath(spark, inputPath, resultClazz) .map(patchResult(), Encoders.bean(resultClazz)) - .filter(Objects::nonNull) + .filter(Objects::nonNull) .map( (MapFunction) value -> resultTagger .enrichContextCriteria( diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java index cfe47f29f..34ca6697c 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java @@ -1,10 +1,14 @@ + package eu.dnetlib.dhp.oa.graph.dump.funderresults; + import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + import java.io.Serializable; import java.util.List; import java.util.Objects; import java.util.Optional; import java.util.stream.Collectors; + import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.FlatMapFunction; @@ -14,29 +18,32 @@ import org.apache.spark.sql.*; import org.jetbrains.annotations.NotNull; import org.slf4j.Logger; import org.slf4j.LoggerFactory; + import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; import eu.dnetlib.dhp.schema.dump.oaf.community.Funder; import eu.dnetlib.dhp.schema.dump.oaf.community.Project; + /** * Splits the dumped results by funder and stores them in a folder named as the funder nsp (for all the funders, but the EC * for the EC it specifies also the fundingStream (FP7 or H2020) */ public class SparkDumpFunderResults implements Serializable { private static final Logger log = LoggerFactory.getLogger(SparkDumpFunderResults.class); + public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils - .toString( - SparkDumpFunderResults.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json")); + .toString( + SparkDumpFunderResults.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json")); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); parser.parseArgument(args); Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); final String inputPath = parser.get("sourcePath"); log.info("inputPath: {}", inputPath); @@ -44,30 +51,32 @@ public class SparkDumpFunderResults implements Serializable { log.info("outputPath: {}", outputPath); SparkConf conf = new SparkConf(); runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - writeResultProjectList(spark, inputPath, outputPath); - }); + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath); + writeResultProjectList(spark, inputPath, outputPath); + }); } + private static void writeResultProjectList(SparkSession spark, String inputPath, String outputPath) { Dataset result = Utils - .readPath(spark, inputPath + "/publication", CommunityResult.class) - .union(Utils.readPath(spark, inputPath + "/dataset", CommunityResult.class)) - .union(Utils.readPath(spark, inputPath + "/otherresearchproduct", CommunityResult.class)) - .union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class)); + .readPath(spark, inputPath + "/publication", CommunityResult.class) + .union(Utils.readPath(spark, inputPath + "/dataset", CommunityResult.class)) + .union(Utils.readPath(spark, inputPath + "/otherresearchproduct", CommunityResult.class)) + .union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class)); log.info("Number of result {}", result.count()); Dataset tmp = result - .flatMap((FlatMapFunction) cr -> cr.getProjects().stream().map(p -> { - return getFunderName(p); - }).collect(Collectors.toList()).iterator(), Encoders.STRING()) - .distinct(); + .flatMap((FlatMapFunction) cr -> cr.getProjects().stream().map(p -> { + return getFunderName(p); + }).collect(Collectors.toList()).iterator(), Encoders.STRING()) + .distinct(); List funderList = tmp.collectAsList(); funderList.forEach(funder -> { dumpResults(funder, result, outputPath); }); } + @NotNull private static String getFunderName(Project p) { Optional ofunder = Optional.ofNullable(p.getFunder()); @@ -97,23 +106,24 @@ public class SparkDumpFunderResults implements Serializable { return fName; } } + private static void dumpResults(String funder, Dataset results, String outputPath) { results.map((MapFunction) r -> { - if (!Optional.ofNullable(r.getProjects()).isPresent()) { - return null; - } - for (Project p : r.getProjects()) { - String fName = getFunderName(p); - if (fName.equalsIgnoreCase(funder)) { - return r; - } - } - return null; - }, Encoders.bean(CommunityResult.class)) - .filter(Objects::nonNull) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath + "/" + funder); + if (!Optional.ofNullable(r.getProjects()).isPresent()) { + return null; + } + for (Project p : r.getProjects()) { + String fName = getFunderName(p); + if (fName.equalsIgnoreCase(funder)) { + return r; + } + } + return null; + }, Encoders.bean(CommunityResult.class)) + .filter(Objects::nonNull) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath + "/" + funder); } -} \ No newline at end of file +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java index 5eed64e89..4b0072944 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java @@ -45,18 +45,18 @@ public class SparkResultLinkedToProject implements Serializable { public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils - .toString( - SparkResultLinkedToProject.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json")); + .toString( + SparkResultLinkedToProject.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json")); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); parser.parseArgument(args); Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); final String inputPath = parser.get("sourcePath"); @@ -78,41 +78,41 @@ public class SparkResultLinkedToProject implements Serializable { SparkConf conf = new SparkConf(); runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - writeResultsLinkedToProjects( - communityMapPath, spark, inputClazz, inputPath, outputPath, resultProjectsPath); - }); + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath); + writeResultsLinkedToProjects( + communityMapPath, spark, inputClazz, inputPath, outputPath, resultProjectsPath); + }); } private static void writeResultsLinkedToProjects(String communityMapPath, SparkSession spark, - Class inputClazz, - String inputPath, String outputPath, String resultProjectsPath) { + Class inputClazz, + String inputPath, String outputPath, String resultProjectsPath) { Dataset results = Utils - .readPath(spark, inputPath, inputClazz) - .filter( - (FilterFunction) r -> !r.getDataInfo().getDeletedbyinference() && - !r.getDataInfo().getInvisible()); + .readPath(spark, inputPath, inputClazz) + .filter( + (FilterFunction) r -> !r.getDataInfo().getDeletedbyinference() && + !r.getDataInfo().getInvisible()); Dataset resultProjectDataset = Utils - .readPath(spark, resultProjectsPath, ResultProject.class); + .readPath(spark, resultProjectsPath, ResultProject.class); CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath); results - .joinWith(resultProjectDataset, results.col("id").equalTo(resultProjectDataset.col("resultId"))) - .map((MapFunction, CommunityResult>) t2 -> { - CommunityResult cr = (CommunityResult) ResultMapper - .map( - t2._1(), - communityMap, Constants.DUMPTYPE.FUNDER.getType()); - cr.setProjects(t2._2().getProjectsList()); - return cr; - }, Encoders.bean(CommunityResult.class)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); + .joinWith(resultProjectDataset, results.col("id").equalTo(resultProjectDataset.col("resultId"))) + .map((MapFunction, CommunityResult>) t2 -> { + CommunityResult cr = (CommunityResult) ResultMapper + .map( + t2._1(), + communityMap, Constants.DUMPTYPE.FUNDER.getType()); + cr.setProjects(t2._2().getProjectsList()); + return cr; + }, Encoders.bean(CommunityResult.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java index 83a9f3464..38eb3cb37 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java @@ -2,9 +2,11 @@ package eu.dnetlib.dhp.oa.graph.dump.projectssubset; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + import java.io.Serializable; import java.util.Objects; import java.util.Optional; + import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; @@ -14,6 +16,7 @@ import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; import org.slf4j.LoggerFactory; + import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.schema.dump.oaf.graph.Project; diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java index c6798ac58..f3b7246b1 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java @@ -35,12 +35,12 @@ public class PrepareResultProjectJobTest { private static Path workingDir; private static final Logger log = LoggerFactory - .getLogger(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class); + .getLogger(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class); @BeforeAll public static void beforeAll() throws IOException { workingDir = Files - .createTempDirectory(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class.getSimpleName()); + .createTempDirectory(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class.getSimpleName()); log.info("using work dir {}", workingDir); SparkConf conf = new SparkConf(); @@ -54,10 +54,10 @@ public class PrepareResultProjectJobTest { conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); spark = SparkSession - .builder() - .appName(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); + .builder() + .appName(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); } @AfterAll @@ -70,23 +70,23 @@ public class PrepareResultProjectJobTest { void testNoMatch() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/no_match") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/no_match") + .getPath(); SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); + .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); assertEquals(0, verificationDataset.count()); @@ -96,37 +96,37 @@ public class PrepareResultProjectJobTest { void testMatchOne() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_one") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_one") + .getPath(); SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); + .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); assertEquals(1, verificationDataset.count()); assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); verificationDataset.createOrReplaceTempView("table"); Dataset check = spark - .sql( - "Select projList.provenance.provenance " + - "from table " + - "lateral view explode (projectsList) pl as projList"); + .sql( + "Select projList.provenance.provenance " + + "from table " + + "lateral view explode (projectsList) pl as projList"); assertEquals(1, check.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); @@ -138,88 +138,88 @@ public class PrepareResultProjectJobTest { void testMatch() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match") + .getPath(); SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); + .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); assertEquals(2, verificationDataset.count()); assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); verificationDataset.createOrReplaceTempView("dataset"); String query = "select resultId, MyT.id project , MyT.title title, MyT.acronym acronym , MyT.provenance.provenance provenance " - + "from dataset " - + "lateral view explode(projectsList) p as MyT "; + + "from dataset " + + "lateral view explode(projectsList) p as MyT "; org.apache.spark.sql.Dataset resultExplodedProvenance = spark.sql(query); assertEquals(3, resultExplodedProvenance.count()); assertEquals( - 2, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") - .count()); + 2, + resultExplodedProvenance + .filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") - .count()); + 1, + resultExplodedProvenance + .filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") + .count()); assertEquals( - 2, - resultExplodedProvenance - .filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'") - .count()); + 2, + resultExplodedProvenance + .filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'") - .count()); + 1, + resultExplodedProvenance + .filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::03376222b28a3aebf2730ac514818d04' and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::03376222b28a3aebf2730ac514818d04' and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") + .count()); assertEquals( - 3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); + 3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); } @@ -227,98 +227,98 @@ public class PrepareResultProjectJobTest { public void testMatchValidated() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_validatedRels") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_validatedRels") + .getPath(); SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); + .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); assertEquals(2, verificationDataset.count()); assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); verificationDataset.createOrReplaceTempView("dataset"); String query = "select resultId, MyT.id project , MyT.title title, MyT.acronym acronym , MyT.provenance.provenance provenance, " - + - "MyT.validated.validatedByFunder, MyT.validated.validationDate " - + "from dataset " - + "lateral view explode(projectsList) p as MyT "; + + + "MyT.validated.validatedByFunder, MyT.validated.validationDate " + + "from dataset " + + "lateral view explode(projectsList) p as MyT "; org.apache.spark.sql.Dataset resultExplodedProvenance = spark.sql(query); assertEquals(3, resultExplodedProvenance.count()); assertEquals(3, resultExplodedProvenance.filter("validatedByFunder = true").count()); assertEquals( - 2, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") - .count()); + 2, + resultExplodedProvenance + .filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") - .count()); + 1, + resultExplodedProvenance + .filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") + .count()); assertEquals( - 2, - resultExplodedProvenance - .filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'") - .count()); + 2, + resultExplodedProvenance + .filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + - "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + - "and validatedByFunder = true " + - "and validationDate = '2021-08-06'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + + "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + + "and validatedByFunder = true " + + "and validationDate = '2021-08-06'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + - "and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80' " + - "and validatedByFunder = true and validationDate = '2021-08-04'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + + "and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80' " + + "and validatedByFunder = true and validationDate = '2021-08-04'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'") - .count()); + 1, + resultExplodedProvenance + .filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::03376222b28a3aebf2730ac514818d04' " + - "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + - "and validatedByFunder = true and validationDate = '2021-08-05'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::03376222b28a3aebf2730ac514818d04' " + + "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + + "and validatedByFunder = true and validationDate = '2021-08-05'") + .count()); assertEquals( - 3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); + 3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); } @@ -326,20 +326,20 @@ public class PrepareResultProjectJobTest { void testMatchx() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match") + .getPath(); SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r))); } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java index 579958a62..7046b02c2 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java @@ -35,15 +35,15 @@ public class ResultLinkedToProjectTest { private static Path workingDir; private static final Logger log = LoggerFactory - .getLogger(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class); + .getLogger(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class); private static final HashMap map = new HashMap<>(); @BeforeAll public static void beforeAll() throws IOException { workingDir = Files - .createTempDirectory( - eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()); + .createTempDirectory( + eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()); log.info("using work dir {}", workingDir); SparkConf conf = new SparkConf(); @@ -57,10 +57,10 @@ public class ResultLinkedToProjectTest { conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); spark = SparkSession - .builder() - .appName(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); + .builder() + .appName(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); } @AfterAll @@ -73,32 +73,32 @@ public class ResultLinkedToProjectTest { void testNoMatch() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json") + .getPath(); final String graphPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo") + .getPath(); final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/communityMapPath") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/communityMapPath") + .getPath(); SparkResultLinkedToProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-graphPath", graphPath, - "-communityMapPath", communityMapPath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath, + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", + "-graphPath", graphPath, + "-communityMapPath", communityMapPath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(0, tmp.count()); @@ -108,32 +108,32 @@ public class ResultLinkedToProjectTest { void testMatchOne() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/papers.json") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/papers.json") + .getPath(); final String graphPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo") + .getPath(); final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/communityMapPath") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/communityMapPath") + .getPath(); SparkResultLinkedToProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-graphPath", graphPath, - "-communityMapPath", communityMapPath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath, + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", + "-graphPath", graphPath, + "-communityMapPath", communityMapPath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(1, tmp.count()); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java index 5bb5a1178..e9d739db2 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java @@ -56,10 +56,10 @@ public class SplitPerFunderTest { conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); spark = SparkSession - .builder() - .appName(SplitPerFunderTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); + .builder() + .appName(SplitPerFunderTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); } @AfterAll @@ -72,13 +72,13 @@ public class SplitPerFunderTest { void test1() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext") + .getPath(); SparkDumpFunderResults.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/split", - "-sourcePath", sourcePath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/split", + "-sourcePath", sourcePath }); @@ -86,64 +86,64 @@ public class SplitPerFunderTest { // FP7 3 and H2020 3 JavaRDD tmp = sc - .textFile(workingDir.toString() + "/split/EC_FP7") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/EC_FP7") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); + .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); Assertions.assertEquals(3, verificationDataset.count()); Assertions - .assertEquals( - 1, verificationDataset.filter("id = '50|dedup_wf_001::0d16b1714ab3077df73893a8ea57d776'").count()); + .assertEquals( + 1, verificationDataset.filter("id = '50|dedup_wf_001::0d16b1714ab3077df73893a8ea57d776'").count()); // CIHR 2 tmp = sc - .textFile(workingDir.toString() + "/split/CIHR") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/CIHR") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(2, tmp.count()); // NWO 1 tmp = sc - .textFile(workingDir.toString() + "/split/NWO") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/NWO") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(1, tmp.count()); // NIH 3 tmp = sc - .textFile(workingDir.toString() + "/split/NIH") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/NIH") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(2, tmp.count()); // NSF 1 tmp = sc - .textFile(workingDir.toString() + "/split/NSF") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/NSF") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(1, tmp.count()); // SNSF 1 tmp = sc - .textFile(workingDir.toString() + "/split/SNSF") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/SNSF") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(1, tmp.count()); // NHMRC 1 tmp = sc - .textFile(workingDir.toString() + "/split/NHMRC") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/NHMRC") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(1, tmp.count()); // H2020 3 tmp = sc - .textFile(workingDir.toString() + "/split/EC_H2020") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/EC_H2020") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(3, tmp.count()); // MZOS 1 tmp = sc - .textFile(workingDir.toString() + "/split/MZOS") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/MZOS") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(1, tmp.count()); } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java index 4ff1e1b96..8cdb285e4 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java @@ -30,7 +30,6 @@ public class ProjectSubsetTest { private static final Logger log = LoggerFactory .getLogger(eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class); - @BeforeAll public static void beforeAll() throws IOException { workingDir = Files From fae681fea1812513f900ad6457455dad9c1f80bc Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Sun, 3 Jul 2022 17:39:58 +0200 Subject: [PATCH 102/214] [Country Propagation] add check to avoid NPE on datasource.getDatasourceType().getClassis() --- .../PrepareDatasourceCountryAssociation.java | 3 +++ 1 file changed, 3 insertions(+) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java index 42b7804ea..b9f3bff52 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java @@ -6,6 +6,7 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.util.Arrays; import java.util.List; +import java.util.Optional; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; @@ -87,6 +88,8 @@ public class PrepareDatasourceCountryAssociation { Dataset datasource = readPath(spark, inputPath + "/datasource", Datasource.class) .filter( (FilterFunction) ds -> !ds.getDataInfo().getDeletedbyinference() && + Optional.ofNullable(ds.getDatasourcetype()).isPresent() && + Optional.ofNullable(ds.getDatasourcetype().getClassid()).isPresent() && (allowedtypes.contains(ds.getDatasourcetype().getClassid()) || whitelist.contains(ds.getId()))); From 0c1cfee39684be0afba50a80e401690cbc5c75d5 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 11 Jul 2022 17:34:59 +0200 Subject: [PATCH 103/214] mapping oaf:fulltext elements in the result.fulltext field --- .../dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java | 2 +- .../test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java | 4 ++++ 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index 739be3df4..a05faab80 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -379,7 +379,7 @@ public abstract class AbstractMdRecordToOafMapper { r.setPublisher(preparePublisher(doc, info)); r.setEmbargoenddate(prepareField(doc, "//oaf:embargoenddate", info)); r.setSource(prepareSources(doc, info)); - r.setFulltext(new ArrayList<>()); // NOT PRESENT IN MDSTORES + r.setFulltext(prepareListFields(doc, "//oaf:fulltext", info)); r.setFormat(prepareFormats(doc, info)); r.setContributor(prepareContributors(doc, info)); r.setResourcetype(prepareResourceType(doc, info)); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index f5cb86bfd..b75f626d6 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -122,6 +122,10 @@ class MappersTest { assertNotNull(p.getBestaccessright()); assertEquals("OPEN", p.getBestaccessright().getClassid()); + assertNotNull(p.getFulltext()); + assertEquals(1, p.getFulltext().size()); + assertEquals("https://oneecosystem.pensoft.net/article/13718/", p.getFulltext().get(0).getValue()); + // RESULT PROJECT List resultProject = list .stream() From 0a4f4d98fa8f73d296ef92f4dbf9f12a760ef735 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Wed, 13 Jul 2022 15:27:17 +0200 Subject: [PATCH 104/214] added PMCId to PmArticle --- .../dnetlib/dhp/sx/bio/pubmed/PMArticle.java | 24 +- .../dnetlib/dhp/sx/bio/pubmed/PMParser.scala | 1 + .../dhp/sx/bio/pubmed/PubMedToOaf.scala | 48 +++- .../eu/dnetlib/dhp/sx/graph/bio/pubmed.xml | 257 ++++++++++++++++-- .../dnetlib/dhp/sx/bio/BioScholixTest.scala | 71 ++++- 5 files changed, 371 insertions(+), 30 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMArticle.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMArticle.java index af0d5169d..9287a8cdd 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMArticle.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMArticle.java @@ -17,6 +17,9 @@ public class PMArticle implements Serializable { * the Pubmed Identifier */ private String pmid; + + private String pmcId; + /** * the DOI */ @@ -122,7 +125,7 @@ public class PMArticle implements Serializable { /** * The full journal title (taken from NLM cataloging data following NLM rules for how to compile a serial name) is exported in this element. - * Some characters that are not part of the NLM MEDLINE/PubMed Character Set reside in a relatively small number of full journal titles. + * Some characters that are not part of the NLM MEDLINE/PubMed Character Set reside in a relatively small number of full journal titles. * The NLM journal title abbreviation is exported in the element. * * @return the pubmed Journal Extracted @@ -140,10 +143,11 @@ public class PMArticle implements Serializable { } /** - * English-language abstracts are taken directly from the published article. - * If the article does not have a published abstract, the National Library of Medicine does not create one, - * thus the record lacks the and elements. However, in the absence of a formally - * labeled abstract in the published article, text from a substantive "summary", "summary and conclusions" or "conclusions and summary" may be used. + * contains the entire title of the journal article. is always in English; + * those titles originally published in a non-English language and translated for are enclosed in square brackets. + * All titles end with a period unless another punctuation mark such as a question mark or bracket is present. + * Explanatory information about the title itself is enclosed in parentheses, e.g.: (author's transl). + * Corporate/collective authors may appear at the end of for citations up to about the year 2000. * * @return the extracted pubmed Title */ @@ -250,4 +254,14 @@ public class PMArticle implements Serializable { public List getGrants() { return grants; } + + + public String getPmcId() { + return pmcId; + } + + public PMArticle setPmcId(String pmcId) { + this.pmcId = pmcId; + return this; + } } diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PMParser.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PMParser.scala index 49a271641..9102c12c4 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PMParser.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PMParser.scala @@ -98,6 +98,7 @@ class PMParser(xml: XMLEventReader) extends Iterator[PMArticle] { case "PMID" => currentArticle.setPmid(text.trim) case "ArticleId" => if ("doi".equalsIgnoreCase(currentArticleType)) currentArticle.setDoi(text.trim) + if ("pmc".equalsIgnoreCase(currentArticleType)) currentArticle.setPmcId(text.trim) case "Language" => currentArticle.setLanguage(text.trim) case "ISSN" => currentJournal.setIssn(text.trim) case "GrantID" => currentGrant.setGrantID(text.trim) diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala index 92ad22c57..24a1fa62b 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala @@ -4,9 +4,12 @@ import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup import eu.dnetlib.dhp.schema.common.ModelConstants import eu.dnetlib.dhp.schema.oaf.utils.{GraphCleaningFunctions, IdentifierFactory, OafMapperUtils, PidType} import eu.dnetlib.dhp.schema.oaf._ -import collection.JavaConverters._ +import eu.dnetlib.dhp.utils.DHPUtils +import org.apache.commons.lang3.StringUtils +import collection.JavaConverters._ import java.util.regex.Pattern +import scala.collection.mutable.ListBuffer /** */ @@ -14,6 +17,9 @@ object PubMedToOaf { val SUBJ_CLASS = "keywords" + val OAI_HEADER = "oai:pubmedcentral.nih.gov:" + val OLD_PMC_PREFIX = "od_______267::" + val urlMap = Map( "pmid" -> "https://pubmed.ncbi.nlm.nih.gov/", "doi" -> "https://dx.doi.org/" @@ -50,6 +56,17 @@ object PubMedToOaf { null } + + def createOriginalOpenaireId(article:PMArticle) :String = { + if (StringUtils.isNotEmpty(article.getPmcId)) { + val md5 = DHPUtils.md5(s"$OAI_HEADER${article.getPmcId.replace("PMC","")}") + s"$OLD_PMC_PREFIX$md5" + } + else + null + + } + /** Create an instance of class extends Result * starting from OAF instanceType value * @@ -122,8 +139,9 @@ object PubMedToOaf { return null // MAP PMID into pid with classid = classname = pmid - val pidList: List[StructuredProperty] = List( - OafMapperUtils.structuredProperty( + val pidList = ListBuffer[StructuredProperty]() + + pidList += OafMapperUtils.structuredProperty( article.getPmid, PidType.pmid.toString, PidType.pmid.toString, @@ -131,7 +149,19 @@ object PubMedToOaf { ModelConstants.DNET_PID_TYPES, dataInfo ) - ) + + + if (StringUtils.isNotBlank(article.getPmcId)) + { + pidList += OafMapperUtils.structuredProperty( + article.getPmcId, + PidType.pmc.toString, + PidType.pmc.toString, + ModelConstants.DNET_PID_TYPES, + ModelConstants.DNET_PID_TYPES, + dataInfo + ) + } if (pidList == null) return null @@ -186,6 +216,7 @@ object PubMedToOaf { val urlLists: List[String] = pidList .map(s => (urlMap.getOrElse(s.getQualifier.getClassid, ""), s.getValue)) .filter(t => t._1.nonEmpty) + .toList .map(t => t._1 + t._2) if (urlLists != null) pubmedInstance.setUrl(urlLists.asJava) @@ -262,7 +293,14 @@ object PubMedToOaf { if (authors != null && authors.nonEmpty) result.setAuthor(authors.asJava) - result.setOriginalId(pidList.map(s => s.getValue).asJava) + + if (StringUtils.isNotEmpty(article.getPmcId)) { + val originalIDS = ListBuffer[String]() + originalIDS += createOriginalOpenaireId(article) + pidList.map(s => s.getValue).foreach(p =>originalIDS += p) + result.setOriginalId(originalIDS.asJava) + } else + result.setOriginalId(pidList.map(s => s.getValue).asJava) result.setId(article.getPmid) diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml index 22da07e29..58a73ae5d 100644 --- a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml @@ -195,7 +195,9 @@ Biochemical and biophysical research communications Biochem Biophys Res Commun - Delineation of the intimate details of the backbone conformation of pyridine nucleotide coenzymes in aqueous solution. + Delineation of the intimate details of the backbone conformation of pyridine nucleotide + coenzymes in aqueous solution. + 1173-9 @@ -473,7 +475,9 @@ Biochemical and biophysical research communications Biochem Biophys Res Commun - Effect of chloroquine on cultured fibroblasts: release of lysosomal hydrolases and inhibition of their uptake. + Effect of chloroquine on cultured fibroblasts: release of lysosomal hydrolases and + inhibition of their uptake. + 1338-43 @@ -657,7 +661,8 @@ Biochemical and biophysical research communications Biochem Biophys Res Commun - Atomic models for the polypeptide backbones of myohemerythrin and hemerythrin. + Atomic models for the polypeptide backbones of myohemerythrin and hemerythrin. + 1349-56 @@ -1627,7 +1632,9 @@ Biochemical pharmacology Biochem Pharmacol - Comparison between procaine and isocarboxazid metabolism in vitro by a liver microsomal amidase-esterase. + Comparison between procaine and isocarboxazid metabolism in vitro by a liver microsomal + amidase-esterase. + 1517-21 @@ -2030,7 +2037,9 @@ Biochemical pharmacology Biochem Pharmacol - Radiochemical assay of glutathione S-epoxide transferase and its enhancement by phenobarbital in rat liver in vivo. + Radiochemical assay of glutathione S-epoxide transferase and its enhancement by + phenobarbital in rat liver in vivo. + 1569-72 @@ -2350,7 +2359,9 @@ Biochemical pharmacology Biochem Pharmacol - Identification of adenylate cyclase-coupled beta-adrenergic receptors with radiolabeled beta-adrenergic antagonists. + Identification of adenylate cyclase-coupled beta-adrenergic receptors with radiolabeled + beta-adrenergic antagonists. + 1651-8 @@ -2598,7 +2609,9 @@ Biochemical pharmacology Biochem Pharmacol - The effect of adrenaline and of alpha- and beta-adrenergic blocking agents on ATP concentration and on incorporation of 32Pi into ATP in rat fat cells. + The effect of adrenaline and of alpha- and beta-adrenergic blocking agents on ATP + concentration and on incorporation of 32Pi into ATP in rat fat cells. + 1659-62 @@ -2851,7 +2864,9 @@ Biochemical pharmacology Biochem Pharmacol - Action of propranolol on mitochondrial functions--effects on energized ion fluxes in the presence of valinomycin. + Action of propranolol on mitochondrial functions--effects on energized ion fluxes in the + presence of valinomycin. + 1701-5 @@ -3265,7 +3280,8 @@ EC 2.6.1.16 - Glutamine-Fructose-6-Phosphate Transaminase (Isomerizing) + Glutamine-Fructose-6-Phosphate Transaminase (Isomerizing) + EC 2.7.- @@ -3324,7 +3340,9 @@ Glucosamine - Glutamine-Fructose-6-Phosphate Transaminase (Isomerizing) + Glutamine-Fructose-6-Phosphate Transaminase + (Isomerizing) + metabolism @@ -3463,7 +3481,8 @@ Biochemical pharmacology Biochem Pharmacol - Inhibition of aldehyde reductase by acidic metabolites of the biogenic amines. + Inhibition of aldehyde reductase by acidic metabolites of the biogenic amines. + 1731-3 @@ -3696,7 +3715,9 @@ Biochemical pharmacology Biochem Pharmacol - Effects of 5,6-dihydroxytryptamine on tyrosine-hydroxylase activity in central catecholaminergic neurons of the rat. + Effects of 5,6-dihydroxytryptamine on tyrosine-hydroxylase activity in central + catecholaminergic neurons of the rat. + 1739-42 @@ -4602,12 +4623,19 @@ Arzneimittel-Forschung Arzneimittelforschung - [Biochemical studies on camomile components/III. In vitro studies about the antipeptic activity of (--)-alpha-bisabolol (author's transl)]. + [Biochemical studies on camomile components/III. In vitro studies about the antipeptic + activity of (--)-alpha-bisabolol (author's transl)]. + 1352-4 - (--)-alpha-Bisabolol has a primary antipeptic action depending on dosage, which is not caused by an alteration of the pH-value. The proteolytic activity of pepsin is reduced by 50 percent through addition of bisabolol in the ratio of 1/0.5. The antipeptic action of bisabolol only occurs in case of direct contact. In case of a previous contact with the substrate, the inhibiting effect is lost. + (--)-alpha-Bisabolol has a primary antipeptic action depending on dosage, which is not + caused by an alteration of the pH-value. The proteolytic activity of pepsin is reduced by 50 + percent through addition of bisabolol in the ratio of 1/0.5. The antipeptic action of bisabolol + only occurs in case of direct contact. In case of a previous contact with the substrate, the + inhibiting effect is lost. + @@ -4626,7 +4654,9 @@ English Abstract Journal Article - Biochemische Untersuchungen von Kamilleninhaltsstoffen. III. In-vitro-Versuche über die antipeptische Wirkung des (-)-alpha-Bisabolols + Biochemische Untersuchungen von Kamilleninhaltsstoffen. III. In-vitro-Versuche über die + antipeptische Wirkung des (-)-alpha-Bisabolols + Germany @@ -4753,12 +4783,37 @@ Arzneimittel-Forschung Arzneimittelforschung - [Demonstration of tumor inhibiting properties of a strongly immunostimulating low-molecular weight substance. Comparative studies with ifosfamide on the immuno-labile DS carcinosarcoma. Stimulation of the autoimmune activity for approx. 20 days by BA 1, a N-(2-cyanoethylene)-urea. Novel prophylactic possibilities]. + [Demonstration of tumor inhibiting properties of a strongly immunostimulating + low-molecular weight substance. Comparative studies with ifosfamide on the immuno-labile DS + carcinosarcoma. Stimulation of the autoimmune activity for approx. 20 days by BA 1, a + N-(2-cyanoethylene)-urea. Novel prophylactic possibilities]. + 1369-79 - A report is given on the recent discovery of outstanding immunological properties in BA 1 [N-(2-cyanoethylene)-urea] having a (low) molecular mass M = 111.104. Experiments in 214 DS carcinosarcoma bearing Wistar rats have shown that BA 1, at a dosage of only about 12 percent LD50 (150 mg kg) and negligible lethality (1.7 percent), results in a recovery rate of 40 percent without hyperglycemia and, in one test, of 80 percent with hyperglycemia. Under otherwise unchanged conditions the reference substance ifosfamide (IF) -- a further development of cyclophosphamide -- applied without hyperglycemia in its most efficient dosage of 47 percent LD50 (150 mg kg) brought about a recovery rate of 25 percent at a lethality of 18 percent. (Contrary to BA 1, 250-min hyperglycemia caused no further improvement of the recovery rate.) However this comparison is characterized by the fact that both substances exhibit two quite different (complementary) mechanisms of action. Leucocyte counts made after application of the said cancerostatics and dosages have shown a pronounced stimulation with BA 1 and with ifosfamide, the known suppression in the post-therapeutic interval usually found with standard cancerostatics. In combination with the cited plaque test for BA 1, blood pictures then allow conclusions on the immunity status. Since IF can be taken as one of the most efficient cancerostatics--there is no other chemotherapeutic known up to now that has a more significant effect on the DS carcinosarcoma in rats -- these findings are of special importance. Finally, the total amount of leucocytes and lymphocytes as well as their time behaviour was determined from the blood picture of tumour-free rats after i.v. application of BA 1. The thus obtained numerical values clearly show that further research work on the prophylactic use of this substance seems to be necessary and very promising. + A report is given on the recent discovery of outstanding immunological properties in + BA 1 [N-(2-cyanoethylene)-urea] having a (low) molecular mass M = 111.104. Experiments in 214 DS + carcinosarcoma bearing Wistar rats have shown that BA 1, at a dosage of only about 12 percent + LD50 (150 mg kg) and negligible lethality (1.7 percent), results in a recovery rate of 40 + percent without hyperglycemia and, in one test, of 80 percent with hyperglycemia. Under + otherwise unchanged conditions the reference substance ifosfamide (IF) -- a further development + of cyclophosphamide -- applied without hyperglycemia in its most efficient dosage of 47 percent + LD50 (150 mg kg) brought about a recovery rate of 25 percent at a lethality of 18 percent. + (Contrary to BA 1, 250-min hyperglycemia caused no further improvement of the recovery rate.) + However this comparison is characterized by the fact that both substances exhibit two quite + different (complementary) mechanisms of action. Leucocyte counts made after application of the + said cancerostatics and dosages have shown a pronounced stimulation with BA 1 and with + ifosfamide, the known suppression in the post-therapeutic interval usually found with standard + cancerostatics. In combination with the cited plaque test for BA 1, blood pictures then allow + conclusions on the immunity status. Since IF can be taken as one of the most efficient + cancerostatics--there is no other chemotherapeutic known up to now that has a more significant + effect on the DS carcinosarcoma in rats -- these findings are of special importance. Finally, + the total amount of leucocytes and lymphocytes as well as their time behaviour was determined + from the blood picture of tumour-free rats after i.v. application of BA 1. The thus obtained + numerical values clearly show that further research work on the prophylactic use of this + substance seems to be necessary and very promising. + @@ -4778,7 +4833,11 @@ English Abstract Journal Article - Nachweis krebshemmender Eigenschaften einer stark immunstimulierenden Verbindung kleiner Molekülmasse. Versuche am immunlabilen DS-Karzinosarkom im Vergleich mit Ifosfamid. Stimulierung der körpereigenen Abwehr über etwa 20 Tage durch BA 1, einen N-(2-Cyanthylen)-harnstoff. Neue prophylaktische Möglichkeiten + Nachweis krebshemmender Eigenschaften einer stark immunstimulierenden Verbindung + kleiner Molekülmasse. Versuche am immunlabilen DS-Karzinosarkom im Vergleich mit Ifosfamid. + Stimulierung der körpereigenen Abwehr über etwa 20 Tage durch BA 1, einen + N-(2-Cyanthylen)-harnstoff. Neue prophylaktische Möglichkeiten + Germany @@ -5016,7 +5075,20 @@ 1400-3 - The distribution of blood flow to the subendocardial, medium and subepicardial layers of the left ventricular free wall was studied in anaesthetized dogs under normoxic (A), hypoxic (B) conditions and under pharmacologically induced (etafenone) coronary vasodilation (C). Regional myocardial blood flow was determined by means of the particle distribution method. In normoxia a transmural gradient of flow was observed, with the subendocardial layers receiving a significantly higher flow rate compared with the subepicardial layers. In hypoxia induced vasodilation this transmural gradient of flow was persistent. In contrast a marked redistribution of regional flow was observed under pharmacologically induced vasodilation. The transmural gradient decreased. In contrast to some findings these experiments demonstrate that a considerable vasodilatory capacity exists in all layers of the myocardium and can be utilized by drugs. The differences observed for the intramural distribution pattern of flow under hypoxia and drug induced vasodilation support the hypothesis that this pattern reflects corresponding gradients of regional myocardial metabolism. + The distribution of blood flow to the subendocardial, medium and subepicardial layers + of the left ventricular free wall was studied in anaesthetized dogs under normoxic (A), hypoxic + (B) conditions and under pharmacologically induced (etafenone) coronary vasodilation (C). + Regional myocardial blood flow was determined by means of the particle distribution method. In + normoxia a transmural gradient of flow was observed, with the subendocardial layers receiving a + significantly higher flow rate compared with the subepicardial layers. In hypoxia induced + vasodilation this transmural gradient of flow was persistent. In contrast a marked + redistribution of regional flow was observed under pharmacologically induced vasodilation. The + transmural gradient decreased. In contrast to some findings these experiments demonstrate that a + considerable vasodilatory capacity exists in all layers of the myocardium and can be utilized by + drugs. The differences observed for the intramural distribution pattern of flow under hypoxia + and drug induced vasodilation support the hypothesis that this pattern reflects corresponding + gradients of regional myocardial metabolism. + @@ -5185,4 +5257,151 @@ + + + 4917185 + + 1970 + 10 + 27 + + + 2018 + 11 + 13 + +
+ + 0003-6919 + + 19 + 6 + + 1970 + Jun + + + Applied microbiology + Appl Microbiol + + Bactericidal activity of a broad-spectrum illumination source. + + 1013-4 + + + + Several hours of exposure to Vita-Lite lamps, which have a unique spectral + distribution, give significant killing of cells of Staphylococcus aureus. + + + + + Himmelfarb + P + P + + + Scott + A + A + + + Thayer + P S + PS + + + eng + + Journal Article + +
+ + United States + Appl Microbiol + 7605802 + 0003-6919 + + IM + + + Bacteriological Techniques + instrumentation + + + Light + + + Radiation Effects + + + Serratia marcescens + growth & development + radiation effects + + + Staphylococcus + growth & development + radiation effects + + + Sterilization + + + + + + + 1970 + 6 + 1 + + + 1970 + 6 + 1 + 0 + 1 + + + 1970 + 6 + 1 + 0 + 0 + + + ppublish + + 4917185 + PMC376844 + + + + Photochem Photobiol. 1969 Jan;9(1):99-102 + + 4889809 + + + + Endocrinology. 1969 Dec;85(6):1218-21 + + 5347623 + + + + Arch Mikrobiol. 1956;24(1):60-79 + + 13327987 + + + + J Bacteriol. 1941 Sep;42(3):353-66 + + 16560457 + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala index ea742a04a..37a5808ec 100644 --- a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala +++ b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala @@ -2,7 +2,8 @@ package eu.dnetlib.dhp.sx.bio import com.fasterxml.jackson.databind.{DeserializationFeature, ObjectMapper, SerializationFeature} import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest -import eu.dnetlib.dhp.schema.oaf.{Oaf, Relation, Result} +import eu.dnetlib.dhp.schema.oaf.utils.PidType +import eu.dnetlib.dhp.schema.oaf.{Oaf, Publication, Relation, Result} import eu.dnetlib.dhp.sx.bio.BioDBToOAF.ScholixResolved import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMParser, PubMedToOaf} import org.json4s.DefaultFormats @@ -16,6 +17,7 @@ import org.mockito.junit.jupiter.MockitoExtension import java.io.{BufferedReader, InputStream, InputStreamReader} import java.util.zip.GZIPInputStream import scala.collection.JavaConverters._ +import scala.collection.mutable.ListBuffer import scala.io.Source import scala.xml.pull.XMLEventReader @@ -72,6 +74,73 @@ class BioScholixTest extends AbstractVocabularyTest { ) println(mapper.writeValueAsString(r.head)) + } + + + private def checkPMArticle(article:PMArticle): Unit = { + assertNotNull(article.getPmid) + assertNotNull(article.getTitle) + assertNotNull(article.getAuthors) + article.getAuthors.asScala.foreach{a => + assertNotNull(a) + assertNotNull(a.getFullName) + } + + } + + @Test + def testParsingPubmedXML():Unit = { + val xml = new XMLEventReader(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml"))) + val parser = new PMParser(xml) + parser.foreach(checkPMArticle) + } + + + private def checkPubmedPublication(o:Oaf): Unit = { + assertTrue(o.isInstanceOf[Publication]) + val p:Publication = o.asInstanceOf[Publication] + assertNotNull(p.getId) + assertNotNull(p.getTitle) + p.getTitle.asScala.foreach(t =>assertNotNull(t.getValue)) + p.getAuthor.asScala.foreach(a =>assertNotNull(a.getFullname)) + assertNotNull(p.getInstance()) + p.getInstance().asScala.foreach { i => + assertNotNull(i.getCollectedfrom) + assertNotNull(i.getPid) + assertNotNull(i.getInstancetype) + } + assertNotNull(p.getOriginalId) + p.getOriginalId.asScala.foreach(oId => assertNotNull(oId)) + + + val hasPMC = p.getInstance().asScala.exists(i => i.getPid.asScala.exists(pid => pid.getQualifier.getClassid.equalsIgnoreCase(PidType.pmc.toString))) + + + + if (hasPMC) { + assertTrue(p.getOriginalId.asScala.exists(oId => oId.startsWith("od_______267::"))) + + + } + + + + } + @Test + def testPubmedMapping() :Unit = { + + val xml = new XMLEventReader(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml"))) + val parser = new PMParser(xml) + val results = ListBuffer[Oaf]() + parser.foreach(x => results += PubMedToOaf.convert(x, vocabularies)) + + + + + results.foreach(checkPubmedPublication) + + + } @Test From 00168303dbb4e14ee453a911d3c072314e686864 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Thu, 14 Jul 2022 10:19:59 +0200 Subject: [PATCH 105/214] Added unit test to verify the generation in the OriginalID the old openaire Identifier generated by OAI --- .../dnetlib/dhp/sx/bio/BioScholixTest.scala | 41 ++++++++++++++++--- 1 file changed, 35 insertions(+), 6 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala index 37a5808ec..b021e5e07 100644 --- a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala +++ b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala @@ -5,7 +5,7 @@ import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest import eu.dnetlib.dhp.schema.oaf.utils.PidType import eu.dnetlib.dhp.schema.oaf.{Oaf, Publication, Relation, Result} import eu.dnetlib.dhp.sx.bio.BioDBToOAF.ScholixResolved -import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMParser, PubMedToOaf} +import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMParser, PMSubject, PubMedToOaf} import org.json4s.DefaultFormats import org.json4s.JsonAST.{JField, JObject, JString} import org.json4s.jackson.JsonMethods.parse @@ -119,13 +119,42 @@ class BioScholixTest extends AbstractVocabularyTest { if (hasPMC) { assertTrue(p.getOriginalId.asScala.exists(oId => oId.startsWith("od_______267::"))) - - } - - - } + + + @Test + def testPubmedOriginalID():Unit = { + val article:PMArticle = new PMArticle + + + article.setPmid("1234") + + article.setTitle("a Title") + + // VERIFY PUBLICATION IS NOT NULL + article.getPublicationTypes.add( new PMSubject("article",null, null)) + var publication = PubMedToOaf.convert(article, vocabularies).asInstanceOf[Publication] + assertNotNull(publication) + assertEquals("50|pmid________::81dc9bdb52d04dc20036dbd8313ed055", publication.getId) + + // VERIFY PUBLICATION ID DOES NOT CHANGE ALSO IF SETTING PMC IDENTIFIER + article.setPmcId("PMC1517292") + publication = PubMedToOaf.convert(article, vocabularies).asInstanceOf[Publication] + assertNotNull(publication) + assertEquals("50|pmid________::81dc9bdb52d04dc20036dbd8313ed055", publication.getId) + + // VERIFY ORIGINAL ID GENERATE IN OLD WAY USING PMC IDENTIFIER EXISTS + + + val oldOpenaireID ="od_______267::0000072375bc0e68fa09d4e6b7658248" + + val hasOldOpenAIREID = publication.getOriginalId.asScala.exists(o => o.equalsIgnoreCase(oldOpenaireID)) + + assertTrue(hasOldOpenAIREID) + } + + @Test def testPubmedMapping() :Unit = { From 5b76321d9cb58f68a52ee01d14ea77f38e81d749 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Wed, 20 Jul 2022 16:34:32 +0200 Subject: [PATCH 106/214] implemented oozie workflow to generate scholix dump filtering relclass semantic --- .../sx/graph/convert_dataset_json_params.json | 1 + .../sx/graph/convert_object_json_params.json | 4 +- .../dumpScholix/oozie_app/config-default.xml | 10 ++ .../graph/dumpScholix/oozie_app/workflow.xml | 145 ++++++++++++++++++ .../sx/graph/SparkConvertObjectToJson.scala | 33 +++- .../sx/graph/SparkConvertRDDtoDataset.scala | 61 +++++--- 6 files changed, 228 insertions(+), 26 deletions(-) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/dumpScholix/oozie_app/config-default.xml create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/dumpScholix/oozie_app/workflow.xml diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/convert_dataset_json_params.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/convert_dataset_json_params.json index 8bfdde5b0..f3e8cdbad 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/convert_dataset_json_params.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/convert_dataset_json_params.json @@ -2,4 +2,5 @@ {"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true}, {"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the source Path", "paramRequired": true}, {"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the path of the raw graph", "paramRequired": true} + {"paramName":"r", "paramLongName":"filterRelation", "paramDescription": "the relation to filter", "paramRequired": false} ] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/convert_object_json_params.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/convert_object_json_params.json index 890570a0b..cbb20bfe7 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/convert_object_json_params.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/convert_object_json_params.json @@ -3,5 +3,7 @@ {"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the source Path", "paramRequired": true}, {"paramName":"su", "paramLongName":"scholixUpdatePath", "paramDescription": "the scholix updated Path", "paramRequired": false}, {"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the path of the raw graph", "paramRequired": true}, - {"paramName":"o", "paramLongName":"objectType", "paramDescription": "should be scholix or Summary", "paramRequired": true} + {"paramName":"o", "paramLongName":"objectType", "paramDescription": "should be scholix or Summary", "paramRequired": true}, + {"paramName":"mp", "paramLongName":"maxPidNumberFilter", "paramDescription": "filter max number of pids in source/target", "paramRequired": false} + ] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/dumpScholix/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/dumpScholix/oozie_app/config-default.xml new file mode 100644 index 000000000..6fb2a1253 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/dumpScholix/oozie_app/config-default.xml @@ -0,0 +1,10 @@ + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/dumpScholix/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/dumpScholix/oozie_app/workflow.xml new file mode 100644 index 000000000..a37d85ad4 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/dumpScholix/oozie_app/workflow.xml @@ -0,0 +1,145 @@ + + + + sourcePath + the working dir base path + + + targetPath + the final graph path + + + relationFilter + Filter relation semantic + + + maxNumberOfPid + filter relation with at least #maxNumberOfPid + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + yarn + cluster + Import JSONRDD to Dataset kryo + eu.dnetlib.dhp.sx.graph.SparkConvertRDDtoDataset + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.shuffle.partitions=3000 + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --masteryarn + --sourcePath${sourcePath} + --targetPath${targetPath} + --filterRelation${relationFilter} + + + + + + + + + yarn + cluster + Convert Entities to summaries + eu.dnetlib.dhp.sx.graph.SparkCreateSummaryObject + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.shuffle.partitions=20000 + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --masteryarn + --sourcePath${targetPath}/entities + --targetPath${targetPath}/provision/summaries + + + + + + + + yarn + cluster + Generate Scholix Dataset + eu.dnetlib.dhp.sx.graph.SparkCreateScholix + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.shuffle.partitions=30000 + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --masteryarn + --summaryPath${targetPath}/provision/summaries + --targetPath${targetPath}/provision/scholix + --relationPath${targetPath}/relation + + + + + + + + + + + + + + + + + yarn + cluster + Serialize scholix to JSON + eu.dnetlib.dhp.sx.graph.SparkConvertObjectToJson + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.shuffle.partitions=6000 + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --masteryarn + --sourcePath${targetPath}/provision/scholix/scholix + --targetPath${targetPath}/json/scholix_json + --objectTypescholix + --maxPidNumberFiltermaxNumberOfPid + + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertObjectToJson.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertObjectToJson.scala index bfa07eb69..6695ebd3c 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertObjectToJson.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertObjectToJson.scala @@ -4,6 +4,7 @@ import com.fasterxml.jackson.databind.ObjectMapper import eu.dnetlib.dhp.application.ArgumentApplicationParser import eu.dnetlib.dhp.schema.sx.scholix.Scholix import eu.dnetlib.dhp.schema.sx.summary.ScholixSummary +import eu.dnetlib.dhp.sx.graph.SparkConvertObjectToJson.toInt import org.apache.commons.io.IOUtils import org.apache.hadoop.io.compress.GzipCodec import org.apache.spark.SparkConf @@ -12,6 +13,14 @@ import org.slf4j.{Logger, LoggerFactory} object SparkConvertObjectToJson { + def toInt(s: String): Option[Int] = { + try { + Some(s.toInt) + } catch { + case e: Exception => None + } + } + def main(args: Array[String]): Unit = { val log: Logger = LoggerFactory.getLogger(getClass) val conf: SparkConf = new SparkConf() @@ -37,6 +46,8 @@ object SparkConvertObjectToJson { log.info(s"objectType -> $objectType") val scholixUpdatePath = parser.get("scholixUpdatePath") log.info(s"scholixUpdatePath -> $scholixUpdatePath") + val maxPidNumberFilter = parser.get("maxPidNumberFilter") + log.info(s"maxPidNumberFilter -> $maxPidNumberFilter") implicit val scholixEncoder: Encoder[Scholix] = Encoders.kryo[Scholix] implicit val summaryEncoder: Encoder[ScholixSummary] = Encoders.kryo[ScholixSummary] @@ -47,12 +58,22 @@ object SparkConvertObjectToJson { case "scholix" => log.info("Serialize Scholix") val d: Dataset[Scholix] = spark.read.load(sourcePath).as[Scholix] - val u: Dataset[Scholix] = spark.read.load(s"$scholixUpdatePath/scholix").as[Scholix] - d.union(u) - .repartition(8000) - .map(s => mapper.writeValueAsString(s))(Encoders.STRING) - .rdd - .saveAsTextFile(targetPath, classOf[GzipCodec]) +// val u: Dataset[Scholix] = spark.read.load(s"$scholixUpdatePath/scholix").as[Scholix] + if (maxPidNumberFilter != null && toInt(maxPidNumberFilter).isDefined) { + val mp = toInt(maxPidNumberFilter).get + d + .filter(s => (s.getSource.getIdentifier.size() <= mp) && (s.getTarget.getIdentifier.size() <= mp)) + .map(s => mapper.writeValueAsString(s))(Encoders.STRING) + .rdd + .saveAsTextFile(targetPath, classOf[GzipCodec]) + } else { + d + .repartition(8000) + .map(s => mapper.writeValueAsString(s))(Encoders.STRING) + .rdd + .saveAsTextFile(targetPath, classOf[GzipCodec]) + } + case "summary" => log.info("Serialize Summary") val d: Dataset[ScholixSummary] = spark.read.load(sourcePath).as[ScholixSummary] diff --git a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala index bd970a5cf..f72f8dd16 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala @@ -4,9 +4,11 @@ import com.fasterxml.jackson.databind.ObjectMapper import eu.dnetlib.dhp.application.ArgumentApplicationParser import eu.dnetlib.dhp.schema.oaf.{OtherResearchProduct, Publication, Relation, Result, Software, Dataset => OafDataset} import org.apache.commons.io.IOUtils +import org.apache.commons.lang3.StringUtils import org.apache.spark.SparkConf import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession} import org.slf4j.{Logger, LoggerFactory} + import scala.collection.JavaConverters._ object SparkConvertRDDtoDataset { @@ -34,6 +36,9 @@ object SparkConvertRDDtoDataset { val t = parser.get("targetPath") log.info(s"targetPath -> $t") + val filterRelation = parser.get("filterRelation") + log.info(s"filterRelation -> $filterRelation") + val entityPath = s"$t/entities" val relPath = s"$t/relation" val mapper = new ObjectMapper() @@ -94,28 +99,46 @@ object SparkConvertRDDtoDataset { log.info("Converting Relation") - val relationSemanticFilter = List( -// "cites", -// "iscitedby", - "merges", - "ismergedin", - "HasAmongTopNSimilarDocuments", - "IsAmongTopNSimilarDocuments" - ) + if (filterRelation != null && StringUtils.isNoneBlank(filterRelation)) { - val rddRelation = spark.sparkContext - .textFile(s"$sourcePath/relation") - .map(s => mapper.readValue(s, classOf[Relation])) - .filter(r => r.getDataInfo != null && r.getDataInfo.getDeletedbyinference == false) - .filter(r => r.getSource.startsWith("50") && r.getTarget.startsWith("50")) - //filter OpenCitations relations - .filter(r => - r.getCollectedfrom != null && r.getCollectedfrom.size() > 0 && !r.getCollectedfrom.asScala.exists(k => - "opencitations".equalsIgnoreCase(k.getValue) + val rddRelation = spark.sparkContext + .textFile(s"$sourcePath/relation") + .map(s => mapper.readValue(s, classOf[Relation])) + .filter(r => r.getDataInfo != null && r.getDataInfo.getDeletedbyinference == false) + .filter(r => r.getSource.startsWith("50") && r.getTarget.startsWith("50")) + //filter OpenCitations relations + .filter(r => + r.getCollectedfrom != null && r.getCollectedfrom.size() > 0 && !r.getCollectedfrom.asScala.exists(k => + "opencitations".equalsIgnoreCase(k.getValue) + ) ) + .filter(r => r.getRelClass != null && r.getRelClass.equalsIgnoreCase(filterRelation)) + spark.createDataset(rddRelation).as[Relation].write.mode(SaveMode.Overwrite).save(s"$relPath") + } else { + + val relationSemanticFilter = List( + // "cites", + // "iscitedby", + "merges", + "ismergedin", + "HasAmongTopNSimilarDocuments", + "IsAmongTopNSimilarDocuments" ) - .filter(r => !relationSemanticFilter.exists(k => k.equalsIgnoreCase(r.getRelClass))) - spark.createDataset(rddRelation).as[Relation].write.mode(SaveMode.Overwrite).save(s"$relPath") + + val rddRelation = spark.sparkContext + .textFile(s"$sourcePath/relation") + .map(s => mapper.readValue(s, classOf[Relation])) + .filter(r => r.getDataInfo != null && r.getDataInfo.getDeletedbyinference == false) + .filter(r => r.getSource.startsWith("50") && r.getTarget.startsWith("50")) + //filter OpenCitations relations + .filter(r => + r.getCollectedfrom != null && r.getCollectedfrom.size() > 0 && !r.getCollectedfrom.asScala.exists(k => + "opencitations".equalsIgnoreCase(k.getValue) + ) + ) + .filter(r => !relationSemanticFilter.exists(k => k.equalsIgnoreCase(r.getRelClass))) + spark.createDataset(rddRelation).as[Relation].write.mode(SaveMode.Overwrite).save(s"$relPath") + } } } From 65cc736e2fb2848bef81f47715370b0f6a9064a4 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 20 Jul 2022 17:05:56 +0200 Subject: [PATCH 107/214] [Clean Country] first implementation to remove country NL from results collected from NARCIS when doi starts with mendely prefix --- .../oa/graph/clean/CleanCountrySparkJob.java | 128 +++++++++++++++++ .../graph/input_clean_country_parameters.json | 43 ++++++ .../dhp/oa/graph/clean/CleanCountryTest.java | 135 ++++++++++++++++++ .../clean/publication_clean_country.json | 7 + 4 files changed, 313 insertions(+) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountrySparkJob.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_country_parameters.json create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountryTest.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/publication_clean_country.json diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountrySparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountrySparkJob.java new file mode 100644 index 000000000..ec82d385c --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountrySparkJob.java @@ -0,0 +1,128 @@ +package eu.dnetlib.dhp.oa.graph.clean; + +/** + * @author miriam.baglioni + * @Date 20/07/22 + */ + +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.oaf.Result; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.FilterFunction; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.Serializable; +import java.util.Optional; +import java.util.stream.Collectors; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + + +public class CleanCountrySparkJob implements Serializable { + private static final Logger log = LoggerFactory.getLogger(CleanCountrySparkJob.class); + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + public static void main(String[] args) throws Exception { + + String jsonConfiguration = IOUtils + .toString( + CleanContextSparkJob.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/input_clean_country_parameters.json")); + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + String inputPath = parser.get("inputPath"); + log.info("inputPath: {}", inputPath); + + String workingPath = parser.get("workingPath"); + log.info("workingPath: {}", workingPath); + + String country = parser.get("country"); + log.info("country: {}", country); + + String verifyParam = parser.get("verifyParam"); + log.info("verifyParam: {}", verifyParam); + + String collectedfrom = parser.get("collectedfrom"); + log.info("collectedfrom: {}", collectedfrom); + + String graphTableClassName = parser.get("graphTableClassName"); + log.info("graphTableClassName: {}", graphTableClassName); + + Class entityClazz = (Class) Class.forName(graphTableClassName); + + SparkConf conf = new SparkConf(); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + + cleanCountry(spark, country, verifyParam, inputPath, entityClazz, workingPath,collectedfrom); + }); + } + + private static void cleanCountry(SparkSession spark, String country, String verifyParam, + String inputPath, Class entityClazz, String workingPath, String collectedfrom) { + Dataset res = spark + .read() + .textFile(inputPath) + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, entityClazz), + Encoders.bean(entityClazz)) + ; + + res.map((MapFunction) r -> { + for(StructuredProperty p: r.getPid()){ + if (p.getQualifier().getClassid().equalsIgnoreCase("doi") && + p.getValue().startsWith(verifyParam) && r.getCollectedfrom().stream().anyMatch(cf -> cf.getValue().equalsIgnoreCase(collectedfrom))) { + + r + .setCountry( + r + .getCountry() + .stream() + .filter( + c -> !c.getClassid() + .equalsIgnoreCase(country)) + .collect(Collectors.toList())); + } + } + + return r; + }, Encoders.bean(entityClazz)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingPath); + + spark + .read() + .textFile(workingPath) + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, entityClazz), + Encoders.bean(entityClazz)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(inputPath); + } + +} + diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_country_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_country_parameters.json new file mode 100644 index 000000000..e46f7b6da --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_country_parameters.json @@ -0,0 +1,43 @@ +[ + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "when true will stop SparkSession after job execution", + "paramRequired": false + }, + { + "paramName": "in", + "paramLongName": "inputPath", + "paramDescription": "the path to the graph data dump to read", + "paramRequired": true + }, + { + "paramName": "wp", + "paramLongName": "workingPath", + "paramDescription": "the path to store the output graph", + "paramRequired": true + }, + { + "paramName": "c", + "paramLongName": "country", + "paramDescription": "the id of the context to be removed", + "paramRequired": true + }, + { + "paramName": "class", + "paramLongName": "graphTableClassName", + "paramDescription": "class name moelling the graph table", + "paramRequired": true + },{ + "paramName": "vf", + "paramLongName": "verifyParam", + "paramDescription": "the parameter to be verified to remove the country", + "paramRequired": true +}, + { + "paramName": "cf", + "paramLongName": "collectedfrom", + "paramDescription": "the collectedfrom value for which we should apply the cleaning", + "paramRequired": true + } +] diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountryTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountryTest.java new file mode 100644 index 000000000..f9dad9fcf --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountryTest.java @@ -0,0 +1,135 @@ +package eu.dnetlib.dhp.oa.graph.clean; +/** + * @author miriam.baglioni + * @Date 20/07/22 + */ + +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.oa.graph.dump.DumpJobTest; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import org.apache.commons.io.FileUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.List; + + +public class CleanCountryTest { + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path workingDir; + + private static final Logger log = LoggerFactory.getLogger(CleanContextTest.class); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files.createTempDirectory(DumpJobTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(DumpJobTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(DumpJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + public void testResultClean() throws Exception { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/clean/publication_clean_country.json") + .getPath(); + final String prefix = "gcube "; + + spark + .read() + .textFile(sourcePath) + .map( + (MapFunction) r -> OBJECT_MAPPER.readValue(r, Publication.class), + Encoders.bean(Publication.class)) + .write() + .json(workingDir.toString() + "/publication"); + + CleanCountrySparkJob.main(new String[] { + "--isSparkSessionManaged", Boolean.FALSE.toString(), + "--inputPath", workingDir.toString() + "/publication", + "-graphTableClassName", Publication.class.getCanonicalName(), + "-workingPath", workingDir.toString() + "/working", + "-country", "NL", + "-verifyParam", "10.17632", + "-collectedfrom", "NARCIS" + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/publication") + .map(item -> OBJECT_MAPPER.readValue(item, Publication.class)); + + Assertions.assertEquals(7, tmp.count()); + + // original result with NL country and doi starting with Mendely prefix, but not collectedfrom NARCIS + Assertions + .assertEquals( + 1, + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::0224aae28af558f21768dbc6439c7a95")) + .collect() + .get(0) + .getCountry() + .size()); + + // original result with NL country and pid not starting with Mendely prefix + Assertions + .assertEquals( + 1, + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")) + .collect() + .get(0) + .getCountry() + .size()); + + // original result with NL country and doi starting with Mendely prefix and collectedfrom NARCIS + Assertions + .assertEquals( + 0, + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")) + .collect() + .get(0) + .getCountry() + .size()); + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/publication_clean_country.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/publication_clean_country.json new file mode 100644 index 000000000..ebceecff9 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/publication_clean_country.json @@ -0,0 +1,7 @@ +{"author":[],"bestaccessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"collectedfrom":[{"dataInfo":null,"key":"10|openaire____::c6df70599aa984f16ee52b4b86d2e89f","value":"DANS (Data Archiving and Networked 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Removed also the deletion of EOSC Jupyter Notebook from subject since now the criteria are searchd for in a different place --- .../eu/dnetlib/dhp/bulktag/SparkEoscTag.java | 82 ++++++------------- pom.xml | 2 +- 2 files changed, 27 insertions(+), 57 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java index b9de5dd11..d31934081 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java @@ -28,28 +28,7 @@ import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; public class SparkEoscTag { private static final Logger log = LoggerFactory.getLogger(SparkEoscTag.class); public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - public static final Qualifier EOSC_QUALIFIER = OafMapperUtils - .qualifier( - "EOSC", - "European Open Science Cloud", - ModelConstants.DNET_SUBJECT_TYPOLOGIES, ModelConstants.DNET_SUBJECT_TYPOLOGIES); - public static final DataInfo EOSC_DATAINFO = OafMapperUtils - .dataInfo( - false, "propagation", true, false, - OafMapperUtils - .qualifier( - "propagation:subject", "Inferred by OpenAIRE", - ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS), - "0.9"); - public final static StructuredProperty EOSC_NOTEBOOK = OafMapperUtils - .structuredProperty( - "EOSC::Jupyter Notebook", EOSC_QUALIFIER, EOSC_DATAINFO); - public final static StructuredProperty EOSC_GALAXY = OafMapperUtils - .structuredProperty( - "EOSC::Galaxy Workflow", EOSC_QUALIFIER, EOSC_DATAINFO); - public final static StructuredProperty EOSC_TWITTER = OafMapperUtils - .structuredProperty( - "EOSC::Twitter Data", EOSC_QUALIFIER, EOSC_DATAINFO); + public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils @@ -84,29 +63,30 @@ public class SparkEoscTag { }); } + public static EoscIfGuidelines newInstance(String code, String label, String url, String semantics){ + EoscIfGuidelines eig = new EoscIfGuidelines(); + eig.setCode( code); + eig.setLabel(label); + eig.setUrl(url); + eig.setSemanticRelation(semantics); + return eig; + + } private static void execEoscTag(SparkSession spark, String inputPath, String workingPath) { readPath(spark, inputPath + "/software", Software.class) .map((MapFunction) s -> { - List sbject; - if (!Optional.ofNullable(s.getSubject()).isPresent()) - s.setSubject(new ArrayList<>()); - sbject = s.getSubject(); if (containsCriteriaNotebook(s)) { - sbject.add(EOSC_NOTEBOOK); - if (sbject.stream().anyMatch(sb -> sb.getValue().equals("EOSC Jupyter Notebook"))) { - sbject = sbject.stream().map(sb -> { - if (sb.getValue().equals("EOSC Jupyter Notebook")) { - return null; - } - return sb; - }).filter(Objects::nonNull).collect(Collectors.toList()); - s.setSubject(sbject); - } + if (!Optional.ofNullable(s.getEoscifguidelines()).isPresent()) + s.setEoscifguidelines(new ArrayList<>()); + s.getEoscifguidelines().add(newInstance("EOSC::Jupyter Notebook", "EOSC::Jupyter Notebook", "", "compliesWith")); } if (containsCriteriaGalaxy(s)) { - sbject.add(EOSC_GALAXY); + if (!Optional.ofNullable(s.getEoscifguidelines()).isPresent()) + s.setEoscifguidelines(new ArrayList<>()); + + s.getEoscifguidelines().add(newInstance("EOSC::Galaxy Workflow", "EOSC::Galaxy Workflow", "", "compliesWith")); } return s; }, Encoders.bean(Software.class)) @@ -124,14 +104,14 @@ public class SparkEoscTag { readPath(spark, inputPath + "/otherresearchproduct", OtherResearchProduct.class) .map((MapFunction) orp -> { List sbject; - if (!Optional.ofNullable(orp.getSubject()).isPresent()) - orp.setSubject(new ArrayList<>()); - sbject = orp.getSubject(); + if (!Optional.ofNullable(orp.getEoscifguidelines()).isPresent()) + orp.setEoscifguidelines(new ArrayList<>()); + if (containsCriteriaGalaxy(orp)) { - sbject.add(EOSC_GALAXY); + orp.getEoscifguidelines().add(newInstance("EOSC::Galaxy Workflow", "EOSC::Galaxy Workflow", "", "compliesWith")); } if (containscriteriaTwitter(orp)) { - sbject.add(EOSC_TWITTER); + orp.getEoscifguidelines().add(newInstance("EOSC::Twitter Data", "EOSC::Twitter Data", "", "compliesWith")); } return orp; }, Encoders.bean(OtherResearchProduct.class)) @@ -149,11 +129,10 @@ public class SparkEoscTag { readPath(spark, inputPath + "/dataset", Dataset.class) .map((MapFunction) d -> { List sbject; - if (!Optional.ofNullable(d.getSubject()).isPresent()) - d.setSubject(new ArrayList<>()); - sbject = d.getSubject(); + if (!Optional.ofNullable(d.getEoscifguidelines()).isPresent()) + d.setEoscifguidelines(new ArrayList<>()); if (containscriteriaTwitter(d)) { - sbject.add(EOSC_TWITTER); + d.getEoscifguidelines().add(newInstance("EOSC::Twitter Data", "EOSC::Twitter Data", "", "compliesWith")); } return d; }, Encoders.bean(Dataset.class)) @@ -212,13 +191,6 @@ public class SparkEoscTag { return false; } - private static Set getSubjects(List s) { - Set subjects = new HashSet<>(); - s.stream().forEach(sbj -> subjects.addAll(Arrays.asList(sbj.getValue().toLowerCase().split(" ")))); - s.stream().forEach(sbj -> subjects.add(sbj.getValue().toLowerCase())); - return subjects; - } - private static Set getWordsSP(List elem) { Set words = new HashSet<>(); Optional @@ -242,9 +214,7 @@ public class SparkEoscTag { t -> words .addAll( Arrays.asList(t.getValue().toLowerCase().replaceAll("[^a-zA-Z ]", "").split(" "))))); -// elem -// .forEach( -// t -> words.addAll(Arrays.asList(t.getValue().toLowerCase().replaceAll("[^a-zA-Z ]", "").split(" ")))); + return words; } diff --git a/pom.xml b/pom.xml index 54070f654..973bc3773 100644 --- a/pom.xml +++ b/pom.xml @@ -801,7 +801,7 @@ 3.3.3 3.4.2 [2.12,3.0) - [2.12.0] + [2.12.2-SNAPSHOT] [4.0.3] [6.0.5] [3.1.6] From 5f651f231650d0e2547bfdf9f7969611e5d43d85 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Thu, 21 Jul 2022 10:11:48 +0200 Subject: [PATCH 109/214] changed filter relation on SubRelType --- .../eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala index f72f8dd16..0073afff5 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala @@ -112,13 +112,11 @@ object SparkConvertRDDtoDataset { "opencitations".equalsIgnoreCase(k.getValue) ) ) - .filter(r => r.getRelClass != null && r.getRelClass.equalsIgnoreCase(filterRelation)) + .filter(r => r.getSubRelType != null && r.getSubRelType.equalsIgnoreCase(filterRelation)) spark.createDataset(rddRelation).as[Relation].write.mode(SaveMode.Overwrite).save(s"$relPath") } else { val relationSemanticFilter = List( - // "cites", - // "iscitedby", "merges", "ismergedin", "HasAmongTopNSimilarDocuments", From 5143a802320b3a64a16b09f298f005d4fbce78e9 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 21 Jul 2022 11:56:51 +0200 Subject: [PATCH 110/214] [EOSC TAG] modification of test class to align with new element --- .../dnetlib/dhp/bulktag/EOSCTagJobTest.java | 174 ++++++++++++++++-- 1 file changed, 155 insertions(+), 19 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java index 1ea254157..b1c0cbb84 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java @@ -126,8 +126,9 @@ public class EOSCTagJobTest { .assertEquals( 4, tmp + .filter(s -> s.getEoscifguidelines()!= null) .filter( - s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook"))) + s -> s.getEoscifguidelines().stream().anyMatch(eig -> eig.getCode().equals("EOSC::Jupyter Notebook"))) .count()); Assertions @@ -136,17 +137,36 @@ public class EOSCTagJobTest { .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) .collect() .get(0) - .getSubject() + .getEoscifguidelines() .size()); + + Assertions + .assertEquals( + 1, tmp + .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) + .collect() + .get(0) + .getSubject() + .size()); Assertions .assertTrue( tmp .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) .collect() .get(0) - .getSubject() + .getEoscifguidelines() .stream() - .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); + .anyMatch(s -> s.getCode().equals("EOSC::Jupyter Notebook"))); + + Assertions + .assertFalse( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) + .collect() + .get(0) + .getSubject() + .stream() + .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); Assertions .assertEquals( @@ -166,16 +186,23 @@ public class EOSCTagJobTest { .stream() .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); + Assertions.assertTrue(tmp + .filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11")) + .collect() + .get(0) + .getEoscifguidelines() == null + ); + Assertions .assertEquals( - 9, tmp + 8, tmp .filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")) .collect() .get(0) .getSubject() .size()); Assertions - .assertTrue( + .assertFalse( tmp .filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")) .collect() @@ -183,6 +210,23 @@ public class EOSCTagJobTest { .getSubject() .stream() .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); + Assertions + .assertEquals( + 1, tmp + .filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")) + .collect() + .get(0) + .getEoscifguidelines() + .size()); + Assertions + .assertTrue( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")) + .collect() + .get(0) + .getEoscifguidelines() + .stream() + .anyMatch(s -> s.getCode().equals("EOSC::Jupyter Notebook"))); Assertions .assertEquals( @@ -201,17 +245,24 @@ public class EOSCTagJobTest { .getSubject() .stream() .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); + Assertions.assertTrue( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::5aec1186054301b66c0c5dc35972a589")) + .collect() + .get(0) + .getEoscifguidelines() == null + ); Assertions .assertEquals( - 9, tmp + 8, tmp .filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0")) .collect() .get(0) .getSubject() .size()); Assertions - .assertTrue( + .assertFalse( tmp .filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0")) .collect() @@ -219,14 +270,27 @@ public class EOSCTagJobTest { .getSubject() .stream() .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); + Assertions.assertEquals(1, + tmp + .filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0")) + .collect() + .get(0) + .getEoscifguidelines() + .size()); + Assertions.assertTrue(tmp + .filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0")) + .collect() + .get(0) + .getEoscifguidelines() + .stream() + .anyMatch(s -> s.getCode().equals("EOSC::Jupyter Notebook"))); List subjects = tmp .filter(sw -> sw.getId().equals("50|od______1582::6e7a9b21a2feef45673890432af34244")) .collect() .get(0) .getSubject(); - Assertions.assertEquals(8, subjects.size()); - Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); + Assertions.assertEquals(7, subjects.size()); Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("jupyter"))); Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("Modeling and Simulation"))); Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("structure granulaire"))); @@ -250,6 +314,14 @@ public class EOSCTagJobTest { .filter( ds -> ds.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook"))) .count()); + Assertions + .assertEquals( + 0, sc + .textFile(workingDir.toString() + "/input/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)) + .filter( + ds -> ds.getEoscifguidelines().stream().anyMatch(eig -> eig.getCode().equals("EOSC::Jupyter Notebook"))) + .count()); Assertions .assertEquals( @@ -264,9 +336,18 @@ public class EOSCTagJobTest { .textFile(workingDir.toString() + "/input/otherresearchproduct") .map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)) .filter( - ds -> ds.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook"))) + orp -> orp.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook"))) .count()); + Assertions + .assertEquals( + 0, sc + .textFile(workingDir.toString() + "/input/otherresearchproduct") + .map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)) + .filter( + orp -> orp.getSubject().stream().anyMatch(eig -> eig.getValue().equals("EOSC::Jupyter Notebook"))) + .count()); + // spark.stop(); } @@ -326,22 +407,37 @@ public class EOSCTagJobTest { Assertions .assertEquals( - 1, + 0, tmp .filter( s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Galaxy Workflow"))) .count()); + Assertions + .assertEquals( + 1, + tmp + .filter( + s -> s.getEoscifguidelines()!=null) + .count()); + Assertions + .assertEquals( + 1, + tmp + .filter( + s -> s.getEoscifguidelines()!=null) + .filter(s -> s.getEoscifguidelines().stream().anyMatch(eig -> eig.getCode().equals("EOSC::Galaxy Workflow"))) + .count()); Assertions .assertEquals( - 2, tmp + 1, tmp .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) .collect() .get(0) .getSubject() .size()); Assertions - .assertTrue( + .assertFalse( tmp .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) .collect() @@ -350,6 +446,19 @@ public class EOSCTagJobTest { .stream() .anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); + Assertions.assertEquals(1, tmp + .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) + .collect() + .get(0) + .getEoscifguidelines() + .size() ); + Assertions.assertTrue(tmp + .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) + .collect() + .get(0) + .getEoscifguidelines() + .stream().anyMatch(eig -> eig.getCode().equals("EOSC::Galaxy Workflow"))); + Assertions .assertEquals( 5, tmp @@ -385,22 +494,26 @@ public class EOSCTagJobTest { Assertions .assertEquals( - 1, + 0, orp .filter( s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Galaxy Workflow"))) .count()); + orp.foreach(o-> System.out.println(OBJECT_MAPPER.writeValueAsString(o))); + + Assertions.assertEquals(1, orp.filter(o -> o.getEoscifguidelines() != null) + .filter(o -> o.getEoscifguidelines().stream().anyMatch(eig -> eig.getCode().equals("EOSC::Galaxy Workflow"))).count()); Assertions .assertEquals( - 3, orp + 2, orp .filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07")) .collect() .get(0) .getSubject() .size()); Assertions - .assertTrue( + .assertFalse( orp .filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07")) .collect() @@ -408,6 +521,23 @@ public class EOSCTagJobTest { .getSubject() .stream() .anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); + Assertions + .assertEquals( + 1, orp + .filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07")) + .collect() + .get(0) + .getEoscifguidelines() + .size()); + Assertions + .assertTrue( + orp + .filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07")) + .collect() + .get(0) + .getEoscifguidelines() + .stream() + .anyMatch(s -> s.getCode().equals("EOSC::Galaxy Workflow"))); Assertions .assertEquals( @@ -516,10 +646,16 @@ public class EOSCTagJobTest { Assertions .assertEquals( - 3, + 0, orp .filter(s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Twitter Data"))) .count()); + Assertions + .assertEquals( + 3, + orp + .filter(s -> s.getEoscifguidelines().stream().anyMatch(eig -> eig.getCode().equals("EOSC::Twitter Data"))) + .count()); JavaRDD dats = sc .textFile(workingDir.toString() + "/input/dataset") @@ -531,7 +667,7 @@ public class EOSCTagJobTest { .assertEquals( 3, dats - .filter(s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Twitter Data"))) + .filter(s -> s.getEoscifguidelines().stream().anyMatch(eig -> eig.getCode().equals("EOSC::Twitter Data"))) .count()); } From 56d09e6348d63d531250ea6f075c1d306c07ed66 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 21 Jul 2022 14:36:48 +0200 Subject: [PATCH 111/214] [EOSC TAG] before adding the tag added a step to verify the same tag is not already present --- .../eu/dnetlib/dhp/bulktag/SparkEoscTag.java | 21 ++++++++++++------- 1 file changed, 14 insertions(+), 7 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java index d31934081..c5ed0b45c 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java @@ -80,13 +80,14 @@ public class SparkEoscTag { if (containsCriteriaNotebook(s)) { if (!Optional.ofNullable(s.getEoscifguidelines()).isPresent()) s.setEoscifguidelines(new ArrayList<>()); - s.getEoscifguidelines().add(newInstance("EOSC::Jupyter Notebook", "EOSC::Jupyter Notebook", "", "compliesWith")); + addEIG(s.getEoscifguidelines(), "EOSC::Jupyter Notebook", "EOSC::Jupyter Notebook", "", "compliesWith"); + } if (containsCriteriaGalaxy(s)) { if (!Optional.ofNullable(s.getEoscifguidelines()).isPresent()) s.setEoscifguidelines(new ArrayList<>()); - s.getEoscifguidelines().add(newInstance("EOSC::Galaxy Workflow", "EOSC::Galaxy Workflow", "", "compliesWith")); + addEIG(s.getEoscifguidelines(),"EOSC::Galaxy Workflow", "EOSC::Galaxy Workflow", "", "compliesWith"); } return s; }, Encoders.bean(Software.class)) @@ -103,15 +104,15 @@ public class SparkEoscTag { readPath(spark, inputPath + "/otherresearchproduct", OtherResearchProduct.class) .map((MapFunction) orp -> { - List sbject; + if (!Optional.ofNullable(orp.getEoscifguidelines()).isPresent()) orp.setEoscifguidelines(new ArrayList<>()); if (containsCriteriaGalaxy(orp)) { - orp.getEoscifguidelines().add(newInstance("EOSC::Galaxy Workflow", "EOSC::Galaxy Workflow", "", "compliesWith")); + addEIG(orp.getEoscifguidelines(),"EOSC::Galaxy Workflow", "EOSC::Galaxy Workflow", "", "compliesWith"); } if (containscriteriaTwitter(orp)) { - orp.getEoscifguidelines().add(newInstance("EOSC::Twitter Data", "EOSC::Twitter Data", "", "compliesWith")); + addEIG(orp.getEoscifguidelines(),"EOSC::Twitter Data", "EOSC::Twitter Data", "", "compliesWith"); } return orp; }, Encoders.bean(OtherResearchProduct.class)) @@ -128,11 +129,11 @@ public class SparkEoscTag { readPath(spark, inputPath + "/dataset", Dataset.class) .map((MapFunction) d -> { - List sbject; + if (!Optional.ofNullable(d.getEoscifguidelines()).isPresent()) d.setEoscifguidelines(new ArrayList<>()); if (containscriteriaTwitter(d)) { - d.getEoscifguidelines().add(newInstance("EOSC::Twitter Data", "EOSC::Twitter Data", "", "compliesWith")); + addEIG(d.getEoscifguidelines(),"EOSC::Twitter Data", "EOSC::Twitter Data", "", "compliesWith"); } return d; }, Encoders.bean(Dataset.class)) @@ -148,6 +149,12 @@ public class SparkEoscTag { .json(inputPath + "/dataset"); } + private static void addEIG(List eoscifguidelines, String code, String label, String url, String sem) { + if (!eoscifguidelines.stream().anyMatch(eig -> eig.getCode().equals(code))) + eoscifguidelines.add(newInstance(code, label, url, sem)); + } + + private static boolean containscriteriaTwitter(Result r) { Set words = getWordsSP(r.getTitle()); words.addAll(getWordsF(r.getDescription())); From 3be036f290f3cb569465cf9566557e51c4660288 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 21 Jul 2022 14:45:43 +0200 Subject: [PATCH 112/214] [EOSC TAG] refactoring after compilation --- .../eu/dnetlib/dhp/bulktag/SparkEoscTag.java | 25 +- .../dnetlib/dhp/bulktag/EOSCTagJobTest.java | 284 ++++++++++-------- 2 files changed, 178 insertions(+), 131 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java index c5ed0b45c..730e8a3fe 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java @@ -29,7 +29,6 @@ public class SparkEoscTag { private static final Logger log = LoggerFactory.getLogger(SparkEoscTag.class); public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils .toString( @@ -63,15 +62,16 @@ public class SparkEoscTag { }); } - public static EoscIfGuidelines newInstance(String code, String label, String url, String semantics){ + public static EoscIfGuidelines newInstance(String code, String label, String url, String semantics) { EoscIfGuidelines eig = new EoscIfGuidelines(); - eig.setCode( code); + eig.setCode(code); eig.setLabel(label); eig.setUrl(url); eig.setSemanticRelation(semantics); return eig; } + private static void execEoscTag(SparkSession spark, String inputPath, String workingPath) { readPath(spark, inputPath + "/software", Software.class) @@ -80,14 +80,17 @@ public class SparkEoscTag { if (containsCriteriaNotebook(s)) { if (!Optional.ofNullable(s.getEoscifguidelines()).isPresent()) s.setEoscifguidelines(new ArrayList<>()); - addEIG(s.getEoscifguidelines(), "EOSC::Jupyter Notebook", "EOSC::Jupyter Notebook", "", "compliesWith"); + addEIG( + s.getEoscifguidelines(), "EOSC::Jupyter Notebook", "EOSC::Jupyter Notebook", "", + "compliesWith"); } if (containsCriteriaGalaxy(s)) { if (!Optional.ofNullable(s.getEoscifguidelines()).isPresent()) s.setEoscifguidelines(new ArrayList<>()); - addEIG(s.getEoscifguidelines(),"EOSC::Galaxy Workflow", "EOSC::Galaxy Workflow", "", "compliesWith"); + addEIG( + s.getEoscifguidelines(), "EOSC::Galaxy Workflow", "EOSC::Galaxy Workflow", "", "compliesWith"); } return s; }, Encoders.bean(Software.class)) @@ -109,10 +112,12 @@ public class SparkEoscTag { orp.setEoscifguidelines(new ArrayList<>()); if (containsCriteriaGalaxy(orp)) { - addEIG(orp.getEoscifguidelines(),"EOSC::Galaxy Workflow", "EOSC::Galaxy Workflow", "", "compliesWith"); + addEIG( + orp.getEoscifguidelines(), "EOSC::Galaxy Workflow", "EOSC::Galaxy Workflow", "", + "compliesWith"); } if (containscriteriaTwitter(orp)) { - addEIG(orp.getEoscifguidelines(),"EOSC::Twitter Data", "EOSC::Twitter Data", "", "compliesWith"); + addEIG(orp.getEoscifguidelines(), "EOSC::Twitter Data", "EOSC::Twitter Data", "", "compliesWith"); } return orp; }, Encoders.bean(OtherResearchProduct.class)) @@ -133,7 +138,7 @@ public class SparkEoscTag { if (!Optional.ofNullable(d.getEoscifguidelines()).isPresent()) d.setEoscifguidelines(new ArrayList<>()); if (containscriteriaTwitter(d)) { - addEIG(d.getEoscifguidelines(),"EOSC::Twitter Data", "EOSC::Twitter Data", "", "compliesWith"); + addEIG(d.getEoscifguidelines(), "EOSC::Twitter Data", "EOSC::Twitter Data", "", "compliesWith"); } return d; }, Encoders.bean(Dataset.class)) @@ -149,12 +154,12 @@ public class SparkEoscTag { .json(inputPath + "/dataset"); } - private static void addEIG(List eoscifguidelines, String code, String label, String url, String sem) { + private static void addEIG(List eoscifguidelines, String code, String label, String url, + String sem) { if (!eoscifguidelines.stream().anyMatch(eig -> eig.getCode().equals(code))) eoscifguidelines.add(newInstance(code, label, url, sem)); } - private static boolean containscriteriaTwitter(Result r) { Set words = getWordsSP(r.getTitle()); words.addAll(getWordsF(r.getDescription())); diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java index b1c0cbb84..5f47da10e 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java @@ -126,9 +126,12 @@ public class EOSCTagJobTest { .assertEquals( 4, tmp - .filter(s -> s.getEoscifguidelines()!= null) + .filter(s -> s.getEoscifguidelines() != null) .filter( - s -> s.getEoscifguidelines().stream().anyMatch(eig -> eig.getCode().equals("EOSC::Jupyter Notebook"))) + s -> s + .getEoscifguidelines() + .stream() + .anyMatch(eig -> eig.getCode().equals("EOSC::Jupyter Notebook"))) .count()); Assertions @@ -141,13 +144,13 @@ public class EOSCTagJobTest { .size()); Assertions - .assertEquals( - 1, tmp - .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) - .collect() - .get(0) - .getSubject() - .size()); + .assertEquals( + 1, tmp + .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) + .collect() + .get(0) + .getSubject() + .size()); Assertions .assertTrue( tmp @@ -159,14 +162,14 @@ public class EOSCTagJobTest { .anyMatch(s -> s.getCode().equals("EOSC::Jupyter Notebook"))); Assertions - .assertFalse( - tmp - .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) - .collect() - .get(0) - .getSubject() - .stream() - .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); + .assertFalse( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) + .collect() + .get(0) + .getSubject() + .stream() + .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); Assertions .assertEquals( @@ -186,12 +189,13 @@ public class EOSCTagJobTest { .stream() .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); - Assertions.assertTrue(tmp - .filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11")) - .collect() - .get(0) - .getEoscifguidelines() == null - ); + Assertions + .assertTrue( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11")) + .collect() + .get(0) + .getEoscifguidelines() == null); Assertions .assertEquals( @@ -211,22 +215,22 @@ public class EOSCTagJobTest { .stream() .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); Assertions - .assertEquals( - 1, tmp - .filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")) - .collect() - .get(0) - .getEoscifguidelines() - .size()); + .assertEquals( + 1, tmp + .filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")) + .collect() + .get(0) + .getEoscifguidelines() + .size()); Assertions - .assertTrue( - tmp - .filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")) - .collect() - .get(0) - .getEoscifguidelines() - .stream() - .anyMatch(s -> s.getCode().equals("EOSC::Jupyter Notebook"))); + .assertTrue( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")) + .collect() + .get(0) + .getEoscifguidelines() + .stream() + .anyMatch(s -> s.getCode().equals("EOSC::Jupyter Notebook"))); Assertions .assertEquals( @@ -245,13 +249,13 @@ public class EOSCTagJobTest { .getSubject() .stream() .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); - Assertions.assertTrue( + Assertions + .assertTrue( tmp - .filter(sw -> sw.getId().equals("50|od______1582::5aec1186054301b66c0c5dc35972a589")) - .collect() - .get(0) - .getEoscifguidelines() == null - ); + .filter(sw -> sw.getId().equals("50|od______1582::5aec1186054301b66c0c5dc35972a589")) + .collect() + .get(0) + .getEoscifguidelines() == null); Assertions .assertEquals( @@ -270,20 +274,24 @@ public class EOSCTagJobTest { .getSubject() .stream() .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); - Assertions.assertEquals(1, + Assertions + .assertEquals( + 1, tmp - .filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0")) - .collect() - .get(0) - .getEoscifguidelines() - .size()); - Assertions.assertTrue(tmp - .filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0")) - .collect() - .get(0) - .getEoscifguidelines() - .stream() - .anyMatch(s -> s.getCode().equals("EOSC::Jupyter Notebook"))); + .filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0")) + .collect() + .get(0) + .getEoscifguidelines() + .size()); + Assertions + .assertTrue( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0")) + .collect() + .get(0) + .getEoscifguidelines() + .stream() + .anyMatch(s -> s.getCode().equals("EOSC::Jupyter Notebook"))); List subjects = tmp .filter(sw -> sw.getId().equals("50|od______1582::6e7a9b21a2feef45673890432af34244")) @@ -315,13 +323,16 @@ public class EOSCTagJobTest { ds -> ds.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook"))) .count()); Assertions - .assertEquals( - 0, sc - .textFile(workingDir.toString() + "/input/dataset") - .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)) - .filter( - ds -> ds.getEoscifguidelines().stream().anyMatch(eig -> eig.getCode().equals("EOSC::Jupyter Notebook"))) - .count()); + .assertEquals( + 0, sc + .textFile(workingDir.toString() + "/input/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)) + .filter( + ds -> ds + .getEoscifguidelines() + .stream() + .anyMatch(eig -> eig.getCode().equals("EOSC::Jupyter Notebook"))) + .count()); Assertions .assertEquals( @@ -336,17 +347,23 @@ public class EOSCTagJobTest { .textFile(workingDir.toString() + "/input/otherresearchproduct") .map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)) .filter( - orp -> orp.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook"))) + orp -> orp + .getSubject() + .stream() + .anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook"))) .count()); Assertions - .assertEquals( - 0, sc - .textFile(workingDir.toString() + "/input/otherresearchproduct") - .map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)) - .filter( - orp -> orp.getSubject().stream().anyMatch(eig -> eig.getValue().equals("EOSC::Jupyter Notebook"))) - .count()); + .assertEquals( + 0, sc + .textFile(workingDir.toString() + "/input/otherresearchproduct") + .map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)) + .filter( + orp -> orp + .getSubject() + .stream() + .anyMatch(eig -> eig.getValue().equals("EOSC::Jupyter Notebook"))) + .count()); // spark.stop(); } @@ -413,20 +430,24 @@ public class EOSCTagJobTest { s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Galaxy Workflow"))) .count()); Assertions - .assertEquals( - 1, - tmp - .filter( - s -> s.getEoscifguidelines()!=null) - .count()); + .assertEquals( + 1, + tmp + .filter( + s -> s.getEoscifguidelines() != null) + .count()); Assertions - .assertEquals( - 1, - tmp - .filter( - s -> s.getEoscifguidelines()!=null) - .filter(s -> s.getEoscifguidelines().stream().anyMatch(eig -> eig.getCode().equals("EOSC::Galaxy Workflow"))) - .count()); + .assertEquals( + 1, + tmp + .filter( + s -> s.getEoscifguidelines() != null) + .filter( + s -> s + .getEoscifguidelines() + .stream() + .anyMatch(eig -> eig.getCode().equals("EOSC::Galaxy Workflow"))) + .count()); Assertions .assertEquals( @@ -446,18 +467,23 @@ public class EOSCTagJobTest { .stream() .anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); - Assertions.assertEquals(1, tmp - .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) - .collect() - .get(0) - .getEoscifguidelines() - .size() ); - Assertions.assertTrue(tmp - .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) - .collect() - .get(0) - .getEoscifguidelines() - .stream().anyMatch(eig -> eig.getCode().equals("EOSC::Galaxy Workflow"))); + Assertions + .assertEquals( + 1, tmp + .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) + .collect() + .get(0) + .getEoscifguidelines() + .size()); + Assertions + .assertTrue( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) + .collect() + .get(0) + .getEoscifguidelines() + .stream() + .anyMatch(eig -> eig.getCode().equals("EOSC::Galaxy Workflow"))); Assertions .assertEquals( @@ -499,10 +525,18 @@ public class EOSCTagJobTest { .filter( s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Galaxy Workflow"))) .count()); - orp.foreach(o-> System.out.println(OBJECT_MAPPER.writeValueAsString(o))); + orp.foreach(o -> System.out.println(OBJECT_MAPPER.writeValueAsString(o))); - Assertions.assertEquals(1, orp.filter(o -> o.getEoscifguidelines() != null) - .filter(o -> o.getEoscifguidelines().stream().anyMatch(eig -> eig.getCode().equals("EOSC::Galaxy Workflow"))).count()); + Assertions + .assertEquals( + 1, orp + .filter(o -> o.getEoscifguidelines() != null) + .filter( + o -> o + .getEoscifguidelines() + .stream() + .anyMatch(eig -> eig.getCode().equals("EOSC::Galaxy Workflow"))) + .count()); Assertions .assertEquals( @@ -522,22 +556,22 @@ public class EOSCTagJobTest { .stream() .anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); Assertions - .assertEquals( - 1, orp - .filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07")) - .collect() - .get(0) - .getEoscifguidelines() - .size()); + .assertEquals( + 1, orp + .filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07")) + .collect() + .get(0) + .getEoscifguidelines() + .size()); Assertions - .assertTrue( - orp - .filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07")) - .collect() - .get(0) - .getEoscifguidelines() - .stream() - .anyMatch(s -> s.getCode().equals("EOSC::Galaxy Workflow"))); + .assertTrue( + orp + .filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07")) + .collect() + .get(0) + .getEoscifguidelines() + .stream() + .anyMatch(s -> s.getCode().equals("EOSC::Galaxy Workflow"))); Assertions .assertEquals( @@ -651,11 +685,15 @@ public class EOSCTagJobTest { .filter(s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Twitter Data"))) .count()); Assertions - .assertEquals( - 3, - orp - .filter(s -> s.getEoscifguidelines().stream().anyMatch(eig -> eig.getCode().equals("EOSC::Twitter Data"))) - .count()); + .assertEquals( + 3, + orp + .filter( + s -> s + .getEoscifguidelines() + .stream() + .anyMatch(eig -> eig.getCode().equals("EOSC::Twitter Data"))) + .count()); JavaRDD dats = sc .textFile(workingDir.toString() + "/input/dataset") @@ -667,7 +705,11 @@ public class EOSCTagJobTest { .assertEquals( 3, dats - .filter(s -> s.getEoscifguidelines().stream().anyMatch(eig -> eig.getCode().equals("EOSC::Twitter Data"))) + .filter( + s -> s + .getEoscifguidelines() + .stream() + .anyMatch(eig -> eig.getCode().equals("EOSC::Twitter Data"))) .count()); } From 317a4a56ef9019bd4cc3280673ec34cc8c5b58d0 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 21 Jul 2022 17:37:48 +0200 Subject: [PATCH 113/214] [EOSC context TAG] first implementation of the logic to tag results imported from datasources registered in the EOSC --- .../dhp/bulktag/eosc/DatasourceMaster.java | 28 ++++ .../eosc/ReadMasterDatasourceFromDB.java | 134 ++++++++++++++++ .../dhp/bulktag/eosc/SparkEoscBulkTag.java | 145 ++++++++++++++++++ pom.xml | 2 +- 4 files changed, 308 insertions(+), 1 deletion(-) create mode 100644 dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/DatasourceMaster.java create mode 100644 dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java create mode 100644 dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/DatasourceMaster.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/DatasourceMaster.java new file mode 100644 index 000000000..537356586 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/DatasourceMaster.java @@ -0,0 +1,28 @@ +package eu.dnetlib.dhp.bulktag.eosc; + +import java.io.Serializable; + +/** + * @author miriam.baglioni + * @Date 21/07/22 + */ +public class DatasourceMaster implements Serializable { + private String datasource; + private String master; + + public String getDatasource() { + return datasource; + } + + public void setDatasource(String datasource) { + this.datasource = datasource; + } + + public String getMaster() { + return master; + } + + public void setMaster(String master) { + this.master = master; + } +} diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java new file mode 100644 index 000000000..7d6964707 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java @@ -0,0 +1,134 @@ + +package eu.dnetlib.dhp.bulktag.eosc; + +/** + * @author miriam.baglioni + * @Date 21/07/22 + */ + +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.DbClient; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.common.RelationInverse; +import eu.dnetlib.dhp.schema.oaf.Relation; +import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FSDataOutputStream; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; + +import java.io.BufferedWriter; +import java.io.Closeable; +import java.io.IOException; +import java.io.OutputStreamWriter; +import java.nio.charset.StandardCharsets; +import java.sql.ResultSet; +import java.sql.SQLException; +import java.util.Arrays; +import java.util.List; +import java.util.function.Consumer; +import java.util.function.Function; + +public class ReadMasterDatasourceFromDB implements Closeable { + + private final DbClient dbClient; + private static final Log log = LogFactory.getLog(ReadMasterDatasourceFromDB.class); + + private final BufferedWriter writer; + private final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static final String QUERY = "SELECT dso.id datasource, d.id master FROM " + + "(SELECT id FROM dsm_services WHERE id like 'eosc%') dso " + + "FULL JOIN " + + "(SELECT id, duplicate FROM dsm_dedup_services WHERE duplicate like 'eosc%')d " + + "ON dso.id = d.duplicate"; + + public static void main(final String[] args) throws Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + ReadMasterDatasourceFromDB.class + .getResourceAsStream( + "/eu/dnetlib/dhp/blacklist/blacklist_parameters.json"))); + + parser.parseArgument(args); + + final String dbUrl = parser.get("postgresUrl"); + final String dbUser = parser.get("postgresUser"); + final String dbPassword = parser.get("postgresPassword"); + final String hdfsPath = parser.get("hdfsPath") + "/datasourceMasters"; + final String hdfsNameNode = parser.get("hdfsNameNode"); + + try (final ReadMasterDatasourceFromDB rmd = new ReadMasterDatasourceFromDB(hdfsPath, hdfsNameNode, dbUrl, dbUser, + dbPassword)) { + + log.info("Processing datasources..."); + rmd.execute(QUERY, rmd::datasourceMasterMap); + + } + } + + public void execute(final String sql, final Function producer) { + + dbClient.processResults(sql, rs -> writeMap(producer.apply(rs))); + } + + public DatasourceMaster datasourceMasterMap(ResultSet rs) { + try { + DatasourceMaster dm = new DatasourceMaster(); + String datasource = rs.getString("datasource"); + dm.setDatasource(datasource); + String master = rs.getString("master"); + if (StringUtils.isNotBlank(master)) + dm.setMaster(OafMapperUtils.createOpenaireId(10, master, true)); + else + dm.setMaster(OafMapperUtils.createOpenaireId(10, datasource, true)); + return dm; + + } catch (final SQLException e) { + throw new RuntimeException(e); + } + } + + @Override + public void close() throws IOException { + dbClient.close(); + writer.close(); + } + + public ReadMasterDatasourceFromDB( + final String hdfsPath, String hdfsNameNode, final String dbUrl, final String dbUser, final String dbPassword) + throws IOException { + + this.dbClient = new DbClient(dbUrl, dbUser, dbPassword); + + Configuration conf = new Configuration(); + conf.set("fs.defaultFS", hdfsNameNode); + + FileSystem fileSystem = FileSystem.get(conf); + Path hdfsWritePath = new Path(hdfsPath); + FSDataOutputStream fsDataOutputStream = null; + if (fileSystem.exists(hdfsWritePath)) { + fsDataOutputStream = fileSystem.append(hdfsWritePath); + } else { + fsDataOutputStream = fileSystem.create(hdfsWritePath); + } + + this.writer = new BufferedWriter(new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8)); + } + + protected void writeMap(final DatasourceMaster dm) { + try { + writer.write(OBJECT_MAPPER.writeValueAsString(dm)); + writer.newLine(); + } catch (final IOException e) { + throw new RuntimeException(e); + } + } + +} diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java new file mode 100644 index 000000000..aa709cb29 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java @@ -0,0 +1,145 @@ +package eu.dnetlib.dhp.bulktag.eosc; + +import com.fasterxml.jackson.databind.ObjectMapper; +import com.google.gson.Gson; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.bulktag.SparkBulkTagJob; +import eu.dnetlib.dhp.bulktag.community.*; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.oaf.Context; +import eu.dnetlib.dhp.schema.oaf.DataInfo; +import eu.dnetlib.dhp.schema.oaf.Qualifier; +import eu.dnetlib.dhp.schema.oaf.Result; +import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import javax.print.attribute.DocAttributeSet; +import java.io.Serializable; +import java.util.*; +import java.util.stream.Collectors; + +import static eu.dnetlib.dhp.PropagationConstant.removeOutputDir; +import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.*; +import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.TAGGING_TRUST; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; +import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PROVENANCE_ACTIONS; + +/** + * @author miriam.baglioni + * @Date 21/07/22 + */ +public class SparkEoscBulkTag implements Serializable { + + private static final Logger log = LoggerFactory.getLogger(SparkEoscBulkTag.class); + public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + SparkEoscBulkTag.class + .getResourceAsStream( + "/eu/dnetlib/dhp/bulktag/input_bulkTag_parameters.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String inputPath = parser.get("sourcePath"); + log.info("inputPath: {}", inputPath); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath: {}", outputPath); + + String datasourceMapPath = parser.get("datasourceMapPath"); + log.info("datasourceMapPath: {}", datasourceMapPath); + + final String resultClassName = parser.get("resultTableName"); + log.info("resultTableName: {}", resultClassName); + + Class resultClazz = (Class) Class.forName(resultClassName); + + SparkConf conf = new SparkConf(); + CommunityConfiguration cc; + + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + removeOutputDir(spark, outputPath); + execBulkTag(spark, inputPath, outputPath, datasourceMapPath, resultClazz); + }); + } + + private static void execBulkTag( + SparkSession spark, + String inputPath, + String outputPath, + String datasourceMapPath, + Class resultClazz) { + + final List hostedByList = Arrays.asList(readPath(spark, datasourceMapPath, DatasourceMaster.class) + .map((MapFunction) dm -> dm.getMaster(), Encoders.STRING()) + .collect()); + + readPath(spark, inputPath, resultClazz) + .map(patchResult(), Encoders.bean(resultClazz)) + .filter(Objects::nonNull) + .map( + (MapFunction) value -> enrich(value, hostedByList), + Encoders.bean(resultClazz)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath); + } + + private static R enrich(R value, List hostedByList) { + if(value.getInstance().stream().anyMatch(i -> hostedByList.contains(i.getHostedby().getKey())) || + (value.getEoscifguidelines() != null && value.getEoscifguidelines().size() > 0)){ + Context context = new Context(); + context.setId("eosc"); + OafMapperUtils.dataInfo(false, BULKTAG_DATA_INFO_TYPE,true,false, + OafMapperUtils.qualifier(CLASS_ID_DATASOURCE, CLASS_NAME_BULKTAG_DATASOURCE, + DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), TAGGING_TRUST); + value.getContext().add(context); + + } + return value; + + } + + public static Dataset readPath( + SparkSession spark, String inputPath, Class clazz) { + return spark + .read() + .textFile(inputPath) + .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz)); + } + + // TODO remove this hack as soon as the values fixed by this method will be provided as NON null + private static MapFunction patchResult() { + return r -> { + if (r.getDataInfo().getDeletedbyinference() == null) { + r.getDataInfo().setDeletedbyinference(false); + } + if (r.getContext() == null) { + r.setContext(new ArrayList<>()); + } + return r; + }; + } + +} diff --git a/pom.xml b/pom.xml index 54070f654..821ce3124 100644 --- a/pom.xml +++ b/pom.xml @@ -801,7 +801,7 @@ 3.3.3 3.4.2 [2.12,3.0) - [2.12.0] + [2.12.1] [4.0.3] [6.0.5] [3.1.6] From ddc414b2586075f2ab32b59480115c826e9a863c Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Fri, 22 Jul 2022 09:43:15 +0200 Subject: [PATCH 114/214] fixed wrong json param --- .../eu/dnetlib/dhp/sx/graph/convert_dataset_json_params.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/convert_dataset_json_params.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/convert_dataset_json_params.json index f3e8cdbad..3a2f90708 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/convert_dataset_json_params.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/convert_dataset_json_params.json @@ -1,6 +1,6 @@ [ {"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true}, {"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the source Path", "paramRequired": true}, - {"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the path of the raw graph", "paramRequired": true} + {"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the path of the raw graph", "paramRequired": true}, {"paramName":"r", "paramLongName":"filterRelation", "paramDescription": "the relation to filter", "paramRequired": false} ] \ No newline at end of file From 7a1c1b6f53b8c7ca51633b440338fffc997e81bb Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 22 Jul 2022 14:36:02 +0200 Subject: [PATCH 115/214] [EOSC context TAG] Add test class and resourcesK --- .../dhp/bulktag/eosc/DatasourceMaster.java | 29 +- .../eosc/ReadMasterDatasourceFromDB.java | 62 ++-- .../dhp/bulktag/eosc/SparkEoscBulkTag.java | 229 +++++++------ .../bulktag/datasourcemaster_parameters.json | 32 ++ .../input_eosc_bulkTag_parameters.json | 34 ++ .../dhp/bulktag/oozie_app/workflow.xml | 139 +++++++- .../dhp/bulktag/EOSCContextTaggingTest.java | 152 +++++++++ .../dhp/bulktag/eosc/dataset/dataset_10.json | 10 + .../datasourceMaster | 318 ++++++++++++++++++ 9 files changed, 855 insertions(+), 150 deletions(-) create mode 100644 dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/datasourcemaster_parameters.json create mode 100644 dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/input_eosc_bulkTag_parameters.json create mode 100644 dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCContextTaggingTest.java create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/eosc/dataset/dataset_10.json create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/eosc/datasourceMasterAssociation/datasourceMaster diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/DatasourceMaster.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/DatasourceMaster.java index 537356586..ee01597e7 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/DatasourceMaster.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/DatasourceMaster.java @@ -1,3 +1,4 @@ + package eu.dnetlib.dhp.bulktag.eosc; import java.io.Serializable; @@ -7,22 +8,22 @@ import java.io.Serializable; * @Date 21/07/22 */ public class DatasourceMaster implements Serializable { - private String datasource; - private String master; + private String datasource; + private String master; - public String getDatasource() { - return datasource; - } + public String getDatasource() { + return datasource; + } - public void setDatasource(String datasource) { - this.datasource = datasource; - } + public void setDatasource(String datasource) { + this.datasource = datasource; + } - public String getMaster() { - return master; - } + public String getMaster() { + return master; + } - public void setMaster(String master) { - this.master = master; - } + public void setMaster(String master) { + this.master = master; + } } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java index 7d6964707..9ad108749 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java @@ -1,27 +1,6 @@ package eu.dnetlib.dhp.bulktag.eosc; -/** - * @author miriam.baglioni - * @Date 21/07/22 - */ - -import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.common.DbClient; -import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.dhp.schema.common.RelationInverse; -import eu.dnetlib.dhp.schema.oaf.Relation; -import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; -import org.apache.commons.io.IOUtils; -import org.apache.commons.lang3.StringUtils; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; -import org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.FSDataOutputStream; -import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.fs.Path; - import java.io.BufferedWriter; import java.io.Closeable; import java.io.IOException; @@ -34,6 +13,28 @@ import java.util.List; import java.util.function.Consumer; import java.util.function.Function; +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FSDataOutputStream; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; + +/** + * @author miriam.baglioni + * @Date 21/07/22 + */ +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.DbClient; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.common.RelationInverse; +import eu.dnetlib.dhp.schema.oaf.Relation; +import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; + public class ReadMasterDatasourceFromDB implements Closeable { private final DbClient dbClient; @@ -43,18 +44,18 @@ public class ReadMasterDatasourceFromDB implements Closeable { private final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); private static final String QUERY = "SELECT dso.id datasource, d.id master FROM " + - "(SELECT id FROM dsm_services WHERE id like 'eosc%') dso " + - "FULL JOIN " + - "(SELECT id, duplicate FROM dsm_dedup_services WHERE duplicate like 'eosc%')d " + - "ON dso.id = d.duplicate"; + "(SELECT id FROM dsm_services WHERE id like 'eosc%') dso " + + "FULL JOIN " + + "(SELECT id, duplicate FROM dsm_dedup_services WHERE duplicate like 'eosc%')d " + + "ON dso.id = d.duplicate"; public static void main(final String[] args) throws Exception { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils .toString( - ReadMasterDatasourceFromDB.class + ReadMasterDatasourceFromDB.class .getResourceAsStream( - "/eu/dnetlib/dhp/blacklist/blacklist_parameters.json"))); + "/eu/dnetlib/dhp/bulktag/datasourcemaster_parameters.json"))); parser.parseArgument(args); @@ -64,8 +65,9 @@ public class ReadMasterDatasourceFromDB implements Closeable { final String hdfsPath = parser.get("hdfsPath") + "/datasourceMasters"; final String hdfsNameNode = parser.get("hdfsNameNode"); - try (final ReadMasterDatasourceFromDB rmd = new ReadMasterDatasourceFromDB(hdfsPath, hdfsNameNode, dbUrl, dbUser, - dbPassword)) { + try ( + final ReadMasterDatasourceFromDB rmd = new ReadMasterDatasourceFromDB(hdfsPath, hdfsNameNode, dbUrl, dbUser, + dbPassword)) { log.info("Processing datasources..."); rmd.execute(QUERY, rmd::datasourceMasterMap); @@ -75,7 +77,7 @@ public class ReadMasterDatasourceFromDB implements Closeable { public void execute(final String sql, final Function producer) { - dbClient.processResults(sql, rs -> writeMap(producer.apply(rs))); + dbClient.processResults(sql, rs -> writeMap(producer.apply(rs))); } public DatasourceMaster datasourceMasterMap(ResultSet rs) { diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java index aa709cb29..600a5cec8 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java @@ -1,18 +1,22 @@ + package eu.dnetlib.dhp.bulktag.eosc; -import com.fasterxml.jackson.databind.ObjectMapper; -import com.google.gson.Gson; -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.bulktag.SparkBulkTagJob; -import eu.dnetlib.dhp.bulktag.community.*; -import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.dhp.schema.oaf.Context; -import eu.dnetlib.dhp.schema.oaf.DataInfo; -import eu.dnetlib.dhp.schema.oaf.Qualifier; -import eu.dnetlib.dhp.schema.oaf.Result; -import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; +import static eu.dnetlib.dhp.PropagationConstant.readPath; +import static eu.dnetlib.dhp.PropagationConstant.removeOutputDir; +import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.*; +import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.TAGGING_TRUST; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; +import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PROVENANCE_ACTIONS; + +import java.io.Serializable; +import java.util.*; +import java.util.stream.Collectors; + +import javax.print.attribute.DocAttributeSet; + import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.ForeachFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; @@ -21,16 +25,15 @@ import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import javax.print.attribute.DocAttributeSet; -import java.io.Serializable; -import java.util.*; -import java.util.stream.Collectors; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.google.gson.Gson; -import static eu.dnetlib.dhp.PropagationConstant.removeOutputDir; -import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.*; -import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.TAGGING_TRUST; -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; -import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PROVENANCE_ACTIONS; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.bulktag.SparkBulkTagJob; +import eu.dnetlib.dhp.bulktag.community.*; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; /** * @author miriam.baglioni @@ -38,108 +41,124 @@ import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PROVENANCE_ACTION */ public class SparkEoscBulkTag implements Serializable { - private static final Logger log = LoggerFactory.getLogger(SparkEoscBulkTag.class); - public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static final Logger log = LoggerFactory.getLogger(SparkEoscBulkTag.class); + public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkEoscBulkTag.class - .getResourceAsStream( - "/eu/dnetlib/dhp/bulktag/input_bulkTag_parameters.json")); + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + SparkEoscBulkTag.class + .getResourceAsStream( + "/eu/dnetlib/dhp/bulktag/input_eosc_bulkTag_parameters.json")); - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); + final String inputPath = parser.get("sourcePath"); + log.info("inputPath: {}", inputPath); - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); + final String workingPath = parser.get("workingPath"); + log.info("workingPath: {}", workingPath); - String datasourceMapPath = parser.get("datasourceMapPath"); - log.info("datasourceMapPath: {}", datasourceMapPath); + String datasourceMapPath = parser.get("datasourceMapPath"); + log.info("datasourceMapPath: {}", datasourceMapPath); - final String resultClassName = parser.get("resultTableName"); - log.info("resultTableName: {}", resultClassName); + final String resultClassName = parser.get("resultTableName"); + log.info("resultTableName: {}", resultClassName); - Class resultClazz = (Class) Class.forName(resultClassName); + Class resultClazz = (Class) Class.forName(resultClassName); - SparkConf conf = new SparkConf(); - CommunityConfiguration cc; + SparkConf conf = new SparkConf(); + CommunityConfiguration cc; - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - removeOutputDir(spark, outputPath); - execBulkTag(spark, inputPath, outputPath, datasourceMapPath, resultClazz); - }); - } + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + removeOutputDir(spark, workingPath); + execBulkTag(spark, inputPath, workingPath, datasourceMapPath, resultClazz); + }); + } - private static void execBulkTag( - SparkSession spark, - String inputPath, - String outputPath, - String datasourceMapPath, - Class resultClazz) { + private static void execBulkTag( + SparkSession spark, + String inputPath, + String workingPath, + String datasourceMapPath, + Class resultClazz) { - final List hostedByList = Arrays.asList(readPath(spark, datasourceMapPath, DatasourceMaster.class) - .map((MapFunction) dm -> dm.getMaster(), Encoders.STRING()) - .collect()); - readPath(spark, inputPath, resultClazz) - .map(patchResult(), Encoders.bean(resultClazz)) - .filter(Objects::nonNull) - .map( - (MapFunction) value -> enrich(value, hostedByList), - Encoders.bean(resultClazz)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); - } + List hostedByList = readPath(spark, datasourceMapPath, DatasourceMaster.class) + .map((MapFunction) dm -> dm.getMaster(), Encoders.STRING()) + .collectAsList(); - private static R enrich(R value, List hostedByList) { - if(value.getInstance().stream().anyMatch(i -> hostedByList.contains(i.getHostedby().getKey())) || - (value.getEoscifguidelines() != null && value.getEoscifguidelines().size() > 0)){ - Context context = new Context(); - context.setId("eosc"); - OafMapperUtils.dataInfo(false, BULKTAG_DATA_INFO_TYPE,true,false, - OafMapperUtils.qualifier(CLASS_ID_DATASOURCE, CLASS_NAME_BULKTAG_DATASOURCE, - DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), TAGGING_TRUST); - value.getContext().add(context); - } - return value; - } - public static Dataset readPath( - SparkSession spark, String inputPath, Class clazz) { - return spark - .read() - .textFile(inputPath) - .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz)); - } + readPath(spark, inputPath, resultClazz) + .map(patchResult(), Encoders.bean(resultClazz)) + .filter(Objects::nonNull) + .map( + (MapFunction) value -> enrich(value, hostedByList), + Encoders.bean(resultClazz)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingPath); - // TODO remove this hack as soon as the values fixed by this method will be provided as NON null - private static MapFunction patchResult() { - return r -> { - if (r.getDataInfo().getDeletedbyinference() == null) { - r.getDataInfo().setDeletedbyinference(false); - } - if (r.getContext() == null) { - r.setContext(new ArrayList<>()); - } - return r; - }; - } + readPath(spark, workingPath, resultClazz) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(inputPath); + + } + + private static R enrich(R value, List hostedByList) { + if (value.getInstance().stream().anyMatch(i -> hostedByList.contains(i.getHostedby().getKey())) || + (value.getEoscifguidelines() != null && value.getEoscifguidelines().size() > 0)) { + Context context = new Context(); + context.setId("eosc"); + OafMapperUtils + .dataInfo( + false, BULKTAG_DATA_INFO_TYPE, true, false, + OafMapperUtils + .qualifier( + CLASS_ID_DATASOURCE, CLASS_NAME_BULKTAG_DATASOURCE, + DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), + TAGGING_TRUST); + value.getContext().add(context); + + } + return value; + + } + + public static Dataset readPath( + SparkSession spark, String inputPath, Class clazz) { + return spark + .read() + .textFile(inputPath) + .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz)); + } + + // TODO remove this hack as soon as the values fixed by this method will be provided as NON null + private static MapFunction patchResult() { + return r -> { + if (r.getDataInfo().getDeletedbyinference() == null) { + r.getDataInfo().setDeletedbyinference(false); + } + if (r.getContext() == null) { + r.setContext(new ArrayList<>()); + } + return r; + }; + } } diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/datasourcemaster_parameters.json b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/datasourcemaster_parameters.json new file mode 100644 index 000000000..9a2eadaa7 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/datasourcemaster_parameters.json @@ -0,0 +1,32 @@ +[ + { + "paramName": "p", + "paramLongName": "hdfsPath", + "paramDescription": "the path where storing the sequential file", + "paramRequired": true + }, + { + "paramName": "nn", + "paramLongName": "hdfsNameNode", + "paramDescription": "the name node on hdfs", + "paramRequired": true + }, + { + "paramName": "pgurl", + "paramLongName": "postgresUrl", + "paramDescription": "postgres url, example: jdbc:postgresql://localhost:5432/testdb", + "paramRequired": true + }, + { + "paramName": "pguser", + "paramLongName": "postgresUser", + "paramDescription": "postgres user", + "paramRequired": false + }, + { + "paramName": "pgpasswd", + "paramLongName": "postgresPassword", + "paramDescription": "postgres password", + "paramRequired": false + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/input_eosc_bulkTag_parameters.json b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/input_eosc_bulkTag_parameters.json new file mode 100644 index 000000000..ebbbd408b --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/input_eosc_bulkTag_parameters.json @@ -0,0 +1,34 @@ +[ + + { + "paramName":"s", + "paramLongName":"sourcePath", + "paramDescription": "the path of the sequencial file to read", + "paramRequired": true + }, + { + "paramName": "dmp", + "paramLongName":"datasourceMapPath", + "paramDescription": "the path where the association datasource master has been stored", + "paramRequired": true + }, + { + "paramName":"tn", + "paramLongName":"resultTableName", + "paramDescription": "the name of the result table we are currently working on", + "paramRequired": true + }, + { + "paramName": "wp", + "paramLongName": "workingPath", + "paramDescription": "the path used to store temporary output files", + "paramRequired": true + }, + { + "paramName": "ssm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "true if the spark session is managed, false otherwise", + "paramRequired": false + } + +] \ No newline at end of file diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml index f34c5110f..6016e0179 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml @@ -16,6 +16,21 @@ outputPath the output path + + + + postgresURL + the url of the postgress server to query + + + postgresUser + the username to access the postgres db + + + postgresPassword + the postgres password + + @@ -29,7 +44,7 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] @@ -226,10 +241,132 @@ --sourcePath${outputPath} --workingPath${workingDir}/eoscTag + + + + + + + eu.dnetlib.dhp.bulktag.eosc.ReadMasterDatasourceFromDB + --hdfsPath${workingDir}/datasourcemaster + --hdfsNameNode${nameNode} + --postgresUrl${postgresURL} + --postgresUser${postgresUser} + --postgresPassword${postgresPassword} + + + + + + + + + + + yarn-cluster + cluster + EOSC_tagging + eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag + dhp-enrichment-${projectVersion}.jar + + --num-executors=${sparkExecutorNumber} + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --sourcePath${outputPath}/publication + --workingPath${workingDir}/eoscContextTag/publication + --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication + --datasourceMapPath${workingDir}/datasourcemaster + + + + + + + + yarn-cluster + cluster + EOSC_tagging + eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag + dhp-enrichment-${projectVersion}.jar + + --num-executors=${sparkExecutorNumber} + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --sourcePath${outputPath}/dataset + --workingPath${workingDir}/eoscContextTag/dataset + --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset + --datasourceMapPath${workingDir}/datasourcemaster + + + + + + + yarn-cluster + cluster + EOSC_tagging + eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag + dhp-enrichment-${projectVersion}.jar + + --num-executors=${sparkExecutorNumber} + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --sourcePath${outputPath}/software + --workingPath${workingDir}/eoscContextTag/software + --resultTableNameeu.dnetlib.dhp.schema.oaf.Software + --datasourceMapPath${workingDir}/datasourcemaster + + + + + + + yarn-cluster + cluster + EOSC_tagging + eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag + dhp-enrichment-${projectVersion}.jar + + --num-executors=${sparkExecutorNumber} + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --sourcePath${outputPath}/otherresearchproduct + --workingPath${workingDir}/eoscContextTag/otherresearchproduct + --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct + --datasourceMapPath${workingDir}/datasourcemaster + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCContextTaggingTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCContextTaggingTest.java new file mode 100644 index 000000000..d6785acc7 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCContextTaggingTest.java @@ -0,0 +1,152 @@ + +package eu.dnetlib.dhp.bulktag; +/** + * @author miriam.baglioni + * @Date 22/07/22 + */ + +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag; +import eu.dnetlib.dhp.schema.oaf.Dataset; +import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct; +import eu.dnetlib.dhp.schema.oaf.Software; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import org.apache.commons.io.FileUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.List; + +//"50|475c1990cbb2::0fecfb874d9395aa69d2f4d7cd1acbea" has instance hostedby eosc +//"50|475c1990cbb2::3185cd5d8a2b0a06bb9b23ef11748eb1" has instance hostedby eosc +//"50|475c1990cbb2::449f28eefccf9f70c04ad70d61e041c7" has two instance one hostedby eosc +//"50|475c1990cbb2::3894c94123e96df8a21249957cf160cb" has EoscTag + +public class EOSCContextTaggingTest { + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path workingDir; + + private static final Logger log = LoggerFactory.getLogger(EOSCContextTaggingTest.class); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files.createTempDirectory(EOSCContextTaggingTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(EOSCContextTaggingTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(EOSCTagJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + void EoscContextTagTest() throws Exception { + + spark + .read() + .textFile(getClass().getResource("/eu/dnetlib/dhp/bulktag/eosc/dataset/dataset_10.json").getPath()) + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, Dataset.class), + Encoders.bean(Dataset.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingDir.toString() + "/input/dataset"); + + + SparkEoscBulkTag + .main( + new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", + workingDir.toString() + "/input/dataset", + "-workingPath", workingDir.toString() + "/working/dataset", + "-datasourceMapPath", getClass().getResource("/eu/dnetlib/dhp/bulktag/eosc/datasourceMasterAssociation/datasourceMaster").getPath(), + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset" + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/input/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); + + Assertions.assertEquals(10, tmp.count()); + + Assertions + .assertEquals( + 4, + tmp + .filter( + s -> s.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))) + .count()); + + Assertions + .assertEquals(1, + tmp + .filter(d -> d.getId().equals("50|475c1990cbb2::0fecfb874d9395aa69d2f4d7cd1acbea") + && + d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))).count() + ); + Assertions + .assertEquals(1, + tmp + .filter(d -> d.getId().equals("50|475c1990cbb2::3185cd5d8a2b0a06bb9b23ef11748eb1") + && + d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))).count() + ); + + + Assertions + .assertEquals(1, + tmp + .filter(d -> d.getId().equals("50|475c1990cbb2::3894c94123e96df8a21249957cf160cb") + && + d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))).count() + ); + + Assertions + .assertEquals(1, + tmp + .filter(d -> d.getId().equals("50|475c1990cbb2::3894c94123e96df8a21249957cf160cb") + && + d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))).count() + ); + } + + +} diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/eosc/dataset/dataset_10.json 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+{"datasource":"eosc________::wenmr::wenmr.disvis_web_portal","master":"10|eosc________::2539ec693b683284c4e243b969ae3fc0"} +{"datasource":"eosc________::wenmr::wenmr.fanten_finding_anisotropy_tensor","master":"10|eosc________::99c793e3f3b856c48eaaa36682038b28"} +{"datasource":"eosc________::wenmr::wenmr.haddock24_web_portal","master":"10|eosc________::0f198f6a0885105809f420be23614be3"} +{"datasource":"eosc________::wenmr::wenmr.metalpdb","master":"10|eosc________::84676bc3d2ce17de70309dc58f428296"} +{"datasource":"eosc________::wenmr::wenmr.pdb-tools_web","master":"10|eosc________::b37eed45624ac30f3476f71640e59a61"} +{"datasource":"eosc________::wenmr::wenmr.powerfit_web_portal","master":"10|eosc________::93d4d621ed1da378c0e7dc891cefc007"} +{"datasource":"eosc________::wenmr::wenmr.spoton","master":"10|eosc________::76e7e0552f9c6b89db94b31ddc366b9f"} \ No newline at end of file From 627332526b4a82b09190d3f3aefd106e274e38dd Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 22 Jul 2022 14:55:11 +0200 Subject: [PATCH 116/214] [EOSC context TAG] workflow start from reset_outputpath action --- .../resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml index 6016e0179..17fc76aad 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml @@ -44,7 +44,7 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] @@ -254,7 +254,7 @@ --postgresUser${postgresUser} --postgresPassword${postgresPassword} - + From 06a95daf60c49d9b0781d0e1f37965fc804a6491 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 22 Jul 2022 14:57:06 +0200 Subject: [PATCH 117/214] [EOSC context TAG] refactoring after compilation --- .../dhp/bulktag/eosc/SparkEoscBulkTag.java | 6 +- .../dhp/bulktag/EOSCContextTaggingTest.java | 224 +++++++++--------- 2 files changed, 118 insertions(+), 112 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java index 600a5cec8..3ed910184 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java @@ -93,13 +93,9 @@ public class SparkEoscBulkTag implements Serializable { String datasourceMapPath, Class resultClazz) { - List hostedByList = readPath(spark, datasourceMapPath, DatasourceMaster.class) .map((MapFunction) dm -> dm.getMaster(), Encoders.STRING()) - .collectAsList(); - - - + .collectAsList(); readPath(spark, inputPath, resultClazz) .map(patchResult(), Encoders.bean(resultClazz)) diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCContextTaggingTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCContextTaggingTest.java index d6785acc7..cbdab7628 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCContextTaggingTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCContextTaggingTest.java @@ -1,16 +1,11 @@ package eu.dnetlib.dhp.bulktag; -/** - * @author miriam.baglioni - * @Date 22/07/22 - */ -import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag; -import eu.dnetlib.dhp.schema.oaf.Dataset; -import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct; -import eu.dnetlib.dhp.schema.oaf.Software; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.List; + import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; @@ -26,10 +21,17 @@ import org.junit.jupiter.api.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.List; +/** + * @author miriam.baglioni + * @Date 22/07/22 + */ +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag; +import eu.dnetlib.dhp.schema.oaf.Dataset; +import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct; +import eu.dnetlib.dhp.schema.oaf.Software; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; //"50|475c1990cbb2::0fecfb874d9395aa69d2f4d7cd1acbea" has instance hostedby eosc //"50|475c1990cbb2::3185cd5d8a2b0a06bb9b23ef11748eb1" has instance hostedby eosc @@ -37,116 +39,124 @@ import java.util.List; //"50|475c1990cbb2::3894c94123e96df8a21249957cf160cb" has EoscTag public class EOSCContextTaggingTest { - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - private static SparkSession spark; + private static SparkSession spark; - private static Path workingDir; + private static Path workingDir; - private static final Logger log = LoggerFactory.getLogger(EOSCContextTaggingTest.class); + private static final Logger log = LoggerFactory.getLogger(EOSCContextTaggingTest.class); - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files.createTempDirectory(EOSCContextTaggingTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files.createTempDirectory(EOSCContextTaggingTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); - SparkConf conf = new SparkConf(); - conf.setAppName(EOSCContextTaggingTest.class.getSimpleName()); + SparkConf conf = new SparkConf(); + conf.setAppName(EOSCContextTaggingTest.class.getSimpleName()); - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - spark = SparkSession - .builder() - .appName(EOSCTagJobTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } + spark = SparkSession + .builder() + .appName(EOSCTagJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } - @Test - void EoscContextTagTest() throws Exception { + @Test + void EoscContextTagTest() throws Exception { - spark - .read() - .textFile(getClass().getResource("/eu/dnetlib/dhp/bulktag/eosc/dataset/dataset_10.json").getPath()) - .map( - (MapFunction) value -> OBJECT_MAPPER.readValue(value, Dataset.class), - Encoders.bean(Dataset.class)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(workingDir.toString() + "/input/dataset"); + spark + .read() + .textFile(getClass().getResource("/eu/dnetlib/dhp/bulktag/eosc/dataset/dataset_10.json").getPath()) + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, Dataset.class), + Encoders.bean(Dataset.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingDir.toString() + "/input/dataset"); + SparkEoscBulkTag + .main( + new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", + workingDir.toString() + "/input/dataset", + "-workingPath", workingDir.toString() + "/working/dataset", + "-datasourceMapPath", + getClass() + .getResource("/eu/dnetlib/dhp/bulktag/eosc/datasourceMasterAssociation/datasourceMaster") + .getPath(), + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset" + }); - SparkEoscBulkTag - .main( - new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", - workingDir.toString() + "/input/dataset", - "-workingPath", workingDir.toString() + "/working/dataset", - "-datasourceMapPath", getClass().getResource("/eu/dnetlib/dhp/bulktag/eosc/datasourceMasterAssociation/datasourceMaster").getPath(), - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset" - }); + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/input/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/input/dataset") - .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); + Assertions.assertEquals(10, tmp.count()); - Assertions.assertEquals(10, tmp.count()); + Assertions + .assertEquals( + 4, + tmp + .filter( + s -> s.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))) + .count()); - Assertions - .assertEquals( - 4, - tmp - .filter( - s -> s.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))) - .count()); + Assertions + .assertEquals( + 1, + tmp + .filter( + d -> d.getId().equals("50|475c1990cbb2::0fecfb874d9395aa69d2f4d7cd1acbea") + && + d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))) + .count()); + Assertions + .assertEquals( + 1, + tmp + .filter( + d -> d.getId().equals("50|475c1990cbb2::3185cd5d8a2b0a06bb9b23ef11748eb1") + && + d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))) + .count()); - Assertions - .assertEquals(1, - tmp - .filter(d -> d.getId().equals("50|475c1990cbb2::0fecfb874d9395aa69d2f4d7cd1acbea") - && - d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))).count() - ); - Assertions - .assertEquals(1, - tmp - .filter(d -> d.getId().equals("50|475c1990cbb2::3185cd5d8a2b0a06bb9b23ef11748eb1") - && - d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))).count() - ); - - - Assertions - .assertEquals(1, - tmp - .filter(d -> d.getId().equals("50|475c1990cbb2::3894c94123e96df8a21249957cf160cb") - && - d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))).count() - ); - - Assertions - .assertEquals(1, - tmp - .filter(d -> d.getId().equals("50|475c1990cbb2::3894c94123e96df8a21249957cf160cb") - && - d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))).count() - ); - } + Assertions + .assertEquals( + 1, + tmp + .filter( + d -> d.getId().equals("50|475c1990cbb2::3894c94123e96df8a21249957cf160cb") + && + d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))) + .count()); + Assertions + .assertEquals( + 1, + tmp + .filter( + d -> d.getId().equals("50|475c1990cbb2::3894c94123e96df8a21249957cf160cb") + && + d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))) + .count()); + } } From a12d28c6444616ac914d79b43e5360c4e92d714b Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 22 Jul 2022 16:23:12 +0200 Subject: [PATCH 118/214] [Clean Country] added logic not to remove country from result if it exist a hosting datasource with that country. Moreover the country will be removed only if added with propagation --- .../{ => country}/CleanCountrySparkJob.java | 40 ++++++-- .../country/GetDatasourceFromCountry.java | 99 +++++++++++++++++++ .../dhp/oa/graph/clean/CleanCountryTest.java | 3 +- 3 files changed, 130 insertions(+), 12 deletions(-) rename dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/{ => country}/CleanCountrySparkJob.java (75%) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/GetDatasourceFromCountry.java diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountrySparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java similarity index 75% rename from dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountrySparkJob.java rename to dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java index ec82d385c..1af1aafc0 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountrySparkJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java @@ -1,4 +1,4 @@ -package eu.dnetlib.dhp.oa.graph.clean; +package eu.dnetlib.dhp.oa.graph.clean.country; /** * @author miriam.baglioni @@ -7,6 +7,7 @@ package eu.dnetlib.dhp.oa.graph.clean; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob; import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.StructuredProperty; import org.apache.commons.io.IOUtils; @@ -21,6 +22,7 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; import java.io.Serializable; +import java.util.List; import java.util.Optional; import java.util.stream.Collectors; @@ -54,10 +56,13 @@ public class CleanCountrySparkJob implements Serializable { String workingPath = parser.get("workingPath"); log.info("workingPath: {}", workingPath); + String datasourcePath = parser.get("datasourcePath"); + log.info("datasourcePath: {}", datasourcePath); + String country = parser.get("country"); log.info("country: {}", country); - String verifyParam = parser.get("verifyParam"); + String[] verifyParam = parser.get("verifyParam").split(";"); log.info("verifyParam: {}", verifyParam); String collectedfrom = parser.get("collectedfrom"); @@ -74,12 +79,17 @@ public class CleanCountrySparkJob implements Serializable { isSparkSessionManaged, spark -> { - cleanCountry(spark, country, verifyParam, inputPath, entityClazz, workingPath,collectedfrom); + cleanCountry(spark, country, verifyParam, inputPath, entityClazz, workingPath,collectedfrom, datasourcePath); }); } - private static void cleanCountry(SparkSession spark, String country, String verifyParam, - String inputPath, Class entityClazz, String workingPath, String collectedfrom) { + private static void cleanCountry(SparkSession spark, String country, String[] verifyParam, + String inputPath, Class entityClazz, String workingPath, String collectedfrom, String datasourcePath) { + + List hostedBy = spark.read().textFile(datasourcePath) + // .filter((FilterFunction) ds -> !ds.equals(collectedfrom)) + .collectAsList(); + Dataset res = spark .read() .textFile(inputPath) @@ -89,11 +99,14 @@ public class CleanCountrySparkJob implements Serializable { ; res.map((MapFunction) r -> { - for(StructuredProperty p: r.getPid()){ - if (p.getQualifier().getClassid().equalsIgnoreCase("doi") && - p.getValue().startsWith(verifyParam) && r.getCollectedfrom().stream().anyMatch(cf -> cf.getValue().equalsIgnoreCase(collectedfrom))) { + if(r.getInstance().stream().anyMatch(i -> hostedBy.contains(i.getHostedby().getKey())) || + !r.getCollectedfrom().stream().anyMatch(cf -> cf.getValue().equals(collectedfrom))){ + return r; + } - r + if(r.getPid().stream().anyMatch(p -> p.getQualifier().getClassid().equals("doi") && pidInParam(p.getValue(), verifyParam)) + && r.getCountry().stream().anyMatch(c -> c.getClassid().equals(country) && c.getDataInfo().getInferenceprovenance().equals("propagation"))) + { r .setCountry( r .getCountry() @@ -102,7 +115,7 @@ public class CleanCountrySparkJob implements Serializable { c -> !c.getClassid() .equalsIgnoreCase(country)) .collect(Collectors.toList())); - } + } return r; @@ -124,5 +137,12 @@ public class CleanCountrySparkJob implements Serializable { .json(inputPath); } + private static boolean pidInParam(String value, String[] verifyParam) { + for (String s : verifyParam ) + if (value.startsWith(s)) + return true; + return false; + } + } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/GetDatasourceFromCountry.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/GetDatasourceFromCountry.java new file mode 100644 index 000000000..cdca96107 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/GetDatasourceFromCountry.java @@ -0,0 +1,99 @@ +package eu.dnetlib.dhp.oa.graph.clean.country; + +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.*; +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.FilterFunction; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import scala.Tuple2; + +import java.io.Serializable; +import java.util.List; +import java.util.Optional; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +/** + * @author miriam.baglioni + * @Date 22/07/22 + */ +public class GetDatasourceFromCountry implements Serializable { + private static final Logger log = LoggerFactory.getLogger(GetDatasourceFromCountry.class); + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + public static void main(String[] args) throws Exception { + + String jsonConfiguration = IOUtils + .toString( + GetDatasourceFromCountry.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/input_clean_country_parameters.json")); + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + String inputPath = parser.get("inputPath"); + log.info("inputPath: {}", inputPath); + + String workingPath = parser.get("workingPath"); + log.info("workingPath: {}", workingPath); + + String country = parser.get("country"); + log.info("country: {}", country); + + SparkConf conf = new SparkConf(); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + + getDatasourceFromCountry(spark, country, inputPath, workingPath); + }); + } + + private static void getDatasourceFromCountry(SparkSession spark, String country, String inputPath, String workingPath) { + + Dataset organization = spark.read().textFile(inputPath + "/organization") + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, Organization.class), + Encoders.bean(Organization.class)) + .filter( + (FilterFunction) o -> !o.getDataInfo().getDeletedbyinference() && + o.getCountry().getClassid().length() > 0 && + o.getCountry().getClassid().equals(country));; + + + // filtering of the relations taking the non deleted by inference and those with IsProvidedBy as relclass + Dataset relation = spark.read().textFile( inputPath + "/relation") + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, Relation.class), + Encoders.bean(Relation.class)) + .filter( + (FilterFunction) rel -> rel.getRelClass().equalsIgnoreCase(ModelConstants.IS_PROVIDED_BY) && + !rel.getDataInfo().getDeletedbyinference()); + + organization.joinWith(relation, organization.col("id").equalTo(relation.col("target")), "left") + .map((MapFunction, String>) t2 -> t2._2().getSource(), Encoders.STRING() ) + .write() + .mode(SaveMode.Overwrite) + .option("compression","gzip") + .json(workingPath); + + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountryTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountryTest.java index f9dad9fcf..a72093156 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountryTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountryTest.java @@ -5,9 +5,9 @@ package eu.dnetlib.dhp.oa.graph.clean; */ import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob; import eu.dnetlib.dhp.oa.graph.dump.DumpJobTest; import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; @@ -25,7 +25,6 @@ import org.slf4j.LoggerFactory; import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; -import java.util.List; public class CleanCountryTest { From 5968ec018db3e9292d8be92552199483791d4ed5 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 22 Jul 2022 16:48:38 +0200 Subject: [PATCH 119/214] [Clean Country] modified workflow and added param file --- .../country/GetDatasourceFromCountry.java | 2 +- .../dhp/oa/graph/clean/oozie_app/workflow.xml | 175 +++++++++++++++++- .../graph/input_clean_country_parameters.json | 6 + .../input_datasource_country_parameters.json | 26 +++ 4 files changed, 204 insertions(+), 5 deletions(-) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_datasource_country_parameters.json diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/GetDatasourceFromCountry.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/GetDatasourceFromCountry.java index cdca96107..c255c445f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/GetDatasourceFromCountry.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/GetDatasourceFromCountry.java @@ -38,7 +38,7 @@ public class GetDatasourceFromCountry implements Serializable { .toString( GetDatasourceFromCountry.class .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/input_clean_country_parameters.json")); + "/eu/dnetlib/dhp/oa/graph/input_datasource_country_parameters.json")); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); parser.parseArgument(args); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml index 0cf6cdd05..2ba0a7ad7 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml @@ -14,8 +14,8 @@ the address of the lookUp service - shouldCleanContext - true if the context have to be cleaned + shouldClean + true if the operation of deletion of not needed values from the results have to be performed contextId @@ -30,6 +30,22 @@ It is the constrint to be verified. This time is hardcoded as gcube and it is searched for in the title. If title starts with gcube than the context sobigdata will be removed by the result if present + + verifyCountryParam + 10.17632;10.5061 + It is the constraints to be verified. This time is hardcoded as the starting doi from mendeley and dryad and it is searched for in + the pid value. If the pid value starts with one of the two prefixes, then the country may be removed + + + country + NL + It is the country to be removed from the set of countries if it is present with provenance propagation. The country will not be removed if in one of the isntances there is a datasource with country `country` + + + collectedfrom + NARCIS + the only datasource for which the country NL will be removed from the country list + sparkDriverMemory @@ -296,7 +312,7 @@ - ${wf:conf('shouldCleanContext') eq true} + ${wf:conf('shouldClean') eq true} @@ -416,7 +432,158 @@ - + + + + + + yarn + cluster + Clean publications context + eu.dnetlib.dhp.oa.graph.clean.country.GetDatasourceFromCountry + dhp-graph-mapper-${projectVersion}.jar + + --executor-cores=${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=7680 + + --inputPath${graphOutputPath} + --workingPath${workingDir}/working/hostedby + --country${country} + + + + + + + + + + + + + + + yarn + cluster + Clean publications counmtry + eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-cores=${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=7680 + + --inputPath${graphOutputPath}/publication + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Publication + --workingPath${workingDir}/working/publication + --country${country} + --verifyParam${verifyCountryParam} + --datasourcePath${workingDir}/working/hostedby + --collectedfrom${collectedfrom} + + + + + + + + yarn + cluster + Clean datasets Country + eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-cores=${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=7680 + + --inputPath${graphOutputPath}/dataset + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Dataset + --workingPath${workingDir}/working/dataset + --country${country} + --verifyParam${verifyCountryParam} + --datasourcePath${workingDir}/working/hostedby + --collectedfrom${collectedfrom} + + + + + + + + yarn + cluster + Clean otherresearchproducts country + eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-cores=${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=7680 + + --inputPath${graphOutputPath}/otherresearchproduct + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct + --workingPath${workingDir}/working/otherresearchproduct + --country${country} + --verifyParam${verifyCountryParam} + --datasourcePath${workingDir}/working/hostedby + --collectedfrom${collectedfrom} + + + + + + + + yarn + cluster + Clean softwares country + eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-cores=${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=7680 + + --inputPath${graphOutputPath}/software + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Software + --workingPath${workingDir}/working/software + --country${country} + --verifyParam${verifyCountryParam} + --datasourcePath${workingDir}/working/hostedby + --collectedfrom${collectedfrom} + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_country_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_country_parameters.json index e46f7b6da..318fb22f8 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_country_parameters.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_country_parameters.json @@ -39,5 +39,11 @@ "paramLongName": "collectedfrom", "paramDescription": "the collectedfrom value for which we should apply the cleaning", "paramRequired": true + }, + { + "paramName": "hb", + "paramLongName": "hostedBy", + "paramDescription": "the set of datasources having the specified country in the graph searched for in the hostedby of the results", + "paramRequired": true } ] diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_datasource_country_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_datasource_country_parameters.json new file mode 100644 index 000000000..e0aa60328 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_datasource_country_parameters.json @@ -0,0 +1,26 @@ +[ + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "when true will stop SparkSession after job execution", + "paramRequired": false + }, + { + "paramName": "in", + "paramLongName": "inputPath", + "paramDescription": "the path to the graph data dump to read", + "paramRequired": true + }, + { + "paramName": "wp", + "paramLongName": "workingPath", + "paramDescription": "the path to store the output graph", + "paramRequired": true + }, + { + "paramName": "c", + "paramLongName": "country", + "paramDescription": "the id of the context to be removed", + "paramRequired": true + } +] From d091866e48ce0f814256c2f40ee5eddeb60511a3 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 25 Jul 2022 11:12:22 +0200 Subject: [PATCH 120/214] [EOSC Context Tagging] refactoring --- .../dhp/bulktag/eosc/SparkEoscBulkTag.java | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java index 3ed910184..99ff92223 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java @@ -121,14 +121,14 @@ public class SparkEoscBulkTag implements Serializable { (value.getEoscifguidelines() != null && value.getEoscifguidelines().size() > 0)) { Context context = new Context(); context.setId("eosc"); - OafMapperUtils - .dataInfo( - false, BULKTAG_DATA_INFO_TYPE, true, false, - OafMapperUtils - .qualifier( - CLASS_ID_DATASOURCE, CLASS_NAME_BULKTAG_DATASOURCE, - DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), - TAGGING_TRUST); + context.setDataInfo(Arrays.asList(OafMapperUtils + .dataInfo( + false, BULKTAG_DATA_INFO_TYPE, true, false, + OafMapperUtils + .qualifier( + CLASS_ID_DATASOURCE, CLASS_NAME_BULKTAG_DATASOURCE, + DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), + TAGGING_TRUST))); value.getContext().add(context); } From 657b0208a25f9597d73ee028579ccdac80f01849 Mon Sep 17 00:00:00 2001 From: Enrico Ottonello Date: Mon, 25 Jul 2022 12:37:39 +0200 Subject: [PATCH 121/214] multiple works download (<=100) for single request --- .../orcid/SparkDownloadOrcidWorks.java | 86 +++++++++++++---- .../doiboost/orcid/xml/XMLRecordParser.java | 92 +++++++++++++++++++ .../oozie_app/workflow.xml | 4 +- .../doiboost/orcid/OrcidClientTest.java | 8 +- .../orcid/xml/XMLRecordParserTest.java | 8 ++ .../0000-0001-7281-6306.compressed.base64 | 1 + .../0000-0003-3028-6161.compressed.base64 | 1 - .../orcid/xml/multiple_downloaded_works.xml | 57 ++++++++++++ 8 files changed, 232 insertions(+), 25 deletions(-) create mode 100644 dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/0000-0001-7281-6306.compressed.base64 delete mode 100644 dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/0000-0003-3028-6161.compressed.base64 create mode 100644 dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/xml/multiple_downloaded_works.xml diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkDownloadOrcidWorks.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkDownloadOrcidWorks.java index 0569bacfd..72122f8b9 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkDownloadOrcidWorks.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkDownloadOrcidWorks.java @@ -3,6 +3,8 @@ package eu.dnetlib.doiboost.orcid; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; +import java.io.IOException; +import java.nio.charset.StandardCharsets; import java.time.LocalDate; import java.time.format.DateTimeFormatter; import java.util.*; @@ -13,6 +15,7 @@ import org.apache.hadoop.io.Text; import org.apache.hadoop.io.compress.GzipCodec; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaPairRDD; +import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.api.java.function.FlatMapFunction; import org.apache.spark.api.java.function.Function; @@ -20,6 +23,7 @@ import org.apache.spark.util.LongAccumulator; import org.slf4j.Logger; import org.slf4j.LoggerFactory; +import com.google.common.collect.Lists; import com.google.gson.JsonElement; import com.google.gson.JsonParser; @@ -42,6 +46,7 @@ public class SparkDownloadOrcidWorks { public static final String ORCID_XML_DATETIME_FORMAT = "yyyy-MM-dd'T'HH:mm:ss.SSS'Z'"; public static final DateTimeFormatter ORCID_XML_DATETIMEFORMATTER = DateTimeFormatter .ofPattern(ORCID_XML_DATETIME_FORMAT); + public static final String DOWNLOAD_WORKS_REQUEST_SEPARATOR = ","; public static void main(String[] args) throws Exception { @@ -56,7 +61,6 @@ public class SparkDownloadOrcidWorks { .ofNullable(parser.get("isSparkSessionManaged")) .map(Boolean::valueOf) .orElse(Boolean.TRUE); - logger.info("isSparkSessionManaged: {}", isSparkSessionManaged); final String workingPath = parser.get("workingPath"); logger.info("workingPath: {}", workingPath); final String outputPath = parser.get("outputPath"); @@ -69,16 +73,12 @@ public class SparkDownloadOrcidWorks { isSparkSessionManaged, spark -> { final String lastUpdateValue = HDFSUtil.readFromTextFile(hdfsServerUri, workingPath, "last_update.txt"); - logger.info("lastUpdateValue: ", lastUpdateValue); JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); LongAccumulator updatedAuthorsAcc = spark.sparkContext().longAccumulator("updated_authors"); LongAccumulator parsedAuthorsAcc = spark.sparkContext().longAccumulator("parsed_authors"); LongAccumulator parsedWorksAcc = spark.sparkContext().longAccumulator("parsed_works"); LongAccumulator modifiedWorksAcc = spark.sparkContext().longAccumulator("modified_works"); - LongAccumulator maxModifiedWorksLimitAcc = spark - .sparkContext() - .longAccumulator("max_modified_works_limit"); LongAccumulator errorCodeFoundAcc = spark.sparkContext().longAccumulator("error_code_found"); LongAccumulator errorLoadingJsonFoundAcc = spark .sparkContext() @@ -94,7 +94,8 @@ public class SparkDownloadOrcidWorks { JavaPairRDD updatedAuthorsRDD = sc .sequenceFile(workingPath + "downloads/updated_authors/*", Text.class, Text.class); - updatedAuthorsAcc.setValue(updatedAuthorsRDD.count()); + long authorsCount = updatedAuthorsRDD.count(); + updatedAuthorsAcc.setValue(authorsCount); FlatMapFunction, String> retrieveWorkUrlFunction = data -> { String orcidId = data._1().toString(); @@ -125,22 +126,38 @@ public class SparkDownloadOrcidWorks { errorCodeFoundAcc.add(1); } parsedAuthorsAcc.add(1); + workIdLastModifiedDate.forEach((k, v) -> { parsedWorksAcc.add(1); if (isModified(orcidId, v, lastUpdateValue)) { modifiedWorksAcc.add(1); - workIds.add(orcidId.concat("/work/").concat(k)); + workIds.add(k); } }); - if (workIdLastModifiedDate.size() > 50) { - maxModifiedWorksLimitAcc.add(1); + if (workIds.isEmpty()) { + return new ArrayList().iterator(); } - return workIds.iterator(); + List worksDownloadUrls = new ArrayList<>(); + + // Creation of url for reading multiple works (up to 100) with ORCID API + // see this https://github.com/ORCID/ORCID-Source/blob/development/orcid-api-web/tutorial/works.md + + List> partitionedWorks = Lists.partition(workIds, 100); + partitionedWorks.stream().forEach(p -> { + String worksDownloadUrl = orcidId.concat("/works/"); + final StringBuffer buffer = new StringBuffer(worksDownloadUrl); + p.forEach(id -> { + buffer.append(id).append(DOWNLOAD_WORKS_REQUEST_SEPARATOR); + }); + String finalUrl = buffer.substring(0, buffer.lastIndexOf(DOWNLOAD_WORKS_REQUEST_SEPARATOR)); + worksDownloadUrls.add(finalUrl); + }); + return worksDownloadUrls.iterator(); }; - Function> downloadWorkFunction = data -> { - String relativeWorkUrl = data; - String orcidId = relativeWorkUrl.split("/")[0]; + Function> downloadWorksFunction = data -> { + String relativeWorksUrl = data; + String orcidId = relativeWorksUrl.split("/")[0]; final DownloadedRecordData downloaded = new DownloadedRecordData(); downloaded.setOrcidId(orcidId); downloaded.setLastModifiedDate(lastUpdateValue); @@ -149,7 +166,7 @@ public class SparkDownloadOrcidWorks { httpConnector.setAuthMethod(MultiAttemptsHttpConnector.BEARER); httpConnector.setAcceptHeaderValue("application/vnd.orcid+xml"); httpConnector.setAuthToken(token); - String apiUrl = "https://api.orcid.org/v3.0/" + relativeWorkUrl; + String apiUrl = "https://api.orcid.org/v3.0/" + relativeWorksUrl; DownloadsReport report = new DownloadsReport(); long startReq = System.currentTimeMillis(); boolean downloadCompleted = false; @@ -185,18 +202,53 @@ public class SparkDownloadOrcidWorks { return downloaded.toTuple2(); }; + FlatMapFunction, Tuple2> splitWorksFunction = data -> { + List> splittedDownloadedWorks = new ArrayList<>(); + String jsonData = data._2().toString(); + JsonElement jElement = new JsonParser().parse(jsonData); + String orcidId = data._1().toString(); + String statusCode = getJsonValue(jElement, "statusCode"); + String lastModifiedDate = getJsonValue(jElement, "lastModifiedDate"); + String compressedData = getJsonValue(jElement, "compressedData"); + String errorMessage = getJsonValue(jElement, "errorMessage"); + String works = ArgumentApplicationParser.decompressValue(compressedData); + + // split a single xml containing multiple works into multiple xml (a single work for each xml) + List splittedWorks = XMLRecordParser + .splitWorks(orcidId, works.getBytes(StandardCharsets.UTF_8)); + + splittedWorks.forEach(w -> { + final DownloadedRecordData downloaded = new DownloadedRecordData(); + downloaded.setOrcidId(orcidId); + downloaded.setLastModifiedDate(lastModifiedDate); + downloaded.setStatusCode(Integer.parseInt(statusCode)); + downloaded.setErrorMessage(errorMessage); + try { + downloaded + .setCompressedData( + ArgumentApplicationParser + .compressArgument(w)); + } catch (IOException e) { + throw new RuntimeException(e); + } + splittedDownloadedWorks.add(downloaded.toTuple2()); + }); + + return splittedDownloadedWorks.iterator(); + }; + updatedAuthorsRDD .flatMap(retrieveWorkUrlFunction) .repartition(100) - .map(downloadWorkFunction) - .mapToPair(t -> new Tuple2<>(new Text(t._1()), new Text(t._2()))) + .map(downloadWorksFunction) + .flatMap(splitWorksFunction) + .mapToPair(w -> new Tuple2<>(new Text(w._1()), new Text(w._2()))) .saveAsTextFile(workingPath.concat(outputPath), GzipCodec.class); logger.info("updatedAuthorsAcc: {}", updatedAuthorsAcc.value()); logger.info("parsedAuthorsAcc: {}", parsedAuthorsAcc.value()); logger.info("parsedWorksAcc: {}", parsedWorksAcc.value()); logger.info("modifiedWorksAcc: {}", modifiedWorksAcc.value()); - logger.info("maxModifiedWorksLimitAcc: {}", maxModifiedWorksLimitAcc.value()); logger.info("errorCodeFoundAcc: {}", errorCodeFoundAcc.value()); logger.info("errorLoadingJsonFoundAcc: {}", errorLoadingJsonFoundAcc.value()); logger.info("errorLoadingXMLFoundAcc: {}", errorLoadingXMLFoundAcc.value()); diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParser.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParser.java index e8745aa96..c1375ee2a 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParser.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParser.java @@ -1,7 +1,11 @@ package eu.dnetlib.doiboost.orcid.xml; +import java.io.ByteArrayOutputStream; +import java.io.IOException; +import java.nio.charset.StandardCharsets; import java.util.*; +import java.util.stream.Collectors; import org.apache.commons.lang3.StringUtils; import org.mortbay.log.Log; @@ -34,6 +38,33 @@ public class XMLRecordParser { private static final String NS_WORK_URL = "http://www.orcid.org/ns/work"; private static final String NS_HISTORY = "history"; private static final String NS_HISTORY_URL = "http://www.orcid.org/ns/history"; + private static final String NS_BULK_URL = "http://www.orcid.org/ns/bulk"; + private static final String NS_BULK = "bulk"; + + private static final String namespaceList = " xmlns:internal=\"http://www.orcid.org/ns/internal\"\n" + + " xmlns:education=\"http://www.orcid.org/ns/education\"\n" + + " xmlns:distinction=\"http://www.orcid.org/ns/distinction\"\n" + + " xmlns:deprecated=\"http://www.orcid.org/ns/deprecated\"\n" + + " xmlns:other-name=\"http://www.orcid.org/ns/other-name\"\n" + + " xmlns:membership=\"http://www.orcid.org/ns/membership\"\n" + + " xmlns:error=\"http://www.orcid.org/ns/error\" xmlns:common=\"http://www.orcid.org/ns/common\"\n" + + " xmlns:record=\"http://www.orcid.org/ns/record\"\n" + + " xmlns:personal-details=\"http://www.orcid.org/ns/personal-details\"\n" + + " xmlns:keyword=\"http://www.orcid.org/ns/keyword\" xmlns:email=\"http://www.orcid.org/ns/email\"\n" + + " xmlns:external-identifier=\"http://www.orcid.org/ns/external-identifier\"\n" + + " xmlns:funding=\"http://www.orcid.org/ns/funding\"\n" + + " xmlns:preferences=\"http://www.orcid.org/ns/preferences\"\n" + + " xmlns:address=\"http://www.orcid.org/ns/address\"\n" + + " xmlns:invited-position=\"http://www.orcid.org/ns/invited-position\"\n" + + " xmlns:work=\"http://www.orcid.org/ns/work\" xmlns:history=\"http://www.orcid.org/ns/history\"\n" + + " xmlns:employment=\"http://www.orcid.org/ns/employment\"\n" + + " xmlns:qualification=\"http://www.orcid.org/ns/qualification\"\n" + + " xmlns:service=\"http://www.orcid.org/ns/service\" xmlns:person=\"http://www.orcid.org/ns/person\"\n" + + " xmlns:activities=\"http://www.orcid.org/ns/activities\"\n" + + " xmlns:researcher-url=\"http://www.orcid.org/ns/researcher-url\"\n" + + " xmlns:peer-review=\"http://www.orcid.org/ns/peer-review\"\n" + + " xmlns:bulk=\"http://www.orcid.org/ns/bulk\"\n" + + " xmlns:research-resource=\"http://www.orcid.org/ns/research-resource\""; private static final String NS_ERROR = "error"; @@ -307,4 +338,65 @@ public class XMLRecordParser { } return authorHistory; } + + public static List splitWorks(String orcidId, byte[] bytes) + throws ParseException, XPathParseException, NavException, XPathEvalException, VtdException, ModifyException, + IOException, TranscodeException { + + final VTDGen vg = new VTDGen(); + vg.setDoc(bytes); + vg.parse(true); + final VTDNav vn = vg.getNav(); + final AutoPilot ap = new AutoPilot(vn); + ap.declareXPathNameSpace(NS_COMMON, NS_COMMON_URL); + ap.declareXPathNameSpace(NS_WORK, NS_WORK_URL); + ap.declareXPathNameSpace(NS_ERROR, NS_ERROR_URL); + ap.declareXPathNameSpace(NS_BULK, NS_BULK_URL); + + List works = new ArrayList<>(); + try { + ap.selectXPath("//work:work"); + while (ap.evalXPath() != -1) { + ByteArrayOutputStream bos = new ByteArrayOutputStream(); + long l = vn.getElementFragment(); + String xmlHeader = ""; + bos.write(xmlHeader.getBytes(StandardCharsets.UTF_8)); + bos.write(vn.getXML().getBytes(), (int) l, (int) (l >> 32)); + works.add(bos.toString()); + bos.close(); + } + } catch (Exception e) { + throw new VtdException(e); + } + + List vgModifiers = Arrays.asList(new VTDGen()); + List xmModifiers = Arrays.asList(new XMLModifier()); + List buffer = Arrays.asList(new ByteArrayOutputStream()); + List updatedWorks = works.stream().map(work -> { + vgModifiers.get(0).setDoc(work.getBytes()); + try { + vgModifiers.get(0).parse(false); + final VTDNav vnModifier = vgModifiers.get(0).getNav(); + xmModifiers.get(0).bind(vnModifier); + vnModifier.toElement(VTDNav.ROOT); + int attr = vnModifier.getAttrVal("put-code"); + if (attr > -1) { + xmModifiers + .get(0) + .insertAttribute( + " path=\"/" + orcidId + "/work/" + vnModifier.toNormalizedString(attr) + "\"" + + " " + namespaceList); + } + buffer.set(0, new ByteArrayOutputStream()); + xmModifiers.get(0).output(buffer.get(0)); + buffer.get(0).close(); + return buffer.get(0).toString(); + } catch (NavException | ModifyException | IOException | TranscodeException | ParseException e) { + e.printStackTrace(); + throw new RuntimeException(e); + } + }).collect(Collectors.toList()); + + return updatedWorks; + } } diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_updates_download/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_updates_download/oozie_app/workflow.xml index f1195a16f..43d7eb1ec 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_updates_download/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_updates_download/oozie_app/workflow.xml @@ -78,7 +78,7 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] @@ -190,7 +190,7 @@ -odownloads/updated_works -t${token} - + diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/OrcidClientTest.java b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/OrcidClientTest.java index d4079058e..70bbd066a 100644 --- a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/OrcidClientTest.java +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/OrcidClientTest.java @@ -161,13 +161,11 @@ public class OrcidClientTest { @Test @Disabled - void testReadBase64CompressedRecord() throws Exception { + void testReadBase64CompressedWork() throws Exception { final String base64CompressedRecord = IOUtils - .toString(getClass().getResourceAsStream("0000-0003-3028-6161.compressed.base64")); + .toString(getClass().getResourceAsStream("0000-0001-7281-6306.compressed.base64")); final String recordFromSeqFile = ArgumentApplicationParser.decompressValue(base64CompressedRecord); logToFile(testPath, "\n\ndownloaded \n\n" + recordFromSeqFile); - final String downloadedRecord = testDownloadRecord("0000-0003-3028-6161", REQUEST_TYPE_RECORD); - assertEquals(recordFromSeqFile, downloadedRecord); } @Test @@ -337,7 +335,7 @@ public class OrcidClientTest { @Ignore void testUpdatedRecord() throws Exception { final String base64CompressedRecord = IOUtils - .toString(getClass().getResourceAsStream("0000-0003-3028-6161.compressed.base64")); + .toString(getClass().getResourceAsStream("0000-0001-7281-6306.compressed.base64")); final String record = ArgumentApplicationParser.decompressValue(base64CompressedRecord); logToFile(testPath, "\n\nrecord updated \n\n" + record); } diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParserTest.java b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParserTest.java index 78760fa96..cb6713009 100644 --- a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParserTest.java +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParserTest.java @@ -108,4 +108,12 @@ public class XMLRecordParserTest { work.setBase64CompressData(ArgumentApplicationParser.compressArgument(xml)); OrcidClientTest.logToFile(testPath, JsonWriter.create(work)); } + + @Test + void testWorksSplit() throws Exception { + String xml = IOUtils + .toString( + this.getClass().getResourceAsStream("multiple_downloaded_works.xml")); + XMLRecordParser.splitWorks("0000-0001-7291-3210", xml.getBytes()); + } } diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/0000-0001-7281-6306.compressed.base64 b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/0000-0001-7281-6306.compressed.base64 new file mode 100644 index 000000000..07b2d46a2 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/0000-0001-7281-6306.compressed.base64 @@ -0,0 +1 @@ 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\ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/0000-0003-3028-6161.compressed.base64 b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/0000-0003-3028-6161.compressed.base64 deleted file mode 100644 index 34de6ba16..000000000 --- a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/0000-0003-3028-6161.compressed.base64 +++ /dev/null @@ -1 +0,0 @@ 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 \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/xml/multiple_downloaded_works.xml b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/xml/multiple_downloaded_works.xml new file mode 100644 index 000000000..b155b16e3 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/xml/multiple_downloaded_works.xml @@ -0,0 +1,57 @@ + + + + 2015-05-23T18:56:52.486Z + 2017-02-28T08:22:12.454Z + + + https://orcid.org/0000-0001-7291-3210 + 0000-0001-7291-3210 + orcid.org + + Paolo Manghi + + + The Query Language TQL + + 5th International Workshop on Web and Data Bases (WebDB02) in conjunction with ACM SIGMOD 2002 + + bibtex + @inproceedings{Conforti2002, Author= {Giovanni Conforti and Giorgio Ghelli and Antonio Albano and Dario Colazzo and Paolo Manghi and Carlo Sartiani}, Bibsource= {DBLP, http://dblp.uni-trier.de}, Booktitle= {5th International Workshop on Web and Data Bases (WebDB02) in conjunction with ACM SIGMOD 2002}, Ee= {http://www.db.ucsd.edu/webdb2002/papers/43.pdf}, Pages= {13-18}, Title= {The Query Language TQL}, Year= {2002}} + + + + conference-paper + + 2002 + + + + + 2015-05-23T18:58:18.492Z + 2017-02-28T08:22:12.455Z + + + https://orcid.org/0000-0001-7291-3210 + 0000-0001-7291-3210 + orcid.org + + Paolo Manghi + + + The Query Language TQL - Demo Presentation + + X Convegno nazionale su Sistemi Evoluti per Basi di Dati (SEBD) + + bibtex + @inproceedings{Conforti2002Demo, Address= {Portoferraio, Italy}, Author= {Giovanni Conforti and Giorgio Ghelli and Antonio Albano and Dario Colazzo and Paolo Manghi and Carlo Sartiani}, Bibsource= {DBLP, http://dblp.uni-trier.de}, Booktitle= {X Convegno nazionale su Sistemi Evoluti per Basi di Dati (SEBD)}, Month= {June}, Pages= {427-431}, Title= {The Query Language TQL - Demo Presentation}, Year= {2002}} + + + + conference-paper + + 2002 + + + + \ No newline at end of file From 144c103b672c3165f8af4bc27f5515f620b3c7d2 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 25 Jul 2022 13:52:45 +0200 Subject: [PATCH 122/214] [EOSC Context Tagging] add check to avoid the insertion of the context if already present --- .../java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java index 99ff92223..24520ff26 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java @@ -117,8 +117,9 @@ public class SparkEoscBulkTag implements Serializable { } private static R enrich(R value, List hostedByList) { - if (value.getInstance().stream().anyMatch(i -> hostedByList.contains(i.getHostedby().getKey())) || - (value.getEoscifguidelines() != null && value.getEoscifguidelines().size() > 0)) { + if (value.getInstance().stream().anyMatch(i -> (hostedByList.contains(i.getHostedby().getKey())) || + (value.getEoscifguidelines() != null && value.getEoscifguidelines().size() > 0)) && + !value.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))) { Context context = new Context(); context.setId("eosc"); context.setDataInfo(Arrays.asList(OafMapperUtils From 0172bab25136b1a3f974c2d66ddee434a712e26f Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 25 Jul 2022 14:16:45 +0200 Subject: [PATCH 123/214] [EOSC Context Tagging] refactoring --- .../dhp/bulktag/eosc/SparkEoscBulkTag.java | 25 +++++++++++++------ 1 file changed, 17 insertions(+), 8 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java index 24520ff26..66e0c8af4 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java @@ -117,19 +117,28 @@ public class SparkEoscBulkTag implements Serializable { } private static R enrich(R value, List hostedByList) { - if (value.getInstance().stream().anyMatch(i -> (hostedByList.contains(i.getHostedby().getKey())) || - (value.getEoscifguidelines() != null && value.getEoscifguidelines().size() > 0)) && - !value.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))) { + if (value + .getInstance() + .stream() + .anyMatch( + i -> (hostedByList.contains(i.getHostedby().getKey())) || + (value.getEoscifguidelines() != null && value.getEoscifguidelines().size() > 0)) + && + !value.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))) { Context context = new Context(); context.setId("eosc"); - context.setDataInfo(Arrays.asList(OafMapperUtils - .dataInfo( - false, BULKTAG_DATA_INFO_TYPE, true, false, + context + .setDataInfo( + Arrays + .asList( OafMapperUtils - .qualifier( + .dataInfo( + false, BULKTAG_DATA_INFO_TYPE, true, false, + OafMapperUtils + .qualifier( CLASS_ID_DATASOURCE, CLASS_NAME_BULKTAG_DATASOURCE, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), - TAGGING_TRUST))); + TAGGING_TRUST))); value.getContext().add(context); } From 1c82acb16835ea7ce3f70f8c847204f0ac487708 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 25 Jul 2022 14:26:39 +0200 Subject: [PATCH 124/214] [EOSC Context Tagging] refactoring: moved EOSC IF tagging in package eosc under bulkTag --- .../eu/dnetlib/dhp/bulktag/{ => eosc}/SparkEoscTag.java | 7 +------ .../eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml | 2 +- .../test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java | 5 +---- 3 files changed, 3 insertions(+), 11 deletions(-) rename dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/{ => eosc}/SparkEoscTag.java (96%) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscTag.java similarity index 96% rename from dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java rename to dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscTag.java index 730e8a3fe..736496641 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscTag.java @@ -1,13 +1,10 @@ -package eu.dnetlib.dhp.bulktag; +package eu.dnetlib.dhp.bulktag.eosc; import static eu.dnetlib.dhp.PropagationConstant.readPath; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.util.*; -import java.util.function.Function; -import java.util.stream.Collectors; -import java.util.stream.Stream; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; @@ -21,9 +18,7 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.*; -import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; public class SparkEoscTag { private static final Logger log = LoggerFactory.getLogger(SparkEoscTag.class); diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml index 17fc76aad..9c1bbdf72 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml @@ -226,7 +226,7 @@ yarn-cluster cluster EOSC_tagging - eu.dnetlib.dhp.bulktag.SparkEoscTag + eu.dnetlib.dhp.bulktag.eosc.SparkEoscTag dhp-enrichment-${projectVersion}.jar --num-executors=${sparkExecutorNumber} diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java index 5f47da10e..17e570fdf 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java @@ -1,21 +1,18 @@ package eu.dnetlib.dhp.bulktag; -import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.ZENODO_COMMUNITY_INDICATOR; - import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; import java.util.List; +import eu.dnetlib.dhp.bulktag.eosc.SparkEoscTag; import org.apache.commons.io.FileUtils; -import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.Row; import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; import org.junit.jupiter.api.AfterAll; From 35bcd9422d60be622a0dd6f71a4a5be03513e07b Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 25 Jul 2022 15:45:22 +0200 Subject: [PATCH 125/214] [EOSC Context Tagging] removed not needed specification in path --- .../eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java index 9ad108749..e9b1d3cfd 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java @@ -62,7 +62,7 @@ public class ReadMasterDatasourceFromDB implements Closeable { final String dbUrl = parser.get("postgresUrl"); final String dbUser = parser.get("postgresUser"); final String dbPassword = parser.get("postgresPassword"); - final String hdfsPath = parser.get("hdfsPath") + "/datasourceMasters"; + final String hdfsPath = parser.get("hdfsPath"); final String hdfsNameNode = parser.get("hdfsNameNode"); try ( From d43663d30f6a3039a28ad8a6ac9723dd3fce4e9c Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 25 Jul 2022 17:54:10 +0200 Subject: [PATCH 126/214] adapted RorActionSet test, it should not create parent/child rels --- .../ror/GenerateRorActionSetJobTest.java | 22 ++++++++----------- 1 file changed, 9 insertions(+), 13 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJobTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJobTest.java index d50c1d5f3..5736bd95e 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJobTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJobTest.java @@ -2,6 +2,7 @@ package eu.dnetlib.dhp.actionmanager.ror; import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertNotNull; import java.io.FileInputStream; import java.util.List; @@ -38,25 +39,20 @@ class GenerateRorActionSetJobTest { .readValue(IOUtils.toString(getClass().getResourceAsStream("ror_org.json")), RorOrganization.class); final List> aas = GenerateRorActionSetJob.convertRorOrg(r); - Assertions.assertEquals(3, aas.size()); + Assertions.assertEquals(1, aas.size()); assertEquals(Organization.class, aas.get(0).getClazz()); - assertEquals(Relation.class, aas.get(1).getClazz()); - assertEquals(Relation.class, aas.get(2).getClazz()); final Organization o = (Organization) aas.get(0).getPayload(); - final Relation r1 = (Relation) aas.get(1).getPayload(); - final Relation r2 = (Relation) aas.get(2).getPayload(); - assertEquals(o.getId(), r1.getSource()); - assertEquals(r1.getSource(), r2.getTarget()); - assertEquals(r2.getSource(), r1.getTarget()); - assertEquals(ModelConstants.IS_PARENT_OF, r1.getRelClass()); - assertEquals(ModelConstants.IS_CHILD_OF, r2.getRelClass()); + assertNotNull(o); + + assertNotNull(o.getCountry()); + assertEquals("AU", o.getCountry().getClassid()); + + assertNotNull(o.getLegalname()); + assertEquals("Mount Stromlo Observatory", o.getLegalname().getValue()); System.out.println(mapper.writeValueAsString(o)); - System.out.println(mapper.writeValueAsString(r1)); - System.out.println(mapper.writeValueAsString(r2)); - } @Test From 67525076ec9ec4ff7b190a0bc1a15b5a31333388 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Tue, 26 Jul 2022 15:35:17 +0200 Subject: [PATCH 127/214] fixed test, now it compiles after commit a6977197b3925c520f76961cfff7b05c37a51d6f --- .../dhp/datacite/DataciteToOAFTest.scala | 17 +++++++--- .../dhp/datacite/DataciteUtilityTest.scala | 31 +++++++++++++++++++ 2 files changed, 43 insertions(+), 5 deletions(-) create mode 100644 dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteUtilityTest.scala diff --git a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala index 31784c7e9..68230b477 100644 --- a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala +++ b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala @@ -2,11 +2,14 @@ package eu.dnetlib.dhp.datacite import com.fasterxml.jackson.databind.{ObjectMapper, SerializationFeature} import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest -import eu.dnetlib.dhp.schema.oaf.Oaf +import eu.dnetlib.dhp.schema.oaf.{Dataset => OafDataset, _} import org.apache.commons.io.FileUtils import org.apache.spark.SparkConf import org.apache.spark.sql.functions.{col, count} import org.apache.spark.sql.{Dataset, Encoder, Encoders, SparkSession} +import org.json4s.DefaultFormats +import org.json4s.JsonAST.{JField, JObject, JString} +import org.json4s.jackson.JsonMethods.parse import org.junit.jupiter.api.Assertions._ import org.junit.jupiter.api.extension.ExtendWith import org.junit.jupiter.api.{AfterEach, BeforeEach, Test} @@ -45,6 +48,9 @@ class DataciteToOAFTest extends AbstractVocabularyTest { } + + + @Test def testConvert(): Unit = { @@ -70,17 +76,18 @@ class DataciteToOAFTest extends AbstractVocabularyTest { assertEquals(100, nativeSize) - spark.read.load(targetPath).printSchema(); + val result: Dataset[String] = spark.read.text(targetPath).as[String].map(DataciteUtilityTest.convertToOAF)(Encoders.STRING) + + + - val result: Dataset[Oaf] = spark.read.load(targetPath).as[Oaf] result - .map(s => s.getClass.getSimpleName) .groupBy(col("value").alias("class")) .agg(count("value").alias("Total")) .show(false) - val t = spark.read.load(targetPath).count() + val t = spark.read.text(targetPath).as[String].count() assertTrue(t > 0) diff --git a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteUtilityTest.scala b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteUtilityTest.scala new file mode 100644 index 000000000..04d3c4a58 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteUtilityTest.scala @@ -0,0 +1,31 @@ +package eu.dnetlib.dhp.datacite + +import org.json4s.DefaultFormats +import org.json4s.JsonAST.{JField, JObject, JString} +import org.json4s.jackson.JsonMethods.parse + +object DataciteUtilityTest { + + def convertToOAF(input:String) : String = { + implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats + lazy val json = parse(input) + + + val isRelation:String = (json \\ "source").extractOrElse("NULL") + + if (isRelation != "NULL") { + return "Relation" + } + + val iType: List[String] = for { + JObject(instance) <- json \\ "instance" + JField("instancetype", JObject(instancetype)) <- instance + JField("classname", JString(classname)) <- instancetype + + } yield classname + + val l:String =iType.head.toLowerCase() + l + } + +} From ed98a6d9d04aafd8ed32212e3e77040d1f8338e0 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 28 Jul 2022 10:15:14 +0200 Subject: [PATCH 128/214] [Datacite mapping] include the older datacite prefixed OpenAIRE id among the originalId[] --- .../dnetlib/dhp/datacite/DataciteToOAFTransformation.scala | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala index ff966aaea..a7863d144 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala @@ -584,7 +584,12 @@ object DataciteToOAFTransformation { JField("awardUri", JString(awardUri)) <- fundingReferences } yield awardUri + val oid = result.getId result.setId(IdentifierFactory.createIdentifier(result)) + if (!result.getId.equalsIgnoreCase(oid)) { + result.getOriginalId.add(oid) + } + var relations: List[Relation] = awardUris.flatMap(a => get_projectRelation(a, result.getId)).filter(r => r != null) From 1dd1e4fe3a224935d3c021f09ae4284e2a22b29e Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 28 Jul 2022 11:27:08 +0200 Subject: [PATCH 129/214] extended test for mapping project_organization relations --- .../raw/MigrateDbEntitiesApplication.java | 2 +- .../raw/MigrateDbEntitiesApplicationTest.java | 62 ++++++++++++++----- .../projectorganization_resultset_entry.json | 17 +++-- 3 files changed, 57 insertions(+), 24 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java index 8296e99cd..f40d3d19b 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java @@ -440,7 +440,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i final List properties = Lists .newArrayList( - keyValue("contribution", String.valueOf(rs.getDouble("totalcost"))), + keyValue("contribution", String.valueOf(rs.getDouble("contribution"))), keyValue("currency", rs.getString("currency"))); final Relation r1 = OafMapperUtils diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java index 9048a22ea..06947103a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java @@ -1,9 +1,7 @@ package eu.dnetlib.dhp.oa.graph.raw; -import static org.junit.jupiter.api.Assertions.assertEquals; -import static org.junit.jupiter.api.Assertions.assertNotNull; -import static org.junit.jupiter.api.Assertions.assertTrue; +import static org.junit.jupiter.api.Assertions.*; import static org.mockito.ArgumentMatchers.anyString; import static org.mockito.Mockito.lenient; @@ -31,11 +29,12 @@ import com.fasterxml.jackson.core.type.TypeReference; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; +import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; @ExtendWith(MockitoExtension.class) -public class MigrateDbEntitiesApplicationTest { +class MigrateDbEntitiesApplicationTest { private MigrateDbEntitiesApplication app; @@ -61,7 +60,7 @@ public class MigrateDbEntitiesApplicationTest { } @Test - public void testProcessService() throws Exception { + void testProcessService() throws Exception { final List fields = prepareMocks("services_resultset_entry.json"); final List list = app.processService(rs); @@ -74,7 +73,7 @@ public class MigrateDbEntitiesApplicationTest { .getCollectedfrom() .stream() .map(KeyValue::getKey) - .forEach(dsId -> assertValidId(dsId)); + .forEach(this::assertValidId); assertEquals(1, ds.getPid().size()); assertEquals("r3d100010218", ds.getPid().get(0).getValue()); @@ -163,14 +162,14 @@ public class MigrateDbEntitiesApplicationTest { .stream() .map(Qualifier::getSchemeid) .collect(Collectors.toCollection(HashSet::new)); - assertTrue(cpSchemeId.size() == 1); + assertEquals(1,cpSchemeId.size()); assertTrue(cpSchemeId.contains("eosc:contentpolicies")); HashSet cpSchemeName = ds .getContentpolicies() .stream() .map(Qualifier::getSchemename) .collect(Collectors.toCollection(HashSet::new)); - assertTrue(cpSchemeName.size() == 1); + assertEquals(1, cpSchemeName.size()); assertTrue(cpSchemeName.contains("eosc:contentpolicies")); assertEquals(2, ds.getContentpolicies().size()); assertEquals("Taxonomic classification", ds.getContentpolicies().get(0).getClassid()); @@ -193,7 +192,7 @@ public class MigrateDbEntitiesApplicationTest { } @Test - public void testProcessProject() throws Exception { + void testProcessProject() throws Exception { final List fields = prepareMocks("projects_resultset_entry.json"); final List list = app.processProject(rs); @@ -211,7 +210,7 @@ public class MigrateDbEntitiesApplicationTest { } @Test - public void testProcessOrganization() throws Exception { + void testProcessOrganization() throws Exception { final List fields = prepareMocks("organizations_resultset_entry.json"); final List list = app.processOrganization(rs); @@ -238,7 +237,7 @@ public class MigrateDbEntitiesApplicationTest { } @Test - public void testProcessDatasourceOrganization() throws Exception { + void testProcessDatasourceOrganization() throws Exception { final List fields = prepareMocks("datasourceorganization_resultset_entry.json"); final List list = app.processServiceOrganization(rs); @@ -255,7 +254,7 @@ public class MigrateDbEntitiesApplicationTest { } @Test - public void testProcessProjectOrganization() throws Exception { + void testProcessProjectOrganization() throws Exception { final List fields = prepareMocks("projectorganization_resultset_entry.json"); final List list = app.processProjectOrganization(rs); @@ -271,6 +270,38 @@ public class MigrateDbEntitiesApplicationTest { assertEquals(r2.getSource(), r1.getTarget()); assertValidId(r1.getCollectedfrom().get(0).getKey()); assertValidId(r2.getCollectedfrom().get(0).getKey()); + + assertEquals(ModelConstants.PROJECT_ORGANIZATION, r1.getRelType()); + assertEquals(ModelConstants.PROJECT_ORGANIZATION, r2.getRelType()); + + assertEquals(ModelConstants.PARTICIPATION, r1.getSubRelType()); + assertEquals(ModelConstants.PARTICIPATION, r2.getSubRelType()); + + if (r1.getSource().startsWith("40")) { + assertEquals(ModelConstants.HAS_PARTICIPANT, r1.getRelClass()); + assertEquals(ModelConstants.IS_PARTICIPANT, r2.getRelClass()); + } else if (r1.getSource().startsWith("20")) { + assertEquals(ModelConstants.IS_PARTICIPANT, r1.getRelClass()); + assertEquals(ModelConstants.HAS_PARTICIPANT, r2.getRelClass()); + } + + assertNotNull(r1.getProperties()); + checkProperty(r1, "contribution", "436754.0"); + checkProperty(r2, "contribution", "436754.0"); + + checkProperty(r1, "currency","EUR"); + checkProperty(r2, "currency", "EUR"); + } + + private void checkProperty(Relation r, String property, String value) { + final List p = r + .getProperties() + .stream() + .filter(kv -> kv.getKey().equals(property)) + .collect(Collectors.toList()); + assertFalse(p.isEmpty()); + assertEquals(1, p.size()); + assertEquals(value, p.get(0).getValue()); } @Test @@ -289,7 +320,7 @@ public class MigrateDbEntitiesApplicationTest { } @Test - public void testProcessClaims_rels() throws Exception { + void testProcessClaims_rels() throws Exception { final List fields = prepareMocks("claimsrel_resultset_entry.json"); final List list = app.processClaims(rs); @@ -320,9 +351,6 @@ public class MigrateDbEntitiesApplicationTest { assertValidId(r1.getCollectedfrom().get(0).getKey()); assertValidId(r2.getCollectedfrom().get(0).getKey()); - - // System.out.println(new ObjectMapper().writeValueAsString(r1)); - // System.out.println(new ObjectMapper().writeValueAsString(r2)); } private List prepareMocks(final String jsonFile) throws IOException, SQLException { @@ -385,7 +413,7 @@ public class MigrateDbEntitiesApplicationTest { final String[] values = ((List) tf.getValue()) .stream() .filter(Objects::nonNull) - .map(o -> o.toString()) + .map(Object::toString) .toArray(String[]::new); Mockito.when(arr.getArray()).thenReturn(values); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/projectorganization_resultset_entry.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/projectorganization_resultset_entry.json index a3305926d..02cebae38 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/projectorganization_resultset_entry.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/projectorganization_resultset_entry.json @@ -2,12 +2,12 @@ { "field": "project", "type": "string", - "value": "nsf_________::1700003" + "value": "corda__h2020::824273" }, { "field": "resporganization", "type": "string", - "value": "nsf_________::University_of_Notre_Dame" + "value": "corda__h2020::999945647" }, { "field": "participantnumber", @@ -16,8 +16,13 @@ }, { "field": "contribution", - "type": "not_used", - "value": null + "type": "double", + "value": 436754 + }, + { + "field": "currency", + "type": "string", + "value": "EUR" }, { "field": "startdate", @@ -52,12 +57,12 @@ { "field": "collectedfromid", "type": "string", - "value": "openaire____::nsf" + "value": "openaire____::corda_h2020" }, { "field": "collectedfromname", "type": "string", - "value": "NSF - National Science Foundation" + "value": "CORDA - COmmon Research DAta Warehouse - Horizon 2020" }, { "field": "semantics", From 3329b6ce6bdccdab25c4bb900cc8ad4f78d8c77c Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 29 Jul 2022 10:54:20 +0200 Subject: [PATCH 130/214] [EOSC TAG] added fix for NPE on subjects --- .../src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscTag.java | 2 ++ 1 file changed, 2 insertions(+) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscTag.java index 736496641..a96e6a3bc 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscTag.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscTag.java @@ -183,6 +183,8 @@ public class SparkEoscTag { } private static boolean containsCriteriaNotebook(Software s) { + if(!Optional.ofNullable(s.getSubject()).isPresent()) + return false; if (s.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("jupyter"))) return true; if (s From 0727f0ef481f783dbfcfd670bd4d91ee88a34f7a Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 29 Jul 2022 11:55:34 +0200 Subject: [PATCH 131/214] [EOSC tag] avoid NPEs --- .../dhp/bulktag/eosc/SparkEoscTag.java | 41 +++++++++++-------- .../dnetlib/dhp/bulktag/EOSCTagJobTest.java | 2 +- 2 files changed, 25 insertions(+), 18 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscTag.java index a96e6a3bc..c131399cc 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscTag.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscTag.java @@ -23,6 +23,10 @@ import eu.dnetlib.dhp.schema.oaf.*; public class SparkEoscTag { private static final Logger log = LoggerFactory.getLogger(SparkEoscTag.class); public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + public static final String EOSC_GALAXY_WORKFLOW = "EOSC::Galaxy Workflow"; + public static final String EOSC_TWITTER_DATA = "EOSC::Twitter Data"; + public static final String EOSC_JUPYTER_NOTEBOOK = "EOSC::Jupyter Notebook"; + public static final String COMPLIES_WITH = "compliesWith"; public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils @@ -76,8 +80,8 @@ public class SparkEoscTag { if (!Optional.ofNullable(s.getEoscifguidelines()).isPresent()) s.setEoscifguidelines(new ArrayList<>()); addEIG( - s.getEoscifguidelines(), "EOSC::Jupyter Notebook", "EOSC::Jupyter Notebook", "", - "compliesWith"); + s.getEoscifguidelines(), EOSC_JUPYTER_NOTEBOOK, EOSC_JUPYTER_NOTEBOOK, "", + COMPLIES_WITH); } if (containsCriteriaGalaxy(s)) { @@ -85,7 +89,7 @@ public class SparkEoscTag { s.setEoscifguidelines(new ArrayList<>()); addEIG( - s.getEoscifguidelines(), "EOSC::Galaxy Workflow", "EOSC::Galaxy Workflow", "", "compliesWith"); + s.getEoscifguidelines(), EOSC_GALAXY_WORKFLOW, EOSC_GALAXY_WORKFLOW, "", COMPLIES_WITH); } return s; }, Encoders.bean(Software.class)) @@ -108,11 +112,11 @@ public class SparkEoscTag { if (containsCriteriaGalaxy(orp)) { addEIG( - orp.getEoscifguidelines(), "EOSC::Galaxy Workflow", "EOSC::Galaxy Workflow", "", - "compliesWith"); + orp.getEoscifguidelines(), EOSC_GALAXY_WORKFLOW, EOSC_GALAXY_WORKFLOW, "", + COMPLIES_WITH); } if (containscriteriaTwitter(orp)) { - addEIG(orp.getEoscifguidelines(), "EOSC::Twitter Data", "EOSC::Twitter Data", "", "compliesWith"); + addEIG(orp.getEoscifguidelines(), EOSC_TWITTER_DATA, EOSC_TWITTER_DATA, "", COMPLIES_WITH); } return orp; }, Encoders.bean(OtherResearchProduct.class)) @@ -133,7 +137,7 @@ public class SparkEoscTag { if (!Optional.ofNullable(d.getEoscifguidelines()).isPresent()) d.setEoscifguidelines(new ArrayList<>()); if (containscriteriaTwitter(d)) { - addEIG(d.getEoscifguidelines(), "EOSC::Twitter Data", "EOSC::Twitter Data", "", "compliesWith"); + addEIG(d.getEoscifguidelines(), EOSC_TWITTER_DATA, EOSC_TWITTER_DATA, "", COMPLIES_WITH); } return d; }, Encoders.bean(Dataset.class)) @@ -163,10 +167,12 @@ public class SparkEoscTag { (words.contains("data") || words.contains("dataset"))) return true; - if (r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("twitter")) && - r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("data"))) - return true; - return false; + return Optional + .ofNullable(r.getSubject()) + .map( + s -> s.stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("twitter")) && + s.stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("data"))) + .orElse(false); } private static boolean containsCriteriaGalaxy(Result r) { @@ -176,14 +182,16 @@ public class SparkEoscTag { words.contains("workflow")) return true; - if (r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("galaxy")) && - r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("workflow"))) - return true; - return false; + return Optional + .ofNullable(r.getSubject()) + .map( + s -> s.stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("galaxy")) && + s.stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("workflow"))) + .orElse(false); } private static boolean containsCriteriaNotebook(Software s) { - if(!Optional.ofNullable(s.getSubject()).isPresent()) + if (!Optional.ofNullable(s.getSubject()).isPresent()) return false; if (s.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("jupyter"))) return true; @@ -225,6 +233,5 @@ public class SparkEoscTag { Arrays.asList(t.getValue().toLowerCase().replaceAll("[^a-zA-Z ]", "").split(" "))))); return words; - } } diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java index 17e570fdf..bfe4f6448 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java @@ -6,7 +6,6 @@ import java.nio.file.Files; import java.nio.file.Path; import java.util.List; -import eu.dnetlib.dhp.bulktag.eosc.SparkEoscTag; import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; @@ -24,6 +23,7 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.bulktag.eosc.SparkEoscTag; import eu.dnetlib.dhp.schema.oaf.*; public class EOSCTagJobTest { From f62c4e05cd239830628154dc09fb7d386f135201 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 29 Jul 2022 11:56:01 +0200 Subject: [PATCH 132/214] code formatting --- .../dnetlib/dhp/sx/bio/pubmed/PMArticle.java | 1 - .../dhp/sx/bio/pubmed/PubMedToOaf.scala | 40 +++++++-------- .../dhp/datacite/DataciteToOAFTest.scala | 10 +--- .../dhp/datacite/DataciteUtilityTest.scala | 11 ++-- .../dnetlib/dhp/sx/bio/BioScholixTest.scala | 51 ++++++++----------- .../raw/MigrateDbEntitiesApplicationTest.java | 12 ++--- 6 files changed, 53 insertions(+), 72 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMArticle.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMArticle.java index 9287a8cdd..3fb814606 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMArticle.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMArticle.java @@ -255,7 +255,6 @@ public class PMArticle implements Serializable { return grants; } - public String getPmcId() { return pmcId; } diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala index 24a1fa62b..42bafc93e 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala @@ -56,13 +56,11 @@ object PubMedToOaf { null } - - def createOriginalOpenaireId(article:PMArticle) :String = { + def createOriginalOpenaireId(article: PMArticle): String = { if (StringUtils.isNotEmpty(article.getPmcId)) { - val md5 = DHPUtils.md5(s"$OAI_HEADER${article.getPmcId.replace("PMC","")}") + val md5 = DHPUtils.md5(s"$OAI_HEADER${article.getPmcId.replace("PMC", "")}") s"$OLD_PMC_PREFIX$md5" - } - else + } else null } @@ -142,26 +140,24 @@ object PubMedToOaf { val pidList = ListBuffer[StructuredProperty]() pidList += OafMapperUtils.structuredProperty( - article.getPmid, - PidType.pmid.toString, - PidType.pmid.toString, + article.getPmid, + PidType.pmid.toString, + PidType.pmid.toString, + ModelConstants.DNET_PID_TYPES, + ModelConstants.DNET_PID_TYPES, + dataInfo + ) + + if (StringUtils.isNotBlank(article.getPmcId)) { + pidList += OafMapperUtils.structuredProperty( + article.getPmcId, + PidType.pmc.toString, + PidType.pmc.toString, ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES, dataInfo ) - - - if (StringUtils.isNotBlank(article.getPmcId)) - { - pidList += OafMapperUtils.structuredProperty( - article.getPmcId, - PidType.pmc.toString, - PidType.pmc.toString, - ModelConstants.DNET_PID_TYPES, - ModelConstants.DNET_PID_TYPES, - dataInfo - ) - } + } if (pidList == null) return null @@ -297,7 +293,7 @@ object PubMedToOaf { if (StringUtils.isNotEmpty(article.getPmcId)) { val originalIDS = ListBuffer[String]() originalIDS += createOriginalOpenaireId(article) - pidList.map(s => s.getValue).foreach(p =>originalIDS += p) + pidList.map(s => s.getValue).foreach(p => originalIDS += p) result.setOriginalId(originalIDS.asJava) } else result.setOriginalId(pidList.map(s => s.getValue).asJava) diff --git a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala index 68230b477..48da049da 100644 --- a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala +++ b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala @@ -48,9 +48,6 @@ class DataciteToOAFTest extends AbstractVocabularyTest { } - - - @Test def testConvert(): Unit = { @@ -76,11 +73,8 @@ class DataciteToOAFTest extends AbstractVocabularyTest { assertEquals(100, nativeSize) - val result: Dataset[String] = spark.read.text(targetPath).as[String].map(DataciteUtilityTest.convertToOAF)(Encoders.STRING) - - - - + val result: Dataset[String] = + spark.read.text(targetPath).as[String].map(DataciteUtilityTest.convertToOAF)(Encoders.STRING) result .groupBy(col("value").alias("class")) diff --git a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteUtilityTest.scala b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteUtilityTest.scala index 04d3c4a58..942e0958e 100644 --- a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteUtilityTest.scala +++ b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteUtilityTest.scala @@ -6,25 +6,24 @@ import org.json4s.jackson.JsonMethods.parse object DataciteUtilityTest { - def convertToOAF(input:String) : String = { + def convertToOAF(input: String): String = { implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats lazy val json = parse(input) - - val isRelation:String = (json \\ "source").extractOrElse("NULL") + val isRelation: String = (json \\ "source").extractOrElse("NULL") if (isRelation != "NULL") { return "Relation" } val iType: List[String] = for { - JObject(instance) <- json \\ "instance" + JObject(instance) <- json \\ "instance" JField("instancetype", JObject(instancetype)) <- instance - JField("classname", JString(classname)) <- instancetype + JField("classname", JString(classname)) <- instancetype } yield classname - val l:String =iType.head.toLowerCase() + val l: String = iType.head.toLowerCase() l } diff --git a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala index b021e5e07..827d23e72 100644 --- a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala +++ b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala @@ -76,12 +76,11 @@ class BioScholixTest extends AbstractVocabularyTest { } - - private def checkPMArticle(article:PMArticle): Unit = { + private def checkPMArticle(article: PMArticle): Unit = { assertNotNull(article.getPmid) assertNotNull(article.getTitle) assertNotNull(article.getAuthors) - article.getAuthors.asScala.foreach{a => + article.getAuthors.asScala.foreach { a => assertNotNull(a) assertNotNull(a.getFullName) } @@ -89,20 +88,21 @@ class BioScholixTest extends AbstractVocabularyTest { } @Test - def testParsingPubmedXML():Unit = { - val xml = new XMLEventReader(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml"))) + def testParsingPubmedXML(): Unit = { + val xml = new XMLEventReader( + Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml")) + ) val parser = new PMParser(xml) parser.foreach(checkPMArticle) } - - private def checkPubmedPublication(o:Oaf): Unit = { + private def checkPubmedPublication(o: Oaf): Unit = { assertTrue(o.isInstanceOf[Publication]) - val p:Publication = o.asInstanceOf[Publication] + val p: Publication = o.asInstanceOf[Publication] assertNotNull(p.getId) assertNotNull(p.getTitle) - p.getTitle.asScala.foreach(t =>assertNotNull(t.getValue)) - p.getAuthor.asScala.foreach(a =>assertNotNull(a.getFullname)) + p.getTitle.asScala.foreach(t => assertNotNull(t.getValue)) + p.getAuthor.asScala.foreach(a => assertNotNull(a.getFullname)) assertNotNull(p.getInstance()) p.getInstance().asScala.foreach { i => assertNotNull(i.getCollectedfrom) @@ -112,28 +112,26 @@ class BioScholixTest extends AbstractVocabularyTest { assertNotNull(p.getOriginalId) p.getOriginalId.asScala.foreach(oId => assertNotNull(oId)) - - val hasPMC = p.getInstance().asScala.exists(i => i.getPid.asScala.exists(pid => pid.getQualifier.getClassid.equalsIgnoreCase(PidType.pmc.toString))) - - + val hasPMC = p + .getInstance() + .asScala + .exists(i => i.getPid.asScala.exists(pid => pid.getQualifier.getClassid.equalsIgnoreCase(PidType.pmc.toString))) if (hasPMC) { assertTrue(p.getOriginalId.asScala.exists(oId => oId.startsWith("od_______267::"))) } } - @Test - def testPubmedOriginalID():Unit = { - val article:PMArticle = new PMArticle - + def testPubmedOriginalID(): Unit = { + val article: PMArticle = new PMArticle article.setPmid("1234") article.setTitle("a Title") // VERIFY PUBLICATION IS NOT NULL - article.getPublicationTypes.add( new PMSubject("article",null, null)) + article.getPublicationTypes.add(new PMSubject("article", null, null)) var publication = PubMedToOaf.convert(article, vocabularies).asInstanceOf[Publication] assertNotNull(publication) assertEquals("50|pmid________::81dc9bdb52d04dc20036dbd8313ed055", publication.getId) @@ -146,30 +144,25 @@ class BioScholixTest extends AbstractVocabularyTest { // VERIFY ORIGINAL ID GENERATE IN OLD WAY USING PMC IDENTIFIER EXISTS - - val oldOpenaireID ="od_______267::0000072375bc0e68fa09d4e6b7658248" + val oldOpenaireID = "od_______267::0000072375bc0e68fa09d4e6b7658248" val hasOldOpenAIREID = publication.getOriginalId.asScala.exists(o => o.equalsIgnoreCase(oldOpenaireID)) assertTrue(hasOldOpenAIREID) } - @Test - def testPubmedMapping() :Unit = { + def testPubmedMapping(): Unit = { - val xml = new XMLEventReader(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml"))) + val xml = new XMLEventReader( + Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml")) + ) val parser = new PMParser(xml) val results = ListBuffer[Oaf]() parser.foreach(x => results += PubMedToOaf.convert(x, vocabularies)) - - - results.foreach(checkPubmedPublication) - - } @Test diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java index 06947103a..069edc5a6 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java @@ -162,7 +162,7 @@ class MigrateDbEntitiesApplicationTest { .stream() .map(Qualifier::getSchemeid) .collect(Collectors.toCollection(HashSet::new)); - assertEquals(1,cpSchemeId.size()); + assertEquals(1, cpSchemeId.size()); assertTrue(cpSchemeId.contains("eosc:contentpolicies")); HashSet cpSchemeName = ds .getContentpolicies() @@ -289,16 +289,16 @@ class MigrateDbEntitiesApplicationTest { checkProperty(r1, "contribution", "436754.0"); checkProperty(r2, "contribution", "436754.0"); - checkProperty(r1, "currency","EUR"); + checkProperty(r1, "currency", "EUR"); checkProperty(r2, "currency", "EUR"); } private void checkProperty(Relation r, String property, String value) { final List p = r - .getProperties() - .stream() - .filter(kv -> kv.getKey().equals(property)) - .collect(Collectors.toList()); + .getProperties() + .stream() + .filter(kv -> kv.getKey().equals(property)) + .collect(Collectors.toList()); assertFalse(p.isEmpty()); assertEquals(1, p.size()); assertEquals(value, p.get(0).getValue()); From 92e48f12f70ce7631a78229f1a4ca4da7ace6e48 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 29 Jul 2022 13:54:00 +0200 Subject: [PATCH 133/214] [metadata collection] updated collector plugin name --- .../main/java/eu/dnetlib/dhp/collection/CollectorWorker.java | 2 +- .../java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java index 9d9400068..c35fbb497 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java @@ -118,7 +118,7 @@ public class CollectorWorker extends ReportingJob { return new RestCollectorPlugin(clientParams); case file: return new FileCollectorPlugin(fileSystem); - case fileGZip: + case fileGzip: return new FileGZipCollectorPlugin(fileSystem); case other: final CollectorPlugin.NAME.OTHER_NAME plugin = Optional diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java index 08084e22a..a19ca5c68 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java @@ -10,7 +10,7 @@ import eu.dnetlib.dhp.common.collection.CollectorException; public interface CollectorPlugin { enum NAME { - oai, other, rest_json2xml, file, fileGZip; + oai, other, rest_json2xml, file, fileGzip; public enum OTHER_NAME { mdstore_mongodb_dump, mdstore_mongodb From 9886fe87ecab8d90473a3c62b5cb83c080ec6864 Mon Sep 17 00:00:00 2001 From: Antonis Lempesis Date: Fri, 29 Jul 2022 16:34:50 +0300 Subject: [PATCH 134/214] - Added FOS classification - Added extra orgs in monitor - Fixed result-project and organization-project tables --- .../oozie_app/scripts/step20-createMonitorDB.sql | 12 +++++++++++- .../dhp/oa/graph/stats/oozie_app/scripts/step6.sql | 4 ++-- .../dhp/oa/graph/stats/oozie_app/scripts/step7.sql | 13 ++++++++++++- 3 files changed, 25 insertions(+), 4 deletions(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql index 7412910a9..cc6b69e34 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql @@ -38,7 +38,14 @@ create table TARGET.result stored as parquet as 'openorgs____::ec3665affa01aeafa28b7852c4176dbd', --Rudjer Boskovic Institute 'openorgs____::5f31346d444a7f06a28c880fb170b0f6', --Ghent University 'openorgs____::2dbe47117fd5409f9c61620813456632', --University of Luxembourg - 'openorgs____::6445d7758d3a40c4d997953b6632a368' --National Institute of Informatics (NII) + 'openorgs____::6445d7758d3a40c4d997953b6632a368', --National Institute of Informatics (NII) + + 'openorgs____::b77c01aa15de3675da34277d48de2ec1', -- Valencia Catholic University Saint Vincent Martyr + 'openorgs____::7fe2f66cdc43983c6b24816bfe9cf6a0', -- Unviersity of Warsaw + 'openorgs____::15e7921fc50d9aa1229a82a84429419e', -- University Of Thessaly + 'openorgs____::11f7919dadc8f8a7251af54bba60c956', -- Technical University of Crete + 'openorgs____::84f0c5f5dbb6daf42748485924efde4b', -- University of Piraeus + 'openorgs____::4ac562f0376fce3539504567649cb373' -- University of Patras ) )) foo; compute stats TARGET.result; @@ -107,6 +114,9 @@ compute stats TARGET.result_sources; create table TARGET.result_topics stored as parquet as select * from SOURCE.result_topics orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.result_topics; +create table TARGET.result_fos stored as parquet as select * from SOURCE.result_fos orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.result_fos; + create view TARGET.foo1 as select * from SOURCE.result_result rr where rr.source in (select id from TARGET.result); create view TARGET.foo2 as select * from SOURCE.result_result rr where rr.target in (select id from TARGET.result); create table TARGET.result_result STORED AS PARQUET as select distinct * from (select * from TARGET.foo1 union all select * from TARGET.foo2) foufou; diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql index dc7c01046..5461afde6 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql @@ -11,13 +11,13 @@ where p.datainfo.deletedbyinference=false and p.datainfo.invisible=false; CREATE TABLE ${stats_db_name}.project_organizations STORED AS PARQUET AS SELECT substr(r.source, 4) AS id, substr(r.target, 4) AS organization from ${openaire_db_name}.relation r -WHERE r.reltype = 'projectOrganization' +WHERE r.reltype = 'projectOrganization' and r.source like '40|%' and r.datainfo.deletedbyinference = false and r.datainfo.invisible=false; CREATE TABLE ${stats_db_name}.project_results STORED AS PARQUET AS SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS result, r.datainfo.provenanceaction.classname as provenance FROM ${openaire_db_name}.relation r -WHERE r.reltype = 'resultProject' +WHERE r.reltype = 'resultProject' and r.target like '40|%' and r.datainfo.deletedbyinference = false and r.datainfo.invisible=false; create table ${stats_db_name}.project_classification STORED AS PARQUET as diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql index b5eba6111..1514ecf52 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql @@ -123,6 +123,16 @@ UNION ALL SELECT * FROM ${stats_db_name}.otherresearchproduct_topics; +create table ${stats_db_name}.result_fos stored as parquet as +with + lvl1 as (select id, topic from ${stats_db_name}.result_topics where topic like '__ %' and type='Fields of Science and Technology classification'), + lvl2 as (select id, topic from ${stats_db_name}.result_topics where topic like '____ %' and type='Fields of Science and Technology classification'), + lvl3 as (select id, topic from ${stats_db_name}.result_topics where topic like '______ %' and type='Fields of Science and Technology classification') +select lvl1.id, lvl1.topic as lvl1, lvl2.topic as lvl2, lvl3.topic as lvl3 +from lvl1 + join lvl2 on lvl1.id=lvl2.id and substr(lvl2.topic, 1, 2)=substr(lvl1.topic, 1, 2) + join lvl3 on lvl3.id=lvl1.id and substr(lvl3.topic, 1, 4)=substr(lvl2.topic, 1, 4); + CREATE TABLE ${stats_db_name}.result_organization STORED AS PARQUET AS SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS organization FROM ${openaire_db_name}.relation r @@ -134,4 +144,5 @@ CREATE TABLE ${stats_db_name}.result_projects STORED AS PARQUET AS select pr.result AS id, pr.id AS project, datediff(p.enddate, p.startdate) AS daysfromend, pr.provenance as provenance FROM ${stats_db_name}.result r JOIN ${stats_db_name}.project_results pr ON r.id = pr.result - JOIN ${stats_db_name}.project_tmp p ON p.id = pr.id; \ No newline at end of file + JOIN ${stats_db_name}.project_tmp p ON p.id = pr.id; + From 64311b8be468c46ad8d03ec206feea5a082ac00c Mon Sep 17 00:00:00 2001 From: Enrico Ottonello Date: Sun, 31 Jul 2022 01:03:29 +0200 Subject: [PATCH 135/214] removed unuseful accumulator --- .../orcid/SparkDownloadOrcidWorks.java | 38 +++++++++---------- .../oozie_app/workflow.xml | 4 +- .../src/test/resources/log4j.properties | 1 + 3 files changed, 22 insertions(+), 21 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkDownloadOrcidWorks.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkDownloadOrcidWorks.java index 72122f8b9..6b9c56005 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkDownloadOrcidWorks.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkDownloadOrcidWorks.java @@ -80,17 +80,10 @@ public class SparkDownloadOrcidWorks { LongAccumulator parsedWorksAcc = spark.sparkContext().longAccumulator("parsed_works"); LongAccumulator modifiedWorksAcc = spark.sparkContext().longAccumulator("modified_works"); LongAccumulator errorCodeFoundAcc = spark.sparkContext().longAccumulator("error_code_found"); - LongAccumulator errorLoadingJsonFoundAcc = spark - .sparkContext() - .longAccumulator("error_loading_json_found"); - LongAccumulator errorLoadingXMLFoundAcc = spark - .sparkContext() - .longAccumulator("error_loading_xml_found"); LongAccumulator errorParsingXMLFoundAcc = spark .sparkContext() .longAccumulator("error_parsing_xml_found"); LongAccumulator downloadedRecordsAcc = spark.sparkContext().longAccumulator("downloaded_records"); - LongAccumulator errorsAcc = spark.sparkContext().longAccumulator("errors"); JavaPairRDD updatedAuthorsRDD = sc .sequenceFile(workingPath + "downloads/updated_authors/*", Text.class, Text.class); @@ -107,11 +100,10 @@ public class SparkDownloadOrcidWorks { if (statusCode.equals("200")) { String compressedData = getJsonValue(jElement, "compressedData"); if (StringUtils.isEmpty(compressedData)) { - errorLoadingJsonFoundAcc.add(1); + } else { String authorSummary = ArgumentApplicationParser.decompressValue(compressedData); if (StringUtils.isEmpty(authorSummary)) { - errorLoadingXMLFoundAcc.add(1); } else { try { workIdLastModifiedDate = XMLRecordParser @@ -184,7 +176,6 @@ public class SparkDownloadOrcidWorks { } else { downloaded.setStatusCode(-4); } - errorsAcc.add(1); } long endReq = System.currentTimeMillis(); long reqTime = endReq - startReq; @@ -193,7 +184,6 @@ public class SparkDownloadOrcidWorks { } if (downloadCompleted) { downloaded.setStatusCode(200); - downloadedRecordsAcc.add(1); downloaded .setCompressedData( ArgumentApplicationParser @@ -214,9 +204,20 @@ public class SparkDownloadOrcidWorks { String works = ArgumentApplicationParser.decompressValue(compressedData); // split a single xml containing multiple works into multiple xml (a single work for each xml) - List splittedWorks = XMLRecordParser - .splitWorks(orcidId, works.getBytes(StandardCharsets.UTF_8)); - + List splittedWorks = null; + try { + splittedWorks = XMLRecordParser + .splitWorks(orcidId, works.getBytes(StandardCharsets.UTF_8)); + } catch (Throwable t) { + final DownloadedRecordData errDownloaded = new DownloadedRecordData(); + errDownloaded.setOrcidId(orcidId); + errDownloaded.setLastModifiedDate(lastModifiedDate); + errDownloaded.setStatusCode(-10); + errDownloaded.setErrorMessage(t.getMessage()); + splittedDownloadedWorks.add(errDownloaded.toTuple2()); + errorParsingXMLFoundAcc.add(1); + return splittedDownloadedWorks.iterator(); + } splittedWorks.forEach(w -> { final DownloadedRecordData downloaded = new DownloadedRecordData(); downloaded.setOrcidId(orcidId); @@ -228,10 +229,12 @@ public class SparkDownloadOrcidWorks { .setCompressedData( ArgumentApplicationParser .compressArgument(w)); - } catch (IOException e) { - throw new RuntimeException(e); + } catch (Throwable t) { + downloaded.setStatusCode(-11); + downloaded.setErrorMessage(t.getMessage()); } splittedDownloadedWorks.add(downloaded.toTuple2()); + downloadedRecordsAcc.add(1); }); return splittedDownloadedWorks.iterator(); @@ -250,11 +253,8 @@ public class SparkDownloadOrcidWorks { logger.info("parsedWorksAcc: {}", parsedWorksAcc.value()); logger.info("modifiedWorksAcc: {}", modifiedWorksAcc.value()); logger.info("errorCodeFoundAcc: {}", errorCodeFoundAcc.value()); - logger.info("errorLoadingJsonFoundAcc: {}", errorLoadingJsonFoundAcc.value()); - logger.info("errorLoadingXMLFoundAcc: {}", errorLoadingXMLFoundAcc.value()); logger.info("errorParsingXMLFoundAcc: {}", errorParsingXMLFoundAcc.value()); logger.info("downloadedRecordsAcc: {}", downloadedRecordsAcc.value()); - logger.info("errorsAcc: {}", errorsAcc.value()); }); } diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_updates_download/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_updates_download/oozie_app/workflow.xml index 43d7eb1ec..f1195a16f 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_updates_download/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_updates_download/oozie_app/workflow.xml @@ -78,7 +78,7 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] @@ -190,7 +190,7 @@ -odownloads/updated_works -t${token} - + diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/log4j.properties b/dhp-workflows/dhp-doiboost/src/test/resources/log4j.properties index 20f56e38d..520bf1a18 100644 --- a/dhp-workflows/dhp-doiboost/src/test/resources/log4j.properties +++ b/dhp-workflows/dhp-doiboost/src/test/resources/log4j.properties @@ -7,5 +7,6 @@ log4j.appender.A1=org.apache.log4j.ConsoleAppender # A1 uses PatternLayout. log4j.logger.org = ERROR log4j.logger.eu.dnetlib = DEBUG +log4j.logger.eu.dnetlib.doiboost.orcid = INFO log4j.appender.A1.layout=org.apache.log4j.PatternLayout log4j.appender.A1.layout.ConversionPattern=%-4r [%t] %-5p %c %x - %m%n \ No newline at end of file From 209c7e9dab323932dba65bb88addf2c8ab848d92 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 1 Aug 2022 09:05:35 +0200 Subject: [PATCH 136/214] [datacite] avoid UnsupportedOperationException --- .../eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala index a7863d144..0f82ecadf 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala @@ -587,7 +587,7 @@ object DataciteToOAFTransformation { val oid = result.getId result.setId(IdentifierFactory.createIdentifier(result)) if (!result.getId.equalsIgnoreCase(oid)) { - result.getOriginalId.add(oid) + result.setOriginalId((oid::List(doi)).asJava) } var relations: List[Relation] = From 1778d40c40654db9bde707ee2ffdc4e3f922bce9 Mon Sep 17 00:00:00 2001 From: Antonis Lempesis Date: Tue, 2 Aug 2022 13:39:34 +0300 Subject: [PATCH 137/214] latest version of indicators --- .../scripts/step16-createIndicatorsTables.sql | 993 +++++++++++++----- 1 file changed, 709 insertions(+), 284 deletions(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql index db40cf973..25776316b 100755 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql @@ -1,60 +1,62 @@ ----- Sprint 1 ---- +-- Sprint 1 ---- create table indi_pub_green_oa stored as parquet as select distinct p.id, coalesce(green_oa, 0) as green_oa from publication p -left outer join ( -select p.id, 1 as green_oa -from publication p -join result_instance ri on ri.id = p.id -join datasource on datasource.id = ri.hostedby -where datasource.type like '%Repository%' -and (ri.accessright = 'Open Access' -or ri.accessright = 'Embargo' or ri.accessright = 'Open Source')) tmp -on p.id= tmp.id; + left outer join ( + select p.id, 1 as green_oa + from publication p + join result_instance ri on ri.id = p.id + join datasource on datasource.id = ri.hostedby + where datasource.type like '%Repository%' + and (ri.accessright = 'Open Access' + or ri.accessright = 'Embargo' or ri.accessright = 'Open Source')) tmp + on p.id= tmp.id; compute stats indi_pub_green_oa; create table indi_pub_grey_lit stored as parquet as select distinct p.id, coalesce(grey_lit, 0) as grey_lit from publication p -left outer join ( -select p.id, 1 as grey_lit -from publication p -join result_classifications rt on rt.id = p.id -where rt.type not in ('Article','Part of book or chapter of book','Book','Doctoral thesis','Master thesis','Data Paper', 'Thesis', 'Bachelor thesis', 'Conference object') and -not exists (select 1 from result_classifications rc where type ='Other literature type' and rc.id=p.id)) tmp on p.id=tmp.id; + left outer join ( + select p.id, 1 as grey_lit + from publication p + join result_classifications rt on rt.id = p.id + where rt.type not in ('Article','Part of book or chapter of book','Book','Doctoral thesis','Master thesis','Data Paper', 'Thesis', 'Bachelor thesis', 'Conference object') and + not exists (select 1 from result_classifications rc where type ='Other literature type' + and rc.id=p.id)) tmp on p.id=tmp.id; compute stats indi_pub_grey_lit; create table indi_pub_doi_from_crossref stored as parquet as select distinct p.id, coalesce(doi_from_crossref, 0) as doi_from_crossref from publication p -left outer join -(select ri.id, 1 as doi_from_crossref from result_instance ri -join datasource d on d.id = ri.collectedfrom -where pidtype='Digital Object Identifier' and d.name ='Crossref') tmp -on tmp.id=p.id; + left outer join + (select ri.id, 1 as doi_from_crossref from result_instance ri + join datasource d on d.id = ri.collectedfrom + where pidtype='Digital Object Identifier' and d.name ='Crossref') tmp + on tmp.id=p.id; compute stats indi_pub_doi_from_crossref; ----- Sprint 2 ---- + +-- Sprint 2 ---- create table indi_result_has_cc_licence stored as parquet as select distinct r.id, (case when lic='' or lic is null then 0 else 1 end) as has_cc_license from result r -left outer join (select r.id, license.type as lic from result r -join result_licenses as license on license.id = r.id -where lower(license.type) LIKE '%creativecommons.org%' OR lower(license.type) LIKE '%cc-%') tmp -on r.id= tmp.id; + left outer join (select r.id, license.type as lic from result r + join result_licenses as license on license.id = r.id + where lower(license.type) LIKE '%creativecommons.org%' OR lower(license.type) LIKE '%cc-%') tmp + on r.id= tmp.id; compute stats indi_result_has_cc_licence; create table indi_result_has_cc_licence_url stored as parquet as select distinct r.id, case when lic_host='' or lic_host is null then 0 else 1 end as has_cc_license_url from result r -left outer join (select r.id, lower(parse_url(license.type, "HOST")) as lic_host -from result r -join result_licenses as license on license.id = r.id -WHERE lower(parse_url(license.type, "HOST")) = "creativecommons.org") tmp -on r.id= tmp.id; + left outer join (select r.id, lower(parse_url(license.type, "HOST")) as lic_host + from result r + join result_licenses as license on license.id = r.id + WHERE lower(parse_url(license.type, "HOST")) = "creativecommons.org") tmp + on r.id= tmp.id; compute stats indi_result_has_cc_licence_url; @@ -67,8 +69,8 @@ compute stats indi_pub_has_abstract; create table indi_result_with_orcid stored as parquet as select distinct r.id, coalesce(has_orcid, 0) as has_orcid from result r -left outer join (select id, 1 as has_orcid from result_orcid) tmp -on r.id= tmp.id; + left outer join (select id, 1 as has_orcid from result_orcid) tmp + on r.id= tmp.id; compute stats indi_result_with_orcid; @@ -76,59 +78,89 @@ compute stats indi_result_with_orcid; create table indi_funded_result_with_fundref stored as parquet as select distinct r.id, coalesce(fundref, 0) as fundref from project_results r -left outer join (select distinct id, 1 as fundref from project_results -where provenance='Harvested') tmp -on r.id= tmp.id; + left outer join (select distinct id, 1 as fundref from project_results + where provenance='Harvested') tmp + on r.id= tmp.id; compute stats indi_funded_result_with_fundref; --- create table indi_result_org_country_collab stored as parquet as --- with tmp as --- (select o.id as id, o.country , ro.id as result,r.type from organization o --- join result_organization ro on o.id=ro.organization --- join result r on r.id=ro.id where o.country <> 'UNKNOWN') --- select o1.id org1,o2.country country2, o1.type, count(distinct o1.result) as collaborations --- from tmp as o1 --- join tmp as o2 on o1.result=o2.result --- where o1.id<>o2.id and o1.country<>o2.country --- group by o1.id, o1.type,o2.country; --- --- compute stats indi_result_org_country_collab; +create table indi_result_org_collab stored as parquet as +select o1.organization org1, o2.organization org2, count(distinct o1.id) as collaborations +from result_organization as o1 + join result_organization as o2 on o1.id=o2.id and o1.organization!=o2.organization +group by o1.organization, o2.organization; --- create table indi_result_org_collab stored as parquet as --- with tmp as --- (select o.id, ro.id as result,r.type from organization o --- join result_organization ro on o.id=ro.organization --- join result r on r.id=ro.id) --- select o1.id org1,o2.id org2, o1.type, count(distinct o1.result) as collaborations --- from tmp as o1 --- join tmp as o2 on o1.result=o2.result --- where o1.id<>o2.id --- group by o1.id, o2.id, o1.type; --- --- compute stats indi_result_org_collab; +compute stats indi_result_org_collab; + +create table indi_result_org_country_collab stored as parquet as + with tmp as + (select o.id as id, o.country , ro.id as result,r.type from organization o + join result_organization ro on o.id=ro.organization + join result r on r.id=ro.id where o.country <> 'UNKNOWN') +select o1.id org1,o2.country country2, o1.type, count(distinct o1.result) as collaborations +from tmp as o1 + join tmp as o2 on o1.result=o2.result +where o1.id<>o2.id and o1.country<>o2.country +group by o1.id, o1.type,o2.country; + +compute stats indi_result_org_country_collab; + +create table indi_result_org_collab stored as parquet as + with tmp as + (select o.id, ro.id as result,r.type from organization o + join result_organization ro on o.id=ro.organization + join result r on r.id=ro.id) +select o1.id org1,o2.id org2, o1.type, count(distinct o1.result) as collaborations +from tmp as o1 + join tmp as o2 on o1.result=o2.result +where o1.id<>o2.id +group by o1.id, o2.id, o1.type; + +compute stats indi_result_org_collab; + +create table indi_project_collab_org stored as parquet as +select o1.id org1,o2.id org2, count(distinct o1.project) as collaborations +from organization_projects as o1 + join organization_projects as o2 on o1.project=o2.project +where o1.id!=o2.id +group by o1.id, o2.id; + +compute stats indi_project_collab_org; + +create table indi_project_collab_org_country stored as parquet as + with tmp as + (select o.id organization, o.country , ro.project as project from organization o + join organization_projects ro on o.id=ro.id + and o.country <> 'UNKNOWN') +select o1.organization org1,o2.country country2, count(distinct o1.project) as collaborations +from tmp as o1 + join tmp as o2 on o1.project=o2.project +where o1.organization<>o2.organization and o1.country<>o2.country +group by o1.organization, o2.country; + +compute stats indi_project_collab_org_country; create table indi_funder_country_collab stored as parquet as -with tmp as (select funder, project, country from organization_projects op -join organization o on o.id=op.id -join project p on p.id=op.project -where country <> 'UNKNOWN') + with tmp as (select funder, project, country from organization_projects op + join organization o on o.id=op.id + join project p on p.id=op.project + where country <> 'UNKNOWN') select f1.funder, f1.country as country1, f2.country as country2, count(distinct f1.project) as collaborations from tmp as f1 -join tmp as f2 on f1.project=f2.project + join tmp as f2 on f1.project=f2.project where f1.country<>f2.country group by f1.funder, f2.country, f1.country; compute stats indi_funder_country_collab; create table indi_result_country_collab stored as parquet as -with tmp as -(select country, ro.id as result,r.type from organization o -join result_organization ro on o.id=ro.organization -join result r on r.id=ro.id) + with tmp as + (select country, ro.id as result,r.type from organization o + join result_organization ro on o.id=ro.organization + join result r on r.id=ro.id where country <> 'UNKNOWN') select o1.country country1, o2.country country2, o1.type, count(distinct o1.result) as collaborations from tmp as o1 -join tmp as o2 on o1.result=o2.result + join tmp as o2 on o1.result=o2.result where o1.country<>o2.country group by o1.country, o2.country, o1.type; @@ -138,255 +170,257 @@ compute stats indi_result_country_collab; create table indi_pub_diamond stored as parquet as select distinct pd.id, coalesce(in_diamond_journal, 0) as in_diamond_journal from publication_datasources pd -left outer join ( -select pd.id, 1 as in_diamond_journal from publication_datasources pd -join datasource d on d.id=pd.datasource -join stats_ext.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_online=d.issn_online) -and (ps.journal_is_in_doaj=true or ps.journal_is_oa=true) and ps.has_apc=false) tmp -on pd.id=tmp.id; + left outer join ( + select pd.id, 1 as in_diamond_journal from publication_datasources pd + join datasource d on d.id=pd.datasource + join stats_ext.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_online=d.issn_online) + and (ps.journal_is_in_doaj=true or ps.journal_is_oa=true) and ps.has_apc=false) tmp + on pd.id=tmp.id; compute stats indi_pub_diamond; create table indi_pub_hybrid stored as parquet as select distinct pd.id, coalesce(is_hybrid, 0) as is_hybrid from publication_datasources pd -left outer join ( -select pd.id, 1 as is_hybrid from publication_datasources pd -join datasource d on d.id=pd.datasource -join stats_ext.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_online=d.issn_online) -and (ps.journal_is_in_doaj=false and ps.journal_is_oa=false)) tmp -on pd.id=tmp.id; + left outer join ( + select pd.id, 1 as is_hybrid from publication_datasources pd + join datasource d on d.id=pd.datasource + join stats_ext.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_online=d.issn_online) + and (ps.journal_is_in_doaj=false and ps.journal_is_oa=false)) tmp + on pd.id=tmp.id; compute stats indi_pub_hybrid; create table indi_pub_in_transformative stored as parquet as select distinct pd.id, coalesce(is_transformative, 0) as is_transformative from publication pd -left outer join ( -select pd.id, 1 as is_transformative from publication_datasources pd -join datasource d on d.id=pd.datasource -join stats_ext.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_online=d.issn_online) -and ps.is_transformative_journal=true) tmp -on pd.id=tmp.id; + left outer join ( + select pd.id, 1 as is_transformative from publication_datasources pd + join datasource d on d.id=pd.datasource + join stats_ext.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_online=d.issn_online) + and ps.is_transformative_journal=true) tmp + on pd.id=tmp.id; compute stats indi_pub_in_transformative; create table indi_pub_closed_other_open stored as parquet as select distinct ri.id, coalesce(pub_closed_other_open, 0) as pub_closed_other_open from result_instance ri -left outer join -(select ri.id, 1 as pub_closed_other_open from result_instance ri -join publication p on p.id=ri.id -join datasource d on ri.hostedby=d.id -where d.type like '%Journal%' and ri.accessright='Closed Access' and -(p.bestlicence='Open Access' or p.bestlicence='Open Source')) tmp -on tmp.id=ri.id; + left outer join + (select ri.id, 1 as pub_closed_other_open from result_instance ri + join publication p on p.id=ri.id + join datasource d on ri.hostedby=d.id + where d.type like '%Journal%' and ri.accessright='Closed Access' and + (p.bestlicence='Open Access' or p.bestlicence='Open Source')) tmp + on tmp.id=ri.id; compute stats indi_pub_closed_other_open; + ---- Sprint 5 ---- create table indi_result_no_of_copies stored as parquet as select id, count(id) as number_of_copies from result_instance group by id; compute stats indi_result_no_of_copies; + ---- Sprint 6 ---- -create table indi_pub_gold_oa stored as parquet as -WITH gold_oa AS ( - SELECT issn_l, journal_is_in_doaj,journal_is_oa, issn_1 as issn - FROM stats_ext.oa_journals - WHERE issn_1 != "" - UNION ALL - SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_2 as issn - FROM stats_ext.oa_journals - WHERE issn_2 != "" ), -issn AS ( - SELECT * FROM - (SELECT id, issn_printed as issn - FROM datasource WHERE issn_printed IS NOT NULL - UNION - SELECT id, issn_online as issn - FROM datasource WHERE issn_online IS NOT NULL) as issn - WHERE LENGTH(issn) > 7) -SELECT DISTINCT pd.id, coalesce(is_gold, 0) as is_gold -FROM publication_datasources pd -LEFT OUTER JOIN ( - SELECT pd.id, 1 as is_gold FROM publication_datasources pd - JOIN issn on issn.id=pd.datasource - JOIN gold_oa on issn.issn = gold_oa.issn) tmp ON pd.id=tmp.id; +--create table indi_pub_gold_oa stored as parquet as +--WITH gold_oa AS ( +-- SELECT issn_l, journal_is_in_doaj,journal_is_oa, issn_1 as issn +-- FROM stats_ext.oa_journals +-- WHERE issn_1 != "" +-- UNION ALL +-- SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_2 as issn +-- FROM stats_ext.oa_journals +-- WHERE issn_2 != "" ), +--issn AS ( +-- SELECT * FROM +-- (SELECT id, issn_printed as issn +-- FROM datasource WHERE issn_printed IS NOT NULL +-- UNION +-- SELECT id, issn_online as issn +-- FROM datasource WHERE issn_online IS NOT NULL) as issn +-- WHERE LENGTH(issn) > 7) +--SELECT DISTINCT pd.id, coalesce(is_gold, 0) as is_gold +--FROM publication_datasources pd +--LEFT OUTER JOIN ( +-- SELECT pd.id, 1 as is_gold FROM publication_datasources pd +-- JOIN issn on issn.id=pd.datasource +-- JOIN gold_oa on issn.issn = gold_oa.issn) tmp ON pd.id=tmp.id; -compute stats indi_pub_gold_oa; +--compute stats indi_pub_gold_oa; +-- +--create table indi_datasets_gold_oa stored as parquet as +--WITH gold_oa AS ( +-- SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_1 as issn +-- FROM stats_ext.oa_journals +-- WHERE issn_1 != "" +-- UNION +-- ALL SELECT issn_l,journal_is_in_doaj,journal_is_oa,issn_2 as issn +-- FROM stats_ext.oa_journals +-- WHERE issn_2 != "" ), +--issn AS ( +-- SELECT * +-- FROM ( +-- SELECT id,issn_printed as issn +-- FROM datasource +-- WHERE issn_printed IS NOT NULL +-- UNION +-- SELECT id, issn_online as issn +-- FROM datasource +-- WHERE issn_online IS NOT NULL ) as issn +-- WHERE LENGTH(issn) > 7) +--SELECT DISTINCT pd.id, coalesce(is_gold, 0) as is_gold +--FROM dataset_datasources pd +--LEFT OUTER JOIN ( +-- SELECT pd.id, 1 as is_gold FROM dataset_datasources pd +-- JOIN issn on issn.id=pd.datasource +-- JOIN gold_oa on issn.issn = gold_oa.issn) tmp ON pd.id=tmp.id; +-- +--compute stats indi_datasets_gold_oa; -create table indi_datasets_gold_oa stored as parquet as -WITH gold_oa AS ( - SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_1 as issn - FROM stats_ext.oa_journals - WHERE issn_1 != "" - UNION - ALL SELECT issn_l,journal_is_in_doaj,journal_is_oa,issn_2 as issn - FROM stats_ext.oa_journals - WHERE issn_2 != "" ), -issn AS ( - SELECT * - FROM ( - SELECT id,issn_printed as issn - FROM datasource - WHERE issn_printed IS NOT NULL - UNION - SELECT id, issn_online as issn - FROM datasource - WHERE issn_online IS NOT NULL ) as issn - WHERE LENGTH(issn) > 7) -SELECT DISTINCT pd.id, coalesce(is_gold, 0) as is_gold -FROM dataset_datasources pd -LEFT OUTER JOIN ( - SELECT pd.id, 1 as is_gold FROM dataset_datasources pd - JOIN issn on issn.id=pd.datasource - JOIN gold_oa on issn.issn = gold_oa.issn) tmp ON pd.id=tmp.id; - -compute stats indi_datasets_gold_oa; - -create table indi_software_gold_oa stored as parquet as -WITH gold_oa AS ( - SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_1 as issn - FROM stats_ext.oa_journals - WHERE issn_1 != "" - UNION - ALL SELECT issn_l,journal_is_in_doaj,journal_is_oa,issn_2 as issn - FROM stats_ext.oa_journals - WHERE issn_2 != "" ), -issn AS ( - SELECT * - FROM ( - SELECT id,issn_printed as issn - FROM datasource - WHERE issn_printed IS NOT NULL - UNION - SELECT id, issn_online as issn - FROM datasource - WHERE issn_online IS NOT NULL ) as issn - WHERE LENGTH(issn) > 7) -SELECT DISTINCT pd.id, coalesce(is_gold, 0) as is_gold -FROM software_datasources pd -LEFT OUTER JOIN ( - SELECT pd.id, 1 as is_gold FROM software_datasources pd - JOIN issn on issn.id=pd.datasource - JOIN gold_oa on issn.issn = gold_oa.issn) tmp ON pd.id=tmp.id; - -compute stats indi_software_gold_oa; - -create table indi_org_findable stored as parquet as -with result_with_pid as ( - select ro.organization organization, count(distinct rp.id) no_result_with_pid from result_organization ro - join result_pids rp on rp.id=ro.id - group by ro.organization), -result_has_abstract as ( - select ro.organization organization, count(distinct rp.id) no_result_with_abstract from result_organization ro - join result rp on rp.id=ro.id where rp.abstract=true - group by ro.organization), -allresults as ( - select organization, count(distinct id) no_allresults from result_organization - group by organization), -result_with_pid_share as ( - select allresults.organization, result_with_pid.no_result_with_pid/allresults.no_allresults pid_share - from allresults - join result_with_pid on result_with_pid.organization=allresults.organization), -result_with_abstract_share as ( - select allresults.organization, result_has_abstract.no_result_with_abstract/allresults.no_allresults abstract_share - from allresults - join result_has_abstract on result_has_abstract.organization=allresults.organization) -select allresults.organization, coalesce((pid_share+abstract_share)/2,pid_share) org_findable -from allresults -join result_with_pid_share on result_with_pid_share.organization=allresults.organization -left outer join ( - select organization, abstract_share from result_with_abstract_share) tmp on tmp.organization=allresults.organization; - -compute stats indi_org_findable; - -create table indi_org_openess stored as parquet as -WITH datasets_oa as ( - SELECT ro.organization, count(dg.id) no_oadatasets FROM indi_datasets_gold_oa dg - join openaire_prod_stats.result_organization ro on dg.id=ro.id - join openaire_prod_stats.dataset ds on dg.id=ds.id - WHERE dg.is_gold=1 - group by ro.organization), -software_oa as ( - SELECT ro.organization, count(dg.id) no_oasoftware FROM indi_software_gold_oa dg - join openaire_prod_stats.result_organization ro on dg.id=ro.id - join openaire_prod_stats.software ds on dg.id=ds.id - WHERE dg.is_gold=1 - group by ro.organization), -pubs_oa as ( - SELECT ro.organization, count(dg.id) no_oapubs FROM indi_pub_gold_oa dg - join openaire_prod_stats.result_organization ro on dg.id=ro.id - join openaire_prod_stats.publication ds on dg.id=ds.id - where dg.is_gold=1 - group by ro.organization), -allpubs as ( - SELECT ro.organization organization, count(ro.id) no_allpubs FROM result_organization ro - join openaire_prod_stats.publication ps on ps.id=ro.id - group by ro.organization), -alldatasets as ( - SELECT ro.organization organization, count(ro.id) no_alldatasets FROM result_organization ro - join openaire_prod_stats.dataset ps on ps.id=ro.id - group by ro.organization), -allsoftware as ( - SELECT ro.organization organization, count(ro.id) no_allsoftware FROM result_organization ro - join openaire_prod_stats.software ps on ps.id=ro.id - group by ro.organization), -allpubsshare as ( - select pubs_oa.organization, pubs_oa.no_oapubs/allpubs.no_allpubs p from allpubs - join pubs_oa on allpubs.organization=pubs_oa.organization), -alldatasetssshare as ( - select datasets_oa.organization, datasets_oa.no_oadatasets/alldatasets.no_alldatasets c - from alldatasets - join datasets_oa on alldatasets.organization=datasets_oa.organization), -allsoftwaresshare as ( - select software_oa.organization, software_oa.no_oasoftware/allsoftware.no_allsoftware s - from allsoftware - join software_oa on allsoftware.organization=software_oa.organization) -select allpubsshare.organization, coalesce((c+p+s)/3, p) org_openess -FROM allpubsshare -left outer join ( - select organization,c from - alldatasetssshare) tmp on tmp.organization=allpubsshare.organization -left outer join ( - select organization,s from allsoftwaresshare) tmp1 on tmp1.organization=allpubsshare.organization; - -compute stats indi_org_openess; +--create table indi_software_gold_oa stored as parquet as +--WITH gold_oa AS ( +-- SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_1 as issn +-- FROM stats_ext.oa_journals +-- WHERE issn_1 != "" +-- UNION +-- ALL SELECT issn_l,journal_is_in_doaj,journal_is_oa,issn_2 as issn +-- FROM stats_ext.oa_journals +-- WHERE issn_2 != "" ), +--issn AS ( +-- SELECT * +-- FROM ( +-- SELECT id,issn_printed as issn +-- FROM datasource +-- WHERE issn_printed IS NOT NULL +-- UNION +-- SELECT id, issn_online as issn +-- FROM datasource +-- WHERE issn_online IS NOT NULL ) as issn +-- WHERE LENGTH(issn) > 7) +--SELECT DISTINCT pd.id, coalesce(is_gold, 0) as is_gold +--FROM software_datasources pd +--LEFT OUTER JOIN ( +-- SELECT pd.id, 1 as is_gold FROM software_datasources pd +-- JOIN issn on issn.id=pd.datasource +-- JOIN gold_oa on issn.issn = gold_oa.issn) tmp ON pd.id=tmp.id; +-- +--compute stats indi_software_gold_oa; +--create table indi_org_findable stored as parquet as +--with result_with_pid as ( +-- select ro.organization organization, count(distinct rp.id) no_result_with_pid from result_organization ro +-- join result_pids rp on rp.id=ro.id +-- group by ro.organization), +--result_has_abstract as ( +-- select ro.organization organization, count(distinct rp.id) no_result_with_abstract from result_organization ro +-- join result rp on rp.id=ro.id where rp.abstract=true +-- group by ro.organization), +--allresults as ( +-- select organization, count(distinct id) no_allresults from result_organization +-- group by organization), +--result_with_pid_share as ( +-- select allresults.organization, result_with_pid.no_result_with_pid/allresults.no_allresults pid_share +-- from allresults +-- join result_with_pid on result_with_pid.organization=allresults.organization), +--result_with_abstract_share as ( +-- select allresults.organization, result_has_abstract.no_result_with_abstract/allresults.no_allresults abstract_share +-- from allresults +-- join result_has_abstract on result_has_abstract.organization=allresults.organization) +--select allresults.organization, coalesce((pid_share+abstract_share)/2,pid_share) org_findable +--from allresults +--join result_with_pid_share on result_with_pid_share.organization=allresults.organization +--left outer join ( +-- select organization, abstract_share from result_with_abstract_share) tmp on tmp.organization=allresults.organization; +-- +--compute stats indi_org_findable; +-- +--create table indi_org_openess stored as parquet as +--WITH datasets_oa as ( +-- SELECT ro.organization, count(dg.id) no_oadatasets FROM indi_datasets_gold_oa dg +-- join result_organization ro on dg.id=ro.id +-- join dataset ds on dg.id=ds.id +-- WHERE dg.is_gold=1 +-- group by ro.organization), +--software_oa as ( +-- SELECT ro.organization, count(dg.id) no_oasoftware FROM indi_software_gold_oa dg +-- join result_organization ro on dg.id=ro.id +-- join software ds on dg.id=ds.id +-- WHERE dg.is_gold=1 +-- group by ro.organization), +--pubs_oa as ( +-- SELECT ro.organization, count(dg.id) no_oapubs FROM indi_pub_gold_oa dg +-- join result_organization ro on dg.id=ro.id +-- join publication ds on dg.id=ds.id +-- where dg.is_gold=1 +-- group by ro.organization), +--allpubs as ( +-- SELECT ro.organization organization, count(ro.id) no_allpubs FROM result_organization ro +-- join publication ps on ps.id=ro.id +-- group by ro.organization), +--alldatasets as ( +-- SELECT ro.organization organization, count(ro.id) no_alldatasets FROM result_organization ro +-- join dataset ps on ps.id=ro.id +-- group by ro.organization), +--allsoftware as ( +-- SELECT ro.organization organization, count(ro.id) no_allsoftware FROM result_organization ro +-- join software ps on ps.id=ro.id +-- group by ro.organization), +--allpubsshare as ( +-- select pubs_oa.organization, pubs_oa.no_oapubs/allpubs.no_allpubs p from allpubs +-- join pubs_oa on allpubs.organization=pubs_oa.organization), +--alldatasetssshare as ( +-- select datasets_oa.organization, datasets_oa.no_oadatasets/alldatasets.no_alldatasets c +-- from alldatasets +-- join datasets_oa on alldatasets.organization=datasets_oa.organization), +--allsoftwaresshare as ( +-- select software_oa.organization, software_oa.no_oasoftware/allsoftware.no_allsoftware s +-- from allsoftware +-- join software_oa on allsoftware.organization=software_oa.organization) +--select allpubsshare.organization, coalesce((c+p+s)/3, p) org_openess +--FROM allpubsshare +--left outer join ( +-- select organization,c from +-- alldatasetssshare) tmp on tmp.organization=allpubsshare.organization +--left outer join ( +-- select organization,s from allsoftwaresshare) tmp1 on tmp1.organization=allpubsshare.organization; +-- +--compute stats indi_org_openess; +-- create table indi_pub_hybrid_oa_with_cc stored as parquet as -WITH hybrid_oa AS ( - SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_print as issn - FROM stats_ext.plan_s_jn - WHERE issn_print != "" - UNION ALL - SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_online as issn - FROM stats_ext.plan_s_jn - WHERE issn_online != "" and (journal_is_in_doaj = FALSE OR journal_is_oa = FALSE)), -issn AS ( - SELECT * - FROM ( - SELECT id, issn_printed as issn - FROM datasource - WHERE issn_printed IS NOT NULL - UNION - SELECT id,issn_online as issn - FROM datasource - WHERE issn_online IS NOT NULL ) as issn + WITH hybrid_oa AS ( + SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_print as issn + FROM stats_ext.plan_s_jn + WHERE issn_print != "" + UNION ALL + SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_online as issn + FROM stats_ext.plan_s_jn + WHERE issn_online != "" and (journal_is_in_doaj = FALSE OR journal_is_oa = FALSE)), + issn AS ( + SELECT * + FROM ( + SELECT id, issn_printed as issn + FROM datasource + WHERE issn_printed IS NOT NULL + UNION + SELECT id,issn_online as issn + FROM datasource + WHERE issn_online IS NOT NULL ) as issn WHERE LENGTH(issn) > 7) SELECT DISTINCT pd.id, coalesce(is_hybrid_oa, 0) as is_hybrid_oa FROM publication_datasources pd -LEFT OUTER JOIN ( + LEFT OUTER JOIN ( SELECT pd.id, 1 as is_hybrid_oa from publication_datasources pd - JOIN datasource d on d.id=pd.datasource - JOIN issn on issn.id=pd.datasource - JOIN hybrid_oa ON issn.issn = hybrid_oa.issn - JOIN indi_result_has_cc_licence cc on pd.id=cc.id + JOIN datasource d on d.id=pd.datasource + JOIN issn on issn.id=pd.datasource + JOIN hybrid_oa ON issn.issn = hybrid_oa.issn + JOIN indi_result_has_cc_licence cc on pd.id=cc.id where cc.has_cc_license=1) tmp on pd.id=tmp.id; compute stats indi_pub_hybrid_oa_with_cc; create table indi_pub_downloads stored as parquet as SELECT result_id, sum(downloads) no_dowloads from openaire_prod_usage_stats.usage_stats -join publication on result_id=id + join publication on result_id=id where downloads>0 GROUP BY result_id order by no_dowloads desc; @@ -395,7 +429,7 @@ compute stats indi_pub_downloads; create table indi_pub_downloads_datasource stored as parquet as SELECT result_id, repository_id, sum(downloads) no_dowloads from openaire_prod_usage_stats.usage_stats -join publication on result_id=id + join publication on result_id=id where downloads>0 GROUP BY result_id, repository_id order by result_id; @@ -404,7 +438,7 @@ compute stats indi_pub_downloads_datasource; create table indi_pub_downloads_year stored as parquet as SELECT result_id, substring(us.`date`, 1,4) as `year`, sum(downloads) no_dowloads from openaire_prod_usage_stats.usage_stats us -join publication on result_id=id where downloads>0 + join publication on result_id=id where downloads>0 GROUP BY result_id, `year` order by `year` asc; @@ -412,9 +446,400 @@ compute stats indi_pub_downloads_year; create table indi_pub_downloads_datasource_year stored as parquet as SELECT result_id, substring(us.`date`, 1,4) as `year`, repository_id, sum(downloads) no_dowloads from openaire_prod_usage_stats.usage_stats us -join publication on result_id=id + join publication on result_id=id where downloads>0 GROUP BY result_id, repository_id, `year` order by `year` asc, result_id; -compute stats indi_pub_downloads_datasource_year; \ No newline at end of file +compute stats indi_pub_downloads_datasource_year; + +---- Sprint 7 ---- +create table indi_pub_gold_oa stored as parquet as + WITH gold_oa AS ( SELECT + issn_l, + journal_is_in_doaj, + journal_is_oa, + issn_1 as issn + FROM + stats_ext.oa_journals + WHERE + issn_1 != "" + UNION + ALL SELECT + issn_l, + journal_is_in_doaj, + journal_is_oa, + issn_2 as issn + FROM + stats_ext.oa_journals + WHERE + issn_2 != "" ), issn AS ( SELECT + * + FROM +( SELECT + id, + issn_printed as issn + FROM + datasource + WHERE + issn_printed IS NOT NULL + UNION + SELECT + id, + issn_online as issn + FROM + datasource + WHERE + issn_online IS NOT NULL or id like '%doajarticles%') as issn + WHERE + LENGTH(issn) > 7) +SELECT + DISTINCT pd.id, coalesce(is_gold, 0) as is_gold +FROM + publication_datasources pd + left outer join( + select pd.id, 1 as is_gold FROM publication_datasources pd + JOIN issn on issn.id=pd.datasource + JOIN gold_oa on issn.issn = gold_oa.issn) tmp + on pd.id=tmp.id; + +compute stats indi_pub_gold_oa; + +create table indi_pub_hybrid stored as parquet as + WITH gold_oa AS ( SELECT + issn_l, + journal_is_in_doaj, + journal_is_oa, + issn_1 as issn, + has_apc + FROM + stats_ext.oa_journals + WHERE + issn_1 != "" + UNION + ALL SELECT + issn_l, + journal_is_in_doaj, + journal_is_oa, + issn_2 as issn, + has_apc + FROM + stats_ext.oa_journals + WHERE + issn_2 != "" ), issn AS ( SELECT + * + FROM +( SELECT + id, + issn_printed as issn + FROM + datasource + WHERE + issn_printed IS NOT NULL + UNION + SELECT + id, + issn_online as issn + FROM + datasource + WHERE + issn_online IS NOT NULL or id like '%doajarticles%') as issn + WHERE + LENGTH(issn) > 7) +select distinct pd.id, coalesce(is_hybrid, 0) as is_hybrid +from publication_datasources pd + left outer join ( + select pd.id, 1 as is_hybrid from publication_datasources pd + join datasource d on d.id=pd.datasource + join issn on issn.id=pd.datasource + join gold_oa on issn.issn=gold_oa.issn + where (gold_oa.journal_is_in_doaj=false or gold_oa.journal_is_oa=false))tmp + on pd.id=tmp.id; + +compute stats indi_pub_hybrid; + +create table indi_org_fairness stored as parquet as +--return results with PIDs, and rich metadata group by organization + with result_fair as + (select ro.organization organization, count(distinct ro.id) no_result_fair from result_organization ro + join result r on r.id=ro.id +--join result_pids rp on r.id=rp.id + where (title is not null) and (publisher is not null) and (abstract is true) and (year is not null) and (authors>0) and year>2003 + group by ro.organization), +--return all results group by organization + allresults as (select organization, count(distinct ro.id) no_allresults from result_organization ro + join result r on r.id=ro.id + where year>2003 + group by organization) +--return results_fair/all_results +select allresults.organization, result_fair.no_result_fair/allresults.no_allresults org_fairness +from allresults + join result_fair on result_fair.organization=allresults.organization; + +compute stats indi_org_fairness; + +create table indi_org_fairness_pub_pr stored as parquet as + with result_fair as + (select ro.organization organization, count(distinct ro.id) no_result_fair + from result_organization ro + join publication p on p.id=ro.id + join indi_pub_doi_from_crossref dc on dc.id=p.id + join indi_pub_grey_lit gl on gl.id=p.id + where (title is not null) and (publisher is not null) and (abstract is true) and (year is not null) + and (authors>0) and cast(year as int)>2003 and dc.doi_from_crossref=1 and gl.grey_lit=0 + group by ro.organization), + allresults as (select organization, count(distinct ro.id) no_allresults from result_organization ro + join publication p on p.id=ro.id + where cast(year as int)>2003 + group by organization) +--return results_fair/all_results +select allresults.organization, result_fair.no_result_fair/allresults.no_allresults org_fairness +from allresults + join result_fair on result_fair.organization=allresults.organization; + +compute stats indi_org_fairness_pub_pr; + +create table indi_org_fairness_pub_year stored as parquet as + with result_fair as + (select year, ro.organization organization, count(distinct ro.id) no_result_fair from result_organization ro + join publication p on p.id=ro.id + where (title is not null) and (publisher is not null) and (abstract is true) and (year is not null) and (authors>0) and cast(year as int)>2003 + group by ro.organization, year), + allresults as (select year, organization, count(distinct ro.id) no_allresults from result_organization ro + join publication p on p.id=ro.id + where cast(year as int)>2003 + group by organization, year) +select allresults.year, allresults.organization, result_fair.no_result_fair/allresults.no_allresults org_fairness +from allresults + join result_fair on result_fair.organization=allresults.organization and result_fair.year=allresults.year; + +compute stats indi_org_fairness_pub_year; + +create table indi_org_fairness_pub as +with result_fair as + (select ro.organization organization, count(distinct ro.id) no_result_fair + from result_organization ro + join publication p on p.id=ro.id + where (title is not null) and (publisher is not null) and (abstract is true) and (year is not null) + and (authors>0) and cast(year as int)>2003 + group by ro.organization), + allresults as (select organization, count(distinct ro.id) no_allresults from result_organization ro + join publication p on p.id=ro.id + where cast(year as int)>2003 + group by organization) +select allresults.organization, result_fair.no_result_fair/allresults.no_allresults org_fairness +from allresults + join result_fair on result_fair.organization=allresults.organization; + +compute stats indi_org_fairness_pub; + +create table indi_org_fairness_year stored as parquet as + with result_fair as + (select year, ro.organization organization, count(distinct ro.id) no_result_fair from result_organization ro + join result r on r.id=ro.id + join result_pids rp on r.id=rp.id + where (title is not null) and (publisher is not null) and (abstract is true) and (year is not null) and (authors>0) and year>2003 + group by ro.organization, year), + allresults as (select year, organization, count(distinct ro.id) no_allresults from result_organization ro + join result r on r.id=ro.id + where year>2003 + group by organization, year) +--return results_fair/all_results +select allresults.year, allresults.organization, result_fair.no_result_fair/allresults.no_allresults org_fairness +from allresults + join result_fair on result_fair.organization=allresults.organization and result_fair.year=allresults.year; + +compute stats indi_org_fairness_year; + +create table indi_org_findable_year stored as parquet as +--return results with PIDs group by organization,year + with result_with_pid as + (select year, ro.organization organization, count(distinct rp.id) no_result_with_pid from result_organization ro + join result_pids rp on rp.id=ro.id + join result r on r.id=rp.id + where year >2003 + group by ro.organization, year), +--return all results group by organization,year + allresults as (select year, organization, count(distinct ro.id) no_allresults from result_organization ro + join result r on r.id=ro.id + where year >2003 + group by organization, year) +--return results_with_pid/all_results +select allresults.year, allresults.organization, result_with_pid.no_result_with_pid/allresults.no_allresults org_findable +from allresults + join result_with_pid on result_with_pid.organization=allresults.organization and result_with_pid.year=allresults.year; + +compute stats indi_org_findable_year; + +create table indi_org_findable stored as parquet as +--return results with PIDs group by organization + with result_with_pid as + (select ro.organization organization, count(distinct rp.id) no_result_with_pid from result_organization ro + join result_pids rp on rp.id=ro.id + join result r on r.id=rp.id + where year >2003 + group by ro.organization), +--return all results group by organization + allresults as (select organization, count(distinct ro.id) no_allresults from result_organization ro + join result r on r.id=ro.id + where year >2003 + group by organization) +--return results_with_pid/all_results +select allresults.organization, result_with_pid.no_result_with_pid/allresults.no_allresults org_findable +from allresults + join result_with_pid on result_with_pid.organization=allresults.organization; + +compute stats indi_org_findable; + +create table indi_org_openess stored as parquet as + WITH pubs_oa as ( + SELECT ro.organization, count(distinct r.id) no_oapubs FROM publication r + join result_organization ro on ro.id=r.id + join result_instance ri on ri.id=r.id + where (ri.accessright = 'Open Access' or ri.accessright = 'Embargo' or ri.accessright = 'Open Source') + and cast(r.year as int)>2003 + group by ro.organization), + datasets_oa as ( + SELECT ro.organization, count(distinct r.id) no_oadatasets FROM dataset r + join result_organization ro on ro.id=r.id + join result_instance ri on ri.id=r.id + where (ri.accessright = 'Open Access' or ri.accessright = 'Embargo' or ri.accessright = 'Open Source') + and cast(r.year as int)>2003 + group by ro.organization), + software_oa as ( + SELECT ro.organization, count(distinct r.id) no_oasoftware FROM software r + join result_organization ro on ro.id=r.id + join result_instance ri on ri.id=r.id + where (ri.accessright = 'Open Access' or ri.accessright = 'Embargo' or ri.accessright = 'Open Source') + and cast(r.year as int)>2003 + group by ro.organization), + allpubs as ( + SELECT ro.organization organization, count(ro.id) no_allpubs FROM result_organization ro + join publication ps on ps.id=ro.id + where cast(ps.year as int)>2003 + group by ro.organization), + alldatasets as ( + SELECT ro.organization organization, count(ro.id) no_alldatasets FROM result_organization ro + join dataset ps on ps.id=ro.id + where cast(ps.year as int)>2003 + group by ro.organization), + allsoftware as ( + SELECT ro.organization organization, count(ro.id) no_allsoftware FROM result_organization ro + join software ps on ps.id=ro.id + where cast(ps.year as int)>2003 + group by ro.organization), + allpubsshare as ( + select pubs_oa.organization, pubs_oa.no_oapubs/allpubs.no_allpubs p from allpubs + join pubs_oa on allpubs.organization=pubs_oa.organization), + alldatasetssshare as ( + select datasets_oa.organization, datasets_oa.no_oadatasets/alldatasets.no_alldatasets d + from alldatasets + join datasets_oa on alldatasets.organization=datasets_oa.organization), + allsoftwaresshare as ( + select software_oa.organization, software_oa.no_oasoftware/allsoftware.no_allsoftware s + from allsoftware + join software_oa on allsoftware.organization=software_oa.organization) +select allpubsshare.organization, + (p+isnull(s,0)+isnull(d,0))/(1+(case when s is null then 0 else 1 end) + +(case when d is null then 0 else 1 end)) + org_openess FROM allpubsshare + left outer join (select organization,d from + alldatasetssshare) tmp1 + on tmp1.organization=allpubsshare.organization + left outer join (select organization,s from + allsoftwaresshare) tmp2 + on tmp2.organization=allpubsshare.organization; + +compute stats indi_org_openess; + +create table indi_org_openess_year stored as parquet as + WITH pubs_oa as ( + SELECT r.year, ro.organization, count(distinct r.id) no_oapubs FROM publication r + join result_organization ro on ro.id=r.id + join result_instance ri on ri.id=r.id + where (ri.accessright = 'Open Access' or ri.accessright = 'Embargo' or ri.accessright = 'Open Source') + and cast(r.year as int)>2003 + group by ro.organization,r.year), + datasets_oa as ( + SELECT r.year,ro.organization, count(distinct r.id) no_oadatasets FROM dataset r + join result_organization ro on ro.id=r.id + join result_instance ri on ri.id=r.id + where (ri.accessright = 'Open Access' or ri.accessright = 'Embargo' or ri.accessright = 'Open Source') + and cast(r.year as int)>2003 + group by ro.organization, r.year), + software_oa as ( + SELECT r.year,ro.organization, count(distinct r.id) no_oasoftware FROM software r + join result_organization ro on ro.id=r.id + join result_instance ri on ri.id=r.id + where (ri.accessright = 'Open Access' or ri.accessright = 'Embargo' or ri.accessright = 'Open Source') + and cast(r.year as int)>2003 + group by ro.organization, r.year), + allpubs as ( + SELECT p.year,ro.organization organization, count(ro.id) no_allpubs FROM result_organization ro + join publication p on p.id=ro.id where cast(p.year as int)>2003 + group by ro.organization, p.year), + alldatasets as ( + SELECT d.year, ro.organization organization, count(ro.id) no_alldatasets FROM result_organization ro + join dataset d on d.id=ro.id where cast(d.year as int)>2003 + group by ro.organization, d.year), + allsoftware as ( + SELECT s.year,ro.organization organization, count(ro.id) no_allsoftware FROM result_organization ro + join software s on s.id=ro.id where cast(s.year as int)>2003 + group by ro.organization, s.year), + allpubsshare as ( + select allpubs.year, pubs_oa.organization, pubs_oa.no_oapubs/allpubs.no_allpubs p from allpubs + join pubs_oa on allpubs.organization=pubs_oa.organization where cast(allpubs.year as INT)=cast(pubs_oa.year as int)), + alldatasetssshare as ( + select alldatasets.year, datasets_oa.organization, datasets_oa.no_oadatasets/alldatasets.no_alldatasets d + from alldatasets + join datasets_oa on alldatasets.organization=datasets_oa.organization where cast(alldatasets.year as INT)=cast(datasets_oa.year as int)), + allsoftwaresshare as ( + select allsoftware.year, software_oa.organization, software_oa.no_oasoftware/allsoftware.no_allsoftware s + from allsoftware + join software_oa on allsoftware.organization=software_oa.organization where cast(allsoftware.year as INT)=cast(software_oa.year as int)) +select allpubsshare.year, allpubsshare.organization, + (p+isnull(s,0)+isnull(d,0))/(1+(case when s is null then 0 else 1 end) + +(case when d is null then 0 else 1 end)) + org_openess FROM allpubsshare + left outer join (select year, organization,d from + alldatasetssshare) tmp1 + on tmp1.organization=allpubsshare.organization and tmp1.year=allpubsshare.year + left outer join (select year, organization,s from + allsoftwaresshare) tmp2 + on tmp2.organization=allpubsshare.organization and tmp2.year=allpubsshare.year; + +compute stats indi_org_openess_year; + +create table indi_pub_has_preprint stored as parquet as +select distinct p.id, coalesce(has_preprint, 0) as has_preprint +from publication_classifications p + left outer join ( + select p.id, 1 as has_preprint + from publication_classifications p + where p.type='Preprint') tmp + on p.id= tmp.id; + +compute stats indi_pub_has_preprint; + +create table indi_pub_in_subscribed stored as parquet as +select distinct p.id, coalesce(is_subscription, 0) as is_subscription +from publication p + left outer join( + select p.id, 1 as is_subscription from publication p + join indi_pub_gold_oa g on p.id=g.id + join indi_pub_hybrid h on p.id=h.id + join indi_pub_in_transformative t on p.id=t.id + where g.is_gold=0 and h.is_hybrid=0 and t.is_transformative=0) tmp + on p.id=tmp.id; + +compute stats indi_pub_in_subscribed; + +create table indi_result_with_pid as +select distinct p.id, coalesce(result_with_pid, 0) as result_with_pid +from result p + left outer join ( + select p.id, 1 as result_with_pid + from result_pids p) tmp + on p.id= tmp.id; + +compute stats indi_result_with_pid; \ No newline at end of file From eb53b52f7c5e1ca1db48171d76379ab9b364b050 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 2 Aug 2022 13:24:47 +0200 Subject: [PATCH 138/214] code formatting --- .../eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala index 0f82ecadf..088a07427 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala @@ -587,7 +587,7 @@ object DataciteToOAFTransformation { val oid = result.getId result.setId(IdentifierFactory.createIdentifier(result)) if (!result.getId.equalsIgnoreCase(oid)) { - result.setOriginalId((oid::List(doi)).asJava) + result.setOriginalId((oid :: List(doi)).asJava) } var relations: List[Relation] = From 8b0407d8ecb8cb793247ec0d72348f78a042d929 Mon Sep 17 00:00:00 2001 From: Antonis Lempesis Date: Wed, 3 Aug 2022 12:26:59 +0300 Subject: [PATCH 139/214] fixed the datasourceOrganization relations --- .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql index 6fa0e6fdf..01bed17cc 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql @@ -93,7 +93,7 @@ where d.datainfo.deletedbyinference=false and d.datainfo.invisible=false; CREATE TABLE ${stats_db_name}.datasource_organizations STORED AS PARQUET AS SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS organization FROM ${openaire_db_name}.relation r -WHERE r.reltype = 'datasourceOrganization' and r.datainfo.deletedbyinference = false and r.target like '20|%' and r.datainfo.invisible=false; +WHERE r.reltype = 'datasourceOrganization' and r.datainfo.deletedbyinference = false and r.source like '20|%' and r.datainfo.invisible=false; -- datasource sources: -- where the datasource info have been collected from. From e62018e95d45cb99442d80576527590a19419194 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 3 Aug 2022 12:26:05 +0200 Subject: [PATCH 140/214] [aggregator graph] added more assertions in test --- .../graph/raw/MigrateDbEntitiesApplicationTest.java | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java index 9048a22ea..408196665 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java @@ -18,6 +18,7 @@ import java.util.Objects; import java.util.Optional; import java.util.stream.Collectors; +import eu.dnetlib.dhp.schema.common.ModelConstants; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; import org.junit.jupiter.api.BeforeEach; @@ -252,6 +253,18 @@ public class MigrateDbEntitiesApplicationTest { assertValidId(r2.getSource()); assertEquals(r1.getSource(), r2.getTarget()); assertEquals(r2.getSource(), r1.getTarget()); + + assertTrue(r1.getSource().startsWith("10|")); + assertTrue(r1.getTarget().startsWith("20|")); + + assertEquals(ModelConstants.DATASOURCE_ORGANIZATION, r1.getRelType()); + assertEquals(ModelConstants.DATASOURCE_ORGANIZATION, r2.getRelType()); + + assertEquals(ModelConstants.PROVISION, r1.getSubRelType()); + assertEquals(ModelConstants.PROVISION, r2.getSubRelType()); + + assertEquals(ModelConstants.IS_PROVIDED_BY, r1.getRelClass()); + assertEquals(ModelConstants.PROVIDES, r2.getRelClass()); } @Test From b09d7ddc74fc13d3d1e7cfefccbfe1e472e88c41 Mon Sep 17 00:00:00 2001 From: Antonis Lempesis Date: Wed, 3 Aug 2022 12:26:59 +0300 Subject: [PATCH 141/214] fixed the datasourceOrganization relations --- .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql index 6fa0e6fdf..01bed17cc 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql @@ -93,7 +93,7 @@ where d.datainfo.deletedbyinference=false and d.datainfo.invisible=false; CREATE TABLE ${stats_db_name}.datasource_organizations STORED AS PARQUET AS SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS organization FROM ${openaire_db_name}.relation r -WHERE r.reltype = 'datasourceOrganization' and r.datainfo.deletedbyinference = false and r.target like '20|%' and r.datainfo.invisible=false; +WHERE r.reltype = 'datasourceOrganization' and r.datainfo.deletedbyinference = false and r.source like '20|%' and r.datainfo.invisible=false; -- datasource sources: -- where the datasource info have been collected from. From 27a91841e7fa2a1b615b4d1e161d606db5bead96 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 4 Aug 2022 11:39:39 +0200 Subject: [PATCH 142/214] WIP: cleaning of subjects --- .../oaf/utils/GraphCleaningFunctions.java | 5 ++ .../dhp/schema/oaf/utils/OafMapperUtils.java | 25 ++++++++++ .../dnetlib/dhp/actionmanager/Constants.java | 13 ++--- .../PrepareFOSSparkJob.java | 3 +- .../PrepareSDGSparkJob.java | 3 +- .../DataciteToOAFTransformation.scala | 6 +-- .../eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala | 2 +- .../dhp/sx/bio/pubmed/PubMedToOaf.scala | 4 +- .../createunresolvedentities/ProduceTest.java | 10 ++-- .../dhp/broker/oa/util/ConversionUtils.java | 33 +++++++------ .../doiboost/DoiBoostMappingUtil.scala | 22 +++++++++ .../doiboost/crossref/Crossref2Oaf.scala | 2 +- .../dnetlib/doiboost/mag/MagDataModel.scala | 12 ++--- .../dnetlib/dhp/bulktag/EOSCTagJobTest.java | 2 +- .../dhp/oa/graph/clean/CleaningRuleMap.java | 1 + .../dhp/oa/graph/dump/ResultMapper.java | 11 ++--- .../raw/AbstractMdRecordToOafMapper.java | 49 +++++++------------ .../dhp/oa/graph/raw/OafToOafMapper.java | 4 +- .../dhp/oa/graph/raw/OdfToOafMapper.java | 4 +- .../resolution/ResolveEntitiesTest.scala | 4 +- pom.xml | 2 +- 21 files changed, 132 insertions(+), 85 deletions(-) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java index 351bd2dd5..151c53685 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java @@ -520,6 +520,11 @@ public class GraphCleaningFunctions extends CleaningFunctions { return s; } + protected static Subject cleanValue(Subject s) { + s.setValue(s.getValue().replaceAll(CLEANING_REGEX, " ")); + return s; + } + protected static Field cleanValue(Field s) { s.setValue(s.getValue().replaceAll(CLEANING_REGEX, " ")); return s; diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java index 6f452e846..d58b354ab 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java @@ -189,6 +189,17 @@ public class OafMapperUtils { return q; } + public static Subject subject( + final String value, + final String classid, + final String classname, + final String schemeid, + final String schemename, + final DataInfo dataInfo) { + + return subject(value, qualifier(classid, classname, schemeid, schemename), dataInfo); + } + public static StructuredProperty structuredProperty( final String value, final String classid, @@ -200,6 +211,20 @@ public class OafMapperUtils { return structuredProperty(value, qualifier(classid, classname, schemeid, schemename), dataInfo); } + public static Subject subject( + final String value, + final Qualifier qualifier, + final DataInfo dataInfo) { + if (value == null) { + return null; + } + final Subject s = new Subject(); + s.setValue(value); + s.setQualifier(qualifier); + s.setDataInfo(dataInfo); + return s; + } + public static StructuredProperty structuredProperty( final String value, final Qualifier qualifier, diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java index aa25ca633..bd223d7c9 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java @@ -13,6 +13,7 @@ import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import eu.dnetlib.dhp.schema.oaf.Subject; import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; public class Constants { @@ -58,13 +59,13 @@ public class Constants { .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz)); } - public static StructuredProperty getSubject(String sbj, String classid, String classname, + public static Subject getSubject(String sbj, String classid, String classname, String diqualifierclassid) { if (sbj.equals(NULL)) return null; - StructuredProperty sp = new StructuredProperty(); - sp.setValue(sbj); - sp + Subject s = new Subject(); + s.setValue(sbj); + s .setQualifier( OafMapperUtils .qualifier( @@ -72,7 +73,7 @@ public class Constants { classname, ModelConstants.DNET_SUBJECT_TYPOLOGIES, ModelConstants.DNET_SUBJECT_TYPOLOGIES)); - sp + s .setDataInfo( OafMapperUtils .dataInfo( @@ -88,7 +89,7 @@ public class Constants { ModelConstants.DNET_PROVENANCE_ACTIONS), "")); - return sp; + return s; } } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareFOSSparkJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareFOSSparkJob.java index 55e391932..4d2d25215 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareFOSSparkJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareFOSSparkJob.java @@ -24,6 +24,7 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import eu.dnetlib.dhp.schema.oaf.Subject; import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; import eu.dnetlib.dhp.utils.DHPUtils; @@ -79,7 +80,7 @@ public class PrepareFOSSparkJob implements Serializable { HashSet level3 = new HashSet<>(); addLevels(level1, level2, level3, first); it.forEachRemaining(v -> addLevels(level1, level2, level3, v)); - List sbjs = new ArrayList<>(); + List sbjs = new ArrayList<>(); level1.forEach(l -> sbjs.add(getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID))); level2.forEach(l -> sbjs.add(getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID))); level3.forEach(l -> sbjs.add(getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID))); diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareSDGSparkJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareSDGSparkJob.java index a31e380fe..bfdf14234 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareSDGSparkJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareSDGSparkJob.java @@ -24,6 +24,7 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import eu.dnetlib.dhp.schema.oaf.Subject; import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; import eu.dnetlib.dhp.utils.DHPUtils; @@ -73,7 +74,7 @@ public class PrepareSDGSparkJob implements Serializable { Result r = new Result(); r.setId(DHPUtils.generateUnresolvedIdentifier(k, DOI)); SDGDataModel first = it.next(); - List sbjs = new ArrayList<>(); + List sbjs = new ArrayList<>(); sbjs.add(getSubject(first.getSbj(), SDG_CLASS_ID, SDG_CLASS_NAME, UPDATE_SUBJECT_SDG_CLASS_ID)); it .forEachRemaining( diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala index 088a07427..c29614d33 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala @@ -19,7 +19,7 @@ import java.time.chrono.ThaiBuddhistDate import java.time.format.DateTimeFormatter import java.util.{Date, Locale} import scala.collection.JavaConverters._ -import scala.io.{Codec, Source} +import scala.io.Source object DataciteToOAFTransformation { @@ -252,7 +252,7 @@ object DataciteToOAFTransformation { .exists(i => i.getHostedby != null && "figshare".equalsIgnoreCase(i.getHostedby.getValue)) if (hosted_by_figshare) { r.getInstance().asScala.foreach(i => i.setAccessright(ModelConstants.OPEN_ACCESS_RIGHT())) - val l: List[StructuredProperty] = List() + val l: List[Subject] = List() r.setSubject(l.asJava) } } @@ -492,7 +492,7 @@ object DataciteToOAFTransformation { subjects .filter(s => s.subject.nonEmpty) .map(s => - OafMapperUtils.structuredProperty( + OafMapperUtils.subject( s.subject.get, SUBJ_CLASS, SUBJ_CLASS, diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala index ffdab1799..670323598 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala @@ -281,7 +281,7 @@ object BioDBToOAF { d.setSubject( subjects .map(s => - OafMapperUtils.structuredProperty( + OafMapperUtils.subject( s, SUBJ_CLASS, SUBJ_CLASS, diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala index 42bafc93e..410686f97 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala @@ -265,8 +265,8 @@ object PubMedToOaf { result.setLanguage(term) } - val subjects: List[StructuredProperty] = article.getSubjects.asScala.map(s => - OafMapperUtils.structuredProperty( + val subjects: List[Subject] = article.getSubjects.asScala.map(s => + OafMapperUtils.subject( s.getValue, SUBJ_CLASS, SUBJ_CLASS, diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/ProduceTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/ProduceTest.java index a5ecaeabf..c3c110f09 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/ProduceTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/ProduceTest.java @@ -72,7 +72,7 @@ public class ProduceTest { JavaRDD tmp = getResultJavaRDD(); - List sbjs = tmp + List sbjs = tmp .filter(row -> row.getSubject() != null && row.getSubject().size() > 0) .flatMap(row -> row.getSubject().iterator()) .collect(); @@ -169,7 +169,7 @@ public class ProduceTest { .getSubject() .size()); - List sbjs = tmp + List sbjs = tmp .filter(row -> row.getId().equals(doi)) .flatMap(row -> row.getSubject().iterator()) .collect(); @@ -396,7 +396,7 @@ public class ProduceTest { .getSubject() .size()); - List sbjs = tmp + List sbjs = tmp .filter(row -> row.getId().equals(doi)) .flatMap(row -> row.getSubject().iterator()) .collect(); @@ -508,7 +508,7 @@ public class ProduceTest { .getSubject() .size()); - List sbjs = tmp + List sbjs = tmp .filter(row -> row.getId().equals(doi)) .flatMap(row -> row.getSubject().iterator()) .collect(); @@ -537,7 +537,7 @@ public class ProduceTest { JavaRDD tmp = getResultJavaRDDPlusSDG(); - List sbjs_sdg = tmp + List sbjs_sdg = tmp .filter(row -> row.getSubject() != null && row.getSubject().size() > 0) .flatMap(row -> row.getSubject().iterator()) .filter(sbj -> sbj.getQualifier().getClassid().equals(Constants.SDG_CLASS_ID)) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java index bc37203d3..5e7adec79 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java @@ -26,20 +26,7 @@ import eu.dnetlib.broker.objects.OaBrokerRelatedPublication; import eu.dnetlib.broker.objects.OaBrokerRelatedSoftware; import eu.dnetlib.broker.objects.OaBrokerTypedValue; import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.oaf.Author; -import eu.dnetlib.dhp.schema.oaf.Dataset; -import eu.dnetlib.dhp.schema.oaf.Datasource; -import eu.dnetlib.dhp.schema.oaf.ExternalReference; -import eu.dnetlib.dhp.schema.oaf.Field; -import eu.dnetlib.dhp.schema.oaf.Instance; -import eu.dnetlib.dhp.schema.oaf.Journal; -import eu.dnetlib.dhp.schema.oaf.KeyValue; -import eu.dnetlib.dhp.schema.oaf.Project; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.Qualifier; -import eu.dnetlib.dhp.schema.oaf.Result; -import eu.dnetlib.dhp.schema.oaf.Software; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import eu.dnetlib.dhp.schema.oaf.*; public class ConversionUtils { @@ -71,6 +58,10 @@ public class ConversionUtils { return sp != null ? new OaBrokerTypedValue(classId(sp.getQualifier()), sp.getValue()) : null; } + public static OaBrokerTypedValue oafSubjectToBrokerTypedValue(final Subject sp) { + return sp != null ? new OaBrokerTypedValue(classId(sp.getQualifier()), sp.getValue()) : null; + } + public static OaBrokerRelatedDataset oafDatasetToBrokerDataset(final Dataset d) { if (d == null) { return null; @@ -115,7 +106,7 @@ public class ConversionUtils { res.setTitles(structPropList(result.getTitle())); res.setAbstracts(fieldList(result.getDescription())); res.setLanguage(classId(result.getLanguage())); - res.setSubjects(structPropTypedList(result.getSubject())); + res.setSubjects(subjectList(result.getSubject())); res.setCreators(mappedList(result.getAuthor(), ConversionUtils::oafAuthorToBrokerAuthor)); res.setPublicationdate(fieldValue(result.getDateofacceptance())); res.setPublisher(fieldValue(result.getPublisher())); @@ -304,6 +295,18 @@ public class ConversionUtils { .collect(Collectors.toList()); } + private static List subjectList(final List list) { + if (list == null) { + return new ArrayList<>(); + } + + return list + .stream() + .map(ConversionUtils::oafSubjectToBrokerTypedValue) + .filter(Objects::nonNull) + .collect(Collectors.toList()); + } + private static List mappedList(final List list, final Function func) { if (list == null) { return new ArrayList<>(); diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala index 20471973a..4789093cd 100644 --- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala +++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala @@ -391,6 +391,28 @@ object DoiBoostMappingUtil { di } + def createSubject(value: String, classId: String, schemeId: String): Subject = { + val s = new Subject + s.setQualifier(OafMapperUtils.qualifier(classId, classId, schemeId, schemeId)) + s.setValue(value) + s + + } + + def createSubject( + value: String, + classId: String, + className: String, + schemeId: String, + schemeName: String + ): Subject = { + val s = new Subject + s.setQualifier(OafMapperUtils.qualifier(classId, className, schemeId, schemeName)) + s.setValue(value) + s + + } + def createSP( value: String, classId: String, diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala index 9eec9e759..7fb10863f 100644 --- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala +++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala @@ -201,7 +201,7 @@ case object Crossref2Oaf { if (subjectList.nonEmpty) { result.setSubject( - subjectList.map(s => createSP(s, "keywords", ModelConstants.DNET_SUBJECT_TYPOLOGIES)).asJava + subjectList.map(s => createSubject(s, "keyword", ModelConstants.DNET_SUBJECT_TYPOLOGIES)).asJava ) } diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/mag/MagDataModel.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/mag/MagDataModel.scala index 18ba864ce..9a0b0d845 100644 --- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/mag/MagDataModel.scala +++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/mag/MagDataModel.scala @@ -2,7 +2,7 @@ package eu.dnetlib.doiboost.mag import eu.dnetlib.dhp.schema.common.ModelConstants import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory -import eu.dnetlib.dhp.schema.oaf.{Instance, Journal, Publication, StructuredProperty} +import eu.dnetlib.dhp.schema.oaf.{Instance, Journal, Publication, StructuredProperty, Subject} import eu.dnetlib.doiboost.DoiBoostMappingUtil import eu.dnetlib.doiboost.DoiBoostMappingUtil._ import org.json4s @@ -210,8 +210,8 @@ case object ConversionUtil { val className = "Microsoft Academic Graph classification" val classid = "MAG" - val p: List[StructuredProperty] = fieldOfStudy.subjects.flatMap(s => { - val s1 = createSP( + val p: List[Subject] = fieldOfStudy.subjects.flatMap(s => { + val s1 = createSubject( s.DisplayName, classid, className, @@ -219,10 +219,10 @@ case object ConversionUtil { ModelConstants.DNET_SUBJECT_TYPOLOGIES ) val di = DoiBoostMappingUtil.generateDataInfo(s.Score.toString) - var resList: List[StructuredProperty] = List(s1) + var resList: List[Subject] = List(s1) if (s.MainType.isDefined) { val maintp = s.MainType.get - val s2 = createSP( + val s2 = createSubject( s.MainType.get, classid, className, @@ -232,7 +232,7 @@ case object ConversionUtil { s2.setDataInfo(di) resList = resList ::: List(s2) if (maintp.contains(".")) { - val s3 = createSP( + val s3 = createSubject( maintp.split("\\.").head, classid, className, diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java index bfe4f6448..a640e2009 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java @@ -290,7 +290,7 @@ public class EOSCTagJobTest { .stream() .anyMatch(s -> s.getCode().equals("EOSC::Jupyter Notebook"))); - List subjects = tmp + List subjects = tmp .filter(sw -> sw.getId().equals("50|od______1582::6e7a9b21a2feef45673890432af34244")) .collect() .get(0) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleMap.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleMap.java index 7a3583289..6c156edb7 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleMap.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleMap.java @@ -27,6 +27,7 @@ public class CleaningRuleMap extends HashMap, SerializableConsumer cleanQualifier(vocabularies, (AccessRight) o)); mapping.put(Country.class, o -> cleanCountry(vocabularies, (Country) o)); mapping.put(Relation.class, o -> cleanRelation(vocabularies, (Relation) o)); + return mapping; } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java index aad3a8706..510f9c3a6 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java @@ -17,6 +17,7 @@ import eu.dnetlib.dhp.schema.dump.oaf.Instance; import eu.dnetlib.dhp.schema.dump.oaf.Measure; import eu.dnetlib.dhp.schema.dump.oaf.OpenAccessRoute; import eu.dnetlib.dhp.schema.dump.oaf.Result; +import eu.dnetlib.dhp.schema.dump.oaf.Subject; import eu.dnetlib.dhp.schema.dump.oaf.community.CfHbKeyValue; import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityInstance; import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; @@ -66,7 +67,7 @@ public class ResultMapper implements Serializable { final List contributorList = new ArrayList<>(); Optional .ofNullable(input.getContributor()) - .ifPresent(value -> value.stream().forEach(c -> contributorList.add(c.getValue()))); + .ifPresent(value -> value.forEach(c -> contributorList.add(c.getValue()))); out.setContributor(contributorList); Optional @@ -103,7 +104,7 @@ public class ResultMapper implements Serializable { final List coverageList = new ArrayList<>(); Optional .ofNullable(input.getCoverage()) - .ifPresent(value -> value.stream().forEach(c -> coverageList.add(c.getValue()))); + .ifPresent(value -> value.forEach(c -> coverageList.add(c.getValue()))); out.setCoverage(coverageList); out.setDateofcollection(input.getDateofcollection()); @@ -114,14 +115,12 @@ public class ResultMapper implements Serializable { .ifPresent(value -> value.forEach(d -> descriptionList.add(d.getValue()))); out.setDescription(descriptionList); Optional> oStr = Optional.ofNullable(input.getEmbargoenddate()); - if (oStr.isPresent()) { - out.setEmbargoenddate(oStr.get().getValue()); - } + oStr.ifPresent(stringField -> out.setEmbargoenddate(stringField.getValue())); final List formatList = new ArrayList<>(); Optional .ofNullable(input.getFormat()) - .ifPresent(value -> value.stream().forEach(f -> formatList.add(f.getValue()))); + .ifPresent(value -> value.forEach(f -> formatList.add(f.getValue()))); out.setFormat(formatList); out.setId(input.getId()); out.setOriginalId(new ArrayList<>()); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index e06327b2a..da1c764e8 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -8,15 +8,7 @@ import static eu.dnetlib.dhp.schema.common.ModelConstants.PRODUCES; import static eu.dnetlib.dhp.schema.common.ModelConstants.REPOSITORY_PROVENANCE_ACTIONS; import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_PROJECT; import static eu.dnetlib.dhp.schema.common.ModelConstants.UNKNOWN; -import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.createOpenaireId; -import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.dataInfo; -import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.field; -import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.journal; -import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.keyValue; -import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.listFields; -import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.oaiIProvenance; -import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.qualifier; -import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.structuredProperty; +import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.*; import java.util.*; @@ -29,26 +21,7 @@ import com.google.common.collect.Sets; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.dhp.schema.oaf.AccessRight; -import eu.dnetlib.dhp.schema.oaf.Author; -import eu.dnetlib.dhp.schema.oaf.Context; -import eu.dnetlib.dhp.schema.oaf.DataInfo; -import eu.dnetlib.dhp.schema.oaf.Dataset; -import eu.dnetlib.dhp.schema.oaf.Field; -import eu.dnetlib.dhp.schema.oaf.GeoLocation; -import eu.dnetlib.dhp.schema.oaf.Instance; -import eu.dnetlib.dhp.schema.oaf.Journal; -import eu.dnetlib.dhp.schema.oaf.KeyValue; -import eu.dnetlib.dhp.schema.oaf.OAIProvenance; -import eu.dnetlib.dhp.schema.oaf.Oaf; -import eu.dnetlib.dhp.schema.oaf.OafEntity; -import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.Qualifier; -import eu.dnetlib.dhp.schema.oaf.Relation; -import eu.dnetlib.dhp.schema.oaf.Result; -import eu.dnetlib.dhp.schema.oaf.Software; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; @@ -411,7 +384,7 @@ public abstract class AbstractMdRecordToOafMapper { protected abstract List prepareTitles(Document doc, DataInfo info); - protected abstract List prepareSubjects(Document doc, DataInfo info); + protected abstract List prepareSubjects(Document doc, DataInfo info); protected abstract Qualifier prepareLanguages(Document doc); @@ -559,6 +532,22 @@ public abstract class AbstractMdRecordToOafMapper { return res; } + protected List prepareSubjectList( + final Node node, + final String xpath, + final DataInfo info) { + final List res = new ArrayList<>(); + for (final Object o : node.selectNodes(xpath)) { + final Node n = (Node) o; + res + .add( + subject( + n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"), + n.valueOf("@schemename"), info)); + } + return res; + } + protected OAIProvenance prepareOAIprovenance(final Document doc) { final Node n = doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']"); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java index b7afd3595..9225e174d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java @@ -84,8 +84,8 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper { } @Override - protected List prepareSubjects(final Document doc, final DataInfo info) { - return prepareListStructProps(doc, "//dc:subject", info); + protected List prepareSubjects(final Document doc, final DataInfo info) { + return prepareSubjectList(doc, "//dc:subject", info); } @Override diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java index 1bbeac9fb..101f74607 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java @@ -249,8 +249,8 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { } @Override - protected List prepareSubjects(final Document doc, final DataInfo info) { - return prepareListStructProps(doc, "//*[local-name()='subject']", info); + protected List prepareSubjects(final Document doc, final DataInfo info) { + return prepareSubjectList(doc, "//*[local-name()='subject']", info); } @Override diff --git a/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/oa/graph/resolution/ResolveEntitiesTest.scala b/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/oa/graph/resolution/ResolveEntitiesTest.scala index c8e41743f..e333da1aa 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/oa/graph/resolution/ResolveEntitiesTest.scala +++ b/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/oa/graph/resolution/ResolveEntitiesTest.scala @@ -59,7 +59,7 @@ class ResolveEntitiesTest extends Serializable { r.setId(id.toLowerCase.trim) r.setSubject( List( - OafMapperUtils.structuredProperty( + OafMapperUtils.subject( FAKE_SUBJECT, OafMapperUtils.qualifier("fos", "fosCS", "fossSchema", "fossiFIgo"), null @@ -250,7 +250,7 @@ class ResolveEntitiesTest extends Serializable { val r = new Result r.setSubject( List( - OafMapperUtils.structuredProperty( + OafMapperUtils.subject( FAKE_SUBJECT, OafMapperUtils.qualifier("fos", "fosCS", "fossSchema", "fossiFIgo"), null diff --git a/pom.xml b/pom.xml index 973bc3773..632ca99b8 100644 --- a/pom.xml +++ b/pom.xml @@ -801,7 +801,7 @@ 3.3.3 3.4.2 [2.12,3.0) - [2.12.2-SNAPSHOT] + [2.13.2-SNAPSHOT] [4.0.3] [6.0.5] [3.1.6] From 499826ead1934f1dbe3f880cdcaa82200ea5f470 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 4 Aug 2022 12:40:48 +0200 Subject: [PATCH 143/214] serialising field eoscifguidelines field in the Solr XML records --- .../dhp/oa/provision/utils/XmlRecordFactory.java | 11 +++++++++++ .../oa/provision/utils/XmlSerializationUtils.java | 13 +++++++++++++ .../dhp/oa/provision/XmlRecordFactoryTest.java | 2 ++ .../eu/dnetlib/dhp/oa/provision/publication.json | 8 ++++++++ 4 files changed, 34 insertions(+) diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java index b34ec9693..45ba840c9 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java @@ -214,6 +214,17 @@ public class XmlRecordFactory implements Serializable { metadata.addAll(measuresAsXml(r.getMeasures())); } + if (r.getEoscifguidelines() != null) { + metadata + .addAll( + r + .getEoscifguidelines() + .stream() + .filter(Objects::nonNull) + .map(e -> XmlSerializationUtils.mapEoscIf(e)) + .collect(Collectors.toList())); + } + if (r.getContext() != null) { contexts.addAll(r.getContext().stream().map(c -> c.getId()).collect(Collectors.toList())); /* FIXME: Workaround for CLARIN mining issue: #3670#note-29 */ diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlSerializationUtils.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlSerializationUtils.java index 73667e056..adf7090d2 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlSerializationUtils.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlSerializationUtils.java @@ -7,6 +7,8 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank; import java.util.List; +import com.google.common.collect.Lists; + import eu.dnetlib.dhp.schema.oaf.*; import scala.Tuple2; @@ -161,4 +163,15 @@ public class XmlSerializationUtils { sb.append("/>"); return sb.toString(); } + + public static String mapEoscIf(EoscIfGuidelines e) { + return asXmlElement( + "eoscifguidelines", Lists + .newArrayList( + new Tuple2<>("code", e.getCode()), + new Tuple2<>("label", e.getLabel()), + new Tuple2<>("url", e.getUrl()), + new Tuple2<>("semanticrelation", e.getSemanticRelation()))); + } + } diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java index 92d9f497f..77d1f9fdb 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java @@ -87,6 +87,8 @@ public class XmlRecordFactoryTest { assertEquals( "C", doc.valueOf("//*[local-name() = 'result']/measure[./@id = 'popularity']/@class")); + assertEquals("EOSC::Jupyter Notebook", doc.valueOf("//*[local-name() = 'result']/eoscifguidelines/@code")); + } @Test diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json index 41ced45ae..5e3f19bd7 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json @@ -1,4 +1,12 @@ { + "eoscifguidelines": [ + { + "code" : "EOSC::Jupyter Notebook", + "label" : "EOSC::Jupyter Notebook", + "url" : "", + "semanticRelation" : "compliesWith" + } + ], "measures": [ { "id": "influence", From a7a18d76306bdae96691a5945ffa84ee32eafcaf Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 4 Aug 2022 17:40:40 +0200 Subject: [PATCH 144/214] [Graph Dump] removed code for the dump from the project. Fixed issues in tests when possible --- .../publication_license_embargo_datetime.json | 4 +- .../graph/datasource/datasource.json | 22 +- .../oa/graph/clean/CleanContextSparkJob.java | 8 - .../dnetlib/dhp/oa/graph/dump/Constants.java | 58 -- .../dhp/oa/graph/dump/DumpProducts.java | 107 -- .../eu/dnetlib/dhp/oa/graph/dump/MakeTar.java | 74 -- .../oa/graph/dump/QueryInformationSystem.java | 74 -- .../dhp/oa/graph/dump/ResultMapper.java | 672 ------------ .../dhp/oa/graph/dump/SaveCommunityMap.java | 99 -- .../dhp/oa/graph/dump/SendToZenodoHDFS.java | 100 -- .../eu/dnetlib/dhp/oa/graph/dump/Utils.java | 77 -- .../oa/graph/dump/community/CommunityMap.java | 8 - .../graph/dump/community/CommunitySplit.java | 81 -- .../graph/dump/community/ResultProject.java | 28 - .../community/SparkDumpCommunityProducts.java | 67 -- .../community/SparkPrepareResultProject.java | 193 ---- .../community/SparkSplitForCommunity.java | 50 - .../community/SparkUpdateProjectInfo.java | 90 -- .../dhp/oa/graph/dump/complete/Constants.java | 26 - .../oa/graph/dump/complete/ContextInfo.java | 84 -- .../dump/complete/CreateContextEntities.java | 110 -- .../dump/complete/CreateContextRelation.java | 128 --- .../dump/complete/DumpGraphEntities.java | 518 ---------- .../dhp/oa/graph/dump/complete/Extractor.java | 201 ---- .../oa/graph/dump/complete/MergedRels.java | 25 - .../graph/dump/complete/OrganizationMap.java | 21 - .../dhp/oa/graph/dump/complete/Process.java | 99 -- .../dump/complete/QueryInformationSystem.java | 195 ---- .../dump/complete/SparkCollectAndSave.java | 122 --- .../dump/complete/SparkDumpEntitiesJob.java | 54 - .../dump/complete/SparkDumpRelationJob.java | 132 --- .../SparkExtractRelationFromEntities.java | 54 - .../complete/SparkOrganizationRelation.java | 176 ---- .../SparkSelectValidRelationsJob.java | 136 --- .../dump/exceptions/MyRuntimeException.java | 30 - .../NoAvailableEntityTypeException.java | 29 - .../funderresults/SparkDumpFunderResults.java | 129 --- .../SparkResultLinkedToProject.java | 118 --- .../ProjectsSubsetSparkJob.java | 82 -- .../graph/raw/PatchRelationsApplication.java | 13 +- .../graph/dump/funder_result_parameters.json | 26 - .../oa/graph/dump/input_cm_parameters.json | 37 - .../oa/graph/dump/input_collect_and_save.json | 30 - .../graph/dump/input_complete_parameters.json | 35 - .../oa/graph/dump/input_entity_parameter.json | 24 - .../graph/dump/input_maketar_parameters.json | 30 - .../dump/input_organization_parameters.json | 36 - .../dump/input_parameter_select_relation.json | 20 - .../dhp/oa/graph/dump/input_parameters.json | 47 - .../graph/dump/input_parameters_link_prj.json | 41 - .../dump/input_relationdump_parameters.json | 32 - .../graph/dump/project_input_parameters.json | 29 - .../graph/dump/project_prep_parameters.json | 20 - .../graph/dump/project_subset_parameters.json | 27 - .../oozie_app/config-default.xml | 30 - .../dump/projectsubset/oozie_app/workflow.xml | 171 ---- 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a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/publication_license_embargo_datetime.json b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/publication_license_embargo_datetime.json index c84e16350..c715e44ed 100644 --- a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/publication_license_embargo_datetime.json +++ b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/publication_license_embargo_datetime.json @@ -1443,7 +1443,7 @@ 17 ] ], -"date-time": "2021-05-17T15:08:12Z", +"date-time": "3021-05-17T15:08:12Z", "timestamp": 1621264092000 }, "score": 1.0, @@ -1461,7 +1461,7 @@ 22 ] ], - "date-time": "2021-05-17T15:08:12Z" + "date-time": "3021-05-17T15:08:12Z" }, "references-count": 83, "journal-issue": { diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/countrypropagation/graph/datasource/datasource.json 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archive","schemeid":"dnet:datasource_typologies_ui","schemename":"dnet:datasource_typologies_ui"},"dateofcollection":"2020-07-10","englishname":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"Estudos Portugueses"},"extraInfo":[],"id":"10|issn___print::a7a2010e75d849442790955162ef4e48","journal":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"issnPrinted":"2447-0546","name":"Estudos Portugueses"},"lastupdatetimestamp":1646230297782,"latitude":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"0.0"},"longitude":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"0.0"},"namespaceprefix":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"jrnl24470546"},"odcontenttypes":[],"odlanguages":[],"odnumberofitems":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"0.0"},"officialname":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"Estudos Portugueses"},"openairecompatibility":{"classid":"hostedBy","classname":"collected from a compatible aggregator","schemeid":"dnet:datasourceCompatibilityLevel","schemename":"dnet:datasourceCompatibilityLevel"},"originalId":["issn___print::2447-0546"],"pid":[],"policies":[],"serviceprovider":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":false},"subjects":[],"thematic":false,"versioning":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":false}} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java index 3e9b17f3f..55fdbac59 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java @@ -4,7 +4,6 @@ package eu.dnetlib.dhp.oa.graph.clean; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.io.Serializable; -import java.util.List; import java.util.Optional; import java.util.stream.Collectors; @@ -21,15 +20,8 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.common.HdfsSupport; -import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.oaf.Context; -import eu.dnetlib.dhp.schema.oaf.Oaf; -import eu.dnetlib.dhp.schema.oaf.OafEntity; import eu.dnetlib.dhp.schema.oaf.Result; -import eu.dnetlib.dhp.utils.ISLookupClientFactory; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; public class CleanContextSparkJob implements Serializable { private static final Logger log = LoggerFactory.getLogger(CleanContextSparkJob.class); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java deleted file mode 100644 index 61167639c..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java +++ /dev/null @@ -1,58 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump; - -import java.util.Map; - -import com.google.common.collect.Maps; - -import eu.dnetlib.dhp.schema.common.ModelConstants; - -public class Constants { - - protected static final Map accessRightsCoarMap = Maps.newHashMap(); - protected static final Map coarCodeLabelMap = Maps.newHashMap(); - - public static final String INFERRED = "Inferred by OpenAIRE"; - public static final String CABF2 = "c_abf2"; - - public static final String HARVESTED = "Harvested"; - public static final String DEFAULT_TRUST = "0.9"; - public static final String USER_CLAIM = "Linked by user"; - - public static final String COAR_ACCESS_RIGHT_SCHEMA = "http://vocabularies.coar-repositories.org/documentation/access_rights/"; - - public static final String ZENODO_COMMUNITY_PREFIX = "https://zenodo.org/communities/"; - - public static final String RESEARCH_COMMUNITY = "Research Community"; - - public static final String RESEARCH_INFRASTRUCTURE = "Research Infrastructure/Initiative"; - - static { - accessRightsCoarMap.put(ModelConstants.ACCESS_RIGHT_OPEN, CABF2); - accessRightsCoarMap.put("RESTRICTED", "c_16ec"); - accessRightsCoarMap.put("OPEN SOURCE", CABF2); - accessRightsCoarMap.put(ModelConstants.ACCESS_RIGHT_CLOSED, "c_14cb"); - accessRightsCoarMap.put(ModelConstants.ACCESS_RIGHT_EMBARGO, "c_f1cf"); - } - - static { - coarCodeLabelMap.put(CABF2, ModelConstants.ACCESS_RIGHT_OPEN); - coarCodeLabelMap.put("c_16ec", "RESTRICTED"); - coarCodeLabelMap.put("c_14cb", ModelConstants.ACCESS_RIGHT_CLOSED); - coarCodeLabelMap.put("c_f1cf", "EMBARGO"); - } - - public enum DUMPTYPE { - COMPLETE("complete"), COMMUNITY("community"), FUNDER("funder"); - - private final String type; - - DUMPTYPE(String type) { - this.type = type; - } - - public String getType() { - return type; - } - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java deleted file mode 100644 index a714cea20..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java +++ /dev/null @@ -1,107 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.util.List; -import java.util.Objects; -import java.util.Optional; -import java.util.Set; -import java.util.stream.Collectors; - -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.FilterFunction; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SaveMode; -import org.apache.spark.sql.SparkSession; - -import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; -import eu.dnetlib.dhp.oa.graph.dump.exceptions.NoAvailableEntityTypeException; -import eu.dnetlib.dhp.schema.oaf.*; - -/** - * It fires the execution of the actual dump for result entities. If the dump is for RC/RI products its checks for each - * result its belongingess to at least one RC/RI before "asking" for its mapping. - */ -public class DumpProducts implements Serializable { - - public void run(Boolean isSparkSessionManaged, String inputPath, String outputPath, String communityMapPath, - Class inputClazz, - Class outputClazz, - String dumpType) { - - SparkConf conf = new SparkConf(); - - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - execDump( - spark, inputPath, outputPath, communityMapPath, inputClazz, outputClazz, dumpType); - }); - } - - public static void execDump( - SparkSession spark, - String inputPath, - String outputPath, - String communityMapPath, - Class inputClazz, - Class outputClazz, - String dumpType) { - - CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath); - - Utils - .readPath(spark, inputPath, inputClazz) - .map((MapFunction) value -> execMap(value, communityMap, dumpType), Encoders.bean(outputClazz)) - .filter((FilterFunction) value -> value != null) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); - - } - - private static O execMap(I value, - CommunityMap communityMap, - String dumpType) throws NoAvailableEntityTypeException { - - Optional odInfo = Optional.ofNullable(value.getDataInfo()); - if (odInfo.isPresent()) { - if (odInfo.get().getDeletedbyinference() || odInfo.get().getInvisible()) { - return null; - } - } else { - return null; - } - - if (Constants.DUMPTYPE.COMMUNITY.getType().equals(dumpType)) { - Set communities = communityMap.keySet(); - - Optional> inputContext = Optional - .ofNullable(((eu.dnetlib.dhp.schema.oaf.Result) value).getContext()); - if (!inputContext.isPresent()) { - return null; - } - List toDumpFor = inputContext.get().stream().map(c -> { - if (communities.contains(c.getId())) { - return c.getId(); - } - if (c.getId().contains("::") && communities.contains(c.getId().substring(0, c.getId().indexOf("::")))) { - return c.getId().substring(0, c.getId().indexOf("::")); - } - return null; - }).filter(Objects::nonNull).collect(Collectors.toList()); - if (toDumpFor.isEmpty()) { - return null; - } - } - - return (O) ResultMapper.map(value, communityMap, dumpType); - - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/MakeTar.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/MakeTar.java deleted file mode 100644 index b56849a3a..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/MakeTar.java +++ /dev/null @@ -1,74 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump; - -import java.io.IOException; -import java.io.Serializable; -import java.util.Optional; - -import org.apache.commons.io.IOUtils; -import org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.fs.LocatedFileStatus; -import org.apache.hadoop.fs.Path; -import org.apache.hadoop.fs.RemoteIterator; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.common.MakeTarArchive; - -public class MakeTar implements Serializable { - - private static final Logger log = LoggerFactory.getLogger(MakeTar.class); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - MakeTar.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_maketar_parameters.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - final String outputPath = parser.get("hdfsPath"); - log.info("hdfsPath: {}", outputPath); - - final String hdfsNameNode = parser.get("nameNode"); - log.info("nameNode: {}", hdfsNameNode); - - final String inputPath = parser.get("sourcePath"); - log.info("input path : {}", inputPath); - - final int gBperSplit = Optional - .ofNullable(parser.get("splitSize")) - .map(Integer::valueOf) - .orElse(10); - - Configuration conf = new Configuration(); - conf.set("fs.defaultFS", hdfsNameNode); - - FileSystem fileSystem = FileSystem.get(conf); - - makeTArArchive(fileSystem, inputPath, outputPath, gBperSplit); - - } - - public static void makeTArArchive(FileSystem fileSystem, String inputPath, String outputPath, int gBperSplit) - throws IOException { - - RemoteIterator dirIterator = fileSystem.listLocatedStatus(new Path(inputPath)); - - while (dirIterator.hasNext()) { - LocatedFileStatus fileStatus = dirIterator.next(); - - Path p = fileStatus.getPath(); - String pathString = p.toString(); - String entity = pathString.substring(pathString.lastIndexOf("/") + 1); - - MakeTarArchive.tarMaxSize(fileSystem, pathString, outputPath + "/" + entity, entity, gBperSplit); - } - - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java deleted file mode 100644 index b972de6e9..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java +++ /dev/null @@ -1,74 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump; - -import java.io.StringReader; -import java.util.List; - -import org.dom4j.Document; -import org.dom4j.DocumentException; -import org.dom4j.Element; -import org.dom4j.io.SAXReader; -import org.xml.sax.SAXException; - -import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; - -public class QueryInformationSystem { - - private ISLookUpService isLookUp; - - private static final String XQUERY_ALL = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') " - + - " where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " + - " and ($x//context/param[./@name = 'status']/text() = 'all') " - + - " return " + - " " + - "{$x//CONFIGURATION/context/@id}" + - "{$x//CONFIGURATION/context/@label}" + - ""; - - private static final String XQUERY_CI = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') " - + - " where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " + - " and $x//CONFIGURATION/context[./@id=%s] " - + - " return " + - " " + - "{$x//CONFIGURATION/context/@id}" + - "{$x//CONFIGURATION/context/@label}" + - ""; - - public CommunityMap getCommunityMap(boolean singleCommunity, String communityId) - throws ISLookUpException, DocumentException, SAXException { - if (singleCommunity) - return getMap(isLookUp.quickSearchProfile(XQUERY_CI.replace("%s", "'" + communityId + "'"))); - return getMap(isLookUp.quickSearchProfile(XQUERY_ALL)); - - } - - public ISLookUpService getIsLookUp() { - return isLookUp; - } - - public void setIsLookUp(ISLookUpService isLookUpService) { - this.isLookUp = isLookUpService; - } - - private CommunityMap getMap(List communityMap) throws DocumentException, SAXException { - final CommunityMap map = new CommunityMap(); - - for (String xml : communityMap) { - final Document doc; - final SAXReader reader = new SAXReader(); - reader.setFeature("http://apache.org/xml/features/disallow-doctype-decl", true); - doc = reader.read(new StringReader(xml)); - Element root = doc.getRootElement(); - map.put(root.attribute("id").getValue(), root.attribute("label").getValue()); - } - - return map; - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java deleted file mode 100644 index aad3a8706..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java +++ /dev/null @@ -1,672 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump; - -import java.io.Serializable; -import java.util.*; -import java.util.stream.Collectors; - -import org.apache.commons.lang3.StringUtils; - -import eu.dnetlib.dhp.oa.graph.dump.exceptions.NoAvailableEntityTypeException; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.dump.oaf.*; -import eu.dnetlib.dhp.schema.dump.oaf.AccessRight; -import eu.dnetlib.dhp.schema.dump.oaf.Author; -import eu.dnetlib.dhp.schema.dump.oaf.GeoLocation; -import eu.dnetlib.dhp.schema.dump.oaf.Instance; -import eu.dnetlib.dhp.schema.dump.oaf.Measure; -import eu.dnetlib.dhp.schema.dump.oaf.OpenAccessRoute; -import eu.dnetlib.dhp.schema.dump.oaf.Result; -import eu.dnetlib.dhp.schema.dump.oaf.community.CfHbKeyValue; -import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityInstance; -import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; -import eu.dnetlib.dhp.schema.dump.oaf.community.Context; -import eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult; -import eu.dnetlib.dhp.schema.oaf.*; - -public class ResultMapper implements Serializable { - - public static Result map( - E in, Map communityMap, String dumpType) throws NoAvailableEntityTypeException { - - Result out; - if (Constants.DUMPTYPE.COMPLETE.getType().equals(dumpType)) { - out = new GraphResult(); - } else { - out = new CommunityResult(); - } - - eu.dnetlib.dhp.schema.oaf.Result input = (eu.dnetlib.dhp.schema.oaf.Result) in; - Optional ort = Optional.ofNullable(input.getResulttype()); - if (ort.isPresent()) { - try { - - addTypeSpecificInformation(out, input, ort); - - Optional - .ofNullable(input.getAuthor()) - .ifPresent( - ats -> out.setAuthor(ats.stream().map(ResultMapper::getAuthor).collect(Collectors.toList()))); - - // I do not map Access Right UNKNOWN or OTHER - - Optional oar = Optional.ofNullable(input.getBestaccessright()); - if (oar.isPresent() && Constants.accessRightsCoarMap.containsKey(oar.get().getClassid())) { - String code = Constants.accessRightsCoarMap.get(oar.get().getClassid()); - out - .setBestaccessright( - - BestAccessRight - .newInstance( - code, - Constants.coarCodeLabelMap.get(code), - Constants.COAR_ACCESS_RIGHT_SCHEMA)); - } - - final List contributorList = new ArrayList<>(); - Optional - .ofNullable(input.getContributor()) - .ifPresent(value -> value.stream().forEach(c -> contributorList.add(c.getValue()))); - out.setContributor(contributorList); - - Optional - .ofNullable(input.getCountry()) - .ifPresent( - value -> out - .setCountry( - value - .stream() - .map( - c -> { - if (c.getClassid().equals((ModelConstants.UNKNOWN))) { - return null; - } - ResultCountry country = new ResultCountry(); - country.setCode(c.getClassid()); - country.setLabel(c.getClassname()); - Optional - .ofNullable(c.getDataInfo()) - .ifPresent( - provenance -> country - .setProvenance( - Provenance - .newInstance( - provenance - .getProvenanceaction() - .getClassname(), - c.getDataInfo().getTrust()))); - return country; - }) - .filter(Objects::nonNull) - .collect(Collectors.toList()))); - - final List coverageList = new ArrayList<>(); - Optional - .ofNullable(input.getCoverage()) - .ifPresent(value -> value.stream().forEach(c -> coverageList.add(c.getValue()))); - out.setCoverage(coverageList); - - out.setDateofcollection(input.getDateofcollection()); - - final List descriptionList = new ArrayList<>(); - Optional - .ofNullable(input.getDescription()) - .ifPresent(value -> value.forEach(d -> descriptionList.add(d.getValue()))); - out.setDescription(descriptionList); - Optional> oStr = Optional.ofNullable(input.getEmbargoenddate()); - if (oStr.isPresent()) { - out.setEmbargoenddate(oStr.get().getValue()); - } - - final List formatList = new ArrayList<>(); - Optional - .ofNullable(input.getFormat()) - .ifPresent(value -> value.stream().forEach(f -> formatList.add(f.getValue()))); - out.setFormat(formatList); - out.setId(input.getId()); - out.setOriginalId(new ArrayList<>()); - Optional - .ofNullable(input.getOriginalId()) - .ifPresent( - v -> out - .setOriginalId( - input - .getOriginalId() - .stream() - .filter(s -> !s.startsWith("50|")) - .collect(Collectors.toList()))); - - Optional> oInst = Optional - .ofNullable(input.getInstance()); - - if (oInst.isPresent()) { - if (Constants.DUMPTYPE.COMPLETE.getType().equals(dumpType)) { - ((GraphResult) out) - .setInstance( - oInst.get().stream().map(ResultMapper::getGraphInstance).collect(Collectors.toList())); - } else { - ((CommunityResult) out) - .setInstance( - oInst - .get() - .stream() - .map(ResultMapper::getCommunityInstance) - .collect(Collectors.toList())); - } - } - - Optional oL = Optional.ofNullable(input.getLanguage()); - if (oL.isPresent()) { - eu.dnetlib.dhp.schema.oaf.Qualifier language = oL.get(); - out.setLanguage(Language.newInstance(language.getClassid(), language.getClassname())); - } - Optional oLong = Optional.ofNullable(input.getLastupdatetimestamp()); - if (oLong.isPresent()) { - out.setLastupdatetimestamp(oLong.get()); - } - Optional> otitle = Optional.ofNullable(input.getTitle()); - if (otitle.isPresent()) { - List iTitle = otitle - .get() - .stream() - .filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("main title")) - .collect(Collectors.toList()); - if (!iTitle.isEmpty()) { - out.setMaintitle(iTitle.get(0).getValue()); - } - - iTitle = otitle - .get() - .stream() - .filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("subtitle")) - .collect(Collectors.toList()); - if (!iTitle.isEmpty()) { - out.setSubtitle(iTitle.get(0).getValue()); - } - - } - - Optional - .ofNullable(input.getPid()) - .ifPresent( - value -> out - .setPid( - value - .stream() - .map( - p -> ResultPid - .newInstance(p.getQualifier().getClassid(), p.getValue())) - .collect(Collectors.toList()))); - - oStr = Optional.ofNullable(input.getDateofacceptance()); - if (oStr.isPresent()) { - out.setPublicationdate(oStr.get().getValue()); - } - oStr = Optional.ofNullable(input.getPublisher()); - if (oStr.isPresent()) { - out.setPublisher(oStr.get().getValue()); - } - - Optional - .ofNullable(input.getSource()) - .ifPresent( - value -> out.setSource(value.stream().map(Field::getValue).collect(Collectors.toList()))); - - List subjectList = new ArrayList<>(); - Optional - .ofNullable(input.getSubject()) - .ifPresent( - value -> value - .forEach(s -> subjectList.add(getSubject(s)))); - - out.setSubjects(subjectList); - - out.setType(input.getResulttype().getClassid()); - - if (!Constants.DUMPTYPE.COMPLETE.getType().equals(dumpType)) { - ((CommunityResult) out) - .setCollectedfrom( - input - .getCollectedfrom() - .stream() - .map(cf -> CfHbKeyValue.newInstance(cf.getKey(), cf.getValue())) - .collect(Collectors.toList())); - - Set communities = communityMap.keySet(); - List contextList = Optional - .ofNullable( - input - .getContext()) - .map( - value -> value - .stream() - .map(c -> { - String communityId = c.getId(); - if (communityId.contains("::")) { - communityId = communityId.substring(0, communityId.indexOf("::")); - } - if (communities.contains(communityId)) { - Context context = new Context(); - context.setCode(communityId); - context.setLabel(communityMap.get(communityId)); - Optional> dataInfo = Optional.ofNullable(c.getDataInfo()); - if (dataInfo.isPresent()) { - List provenance = new ArrayList<>(); - provenance - .addAll( - dataInfo - .get() - .stream() - .map( - di -> Optional - .ofNullable(di.getProvenanceaction()) - .map( - provenanceaction -> Provenance - .newInstance( - provenanceaction.getClassname(), - di.getTrust())) - .orElse(null)) - .filter(Objects::nonNull) - .collect(Collectors.toSet())); - - try { - context.setProvenance(getUniqueProvenance(provenance)); - } catch (NoAvailableEntityTypeException e) { - e.printStackTrace(); - } - } - return context; - } - return null; - }) - .filter(Objects::nonNull) - .collect(Collectors.toList())) - .orElse(new ArrayList<>()); - - if (!contextList.isEmpty()) { - Set hashValue = new HashSet<>(); - List remainigContext = new ArrayList<>(); - contextList.forEach(c -> { - if (!hashValue.contains(c.hashCode())) { - remainigContext.add(c); - hashValue.add(c.hashCode()); - } - }); - ((CommunityResult) out).setContext(remainigContext); - } - } - } catch (ClassCastException cce) { - return out; - } - } - - return out; - - } - - private static void addTypeSpecificInformation(Result out, eu.dnetlib.dhp.schema.oaf.Result input, - Optional ort) throws NoAvailableEntityTypeException { - switch (ort.get().getClassid()) { - case "publication": - Optional journal = Optional - .ofNullable(((Publication) input).getJournal()); - if (journal.isPresent()) { - Journal j = journal.get(); - Container c = new Container(); - c.setConferencedate(j.getConferencedate()); - c.setConferenceplace(j.getConferenceplace()); - c.setEdition(j.getEdition()); - c.setEp(j.getEp()); - c.setIss(j.getIss()); - c.setIssnLinking(j.getIssnLinking()); - c.setIssnOnline(j.getIssnOnline()); - c.setIssnPrinted(j.getIssnPrinted()); - c.setName(j.getName()); - c.setSp(j.getSp()); - c.setVol(j.getVol()); - out.setContainer(c); - out.setType(ModelConstants.PUBLICATION_DEFAULT_RESULTTYPE.getClassname()); - } - break; - case "dataset": - Dataset id = (Dataset) input; - Optional.ofNullable(id.getSize()).ifPresent(v -> out.setSize(v.getValue())); - Optional.ofNullable(id.getVersion()).ifPresent(v -> out.setVersion(v.getValue())); - - out - .setGeolocation( - Optional - .ofNullable(id.getGeolocation()) - .map( - igl -> igl - .stream() - .filter(Objects::nonNull) - .map(gli -> { - GeoLocation gl = new GeoLocation(); - gl.setBox(gli.getBox()); - gl.setPlace(gli.getPlace()); - gl.setPoint(gli.getPoint()); - return gl; - }) - .collect(Collectors.toList())) - .orElse(null)); - - out.setType(ModelConstants.DATASET_DEFAULT_RESULTTYPE.getClassname()); - break; - case "software": - - Software is = (Software) input; - Optional - .ofNullable(is.getCodeRepositoryUrl()) - .ifPresent(value -> out.setCodeRepositoryUrl(value.getValue())); - Optional - .ofNullable(is.getDocumentationUrl()) - .ifPresent( - value -> out - .setDocumentationUrl( - value - .stream() - .map(Field::getValue) - .collect(Collectors.toList()))); - - Optional - .ofNullable(is.getProgrammingLanguage()) - .ifPresent(value -> out.setProgrammingLanguage(value.getClassid())); - - out.setType(ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE.getClassname()); - break; - case "other": - - OtherResearchProduct ir = (OtherResearchProduct) input; - out - .setContactgroup( - Optional - .ofNullable(ir.getContactgroup()) - .map(value -> value.stream().map(Field::getValue).collect(Collectors.toList())) - .orElse(null)); - - out - .setContactperson( - Optional - .ofNullable(ir.getContactperson()) - .map(value -> value.stream().map(Field::getValue).collect(Collectors.toList())) - .orElse(null)); - out - .setTool( - Optional - .ofNullable(ir.getTool()) - .map(value -> value.stream().map(Field::getValue).collect(Collectors.toList())) - .orElse(null)); - - out.setType(ModelConstants.ORP_DEFAULT_RESULTTYPE.getClassname()); - - break; - default: - throw new NoAvailableEntityTypeException(); - } - } - - private static Instance getGraphInstance(eu.dnetlib.dhp.schema.oaf.Instance i) { - Instance instance = new Instance(); - - setCommonValue(i, instance); - - return instance; - - } - - private static CommunityInstance getCommunityInstance(eu.dnetlib.dhp.schema.oaf.Instance i) { - CommunityInstance instance = new CommunityInstance(); - - setCommonValue(i, instance); - - instance - .setCollectedfrom( - CfHbKeyValue - .newInstance(i.getCollectedfrom().getKey(), i.getCollectedfrom().getValue())); - - instance - .setHostedby( - CfHbKeyValue.newInstance(i.getHostedby().getKey(), i.getHostedby().getValue())); - - return instance; - - } - - private static void setCommonValue(eu.dnetlib.dhp.schema.oaf.Instance i, I instance) { - Optional opAr = Optional.ofNullable(i.getAccessright()); - - if (opAr.isPresent() && Constants.accessRightsCoarMap.containsKey(opAr.get().getClassid())) { - String code = Constants.accessRightsCoarMap.get(opAr.get().getClassid()); - - instance - .setAccessright( - AccessRight - .newInstance( - code, - Constants.coarCodeLabelMap.get(code), - Constants.COAR_ACCESS_RIGHT_SCHEMA)); - - Optional> mes = Optional.ofNullable(i.getMeasures()); - if (mes.isPresent()) { - List measure = new ArrayList<>(); - mes - .get() - .forEach( - m -> m.getUnit().forEach(u -> measure.add(Measure.newInstance(m.getId(), u.getValue())))); - instance.setMeasures(measure); - } - - if (opAr.get().getOpenAccessRoute() != null) { - switch (opAr.get().getOpenAccessRoute()) { - case hybrid: - instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.hybrid); - break; - case gold: - instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.gold); - break; - case green: - instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.green); - break; - case bronze: - instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.bronze); - break; - - } - } - - } - - Optional - .ofNullable(i.getPid()) - .ifPresent( - pid -> instance - .setPid( - pid - .stream() - .map(p -> ResultPid.newInstance(p.getQualifier().getClassid(), p.getValue())) - .collect(Collectors.toList()))); - - Optional - .ofNullable(i.getAlternateIdentifier()) - .ifPresent( - ai -> instance - .setAlternateIdentifier( - ai - .stream() - .map(p -> AlternateIdentifier.newInstance(p.getQualifier().getClassid(), p.getValue())) - .collect(Collectors.toList()))); - - Optional - .ofNullable(i.getLicense()) - .ifPresent(value -> instance.setLicense(value.getValue())); - Optional - .ofNullable(i.getDateofacceptance()) - .ifPresent(value -> instance.setPublicationdate(value.getValue())); - Optional - .ofNullable(i.getRefereed()) - .ifPresent(value -> instance.setRefereed(value.getClassname())); - Optional - .ofNullable(i.getInstancetype()) - .ifPresent(value -> instance.setType(value.getClassname())); - Optional.ofNullable(i.getUrl()).ifPresent(value -> instance.setUrl(value)); - Optional> oPca = Optional.ofNullable(i.getProcessingchargeamount()); - Optional> oPcc = Optional.ofNullable(i.getProcessingchargecurrency()); - if (oPca.isPresent() && oPcc.isPresent()) { - Field pca = oPca.get(); - Field pcc = oPcc.get(); - if (!pca.getValue().trim().equals("") && !pcc.getValue().trim().equals("")) { - APC apc = new APC(); - apc.setCurrency(oPcc.get().getValue()); - apc.setAmount(oPca.get().getValue()); - instance.setArticleprocessingcharge(apc); - } - - } - Optional.ofNullable(i.getUrl()).ifPresent(instance::setUrl); - - } - - private static List getUniqueProvenance(List provenance) - throws NoAvailableEntityTypeException { - Provenance iProv = new Provenance(); - - Provenance hProv = new Provenance(); - Provenance lProv = new Provenance(); - - for (Provenance p : provenance) { - switch (p.getProvenance()) { - case Constants.HARVESTED: - hProv = getHighestTrust(hProv, p); - break; - case Constants.INFERRED: - iProv = getHighestTrust(iProv, p); - // To be removed as soon as the new beta run has been done - // this fixex issue of not set trust during bulktagging - if (StringUtils.isEmpty(iProv.getTrust())) { - iProv.setTrust(Constants.DEFAULT_TRUST); - } - break; - case Constants.USER_CLAIM: - lProv = getHighestTrust(lProv, p); - break; - default: - throw new NoAvailableEntityTypeException(); - } - - } - - return Arrays - .asList(iProv, hProv, lProv) - .stream() - .filter(p -> !StringUtils.isEmpty(p.getProvenance())) - .collect(Collectors.toList()); - - } - - private static Provenance getHighestTrust(Provenance hProv, Provenance p) { - if (StringUtils.isNoneEmpty(hProv.getTrust(), p.getTrust())) - return hProv.getTrust().compareTo(p.getTrust()) > 0 ? hProv : p; - - return (StringUtils.isEmpty(p.getTrust()) && !StringUtils.isEmpty(hProv.getTrust())) ? hProv : p; - - } - - private static Subject getSubject(StructuredProperty s) { - Subject subject = new Subject(); - subject.setSubject(SubjectSchemeValue.newInstance(s.getQualifier().getClassid(), s.getValue())); - Optional di = Optional.ofNullable(s.getDataInfo()); - if (di.isPresent()) { - Provenance p = new Provenance(); - p.setProvenance(di.get().getProvenanceaction().getClassname()); - p.setTrust(di.get().getTrust()); - subject.setProvenance(p); - } - - return subject; - } - - private static Author getAuthor(eu.dnetlib.dhp.schema.oaf.Author oa) { - Author a = new Author(); - a.setFullname(oa.getFullname()); - a.setName(oa.getName()); - a.setSurname(oa.getSurname()); - a.setRank(oa.getRank()); - - Optional> oPids = Optional - .ofNullable(oa.getPid()); - if (oPids.isPresent()) { - AuthorPid pid = getOrcid(oPids.get()); - if (pid != null) { - a.setPid(pid); - } - } - - return a; - } - - private static AuthorPid getAuthorPid(StructuredProperty pid) { - Optional di = Optional.ofNullable(pid.getDataInfo()); - if (di.isPresent()) { - return AuthorPid - .newInstance( - AuthorPidSchemeValue - .newInstance( - pid.getQualifier().getClassid(), - pid.getValue()), - Provenance - .newInstance( - di.get().getProvenanceaction().getClassname(), - di.get().getTrust())); - } else { - return AuthorPid - .newInstance( - AuthorPidSchemeValue - .newInstance( - pid.getQualifier().getClassid(), - pid.getValue()) - - ); - } - } - - private static AuthorPid getOrcid(List p) { - List pidList = p.stream().map(pid -> { - if (pid.getQualifier().getClassid().equals(ModelConstants.ORCID) || - (pid.getQualifier().getClassid().equals(ModelConstants.ORCID_PENDING))) { - return pid; - } - return null; - }).filter(Objects::nonNull).collect(Collectors.toList()); - - if (pidList.size() == 1) { - return getAuthorPid(pidList.get(0)); - } - - List orcid = pidList - .stream() - .filter( - ap -> ap - .getQualifier() - .getClassid() - .equals(ModelConstants.ORCID)) - .collect(Collectors.toList()); - if (orcid.size() == 1) { - return getAuthorPid(orcid.get(0)); - } - orcid = pidList - .stream() - .filter( - ap -> ap - .getQualifier() - .getClassid() - .equals(ModelConstants.ORCID_PENDING)) - .collect(Collectors.toList()); - if (orcid.size() == 1) { - return getAuthorPid(orcid.get(0)); - } - - return null; - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SaveCommunityMap.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SaveCommunityMap.java deleted file mode 100644 index a6595d756..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SaveCommunityMap.java +++ /dev/null @@ -1,99 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump; - -import java.io.BufferedWriter; -import java.io.IOException; -import java.io.OutputStreamWriter; -import java.io.Serializable; -import java.nio.charset.StandardCharsets; -import java.util.Optional; - -import org.apache.commons.io.IOUtils; -import org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.FSDataOutputStream; -import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.fs.Path; -import org.dom4j.DocumentException; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; -import org.xml.sax.SAXException; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; - -/** - * This class connects with the IS related to the isLookUpUrl got as parameter. It saves the information about the - * context that will guide the dump of the results. The information saved is a HashMap. The key is the id of a community - * - research infrastructure/initiative , the value is the label of the research community - research - * infrastructure/initiative. - */ - -public class SaveCommunityMap implements Serializable { - - private static final Logger log = LoggerFactory.getLogger(SaveCommunityMap.class); - private final transient QueryInformationSystem queryInformationSystem; - - private final transient BufferedWriter writer; - - public SaveCommunityMap(String hdfsPath, String hdfsNameNode, String isLookUpUrl) throws IOException { - final Configuration conf = new Configuration(); - conf.set("fs.defaultFS", hdfsNameNode); - FileSystem fileSystem = FileSystem.get(conf); - Path hdfsWritePath = new Path(hdfsPath); - - if (fileSystem.exists(hdfsWritePath)) { - fileSystem.delete(hdfsWritePath, true); - } - - queryInformationSystem = new QueryInformationSystem(); - queryInformationSystem.setIsLookUp(Utils.getIsLookUpService(isLookUpUrl)); - - FSDataOutputStream fos = fileSystem.create(hdfsWritePath); - writer = new BufferedWriter(new OutputStreamWriter(fos, StandardCharsets.UTF_8)); - } - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SaveCommunityMap.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_cm_parameters.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - final String nameNode = parser.get("nameNode"); - log.info("nameNode: {}", nameNode); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - final String isLookUpUrl = parser.get("isLookUpUrl"); - log.info("isLookUpUrl: {}", isLookUpUrl); - - final Boolean singleCommunity = Optional - .ofNullable(parser.get("singleDeposition")) - .map(Boolean::valueOf) - .orElse(false); - - final String community_id = Optional.ofNullable(parser.get("communityId")).orElse(null); - - final SaveCommunityMap scm = new SaveCommunityMap(outputPath, nameNode, isLookUpUrl); - - scm.saveCommunityMap(singleCommunity, community_id); - - } - - private void saveCommunityMap(boolean singleCommunity, String communityId) - throws ISLookUpException, IOException, DocumentException, SAXException { - final String communityMapString = Utils.OBJECT_MAPPER - .writeValueAsString(queryInformationSystem.getCommunityMap(singleCommunity, communityId)); - log.info("communityMap {} ", communityMapString); - writer - .write( - communityMapString); - writer.close(); - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SendToZenodoHDFS.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SendToZenodoHDFS.java deleted file mode 100644 index a19a3a5b6..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SendToZenodoHDFS.java +++ /dev/null @@ -1,100 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump; - -import java.io.Serializable; -import java.util.Optional; - -import org.apache.commons.io.IOUtils; -import org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.*; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.common.api.MissingConceptDoiException; -import eu.dnetlib.dhp.common.api.ZenodoAPIClient; -import eu.dnetlib.dhp.oa.graph.dump.exceptions.NoAvailableEntityTypeException; - -public class SendToZenodoHDFS implements Serializable { - - private static final String NEW = "new"; // to be used for a brand new deposition in zenodo - private static final String VERSION = "version"; // to be used to upload a new version of a published deposition - private static final String UPDATE = "update"; // to upload content to an open deposition not published - - public static void main(final String[] args) throws Exception, MissingConceptDoiException { - final ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils - .toString( - SendToZenodoHDFS.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/upload_zenodo.json"))); - - parser.parseArgument(args); - - final String hdfsPath = parser.get("hdfsPath"); - final String hdfsNameNode = parser.get("nameNode"); - final String access_token = parser.get("accessToken"); - final String connection_url = parser.get("connectionUrl"); - final String metadata = parser.get("metadata"); - final String depositionType = parser.get("depositionType"); - final String concept_rec_id = Optional - .ofNullable(parser.get("conceptRecordId")) - .orElse(null); - final Boolean publish = Optional - .ofNullable(parser.get("publish")) - .map(Boolean::valueOf) - .orElse(false); - - final String depositionId = Optional.ofNullable(parser.get("depositionId")).orElse(null); - - Configuration conf = new Configuration(); - conf.set("fs.defaultFS", hdfsNameNode); - - FileSystem fileSystem = FileSystem.get(conf); - - RemoteIterator fileStatusListIterator = fileSystem - .listFiles( - new Path(hdfsPath), true); - ZenodoAPIClient zenodoApiClient = new ZenodoAPIClient(connection_url, access_token); - switch (depositionType) { - case NEW: - zenodoApiClient.newDeposition(); - break; - case VERSION: - if (concept_rec_id == null) { - throw new MissingConceptDoiException("No concept record id has been provided"); - } - zenodoApiClient.newVersion(concept_rec_id); - break; - case UPDATE: - if (depositionId == null) { - throw new MissingConceptDoiException("No deposition id has been provided"); - } - zenodoApiClient.uploadOpenDeposition(depositionId); - break; - default: - throw new NoAvailableEntityTypeException(); - } - - while (fileStatusListIterator.hasNext()) { - LocatedFileStatus fileStatus = fileStatusListIterator.next(); - - Path p = fileStatus.getPath(); - String pString = p.toString(); - if (!pString.endsWith("_SUCCESS")) { - String name = pString.substring(pString.lastIndexOf("/") + 1); - - FSDataInputStream inputStream = fileSystem.open(p); - zenodoApiClient.uploadIS(inputStream, name, fileStatus.getLen()); - - } - - } - if (!metadata.equals("")) { - zenodoApiClient.sendMretadata(metadata); - } - - if (Boolean.TRUE.equals(publish)) { - zenodoApiClient.publish(); - } - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Utils.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Utils.java deleted file mode 100644 index 8e75e9d92..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Utils.java +++ /dev/null @@ -1,77 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump; - -import java.io.BufferedReader; -import java.io.IOException; -import java.io.InputStreamReader; - -import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.fs.Path; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SparkSession; - -import com.fasterxml.jackson.databind.ObjectMapper; -import com.google.gson.Gson; - -import eu.dnetlib.dhp.common.HdfsSupport; -import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; -import eu.dnetlib.dhp.oa.graph.dump.complete.Constants; -import eu.dnetlib.dhp.utils.DHPUtils; -import eu.dnetlib.dhp.utils.ISLookupClientFactory; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; - -public class Utils { - public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private Utils() { - } - - public static void removeOutputDir(SparkSession spark, String path) { - HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); - } - - public static Dataset readPath( - SparkSession spark, String inputPath, Class clazz) { - return spark - .read() - .textFile(inputPath) - .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz)); - } - - public static ISLookUpService getIsLookUpService(String isLookUpUrl) { - return ISLookupClientFactory.getLookUpService(isLookUpUrl); - } - - public static String getContextId(String id) { - - return String - .format( - "%s|%s::%s", Constants.CONTEXT_ID, Constants.CONTEXT_NS_PREFIX, - DHPUtils.md5(id)); - } - - public static CommunityMap getCommunityMap(SparkSession spark, String communityMapPath) { - - return new Gson().fromJson(spark.read().textFile(communityMapPath).collectAsList().get(0), CommunityMap.class); - - } - - public static CommunityMap readCommunityMap(FileSystem fileSystem, String communityMapPath) throws IOException { - BufferedReader br = new BufferedReader(new InputStreamReader(fileSystem.open(new Path(communityMapPath)))); - StringBuilder sb = new StringBuilder(); - try { - String line; - while ((line = br.readLine()) != null) { - sb.append(line); - } - } finally { - br.close(); - - } - - return new Gson().fromJson(sb.toString(), CommunityMap.class); - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunityMap.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunityMap.java deleted file mode 100644 index d45906337..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunityMap.java +++ /dev/null @@ -1,8 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.community; - -import java.io.Serializable; -import java.util.HashMap; - -public class CommunityMap extends HashMap implements Serializable { -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java deleted file mode 100644 index ee6341f84..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java +++ /dev/null @@ -1,81 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.community; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.util.Optional; -import java.util.stream.Collectors; - -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.FilterFunction; -import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.SaveMode; -import org.apache.spark.sql.SparkSession; - -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; -import eu.dnetlib.dhp.schema.dump.oaf.community.Context; - -/** - * This class splits the dumped results according to the research community - research initiative/infrastructure they - * are related to. The information about the community is found in the element "context.id" in the result. Since the - * context that can be found in the result can be associated not only to communities, a community Map is provided. It - * will guide the splitting process. Note: the repartition(1) just before writing the results related to a community. - * This is a choice due to uploading constraints (just one file for each community) As soon as a better solution will be - * in place remove the repartition - */ -public class CommunitySplit implements Serializable { - - public void run(Boolean isSparkSessionManaged, String inputPath, String outputPath, String communityMapPath) { - SparkConf conf = new SparkConf(); - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath); - execSplit(spark, inputPath, outputPath, communityMap); - }); - } - - private static void execSplit(SparkSession spark, String inputPath, String outputPath, - CommunityMap communities) { - - Dataset result = Utils - .readPath(spark, inputPath + "/publication", CommunityResult.class) - .union(Utils.readPath(spark, inputPath + "/dataset", CommunityResult.class)) - .union(Utils.readPath(spark, inputPath + "/orp", CommunityResult.class)) - .union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class)); - - communities - .keySet() - .stream() - .forEach(c -> printResult(c, result, outputPath + "/" + communities.get(c).replace(" ", "_"))); - - } - - private static void printResult(String c, Dataset result, String outputPath) { - Dataset communityProducts = result - .filter((FilterFunction) r -> containsCommunity(r, c)); - - communityProducts - .write() - .option("compression", "gzip") - .mode(SaveMode.Overwrite) - .json(outputPath); - - } - - private static boolean containsCommunity(CommunityResult r, String c) { - if (Optional.ofNullable(r.getContext()).isPresent()) { - return r - .getContext() - .stream() - .map(Context::getCode) - .collect(Collectors.toList()) - .contains(c); - } - return false; - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/ResultProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/ResultProject.java deleted file mode 100644 index 300af62f3..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/ResultProject.java +++ /dev/null @@ -1,28 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.community; - -import java.io.Serializable; -import java.util.List; - -import eu.dnetlib.dhp.schema.dump.oaf.community.Project; - -public class ResultProject implements Serializable { - private String resultId; - private List projectsList; - - public String getResultId() { - return resultId; - } - - public void setResultId(String resultId) { - this.resultId = resultId; - } - - public List getProjectsList() { - return projectsList; - } - - public void setProjectsList(List projectsList) { - this.projectsList = projectsList; - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkDumpCommunityProducts.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkDumpCommunityProducts.java deleted file mode 100644 index 7ab8a7540..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkDumpCommunityProducts.java +++ /dev/null @@ -1,67 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.community; - -import java.io.Serializable; -import java.util.Optional; - -import org.apache.commons.io.IOUtils; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.DumpProducts; -import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; -import eu.dnetlib.dhp.schema.oaf.Result; - -/** - * Spark action to trigger the dump of results associated to research community - reseach initiative/infrasctructure The - * actual dump if performed via the class DumpProducts that is used also for the entire graph dump - */ -public class SparkDumpCommunityProducts implements Serializable { - - private static final Logger log = LoggerFactory.getLogger(SparkDumpCommunityProducts.class); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkDumpCommunityProducts.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - final String resultClassName = parser.get("resultTableName"); - log.info("resultTableName: {}", resultClassName); - - String communityMapPath = parser.get("communityMapPath"); - - final String dumpType = Optional - .ofNullable(parser.get("dumpType")) - .map(String::valueOf) - .orElse("community"); - - Class inputClazz = (Class) Class.forName(resultClassName); - - DumpProducts dump = new DumpProducts(); - - dump - .run( - isSparkSessionManaged, inputPath, outputPath, communityMapPath, inputClazz, CommunityResult.class, - dumpType); - - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java deleted file mode 100644 index 410feea02..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java +++ /dev/null @@ -1,193 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.community; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.io.StringReader; -import java.util.*; -import java.util.stream.Collectors; - -import org.apache.commons.io.IOUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.FilterFunction; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.api.java.function.MapGroupsFunction; -import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SaveMode; -import org.apache.spark.sql.SparkSession; -import org.dom4j.Document; -import org.dom4j.DocumentException; -import org.dom4j.Node; -import org.dom4j.io.SAXReader; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; -import org.xml.sax.SAXException; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.dump.oaf.Provenance; -import eu.dnetlib.dhp.schema.dump.oaf.community.Funder; -import eu.dnetlib.dhp.schema.dump.oaf.community.Project; -import eu.dnetlib.dhp.schema.dump.oaf.community.Validated; -import eu.dnetlib.dhp.schema.oaf.DataInfo; -import eu.dnetlib.dhp.schema.oaf.Field; -import eu.dnetlib.dhp.schema.oaf.Relation; -import scala.Tuple2; - -/** - * Preparation of the Project information to be added to the dumped results. For each result associated to at least one - * Project, a serialization of an instance af ResultProject class is done. ResultProject contains the resultId, and the - * list of Projects (as in eu.dnetlib.dhp.schema.dump.oaf.community.Project) it is associated to - */ -public class SparkPrepareResultProject implements Serializable { - private static final Logger log = LoggerFactory.getLogger(SparkPrepareResultProject.class); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkPrepareResultProject.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/project_prep_parameters.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - SparkConf conf = new SparkConf(); - - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - prepareResultProjectList(spark, inputPath, outputPath); - }); - } - - private static void prepareResultProjectList(SparkSession spark, String inputPath, String outputPath) { - Dataset relation = Utils - .readPath(spark, inputPath + "/relation", Relation.class) - .filter( - (FilterFunction) r -> !r.getDataInfo().getDeletedbyinference() && - r.getRelClass().equalsIgnoreCase(ModelConstants.IS_PRODUCED_BY)); - - Dataset projects = Utils - .readPath(spark, inputPath + "/project", eu.dnetlib.dhp.schema.oaf.Project.class); - - projects - .joinWith(relation, projects.col("id").equalTo(relation.col("target")), "inner") - .groupByKey( - (MapFunction, String>) value -> value - ._2() - .getSource(), - Encoders.STRING()) - .mapGroups( - (MapGroupsFunction, ResultProject>) (s, - it) -> { - Set projectSet = new HashSet<>(); - Tuple2 first = it.next(); - ResultProject rp = new ResultProject(); - rp.setResultId(s); - eu.dnetlib.dhp.schema.oaf.Project p = first._1(); - projectSet.add(p.getId()); - Project ps = getProject(p, first._2); - - List projList = new ArrayList<>(); - projList.add(ps); - rp.setProjectsList(projList); - it.forEachRemaining(c -> { - eu.dnetlib.dhp.schema.oaf.Project op = c._1(); - if (!projectSet.contains(op.getId())) { - projList - .add(getProject(op, c._2)); - - projectSet.add(op.getId()); - - } - - }); - return rp; - }, Encoders.bean(ResultProject.class)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); - } - - private static Project getProject(eu.dnetlib.dhp.schema.oaf.Project op, Relation relation) { - Project p = Project - .newInstance( - op.getId(), - op.getCode().getValue(), - Optional - .ofNullable(op.getAcronym()) - .map(Field::getValue) - .orElse(null), - Optional - .ofNullable(op.getTitle()) - .map(Field::getValue) - .orElse(null), - Optional - .ofNullable(op.getFundingtree()) - .map(value -> { - List tmp = value - .stream() - .map(ft -> getFunder(ft.getValue())) - .collect(Collectors.toList()); - if (!tmp.isEmpty()) { - return tmp.get(0); - } else { - return null; - } - }) - .orElse(null)); - - Optional di = Optional.ofNullable(op.getDataInfo()); - Provenance provenance = new Provenance(); - if (di.isPresent()) { - provenance.setProvenance(di.get().getProvenanceaction().getClassname()); - provenance.setTrust(di.get().getTrust()); - p.setProvenance(provenance); - } - if (Boolean.TRUE.equals(relation.getValidated())) { - p.setValidated(Validated.newInstance(relation.getValidated(), relation.getValidationDate())); - } - return p; - - } - - private static Funder getFunder(String fundingtree) { - final Funder f = new Funder(); - final Document doc; - try { - final SAXReader reader = new SAXReader(); - reader.setFeature("http://apache.org/xml/features/disallow-doctype-decl", true); - doc = reader.read(new StringReader(fundingtree)); - f.setShortName(((Node) (doc.selectNodes("//funder/shortname").get(0))).getText()); - f.setName(((Node) (doc.selectNodes("//funder/name").get(0))).getText()); - f.setJurisdiction(((Node) (doc.selectNodes("//funder/jurisdiction").get(0))).getText()); - for (Object o : doc.selectNodes("//funding_level_0")) { - List node = ((Node) o).selectNodes("./name"); - f.setFundingStream((node.get(0)).getText()); - } - - return f; - } catch (DocumentException | SAXException e) { - throw new IllegalArgumentException(e); - } - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkSplitForCommunity.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkSplitForCommunity.java deleted file mode 100644 index b62bf18e7..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkSplitForCommunity.java +++ /dev/null @@ -1,50 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.community; - -import java.io.Serializable; -import java.util.Optional; - -import org.apache.commons.io.IOUtils; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; - -/** - * Spark job to trigger the split of results associated to research community - reseach initiative/infrasctructure. The - * actual split is performed by the class CommunitySplit - */ -public class SparkSplitForCommunity implements Serializable { - - private static final Logger log = LoggerFactory.getLogger(SparkSplitForCommunity.class); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkSplitForCommunity.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/split_parameters.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - final String communityMapPath = parser.get("communityMapPath"); - - CommunitySplit split = new CommunitySplit(); - split.run(isSparkSessionManaged, inputPath, outputPath, communityMapPath); - - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkUpdateProjectInfo.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkUpdateProjectInfo.java deleted file mode 100644 index 39ae32053..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkUpdateProjectInfo.java +++ /dev/null @@ -1,90 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.community; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.util.Optional; - -import org.apache.commons.io.IOUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SaveMode; -import org.apache.spark.sql.SparkSession; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; -import scala.Tuple2; - -public class SparkUpdateProjectInfo implements Serializable { - - private static final Logger log = LoggerFactory.getLogger(SparkUpdateProjectInfo.class); - public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkUpdateProjectInfo.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/project_input_parameters.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - final String preparedInfoPath = parser.get("preparedInfoPath"); - log.info("preparedInfoPath: {}", preparedInfoPath); - - SparkConf conf = new SparkConf(); - - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - extend(spark, inputPath, outputPath, preparedInfoPath); - }); - } - - private static void extend( - SparkSession spark, - String inputPath, - String outputPath, - String preparedInfoPath) { - Dataset result = Utils.readPath(spark, inputPath, CommunityResult.class); - Dataset resultProject = Utils.readPath(spark, preparedInfoPath, ResultProject.class); - result - .joinWith( - resultProject, result.col("id").equalTo(resultProject.col("resultId")), - "left") - .map((MapFunction, CommunityResult>) value -> { - CommunityResult r = value._1(); - Optional.ofNullable(value._2()).ifPresent(rp -> r.setProjects(rp.getProjectsList())); - return r; - }, Encoders.bean(CommunityResult.class)) - .write() - .option("compression", "gzip") - .mode(SaveMode.Append) - .json(outputPath); - - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Constants.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Constants.java deleted file mode 100644 index 57708a78d..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Constants.java +++ /dev/null @@ -1,26 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import java.io.Serializable; - -public class Constants implements Serializable { - - public static final String IS_HOSTED_BY = "isHostedBy"; - public static final String HOSTS = "hosts"; - - public static final String IS_FUNDED_BY = "isFundedBy"; - public static final String FUNDS = "funds"; - - public static final String FUNDINGS = "fundings"; - - public static final String RESULT_ENTITY = "result"; - public static final String DATASOURCE_ENTITY = "datasource"; - public static final String CONTEXT_ENTITY = "context"; - public static final String ORGANIZATION_ENTITY = "organization"; - public static final String PROJECT_ENTITY = "project"; - - public static final String CONTEXT_ID = "00"; - public static final String CONTEXT_NS_PREFIX = "context_____"; - public static final String UNKNOWN = "UNKNOWN"; - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/ContextInfo.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/ContextInfo.java deleted file mode 100644 index 982a69afb..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/ContextInfo.java +++ /dev/null @@ -1,84 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import java.io.Serializable; -import java.util.List; - -/** - * Deserialization of the information in the context needed to create Context Entities, and relations between context - * entities and datasources and projects - */ -public class ContextInfo implements Serializable { - private String id; - private String description; - private String type; - private String zenodocommunity; - private String name; - private List projectList; - private List datasourceList; - private List subject; - - public List getSubject() { - return subject; - } - - public void setSubject(List subject) { - this.subject = subject; - } - - public String getName() { - return name; - } - - public void setName(String name) { - this.name = name; - } - - public String getId() { - return id; - } - - public void setId(String id) { - this.id = id; - } - - public String getDescription() { - return description; - } - - public void setDescription(String description) { - this.description = description; - } - - public String getType() { - return type; - } - - public void setType(String type) { - this.type = type; - } - - public String getZenodocommunity() { - return zenodocommunity; - } - - public void setZenodocommunity(String zenodocommunity) { - this.zenodocommunity = zenodocommunity; - } - - public List getProjectList() { - return projectList; - } - - public void setProjectList(List projectList) { - this.projectList = projectList; - } - - public List getDatasourceList() { - return datasourceList; - } - - public void setDatasourceList(List datasourceList) { - this.datasourceList = datasourceList; - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextEntities.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextEntities.java deleted file mode 100644 index c422c3b40..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextEntities.java +++ /dev/null @@ -1,110 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import java.io.BufferedWriter; -import java.io.IOException; -import java.io.OutputStreamWriter; -import java.io.Serializable; -import java.nio.charset.StandardCharsets; -import java.util.function.Consumer; -import java.util.function.Function; - -import org.apache.commons.io.IOUtils; -import org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.FSDataOutputStream; -import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.fs.Path; -import org.apache.hadoop.io.compress.CompressionCodec; -import org.apache.hadoop.io.compress.CompressionCodecFactory; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.schema.dump.oaf.graph.ResearchInitiative; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; - -/** - * Writes on HDFS Context entities. It queries the Information System at the lookup url provided as parameter and - * collects the general information for contexes of type community or ri. The general information is the id of the - * context, its label, the subjects associated to the context, its zenodo community, description and type. This - * information is used to create a new Context Entity - */ -public class CreateContextEntities implements Serializable { - - private static final Logger log = LoggerFactory.getLogger(CreateContextEntities.class); - private final transient Configuration conf; - private final transient BufferedWriter writer; - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - CreateContextEntities.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_entity_parameter.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - final String hdfsPath = parser.get("hdfsPath"); - log.info("hdfsPath: {}", hdfsPath); - - final String hdfsNameNode = parser.get("nameNode"); - log.info("nameNode: {}", hdfsNameNode); - - final String isLookUpUrl = parser.get("isLookUpUrl"); - log.info("isLookUpUrl: {}", isLookUpUrl); - - final CreateContextEntities cce = new CreateContextEntities(hdfsPath, hdfsNameNode); - - log.info("Processing contexts..."); - cce.execute(Process::getEntity, isLookUpUrl); - - cce.close(); - - } - - private void close() throws IOException { - writer.close(); - } - - public CreateContextEntities(String hdfsPath, String hdfsNameNode) throws IOException { - this.conf = new Configuration(); - this.conf.set("fs.defaultFS", hdfsNameNode); - FileSystem fileSystem = FileSystem.get(this.conf); - Path hdfsWritePath = new Path(hdfsPath); - FSDataOutputStream fsDataOutputStream = null; - if (fileSystem.exists(hdfsWritePath)) { - fsDataOutputStream = fileSystem.append(hdfsWritePath); - } else { - fsDataOutputStream = fileSystem.create(hdfsWritePath); - } - CompressionCodecFactory factory = new CompressionCodecFactory(conf); - CompressionCodec codec = factory.getCodecByClassName("org.apache.hadoop.io.compress.GzipCodec"); - - this.writer = new BufferedWriter(new OutputStreamWriter(codec.createOutputStream(fsDataOutputStream), - StandardCharsets.UTF_8)); - - } - - public void execute(final Function producer, String isLookUpUrl) - throws ISLookUpException { - - QueryInformationSystem queryInformationSystem = new QueryInformationSystem(); - queryInformationSystem.setIsLookUp(Utils.getIsLookUpService(isLookUpUrl)); - - final Consumer consumer = ci -> writeEntity(producer.apply(ci)); - - queryInformationSystem.getContextInformation(consumer); - } - - protected void writeEntity(final R r) { - try { - writer.write(Utils.OBJECT_MAPPER.writeValueAsString(r)); - writer.newLine(); - } catch (final IOException e) { - throw new IllegalArgumentException(e); - } - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextRelation.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextRelation.java deleted file mode 100644 index 03f53de64..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextRelation.java +++ /dev/null @@ -1,128 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import java.io.BufferedWriter; -import java.io.IOException; -import java.io.OutputStreamWriter; -import java.io.Serializable; -import java.nio.charset.StandardCharsets; -import java.util.List; -import java.util.Objects; -import java.util.Optional; -import java.util.function.Consumer; -import java.util.function.Function; - -import org.apache.commons.io.IOUtils; -import org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.FSDataOutputStream; -import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.fs.Path; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.oa.graph.dump.exceptions.MyRuntimeException; -import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.dhp.schema.dump.oaf.graph.*; -import eu.dnetlib.dhp.schema.oaf.Datasource; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; - -/** - * Writes the set of new Relation between the context and datasources. At the moment the relation between the context - * and the project is not created because of a low coverage in the profiles of openaire ids related to projects - */ -public class CreateContextRelation implements Serializable { - private static final Logger log = LoggerFactory.getLogger(CreateContextRelation.class); - private final transient Configuration conf; - private final transient BufferedWriter writer; - private final transient QueryInformationSystem queryInformationSystem; - - private static final String CONTEX_RELATION_DATASOURCE = "contentproviders"; - private static final String CONTEX_RELATION_PROJECT = "projects"; - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - Objects - .requireNonNull( - CreateContextRelation.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_entity_parameter.json"))); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String hdfsPath = parser.get("hdfsPath"); - log.info("hdfsPath: {}", hdfsPath); - - final String hdfsNameNode = parser.get("nameNode"); - log.info("nameNode: {}", hdfsNameNode); - - final String isLookUpUrl = parser.get("isLookUpUrl"); - log.info("isLookUpUrl: {}", isLookUpUrl); - - final CreateContextRelation cce = new CreateContextRelation(hdfsPath, hdfsNameNode, isLookUpUrl); - - log.info("Creating relation for datasource..."); - cce.execute(Process::getRelation, CONTEX_RELATION_DATASOURCE, ModelSupport.getIdPrefix(Datasource.class)); - - log.info("Creating relations for projects... "); - cce - .execute( - Process::getRelation, CONTEX_RELATION_PROJECT, - ModelSupport.getIdPrefix(eu.dnetlib.dhp.schema.oaf.Project.class)); - - cce.close(); - - } - - private void close() throws IOException { - writer.close(); - } - - public CreateContextRelation(String hdfsPath, String hdfsNameNode, String isLookUpUrl) - throws IOException, ISLookUpException { - this.conf = new Configuration(); - this.conf.set("fs.defaultFS", hdfsNameNode); - - queryInformationSystem = new QueryInformationSystem(); - queryInformationSystem.setIsLookUp(Utils.getIsLookUpService(isLookUpUrl)); - queryInformationSystem.execContextRelationQuery(); - - FileSystem fileSystem = FileSystem.get(this.conf); - Path hdfsWritePath = new Path(hdfsPath); - FSDataOutputStream fsDataOutputStream = null; - if (fileSystem.exists(hdfsWritePath)) { - fsDataOutputStream = fileSystem.append(hdfsWritePath); - } else { - fsDataOutputStream = fileSystem.create(hdfsWritePath); - } - - this.writer = new BufferedWriter(new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8)); - - } - - public void execute(final Function> producer, String category, String prefix) { - - final Consumer consumer = ci -> producer.apply(ci).forEach(this::writeEntity); - - queryInformationSystem.getContextRelation(consumer, category, prefix); - } - - protected void writeEntity(final Relation r) { - try { - writer.write(Utils.OBJECT_MAPPER.writeValueAsString(r)); - writer.newLine(); - } catch (final Exception e) { - throw new MyRuntimeException(e); - } - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpGraphEntities.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpGraphEntities.java deleted file mode 100644 index c9de86613..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpGraphEntities.java +++ /dev/null @@ -1,518 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.io.StringReader; -import java.util.*; -import java.util.stream.Collectors; - -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.FilterFunction; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SaveMode; -import org.apache.spark.sql.SparkSession; -import org.dom4j.Document; -import org.dom4j.DocumentException; -import org.dom4j.Node; -import org.dom4j.io.SAXReader; - -import eu.dnetlib.dhp.oa.graph.dump.DumpProducts; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.dhp.schema.dump.oaf.*; -import eu.dnetlib.dhp.schema.dump.oaf.graph.*; -import eu.dnetlib.dhp.schema.dump.oaf.graph.Funder; -import eu.dnetlib.dhp.schema.dump.oaf.graph.Project; -import eu.dnetlib.dhp.schema.oaf.Field; -import eu.dnetlib.dhp.schema.oaf.Journal; -import eu.dnetlib.dhp.schema.oaf.OafEntity; - -/** - * Dumps of entities in the model defined in eu.dnetlib.dhp.schema.dump.oaf.graph. Results are dumped using the same - * Mapper as for eu.dnetlib.dhp.schema.dump.oaf.community, while for the other entities the mapping is defined below - */ -public class DumpGraphEntities implements Serializable { - - public void run(Boolean isSparkSessionManaged, - String inputPath, - String outputPath, - Class inputClazz, - String communityMapPath) { - - SparkConf conf = new SparkConf(); - - switch (ModelSupport.idPrefixMap.get(inputClazz)) { - case "50": - DumpProducts d = new DumpProducts(); - d - .run( - isSparkSessionManaged, inputPath, outputPath, communityMapPath, inputClazz, GraphResult.class, - eu.dnetlib.dhp.oa.graph.dump.Constants.DUMPTYPE.COMPLETE.getType()); - break; - case "40": - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - projectMap(spark, inputPath, outputPath, inputClazz); - - }); - break; - case "20": - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - organizationMap(spark, inputPath, outputPath, inputClazz); - - }); - break; - case "10": - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - datasourceMap(spark, inputPath, outputPath, inputClazz); - - }); - break; - } - - } - - private static void datasourceMap(SparkSession spark, String inputPath, String outputPath, - Class inputClazz) { - Utils - .readPath(spark, inputPath, inputClazz) - .map( - (MapFunction) d -> mapDatasource((eu.dnetlib.dhp.schema.oaf.Datasource) d), - Encoders.bean(Datasource.class)) - .filter(Objects::nonNull) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); - } - - private static void projectMap(SparkSession spark, String inputPath, String outputPath, - Class inputClazz) { - Utils - .readPath(spark, inputPath, inputClazz) - .map( - (MapFunction) p -> mapProject((eu.dnetlib.dhp.schema.oaf.Project) p), - Encoders.bean(Project.class)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); - } - - private static Datasource mapDatasource(eu.dnetlib.dhp.schema.oaf.Datasource d) { - Datasource datasource = new Datasource(); - - datasource.setId(d.getId()); - - Optional - .ofNullable(d.getOriginalId()) - .ifPresent( - oId -> datasource.setOriginalId(oId.stream().filter(Objects::nonNull).collect(Collectors.toList()))); - - Optional - .ofNullable(d.getPid()) - .ifPresent( - pids -> pids - .stream() - .map(p -> DatasourcePid.newInstance(p.getQualifier().getClassid(), p.getValue())) - .collect(Collectors.toList())); - - Optional - .ofNullable(d.getDatasourcetype()) - .ifPresent( - dsType -> datasource - .setDatasourcetype(DatasourceSchemeValue.newInstance(dsType.getClassid(), dsType.getClassname()))); - - Optional - .ofNullable(d.getOpenairecompatibility()) - .ifPresent(v -> datasource.setOpenairecompatibility(v.getClassname())); - - Optional - .ofNullable(d.getOfficialname()) - .ifPresent(oname -> datasource.setOfficialname(oname.getValue())); - - Optional - .ofNullable(d.getEnglishname()) - .ifPresent(ename -> datasource.setEnglishname(ename.getValue())); - - Optional - .ofNullable(d.getWebsiteurl()) - .ifPresent(wsite -> datasource.setWebsiteurl(wsite.getValue())); - - Optional - .ofNullable(d.getLogourl()) - .ifPresent(lurl -> datasource.setLogourl(lurl.getValue())); - - Optional - .ofNullable(d.getDateofvalidation()) - .ifPresent(dval -> datasource.setDateofvalidation(dval.getValue())); - - Optional - .ofNullable(d.getDescription()) - .ifPresent(dex -> datasource.setDescription(dex.getValue())); - - Optional - .ofNullable(d.getSubjects()) - .ifPresent( - sbjs -> datasource.setSubjects(sbjs.stream().map(sbj -> sbj.getValue()).collect(Collectors.toList()))); - - Optional - .ofNullable(d.getOdpolicies()) - .ifPresent(odp -> datasource.setPolicies(Arrays.asList(odp.getValue()))); - - Optional - .ofNullable(d.getOdlanguages()) - .ifPresent( - langs -> datasource - .setLanguages(langs.stream().map(lang -> lang.getValue()).collect(Collectors.toList()))); - - Optional - .ofNullable(d.getOdcontenttypes()) - .ifPresent( - ctypes -> datasource - .setContenttypes(ctypes.stream().map(ctype -> ctype.getValue()).collect(Collectors.toList()))); - - Optional - .ofNullable(d.getReleasestartdate()) - .ifPresent(rd -> datasource.setReleasestartdate(rd.getValue())); - - Optional - .ofNullable(d.getReleaseenddate()) - .ifPresent(ed -> datasource.setReleaseenddate(ed.getValue())); - - Optional - .ofNullable(d.getMissionstatementurl()) - .ifPresent(ms -> datasource.setMissionstatementurl(ms.getValue())); - - Optional - .ofNullable(d.getDatabaseaccesstype()) - .ifPresent(ar -> datasource.setAccessrights(ar.getValue())); - - Optional - .ofNullable(d.getDatauploadtype()) - .ifPresent(dut -> datasource.setUploadrights(dut.getValue())); - - Optional - .ofNullable(d.getDatabaseaccessrestriction()) - .ifPresent(dar -> datasource.setDatabaseaccessrestriction(dar.getValue())); - - Optional - .ofNullable(d.getDatauploadrestriction()) - .ifPresent(dur -> datasource.setDatauploadrestriction(dur.getValue())); - - Optional - .ofNullable(d.getVersioning()) - .ifPresent(v -> datasource.setVersioning(v.getValue())); - - Optional - .ofNullable(d.getCitationguidelineurl()) - .ifPresent(cu -> datasource.setCitationguidelineurl(cu.getValue())); - - Optional - .ofNullable(d.getPidsystems()) - .ifPresent(ps -> datasource.setPidsystems(ps.getValue())); - - Optional - .ofNullable(d.getCertificates()) - .ifPresent(c -> datasource.setCertificates(c.getValue())); - - Optional - .ofNullable(d.getPolicies()) - .ifPresent(ps -> datasource.setPolicies(ps.stream().map(p -> p.getValue()).collect(Collectors.toList()))); - - Optional - .ofNullable(d.getJournal()) - .ifPresent(j -> datasource.setJournal(getContainer(j))); - - return datasource; - - } - - private static Container getContainer(Journal j) { - Container c = new Container(); - - Optional - .ofNullable(j.getName()) - .ifPresent(n -> c.setName(n)); - - Optional - .ofNullable(j.getIssnPrinted()) - .ifPresent(issnp -> c.setIssnPrinted(issnp)); - - Optional - .ofNullable(j.getIssnOnline()) - .ifPresent(issno -> c.setIssnOnline(issno)); - - Optional - .ofNullable(j.getIssnLinking()) - .ifPresent(isnl -> c.setIssnLinking(isnl)); - - Optional - .ofNullable(j.getEp()) - .ifPresent(ep -> c.setEp(ep)); - - Optional - .ofNullable(j.getIss()) - .ifPresent(iss -> c.setIss(iss)); - - Optional - .ofNullable(j.getSp()) - .ifPresent(sp -> c.setSp(sp)); - - Optional - .ofNullable(j.getVol()) - .ifPresent(vol -> c.setVol(vol)); - - Optional - .ofNullable(j.getEdition()) - .ifPresent(edition -> c.setEdition(edition)); - - Optional - .ofNullable(j.getConferencedate()) - .ifPresent(cdate -> c.setConferencedate(cdate)); - - Optional - .ofNullable(j.getConferenceplace()) - .ifPresent(cplace -> c.setConferenceplace(cplace)); - - return c; - } - - private static Project mapProject(eu.dnetlib.dhp.schema.oaf.Project p) throws DocumentException { - Project project = new Project(); - - Optional - .ofNullable(p.getId()) - .ifPresent(id -> project.setId(id)); - - Optional - .ofNullable(p.getWebsiteurl()) - .ifPresent(w -> project.setWebsiteurl(w.getValue())); - - Optional - .ofNullable(p.getCode()) - .ifPresent(code -> project.setCode(code.getValue())); - - Optional - .ofNullable(p.getAcronym()) - .ifPresent(acronynim -> project.setAcronym(acronynim.getValue())); - - Optional - .ofNullable(p.getTitle()) - .ifPresent(title -> project.setTitle(title.getValue())); - - Optional - .ofNullable(p.getStartdate()) - .ifPresent(sdate -> project.setStartdate(sdate.getValue())); - - Optional - .ofNullable(p.getEnddate()) - .ifPresent(edate -> project.setEnddate(edate.getValue())); - - Optional - .ofNullable(p.getCallidentifier()) - .ifPresent(cide -> project.setCallidentifier(cide.getValue())); - - Optional - .ofNullable(p.getKeywords()) - .ifPresent(key -> project.setKeywords(key.getValue())); - - Optional> omandate = Optional.ofNullable(p.getOamandatepublications()); - Optional> oecsc39 = Optional.ofNullable(p.getEcsc39()); - boolean mandate = false; - if (omandate.isPresent()) { - if (omandate.get().getValue().equals("true")) { - mandate = true; - } - } - if (oecsc39.isPresent()) { - if (oecsc39.get().getValue().equals("true")) { - mandate = true; - } - } - - project.setOpenaccessmandateforpublications(mandate); - project.setOpenaccessmandatefordataset(false); - - Optional - .ofNullable(p.getEcarticle29_3()) - .ifPresent(oamandate -> project.setOpenaccessmandatefordataset(oamandate.getValue().equals("true"))); - - project - .setSubject( - Optional - .ofNullable(p.getSubjects()) - .map(subjs -> subjs.stream().map(s -> s.getValue()).collect(Collectors.toList())) - .orElse(new ArrayList<>())); - - Optional - .ofNullable(p.getSummary()) - .ifPresent(summary -> project.setSummary(summary.getValue())); - - Optional ofundedamount = Optional.ofNullable(p.getFundedamount()); - Optional> ocurrency = Optional.ofNullable(p.getCurrency()); - Optional ototalcost = Optional.ofNullable(p.getTotalcost()); - - if (ocurrency.isPresent()) { - if (ofundedamount.isPresent()) { - if (ototalcost.isPresent()) { - project - .setGranted( - Granted.newInstance(ocurrency.get().getValue(), ototalcost.get(), ofundedamount.get())); - } else { - project.setGranted(Granted.newInstance(ocurrency.get().getValue(), ofundedamount.get())); - } - } - } - - project - .setH2020programme( - Optional - .ofNullable(p.getH2020classification()) - .map( - classification -> classification - .stream() - .map( - c -> Programme - .newInstance( - c.getH2020Programme().getCode(), c.getH2020Programme().getDescription())) - .collect(Collectors.toList())) - .orElse(new ArrayList<>())); - - Optional>> ofundTree = Optional - .ofNullable(p.getFundingtree()); - List funList = new ArrayList<>(); - if (ofundTree.isPresent()) { - for (Field fundingtree : ofundTree.get()) { - funList.add(getFunder(fundingtree.getValue())); - } - } - project.setFunding(funList); - - return project; - } - - public static Funder getFunder(String fundingtree) throws DocumentException { - Funder f = new Funder(); - final Document doc; - - doc = new SAXReader().read(new StringReader(fundingtree)); - f.setShortName(((org.dom4j.Node) (doc.selectNodes("//funder/shortname").get(0))).getText()); - f.setName(((org.dom4j.Node) (doc.selectNodes("//funder/name").get(0))).getText()); - f.setJurisdiction(((org.dom4j.Node) (doc.selectNodes("//funder/jurisdiction").get(0))).getText()); - // f.setId(((org.dom4j.Node) (doc.selectNodes("//funder/id").get(0))).getText()); - - String id = ""; - String description = ""; - // List fundings = new ArrayList<>(); - int level = 0; - List nodes = doc.selectNodes("//funding_level_" + level); - while (nodes.size() > 0) { - for (org.dom4j.Node n : nodes) { - - List node = n.selectNodes("./id"); - id = ((org.dom4j.Node) node.get(0)).getText(); - id = id.substring(id.indexOf("::") + 2); - - node = n.selectNodes("./description"); - description += ((Node) node.get(0)).getText() + " - "; - - } - level += 1; - nodes = doc.selectNodes("//funding_level_" + level); - } - - if (!id.equals("")) { - Fundings fundings = new Fundings(); - fundings.setId(id); - fundings.setDescription(description.substring(0, description.length() - 3).trim()); - f.setFunding_stream(fundings); - } - - return f; - - } - - private static void organizationMap(SparkSession spark, String inputPath, String outputPath, - Class inputClazz) { - Utils - .readPath(spark, inputPath, inputClazz) - .map( - (MapFunction) o -> mapOrganization((eu.dnetlib.dhp.schema.oaf.Organization) o), - Encoders.bean(Organization.class)) - .filter((FilterFunction) o -> o != null) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); - } - - private static eu.dnetlib.dhp.schema.dump.oaf.graph.Organization mapOrganization( - eu.dnetlib.dhp.schema.oaf.Organization org) { - if (org.getDataInfo().getDeletedbyinference()) - return null; - Organization organization = new Organization(); - - Optional - .ofNullable(org.getLegalshortname()) - .ifPresent(value -> organization.setLegalshortname(value.getValue())); - - Optional - .ofNullable(org.getLegalname()) - .ifPresent(value -> organization.setLegalname(value.getValue())); - - Optional - .ofNullable(org.getWebsiteurl()) - .ifPresent(value -> organization.setWebsiteurl(value.getValue())); - - Optional - .ofNullable(org.getAlternativeNames()) - .ifPresent( - value -> organization - .setAlternativenames( - value - .stream() - .map(v -> v.getValue()) - .collect(Collectors.toList()))); - - Optional - .ofNullable(org.getCountry()) - .ifPresent( - value -> { - if (!value.getClassid().equals(Constants.UNKNOWN)) { - organization.setCountry(Country.newInstance(value.getClassid(), value.getClassname())); - } - - }); - - Optional - .ofNullable(org.getId()) - .ifPresent(value -> organization.setId(value)); - - Optional - .ofNullable(org.getPid()) - .ifPresent( - value -> organization - .setPid( - value - .stream() - .map(p -> OrganizationPid.newInstance(p.getQualifier().getClassid(), p.getValue())) - .collect(Collectors.toList()))); - - return organization; - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Extractor.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Extractor.java deleted file mode 100644 index cb4e42ac7..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Extractor.java +++ /dev/null @@ -1,201 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.util.*; - -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.FlatMapFunction; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SaveMode; -import org.apache.spark.sql.SparkSession; - -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.dump.oaf.Provenance; -import eu.dnetlib.dhp.schema.dump.oaf.graph.Node; -import eu.dnetlib.dhp.schema.dump.oaf.graph.RelType; -import eu.dnetlib.dhp.schema.dump.oaf.graph.Relation; -import eu.dnetlib.dhp.schema.oaf.KeyValue; -import eu.dnetlib.dhp.schema.oaf.Result; - -/** - * Creates new Relations (as in eu.dnetlib.dhp.schema.dump.oaf.graph.Relation) from the information in the Entity. The - * new Relations are created for the datasource in the collectedfrom and hostedby elements and for the context related - * to communities and research initiative/infrastructures. For collectedfrom elements it creates: datasource -> provides - * -> result and result -> isProvidedBy -> datasource For hostedby elements it creates: datasource -> hosts -> result - * and result -> isHostedBy -> datasource For context elements it creates: context <-> isRelatedTo <-> result. Note for - * context: it gets the first provenance in the dataInfo. If more than one is present the others are not dumped - */ -public class Extractor implements Serializable { - - public void run(Boolean isSparkSessionManaged, - String inputPath, - String outputPath, - Class inputClazz, - String communityMapPath) { - - SparkConf conf = new SparkConf(); - - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - extractRelationResult( - spark, inputPath, outputPath, inputClazz, Utils.getCommunityMap(spark, communityMapPath)); - }); - } - - private void extractRelationResult(SparkSession spark, - String inputPath, - String outputPath, - Class inputClazz, - CommunityMap communityMap) { - - Set hashCodes = new HashSet<>(); - - Utils - .readPath(spark, inputPath, inputClazz) - .flatMap((FlatMapFunction) value -> { - List relationList = new ArrayList<>(); - extractRelationsFromInstance(hashCodes, value, relationList); - Set communities = communityMap.keySet(); - Optional - .ofNullable(value.getContext()) - .ifPresent(contexts -> contexts.forEach(context -> { - String id = context.getId(); - if (id.contains(":")) { - id = id.substring(0, id.indexOf(":")); - } - if (communities.contains(id)) { - String contextId = Utils.getContextId(id); - Provenance provenance = Optional - .ofNullable(context.getDataInfo()) - .map( - dinfo -> Optional - .ofNullable(dinfo.get(0).getProvenanceaction()) - .map( - paction -> Provenance - .newInstance( - paction.getClassid(), - dinfo.get(0).getTrust())) - .orElse(null)) - .orElse(null); - Relation r = getRelation( - value.getId(), contextId, - Constants.RESULT_ENTITY, - Constants.CONTEXT_ENTITY, - ModelConstants.IS_RELATED_TO, ModelConstants.RELATIONSHIP, provenance); - if (!hashCodes.contains(r.hashCode())) { - relationList - .add(r); - hashCodes.add(r.hashCode()); - } - r = getRelation( - contextId, value.getId(), - Constants.CONTEXT_ENTITY, - Constants.RESULT_ENTITY, - ModelConstants.IS_RELATED_TO, - ModelConstants.RELATIONSHIP, provenance); - if (!hashCodes.contains(r.hashCode())) { - relationList - .add( - r); - hashCodes.add(r.hashCode()); - } - - } - - })); - - return relationList.iterator(); - }, Encoders.bean(Relation.class)) - .write() - .option("compression", "gzip") - .mode(SaveMode.Overwrite) - .json(outputPath); - - } - - private void extractRelationsFromInstance(Set hashCodes, R value, - List relationList) { - Optional - .ofNullable(value.getInstance()) - .ifPresent(inst -> inst.forEach(instance -> { - Optional - .ofNullable(instance.getCollectedfrom()) - .ifPresent( - cf -> getRelatioPair( - value, relationList, cf, - ModelConstants.IS_PROVIDED_BY, ModelConstants.PROVIDES, hashCodes)); - Optional - .ofNullable(instance.getHostedby()) - .ifPresent( - hb -> getRelatioPair( - value, relationList, hb, - Constants.IS_HOSTED_BY, Constants.HOSTS, hashCodes)); - })); - } - - private static void getRelatioPair(R value, List relationList, KeyValue cf, - String resultDatasource, String datasourceResult, - Set hashCodes) { - Provenance provenance = Optional - .ofNullable(cf.getDataInfo()) - .map( - dinfo -> Optional - .ofNullable(dinfo.getProvenanceaction()) - .map( - paction -> Provenance - .newInstance( - paction.getClassname(), - dinfo.getTrust())) - .orElse( - Provenance - .newInstance( - eu.dnetlib.dhp.oa.graph.dump.Constants.HARVESTED, - eu.dnetlib.dhp.oa.graph.dump.Constants.DEFAULT_TRUST))) - .orElse( - Provenance - .newInstance( - eu.dnetlib.dhp.oa.graph.dump.Constants.HARVESTED, - eu.dnetlib.dhp.oa.graph.dump.Constants.DEFAULT_TRUST)); - Relation r = getRelation( - value.getId(), - cf.getKey(), Constants.RESULT_ENTITY, Constants.DATASOURCE_ENTITY, - resultDatasource, ModelConstants.PROVISION, - provenance); - if (!hashCodes.contains(r.hashCode())) { - relationList - .add(r); - hashCodes.add(r.hashCode()); - } - - r = getRelation( - cf.getKey(), value.getId(), - Constants.DATASOURCE_ENTITY, Constants.RESULT_ENTITY, - datasourceResult, ModelConstants.PROVISION, - provenance); - - if (!hashCodes.contains(r.hashCode())) { - relationList - .add(r); - hashCodes.add(r.hashCode()); - } - - } - - private static Relation getRelation(String source, String target, String sourceType, String targetType, - String relName, String relType, Provenance provenance) { - Relation r = new Relation(); - r.setSource(Node.newInstance(source, sourceType)); - r.setTarget(Node.newInstance(target, targetType)); - r.setReltype(RelType.newInstance(relName, relType)); - r.setProvenance(provenance); - return r; - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/MergedRels.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/MergedRels.java deleted file mode 100644 index 30088e8d0..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/MergedRels.java +++ /dev/null @@ -1,25 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import java.io.Serializable; - -public class MergedRels implements Serializable { - private String organizationId; - private String representativeId; - - public String getOrganizationId() { - return organizationId; - } - - public void setOrganizationId(String organizationId) { - this.organizationId = organizationId; - } - - public String getRepresentativeId() { - return representativeId; - } - - public void setRepresentativeId(String representativeId) { - this.representativeId = representativeId; - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/OrganizationMap.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/OrganizationMap.java deleted file mode 100644 index bf6cdbd14..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/OrganizationMap.java +++ /dev/null @@ -1,21 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import java.util.ArrayList; -import java.util.HashMap; -import java.util.List; - -public class OrganizationMap extends HashMap> { - - public OrganizationMap() { - super(); - } - - public List get(String key) { - - if (super.get(key) == null) { - return new ArrayList<>(); - } - return super.get(key); - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Process.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Process.java deleted file mode 100644 index e1cb0e753..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Process.java +++ /dev/null @@ -1,99 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import java.io.Serializable; -import java.util.ArrayList; -import java.util.List; - -import org.apache.commons.lang3.StringUtils; - -import eu.dnetlib.dhp.oa.graph.dump.Constants; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.oa.graph.dump.exceptions.MyRuntimeException; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.dhp.schema.dump.oaf.Provenance; -import eu.dnetlib.dhp.schema.dump.oaf.graph.*; - -/** - * It process the ContextInfo information to produce a new Context Entity or a set of Relations between the generic - * context entity and datasource/projects related to the context. - */ -public class Process implements Serializable { - - @SuppressWarnings("unchecked") - public static R getEntity(ContextInfo ci) { - try { - ResearchInitiative ri; - if (ci.getType().equals("community")) { - ri = new ResearchCommunity(); - ((ResearchCommunity) ri).setSubject(ci.getSubject()); - ri.setType(Constants.RESEARCH_COMMUNITY); - } else { - ri = new ResearchInitiative(); - ri.setType(Constants.RESEARCH_INFRASTRUCTURE); - } - ri.setId(Utils.getContextId(ci.getId())); - ri.setAcronym(ci.getId()); - - ri.setDescription(ci.getDescription()); - ri.setName(ci.getName()); - if (StringUtils.isNotEmpty(ci.getZenodocommunity())) { - ri.setZenodo_community(Constants.ZENODO_COMMUNITY_PREFIX + ci.getZenodocommunity()); - } - return (R) ri; - - } catch (final Exception e) { - throw new MyRuntimeException(e); - } - } - - public static List getRelation(ContextInfo ci) { - try { - - List relationList = new ArrayList<>(); - ci - .getDatasourceList() - .forEach(ds -> { - - String nodeType = ModelSupport.idPrefixEntity.get(ds.substring(0, 2)); - - String contextId = Utils.getContextId(ci.getId()); - relationList - .add( - Relation - .newInstance( - Node - .newInstance( - contextId, eu.dnetlib.dhp.schema.dump.oaf.graph.Constants.CONTEXT_ENTITY), - Node.newInstance(ds, nodeType), - RelType.newInstance(ModelConstants.IS_RELATED_TO, ModelConstants.RELATIONSHIP), - Provenance - .newInstance( - Constants.USER_CLAIM, - Constants.DEFAULT_TRUST))); - - relationList - .add( - Relation - .newInstance( - Node.newInstance(ds, nodeType), - Node - .newInstance( - contextId, eu.dnetlib.dhp.schema.dump.oaf.graph.Constants.CONTEXT_ENTITY), - RelType.newInstance(ModelConstants.IS_RELATED_TO, ModelConstants.RELATIONSHIP), - Provenance - .newInstance( - Constants.USER_CLAIM, - Constants.DEFAULT_TRUST))); - - }); - - return relationList; - - } catch (final Exception e) { - throw new MyRuntimeException(e); - } - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystem.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystem.java deleted file mode 100644 index fcc4bf39c..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystem.java +++ /dev/null @@ -1,195 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import java.io.StringReader; -import java.util.*; -import java.util.function.Consumer; - -import org.dom4j.Document; -import org.dom4j.DocumentException; -import org.dom4j.Element; -import org.dom4j.Node; -import org.dom4j.io.SAXReader; -import org.jetbrains.annotations.NotNull; -import org.xml.sax.SAXException; - -import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.dhp.utils.DHPUtils; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; - -public class QueryInformationSystem { - - private ISLookUpService isLookUp; - private List contextRelationResult; - - private static final String XQUERY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') " - + - " where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " + - " and $x//context/param[./@name = 'status']/text() = 'all' " + - " return " + - "$x//context"; - - private static final String XQUERY_ENTITY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') " - + - "where $x//context[./@type='community' or ./@type = 'ri'] and $x//context/param[./@name = 'status']/text() = 'all' return " - + - "concat(data($x//context/@id) , '@@', $x//context/param[./@name =\"name\"]/text(), '@@', " + - "$x//context/param[./@name=\"description\"]/text(), '@@', $x//context/param[./@name = \"subject\"]/text(), '@@', " - + - "$x//context/param[./@name = \"zenodoCommunity\"]/text(), '@@', $x//context/@type)"; - - public void getContextInformation(final Consumer consumer) throws ISLookUpException { - - isLookUp - .quickSearchProfile(XQUERY_ENTITY) - .forEach(c -> { - ContextInfo cinfo = new ContextInfo(); - String[] cSplit = c.split("@@"); - cinfo.setId(cSplit[0]); - cinfo.setName(cSplit[1]); - cinfo.setDescription(cSplit[2]); - if (!cSplit[3].trim().equals("")) { - cinfo.setSubject(Arrays.asList(cSplit[3].split(","))); - } - cinfo.setZenodocommunity(cSplit[4]); - cinfo.setType(cSplit[5]); - consumer.accept(cinfo); - }); - - } - - public List getContextRelationResult() { - return contextRelationResult; - } - - public void setContextRelationResult(List contextRelationResult) { - this.contextRelationResult = contextRelationResult; - } - - public ISLookUpService getIsLookUp() { - return isLookUp; - } - - public void setIsLookUp(ISLookUpService isLookUpService) { - this.isLookUp = isLookUpService; - } - - public void execContextRelationQuery() throws ISLookUpException { - contextRelationResult = isLookUp.quickSearchProfile(XQUERY); - - } - - public void getContextRelation(final Consumer consumer, String category, String prefix) { - - contextRelationResult.forEach(xml -> { - ContextInfo cinfo = new ContextInfo(); - final Document doc; - - try { - final SAXReader reader = new SAXReader(); - reader.setFeature("http://apache.org/xml/features/disallow-doctype-decl", true); - doc = reader.read(new StringReader(xml)); - Element root = doc.getRootElement(); - cinfo.setId(root.attributeValue("id")); - - Iterator it = root.elementIterator(); - while (it.hasNext()) { - Element el = it.next(); - if (el.getName().equals("category")) { - String categoryId = el.attributeValue("id"); - categoryId = categoryId.substring(categoryId.lastIndexOf("::") + 2); - if (categoryId.equals(category)) { - cinfo.setDatasourceList(getCategoryList(el, prefix)); - } - } - - } - consumer.accept(cinfo); - } catch (DocumentException | SAXException e) { - e.printStackTrace(); - } - - }); - - } - - @NotNull - private List getCategoryList(Element el, String prefix) { - List datasourceList = new ArrayList<>(); - for (Object node : el.selectNodes(".//concept")) { - String oid = getOpenaireId((Node) node, prefix); - if (oid != null) - datasourceList.add(oid); - } - - return datasourceList; - } - - private String getOpenaireId(Node el, String prefix) { - for (Object node : el.selectNodes(".//param")) { - Node n = (Node) node; - if (n.valueOf("./@name").equals("openaireId")) { - return prefix + "|" + n.getText(); - } - } - - return makeOpenaireId(el, prefix); - - } - - private String makeOpenaireId(Node el, String prefix) { - if (!prefix.equals(ModelSupport.entityIdPrefix.get("project"))) { - return null; - } - String funder = ""; - String grantId = null; - String funding = null; - for (Object node : el.selectNodes(".//param")) { - Node n = (Node) node; - switch (n.valueOf("./@name")) { - case "funding": - funding = n.getText(); - break; - case "funder": - funder = n.getText(); - break; - case "CD_PROJECT_NUMBER": - grantId = n.getText(); - break; - default: - break; - } - } - String nsp = null; - - switch (funder.toLowerCase()) { - case "ec": - if (funding == null) { - return null; - } - if (funding.toLowerCase().contains("h2020")) { - nsp = "corda__h2020::"; - } else { - nsp = "corda_______::"; - } - break; - case "tubitak": - nsp = "tubitakf____::"; - break; - case "dfg": - nsp = "dfgf________::"; - break; - default: - StringBuilder bld = new StringBuilder(); - bld.append(funder.toLowerCase()); - for (int i = funder.length(); i < 12; i++) - bld.append("_"); - bld.append("::"); - nsp = bld.toString(); - } - - return prefix + "|" + nsp + DHPUtils.md5(grantId); - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkCollectAndSave.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkCollectAndSave.java deleted file mode 100644 index 1c98ea6cb..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkCollectAndSave.java +++ /dev/null @@ -1,122 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.util.Optional; - -import org.apache.commons.io.IOUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.SaveMode; -import org.apache.spark.sql.SparkSession; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult; -import eu.dnetlib.dhp.schema.dump.oaf.graph.Relation; - -/** - * Reads all the entities of the same type (Relation / Results) and saves them in the same folder - */ -public class SparkCollectAndSave implements Serializable { - - private static final Logger log = LoggerFactory.getLogger(SparkCollectAndSave.class); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkCollectAndSave.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_collect_and_save.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - final Boolean aggregateResult = Optional - .ofNullable(parser.get("resultAggregation")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - - SparkConf conf = new SparkConf(); - - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath + "/result"); - run(spark, inputPath, outputPath, aggregateResult); - - }); - - } - - private static void run(SparkSession spark, String inputPath, String outputPath, boolean aggregate) { - if (aggregate) { - Utils - .readPath(spark, inputPath + "/result/publication", GraphResult.class) - .union(Utils.readPath(spark, inputPath + "/result/dataset", GraphResult.class)) - .union(Utils.readPath(spark, inputPath + "/result/otherresearchproduct", GraphResult.class)) - .union(Utils.readPath(spark, inputPath + "/result/software", GraphResult.class)) - .write() - .option("compression", "gzip") - .mode(SaveMode.Overwrite) - .json(outputPath + "/result"); - } else { - write( - Utils - .readPath(spark, inputPath + "/result/publication", GraphResult.class), - outputPath + "/publication"); - write( - Utils - .readPath(spark, inputPath + "/result/dataset", GraphResult.class), - outputPath + "/dataset"); - write( - Utils - .readPath(spark, inputPath + "/result/otherresearchproduct", GraphResult.class), - outputPath + "/otheresearchproduct"); - write( - Utils - .readPath(spark, inputPath + "/result/software", GraphResult.class), - outputPath + "/software"); - - } - - Utils - .readPath(spark, inputPath + "/relation/publication", Relation.class) - .union(Utils.readPath(spark, inputPath + "/relation/dataset", Relation.class)) - .union(Utils.readPath(spark, inputPath + "/relation/orp", Relation.class)) - .union(Utils.readPath(spark, inputPath + "/relation/software", Relation.class)) - .union(Utils.readPath(spark, inputPath + "/relation/contextOrg", Relation.class)) - .union(Utils.readPath(spark, inputPath + "/relation/context", Relation.class)) - .union(Utils.readPath(spark, inputPath + "/relation/relation", Relation.class)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath + "/relation"); - - } - - private static void write(Dataset dataSet, String outputPath) { - dataSet - .write() - .option("compression", "gzip") - .mode(SaveMode.Overwrite) - .json(outputPath); - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpEntitiesJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpEntitiesJob.java deleted file mode 100644 index 7cc05a821..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpEntitiesJob.java +++ /dev/null @@ -1,54 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import java.io.Serializable; -import java.util.Optional; - -import org.apache.commons.io.IOUtils; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.schema.oaf.OafEntity; - -/** - * Spark Job that fires the dump for the entites - */ -public class SparkDumpEntitiesJob implements Serializable { - private static final Logger log = LoggerFactory.getLogger(SparkDumpEntitiesJob.class); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkDumpEntitiesJob.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - final String resultClassName = parser.get("resultTableName"); - log.info("resultTableName: {}", resultClassName); - - final String communityMapPath = parser.get("communityMapPath"); - - Class inputClazz = (Class) Class.forName(resultClassName); - - DumpGraphEntities dg = new DumpGraphEntities(); - dg.run(isSparkSessionManaged, inputPath, outputPath, inputClazz, communityMapPath); - - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpRelationJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpRelationJob.java deleted file mode 100644 index 0ac97dcb6..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpRelationJob.java +++ /dev/null @@ -1,132 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.util.*; - -import org.apache.commons.io.IOUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.FilterFunction; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SaveMode; -import org.apache.spark.sql.SparkSession; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.dhp.schema.dump.oaf.Provenance; -import eu.dnetlib.dhp.schema.dump.oaf.graph.Node; -import eu.dnetlib.dhp.schema.dump.oaf.graph.RelType; -import eu.dnetlib.dhp.schema.oaf.DataInfo; -import eu.dnetlib.dhp.schema.oaf.Relation; - -/** - * Dumps eu.dnetlib.dhp.schema.oaf.Relation in eu.dnetlib.dhp.schema.dump.oaf.graph.Relation - */ -public class SparkDumpRelationJob implements Serializable { - - private static final Logger log = LoggerFactory.getLogger(SparkDumpRelationJob.class); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkDumpRelationJob.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_relationdump_parameters.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - Optional rs = Optional.ofNullable(parser.get("removeSet")); - final Set removeSet = new HashSet<>(); - if (rs.isPresent()) { - Collections.addAll(removeSet, rs.get().split(";")); - } - - SparkConf conf = new SparkConf(); - - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - dumpRelation(spark, inputPath, outputPath, removeSet); - - }); - - } - - private static void dumpRelation(SparkSession spark, String inputPath, String outputPath, Set removeSet) { - Dataset relations = Utils.readPath(spark, inputPath, Relation.class); - relations - .filter((FilterFunction) r -> !removeSet.contains(r.getRelClass())) - .map((MapFunction) relation -> { - eu.dnetlib.dhp.schema.dump.oaf.graph.Relation relNew = new eu.dnetlib.dhp.schema.dump.oaf.graph.Relation(); - relNew - .setSource( - Node - .newInstance( - relation.getSource(), - ModelSupport.idPrefixEntity.get(relation.getSource().substring(0, 2)))); - - relNew - .setTarget( - Node - .newInstance( - relation.getTarget(), - ModelSupport.idPrefixEntity.get(relation.getTarget().substring(0, 2)))); - - relNew - .setReltype( - RelType - .newInstance( - relation.getRelClass(), - relation.getSubRelType())); - - Optional odInfo = Optional.ofNullable(relation.getDataInfo()); - if (odInfo.isPresent()) { - DataInfo dInfo = odInfo.get(); - if (Optional.ofNullable(dInfo.getProvenanceaction()).isPresent() && - Optional.ofNullable(dInfo.getProvenanceaction().getClassname()).isPresent()) { - relNew - .setProvenance( - Provenance - .newInstance( - dInfo.getProvenanceaction().getClassname(), - dInfo.getTrust())); - } - } - if (Boolean.TRUE.equals(relation.getValidated())) { - relNew.setValidated(relation.getValidated()); - relNew.setValidationDate(relation.getValidationDate()); - } - - return relNew; - - }, Encoders.bean(eu.dnetlib.dhp.schema.dump.oaf.graph.Relation.class)) - .write() - .option("compression", "gzip") - .mode(SaveMode.Overwrite) - .json(outputPath); - - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkExtractRelationFromEntities.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkExtractRelationFromEntities.java deleted file mode 100644 index ec91bd8d6..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkExtractRelationFromEntities.java +++ /dev/null @@ -1,54 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import java.io.Serializable; -import java.util.*; - -import org.apache.commons.io.IOUtils; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.schema.oaf.Result; - -/** - * Spark job that fires the extraction of relations from entities - */ -public class SparkExtractRelationFromEntities implements Serializable { - private static final Logger log = LoggerFactory.getLogger(SparkExtractRelationFromEntities.class); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkExtractRelationFromEntities.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - final String resultClassName = parser.get("resultTableName"); - log.info("resultTableName: {}", resultClassName); - - final String communityMapPath = parser.get("communityMapPath"); - - Class inputClazz = (Class) Class.forName(resultClassName); - - Extractor extractor = new Extractor(); - extractor.run(isSparkSessionManaged, inputPath, outputPath, inputClazz, communityMapPath); - - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkOrganizationRelation.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkOrganizationRelation.java deleted file mode 100644 index dff1a1066..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkOrganizationRelation.java +++ /dev/null @@ -1,176 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.util.*; -import java.util.function.Consumer; - -import org.apache.commons.io.IOUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.*; -import org.jetbrains.annotations.NotNull; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.google.gson.Gson; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.dhp.schema.dump.oaf.Provenance; -import eu.dnetlib.dhp.schema.dump.oaf.graph.Node; -import eu.dnetlib.dhp.schema.dump.oaf.graph.RelType; -import eu.dnetlib.dhp.schema.oaf.Relation; - -/** - * Create new Relations between Context Entities and Organizations whose products are associated to the context. It - * produces relation such as: organization <-> isRelatedTo <-> context - */ -public class SparkOrganizationRelation implements Serializable { - private static final Logger log = LoggerFactory.getLogger(SparkOrganizationRelation.class); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkOrganizationRelation.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_organization_parameters.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - final OrganizationMap organizationMap = new Gson() - .fromJson(parser.get("organizationCommunityMap"), OrganizationMap.class); - final String serializedOrganizationMap = new Gson().toJson(organizationMap); - log.info("organization map : {}", serializedOrganizationMap); - - final String communityMapPath = parser.get("communityMapPath"); - log.info("communityMapPath: {}", communityMapPath); - - SparkConf conf = new SparkConf(); - - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - extractRelation(spark, inputPath, organizationMap, outputPath, communityMapPath); - - }); - - } - - private static void extractRelation(SparkSession spark, String inputPath, OrganizationMap organizationMap, - String outputPath, String communityMapPath) { - - CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath); - - Dataset relationDataset = Utils.readPath(spark, inputPath, Relation.class); - - relationDataset.createOrReplaceTempView("relation"); - - List relList = new ArrayList<>(); - - Dataset mergedRelsDataset = spark - .sql( - "SELECT target organizationId, source representativeId " + - "FROM relation " + - "WHERE datainfo.deletedbyinference = false " + - "AND relclass = 'merges' " + - "AND substr(source, 1, 2) = '20'") - .as(Encoders.bean(MergedRels.class)); - - mergedRelsDataset.map((MapFunction) mergedRels -> { - if (organizationMap.containsKey(mergedRels.getOrganizationId())) { - return mergedRels; - } - return null; - }, Encoders.bean(MergedRels.class)) - .filter(Objects::nonNull) - .collectAsList() - .forEach(getMergedRelsConsumer(organizationMap, relList, communityMap)); - - organizationMap - .keySet() - .forEach( - oId -> organizationMap - .get(oId) - .forEach(community -> { - if (communityMap.containsKey(community)) { - addRelations(relList, community, oId); - } - })); - - spark - .createDataset(relList, Encoders.bean(eu.dnetlib.dhp.schema.dump.oaf.graph.Relation.class)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); - } - - @NotNull - private static Consumer getMergedRelsConsumer(OrganizationMap organizationMap, - List relList, CommunityMap communityMap) { - return mergedRels -> { - String oId = mergedRels.getOrganizationId(); - organizationMap - .get(oId) - .forEach(community -> { - if (communityMap.containsKey(community)) { - addRelations(relList, community, mergedRels.getRepresentativeId()); - } - - }); - organizationMap.remove(oId); - }; - } - - private static void addRelations(List relList, String community, - String organization) { - - String id = Utils.getContextId(community); - log.info("create relation for organization: {}", organization); - relList - .add( - eu.dnetlib.dhp.schema.dump.oaf.graph.Relation - .newInstance( - Node.newInstance(id, Constants.CONTEXT_ENTITY), - Node.newInstance(organization, ModelSupport.idPrefixEntity.get(organization.substring(0, 2))), - RelType.newInstance(ModelConstants.IS_RELATED_TO, ModelConstants.RELATIONSHIP), - Provenance - .newInstance( - eu.dnetlib.dhp.oa.graph.dump.Constants.USER_CLAIM, - eu.dnetlib.dhp.oa.graph.dump.Constants.DEFAULT_TRUST))); - - relList - .add( - eu.dnetlib.dhp.schema.dump.oaf.graph.Relation - .newInstance( - Node.newInstance(organization, ModelSupport.idPrefixEntity.get(organization.substring(0, 2))), - Node.newInstance(id, Constants.CONTEXT_ENTITY), - RelType.newInstance(ModelConstants.IS_RELATED_TO, ModelConstants.RELATIONSHIP), - Provenance - .newInstance( - eu.dnetlib.dhp.oa.graph.dump.Constants.USER_CLAIM, - eu.dnetlib.dhp.oa.graph.dump.Constants.DEFAULT_TRUST))); - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkSelectValidRelationsJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkSelectValidRelationsJob.java deleted file mode 100644 index 1e5675e5f..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkSelectValidRelationsJob.java +++ /dev/null @@ -1,136 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.util.Optional; - -import org.apache.commons.io.IOUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SaveMode; -import org.apache.spark.sql.SparkSession; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.schema.oaf.*; - -/** - * It selects the valid relations among those present in the graph. One relation is valid if it is not deletedbyinference - * and if both the source and the target node are present in the graph and are not deleted by inference nor invisible. - * To check this I made a view of the ids of all the entities in the graph, and select the relations for which a join exists - * with this view for both the source and the target - */ - -public class SparkSelectValidRelationsJob implements Serializable { - - private static final Logger log = LoggerFactory.getLogger(SparkSelectValidRelationsJob.class); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkSelectValidRelationsJob.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_relationdump_parameters.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - SparkConf conf = new SparkConf(); - - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - selectValidRelation(spark, inputPath, outputPath); - - }); - - } - - private static void selectValidRelation(SparkSession spark, String inputPath, String outputPath) { - Dataset relation = Utils.readPath(spark, inputPath + "/relation", Relation.class); - Dataset publication = Utils.readPath(spark, inputPath + "/publication", Publication.class); - Dataset dataset = Utils - .readPath(spark, inputPath + "/dataset", eu.dnetlib.dhp.schema.oaf.Dataset.class); - Dataset software = Utils.readPath(spark, inputPath + "/software", Software.class); - Dataset other = Utils - .readPath(spark, inputPath + "/otherresearchproduct", OtherResearchProduct.class); - Dataset organization = Utils.readPath(spark, inputPath + "/organization", Organization.class); - Dataset project = Utils.readPath(spark, inputPath + "/project", Project.class); - Dataset datasource = Utils.readPath(spark, inputPath + "/datasource", Datasource.class); - - relation.createOrReplaceTempView("relation"); - publication.createOrReplaceTempView("publication"); - dataset.createOrReplaceTempView("dataset"); - other.createOrReplaceTempView("other"); - software.createOrReplaceTempView("software"); - organization.createOrReplaceTempView("organization"); - project.createOrReplaceTempView("project"); - datasource.createOrReplaceTempView("datasource"); - - spark - .sql( - "SELECT id " + - "FROM publication " + - "WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " + - "UNION ALL " + - "SELECT id " + - "FROM dataset " + - "WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " + - "UNION ALL " + - "SELECT id " + - "FROM other " + - "WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " + - "UNION ALL " + - "SELECT id " + - "FROM software " + - "WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " + - "UNION ALL " + - "SELECT id " + - "FROM organization " + - "WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " + - "UNION ALL " + - "SELECT id " + - "FROM project " + - "WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " + - "UNION ALL " + - "SELECT id " + - "FROM datasource " + - "WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false ") - .createOrReplaceTempView("identifiers"); - - spark - .sql( - "SELECT relation.* " + - "FROM relation " + - "JOIN identifiers i1 " + - "ON source = i1.id " + - "JOIN identifiers i2 " + - "ON target = i2.id " + - "WHERE datainfo.deletedbyinference = false") - .as(Encoders.bean(Relation.class)) - .write() - .option("compression", "gzip") - .mode(SaveMode.Overwrite) - .json(outputPath); - - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/MyRuntimeException.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/MyRuntimeException.java deleted file mode 100644 index e325c4334..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/MyRuntimeException.java +++ /dev/null @@ -1,30 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.exceptions; - -public class MyRuntimeException extends RuntimeException { - - public MyRuntimeException() { - super(); - } - - public MyRuntimeException( - final String message, - final Throwable cause, - final boolean enableSuppression, - final boolean writableStackTrace) { - super(message, cause, enableSuppression, writableStackTrace); - } - - public MyRuntimeException(final String message, final Throwable cause) { - super(message, cause); - } - - public MyRuntimeException(final String message) { - super(message); - } - - public MyRuntimeException(final Throwable cause) { - super(cause); - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/NoAvailableEntityTypeException.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/NoAvailableEntityTypeException.java deleted file mode 100644 index f3fbf740a..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/NoAvailableEntityTypeException.java +++ /dev/null @@ -1,29 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.exceptions; - -public class NoAvailableEntityTypeException extends Exception { - public NoAvailableEntityTypeException() { - super(); - } - - public NoAvailableEntityTypeException( - final String message, - final Throwable cause, - final boolean enableSuppression, - final boolean writableStackTrace) { - super(message, cause, enableSuppression, writableStackTrace); - } - - public NoAvailableEntityTypeException(final String message, final Throwable cause) { - super(message, cause); - } - - public NoAvailableEntityTypeException(final String message) { - super(message); - } - - public NoAvailableEntityTypeException(final Throwable cause) { - super(cause); - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java deleted file mode 100644 index 34ca6697c..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java +++ /dev/null @@ -1,129 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.funderresults; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.util.List; -import java.util.Objects; -import java.util.Optional; -import java.util.stream.Collectors; - -import org.apache.commons.io.IOUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.FlatMapFunction; -import org.apache.spark.api.java.function.ForeachFunction; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.*; -import org.jetbrains.annotations.NotNull; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; -import eu.dnetlib.dhp.schema.dump.oaf.community.Funder; -import eu.dnetlib.dhp.schema.dump.oaf.community.Project; - -/** - * Splits the dumped results by funder and stores them in a folder named as the funder nsp (for all the funders, but the EC - * for the EC it specifies also the fundingStream (FP7 or H2020) - */ -public class SparkDumpFunderResults implements Serializable { - private static final Logger log = LoggerFactory.getLogger(SparkDumpFunderResults.class); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkDumpFunderResults.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json")); - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - SparkConf conf = new SparkConf(); - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - writeResultProjectList(spark, inputPath, outputPath); - }); - } - - private static void writeResultProjectList(SparkSession spark, String inputPath, String outputPath) { - Dataset result = Utils - .readPath(spark, inputPath + "/publication", CommunityResult.class) - .union(Utils.readPath(spark, inputPath + "/dataset", CommunityResult.class)) - .union(Utils.readPath(spark, inputPath + "/otherresearchproduct", CommunityResult.class)) - .union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class)); - log.info("Number of result {}", result.count()); - Dataset tmp = result - .flatMap((FlatMapFunction) cr -> cr.getProjects().stream().map(p -> { - return getFunderName(p); - }).collect(Collectors.toList()).iterator(), Encoders.STRING()) - .distinct(); - List funderList = tmp.collectAsList(); - funderList.forEach(funder -> { - dumpResults(funder, result, outputPath); - }); - } - - @NotNull - private static String getFunderName(Project p) { - Optional ofunder = Optional.ofNullable(p.getFunder()); - if (ofunder.isPresent()) { - String fName = ofunder.get().getShortName(); - if (fName.equalsIgnoreCase("ec")) { - fName += "_" + ofunder.get().getFundingStream(); - } - return fName; - } else { - String fName = p.getId().substring(3, p.getId().indexOf("_")).toUpperCase(); - if (fName.equalsIgnoreCase("ec")) { - if (p.getId().contains("h2020")) { - fName += "_H2020"; - } else { - fName += "_FP7"; - } - } else if (fName.equalsIgnoreCase("conicytf")) { - fName = "CONICYT"; - } else if (fName.equalsIgnoreCase("dfgf")) { - fName = "DFG"; - } else if (fName.equalsIgnoreCase("tubitakf")) { - fName = "TUBITAK"; - } else if (fName.equalsIgnoreCase("euenvagency")) { - fName = "EEA"; - } - return fName; - } - } - - private static void dumpResults(String funder, Dataset results, String outputPath) { - results.map((MapFunction) r -> { - if (!Optional.ofNullable(r.getProjects()).isPresent()) { - return null; - } - for (Project p : r.getProjects()) { - String fName = getFunderName(p); - if (fName.equalsIgnoreCase(funder)) { - return r; - } - } - return null; - }, Encoders.bean(CommunityResult.class)) - .filter(Objects::nonNull) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath + "/" + funder); - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java deleted file mode 100644 index 4b0072944..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java +++ /dev/null @@ -1,118 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.funderresults; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.util.Optional; -import java.util.stream.Collectors; - -import org.apache.commons.io.IOUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.FilterFunction; -import org.apache.spark.api.java.function.FlatMapFunction; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.api.java.function.MapGroupsFunction; -import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SaveMode; -import org.apache.spark.sql.SparkSession; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Constants; -import eu.dnetlib.dhp.oa.graph.dump.DumpProducts; -import eu.dnetlib.dhp.oa.graph.dump.ResultMapper; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; -import eu.dnetlib.dhp.oa.graph.dump.community.ResultProject; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; -import eu.dnetlib.dhp.schema.oaf.Project; -import eu.dnetlib.dhp.schema.oaf.Relation; -import eu.dnetlib.dhp.schema.oaf.Result; -import scala.Tuple2; - -/** - * Selects the results linked to projects. Only for these results the dump will be performed. - * The code to perform the dump and to expend the dumped results with the information related to projects - * is the one used for the dump of the community products - */ -public class SparkResultLinkedToProject implements Serializable { - - private static final Logger log = LoggerFactory.getLogger(SparkResultLinkedToProject.class); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkResultLinkedToProject.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - final String resultClassName = parser.get("resultTableName"); - log.info("resultTableName: {}", resultClassName); - - final String resultProjectsPath = parser.get("graphPath"); - log.info("graphPath: {}", resultProjectsPath); - - String communityMapPath = parser.get("communityMapPath"); - - @SuppressWarnings("unchecked") - Class inputClazz = (Class) Class.forName(resultClassName); - SparkConf conf = new SparkConf(); - - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - writeResultsLinkedToProjects( - communityMapPath, spark, inputClazz, inputPath, outputPath, resultProjectsPath); - }); - } - - private static void writeResultsLinkedToProjects(String communityMapPath, SparkSession spark, - Class inputClazz, - String inputPath, String outputPath, String resultProjectsPath) { - - Dataset results = Utils - .readPath(spark, inputPath, inputClazz) - .filter( - (FilterFunction) r -> !r.getDataInfo().getDeletedbyinference() && - !r.getDataInfo().getInvisible()); - Dataset resultProjectDataset = Utils - .readPath(spark, resultProjectsPath, ResultProject.class); - CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath); - results - .joinWith(resultProjectDataset, results.col("id").equalTo(resultProjectDataset.col("resultId"))) - .map((MapFunction, CommunityResult>) t2 -> { - CommunityResult cr = (CommunityResult) ResultMapper - .map( - t2._1(), - communityMap, Constants.DUMPTYPE.FUNDER.getType()); - cr.setProjects(t2._2().getProjectsList()); - return cr; - }, Encoders.bean(CommunityResult.class)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); - - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java deleted file mode 100644 index 38eb3cb37..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java +++ /dev/null @@ -1,82 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.projectssubset; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.util.Objects; -import java.util.Optional; - -import org.apache.commons.io.IOUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SaveMode; -import org.apache.spark.sql.SparkSession; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.schema.dump.oaf.graph.Project; -import scala.Tuple2; - -public class ProjectsSubsetSparkJob implements Serializable { - private static final Logger log = LoggerFactory.getLogger(ProjectsSubsetSparkJob.class); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - ProjectsSubsetSparkJob.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/project_subset_parameters.json")); - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - final String projectListPath = parser.get("projectListPath"); - log.info("projectListPath: {}", projectListPath); - SparkConf conf = new SparkConf(); - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - getNewProjectList(spark, inputPath, outputPath, projectListPath); - }); - } - - private static void getNewProjectList(SparkSession spark, String inputPath, String outputPath, - String projectListPath) { - Dataset projectList = spark.read().textFile(projectListPath); - Dataset projects; - projects = Utils.readPath(spark, inputPath, Project.class); - projects - .joinWith(projectList, projects.col("id").equalTo(projectList.col("value")), "left") - .map((MapFunction, Project>) t2 -> { - if (Optional.ofNullable(t2._2()).isPresent()) - return null; - return t2._1(); - }, Encoders.bean(Project.class)) - .filter(Objects::nonNull) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); - Utils - .readPath(spark, outputPath, Project.class) - .map((MapFunction) p -> p.getId(), Encoders.STRING()) - .write() - .mode(SaveMode.Append) - .option("compression", "gzip") - .text(projectListPath); - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationsApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationsApplication.java index edfd65299..615b4a824 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationsApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationsApplication.java @@ -19,7 +19,6 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.oa.graph.raw.common.RelationIdMapping; import eu.dnetlib.dhp.schema.oaf.Relation; import scala.Tuple2; @@ -78,8 +77,8 @@ public class PatchRelationsApplication { final String relationPath = graphBasePath + "/relation"; - final Dataset rels = Utils.readPath(spark, relationPath, Relation.class); - final Dataset idMapping = Utils.readPath(spark, idMappingPath, RelationIdMapping.class); + final Dataset rels = readPath(spark, relationPath, Relation.class); + final Dataset idMapping = readPath(spark, idMappingPath, RelationIdMapping.class); log.info("relations: {}", rels.count()); log.info("idMapping: {}", idMapping.count()); @@ -122,4 +121,12 @@ public class PatchRelationsApplication { .text(relationPath); } + public static Dataset readPath( + SparkSession spark, String inputPath, Class clazz) { + return spark + .read() + .textFile(inputPath) + .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz)); + } + } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json deleted file mode 100644 index 5669dca37..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json +++ /dev/null @@ -1,26 +0,0 @@ -[ - { - "paramName":"s", - "paramLongName":"sourcePath", - "paramDescription": "the path of the sequencial file to read", - "paramRequired": true - }, - { - "paramName": "out", - "paramLongName": "outputPath", - "paramDescription": "the path used to store temporary output files", - "paramRequired": true - }, - { - "paramName": "ssm", - "paramLongName": "isSparkSessionManaged", - "paramDescription": "true if the spark session is managed, false otherwise", - "paramRequired": false - }, - { - "paramName": "gp", - "paramLongName": "graphPath", - "paramDescription": "the relationPath", - "paramRequired": false - } -] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_cm_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_cm_parameters.json deleted file mode 100644 index 677715847..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_cm_parameters.json +++ /dev/null @@ -1,37 +0,0 @@ - -[ - - { - "paramName":"is", - "paramLongName":"isLookUpUrl", - "paramDescription": "URL of the isLookUp Service", - "paramRequired": true - }, - { - "paramName":"nn", - "paramLongName":"nameNode", - "paramDescription": "the name node", - "paramRequired": true - }, - { - "paramName": "out", - "paramLongName": "outputPath", - "paramDescription": "the path used to store temporary output files", - "paramRequired": true - }, - { - "paramName": "sd", - "paramLongName": "singleDeposition", - "paramDescription": "true if the dump should be created for a single community", - "paramRequired": true - }, - { - "paramName": "ci", - "paramLongName": "communityId", - "paramDescription": "the id of the community for which to create the dump", - "paramRequired": true - } -] - - - diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_collect_and_save.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_collect_and_save.json deleted file mode 100644 index 2b422176c..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_collect_and_save.json +++ /dev/null @@ -1,30 +0,0 @@ -[ - - { - "paramName":"s", - "paramLongName":"sourcePath", - "paramDescription": "the path of the sequencial file to read", - "paramRequired": true - }, - { - "paramName": "out", - "paramLongName": "outputPath", - "paramDescription": "the path used to store temporary output files", - "paramRequired": true - }, - { - "paramName": "ssm", - "paramLongName": "isSparkSessionManaged", - "paramDescription": "true if the spark session is managed, false otherwise", - "paramRequired": false - }, - { - "paramName": "ra", - "paramLongName": "resultAggregation", - "paramDescription": "true if all the result type should be saved under the generic result name. false to get a different dump for each result type", - "paramRequired": true -} -] - - - diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_complete_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_complete_parameters.json deleted file mode 100644 index bc3e0cd51..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_complete_parameters.json +++ /dev/null @@ -1,35 +0,0 @@ -[ - { - "paramName":"cmp", - "paramLongName":"communityMapPath", - "paramDescription": "the path to the serialization of the community map", - "paramRequired": true - }, - { - "paramName":"s", - "paramLongName":"sourcePath", - "paramDescription": "the path of the sequencial file to read", - "paramRequired": true - }, - { - "paramName": "out", - "paramLongName": "outputPath", - "paramDescription": "the path used to store temporary output files", - "paramRequired": true - }, - { - "paramName": "ssm", - "paramLongName": "isSparkSessionManaged", - "paramDescription": "true if the spark session is managed, false otherwise", - "paramRequired": false - }, - { - "paramName":"tn", - "paramLongName":"resultTableName", - "paramDescription": "the name of the result table we are currently working on", - "paramRequired": true - } -] - - - diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_entity_parameter.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_entity_parameter.json deleted file mode 100644 index 87de13d63..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_entity_parameter.json +++ /dev/null @@ -1,24 +0,0 @@ -[ - - { - "paramName":"is", - "paramLongName":"isLookUpUrl", - "paramDescription": "URL of the isLookUp Service", - "paramRequired": false - }, - { - "paramName": "hdfs", - "paramLongName": "hdfsPath", - "paramDescription": "the path used to store temporary output files", - "paramRequired": true - }, - { - "paramName": "nn", - "paramLongName": "nameNode", - "paramDescription": "the name node", - "paramRequired": true - } -] - - - diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_maketar_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_maketar_parameters.json deleted file mode 100644 index a15318865..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_maketar_parameters.json +++ /dev/null @@ -1,30 +0,0 @@ -[ - - { - "paramName":"s", - "paramLongName":"sourcePath", - "paramDescription": "the path of the sequencial file to read", - "paramRequired": true - }, - { - "paramName": "hdp", - "paramLongName": "hdfsPath", - "paramDescription": "the path used to store the output archive", - "paramRequired": true - }, - { - "paramName":"nn", - "paramLongName":"nameNode", - "paramDescription": "the name node", - "paramRequired": true - }, - { - "paramName":"ss", - "paramLongName":"splitSize", - "paramDescription": "the maximum size of the archive", - "paramRequired": false - } -] - - - diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_organization_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_organization_parameters.json deleted file mode 100644 index c27a9234d..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_organization_parameters.json +++ /dev/null @@ -1,36 +0,0 @@ -[ - - { - "paramName":"ocm", - "paramLongName":"organizationCommunityMap", - "paramDescription": "the organization community map association", - "paramRequired": false - }, - { - "paramName":"s", - "paramLongName":"sourcePath", - "paramDescription": "the path of the sequencial file to read", - "paramRequired": true - }, - { - "paramName": "out", - "paramLongName": "outputPath", - "paramDescription": "the path used to store temporary output files", - "paramRequired": true - }, - { - "paramName": "ssm", - "paramLongName": "isSparkSessionManaged", - "paramDescription": "true if the spark session is managed, false otherwise", - "paramRequired": false - }, - { - "paramName":"cmp", - "paramLongName":"communityMapPath", - "paramDescription": "the path to the serialization of the community map", - "paramRequired": true - } -] - - - diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameter_select_relation.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameter_select_relation.json deleted file mode 100644 index 1a67134a6..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameter_select_relation.json +++ /dev/null @@ -1,20 +0,0 @@ -[ - { - "paramName":"s", - "paramLongName":"sourcePath", - "paramDescription": "the path of the sequencial file to read", - "paramRequired": true - }, - { - "paramName": "out", - "paramLongName": "outputPath", - "paramDescription": "the path used to store temporary output files", - "paramRequired": true - }, - { - "paramName": "ssm", - "paramLongName": "isSparkSessionManaged", - "paramDescription": "true if the spark session is managed, false otherwise", - "paramRequired": false - } -] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json deleted file mode 100644 index e86f6e3d2..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json +++ /dev/null @@ -1,47 +0,0 @@ -[ - - { - "paramName":"cmp", - "paramLongName":"communityMapPath", - "paramDescription": "the path to the serialization of the community map", - "paramRequired": true - }, - { - "paramName":"s", - "paramLongName":"sourcePath", - "paramDescription": "the path of the sequencial file to read", - "paramRequired": true - }, - { - "paramName": "out", - "paramLongName": "outputPath", - "paramDescription": "the path used to store temporary output files", - "paramRequired": true - }, - { - "paramName": "ssm", - "paramLongName": "isSparkSessionManaged", - "paramDescription": "true if the spark session is managed, false otherwise", - "paramRequired": false - }, - { - "paramName":"tn", - "paramLongName":"resultTableName", - "paramDescription": "the name of the result table we are currently working on", - "paramRequired": true - }, - { - "paramName":"dt", - "paramLongName":"dumpType", - "paramDescription": "the type of the dump (complete for the whole graph, community for the products related to communities, funder for the results with at least a link to project", - "paramRequired": false - }, { - "paramName":"cid", - "paramLongName":"communityId", - "paramDescription": "the id of the community to be dumped", - "paramRequired": false -} -] - - - diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json deleted file mode 100644 index 6c45538cf..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json +++ /dev/null @@ -1,41 +0,0 @@ -[ - { - "paramName":"s", - "paramLongName":"sourcePath", - "paramDescription": "the path of the sequencial file to read", - "paramRequired": true - }, - { - "paramName": "out", - "paramLongName": "outputPath", - "paramDescription": "the path used to store temporary output files", - "paramRequired": true - }, - { - "paramName": "ssm", - "paramLongName": "isSparkSessionManaged", - "paramDescription": "true if the spark session is managed, false otherwise", - "paramRequired": false - }, - { - "paramName":"tn", - "paramLongName":"resultTableName", - "paramDescription": "the name of the result table we are currently working on", - "paramRequired": true - }, - { - "paramName":"gp", - "paramLongName":"graphPath", - "paramDescription": "the path to the relations", - "paramRequired": true - }, - { - "paramName":"cmp", - "paramLongName":"communityMapPath", - "paramDescription": "the path to the relations", - "paramRequired": true - } -] - - - diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_relationdump_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_relationdump_parameters.json deleted file mode 100644 index 5c26ea7d1..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_relationdump_parameters.json +++ /dev/null @@ -1,32 +0,0 @@ - - -[ - - { - "paramName":"s", - "paramLongName":"sourcePath", - "paramDescription": "the path of the sequencial file to read", - "paramRequired": true - }, - { - "paramName": "out", - "paramLongName": "outputPath", - "paramDescription": "the path used to store temporary output files", - "paramRequired": true - }, - { - "paramName": "ssm", - "paramLongName": "isSparkSessionManaged", - "paramDescription": "true if the spark session is managed, false otherwise", - "paramRequired": false - }, - { - "paramName": "rs", - "paramLongName": "removeSet", - "paramDescription": "the list of classname relations, split by ';', not to be dumped", - "paramRequired": false - } -] - - - diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/project_input_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/project_input_parameters.json deleted file mode 100644 index f2dc02ba9..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/project_input_parameters.json +++ /dev/null @@ -1,29 +0,0 @@ -[ - - { - "paramName":"s", - "paramLongName":"sourcePath", - "paramDescription": "the path of the sequencial file to read", - "paramRequired": true - }, - { - "paramName": "out", - "paramLongName": "outputPath", - "paramDescription": "the path used to store temporary output files", - "paramRequired": true - }, - { - "paramName": "ssm", - "paramLongName": "isSparkSessionManaged", - "paramDescription": "true if the spark session is managed, false otherwise", - "paramRequired": false - }, - { - "paramName": "pip", - "paramLongName": "preparedInfoPath", - "paramDescription": "the path of the association result projectlist", - "paramRequired": true - } -] - - diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/project_prep_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/project_prep_parameters.json deleted file mode 100644 index 82714d973..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/project_prep_parameters.json +++ /dev/null @@ -1,20 +0,0 @@ -[ - { - "paramName":"s", - "paramLongName":"sourcePath", - "paramDescription": "the path of the sequencial file to read", - "paramRequired": true - }, - { - "paramName": "out", - "paramLongName": "outputPath", - "paramDescription": "the path used to store temporary output files", - "paramRequired": true - }, - { - "paramName": "ssm", - "paramLongName": "isSparkSessionManaged", - "paramDescription": "true if the spark session is managed, false otherwise", - "paramRequired": false - } -] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/project_subset_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/project_subset_parameters.json deleted file mode 100644 index ed2313680..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/project_subset_parameters.json +++ /dev/null @@ -1,27 +0,0 @@ -[ - { - "paramName":"s", - "paramLongName":"sourcePath", - "paramDescription": "the path of the sequencial file to read", - "paramRequired": true - }, - { - "paramName": "out", - "paramLongName": "outputPath", - "paramDescription": "the path used to store temporary output files", - "paramRequired": true - }, - { - "paramName": "ssm", - "paramLongName": "isSparkSessionManaged", - "paramDescription": "true if the spark session is managed, false otherwise", - "paramRequired": false - }, - { - "paramName": "pl", - "paramLongName": "projectListPath", - "paramDescription": "the path of the association result projectlist", - "paramRequired": true - } -] - diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/oozie_app/config-default.xml deleted file mode 100644 index d262cb6e0..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/oozie_app/config-default.xml +++ /dev/null @@ -1,30 +0,0 @@ - - - jobTracker - yarnRM - - - nameNode - hdfs://nameservice1 - - - oozie.use.system.libpath - true - - - hiveMetastoreUris - thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 - - - hiveJdbcUrl - jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000 - - - hiveDbName - openaire - - - oozie.launcher.mapreduce.user.classpath.first - true - - diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/oozie_app/workflow.xml deleted file mode 100644 index 619e3aa20..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/oozie_app/workflow.xml +++ /dev/null @@ -1,171 +0,0 @@ - - - - sourcePath - the source path - - - projectListPath - the path to the project list - - - outputPath - the output path - - - accessToken - the access token used for the deposition in Zenodo - - - connectionUrl - the connection url for Zenodo - - - metadata - the metadata associated to the deposition - - - depositionType - the type of deposition we want to perform. "new" for brand new deposition, "version" for a new version of a published deposition (in this case the concept record id must be provided), "upload" to upload content to an open deposition for which we already have the deposition id (in this case the deposition id should be provided) - - - conceptRecordId - for new version, the id of the record for the old deposition - - - depositionId - the depositionId of a deposition open that has to be added content - - - sparkDriverMemory - memory for driver process - - - sparkExecutorMemory - memory for individual executor - - - sparkExecutorCores - number of cores used by single executor - - - oozieActionShareLibForSpark2 - oozie action sharelib for spark 2.* - - - spark2ExtraListeners - com.cloudera.spark.lineage.NavigatorAppListener - spark 2.* extra listeners classname - - - spark2SqlQueryExecutionListeners - com.cloudera.spark.lineage.NavigatorQueryListener - spark 2.* sql query execution listeners classname - - - spark2YarnHistoryServerAddress - spark 2.* yarn history server address - - - spark2EventLogDir - spark 2.* event log dir location - - - - ${jobTracker} - ${nameNode} - - - mapreduce.job.queuename - ${queueName} - - - oozie.launcher.mapred.job.queue.name - ${oozieLauncherQueueName} - - - oozie.action.sharelib.for.spark - ${oozieActionShareLibForSpark2} - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - yarn - cluster - Dump table project - eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath}/project - --resultTableNameeu.dnetlib.dhp.schema.oaf.Project - --outputPath${workingDir}/project - --communityMapPathnoneed - - - - - - - yarn - cluster - Dump table project - eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectsSubsetSparkJob - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${workingDir}/project - --outputPath${workingDir}/tar/project - --projectListPath${projectListPath} - - - - - - - eu.dnetlib.dhp.oa.graph.dump.MakeTar - --hdfsPath${outputPath} - --nameNode${nameNode} - --sourcePath${workingDir}/tar - - - - - - - eu.dnetlib.dhp.oa.graph.dump.SendToZenodoHDFS - --hdfsPath${outputPath} - --nameNode${nameNode} - --accessToken${accessToken} - --connectionUrl${connectionUrl} - --metadata${metadata} - --conceptRecordId${conceptRecordId} - --depositionType${depositionType} - --depositionId${depositionId} - - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/split_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/split_parameters.json deleted file mode 100644 index dec82bc97..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/split_parameters.json +++ /dev/null @@ -1,37 +0,0 @@ - -[ - - { - "paramName":"cmp", - "paramLongName":"communityMapPath", - "paramDescription": "the path to the serialization of the community map", - "paramRequired": false - }, - - { - "paramName":"s", - "paramLongName":"sourcePath", - "paramDescription": "the path of the sequencial file to read", - "paramRequired": true - }, - { - "paramName": "out", - "paramLongName": "outputPath", - "paramDescription": "the path used to store temporary output files", - "paramRequired": true - }, - { - "paramName": "ssm", - "paramLongName": "isSparkSessionManaged", - "paramDescription": "true if the spark session is managed, false otherwise", - "paramRequired": false - }, { - "paramName":"cid", - "paramLongName":"communityId", - "paramDescription": "the id of the community to be dumped", - "paramRequired": false -} -] - - - diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/upload_zenodo.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/upload_zenodo.json deleted file mode 100644 index b02062ede..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/upload_zenodo.json +++ /dev/null @@ -1,58 +0,0 @@ - -[ - { - "paramName":"dt", - "paramLongName":"depositionType", - "paramDescription": "the type of the deposition (new, version, update)", - "paramRequired": true - }, - { - "paramName":"cri", - "paramLongName":"conceptRecordId", - "paramDescription": "The id of the concept record for a new version", - "paramRequired": false - }, - - { - "paramName":"di", - "paramLongName":"depositionId", - "paramDescription": "the id of an open deposition which has not been published", - "paramRequired": false - }, -{ -"paramName":"hdfsp", -"paramLongName":"hdfsPath", -"paramDescription": "the path of the folder tofind files to send to Zenodo", -"paramRequired": true -}, -{ -"paramName": "nn", -"paramLongName": "nameNode", -"paramDescription": "the name node", -"paramRequired": true -}, -{ -"paramName": "at", -"paramLongName": "accessToken", -"paramDescription": "the access token for the deposition", -"paramRequired": false -}, -{ -"paramName":"cu", -"paramLongName":"connectionUrl", -"paramDescription": "the url to connect to deposit", -"paramRequired": false -}, -{ -"paramName":"m", -"paramLongName":"metadata", -"paramDescription": "metadata associated to the deposition", -"paramRequired": false -}, - { - "paramName":"p", - "paramLongName":"publish", - "paramDescription": "if to publish the upload", - "paramRequired": false - } -] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/config-default.xml deleted file mode 100644 index d262cb6e0..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/config-default.xml +++ /dev/null @@ -1,30 +0,0 @@ - - - jobTracker - yarnRM - - - nameNode - hdfs://nameservice1 - - - oozie.use.system.libpath - true - - - hiveMetastoreUris - thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 - - - hiveJdbcUrl - jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000 - - - hiveDbName - openaire - - - oozie.launcher.mapreduce.user.classpath.first - true - - diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/import.txt b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/import.txt deleted file mode 100644 index bf55947d1..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/import.txt +++ /dev/null @@ -1,4 +0,0 @@ -## This is a classpath-based import file (this header is required) -dump_complete classpath eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app -dump_funder classpath eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app -dump_community classpath eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/workflow.xml deleted file mode 100644 index 2a612dec5..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/workflow.xml +++ /dev/null @@ -1,306 +0,0 @@ - - - - - singleDeposition - Indicates if it is a single community deposition - - - communityId - the id of the community to be dumped if a dump for a single community should be done - - - dumpType - the type of the dump one of {complete, community, funder} - - - onlyUpload - true if the dump is already done and should only be upload in zenodo - - - upload - true if the dump should be upload in zenodo - - - sourcePath - the source path - - - isLookUpUrl - the isLookup service endpoint - - - outputPath - the output path - - - resultAggregation - true if all the result type have to be dumped under result. false otherwise - - - accessToken - the access token used for the deposition in Zenodo - - - connectionUrl - the connection url for Zenodo - - - metadata - the metadata associated to the deposition - - - depositionType - the type of deposition we want to perform. "new" for brand new deposition, "version" for a new version of a published deposition (in this case the concept record id must be provided), "upload" to upload content to an open deposition for which we already have the deposition id (in this case the deposition id should be provided) - - - conceptRecordId - for new version, the id of the record for the old deposition - - - depositionId - the depositionId of a deposition open that has to be added content - - - organizationCommunityMap - the organization community map - - - - hiveDbName - the target hive database name - - - hiveJdbcUrl - hive server jdbc url - - - hiveMetastoreUris - hive server metastore URIs - - - sparkDriverMemory - memory for driver process - - - sparkExecutorMemory - memory for individual executor - - - sparkExecutorCores - number of cores used by single executor - - - oozieActionShareLibForSpark2 - oozie action sharelib for spark 2.* - - - spark2ExtraListeners - com.cloudera.spark.lineage.NavigatorAppListener - spark 2.* extra listeners classname - - - spark2SqlQueryExecutionListeners - com.cloudera.spark.lineage.NavigatorQueryListener - spark 2.* sql query execution listeners classname - - - spark2YarnHistoryServerAddress - spark 2.* yarn history server address - - - spark2EventLogDir - spark 2.* event log dir location - - - - - ${jobTracker} - ${nameNode} - - - mapreduce.job.queuename - ${queueName} - - - oozie.launcher.mapred.job.queue.name - ${oozieLauncherQueueName} - - - oozie.action.sharelib.for.spark - ${oozieActionShareLibForSpark2} - - - - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - ${wf:conf('onlyUpload') eq true} - - - - - - - - - - - - - - - - eu.dnetlib.dhp.oa.graph.dump.SaveCommunityMap - --outputPath${workingDir}/communityMap - --nameNode${nameNode} - --isLookUpUrl${isLookUpUrl} - --singleDeposition${singleDeposition} - --communityId${communityId} - - - - - - - - ${wf:conf('dumpType') eq "funder"} - ${wf:conf('dumpType') eq "community"} - - - - - - - - ${wf:appPath()}/dump_complete - - - - - communityMapPath - ${workingDir}/communityMap - - - outputPath - ${workingDir}/tar - - - sourcePath - ${sourcePath} - - - organizationCommunityMap - ${organizationCommunityMap} - - - isLookUpUrl - ${isLookUpUrl} - - - resultAggregation - ${resultAggregation} - - - - - - - - - - - ${wf:appPath()}/dump_community - - - - - sourcePath - ${sourcePath} - - - communityMapPath - ${workingDir}/communityMap - - - outputPath - ${workingDir}/tar - - - - - - - - - - ${wf:appPath()}/dump_funder - - - - - communityMapPath - ${workingDir}/communityMap - - - outputPath - ${workingDir}/tar - - - sourcePath - ${sourcePath} - - - dumpType - ${dumpType} - - - - - - - - - - eu.dnetlib.dhp.oa.graph.dump.MakeTar - --hdfsPath${outputPath} - --nameNode${nameNode} - --sourcePath${workingDir}/tar - - - - - - - - ${wf:conf('upload') eq true} - - - - - - - eu.dnetlib.dhp.oa.graph.dump.SendToZenodoHDFS - --hdfsPath${outputPath} - --nameNode${nameNode} - --accessToken${accessToken} - --connectionUrl${connectionUrl} - --metadata${metadata} - --conceptRecordId${conceptRecordId} - --depositionType${depositionType} - --depositionId${depositionId} - - - - - - - - diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/config-default.xml deleted file mode 100644 index e5ec3d0ae..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/config-default.xml +++ /dev/null @@ -1,30 +0,0 @@ - - - jobTracker - yarnRM - - - nameNode - hdfs://nameservice1 - - - oozie.use.system.libpath - true - - - hiveMetastoreUris - thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 - - - hiveJdbcUrl - jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000 - - - hiveDbName - openaire - - - oozie.launcher.mapreduce.user.classpath.first - true - - \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml deleted file mode 100644 index dfbe93b67..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml +++ /dev/null @@ -1,362 +0,0 @@ - - - - - sourcePath - the source path - - - outputPath - the output path - - - hiveDbName - the target hive database name - - - hiveJdbcUrl - hive server jdbc url - - - hiveMetastoreUris - hive server metastore URIs - - - sparkDriverMemory - memory for driver process - - - sparkExecutorMemory - memory for individual executor - - - sparkExecutorCores - number of cores used by single executor - - - oozieActionShareLibForSpark2 - oozie action sharelib for spark 2.* - - - spark2ExtraListeners - com.cloudera.spark.lineage.NavigatorAppListener - spark 2.* extra listeners classname - - - spark2SqlQueryExecutionListeners - com.cloudera.spark.lineage.NavigatorQueryListener - spark 2.* sql query execution listeners classname - - - spark2YarnHistoryServerAddress - spark 2.* yarn history server address - - - spark2EventLogDir - spark 2.* event log dir location - - - - - ${jobTracker} - ${nameNode} - - - mapreduce.job.queuename - ${queueName} - - - oozie.launcher.mapred.job.queue.name - ${oozieLauncherQueueName} - - - oozie.action.sharelib.for.spark - ${oozieActionShareLibForSpark2} - - - - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - - - - - - - - yarn - cluster - Dump table publication for community/funder related products - eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath}/publication - --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication - --outputPath${workingDir}/dump/publication - --communityMapPath${communityMapPath} - --dumpType${dumpType} - - - - - - - - yarn - cluster - Dump table dataset for community/funder related products - eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath}/dataset - --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset - --outputPath${workingDir}/dump/dataset - --communityMapPath${communityMapPath} - - - - - - - - yarn - cluster - Dump table ORP for community related products - eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath}/otherresearchproduct - --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct - --outputPath${workingDir}/dump/otherresearchproduct - --communityMapPath${communityMapPath} - - - - - - - - yarn - cluster - Dump table software for community related products - eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath}/software - --resultTableNameeu.dnetlib.dhp.schema.oaf.Software - --outputPath${workingDir}/dump/software - --communityMapPath${communityMapPath} - - - - - - - - - - yarn - cluster - Prepare association result subset of project info - eu.dnetlib.dhp.oa.graph.dump.community.SparkPrepareResultProject - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath} - --outputPath${workingDir}/preparedInfo - - - - - - - - - - - - - - - yarn - cluster - Extend dumped publications with information about project - eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${workingDir}/dump/publication - --outputPath${workingDir}/ext/publication - --preparedInfoPath${workingDir}/preparedInfo - - - - - - - - yarn - cluster - Extend dumped dataset with information about project - eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${workingDir}/dump/dataset - --outputPath${workingDir}/ext/dataset - --preparedInfoPath${workingDir}/preparedInfo - - - - - - - - yarn - cluster - Extend dumped ORP with information about project - eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${workingDir}/dump/otherresearchproduct - --outputPath${workingDir}/ext/orp - --preparedInfoPath${workingDir}/preparedInfo - - - - - - - - yarn - cluster - Extend dumped software with information about project - eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${workingDir}/dump/software - --outputPath${workingDir}/ext/software - --preparedInfoPath${workingDir}/preparedInfo - - - - - - - - - - yarn - cluster - Split dumped result for community - eu.dnetlib.dhp.oa.graph.dump.community.SparkSplitForCommunity - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${workingDir}/ext - --outputPath${outputPath} - --communityMapPath${communityMapPath} - - - - - - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/config-default.xml deleted file mode 100644 index e5ec3d0ae..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/config-default.xml +++ /dev/null @@ -1,30 +0,0 @@ - - - jobTracker - yarnRM - - - nameNode - hdfs://nameservice1 - - - oozie.use.system.libpath - true - - - hiveMetastoreUris - thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 - - - hiveJdbcUrl - jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000 - - - hiveDbName - openaire - - - oozie.launcher.mapreduce.user.classpath.first - true - - \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/workflow.xml deleted file mode 100644 index 7cc133323..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/workflow.xml +++ /dev/null @@ -1,539 +0,0 @@ - - - - sourcePath - the source path - - - outputPath - the output path - - - resultAggregation - true if all the result type have to be dumped under result. false otherwise - - - organizationCommunityMap - the organization community map - - - - hiveDbName - the target hive database name - - - hiveJdbcUrl - hive server jdbc url - - - hiveMetastoreUris - hive server metastore URIs - - - sparkDriverMemory - memory for driver process - - - sparkExecutorMemory - memory for individual executor - - - sparkExecutorCores - number of cores used by single executor - - - oozieActionShareLibForSpark2 - oozie action sharelib for spark 2.* - - - spark2ExtraListeners - com.cloudera.spark.lineage.NavigatorAppListener - spark 2.* extra listeners classname - - - spark2SqlQueryExecutionListeners - com.cloudera.spark.lineage.NavigatorQueryListener - spark 2.* sql query execution listeners classname - - - spark2YarnHistoryServerAddress - spark 2.* yarn history server address - - - spark2EventLogDir - spark 2.* event log dir location - - - - - ${jobTracker} - ${nameNode} - - - mapreduce.job.queuename - ${queueName} - - - oozie.launcher.mapred.job.queue.name - ${oozieLauncherQueueName} - - - oozie.action.sharelib.for.spark - ${oozieActionShareLibForSpark2} - - - - - - - - - - - - - - - - - - - - - - - yarn - cluster - Dump table publication - eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath}/publication - --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication - --outputPath${workingDir}/result/publication - --communityMapPath${communityMapPath} - - - - - - - - yarn - cluster - Dump table dataset - eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath}/dataset - --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset - --outputPath${workingDir}/result/dataset - --communityMapPath${communityMapPath} - - - - - - - - yarn - cluster - Dump table ORP - eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath}/otherresearchproduct - --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct - --outputPath${workingDir}/result/otherresearchproduct - --communityMapPath${communityMapPath} - - - - - - - - yarn - cluster - Dump table software - eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath}/software - --resultTableNameeu.dnetlib.dhp.schema.oaf.Software - --outputPath${workingDir}/result/software - --communityMapPath${communityMapPath} - - - - - - - - yarn - cluster - Dump table organization - eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath}/organization - --resultTableNameeu.dnetlib.dhp.schema.oaf.Organization - --outputPath${outputPath}/organization - --communityMapPath${communityMapPath} - - - - - - - - yarn - cluster - Dump table project - eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath}/project - --resultTableNameeu.dnetlib.dhp.schema.oaf.Project - --outputPath${outputPath}/project - --communityMapPath${communityMapPath} - - - - - - - - yarn - cluster - Dump table datasource - eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath}/datasource - --resultTableNameeu.dnetlib.dhp.schema.oaf.Datasource - --outputPath${outputPath}/datasource - --communityMapPath${workingDir}/communityMap - - - - - - - - yarn - cluster - Select valid table relation - eu.dnetlib.dhp.oa.graph.dump.complete.SparkSelectValidRelationsJob - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - --conf spark.sql.shuffle.partitions=3840 - - --sourcePath${sourcePath} - --outputPath${workingDir}/validrelation - - - - - - - - yarn - cluster - Dump table relation - eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpRelationJob - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${workingDir}/validrelation - --outputPath${workingDir}/relation/relation - --removeSet${removeSet} - - - - - - - - - - - - - - - - eu.dnetlib.dhp.oa.graph.dump.complete.CreateContextEntities - --hdfsPath${outputPath}/communities_infrastructures/communities_infrastructure.json.gz - --nameNode${nameNode} - --isLookUpUrl${isLookUpUrl} - - - - - - - - eu.dnetlib.dhp.oa.graph.dump.complete.CreateContextRelation - --hdfsPath${workingDir}/relation/context - --nameNode${nameNode} - --isLookUpUrl${isLookUpUrl} - - - - - - - - yarn - cluster - Dump table relation - eu.dnetlib.dhp.oa.graph.dump.complete.SparkOrganizationRelation - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath}/relation - --outputPath${workingDir}/relation/contextOrg - --organizationCommunityMap${organizationCommunityMap} - --communityMapPath${communityMapPath} - - - - - - - - - - - - - - - - - yarn - cluster - Extract Relations from publication - eu.dnetlib.dhp.oa.graph.dump.complete.SparkExtractRelationFromEntities - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath}/publication - --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication - --outputPath${workingDir}/relation/publication - --communityMapPath${communityMapPath} - - - - - - - - yarn - cluster - Dump table dataset - eu.dnetlib.dhp.oa.graph.dump.complete.SparkExtractRelationFromEntities - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath}/dataset - --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset - --outputPath${workingDir}/relation/dataset - --communityMapPath${communityMapPath} - - - - - - - - yarn - cluster - Dump table ORP - eu.dnetlib.dhp.oa.graph.dump.complete.SparkExtractRelationFromEntities - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath}/otherresearchproduct - --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct - --outputPath${workingDir}/relation/orp - --communityMapPath${communityMapPath} - - - - - - - - yarn - cluster - Dump table software - eu.dnetlib.dhp.oa.graph.dump.complete.SparkExtractRelationFromEntities - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath}/software - --resultTableNameeu.dnetlib.dhp.schema.oaf.Software - --outputPath${workingDir}/relation/software - --communityMapPath${communityMapPath} - - - - - - - - - - yarn - cluster - Collect Results and Relations and put them in the right path - eu.dnetlib.dhp.oa.graph.dump.complete.SparkCollectAndSave - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${workingDir} - --outputPath${outputPath} - --resultAggregation${resultAggregation} - - - - - - - - - Sub-workflow dump complete failed with error message ${wf:errorMessage()} - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/config-default.xml deleted file mode 100644 index e5ec3d0ae..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/config-default.xml +++ /dev/null @@ -1,30 +0,0 @@ - - - jobTracker - yarnRM - - - nameNode - hdfs://nameservice1 - - - oozie.use.system.libpath - true - - - hiveMetastoreUris - thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 - - - hiveJdbcUrl - jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000 - - - hiveDbName - openaire - - - oozie.launcher.mapreduce.user.classpath.first - true - - \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/workflow.xml deleted file mode 100644 index 2c05256cf..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/workflow.xml +++ /dev/null @@ -1,255 +0,0 @@ - - - - - sourcePath - the source path - - - outputPath - the output path - - - hiveDbName - the target hive database name - - - hiveJdbcUrl - hive server jdbc url - - - hiveMetastoreUris - hive server metastore URIs - - - sparkDriverMemory - memory for driver process - - - sparkExecutorMemory - memory for individual executor - - - sparkExecutorCores - number of cores used by single executor - - - oozieActionShareLibForSpark2 - oozie action sharelib for spark 2.* - - - spark2ExtraListeners - com.cloudera.spark.lineage.NavigatorAppListener - spark 2.* extra listeners classname - - - spark2SqlQueryExecutionListeners - com.cloudera.spark.lineage.NavigatorQueryListener - spark 2.* sql query execution listeners classname - - - spark2YarnHistoryServerAddress - spark 2.* yarn history server address - - - spark2EventLogDir - spark 2.* event log dir location - - - - - ${jobTracker} - ${nameNode} - - - mapreduce.job.queuename - ${queueName} - - - oozie.launcher.mapred.job.queue.name - ${oozieLauncherQueueName} - - - oozie.action.sharelib.for.spark - ${oozieActionShareLibForSpark2} - - - - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - yarn - cluster - Prepare association result subset of project info - eu.dnetlib.dhp.oa.graph.dump.community.SparkPrepareResultProject - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath} - --outputPath${workingDir}/preparedInfo - - - - - - - - - - - - - - - - yarn - cluster - Dump funder results - eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath}/publication - --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication - --outputPath${workingDir}/result/publication - --graphPath${workingDir}/preparedInfo - --communityMapPath${communityMapPath} - - - - - - - - yarn - cluster - Dump funder results - eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath}/dataset - --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset - --outputPath${workingDir}/result/dataset - --graphPath${workingDir}/preparedInfo - --communityMapPath${communityMapPath} - - - - - - - - yarn - cluster - Dump funder results - eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath}/otherresearchproduct - --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct - --outputPath${workingDir}/result/otherresearchproduct - --graphPath${workingDir}/preparedInfo - --communityMapPath${communityMapPath} - - - - - - - - yarn - cluster - Dump funder results - eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath}/software - --resultTableNameeu.dnetlib.dhp.schema.oaf.Software - --outputPath${workingDir}/result/software - --graphPath${workingDir}/preparedInfo - --communityMapPath${communityMapPath} - - - - - - - - - - yarn - cluster - Dump funder results - eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkDumpFunderResults - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${workingDir}/result - --outputPath${outputPath} - - - - - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java index 472d3781d..e206c7c5a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java @@ -5,7 +5,6 @@ import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; import java.util.List; -import java.util.Locale; import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; @@ -21,19 +20,9 @@ import org.junit.jupiter.api.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import com.fasterxml.jackson.core.JsonProcessingException; import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.oa.graph.dump.Constants; -import eu.dnetlib.dhp.oa.graph.dump.DumpJobTest; -import eu.dnetlib.dhp.oa.graph.dump.DumpProducts; -import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.dump.oaf.Instance; -import eu.dnetlib.dhp.schema.dump.oaf.OpenAccessRoute; -import eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult; import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.Software; import eu.dnetlib.dhp.schema.oaf.StructuredProperty; public class CleanContextTest { @@ -48,11 +37,11 @@ public class CleanContextTest { @BeforeAll public static void beforeAll() throws IOException { - workingDir = Files.createTempDirectory(DumpJobTest.class.getSimpleName()); + workingDir = Files.createTempDirectory(CleanContextTest.class.getSimpleName()); log.info("using work dir {}", workingDir); SparkConf conf = new SparkConf(); - conf.setAppName(DumpJobTest.class.getSimpleName()); + conf.setAppName(CleanContextTest.class.getSimpleName()); conf.setMaster("local[*]"); conf.set("spark.driver.host", "localhost"); @@ -63,7 +52,7 @@ public class CleanContextTest { spark = SparkSession .builder() - .appName(DumpJobTest.class.getSimpleName()) + .appName(CleanContextTest.class.getSimpleName()) .config(conf) .getOrCreate(); } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java deleted file mode 100644 index 7300ce860..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java +++ /dev/null @@ -1,967 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.Arrays; -import java.util.List; - -import org.apache.commons.io.FileUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.Row; -import org.apache.spark.sql.SparkSession; -import org.junit.jupiter.api.*; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.core.JsonProcessingException; -import com.fasterxml.jackson.databind.ObjectMapper; -import com.google.gson.Gson; - -import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.dump.oaf.Instance; -import eu.dnetlib.dhp.schema.dump.oaf.OpenAccessRoute; -import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; -import eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult; -import eu.dnetlib.dhp.schema.oaf.Dataset; -import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.Software; - -//@Disabled -public class DumpJobTest { - - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private static SparkSession spark; - - private static Path workingDir; - - private static final Logger log = LoggerFactory.getLogger(DumpJobTest.class); - - private static final CommunityMap map = new CommunityMap(); - - static { - map.put("egi", "EGI Federation"); - map.put("fet-fp7", "FET FP7"); - map.put("fet-h2020", "FET H2020"); - map.put("clarin", "CLARIN"); - map.put("fam", "Fisheries and Aquaculture Management"); - map.put("ni", "Neuroinformatics"); - map.put("mes", "European Marine Scinece"); - map.put("instruct", "Instruct-Eric"); - map.put("rda", "Research Data Alliance"); - map.put("elixir-gr", "ELIXIR GR"); - map.put("aginfra", "Agricultural and Food Sciences"); - map.put("dariah", "DARIAH EU"); - map.put("risis", "RISI"); - map.put("ee", "SDSN - Greece"); - map.put("oa-pg", "EC Post-Grant Open Access Pilot"); - map.put("beopen", "Transport Research"); - map.put("euromarine", "Euromarine"); - map.put("ifremer", "Ifremer"); - map.put("dh-ch", "Digital Humanities and Cultural Heritage"); - map.put("science-innovation-policy", "Science and Innovation Policy Studies"); - map.put("covid-19", "COVID-19"); - map.put("enrmaps", "Energy Research"); - map.put("epos", "EPOS"); - - } - - List communityMap = Arrays - .asList( - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - ""); - - private static final String XQUERY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') " - + - " where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " + - " return " + - " " + - "{$x//CONFIGURATION/context/@id}" + - "{$x//CONFIGURATION/context/@label}" + - ""; - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files.createTempDirectory(DumpJobTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - - SparkConf conf = new SparkConf(); - conf.setAppName(DumpJobTest.class.getSimpleName()); - - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - - spark = SparkSession - .builder() - .appName(DumpJobTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Test - public void testMap() { - System.out.println(new Gson().toJson(map)); - } - - @Test - public void testPublicationDump() { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication_extendedinstance") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - DumpProducts dump = new DumpProducts(); - dump - .run( - // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, - false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, - GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType()); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(GraphResult.class)); - - Assertions.assertEquals(1, verificationDataset.count()); - - GraphResult gr = verificationDataset.first(); - - Assertions.assertEquals(6, gr.getAuthor().size()); - Assertions - .assertTrue( - gr - .getAuthor() - .stream() - .anyMatch( - a -> a.getFullname().equals("Nikolaidou,Charitini") && - a.getName().equals("Charitini") && a.getSurname().equals("Nikolaidou") - && a.getRank() == 1 && a.getPid() == null)); - - Assertions - .assertTrue( - gr - .getAuthor() - .stream() - .anyMatch( - a -> a.getFullname().equals("Votsi,Nefta") && - a.getName().equals("Nefta") && a.getSurname().equals("Votsi") - && a.getRank() == 2 && a.getPid().getId().getScheme().equals(ModelConstants.ORCID) - && a.getPid().getId().getValue().equals("0000-0001-6651-1178") - && a.getPid().getProvenance() != null)); - - Assertions - .assertTrue( - gr - .getAuthor() - .stream() - .anyMatch( - a -> a.getFullname().equals("Sgardelis,Steanos") && - a.getName().equals("Steanos") && a.getSurname().equals("Sgardelis") - && a.getRank() == 3 && a.getPid().getId().getScheme().equals(ModelConstants.ORCID_PENDING) - && a.getPid().getId().getValue().equals("0000-0001-6651-1178") - && a.getPid().getProvenance() != null)); - - Assertions - .assertTrue( - gr - .getAuthor() - .stream() - .anyMatch( - a -> a.getFullname().equals("Halley,John") && - a.getName().equals("John") && a.getSurname().equals("Halley") - && a.getRank() == 4 && a.getPid() == null)); - - Assertions - .assertTrue( - gr - .getAuthor() - .stream() - .anyMatch( - a -> a.getFullname().equals("Pantis,John") && - a.getName().equals("John") && a.getSurname().equals("Pantis") - && a.getRank() == 5 && a.getPid().getId().getScheme().equals(ModelConstants.ORCID) - && a.getPid().getId().getValue().equals("0000-0001-6651-1178") - && a.getPid().getProvenance() != null)); - - Assertions - .assertTrue( - gr - .getAuthor() - .stream() - .anyMatch( - a -> a.getFullname().equals("Tsiafouli,Maria") && - a.getName().equals("Maria") && a.getSurname().equals("Tsiafouli") - && a.getRank() == 6 && a.getPid().getId().getScheme().equals(ModelConstants.ORCID_PENDING) - && a.getPid().getId().getValue().equals("0000-0001-6651-1178") - && a.getPid().getProvenance() != null)); - - Assertions.assertEquals("publication", gr.getType()); - - Assertions.assertEquals("eng", gr.getLanguage().getCode()); - Assertions.assertEquals("English", gr.getLanguage().getLabel()); - - Assertions.assertEquals(1, gr.getCountry().size()); - Assertions.assertEquals("IT", gr.getCountry().get(0).getCode()); - Assertions.assertEquals("Italy", gr.getCountry().get(0).getLabel()); - Assertions.assertTrue(gr.getCountry().get(0).getProvenance() == null); - - Assertions.assertEquals(12, gr.getSubjects().size()); - Assertions - .assertTrue( - gr - .getSubjects() - .stream() - .anyMatch( - s -> s.getSubject().getValue().equals("Ecosystem Services hotspots") - && s.getSubject().getScheme().equals("ACM") && s.getProvenance() != null && - s.getProvenance().getProvenance().equals("sysimport:crosswalk:repository"))); - Assertions - .assertTrue( - gr - .getSubjects() - .stream() - .anyMatch( - s -> s.getSubject().getValue().equals("Natura 2000") - && s.getSubject().getScheme().equals("") && s.getProvenance() != null && - s.getProvenance().getProvenance().equals("sysimport:crosswalk:repository"))); - - Assertions - .assertEquals( - "Ecosystem Service capacity is higher in areas of multiple designation types", - gr.getMaintitle()); - - Assertions.assertEquals(null, gr.getSubtitle()); - - Assertions.assertEquals(1, gr.getDescription().size()); - - Assertions - .assertTrue( - gr - .getDescription() - .get(0) - .startsWith("The implementation of the Ecosystem Service (ES) concept into practice")); - Assertions - .assertTrue( - gr - .getDescription() - .get(0) - .endsWith( - "start complying with new standards and demands for nature conservation and environmental management.")); - - Assertions.assertEquals("2017-01-01", gr.getPublicationdate()); - - Assertions.assertEquals("Pensoft Publishers", gr.getPublisher()); - - Assertions.assertEquals(null, gr.getEmbargoenddate()); - - Assertions.assertEquals(1, gr.getSource().size()); - Assertions.assertEquals("One Ecosystem 2: e13718", gr.getSource().get(0)); - - Assertions.assertEquals(1, gr.getFormat().size()); - Assertions.assertEquals("text/html", gr.getFormat().get(0)); - - Assertions.assertEquals(0, gr.getContributor().size()); - - Assertions.assertEquals(0, gr.getCoverage().size()); - - Assertions.assertEquals(ModelConstants.ACCESS_RIGHT_OPEN, gr.getBestaccessright().getLabel()); - Assertions - .assertEquals( - Constants.accessRightsCoarMap.get(ModelConstants.ACCESS_RIGHT_OPEN), gr.getBestaccessright().getCode()); - - Assertions.assertEquals("One Ecosystem", gr.getContainer().getName()); - Assertions.assertEquals("2367-8194", gr.getContainer().getIssnOnline()); - Assertions.assertEquals("", gr.getContainer().getIssnPrinted()); - Assertions.assertEquals("", gr.getContainer().getIssnLinking()); - - Assertions.assertTrue(null == gr.getDocumentationUrl() || gr.getDocumentationUrl().size() == 0); - - Assertions.assertTrue(null == gr.getCodeRepositoryUrl()); - - Assertions.assertEquals(null, gr.getProgrammingLanguage()); - - Assertions.assertTrue(null == gr.getContactperson() || gr.getContactperson().size() == 0); - - Assertions.assertTrue(null == gr.getContactgroup() || gr.getContactgroup().size() == 0); - - Assertions.assertTrue(null == gr.getTool() || gr.getTool().size() == 0); - - Assertions.assertEquals(null, gr.getSize()); - - Assertions.assertEquals(null, gr.getVersion()); - - Assertions.assertTrue(null == gr.getGeolocation() || gr.getGeolocation().size() == 0); - - Assertions.assertEquals("50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2", gr.getId()); - - Assertions.assertEquals(1, gr.getOriginalId().size()); - Assertions - .assertTrue( - gr.getOriginalId().contains("10.3897/oneeco.2.e13718")); - - Assertions.assertEquals(1, gr.getPid().size()); - Assertions - .assertTrue( - gr.getPid().get(0).getScheme().equals("doi") - && gr.getPid().get(0).getValue().equals("10.1016/j.triboint.2014.05.004")); - - Assertions.assertEquals("2020-03-23T00:20:51.392Z", gr.getDateofcollection()); - - Assertions.assertEquals(1, gr.getInstance().size()); - - Instance instance = gr.getInstance().get(0); - Assertions.assertEquals(0, instance.getPid().size()); - Assertions.assertEquals(1, instance.getAlternateIdentifier().size()); - Assertions - .assertTrue( - instance.getAlternateIdentifier().get(0).getScheme().equals("doi") - && instance.getAlternateIdentifier().get(0).getValue().equals("10.3897/oneeco.2.e13718")); - Assertions.assertEquals(null, instance.getLicense()); - Assertions - .assertTrue( - instance - .getAccessright() - .getCode() - .equals( - Constants.accessRightsCoarMap - .get(ModelConstants.ACCESS_RIGHT_OPEN))); - Assertions.assertTrue(instance.getAccessright().getLabel().equals(ModelConstants.ACCESS_RIGHT_OPEN)); - Assertions.assertTrue(instance.getAccessright().getOpenAccessRoute().equals(OpenAccessRoute.green)); - Assertions.assertTrue(instance.getType().equals("Article")); - Assertions.assertEquals(2, instance.getUrl().size()); - Assertions - .assertTrue( - instance.getUrl().contains("https://doi.org/10.3897/oneeco.2.e13718") - && instance.getUrl().contains("https://oneecosystem.pensoft.net/article/13718/")); - Assertions.assertEquals("2017-01-01", instance.getPublicationdate()); - Assertions.assertEquals(null, instance.getArticleprocessingcharge()); - Assertions.assertEquals("peerReviewed", instance.getRefereed()); - } - - @Test - public void testDatasetDump() { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/dataset_extendedinstance") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - DumpProducts dump = new DumpProducts(); - dump - .run( - false, sourcePath, workingDir.toString() + "/result", - communityMapPath, Dataset.class, - GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType()); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(GraphResult.class)); - - Assertions.assertEquals(1, verificationDataset.count()); - - Assertions.assertEquals(1, verificationDataset.filter("type = 'dataset'").count()); - - // the common fields in the result have been already checked. Now checking only - // community specific fields - - GraphResult gr = verificationDataset.first(); - - Assertions.assertEquals(2, gr.getGeolocation().size()); - Assertions.assertEquals(2, gr.getGeolocation().stream().filter(gl -> gl.getBox().equals("")).count()); - Assertions.assertEquals(1, gr.getGeolocation().stream().filter(gl -> gl.getPlace().equals("")).count()); - Assertions.assertEquals(1, gr.getGeolocation().stream().filter(gl -> gl.getPoint().equals("")).count()); - Assertions - .assertEquals( - 1, - gr - .getGeolocation() - .stream() - .filter(gl -> gl.getPlace().equals("18 York St, Ottawa, ON K1N 5S6; Ottawa; Ontario; Canada")) - .count()); - Assertions - .assertEquals( - 1, gr.getGeolocation().stream().filter(gl -> gl.getPoint().equals("45.427242 -75.693904")).count()); - Assertions - .assertEquals( - 1, - gr - .getGeolocation() - .stream() - .filter(gl -> gl.getPoint().equals("") && !gl.getPlace().equals("")) - .count()); - Assertions - .assertEquals( - 1, - gr - .getGeolocation() - .stream() - .filter(gl -> !gl.getPoint().equals("") && gl.getPlace().equals("")) - .count()); - - Assertions.assertEquals("1024Gb", gr.getSize()); - - Assertions.assertEquals("1.01", gr.getVersion()); - - Assertions.assertEquals(null, gr.getContainer()); - Assertions.assertEquals(null, gr.getCodeRepositoryUrl()); - Assertions.assertEquals(null, gr.getProgrammingLanguage()); - Assertions.assertEquals(null, gr.getDocumentationUrl()); - Assertions.assertEquals(null, gr.getContactperson()); - Assertions.assertEquals(null, gr.getContactgroup()); - Assertions.assertEquals(null, gr.getTool()); - - } - - @Test - public void testSoftwareDump() { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/software_extendedinstance") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - DumpProducts dump = new DumpProducts(); - dump - .run( - false, sourcePath, workingDir.toString() + "/result", - communityMapPath, Software.class, - GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType()); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(GraphResult.class)); - - Assertions.assertEquals(1, verificationDataset.count()); - - Assertions.assertEquals(1, verificationDataset.filter("type = 'software'").count()); - - GraphResult gr = verificationDataset.first(); - - Assertions.assertEquals(2, gr.getDocumentationUrl().size()); - Assertions.assertTrue(gr.getDocumentationUrl().contains("doc_url_1")); - Assertions.assertTrue(gr.getDocumentationUrl().contains("doc_url_2")); - - Assertions.assertEquals("code_repo", gr.getCodeRepositoryUrl()); - - Assertions.assertEquals("perl", gr.getProgrammingLanguage()); - - Assertions.assertEquals(null, gr.getContainer()); - Assertions.assertEquals(null, gr.getContactperson()); - Assertions.assertEquals(null, gr.getContactgroup()); - Assertions.assertEquals(null, gr.getTool()); - Assertions.assertEquals(null, gr.getGeolocation()); - Assertions.assertEquals(null, gr.getSize()); - Assertions.assertEquals(null, gr.getVersion()); - - } - - @Test - public void testOrpDump() { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/orp_extendedinstance") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - DumpProducts dump = new DumpProducts(); - dump - .run( - false, sourcePath, workingDir.toString() + "/result", - communityMapPath, OtherResearchProduct.class, - GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType()); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(GraphResult.class)); - - Assertions.assertEquals(1, verificationDataset.count()); - - Assertions.assertEquals(1, verificationDataset.filter("type = 'other'").count()); - - GraphResult gr = verificationDataset.first(); - - Assertions.assertEquals(2, gr.getContactperson().size()); - Assertions.assertTrue(gr.getContactperson().contains(("contact_person1"))); - Assertions.assertTrue(gr.getContactperson().contains(("contact_person2"))); - - Assertions.assertEquals(1, gr.getContactgroup().size()); - Assertions.assertTrue(gr.getContactgroup().contains(("contact_group"))); - - Assertions.assertEquals(2, gr.getTool().size()); - Assertions.assertTrue(gr.getTool().contains("tool1")); - Assertions.assertTrue(gr.getTool().contains("tool2")); - - Assertions.assertEquals(null, gr.getContainer()); - Assertions.assertEquals(null, gr.getDocumentationUrl()); - Assertions.assertEquals(null, gr.getCodeRepositoryUrl()); - Assertions.assertEquals(null, gr.getProgrammingLanguage()); - Assertions.assertEquals(null, gr.getGeolocation()); - Assertions.assertEquals(null, gr.getSize()); - Assertions.assertEquals(null, gr.getVersion()); - - } - - @Test - public void testPublicationDumpCommunity() throws JsonProcessingException { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication_extendedinstance") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - DumpProducts dump = new DumpProducts(); - dump - .run( - false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, - CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - Assertions.assertEquals(1, verificationDataset.count()); - - Assertions.assertEquals(1, verificationDataset.filter("type = 'publication'").count()); - - // the common fields in the result have been already checked. Now checking only - // community specific fields - - CommunityResult cr = verificationDataset.first(); - - Assertions.assertEquals(1, cr.getContext().size()); - Assertions.assertEquals("dh-ch", cr.getContext().get(0).getCode()); - Assertions.assertEquals("Digital Humanities and Cultural Heritage", cr.getContext().get(0).getLabel()); - Assertions.assertEquals(1, cr.getContext().get(0).getProvenance().size()); - Assertions.assertEquals("Inferred by OpenAIRE", cr.getContext().get(0).getProvenance().get(0).getProvenance()); - Assertions.assertEquals("0.9", cr.getContext().get(0).getProvenance().get(0).getTrust()); - - Assertions.assertEquals(1, cr.getCollectedfrom().size()); - Assertions - .assertEquals("10|openaire____::fdc7e0400d8c1634cdaf8051dbae23db", cr.getCollectedfrom().get(0).getKey()); - Assertions.assertEquals("Pensoft", cr.getCollectedfrom().get(0).getValue()); - - Assertions.assertEquals(1, cr.getInstance().size()); - Assertions - .assertEquals( - "10|openaire____::fdc7e0400d8c1634cdaf8051dbae23db", - cr.getInstance().get(0).getCollectedfrom().getKey()); - Assertions.assertEquals("Pensoft", cr.getInstance().get(0).getCollectedfrom().getValue()); - Assertions - .assertEquals( - "10|openaire____::e707e544b9a5bd23fc27fbfa65eb60dd", cr.getInstance().get(0).getHostedby().getKey()); - Assertions.assertEquals("One Ecosystem", cr.getInstance().get(0).getHostedby().getValue()); - - } - - @Test - public void testDataset() { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/dataset.json") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - DumpProducts dump = new DumpProducts(); - dump - .run( - false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, - CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - Assertions.assertEquals(90, verificationDataset.count()); - - Assertions - .assertTrue( - verificationDataset.filter("bestAccessright.code = 'c_abf2'").count() == verificationDataset - .filter("bestAccessright.code = 'c_abf2' and bestAccessright.label = 'OPEN'") - .count()); - - Assertions - .assertTrue( - verificationDataset.filter("bestAccessright.code = 'c_16ec'").count() == verificationDataset - .filter("bestAccessright.code = 'c_16ec' and bestAccessright.label = 'RESTRICTED'") - .count()); - - Assertions - .assertTrue( - verificationDataset.filter("bestAccessright.code = 'c_14cb'").count() == verificationDataset - .filter("bestAccessright.code = 'c_14cb' and bestAccessright.label = 'CLOSED'") - .count()); - - Assertions - .assertTrue( - verificationDataset.filter("bestAccessright.code = 'c_f1cf'").count() == verificationDataset - .filter("bestAccessright.code = 'c_f1cf' and bestAccessright.label = 'EMBARGO'") - .count()); - - Assertions.assertTrue(verificationDataset.filter("size(context) > 0").count() == 90); - - Assertions.assertTrue(verificationDataset.filter("type = 'dataset'").count() == 90); - - } - - @Test - public void testDataset2All() { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/dataset_cleaned") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - DumpProducts dump = new DumpProducts(); - dump - .run( - // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, - false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, - GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType()); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult.class)); - - Assertions.assertEquals(5, verificationDataset.count()); - - } - - @Test - public void testDataset2Communities() { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/dataset_cleaned") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - DumpProducts dump = new DumpProducts(); - dump - .run( - false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, - CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - Assertions.assertEquals(0, verificationDataset.count()); - - } - - @Test - public void testPublication() { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication.json") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - DumpProducts dump = new DumpProducts(); - dump - .run( - // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, - false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, - CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - Assertions.assertEquals(74, verificationDataset.count()); - verificationDataset.show(false); - - Assertions.assertEquals(74, verificationDataset.filter("type = 'publication'").count()); - - } - - @Test - public void testSoftware() { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/software.json") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - DumpProducts dump = new DumpProducts(); - dump - .run( - // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Software.class, - false, sourcePath, workingDir.toString() + "/result", communityMapPath, Software.class, - CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - Assertions.assertEquals(6, verificationDataset.count()); - - Assertions.assertEquals(6, verificationDataset.filter("type = 'software'").count()); - - } - - @Test - public void testORP() { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/orp.json") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - DumpProducts dump = new DumpProducts(); - dump - .run( - // false, sourcePath, workingDir.toString() + "/result", communityMapPath, OtherResearchProduct.class, - false, sourcePath, workingDir.toString() + "/result", communityMapPath, OtherResearchProduct.class, - CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - Assertions.assertEquals(3, verificationDataset.count()); - - Assertions.assertEquals(3, verificationDataset.filter("type = 'other'").count()); - - } - - @Test - public void testRecord() { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/singelRecord_pub.json") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - DumpProducts dump = new DumpProducts(); - dump - .run( - false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, - CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - Assertions.assertEquals(2, verificationDataset.count()); - verificationDataset.show(false); - - Assertions.assertEquals(2, verificationDataset.filter("type = 'publication'").count()); - - } - - @Test - public void testArticlePCA() { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication_pca") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - DumpProducts dump = new DumpProducts(); - dump - .run( - false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, - GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType()); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(GraphResult.class)); - - Assertions.assertEquals(23, verificationDataset.count()); - - Assertions.assertEquals(23, verificationDataset.filter("type = 'publication'").count()); - - verificationDataset.createOrReplaceTempView("check"); - - org.apache.spark.sql.Dataset temp = spark - .sql( - "select id " + - "from check " + - "lateral view explode (instance) i as inst " + - "where inst.articleprocessingcharge is not null"); - - Assertions.assertTrue(temp.count() == 2); - - Assertions.assertTrue(temp.filter("id = '50|datacite____::05c611fdfc93d7a2a703d1324e28104a'").count() == 1); - - Assertions.assertTrue(temp.filter("id = '50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8'").count() == 1); - - temp = spark - .sql( - "select id, inst.articleprocessingcharge.amount, inst.articleprocessingcharge.currency " + - "from check " + - "lateral view explode (instance) i as inst " + - "where inst.articleprocessingcharge is not null"); - - Assertions - .assertEquals( - "3131.64", - temp - .filter("id = '50|datacite____::05c611fdfc93d7a2a703d1324e28104a'") - .collectAsList() - .get(0) - .getString(1)); - Assertions - .assertEquals( - "EUR", - temp - .filter("id = '50|datacite____::05c611fdfc93d7a2a703d1324e28104a'") - .collectAsList() - .get(0) - .getString(2)); - - Assertions - .assertEquals( - "2578.35", - temp - .filter("id = '50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8'") - .collectAsList() - .get(0) - .getString(1)); - Assertions - .assertEquals( - "EUR", - temp - .filter("id = '50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8'") - .collectAsList() - .get(0) - .getString(2)); - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/GenerateJsonSchema.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/GenerateJsonSchema.java deleted file mode 100644 index 2cc53027e..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/GenerateJsonSchema.java +++ /dev/null @@ -1,28 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump; - -import org.junit.jupiter.api.Disabled; -import org.junit.jupiter.api.Test; - -import com.fasterxml.jackson.databind.JsonNode; -import com.github.victools.jsonschema.generator.*; - -import eu.dnetlib.dhp.schema.dump.oaf.graph.*; - -//@Disabled -class GenerateJsonSchema { - - @Test - void generateSchema() { - SchemaGeneratorConfigBuilder configBuilder = new SchemaGeneratorConfigBuilder(SchemaVersion.DRAFT_7, - OptionPreset.PLAIN_JSON) - .with(Option.SCHEMA_VERSION_INDICATOR) - .without(Option.NONPUBLIC_NONSTATIC_FIELDS_WITHOUT_GETTERS); - configBuilder.forFields().withDescriptionResolver(field -> "Description of " + field.getDeclaredName()); - SchemaGeneratorConfig config = configBuilder.build(); - SchemaGenerator generator = new SchemaGenerator(config); - JsonNode jsonSchema = generator.generateSchema(GraphResult.class); - - System.out.println(jsonSchema.toString()); - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/MakeTarTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/MakeTarTest.java deleted file mode 100644 index 41b906e58..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/MakeTarTest.java +++ /dev/null @@ -1,60 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump; - -import java.io.IOException; -import java.nio.file.Files; - -import org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.*; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.Disabled; -import org.junit.jupiter.api.Test; - -@Disabled -public class MakeTarTest { - private static String workingDir; - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory(MakeTarTest.class.getSimpleName()) - .toString(); - } - - @Test - void testTar() throws IOException { - LocalFileSystem fs = FileSystem.getLocal(new Configuration()); - - fs - .copyFromLocalFile( - false, new Path(getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/ni") - .getPath()), - new Path(workingDir + "/zenodo/ni/part-00000")); - - fs - .copyFromLocalFile( - false, new Path(getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/egi") - .getPath()), - new Path(workingDir + "/zenodo/ni/part-00001")); - - fs - .copyFromLocalFile( - false, new Path(getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/dh-ch") - .getPath()), - new Path(workingDir + "/zenodo/dh-ch/part-00000")); - fs - .copyFromLocalFile( - false, new Path(getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/science-innovation-policy") - .getPath()), - new Path(workingDir + "/zenodo/ni/part-00002")); - - String inputPath = workingDir + "/zenodo/"; - - MakeTar.makeTArArchive(fs, inputPath, "/tmp/out", 0); - - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java deleted file mode 100644 index f3b7246b1..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java +++ /dev/null @@ -1,347 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump; - -import static org.junit.jupiter.api.Assertions.assertEquals; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; - -import org.apache.commons.io.FileUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.Row; -import org.apache.spark.sql.SparkSession; -import org.junit.jupiter.api.AfterAll; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.Test; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.oa.graph.dump.community.ResultProject; -import eu.dnetlib.dhp.oa.graph.dump.community.SparkPrepareResultProject; - -public class PrepareResultProjectJobTest { - - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private static SparkSession spark; - - private static Path workingDir; - - private static final Logger log = LoggerFactory - .getLogger(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class); - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - - SparkConf conf = new SparkConf(); - conf.setAppName(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class.getSimpleName()); - - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - - spark = SparkSession - .builder() - .appName(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Test - void testNoMatch() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/no_match") - .getPath(); - - SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); - - assertEquals(0, verificationDataset.count()); - - } - - @Test - void testMatchOne() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_one") - .getPath(); - - SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); - - assertEquals(1, verificationDataset.count()); - - assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); - - verificationDataset.createOrReplaceTempView("table"); - - Dataset check = spark - .sql( - "Select projList.provenance.provenance " + - "from table " + - "lateral view explode (projectsList) pl as projList"); - - assertEquals(1, check.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); - - verificationDataset.show(false); - - } - - @Test - void testMatch() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match") - .getPath(); - - SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); - - assertEquals(2, verificationDataset.count()); - - assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); - assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); - - verificationDataset.createOrReplaceTempView("dataset"); - - String query = "select resultId, MyT.id project , MyT.title title, MyT.acronym acronym , MyT.provenance.provenance provenance " - + "from dataset " - + "lateral view explode(projectsList) p as MyT "; - - org.apache.spark.sql.Dataset resultExplodedProvenance = spark.sql(query); - assertEquals(3, resultExplodedProvenance.count()); - assertEquals( - 2, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") - .count()); - - assertEquals( - 1, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") - .count()); - - assertEquals( - 2, - resultExplodedProvenance - .filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'") - .count()); - - assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") - .count()); - - assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") - .count()); - - assertEquals( - 1, - resultExplodedProvenance - .filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'") - .count()); - - assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::03376222b28a3aebf2730ac514818d04' and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") - .count()); - - assertEquals( - 3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); - - } - - @Test - public void testMatchValidated() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_validatedRels") - .getPath(); - - SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); - - assertEquals(2, verificationDataset.count()); - - assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); - assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); - - verificationDataset.createOrReplaceTempView("dataset"); - - String query = "select resultId, MyT.id project , MyT.title title, MyT.acronym acronym , MyT.provenance.provenance provenance, " - + - "MyT.validated.validatedByFunder, MyT.validated.validationDate " - + "from dataset " - + "lateral view explode(projectsList) p as MyT "; - - org.apache.spark.sql.Dataset resultExplodedProvenance = spark.sql(query); - assertEquals(3, resultExplodedProvenance.count()); - assertEquals(3, resultExplodedProvenance.filter("validatedByFunder = true").count()); - assertEquals( - 2, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") - .count()); - - assertEquals( - 1, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") - .count()); - - assertEquals( - 2, - resultExplodedProvenance - .filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'") - .count()); - - assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + - "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + - "and validatedByFunder = true " + - "and validationDate = '2021-08-06'") - .count()); - - assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + - "and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80' " + - "and validatedByFunder = true and validationDate = '2021-08-04'") - .count()); - - assertEquals( - 1, - resultExplodedProvenance - .filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'") - .count()); - - assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::03376222b28a3aebf2730ac514818d04' " + - "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + - "and validatedByFunder = true and validationDate = '2021-08-05'") - .count()); - - assertEquals( - 3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); - - } - - @Test - void testMatchx() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match") - .getPath(); - - SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); - - tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r))); - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystemTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystemTest.java deleted file mode 100644 index 8391c8963..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystemTest.java +++ /dev/null @@ -1,117 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump; - -import static org.mockito.Mockito.lenient; - -import java.util.Arrays; -import java.util.List; -import java.util.Map; - -import org.dom4j.DocumentException; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeEach; -import org.junit.jupiter.api.Test; -import org.junit.jupiter.api.extension.ExtendWith; -import org.mockito.Mock; -import org.mockito.junit.jupiter.MockitoExtension; -import org.xml.sax.SAXException; - -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; - -@ExtendWith(MockitoExtension.class) -class QueryInformationSystemTest { - - private static final String XQUERY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') " - + - " where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " + - " and ($x//context/param[./@name = 'status']/text() = 'all') " - + - " return " + - " " + - "{$x//CONFIGURATION/context/@id}" + - "{$x//CONFIGURATION/context/@label}" + - ""; - - List communityMap = Arrays - .asList( - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - ""); - - @Mock - private ISLookUpService isLookUpService; - - private QueryInformationSystem queryInformationSystem; - - private Map map; - - @BeforeEach - public void setUp() throws ISLookUpException, DocumentException, SAXException { - lenient().when(isLookUpService.quickSearchProfile(XQUERY)).thenReturn(communityMap); - queryInformationSystem = new QueryInformationSystem(); - queryInformationSystem.setIsLookUp(isLookUpService); - map = queryInformationSystem.getCommunityMap(false, null); - } - - @Test - void testSize() throws ISLookUpException { - - Assertions.assertEquals(23, map.size()); - } - - @Test - void testContent() { - Assertions.assertTrue(map.containsKey("egi") && map.get("egi").equals("EGI Federation")); - - Assertions.assertTrue(map.containsKey("fet-fp7") && map.get("fet-fp7").equals("FET FP7")); - Assertions.assertTrue(map.containsKey("fet-h2020") && map.get("fet-h2020").equals("FET H2020")); - Assertions.assertTrue(map.containsKey("clarin") && map.get("clarin").equals("CLARIN")); - Assertions.assertTrue(map.containsKey("rda") && map.get("rda").equals("Research Data Alliance")); - Assertions.assertTrue(map.containsKey("ee") && map.get("ee").equals("SDSN - Greece")); - Assertions - .assertTrue( - map.containsKey("dh-ch") && map.get("dh-ch").equals("Digital Humanities and Cultural Heritage")); - Assertions.assertTrue(map.containsKey("fam") && map.get("fam").equals("Fisheries and Aquaculture Management")); - Assertions.assertTrue(map.containsKey("ni") && map.get("ni").equals("Neuroinformatics")); - Assertions.assertTrue(map.containsKey("mes") && map.get("mes").equals("European Marine Science")); - Assertions.assertTrue(map.containsKey("instruct") && map.get("instruct").equals("Instruct-ERIC")); - Assertions.assertTrue(map.containsKey("elixir-gr") && map.get("elixir-gr").equals("ELIXIR GR")); - Assertions - .assertTrue(map.containsKey("aginfra") && map.get("aginfra").equals("Agricultural and Food Sciences")); - Assertions.assertTrue(map.containsKey("dariah") && map.get("dariah").equals("DARIAH EU")); - Assertions.assertTrue(map.containsKey("risis") && map.get("risis").equals("RISIS")); - Assertions.assertTrue(map.containsKey("epos") && map.get("epos").equals("EPOS")); - Assertions.assertTrue(map.containsKey("beopen") && map.get("beopen").equals("Transport Research")); - Assertions.assertTrue(map.containsKey("euromarine") && map.get("euromarine").equals("EuroMarine")); - Assertions.assertTrue(map.containsKey("ifremer") && map.get("ifremer").equals("Ifremer")); - Assertions.assertTrue(map.containsKey("oa-pg") && map.get("oa-pg").equals("EC Post-Grant Open Access Pilot")); - Assertions - .assertTrue( - map.containsKey("science-innovation-policy") - && map.get("science-innovation-policy").equals("Science and Innovation Policy Studies")); - Assertions.assertTrue(map.containsKey("covid-19") && map.get("covid-19").equals("COVID-19")); - Assertions.assertTrue(map.containsKey("enermaps") && map.get("enermaps").equals("Energy Research")); - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/SplitForCommunityTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/SplitForCommunityTest.java deleted file mode 100644 index 4209caad3..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/SplitForCommunityTest.java +++ /dev/null @@ -1,143 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; - -import org.apache.commons.io.FileUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SparkSession; -import org.junit.jupiter.api.AfterAll; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.Test; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.oa.graph.dump.community.CommunitySplit; -import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; - -public class SplitForCommunityTest { - - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private static SparkSession spark; - - private static Path workingDir; - - private static final Logger log = LoggerFactory.getLogger(DumpJobTest.class); - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files.createTempDirectory(SplitForCommunityTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - - SparkConf conf = new SparkConf(); - conf.setAppName(SplitForCommunityTest.class.getSimpleName()); - - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - - spark = SparkSession - .builder() - .appName(SplitForCommunityTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Test - void testCommunitySplit() { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/splitForCommunity") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - CommunitySplit split = new CommunitySplit(); - - split.run(false, sourcePath, workingDir.toString() + "/split", communityMapPath); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/split/Digital_Humanities_and_Cultural_Heritage") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - Assertions.assertEquals(19, verificationDataset.count()); - - Assertions - .assertEquals( - 1, verificationDataset.filter("id = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); - - tmp = sc - .textFile(workingDir.toString() + "/split/EGI_Federation") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - Assertions.assertEquals(1, verificationDataset.count()); - - Assertions - .assertEquals( - 1, verificationDataset.filter("id = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); - - tmp = sc - .textFile(workingDir.toString() + "/split/Neuroinformatics") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - Assertions.assertEquals(5, verificationDataset.count()); - - Assertions - .assertEquals( - 1, verificationDataset.filter("id = '50|datacite____::6b1e3a2fa60ed8c27317a66d6357f795'").count()); - - tmp = sc - .textFile(workingDir.toString() + "/split/Science_and_Innovation_Policy_Studies") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - Assertions.assertEquals(4, verificationDataset.count()); - - Assertions - .assertEquals( - 1, verificationDataset.filter("id = '50|dedup_wf_001::0347b1cd516fc59e41ba92e0d74e4e9f'").count()); - Assertions - .assertEquals( - 1, verificationDataset.filter("id = '50|dedup_wf_001::1432beb6171baa5da8a85a7f99545d69'").count()); - Assertions - .assertEquals( - 1, verificationDataset.filter("id = '50|dedup_wf_001::1c8bd19e633976e314b88ce5c3f92d69'").count()); - Assertions - .assertEquals( - 1, verificationDataset.filter("id = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); - - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/UpdateProjectInfoTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/UpdateProjectInfoTest.java deleted file mode 100644 index 9710e4553..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/UpdateProjectInfoTest.java +++ /dev/null @@ -1,236 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.HashMap; -import java.util.logging.Filter; -import java.util.stream.Collectors; - -import org.apache.commons.io.FileUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.api.java.function.FilterFunction; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.Row; -import org.apache.spark.sql.SparkSession; -import org.junit.jupiter.api.AfterAll; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.Test; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo; -import eu.dnetlib.dhp.schema.dump.oaf.Result; -import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; -import eu.dnetlib.dhp.schema.dump.oaf.community.Funder; -import eu.dnetlib.dhp.schema.dump.oaf.community.Project; - -public class UpdateProjectInfoTest { - - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private static SparkSession spark; - - private static Path workingDir; - - private static final Logger log = LoggerFactory.getLogger(eu.dnetlib.dhp.oa.graph.dump.UpdateProjectInfoTest.class); - - private static final HashMap map = new HashMap<>(); - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory(eu.dnetlib.dhp.oa.graph.dump.UpdateProjectInfoTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - - SparkConf conf = new SparkConf(); - conf.setAppName(eu.dnetlib.dhp.oa.graph.dump.UpdateProjectInfoTest.class.getSimpleName()); - - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - - spark = SparkSession - .builder() - .appName(eu.dnetlib.dhp.oa.graph.dump.UpdateProjectInfoTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Test - void test1() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/addProjectInfo") - .getPath(); - - SparkUpdateProjectInfo.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-preparedInfoPath", sourcePath + "/preparedInfo", - "-outputPath", workingDir.toString() + "/result", - "-sourcePath", sourcePath + "/software.json" - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - verificationDataset.show(false); - - Assertions.assertEquals(6, verificationDataset.count()); - verificationDataset.createOrReplaceTempView("dataset"); - - String query = "select id, MyT.code code, MyT.title title, MyT.funder.name funderName, MyT.funder.shortName funderShortName, " - + - "MyT.funder.jurisdiction funderJurisdiction, MyT.funder.fundingStream fundingStream " - + "from dataset " + - "lateral view explode(projects) p as MyT "; - - org.apache.spark.sql.Dataset resultExplodedProvenance = spark.sql(query); - - Assertions.assertEquals(3, resultExplodedProvenance.count()); - resultExplodedProvenance.show(false); - - Assertions - .assertEquals( - 2, - resultExplodedProvenance.filter("id = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); - - Assertions - .assertEquals( - 1, - resultExplodedProvenance - .filter("id = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' and code = '123455'") - .count()); - - Assertions - .assertEquals( - 1, - resultExplodedProvenance - .filter("id = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' and code = '119027'") - .count()); - - Assertions - .assertEquals( - 1, - resultExplodedProvenance - .filter("id = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80' and code = '123455'") - .count()); - - resultExplodedProvenance.show(false); - } - - @Test - public void testValidatedRelation() throws Exception { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/addProjectInfo") - .getPath(); - - SparkUpdateProjectInfo.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-preparedInfoPath", sourcePath + "/preparedInfoValidated", - "-outputPath", workingDir.toString() + "/result", - "-sourcePath", sourcePath + "/publication_extendedmodel" - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - verificationDataset.show(false); - - Assertions.assertEquals(2, verificationDataset.count()); - verificationDataset.createOrReplaceTempView("dataset"); - - String query = "select id, MyT.code code, MyT.title title, MyT.funder.name funderName, MyT.funder.shortName funderShortName, " - + - "MyT.funder.jurisdiction funderJurisdiction, MyT.funder.fundingStream fundingStream, MyT.validated " - + "from dataset " + - "lateral view explode(projects) p as MyT "; - - org.apache.spark.sql.Dataset resultExplodedProvenance = spark.sql(query); - - Assertions.assertEquals(2, resultExplodedProvenance.count()); - resultExplodedProvenance.show(false); - - Assertions - .assertEquals( - 2, - resultExplodedProvenance.filter("id = '50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2'").count()); - - Assertions - .assertEquals( - 1, - resultExplodedProvenance - .filter("id = '50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2' and code = '123455'") - .count()); - - Assertions - .assertEquals( - 1, - resultExplodedProvenance - .filter("id = '50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2' and code = '119027'") - .count()); - - Project project = verificationDataset - .map( - (MapFunction) cr -> cr - .getProjects() - .stream() - .filter(p -> p.getValidated() != null) - .collect(Collectors.toList()) - .get(0), - Encoders.bean(Project.class)) - .first(); - - Assertions.assertTrue(project.getFunder().getName().equals("Academy of Finland")); - Assertions.assertTrue(project.getFunder().getShortName().equals("AKA")); - Assertions.assertTrue(project.getFunder().getJurisdiction().equals("FI")); - Assertions.assertTrue(project.getFunder().getFundingStream() == null); - Assertions.assertTrue(project.getValidated().getValidationDate().equals("2021-08-06")); - - project = verificationDataset - .map( - (MapFunction) cr -> cr - .getProjects() - .stream() - .filter(p -> p.getValidated() == null) - .collect(Collectors.toList()) - .get(0), - Encoders.bean(Project.class)) - .first(); - - Assertions.assertTrue(project.getFunder().getName().equals("European Commission")); - Assertions.assertTrue(project.getFunder().getShortName().equals("EC")); - Assertions.assertTrue(project.getFunder().getJurisdiction().equals("EU")); - Assertions.assertTrue(project.getFunder().getFundingStream().equals("H2020")); - - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/ZenodoUploadTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/ZenodoUploadTest.java deleted file mode 100644 index 8d06758a8..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/ZenodoUploadTest.java +++ /dev/null @@ -1,153 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump; - -import java.io.*; -import java.nio.file.Files; - -import org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.*; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.Disabled; -import org.junit.jupiter.api.Test; - -import com.google.gson.Gson; - -import eu.dnetlib.dhp.common.api.MissingConceptDoiException; -import eu.dnetlib.dhp.common.api.ZenodoAPIClient; -import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; - -@Disabled -public class ZenodoUploadTest { - - private static String workingDir; - - private final String URL_STRING = "https://sandbox.zenodo.org/api/deposit/depositions"; - private final String ACCESS_TOKEN = ""; - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory(eu.dnetlib.dhp.oa.graph.dump.UpdateProjectInfoTest.class.getSimpleName()) - .toString(); - } - - @Test - void testNewDeposition() throws IOException { - CommunityMap communityMap = new CommunityMap(); - communityMap.put("ni", "Neuroinformatics"); - communityMap.put("dh-ch", "Digital Humanities and Cultural Heritage"); - LocalFileSystem fs = FileSystem.getLocal(new Configuration()); - - fs - .copyFromLocalFile( - false, new Path(getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/ni") - .getPath()), - new Path(workingDir + "/zenodo/ni/ni")); - fs - .copyFromLocalFile( - false, new Path(getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/dh-ch") - .getPath()), - new Path(workingDir + "/zenodo/dh-ch/dh-ch")); - - ZenodoAPIClient client = new ZenodoAPIClient(URL_STRING, - ACCESS_TOKEN); - client.newDeposition(); - - // the second boolean parameter here sets the recursion to true - RemoteIterator fileStatusListIterator = fs - .listFiles( - new Path(workingDir + "/zenodo"), true); - while (fileStatusListIterator.hasNext()) { - LocatedFileStatus fileStatus = fileStatusListIterator.next(); - - String p_string = fileStatus.getPath().toString(); - - int index = p_string.lastIndexOf("/"); - String community = p_string.substring(0, index); - community = community.substring(community.lastIndexOf("/") + 1); - String community_name = communityMap.get(community).replace(" ", "_"); - // fs.copyToLocalFile(fileStatus.getPath(), new Path("/tmp/" + community_name)); - System.out.println(community); - - // File f = new File("/tmp/" + community_name); - FSDataInputStream inputStream = fs.open(fileStatus.getPath()); - System.out.println(client.uploadIS(inputStream, community_name, fileStatus.getLen())); - - } - - String metadata = "{\"metadata\":{\"access_right\":\"open\",\"communities\":[{\"identifier\":\"openaire-research-graph\"}],\"creators\":[{\"affiliation\":\"CNR - ISTI\",\"name\":\"Manghi, Paolo\",\"orcid\":\"0000-0001-7291-3210\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"Atzori, Claudio\",\"orcid\":\"0000-0001-9613-6639\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"Bardi, Alessia\",\"orcid\":\"0000-0002-1112-1292\"},{\"affiliation\":\"ISTI - CNR\",\"name\":\"Baglioni, Miriam\",\"orcid\":\"0000-0002-2273-9004\"},{\"affiliation\":\"University of Bielefeld\",\"name\":\"Shirrwagen, Jochen\"},{\"affiliation\":\"Athena Research and Innovation Centre\",\"name\":\"Dimitropoulos, Harry\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"La Bruzzo, Sandro\",\"orcid\":\"0000-0003-2855-1245\"},{\"affiliation\":\"Athena Research and Innovation Centre\",\"name\":\"Foufoulas, Ioannis\"},{\"affiliation\":\"University of Bielefeld\",\"name\":\"Löhden, Aenne\"},{\"affiliation\":\"University of Bielefeld\",\"name\":\"Bäcker, Amelie\",\"orcid\":\"0000-0001-6015-2063\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"Mannocci, Andrea\",\"orcid\":\"0000-0002-5193-7851\"},{\"affiliation\":\"University of Warsaw\",\"name\":\"Horst, Marek\"},{\"affiliation\":\"University of Bielefeld\",\"name\":\"Czerniak, Andreas\",\"orcid\":\"0000-0003-3883-4169\"},{\"affiliation\":\"Athena Research and Innovation Centre\",\"name\":\"Kiatropoulou, Katerina\"},{\"affiliation\":\"Athena Research and Innovation Centre\",\"name\":\"Kokogiannaki, Argiro\",\"orcid\":\"0000-0002-3880-0244\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"De Bonis, Michele\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"Artini, Michele\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"Ottonello, Enrico\"},{\"affiliation\":\"Athena Research and Innovation Centre\",\"name\":\"Lempesis, Antonis\"},{\"affiliation\":\"CERN\",\"name\":\"Ioannidis, Alexandros\"},{\"affiliation\":\"University of Bielefeld\",\"name\":\"Summan, Friedrich\"}],\"description\":\"\\u003cp\\u003eThis dataset contains dumps of the OpenAIRE Research Graph containing metadata records relevant for the research communities and initiatives collaborating with OpenAIRE\\u003c/p\\u003e. \\u003cp\\u003eEach dataset is a zip containing a file with one json per line. Each json is compliant to the schema available at XXXX\\u003c/p\\u003e Note that the file that is offered is not a typical json file: each line contains a separate, self-contained json object. For more information please see http://jsonlines.org\",\"grants\":[{\"id\":\"777541\"},{\"id\":\"824091\"},{\"id\":\"824323\"}],\"keywords\":[\"Open Science\",\"Scholarly Communication\",\"Information Science\"],\"language\":\"eng\",\"license\":\"CC-BY-4.0\",\"title\":\"OpenAIRE Research Graph: Dumps for research communities and initiatives.\",\"upload_type\":\"dataset\",\"version\":\"1.0\"}}"; - - System.out.println(client.sendMretadata(metadata)); - - System.out.println(client.publish()); - - } - - @Test - void testNewVersion() throws IOException, MissingConceptDoiException { - - ZenodoAPIClient client = new ZenodoAPIClient(URL_STRING, - ACCESS_TOKEN); - - client.newVersion("656628"); - - CommunityMap communityMap = new CommunityMap(); - communityMap.put("ni", "Neuroinformatics"); - communityMap.put("dh-ch", "Digital Humanities and Cultural Heritage"); - LocalFileSystem fs = FileSystem.getLocal(new Configuration()); - - fs - .copyFromLocalFile( - false, new Path(getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/ni") - .getPath()), - new Path(workingDir + "/zenodo/ni/ni")); - fs - .copyFromLocalFile( - false, new Path(getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/dh-ch") - .getPath()), - new Path(workingDir + "/zenodo/dh-ch/dh-ch")); - - RemoteIterator fileStatusListIterator = fs - .listFiles( - new Path(workingDir + "/zenodo"), true); - while (fileStatusListIterator.hasNext()) { - LocatedFileStatus fileStatus = fileStatusListIterator.next(); - - String p_string = fileStatus.getPath().toString(); - - int index = p_string.lastIndexOf("/"); - String community = p_string.substring(0, index); - community = community.substring(community.lastIndexOf("/") + 1); - String community_name = communityMap.get(community).replace(" ", "_"); - // fs.copyToLocalFile(fileStatus.getPath(), new Path("/tmp/" + community_name)); - System.out.println(community); - - // File f = new File("/tmp/" + community_name); - FSDataInputStream inputStream = fs.open(fileStatus.getPath()); - System.out.println(client.uploadIS(inputStream, community_name, fileStatus.getLen())); - - } - - System.out.println(client.publish()); - - } - - @Test - void readCommunityMap() throws IOException { - LocalFileSystem fs = FileSystem.getLocal(new Configuration()); - System.out - .println( - new Gson() - .toJson( - Utils - .readCommunityMap( - fs, getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath()))); - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java deleted file mode 100644 index b5f73da71..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java +++ /dev/null @@ -1,173 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import static org.mockito.Mockito.lenient; - -import java.io.BufferedWriter; -import java.io.IOException; -import java.io.OutputStreamWriter; -import java.nio.charset.StandardCharsets; -import java.nio.file.Files; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.List; -import java.util.function.Consumer; - -import org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.FSDataOutputStream; -import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.fs.LocalFileSystem; -import org.apache.hadoop.fs.Path; -import org.apache.hadoop.io.compress.CompressionCodec; -import org.apache.hadoop.io.compress.CompressionCodecFactory; -import org.junit.jupiter.api.*; -import org.junit.jupiter.api.extension.ExtendWith; -import org.mockito.Mock; -import org.mockito.junit.jupiter.MockitoExtension; - -import com.google.gson.Gson; - -import eu.dnetlib.dhp.schema.dump.oaf.graph.ResearchCommunity; -import eu.dnetlib.dhp.schema.dump.oaf.graph.ResearchInitiative; -import eu.dnetlib.dhp.utils.DHPUtils; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; - -@ExtendWith(MockitoExtension.class) -public class CreateEntityTest { - - private static final String XQUERY_ENTITY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') " - + - "where $x//context[./@type='community' or ./@type = 'ri'] and $x//context/param[./@name = 'status']/text() = 'all' return " - + - "concat(data($x//context/@id) , '@@', $x//context/param[./@name =\"name\"]/text(), '@@', " + - "$x//context/param[./@name=\"description\"]/text(), '@@', $x//context/param[./@name = \"subject\"]/text(), '@@', " - + - "$x//context/param[./@name = \"zenodoCommunity\"]/text(), '@@', $x//context/@type)"; - - List communityMap = Arrays - .asList( - "clarin@@Common Language Resources and Technology Infrastructure@@CLARIN@@@@oac_clarin@@ri", - "ee@@Sustainable Development Solutions Network - Greece@@The UN Sustainable Development Solutions Network (SDSN) has been operating since 2012 under the auspices of the UN Secretary-General. " - + - "SDSN mobilizes global scientific and technological expertise to promote practical solutions for sustainable development, including the implementation of the Sustainable Development Goals (SDGs) and the Paris Climate Agreement. The Greek hub of SDSN has been included in the SDSN network in 2017 and is co-hosted by ICRE8: International Center for Research on the Environment and the Economy and the Political Economy of Sustainable Development Lab.@@SDG13 - Climate action,SDG8 - Decent work and economic growth,SDG15 - " - + - "Life on land,SDG2 - Zero hunger,SDG17 - Partnerships for the ´goals,SDG10 - Reduced inequalities,SDG5 - Gender equality,SDG12 - Responsible consumption and production,SDG14 - Life below water,SDG6 - Clean water and sanitation,SDG11 - Sustainable cities and communities,SDG1 - No poverty,SDG3 - Good health and well being,SDG7 - Affordable and clean energy,SDG4 - Quality education,SDG9 - Industry innovation and infrastructure,SDG16 - Peace justice and strong institutions@@oac_sdsn-greece@@community", - "dh-ch@@Digital Humanities and Cultural Heritage@@This community gathers research results, data, scientific publications and projects related to the domain of Digital Humanities. This broad definition includes Humanities, Cultural Heritage, History, Archaeology and related fields.@@modern art,monuments,europeana data model,sites,field walking,frescoes,LIDO metadata schema,art history,excavation,Arts and Humanities General,cities,coins,temples,numismatics,lithics,roads,environmental archaeology,digital cultural heritage,archaeological reports,history,CRMba,churches,cultural heritage,archaeological stratigraphy,religious art,buidings,digital humanities,survey,archaeological sites,linguistic studies,bioarchaeology,architectural orders,palaeoanthropology,fine arts,europeana,CIDOC CRM,decorations,classic art,stratigraphy,digital archaeology,intangible cultural heritage,walls,humanities,chapels,CRMtex,Language and Literature,paintings,archaeology,fair data,mosaics,burials,architecture,medieval art,castles,CARARE metadata schema,statues,natural language processing,inscriptions,CRMsci,vaults,contemporary art,Arts and Humanities,CRMarchaeo,pottery,site,architectural,vessels@@oac_dh-ch@@community", - "fam@@Fisheries and Aquaculture Management@@Conservation of marine resources for sustainable development. The Fisheries and Aquaculture community focus on resources (document, data, codes..) which have been produced in the framework of projects (H2020, FP7, ..) related to the domain of fisheries and aquaculture.@@Stock Assessment,pelagic,Acoustic,Fish farming,Fisheries,Fishermen,maximum sustainable yield,trawler,Fishing vessel,Fisherman,Fishing gear,mackerel,RFMO,Fish Aggregating Device,Bycatch,Fishery,common fisheries policy,Fishing fleet,Aquaculture@@fisheries@@community", - "ni@@Neuroinformatics@@The neuroinformatics dashboard gathers research outputs from the 'neuroinformatics' community at large including the fields of: neuroscience, neuroinformatics, brain imaging databases and standards, brain imaging techniques, neuroimaging methods including statistics and machine learning. The dashboard covers a wide range of imaging methods including (but not limited to): MRI, TEP, EEG, MEG, and studies involving human participants as well as animal studies.@@brain mapping,brain imaging,electroencephalography,arterial spin labelling,brain fingerprinting,brain,neuroimaging,Multimodal Brain Image Analysis,fMRI,neuroinformatics,fetal brain,brain ultrasonic imaging,topographic brain mapping,diffusion tensor imaging,computerized knowledge assessment,connectome mapping,brain magnetic resonance imaging,brain abnormalities@@oac_ni@@community", - "mes@@European Marine Science@@This community was initially defined to include a very broad range of topics, with the intention to generate a number of more focused and sustainable dashboards for research communities and initiatives. As outlined in the logo of this community, we intend to setup a community dashboard for EuroMarine (a consortium of 56 research and academic organisations) and monitoring dashboards for marine research initiatives, including infrastructures (e.g. EMBRC & EMSO), advisory boards (e.g. Marine Boards & ICES), and transnational funding bodies (e.g. JPI-Oceans and Tara Foundation).@@marine,ocean,fish,aqua,sea@@oac_mes@@community", - "instruct@@Instruct-ERIC@@Instruct-ERIC is the European Research Infrastructure for Structural Biology@@@@oac_instruct@@community", - "elixir-gr@@The Greek National Node of the ESFRI European RI ELIXIR@@ELIXIR-GR enhances the potential of the Greek bioinformatics community to offer open, easily accessible and state -of- the- art services to the Greek and the international academic community and other stakeholders, such as industry and the health sector. More importantly, by providing these services, the infrastructure facilitates discoveries in the field of the life-sciences, having strong spill over effects in promoting innovation in sectors such as discovery of new drug targets and development of novel therapeutic agents, development of innovative diagnostics, personalized medicine, and development of innovative biotechnological products and processes.@@@@oaa_elixir-gr@@ri", - "aginfra@@Agricultural and Food Sciences@@The scope of this community is to provide access to publications, research data, projects and software that are related to agricultural and food sciences@@animal production and health,fisheries and aquaculture,food safety and human nutrition,information management,food technology,agri-food education and extension,natural resources and environment,food system,engineering technology and Research,agriculture,food safety risk assessment,food security,farming practices and systems,plant production and protection,agri-food economics and policy,Agri-food,food distribution,forestry@@oac_aginfra@@community", - "dariah@@DARIAH EU@@The Digital Research Infrastructure for the Arts and Humanities (DARIAH) aims to enhance and support digitally-enabled research and teaching across the arts and humanities. It develops, maintains and operates an infrastructure in support of ICT-based research practices and sustains researchers in using them to build, analyse and interpret digital resources. DARIAH was established as a European Research Infrastructure Consortium (ERIC) in August 2014. Currently, DARIAH has 18 Members and several cooperating partners in eight non-member countries. Here you will find a growing collection of DARIAH-affiliated research outputs and other documents. @@@@dariah@@ri", - "epos@@European Plate Observing System@@EPOS, the European Plate Observing System, is a long-term plan to facilitate integrated use of data, data products, and facilities from distributed research infrastructures for solid Earth science in Europe.@@@@@@ri", - "covid-19@@Corona Virus Disease@@This portal provides access to publications, research data, projects and software that may be relevant to the Corona Virus Disease (COVID-19). The OpenAIRE COVID-19 Gateway aggregates COVID-19 related records, links them and provides a single access point for discovery and navigation. We tag content from the OpenAIRE Research Graph (10,000+ data sources) and additional sources. All COVID-19 related research results are linked to people, organizations and projects, providing a contextualized navigation.@@COVID19,SARS-CoV,HCoV-19,mesh:C000657245,MERS-CoV,Síndrome Respiratorio Agudo Severo,mesh:COVID-19,COVID2019,COVID-19,SARS-CoV-2,2019 novel coronavirus,severe acute respiratory syndrome coronavirus 2,Orthocoronavirinae,Coronaviridae,mesh:D045169,coronavirus,SARS,coronaviruses,coronavirus disease-19,sars cov 2,Middle East Respiratory Syndrome,Severe acute respiratory syndrome coronavirus 2,Severe Acute Respiratory Syndrome,coronavirus disease 2019,2019-nCoV@@covid-19@@community"); - - @Mock - private ISLookUpService isLookUpService; - - private QueryInformationSystem queryInformationSystem; - - private static String workingDir; - - @BeforeEach - public void setUp() throws ISLookUpException { - lenient().when(isLookUpService.quickSearchProfile(XQUERY_ENTITY)).thenReturn(communityMap); - queryInformationSystem = new QueryInformationSystem(); - queryInformationSystem.setIsLookUp(isLookUpService); - } - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory(eu.dnetlib.dhp.oa.graph.dump.complete.CreateEntityTest.class.getSimpleName()) - .toString(); - } - - @Test - void test1() throws ISLookUpException, IOException { - List cInfoList = new ArrayList<>(); - final Consumer consumer = ci -> cInfoList.add(ci); - queryInformationSystem.getContextInformation(consumer); - - List riList = new ArrayList<>(); - cInfoList.forEach(cInfo -> riList.add(Process.getEntity(cInfo))); - - Assertions.assertEquals(12, riList.size()); - - riList.stream().forEach(c -> { - switch (c.getAcronym()) { - case "mes": - Assertions - .assertTrue(c.getType().equals(eu.dnetlib.dhp.oa.graph.dump.Constants.RESEARCH_COMMUNITY)); - Assertions.assertTrue(((ResearchCommunity) c).getSubject().size() == 5); - Assertions.assertTrue(((ResearchCommunity) c).getSubject().contains("marine")); - Assertions.assertTrue(((ResearchCommunity) c).getSubject().contains("ocean")); - Assertions.assertTrue(((ResearchCommunity) c).getSubject().contains("fish")); - Assertions.assertTrue(((ResearchCommunity) c).getSubject().contains("aqua")); - Assertions.assertTrue(((ResearchCommunity) c).getSubject().contains("sea")); - Assertions - .assertTrue( - c - .getId() - .equals( - String - .format( - "%s|%s::%s", Constants.CONTEXT_ID, Constants.CONTEXT_NS_PREFIX, - DHPUtils.md5(c.getAcronym())))); - Assertions.assertTrue(c.getZenodo_community().equals("https://zenodo.org/communities/oac_mes")); - Assertions.assertTrue("mes".equals(c.getAcronym())); - break; - case "clarin": - Assertions - .assertTrue(c.getType().equals(eu.dnetlib.dhp.oa.graph.dump.Constants.RESEARCH_INFRASTRUCTURE)); - Assertions - .assertTrue( - c - .getId() - .equals( - String - .format( - "%s|%s::%s", Constants.CONTEXT_ID, Constants.CONTEXT_NS_PREFIX, - DHPUtils.md5(c.getAcronym())))); - Assertions.assertTrue(c.getZenodo_community().equals("https://zenodo.org/communities/oac_clarin")); - Assertions.assertTrue("clarin".equals(c.getAcronym())); - break; - } - // TODO add check for all the others Entities - - }); - - riList.forEach(c -> System.out.println(new Gson().toJson(c))); - } - - @Test - @Disabled - void test2() throws IOException, ISLookUpException { - LocalFileSystem fs = FileSystem.getLocal(new Configuration()); - - Path hdfsWritePath = new Path(workingDir + "/prova"); - FSDataOutputStream fsDataOutputStream = null; - if (fs.exists(hdfsWritePath)) { - fsDataOutputStream = fs.append(hdfsWritePath); - } else { - fsDataOutputStream = fs.create(hdfsWritePath); - } - CompressionCodecFactory factory = new CompressionCodecFactory(fs.getConf()); - CompressionCodec codec = factory.getCodecByClassName("org.apache.hadoop.io.compress.GzipCodec"); - - BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(codec.createOutputStream(fsDataOutputStream), - StandardCharsets.UTF_8)); - - List cInfoList = new ArrayList<>(); - final Consumer consumer = ci -> cInfoList.add(ci); - queryInformationSystem.getContextInformation(consumer); - - for (ContextInfo cInfo : cInfoList) { - writer.write(new Gson().toJson(Process.getEntity(cInfo))); - } - writer.close(); - - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateRelationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateRelationTest.java deleted file mode 100644 index d2343d274..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateRelationTest.java +++ /dev/null @@ -1,723 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import java.util.*; -import java.util.function.Consumer; -import java.util.stream.Collectors; - -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeEach; -import org.junit.jupiter.api.Test; - -import com.google.gson.Gson; - -import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.dhp.schema.dump.oaf.graph.Relation; -import eu.dnetlib.dhp.schema.oaf.Datasource; -import eu.dnetlib.dhp.schema.oaf.Project; -import eu.dnetlib.dhp.utils.DHPUtils; - -class CreateRelationTest { - - List communityContext = Arrays - .asList( - "\n" + - " all\n" + - " CLARIN\n" + - " https://www.clarin.eu/sites/default/files/clarin-frontpage-logo.jpg\n" - + - " Common Language Resources and Technology Infrastructure\n" + - " maria@clarin.eu,dieter@clarin.eu,f.m.g.dejong@uu.nl,paolo.manghi@isti.cnr.it\n" - + - " \n" + - " (Part of) the work reported here was made possible by using the CLARIN infrastructure.\n" - + - " The work reported here has received funding through <CLARIN national consortium member, e.g. CLARIN.SI>, <XYZ> project, grant no. <XYZ>.\n" - + - " The work reported here has received funding (through CLARIN ERIC) from the European Union’s Horizon 2020 research and innovation programme under grant agreement No <0-9> for project <XYZ>.\n" - + - " (E.g. No 676529 for project CLARIN-PLUS.)\n" + - " oac_clarin\n" + - " 2018-03-01T12:00:00\n" + - " \n" + - " \n" + - " CLARIN-PLUS\n" + - " \n" + - " \n" + - " 676529\n" + - " http://www.clarin.eu\n" + - " EC\n" + - " H2020-INFRADEV-1-2015-1\n" + - " CLARIN+\n" + - " \n" + - " \n" + - " Common Language Resources and Technology Infrastructure\n" - + - " CLARIN\n" + - " 212230\n" + - " EC\n" + - " corda_______::ef782b2d85676aa3e5a907427feb18c4\n" + - " \n" + - " \n" + - " " + - "\n" + - " \n" + - " LINDAT/CLARIN repository\n" + - " LINDAT/CLARIN repository\n" + - " true\n" + - " \n" + - " \n" + - " \n" + - " \n" + - " CLARIN-D\n" + - " https://www.clarin-d.de/en/\n" + - " \n" + - " http://www.lrec-conf.org/proceedings/lrec2018/pdf/504.pdf\n" - + - " Germany\n" + - " \n" + - " \n" + - " \n" - + - " \n" + - "", - "\n" + - " all\n" + - " This community gathers research results, data, scientific publications and projects related to the domain of Digital Humanities. This broad definition includes Humanities, Cultural Heritage, History, Archaeology and related fields.\n" - + - " http://sanmamante.org/DH_CH_logo.png\n" + - " Digital Humanities and Cultural Heritage\n" + - " ileniagalluccio87@gmail.com,achille.felicetti@gmail.com,paolo.manghi@isti.cnr.it,tim.evans@york.ac.uk\n" - + - " modern art,monuments,europeana data model,sites,field walking,frescoes,LIDO metadata schema,art history,excavation,Arts and Humanities General,cities,coins,temples,numismatics,lithics,roads,environmental archaeology,digital cultural heritage,archaeological reports,history,CRMba,churches,cultural heritage,archaeological stratigraphy,religious art,buidings,digital humanities,survey,archaeological sites,linguistic studies,bioarchaeology,architectural orders,palaeoanthropology,fine arts,europeana,CIDOC CRM,decorations,classic art,stratigraphy,digital archaeology,intangible cultural heritage,walls,humanities,chapels,CRMtex,Language and Literature,paintings,archaeology,fair data,mosaics,burials,architecture,medieval art,castles,CARARE metadata schema,statues,natural language processing,inscriptions,CRMsci,vaults,contemporary art,Arts and Humanities,CRMarchaeo,pottery,site,architectural,vessels\n" - + - " The present work has been partially supported by the PARTHENOS project, funded by the European Commission (Grant Agreement No. 654119) under the HORIZON 2020 - INFRADEV-4-2014/2015 call\n" - + - " oac_dh-ch\n" + - " 2018-03-01T12:00:00\n" + - " \n" + - " \n" - + - " Pooling Activities, Resources and Tools for Heritage E-research Networking, Optimization and Synergies\n" - + - " The present work has been partially supported by the PARTHENOS project, funded by the European Commission (Grant Agreement No. 654119) under the HORIZON 2020 - INFRADEV-4-2014/2015 call\n" - + - " \n" + - " 654119\n" + - " http://www.parthenos-project.eu\n" + - " EC\n" + - " PARTHENOS\n" + - " \n" + - " \n" + - " \n" + - " \n" - + - " re3data_____::9ebe127e5f3a0bf401875690f3bb6b81\n" + - " The UK's largest collection of digital research data in the social sciences and humanities\n" - + - " UK Data Archive\n" + - " true\n" + - " \n" + - " \n" - + - " doajarticles::c6cd4b532e12868c1d760a8d7cda6815\n" + - " Journal of Data Mining and Digital Humanities\n" + - " Journal of Data Mining and Digital Humanities\n" + - " true\n" + - " \n" + - " \n" - + - " doajarticles::a6de4499bb87bf3c01add0a9e2c9ed0b\n" + - " Frontiers in Digital Humanities\n" + - " Frontiers in Digital Humanities\n" + - " true\n" + - " \n" + - " \n" - + - " doajarticles::6eb31d13b12bc06bbac06aef63cf33c9\n" + - " Il Capitale Culturale: Studies on the Value of Cultural Heritage\n" - + - " Il Capitale Culturale: Studies on the Value of Cultural Heritage\n" - + - " true\n" + - " \n" + - " \n" - + - " doajarticles::0da84e9dfdc8419576169e027baa8028\n" + - " Conservation Science in Cultural Heritage\n" + - " Conservation Science in Cultural Heritage\n" + - " true\n" + - " \n" + - " \n" - + - " re3data_____::84e123776089ce3c7a33db98d9cd15a8\n" + - " Electronic Archiving System\n" + - " EASY\n" + - " true\n" + - " \n" + - " \n" + - " openaire____::c5502a43e76feab55dd00cf50f519125\n" + - " DANS-KB Harvester\n" + - " Gemeenschappelijke Harvester DANS-KB\n" + - " true\n" + - " \n" + - " \n" + - " re3data_____::a48f09c562b247a9919acfe195549b47\n" + - " ads\n" + - " Archaeology Data Service\n" + - " true\n" + - " \n" + - " \n" + - " opendoar____::97275a23ca44226c9964043c8462be96\n" + - " KNAW Repository\n" + - " KNAW Repository\n" + - " true\n" + - " \n" + - " \n" - + - " doajarticles::2899208a99aa7d142646e0a80bfeef05\n" + - " Internet Archaeology\n" + - " Internet Archaeology\n" + - " true\n" + - " \n" + - " \n" + - " \n" + - "\n", - "\n" + - " all\n" + - " The neuroinformatics dashboard gathers research outputs from the 'neuroinformatics' community at large including the fields of: neuroscience, neuroinformatics, brain imaging databases and standards, brain imaging techniques, neuroimaging methods including statistics and machine learning. The dashboard covers a wide range of imaging methods including (but not limited to): MRI, TEP, EEG, MEG, and studies involving human participants as well as animal studies.\n" - + - " https://docs.google.com/drawings/u/0/d/10e191xGoGf4uaRluMqbt_7cCj6LSCs2a29im4CmWjqU/export/png\n" - + - " Neuroinformatics\n" + - " sorina.pop@creatis.insa-lyon.fr,camille.maumet@inria.fr,christian.barillot@irisa.fr,xavier.rolland@irisa.fr,axel.bonnet@creatis.insa-lyon.fr,paolo.manghi@isti.cnr.it\n" - + - " brain mapping,brain imaging,electroencephalography,arterial spin labelling,brain fingerprinting,brain,neuroimaging,Multimodal Brain Image Analysis,fMRI,neuroinformatics,fetal brain,brain ultrasonic imaging,topographic brain mapping,diffusion tensor imaging,computerized knowledge assessment,connectome mapping,brain magnetic resonance imaging,brain abnormalities\n" - + - " \n" + - " oac_ni\n" + - " 2018-03-01T12:00:00\n" + - " \n" + - " \n" + - " \n" + - " re3data_____::5b9bf9171d92df854cf3c520692e9122\n" + - " Formerly:OpenFMRI\n" + - " OpenNeuro\n" + - " true\n" + - " \n" + - " \n" + - " doajarticles::c7d3de67dc77af72f6747157441252ec\n" + - " Research Ideas and Outcomes\n" + - " Research Ideas and Outcomes\n" + - " true\n" + - " \n" + - " \n" + - " re3data_____::8515794670370f49c1d176c399c714f5\n" + - " Neuroimaging Informatics Tools and Resources Clearinghouse\n" - + - " NITRC\n" + - " true\n" + - " \n" + - " \n" + - " doajarticles::d640648c84b10d425f96f11c3de468f3\n" + - " Frontiers in Neuroinformatics\n" + - " Frontiers in Neuroinformatics\n" + - " true\n" + - " \n" + - " \n" + - " doajarticles::0c0e74daa5d95504eade9c81ebbd5b8a\n" + - " NeuroImage: Clinical\n" + - " NeuroImage: Clinical\n" + - " true\n" + - " \n" + - " \n" + - " rest________::fb1a3d4523c95e63496e3bc7ba36244b\n" + - " NeuroVault\n" + - " NeuroVault\n" + - " true\n" + - " \n" + - " \n" + - "\n", - "\n" + - " all\n" + - " Instruct-ERIC is the European Research Infrastructure for Structural Biology\n" - + - " https://instruct-eric.eu/templates/instructeric/images/logos/instruct-eric-logo-noline.png\n" - + - " Instruct-ERIC\n" + - " claudia@instruct-eric.eu,carazo@cnb.csic.es,echrysina@eie.gr,susan@instruct-eric.eu,naomi@instruct-eric.eu,natalie@instruct-eric.eu,pmarie@igbmc.fr,darren.hart@ibs.fr,claudia@strubi.ox.ac.uk,paolo.manghi@isti.cnr.it\n" - + - " \n" + - " The authors acknowledge the support and the use of resources of Instruct-ERIC.\n" - + - " The authors acknowledge the support and the use of resources of Instruct (PID # or APPID #), a Landmark ESFRI project\n" - + - " oac_instruct\n" + - " 2018-03-01T12:00:00\n" + - " \n" + - " \n" - + - " Authentication and Authorisation For Research and Collaboration\n" - + - " \n" + - " 730941\n" + - " \n" + - " H2020-EINFRA-2016-1\n" + - " AARC2\n" + - " EC\n" + - " \n" + - " \n" - + - " Building data bridges between biological and medical infrastructures in Europe\n" - + - " \n" + - " 284209\n" + - " \n" + - " FP7-INFRASTRUCTURES-2011-1\n" + - " EC\n" + - " BioMedBridges\n" + - " \n" + - " \n" - + - " Transnational access and enhancement of integrated Biological Structure determination at synchrotron X-ray radiation facilities\n" - + - " \n" + - " 283570\n" + - " \n" + - " FP7-INFRASTRUCTURES-2011-1\n" + - " EC\n" + - " BioStruct-X\n" + - " \n" + - " \n" - + - " Coordinated Research Infrastructures Building Enduring Life-science services\n" - + - " \n" + - " 654248\n" + - " \n" + - " H2020-INFRADEV-1-2014-1\n" + - " EC\n" + - " CORBEL\n" + - " \n" + - " \n" - + - " Infrastructure for NMR, EM and X-rays for translational research\n" - + - " \n" + - " 653706\n" + - " \n" + - " H2020-INFRAIA-2014-2015\n" + - " EC\n" + - " iNEXT\n" + - " \n" + - " \n" - + - " Integrated Structural Biology Infrastructure\n" + - " \n" + - " 211252\n" + - " \n" + - " FP7-INFRASTRUCTURES-2007-1\n" + - " EC\n" + - " INSTRUCT\n" + - " \n" + - " \n" - + - " Releasing the full potential of Instruct to expand and consolidate infrastructure services for integrated structural life science research\n" - + - " \n" + - " 731005\n" + - " \n" + - " H2020-INFRADEV-2016-1\n" + - " EC\n" + - " INSTRUCT-ULTRA\n" + - " \n" + - " \n" - + - " Opening Synchrotron Light for Experimental Science and Applications in the Middle East\n" - + - " \n" + - " 730943\n" + - " \n" + - " H2020-INFRASUPP-2016-1\n" + - " EC\n" + - " OPEN SESAME\n" + - " \n" + - " \n" - + - " Infrastructure for Protein Production Platforms\n" - + - " \n" + - " 227764\n" + - " \n" + - " FP7-INFRASTRUCTURES-2008-1\n" + - " EC\n" + - " PCUBE\n" + - " \n" + - " \n" - + - " European Vaccine Research and Development Infrastructure\n" - + - " \n" + - " 730964\n" + - " \n" + - " H2020-INFRAIA-2016-1\n" + - " EC\n" + - " TRAMSVAC2\n" + - " \n" + - " \n" - + - " World-wide E-infrastructure for structural biology\n" - + - " \n" + - " 675858\n" + - " \n" + - " EC | H2020 | RIA\n" + - " EC\n" + - " West-Life\n" + - " \n" + - " \n" + - " Expanding research infrastructure visibility to strengthen strategic partnerships\n" - + - " RI-VIS\n" + - " 824063\n" + - " EC\n" + - " corda__h2020::af93b591b76991d8437993a8f6fc6538\n" + - " \n" + - " \n" + - " \n" - + - " \n" - + - " \n" + - " instruct\n" + - " \n" + - " \n" + - " \n" - + - " west-life\n" + - " \n" + - " \n" + - " \n" + - " \n" - + - " \n" + - " FRISBI\n" + - " aHR0cDovL2ZyaXNiaS5ldS9zdGF0aWMvaW1hZ2VzL2xvZ29zL2xvZ28tZnJpc2JpLnBuZw==\n" - + - " aHR0cDovL2ZyaXNiaS5ldS8=\n" + - " \n" + - " \n" + - " RI-VIS\n" + - " aHR0cHM6Ly9yaS12aXMuZXUvbmV0d29yay9yaXZpcy90ZW1wbGF0ZXMvcml2aXMvaW1hZ2VzL1JJLVZJU0xvZ29GaW5hbC0wNi5wbmc=\n" - + - " aHR0cHM6Ly9yaS12aXMuZXU=\n" + - " \n" + - " \n" + - " CIISB\n" + - " aHR0cDovL2JpYy5jZWl0ZWMuY3ovZmlsZXMvMjkyLzEyNS5KUEc=\n" + - " aHR0cHM6Ly93d3cuY2lpc2Iub3Jn\n" + - " \n" + - " \n" + - "\n", - "\n" + - " all\n" + - " ELIXIR-GR enhances the potential of the Greek bioinformatics community to offer open, easily accessible and state -of- the- art services to the Greek and the international academic community and other stakeholders, such as industry and the health sector. More importantly, by providing these services, the infrastructure facilitates discoveries in the field of the life-sciences, having strong spill over effects in promoting innovation in sectors such as discovery of new drug targets and development of novel therapeutic agents, development of innovative diagnostics, personalized medicine, and development of innovative biotechnological products and processes.\n" - + - " https://elixir-greece.org/sites/default/files/ELIXIR_GREECE_white_background.png\n" - + - " The Greek National Node of the ESFRI European RI ELIXIR\n" + - " vergoulis@imis.athena-innovation.gr,schatz@imis.athena-innovation.gr,paolo.manghi@isti.cnr.it\n" - + - " \n" + - " \n" + - " oaa_elixir-gr\n" + - " 2018-03-01T12:00:00\n" + - " \n" + - " \n" + - " BIO-INFORMATICS RESEARCH NETWORK COORDINATING CENTER (BIRN-CC)\n" - + - " \n" + - " 1U24RR025736-01\n" + - " NIH\n" + - " \n" + - " \n" + - " COLLABORATIVE RESEARCH: The Cognitive Neuroscience of Category Learning\n" - + - " \n" + - " 0223843\n" + - " NSF\n" + - " \n" + - " \n" + - " The Cognitive Atlas: Developing an Interdisciplinary Knowledge Base Through Socia\n" - + - " \n" + - " 5R01MH082795-05\n" + - " NIH\n" + - " \n" + - " \n" + - " Fragmented early life environmental and emotional / cognitive vulnerabilities\n" - + - " \n" + - " 1P50MH096889-01A1\n" + - " NIH\n" + - " \n" + - " \n" + - " Enhancement of the 1000 Functional Connectome Project\n" - + - " \n" + - " 1R03MH096321-01A1\n" + - " TUBITAK\n" + - " \n" + - " \n" + - " CRCNS Data Sharing: An open data repository for cognitive neuroscience: The OpenfMRI Project\n" - + - " \n" + - " 1131441\n" + - " NSF\n" + - " \n" + - " \n" + - " Enhancing Human Cortical Plasticity: Visual Psychophysics and fMRI\n" - + - " \n" + - " 0121950\n" + - " NSF\n" + - " \n" + - " \n" + - " Transforming statistical methodology for neuroimaging meta-analysis.\n" - + - " \n" + - " 100309\n" + - " WT\n" + - " \n" + - " " + - - " \n" - + - " \n" + - " rest________::b8e502674c3c3499d5374e9b2ea6d8d5\n" + - " bio.tools\n" + - " bio.tools\n" + - " false\n" + - " \n" + - " \n" + - " \n" + - " \n" - + - " \n" + - " \n" + - " ATHENA RC\n" + - " aHR0cHM6Ly9lbGl4aXItZ3JlZWNlLm9yZy9zaXRlcy9kZWZhdWx0L2ZpbGVzL3N0eWxlcy90aHVtYm5haWwvcHVibGljL3BhcnRuZXJfbG9nb3MvYXRoZW5hX2xvZ28uanBnP2l0b2s9VXdGWFNpZng=\n" - + - " aHR0cHM6Ly93d3cuYXRoZW5hLWlubm92YXRpb24uZ3IvZW4=\n" + - " \n" + - " \n" - + - ""); - - private QueryInformationSystem queryInformationSystem; - - private Map map; - - @BeforeEach - public void setUp() { - - queryInformationSystem = new QueryInformationSystem(); - queryInformationSystem.setContextRelationResult(communityContext); - } - - @Test - void test1() { - List cInfoList = new ArrayList<>(); - final Consumer consumer = ci -> cInfoList.add(ci); - - queryInformationSystem - .getContextRelation(consumer, "contentproviders", ModelSupport.getIdPrefix(Datasource.class)); - - cInfoList.forEach(c -> System.out.println(new Gson().toJson(c))); - - List rList = new ArrayList<>(); - - cInfoList.forEach(cInfo -> Process.getRelation(cInfo).forEach(rList::add)); - - Assertions.assertEquals(34, rList.size()); - - Assertions - .assertTrue( - rList - .stream() - .map(r -> r.getSource().getId()) - .collect(Collectors.toSet()) - .contains( - String - .format( - "%s|%s::%s", Constants.CONTEXT_ID, - Constants.CONTEXT_NS_PREFIX, - DHPUtils.md5("dh-ch")))); - - Assertions - .assertEquals( - 10, - rList - .stream() - .filter( - r -> r - .getSource() - .getId() - .equals( - String - .format( - "%s|%s::%s", Constants.CONTEXT_ID, - Constants.CONTEXT_NS_PREFIX, - DHPUtils.md5("dh-ch")))) - .collect(Collectors.toList()) - .size()); - - Assertions - .assertEquals( - 10, - rList - .stream() - .filter( - r -> r - .getTarget() - .getId() - .equals( - String - .format( - "%s|%s::%s", Constants.CONTEXT_ID, - Constants.CONTEXT_NS_PREFIX, - DHPUtils.md5("dh-ch")))) - .collect(Collectors.toList()) - .size()); - - Set tmp = rList - .stream() - .filter( - r -> r - .getSource() - .getId() - .equals( - String - .format( - "%s|%s::%s", Constants.CONTEXT_ID, - Constants.CONTEXT_NS_PREFIX, - DHPUtils.md5("dh-ch")))) - .map(r -> r.getTarget().getId()) - .collect(Collectors.toSet()); - - Assertions - .assertTrue( - tmp.contains("10|re3data_____::9ebe127e5f3a0bf401875690f3bb6b81") && - tmp.contains("10|doajarticles::c6cd4b532e12868c1d760a8d7cda6815") && - tmp.contains("10|doajarticles::a6de4499bb87bf3c01add0a9e2c9ed0b") && - tmp.contains("10|doajarticles::6eb31d13b12bc06bbac06aef63cf33c9") && - tmp.contains("10|doajarticles::0da84e9dfdc8419576169e027baa8028") && - tmp.contains("10|re3data_____::84e123776089ce3c7a33db98d9cd15a8") && - tmp.contains("10|openaire____::c5502a43e76feab55dd00cf50f519125") && - tmp.contains("10|re3data_____::a48f09c562b247a9919acfe195549b47") && - tmp.contains("10|opendoar____::97275a23ca44226c9964043c8462be96") && - tmp.contains("10|doajarticles::2899208a99aa7d142646e0a80bfeef05")); - - } - - @Test - public void test2() { - List cInfoList = new ArrayList<>(); - final Consumer consumer = ci -> cInfoList.add(ci); - - queryInformationSystem - .getContextRelation(consumer, "projects", ModelSupport.getIdPrefix(Project.class)); - - cInfoList.forEach(c -> System.out.println(new Gson().toJson(c))); - - List rList = new ArrayList<>(); - - cInfoList.forEach(cInfo -> Process.getRelation(cInfo).forEach(rList::add)); - - Assertions.assertEquals(44, rList.size()); - - Assertions - .assertFalse( - rList - .stream() - .map(r -> r.getSource().getId()) - .collect(Collectors.toSet()) - .contains( - String - .format( - "%s|%s::%s", Constants.CONTEXT_ID, - Constants.CONTEXT_NS_PREFIX, - DHPUtils.md5("dh-ch")))); - - Assertions - .assertEquals( - 2, - rList - .stream() - .filter( - r -> r - .getSource() - .getId() - .equals( - String - .format( - "%s|%s::%s", Constants.CONTEXT_ID, - Constants.CONTEXT_NS_PREFIX, - DHPUtils.md5("clarin")))) - .collect(Collectors.toList()) - .size()); - - Assertions - .assertEquals( - 2, - rList - .stream() - .filter( - r -> r - .getTarget() - .getId() - .equals( - String - .format( - "%s|%s::%s", Constants.CONTEXT_ID, - Constants.CONTEXT_NS_PREFIX, - DHPUtils.md5("clarin")))) - .collect(Collectors.toList()) - .size()); - - Set tmp = rList - .stream() - .filter( - r -> r - .getSource() - .getId() - .equals( - String - .format( - "%s|%s::%s", Constants.CONTEXT_ID, - Constants.CONTEXT_NS_PREFIX, - DHPUtils.md5("clarin")))) - .map(r -> r.getTarget().getId()) - .collect(Collectors.toSet()); - - Assertions - .assertTrue( - tmp.contains("40|corda__h2020::b5a4eb56bf84bef2ebc193306b4d423f") && - tmp.contains("40|corda_______::ef782b2d85676aa3e5a907427feb18c4")); - - rList.forEach(rel -> { - if (rel.getSource().getId().startsWith("40|")) { - String proj = rel.getSource().getId().substring(3); - Assertions.assertTrue(proj.substring(0, proj.indexOf("::")).length() == 12); - } - }); - - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpOrganizationProjectDatasourceTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpOrganizationProjectDatasourceTest.java deleted file mode 100644 index 80b5fd89e..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpOrganizationProjectDatasourceTest.java +++ /dev/null @@ -1,157 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.HashMap; - -import org.apache.commons.io.FileUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.api.java.function.ForeachFunction; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SparkSession; -import org.junit.jupiter.api.AfterAll; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.Test; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.oa.graph.dump.exceptions.NoAvailableEntityTypeException; -import eu.dnetlib.dhp.schema.oaf.Datasource; -import eu.dnetlib.dhp.schema.oaf.Organization; -import eu.dnetlib.dhp.schema.oaf.Project; - -public class DumpOrganizationProjectDatasourceTest { - - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private static SparkSession spark; - - private static Path workingDir; - - private static final Logger log = LoggerFactory - .getLogger(DumpOrganizationProjectDatasourceTest.class); - - private static final HashMap map = new HashMap<>(); - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory(DumpOrganizationProjectDatasourceTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - - SparkConf conf = new SparkConf(); - conf.setAppName(DumpOrganizationProjectDatasourceTest.class.getSimpleName()); - - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - - spark = SparkSession - .builder() - .appName(DumpOrganizationProjectDatasourceTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Test - public void dumpOrganizationTest() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/complete/organization") - .getPath(); - - DumpGraphEntities dg = new DumpGraphEntities(); - - dg.run(false, sourcePath, workingDir.toString() + "/dump", Organization.class, null); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/dump") - .map(item -> OBJECT_MAPPER.readValue(item, eu.dnetlib.dhp.schema.dump.oaf.graph.Organization.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(eu.dnetlib.dhp.schema.dump.oaf.graph.Organization.class)); - - Assertions.assertEquals(15, verificationDataset.count()); - - verificationDataset - .foreach( - (ForeachFunction) o -> System.out - .println(OBJECT_MAPPER.writeValueAsString(o))); - - } - - @Test - public void dumpProjectTest() throws NoAvailableEntityTypeException { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/complete/project") - .getPath(); - - DumpGraphEntities dg = new DumpGraphEntities(); - - dg.run(false, sourcePath, workingDir.toString() + "/dump", Project.class, null); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/dump") - .map(item -> OBJECT_MAPPER.readValue(item, eu.dnetlib.dhp.schema.dump.oaf.graph.Project.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(eu.dnetlib.dhp.schema.dump.oaf.graph.Project.class)); - - Assertions.assertEquals(12, verificationDataset.count()); - - verificationDataset - .foreach( - (ForeachFunction) o -> System.out - .println(OBJECT_MAPPER.writeValueAsString(o))); - - } - - @Test - public void dumpDatasourceTest() throws NoAvailableEntityTypeException { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/complete/datasource") - .getPath(); - - DumpGraphEntities dg = new DumpGraphEntities(); - - dg.run(false, sourcePath, workingDir.toString() + "/dump", Datasource.class, null); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/dump") - .map(item -> OBJECT_MAPPER.readValue(item, eu.dnetlib.dhp.schema.dump.oaf.graph.Datasource.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(eu.dnetlib.dhp.schema.dump.oaf.graph.Datasource.class)); - - Assertions.assertEquals(5, verificationDataset.count()); - - verificationDataset - .foreach( - (ForeachFunction) o -> System.out - .println(OBJECT_MAPPER.writeValueAsString(o))); - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpRelationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpRelationTest.java deleted file mode 100644 index 763318ae4..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpRelationTest.java +++ /dev/null @@ -1,305 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.HashMap; - -import org.apache.commons.io.FileUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.api.java.function.ForeachFunction; -import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.Row; -import org.apache.spark.sql.SparkSession; -import org.junit.jupiter.api.AfterAll; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.Test; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.schema.dump.oaf.graph.Relation; - -public class DumpRelationTest { - - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private static SparkSession spark; - - private static Path workingDir; - - private static final Logger log = LoggerFactory - .getLogger(DumpRelationTest.class); - - private static final HashMap map = new HashMap<>(); - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory(DumpRelationTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - - SparkConf conf = new SparkConf(); - conf.setAppName(DumpRelationTest.class.getSimpleName()); - - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - - spark = SparkSession - .builder() - .appName(DumpRelationTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Test - public void test1() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/relation/relation") - .getPath(); - - SparkDumpRelationJob.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/relation", - "-sourcePath", sourcePath - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/relation") - .map(item -> OBJECT_MAPPER.readValue(item, Relation.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Relation.class)); - - verificationDataset.createOrReplaceTempView("table"); - - verificationDataset - .foreach((ForeachFunction) r -> System.out.println(new ObjectMapper().writeValueAsString(r))); - - Dataset check = spark - .sql( - "SELECT reltype.name, source.id source, source.type stype, target.id target,target.type ttype, provenance.provenance " - + - "from table "); - - Assertions.assertEquals(22, check.filter("name = 'isProvidedBy'").count()); - Assertions - .assertEquals( - 22, check - .filter( - "name = 'isProvidedBy' and stype = 'datasource' and ttype = 'organization' and " + - "provenance = 'Harvested'") - .count()); - - Assertions.assertEquals(7, check.filter("name = 'isParticipant'").count()); - Assertions - .assertEquals( - 7, check - .filter( - "name = 'isParticipant' and stype = 'organization' and ttype = 'project' " + - "and provenance = 'Harvested'") - .count()); - - Assertions.assertEquals(1, check.filter("name = 'isAuthorInstitutionOf'").count()); - Assertions - .assertEquals( - 1, check - .filter( - "name = 'isAuthorInstitutionOf' and stype = 'organization' and ttype = 'result' " + - "and provenance = 'Inferred by OpenAIRE'") - .count()); - } - - @Test - public void test2() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/relation/relation_validated") - .getPath(); - - SparkDumpRelationJob.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/relation", - "-sourcePath", sourcePath - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/relation") - .map(item -> OBJECT_MAPPER.readValue(item, Relation.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Relation.class)); - - verificationDataset.createOrReplaceTempView("table"); - - verificationDataset - .foreach((ForeachFunction) r -> System.out.println(new ObjectMapper().writeValueAsString(r))); - - Dataset check = spark - .sql( - "SELECT reltype.name, source.id source, source.type stype, target.id target,target.type ttype, provenance.provenance " - + - "from table "); - - Assertions.assertEquals(20, check.filter("name = 'isProvidedBy'").count()); - Assertions - .assertEquals( - 20, check - .filter( - "name = 'isProvidedBy' and stype = 'datasource' and ttype = 'organization' and " + - "provenance = 'Harvested'") - .count()); - - Assertions.assertEquals(7, check.filter("name = 'isParticipant'").count()); - Assertions - .assertEquals( - 7, check - .filter( - "name = 'isParticipant' and stype = 'organization' and ttype = 'project' " + - "and provenance = 'Harvested'") - .count()); - - Assertions.assertEquals(1, check.filter("name = 'isAuthorInstitutionOf'").count()); - Assertions - .assertEquals( - 1, check - .filter( - "name = 'isAuthorInstitutionOf' and stype = 'organization' and ttype = 'result' " + - "and provenance = 'Inferred by OpenAIRE'") - .count()); - - Assertions.assertEquals(2, check.filter("name = 'isProducedBy'").count()); - Assertions - .assertEquals( - 2, check - .filter( - "name = 'isProducedBy' and stype = 'project' and ttype = 'result' " + - "and provenance = 'Harvested' and validated = true " + - "and validationDate = '2021-08-06'") - .count()); - } - - @Test - public void test3() throws Exception {// - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/relation/relation") - .getPath(); - - SparkDumpRelationJob.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/relation", - "-sourcePath", sourcePath, - "-removeSet", "isParticipant" - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/relation") - .map(item -> OBJECT_MAPPER.readValue(item, Relation.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Relation.class)); - - verificationDataset.createOrReplaceTempView("table"); - - verificationDataset - .foreach((ForeachFunction) r -> System.out.println(new ObjectMapper().writeValueAsString(r))); - - Dataset check = spark - .sql( - "SELECT reltype.name, source.id source, source.type stype, target.id target,target.type ttype, provenance.provenance " - + - "from table "); - - Assertions.assertEquals(22, check.filter("name = 'isProvidedBy'").count()); - Assertions - .assertEquals( - 22, check - .filter( - "name = 'isProvidedBy' and stype = 'datasource' and ttype = 'organization' and " + - "provenance = 'Harvested'") - .count()); - - Assertions.assertEquals(0, check.filter("name = 'isParticipant'").count()); - - Assertions.assertEquals(1, check.filter("name = 'isAuthorInstitutionOf'").count()); - Assertions - .assertEquals( - 1, check - .filter( - "name = 'isAuthorInstitutionOf' and stype = 'organization' and ttype = 'result' " + - "and provenance = 'Inferred by OpenAIRE'") - .count()); - } - - @Test - public void test4() throws Exception {// - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/relation/relation") - .getPath(); - - SparkDumpRelationJob.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/relation", - "-sourcePath", sourcePath, - "-removeSet", "isParticipant;isAuthorInstitutionOf" - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/relation") - .map(item -> OBJECT_MAPPER.readValue(item, Relation.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Relation.class)); - - verificationDataset.createOrReplaceTempView("table"); - - verificationDataset - .foreach((ForeachFunction) r -> System.out.println(new ObjectMapper().writeValueAsString(r))); - - Dataset check = spark - .sql( - "SELECT reltype.name, source.id source, source.type stype, target.id target,target.type ttype, provenance.provenance " - + - "from table "); - - Assertions.assertEquals(22, check.filter("name = 'isProvidedBy'").count()); - Assertions - .assertEquals( - 22, check - .filter( - "name = 'isProvidedBy' and stype = 'datasource' and ttype = 'organization' and " + - "provenance = 'Harvested'") - .count()); - - Assertions.assertEquals(0, check.filter("name = 'isParticipant'").count()); - - Assertions.assertEquals(0, check.filter("name = 'isAuthorInstitutionOf'").count()); - - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/ExtractRelationFromEntityTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/ExtractRelationFromEntityTest.java deleted file mode 100644 index 27573bb32..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/ExtractRelationFromEntityTest.java +++ /dev/null @@ -1,172 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; - -import org.apache.commons.io.FileUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.api.java.function.FilterFunction; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SparkSession; -import org.junit.jupiter.api.*; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.schema.dump.oaf.graph.Relation; - -public class ExtractRelationFromEntityTest { - - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private static SparkSession spark; - - private static Path workingDir; - - private static final Logger log = LoggerFactory - .getLogger(ExtractRelationFromEntityTest.class); - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory(ExtractRelationFromEntityTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - - SparkConf conf = new SparkConf(); - conf.setAppName(ExtractRelationFromEntityTest.class.getSimpleName()); - - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - - spark = SparkSession - .builder() - .appName(ExtractRelationFromEntityTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Test - void test1() { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/singelRecord_pub.json") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - Extractor ex = new Extractor(); - ex - .run( - false, sourcePath, workingDir.toString() + "/relation", - // eu.dnetlib.dhp.schema.oaf.Publication.class, communityMapPath); - eu.dnetlib.dhp.schema.oaf.Publication.class, communityMapPath); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/relation") - .map(item -> OBJECT_MAPPER.readValue(item, Relation.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Relation.class)); - - Assertions - .assertEquals( - 9, - verificationDataset.filter("source.id = '50|dedup_wf_001::15270b996fa8fd2fb5723daeab3685c3'").count()); - - Assertions - .assertEquals( - 9, - verificationDataset.filter("source.id = '50|dedup_wf_001::15270b996fa8fd2fb5723daxab3685c3'").count()); - - Assertions - .assertEquals( - "IsRelatedTo", verificationDataset - .filter((FilterFunction) row -> row.getSource().getId().startsWith("00")) - .collectAsList() - .get(0) - .getReltype() - .getName()); - - Assertions - .assertEquals( - "relationship", verificationDataset - .filter((FilterFunction) row -> row.getSource().getId().startsWith("00")) - .collectAsList() - .get(0) - .getReltype() - .getType()); - - Assertions - .assertEquals( - "context", verificationDataset - .filter((FilterFunction) row -> row.getSource().getId().startsWith("00")) - .collectAsList() - .get(0) - .getSource() - .getType()); - - Assertions - .assertEquals( - "result", verificationDataset - .filter((FilterFunction) row -> row.getSource().getId().startsWith("00")) - .collectAsList() - .get(0) - .getTarget() - .getType()); - Assertions - .assertEquals( - "IsRelatedTo", verificationDataset - .filter((FilterFunction) row -> row.getTarget().getId().startsWith("00")) - .collectAsList() - .get(0) - .getReltype() - .getName()); - - Assertions - .assertEquals( - "relationship", verificationDataset - .filter((FilterFunction) row -> row.getTarget().getId().startsWith("00")) - .collectAsList() - .get(0) - .getReltype() - .getType()); - - Assertions - .assertEquals( - "context", verificationDataset - .filter((FilterFunction) row -> row.getTarget().getId().startsWith("00")) - .collectAsList() - .get(0) - .getTarget() - .getType()); - - Assertions - .assertEquals( - "result", verificationDataset - .filter((FilterFunction) row -> row.getTarget().getId().startsWith("00")) - .collectAsList() - .get(0) - .getSource() - .getType()); - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/FunderParsingTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/FunderParsingTest.java deleted file mode 100644 index eb5919fd5..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/FunderParsingTest.java +++ /dev/null @@ -1,70 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import org.dom4j.DocumentException; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.Test; -import org.xml.sax.SAXException; - -import eu.dnetlib.dhp.schema.dump.oaf.graph.Funder; - -class FunderParsingTest { - - @Test - void testFunderTwoLevels() throws DocumentException { - - String funding_Stream = "nsf_________::NSFNSFNational Science " - + - "FoundationUSnsf_________::NSF::CISE/OAD::CISE/CCFDivision " - + - "of Computing and Communication FoundationsDivision of Computing and Communication " + - "Foundationsnsf_________::NSF::CISE/OADDirectorate for " - + - "Computer & Information Science & EngineeringDirectorate for Computer & " + - "Information Science & Engineeringnsf:fundingStream"; - - Funder f = DumpGraphEntities.getFunder(funding_Stream); - - Assertions.assertEquals("NSF", f.getShortName()); - Assertions.assertEquals("National Science Foundation", f.getName()); - Assertions.assertEquals("US", f.getJurisdiction()); - - Assertions.assertEquals("NSF::CISE/OAD::CISE/CCF", f.getFunding_stream().getId()); - Assertions - .assertEquals( - "Directorate for Computer & Information Science & Engineering - Division of Computing and Communication Foundations", - f.getFunding_stream().getDescription()); - - } - - @Test - void testFunderThreeeLevels() throws DocumentException, SAXException { - String funding_stream = "ec__________::EC" + - "EC" + - "European Commission" + - "EU" + - "" + - "ec__________::EC::H2020::ERC::ERC-COG" + - "Consolidator Grant" + - "ERC-COGec:h2020toas" + - "ec__________::EC::H2020::ERC" + - "European Research Council" + - "ERCec:h2020fundings" + - "ec__________::EC::H2020H2020" + - "Horizon 2020 Framework Programme" + - "ec:h2020fundings"; - - Funder f = DumpGraphEntities.getFunder(funding_stream); - - Assertions.assertEquals("EC", f.getShortName()); - Assertions.assertEquals("European Commission", f.getName()); - Assertions.assertEquals("EU", f.getJurisdiction()); - - Assertions.assertEquals("EC::H2020::ERC::ERC-COG", f.getFunding_stream().getId()); - Assertions - .assertEquals( - "Horizon 2020 Framework Programme - European Research Council - Consolidator Grant", - f.getFunding_stream().getDescription()); - - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystemTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystemTest.java deleted file mode 100644 index 08fcd49a8..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystemTest.java +++ /dev/null @@ -1,810 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import static org.mockito.Mockito.lenient; - -import java.util.*; -import java.util.function.Consumer; - -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeEach; -import org.junit.jupiter.api.Test; -import org.junit.jupiter.api.extension.ExtendWith; -import org.mockito.Mock; -import org.mockito.junit.jupiter.MockitoExtension; - -import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; - -@ExtendWith(MockitoExtension.class) -class QueryInformationSystemTest { - - private static final String XQUERY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') " - + - " where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " + - " and $x//context/param[./@name = 'status']/text() = 'all' " + - " return " + - "$x//context"; - - private static final String XQUERY_ENTITY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') " - + - "where $x//context[./@type='community' or ./@type = 'ri'] and $x//context/param[./@name = 'status']/text() = 'all' return " - + - "concat(data($x//context/@id) , '@@', $x//context/param[./@name =\"name\"]/text(), '@@', " + - "$x//context/param[./@name=\"description\"]/text(), '@@', $x//context/param[./@name = \"subject\"]/text(), '@@', " - + - "$x//context/param[./@name = \"zenodoCommunity\"]/text(), '@@', $x//context/@type)"; - - List communityMap = Arrays - .asList( - "clarin@@Common Language Resources and Technology Infrastructure@@CLARIN@@@@oac_clarin@@ri", - "ee@@Sustainable Development Solutions Network - Greece@@The UN Sustainable Development Solutions Network (SDSN) has been operating since 2012 under the auspices of the UN Secretary-General. " - + - "SDSN mobilizes global scientific and technological expertise to promote practical solutions for sustainable development, including the implementation of the Sustainable Development Goals (SDGs) and the Paris Climate Agreement. The Greek hub of SDSN has been included in the SDSN network in 2017 and is co-hosted by ICRE8: International Center for Research on the Environment and the Economy and the Political Economy of Sustainable Development Lab.@@SDG13 - Climate action,SDG8 - Decent work and economic growth,SDG15 - " - + - "Life on land,SDG2 - Zero hunger,SDG17 - Partnerships for the ´goals,SDG10 - Reduced inequalities,SDG5 - Gender equality,SDG12 - Responsible consumption and production,SDG14 - Life below water,SDG6 - Clean water and sanitation,SDG11 - Sustainable cities and communities,SDG1 - No poverty,SDG3 - Good health and well being,SDG7 - Affordable and clean energy,SDG4 - Quality education,SDG9 - Industry innovation and infrastructure,SDG16 - Peace justice and strong institutions@@oac_sdsn-greece@@community", - "dh-ch@@Digital Humanities and Cultural Heritage@@This community gathers research results, data, scientific publications and projects related to the domain of Digital Humanities. This broad definition includes Humanities, Cultural Heritage, History, Archaeology and related fields.@@modern art,monuments,europeana data model,sites,field walking,frescoes,LIDO metadata schema,art history,excavation,Arts and Humanities General,cities,coins,temples,numismatics,lithics,roads,environmental archaeology,digital cultural heritage,archaeological reports,history,CRMba,churches,cultural heritage,archaeological stratigraphy,religious art,buidings,digital humanities,survey,archaeological sites,linguistic studies,bioarchaeology,architectural orders,palaeoanthropology,fine arts,europeana,CIDOC CRM,decorations,classic art,stratigraphy,digital archaeology,intangible cultural heritage,walls,humanities,chapels,CRMtex,Language and Literature,paintings,archaeology,fair data,mosaics,burials,architecture,medieval art,castles,CARARE metadata schema,statues,natural language processing,inscriptions,CRMsci,vaults,contemporary art,Arts and Humanities,CRMarchaeo,pottery,site,architectural,vessels@@oac_dh-ch@@community", - "fam@@Fisheries and Aquaculture Management@@Conservation of marine resources for sustainable development. The Fisheries and Aquaculture community focus on resources (document, data, codes..) which have been produced in the framework of projects (H2020, FP7, ..) related to the domain of fisheries and aquaculture.@@Stock Assessment,pelagic,Acoustic,Fish farming,Fisheries,Fishermen,maximum sustainable yield,trawler,Fishing vessel,Fisherman,Fishing gear,mackerel,RFMO,Fish Aggregating Device,Bycatch,Fishery,common fisheries policy,Fishing fleet,Aquaculture@@fisheries@@community", - "ni@@Neuroinformatics@@The neuroinformatics dashboard gathers research outputs from the 'neuroinformatics' community at large including the fields of: neuroscience, neuroinformatics, brain imaging databases and standards, brain imaging techniques, neuroimaging methods including statistics and machine learning. The dashboard covers a wide range of imaging methods including (but not limited to): MRI, TEP, EEG, MEG, and studies involving human participants as well as animal studies.@@brain mapping,brain imaging,electroencephalography,arterial spin labelling,brain fingerprinting,brain,neuroimaging,Multimodal Brain Image Analysis,fMRI,neuroinformatics,fetal brain,brain ultrasonic imaging,topographic brain mapping,diffusion tensor imaging,computerized knowledge assessment,connectome mapping,brain magnetic resonance imaging,brain abnormalities@@oac_ni@@community", - "mes@@European Marine Science@@This community was initially defined to include a very broad range of topics, with the intention to generate a number of more focused and sustainable dashboards for research communities and initiatives. As outlined in the logo of this community, we intend to setup a community dashboard for EuroMarine (a consortium of 56 research and academic organisations) and monitoring dashboards for marine research initiatives, including infrastructures (e.g. EMBRC & EMSO), advisory boards (e.g. Marine Boards & ICES), and transnational funding bodies (e.g. JPI-Oceans and Tara Foundation).@@marine,ocean,fish,aqua,sea@@oac_mes@@community", - "instruct@@Instruct-ERIC@@Instruct-ERIC is the European Research Infrastructure for Structural Biology@@@@oac_instruct@@community", - "elixir-gr@@The Greek National Node of the ESFRI European RI ELIXIR@@ELIXIR-GR enhances the potential of the Greek bioinformatics community to offer open, easily accessible and state -of- the- art services to the Greek and the international academic community and other stakeholders, such as industry and the health sector. More importantly, by providing these services, the infrastructure facilitates discoveries in the field of the life-sciences, having strong spill over effects in promoting innovation in sectors such as discovery of new drug targets and development of novel therapeutic agents, development of innovative diagnostics, personalized medicine, and development of innovative biotechnological products and processes.@@@@oaa_elixir-gr@@ri", - "aginfra@@Agricultural and Food Sciences@@The scope of this community is to provide access to publications, research data, projects and software that are related to agricultural and food sciences@@animal production and health,fisheries and aquaculture,food safety and human nutrition,information management,food technology,agri-food education and extension,natural resources and environment,food system,engineering technology and Research,agriculture,food safety risk assessment,food security,farming practices and systems,plant production and protection,agri-food economics and policy,Agri-food,food distribution,forestry@@oac_aginfra@@community", - "dariah@@DARIAH EU@@The Digital Research Infrastructure for the Arts and Humanities (DARIAH) aims to enhance and support digitally-enabled research and teaching across the arts and humanities. It develops, maintains and operates an infrastructure in support of ICT-based research practices and sustains researchers in using them to build, analyse and interpret digital resources. DARIAH was established as a European Research Infrastructure Consortium (ERIC) in August 2014. Currently, DARIAH has 18 Members and several cooperating partners in eight non-member countries. Here you will find a growing collection of DARIAH-affiliated research outputs and other documents. @@@@dariah@@ri", - "epos@@European Plate Observing System@@EPOS, the European Plate Observing System, is a long-term plan to facilitate integrated use of data, data products, and facilities from distributed research infrastructures for solid Earth science in Europe.@@@@@@ri", - "covid-19@@Corona Virus Disease@@This portal provides access to publications, research data, projects and software that may be relevant to the Corona Virus Disease (COVID-19). The OpenAIRE COVID-19 Gateway aggregates COVID-19 related records, links them and provides a single access point for discovery and navigation. We tag content from the OpenAIRE Research Graph (10,000+ data sources) and additional sources. All COVID-19 related research results are linked to people, organizations and projects, providing a contextualized navigation.@@COVID19,SARS-CoV,HCoV-19,mesh:C000657245,MERS-CoV,Síndrome Respiratorio Agudo Severo,mesh:COVID-19,COVID2019,COVID-19,SARS-CoV-2,2019 novel coronavirus,severe acute respiratory syndrome coronavirus 2,Orthocoronavirinae,Coronaviridae,mesh:D045169,coronavirus,SARS,coronaviruses,coronavirus disease-19,sars cov 2,Middle East Respiratory Syndrome,Severe acute respiratory syndrome coronavirus 2,Severe Acute Respiratory Syndrome,coronavirus disease 2019,2019-nCoV@@covid-19@@community"); - - List communityContext = Arrays - .asList( - "\n" + - " all\n" + - " CLARIN\n" + - " https://www.clarin.eu/sites/default/files/clarin-frontpage-logo.jpg\n" - + - " Common Language Resources and Technology Infrastructure\n" + - " maria@clarin.eu,dieter@clarin.eu,f.m.g.dejong@uu.nl,paolo.manghi@isti.cnr.it\n" - + - " \n" + - " (Part of) the work reported here was made possible by using the CLARIN infrastructure.\n" - + - " The work reported here has received funding through <CLARIN national consortium member, e.g. CLARIN.SI>, <XYZ> project, grant no. <XYZ>.\n" - + - " The work reported here has received funding (through CLARIN ERIC) from the European Union’s Horizon 2020 research and innovation programme under grant agreement No <0-9> for project <XYZ>.\n" - + - " (E.g. No 676529 for project CLARIN-PLUS.)\n" + - " oac_clarin\n" + - " 2018-03-01T12:00:00\n" + - " \n" + - " \n" + - " CLARIN-PLUS\n" + - " \n" + - " \n" + - " 676529\n" + - " http://www.clarin.eu\n" + - " EC\n" + - " H2020-INFRADEV-1-2015-1\n" + - " CLARIN+\n" + - " \n" + - " \n" + - " Common Language Resources and Technology Infrastructure\n" - + - " CLARIN\n" + - " 212230\n" + - " EC\n" + - " corda_______::ef782b2d85676aa3e5a907427feb18c4\n" + - " \n" + - " \n" + - " " + - "\n" + - " \n" + - " LINDAT/CLARIN repository\n" + - " LINDAT/CLARIN repository\n" + - " true\n" + - " \n" + - " \n" + - " \n" + - " \n" + - " CLARIN-D\n" + - " https://www.clarin-d.de/en/\n" + - " \n" + - " http://www.lrec-conf.org/proceedings/lrec2018/pdf/504.pdf\n" - + - " Germany\n" + - " \n" + - " \n" + - " \n" - + - " \n" + - "", - "\n" + - " all\n" + - " This community gathers research results, data, scientific publications and projects related to the domain of Digital Humanities. This broad definition includes Humanities, Cultural Heritage, History, Archaeology and related fields.\n" - + - " http://sanmamante.org/DH_CH_logo.png\n" + - " Digital Humanities and Cultural Heritage\n" + - " ileniagalluccio87@gmail.com,achille.felicetti@gmail.com,paolo.manghi@isti.cnr.it,tim.evans@york.ac.uk\n" - + - " modern art,monuments,europeana data model,sites,field walking,frescoes,LIDO metadata schema,art history,excavation,Arts and Humanities General,cities,coins,temples,numismatics,lithics,roads,environmental archaeology,digital cultural heritage,archaeological reports,history,CRMba,churches,cultural heritage,archaeological stratigraphy,religious art,buidings,digital humanities,survey,archaeological sites,linguistic studies,bioarchaeology,architectural orders,palaeoanthropology,fine arts,europeana,CIDOC CRM,decorations,classic art,stratigraphy,digital archaeology,intangible cultural heritage,walls,humanities,chapels,CRMtex,Language and Literature,paintings,archaeology,fair data,mosaics,burials,architecture,medieval art,castles,CARARE metadata schema,statues,natural language processing,inscriptions,CRMsci,vaults,contemporary art,Arts and Humanities,CRMarchaeo,pottery,site,architectural,vessels\n" - + - " The present work has been partially supported by the PARTHENOS project, funded by the European Commission (Grant Agreement No. 654119) under the HORIZON 2020 - INFRADEV-4-2014/2015 call\n" - + - " oac_dh-ch\n" + - " 2018-03-01T12:00:00\n" + - " \n" + - " \n" - + - " Pooling Activities, Resources and Tools for Heritage E-research Networking, Optimization and Synergies\n" - + - " The present work has been partially supported by the PARTHENOS project, funded by the European Commission (Grant Agreement No. 654119) under the HORIZON 2020 - INFRADEV-4-2014/2015 call\n" - + - " \n" + - " 654119\n" + - " http://www.parthenos-project.eu\n" + - " EC\n" + - " PARTHENOS\n" + - " \n" + - " \n" + - " \n" + - " \n" - + - " re3data_____::9ebe127e5f3a0bf401875690f3bb6b81\n" + - " The UK's largest collection of digital research data in the social sciences and humanities\n" - + - " UK Data Archive\n" + - " true\n" + - " \n" + - " \n" - + - " doajarticles::c6cd4b532e12868c1d760a8d7cda6815\n" + - " Journal of Data Mining and Digital Humanities\n" + - " Journal of Data Mining and Digital Humanities\n" + - " true\n" + - " \n" + - " \n" - + - " doajarticles::a6de4499bb87bf3c01add0a9e2c9ed0b\n" + - " Frontiers in Digital Humanities\n" + - " Frontiers in Digital Humanities\n" + - " true\n" + - " \n" + - " \n" - + - " doajarticles::6eb31d13b12bc06bbac06aef63cf33c9\n" + - " Il Capitale Culturale: Studies on the Value of Cultural Heritage\n" - + - " Il Capitale Culturale: Studies on the Value of Cultural Heritage\n" - + - " true\n" + - " \n" + - " \n" - + - " doajarticles::0da84e9dfdc8419576169e027baa8028\n" + - " Conservation Science in Cultural Heritage\n" + - " Conservation Science in Cultural Heritage\n" + - " true\n" + - " \n" + - " \n" - + - " re3data_____::84e123776089ce3c7a33db98d9cd15a8\n" + - " Electronic Archiving System\n" + - " EASY\n" + - " true\n" + - " \n" + - " \n" + - " openaire____::c5502a43e76feab55dd00cf50f519125\n" + - " DANS-KB Harvester\n" + - " Gemeenschappelijke Harvester DANS-KB\n" + - " true\n" + - " \n" + - " \n" + - " re3data_____::a48f09c562b247a9919acfe195549b47\n" + - " ads\n" + - " Archaeology Data Service\n" + - " true\n" + - " \n" + - " \n" + - " opendoar____::97275a23ca44226c9964043c8462be96\n" + - " KNAW Repository\n" + - " KNAW Repository\n" + - " true\n" + - " \n" + - " \n" - + - " doajarticles::2899208a99aa7d142646e0a80bfeef05\n" + - " Internet Archaeology\n" + - " Internet Archaeology\n" + - " true\n" + - " \n" + - " \n" + - " \n" + - "\n", - "\n" + - " all\n" + - " The neuroinformatics dashboard gathers research outputs from the 'neuroinformatics' community at large including the fields of: neuroscience, neuroinformatics, brain imaging databases and standards, brain imaging techniques, neuroimaging methods including statistics and machine learning. The dashboard covers a wide range of imaging methods including (but not limited to): MRI, TEP, EEG, MEG, and studies involving human participants as well as animal studies.\n" - + - " https://docs.google.com/drawings/u/0/d/10e191xGoGf4uaRluMqbt_7cCj6LSCs2a29im4CmWjqU/export/png\n" - + - " Neuroinformatics\n" + - " sorina.pop@creatis.insa-lyon.fr,camille.maumet@inria.fr,christian.barillot@irisa.fr,xavier.rolland@irisa.fr,axel.bonnet@creatis.insa-lyon.fr,paolo.manghi@isti.cnr.it\n" - + - " brain mapping,brain imaging,electroencephalography,arterial spin labelling,brain fingerprinting,brain,neuroimaging,Multimodal Brain Image Analysis,fMRI,neuroinformatics,fetal brain,brain ultrasonic imaging,topographic brain mapping,diffusion tensor imaging,computerized knowledge assessment,connectome mapping,brain magnetic resonance imaging,brain abnormalities\n" - + - " \n" + - " oac_ni\n" + - " 2018-03-01T12:00:00\n" + - " \n" + - " \n" + - " re3data_____::5b9bf9171d92df854cf3c520692e9122\n" + - " Formerly:OpenFMRI\n" + - " OpenNeuro\n" + - " true\n" + - " \n" + - " \n" + - " doajarticles::c7d3de67dc77af72f6747157441252ec\n" + - " Research Ideas and Outcomes\n" + - " Research Ideas and Outcomes\n" + - " true\n" + - " \n" + - " \n" + - " re3data_____::8515794670370f49c1d176c399c714f5\n" + - " Neuroimaging Informatics Tools and Resources Clearinghouse\n" - + - " NITRC\n" + - " true\n" + - " \n" + - " \n" + - " doajarticles::d640648c84b10d425f96f11c3de468f3\n" + - " Frontiers in Neuroinformatics\n" + - " Frontiers in Neuroinformatics\n" + - " true\n" + - " \n" + - " \n" + - " doajarticles::0c0e74daa5d95504eade9c81ebbd5b8a\n" + - " NeuroImage: Clinical\n" + - " NeuroImage: Clinical\n" + - " true\n" + - " \n" + - " \n" + - " rest________::fb1a3d4523c95e63496e3bc7ba36244b\n" + - " NeuroVault\n" + - " NeuroVault\n" + - " true\n" + - " \n" + - " \n" + - "\n", - "\n" + - " all\n" + - " Instruct-ERIC is the European Research Infrastructure for Structural Biology\n" - + - " https://instruct-eric.eu/templates/instructeric/images/logos/instruct-eric-logo-noline.png\n" - + - " Instruct-ERIC\n" + - " claudia@instruct-eric.eu,carazo@cnb.csic.es,echrysina@eie.gr,susan@instruct-eric.eu,naomi@instruct-eric.eu,natalie@instruct-eric.eu,pmarie@igbmc.fr,darren.hart@ibs.fr,claudia@strubi.ox.ac.uk,paolo.manghi@isti.cnr.it\n" - + - " \n" + - " The authors acknowledge the support and the use of resources of Instruct-ERIC.\n" - + - " The authors acknowledge the support and the use of resources of Instruct (PID # or APPID #), a Landmark ESFRI project\n" - + - " oac_instruct\n" + - " 2018-03-01T12:00:00\n" + - " \n" + - " \n" - + - " Authentication and Authorisation For Research and Collaboration\n" - + - " \n" + - " 730941\n" + - " \n" + - " H2020-EINFRA-2016-1\n" + - " AARC2\n" + - " EC\n" + - " \n" + - " \n" - + - " Building data bridges between biological and medical infrastructures in Europe\n" - + - " \n" + - " 284209\n" + - " \n" + - " FP7-INFRASTRUCTURES-2011-1\n" + - " EC\n" + - " BioMedBridges\n" + - " \n" + - " \n" - + - " Transnational access and enhancement of integrated Biological Structure determination at synchrotron X-ray radiation facilities\n" - + - " \n" + - " 283570\n" + - " \n" + - " FP7-INFRASTRUCTURES-2011-1\n" + - " EC\n" + - " BioStruct-X\n" + - " \n" + - " \n" - + - " Coordinated Research Infrastructures Building Enduring Life-science services\n" - + - " \n" + - " 654248\n" + - " \n" + - " H2020-INFRADEV-1-2014-1\n" + - " EC\n" + - " CORBEL\n" + - " \n" + - " \n" - + - " Infrastructure for NMR, EM and X-rays for translational research\n" - + - " \n" + - " 653706\n" + - " \n" + - " H2020-INFRAIA-2014-2015\n" + - " EC\n" + - " iNEXT\n" + - " \n" + - " \n" - + - " Integrated Structural Biology Infrastructure\n" + - " \n" + - " 211252\n" + - " \n" + - " FP7-INFRASTRUCTURES-2007-1\n" + - " EC\n" + - " INSTRUCT\n" + - " \n" + - " \n" - + - " Releasing the full potential of Instruct to expand and consolidate infrastructure services for integrated structural life science research\n" - + - " \n" + - " 731005\n" + - " \n" + - " H2020-INFRADEV-2016-1\n" + - " EC\n" + - " INSTRUCT-ULTRA\n" + - " \n" + - " \n" - + - " Opening Synchrotron Light for Experimental Science and Applications in the Middle East\n" - + - " \n" + - " 730943\n" + - " \n" + - " H2020-INFRASUPP-2016-1\n" + - " EC\n" + - " OPEN SESAME\n" + - " \n" + - " \n" - + - " Infrastructure for Protein Production Platforms\n" - + - " \n" + - " 227764\n" + - " \n" + - " FP7-INFRASTRUCTURES-2008-1\n" + - " EC\n" + - " PCUBE\n" + - " \n" + - " \n" - + - " European Vaccine Research and Development Infrastructure\n" - + - " \n" + - " 730964\n" + - " \n" + - " H2020-INFRAIA-2016-1\n" + - " EC\n" + - " TRAMSVAC2\n" + - " \n" + - " \n" - + - " World-wide E-infrastructure for structural biology\n" - + - " \n" + - " 675858\n" + - " \n" + - " H2020-EINFRA-2015-1\n" + - " EC\n" + - " West-Life\n" + - " \n" + - " \n" + - " Expanding research infrastructure visibility to strengthen strategic partnerships\n" - + - " RI-VIS\n" + - " 824063\n" + - " EC\n" + - " corda__h2020::af93b591b76991d8437993a8f6fc6538\n" + - " \n" + - " \n" + - " \n" - + - " \n" - + - " \n" + - " instruct\n" + - " \n" + - " \n" + - " \n" - + - " west-life\n" + - " \n" + - " \n" + - " \n" + - " \n" - + - " \n" + - " FRISBI\n" + - " aHR0cDovL2ZyaXNiaS5ldS9zdGF0aWMvaW1hZ2VzL2xvZ29zL2xvZ28tZnJpc2JpLnBuZw==\n" - + - " aHR0cDovL2ZyaXNiaS5ldS8=\n" + - " \n" + - " \n" + - " RI-VIS\n" + - " aHR0cHM6Ly9yaS12aXMuZXUvbmV0d29yay9yaXZpcy90ZW1wbGF0ZXMvcml2aXMvaW1hZ2VzL1JJLVZJU0xvZ29GaW5hbC0wNi5wbmc=\n" - + - " aHR0cHM6Ly9yaS12aXMuZXU=\n" + - " \n" + - " \n" + - " CIISB\n" + - " aHR0cDovL2JpYy5jZWl0ZWMuY3ovZmlsZXMvMjkyLzEyNS5KUEc=\n" + - " aHR0cHM6Ly93d3cuY2lpc2Iub3Jn\n" + - " \n" + - " \n" + - "\n", - "\n" + - " all\n" + - " ELIXIR-GR enhances the potential of the Greek bioinformatics community to offer open, easily accessible and state -of- the- art services to the Greek and the international academic community and other stakeholders, such as industry and the health sector. More importantly, by providing these services, the infrastructure facilitates discoveries in the field of the life-sciences, having strong spill over effects in promoting innovation in sectors such as discovery of new drug targets and development of novel therapeutic agents, development of innovative diagnostics, personalized medicine, and development of innovative biotechnological products and processes.\n" - + - " https://elixir-greece.org/sites/default/files/ELIXIR_GREECE_white_background.png\n" - + - " The Greek National Node of the ESFRI European RI ELIXIR\n" + - " vergoulis@imis.athena-innovation.gr,schatz@imis.athena-innovation.gr,paolo.manghi@isti.cnr.it\n" - + - " \n" + - " \n" + - " oaa_elixir-gr\n" + - " 2018-03-01T12:00:00\n" + - " \n" + - " \n" - + - " \n" + - " rest________::b8e502674c3c3499d5374e9b2ea6d8d5\n" + - " bio.tools\n" + - " bio.tools\n" + - " false\n" + - " \n" + - " \n" + - " \n" + - " \n" - + - " \n" + - " \n" + - " ATHENA RC\n" + - " aHR0cHM6Ly9lbGl4aXItZ3JlZWNlLm9yZy9zaXRlcy9kZWZhdWx0L2ZpbGVzL3N0eWxlcy90aHVtYm5haWwvcHVibGljL3BhcnRuZXJfbG9nb3MvYXRoZW5hX2xvZ28uanBnP2l0b2s9VXdGWFNpZng=\n" - + - " aHR0cHM6Ly93d3cuYXRoZW5hLWlubm92YXRpb24uZ3IvZW4=\n" + - " \n" + - " \n" - + - ""); - - @Mock - private ISLookUpService isLookUpService; - - private QueryInformationSystem queryInformationSystem; - - private Map map; - - @BeforeEach - public void setUp() throws ISLookUpException { - lenient().when(isLookUpService.quickSearchProfile(XQUERY_ENTITY)).thenReturn(communityMap); - lenient().when(isLookUpService.quickSearchProfile(XQUERY)).thenReturn(communityContext); - queryInformationSystem = new QueryInformationSystem(); - queryInformationSystem.setIsLookUp(isLookUpService); - } - - @Test - void testSizeEntity() throws ISLookUpException { - - List cInfoList = new ArrayList<>(); - final Consumer consumer = ci -> cInfoList.add(ci); - queryInformationSystem.getContextInformation(consumer); - - Assertions.assertEquals(12, cInfoList.size()); - } - - @Test - void testSizeRelation() throws ISLookUpException { - - List cInfoList = new ArrayList<>(); - final Consumer consumer = ci -> cInfoList.add(ci); - queryInformationSystem.execContextRelationQuery(); - queryInformationSystem - .getContextRelation(consumer, "contentproviders", ModelSupport.entityIdPrefix.get("datasource")); - - Assertions.assertEquals(5, cInfoList.size()); - } - - @Test - void testContentRelation() throws ISLookUpException { - - List cInfoList = new ArrayList<>(); - final Consumer consumer = ci -> cInfoList.add(ci); - queryInformationSystem.execContextRelationQuery(); - queryInformationSystem - .getContextRelation(consumer, "contentproviders", ModelSupport.entityIdPrefix.get("datasource")); - - cInfoList.forEach(contextInfo -> { - switch (contextInfo.getId()) { - case "elixir-gr": - Assertions.assertEquals(1, contextInfo.getDatasourceList().size()); - Assertions - .assertEquals( - "10|rest________::b8e502674c3c3499d5374e9b2ea6d8d5", - contextInfo.getDatasourceList().get(0)); - break; - case "instruct": - Assertions.assertEquals(0, contextInfo.getDatasourceList().size()); - break; - case "ni": - Assertions.assertEquals(6, contextInfo.getDatasourceList().size()); - Assertions - .assertTrue( - contextInfo - .getDatasourceList() - .contains("10|rest________::fb1a3d4523c95e63496e3bc7ba36244b")); - break; - case "dh-ch": - Assertions.assertEquals(10, contextInfo.getDatasourceList().size()); - break; - case "clarin": - Assertions.assertEquals(0, contextInfo.getDatasourceList().size()); - break; - } - }); - } - - @Test - void testContentEntity() throws ISLookUpException { - - List cInfoList = new ArrayList<>(); - final Consumer consumer = ci -> cInfoList.add(ci); - queryInformationSystem.getContextInformation(consumer); - - cInfoList.forEach(context -> { - switch (context.getId()) { - case "clarin":// clarin@@Common Language Resources and Technology Infrastructure@@CLARIN@@@@oac_clarin", - Assertions - .assertEquals("Common Language Resources and Technology Infrastructure", context.getName()); - Assertions.assertEquals("CLARIN", context.getDescription()); - Assertions - .assertTrue( - Optional - .ofNullable(context.getSubject()) - .map(value -> false) - .orElse(true)); - Assertions.assertEquals("oac_clarin", context.getZenodocommunity()); - Assertions.assertEquals("ri", context.getType()); - break; - case "ee": - Assertions.assertEquals("Sustainable Development Solutions Network - Greece", context.getName()); - Assertions.assertTrue(context.getDescription().length() > 0); - Assertions - .assertFalse( - Optional - .ofNullable(context.getSubject()) - .map(value -> false) - .orElse(true)); - Assertions.assertEquals(17, context.getSubject().size()); - Assertions.assertEquals("oac_sdsn-greece", context.getZenodocommunity()); - Assertions.assertEquals("community", context.getType()); - break; - case "dh-ch": - Assertions.assertEquals("Digital Humanities and Cultural Heritage", context.getName()); - Assertions.assertTrue(context.getDescription().length() > 0); - Assertions - .assertFalse( - Optional - .ofNullable(context.getSubject()) - .map(value -> false) - .orElse(true)); - Assertions.assertEquals(67, context.getSubject().size()); - Assertions.assertEquals("oac_dh-ch", context.getZenodocommunity()); - Assertions.assertEquals("community", context.getType()); - break; - case "fam": - Assertions.assertEquals("Fisheries and Aquaculture Management", context.getName()); - Assertions.assertTrue(context.getDescription().length() > 0); - Assertions - .assertTrue( - context - .getDescription() - .startsWith("Conservation of marine resources for sustainable development")); - Assertions - .assertFalse( - Optional - .ofNullable(context.getSubject()) - .map(value -> false) - .orElse(true)); - Assertions.assertEquals(19, context.getSubject().size()); - Assertions.assertEquals("fisheries", context.getZenodocommunity()); - Assertions.assertEquals("community", context.getType()); - break; - case "ni": - Assertions.assertEquals("Neuroinformatics", context.getName()); - Assertions.assertTrue(context.getDescription().length() > 0); - Assertions - .assertTrue( - context - .getDescription() - .startsWith("The neuroinformatics dashboard gathers research outputs from the")); - Assertions - .assertFalse( - Optional - .ofNullable(context.getSubject()) - .map(value -> false) - .orElse(true)); - Assertions.assertEquals(18, context.getSubject().size()); - Assertions.assertEquals("oac_ni", context.getZenodocommunity()); - Assertions.assertEquals("community", context.getType()); - Assertions.assertTrue(context.getSubject().contains("brain")); - break; - case "mes": - Assertions.assertEquals("European Marine Science", context.getName()); - Assertions.assertTrue(context.getDescription().length() > 0); - Assertions - .assertTrue( - context - .getDescription() - .startsWith( - "This community was initially defined to include a very broad range of topics")); - Assertions - .assertFalse( - Optional - .ofNullable(context.getSubject()) - .map(value -> false) - .orElse(true)); - Assertions.assertEquals(5, context.getSubject().size()); - Assertions.assertEquals("oac_mes", context.getZenodocommunity()); - Assertions.assertEquals("community", context.getType()); - Assertions.assertTrue(context.getSubject().contains("sea")); - Assertions.assertTrue(context.getSubject().contains("fish")); - Assertions.assertTrue(context.getSubject().contains("ocean")); - Assertions.assertTrue(context.getSubject().contains("aqua")); - Assertions.assertTrue(context.getSubject().contains("marine")); - break; - case "instruct": - Assertions.assertEquals("Instruct-ERIC", context.getName()); - Assertions.assertTrue(context.getDescription().length() > 0); - Assertions - .assertTrue( - context - .getDescription() - .equals( - "Instruct-ERIC is the European Research Infrastructure for Structural Biology")); - Assertions - .assertTrue( - Optional - .ofNullable(context.getSubject()) - .map(value -> false) - .orElse(true)); - Assertions.assertEquals("oac_instruct", context.getZenodocommunity()); - Assertions.assertEquals("community", context.getType()); - - break; - case "elixir-gr": - Assertions - .assertEquals("The Greek National Node of the ESFRI European RI ELIXIR", context.getName()); - Assertions.assertTrue(context.getDescription().length() > 0); - Assertions - .assertTrue( - context - .getDescription() - .startsWith( - "ELIXIR-GR enhances the potential of the Greek bioinformatics community to offer open")); - Assertions - .assertTrue( - Optional - .ofNullable(context.getSubject()) - .map(value -> false) - .orElse(true)); - Assertions.assertEquals("oaa_elixir-gr", context.getZenodocommunity()); - Assertions.assertEquals("ri", context.getType()); - - break; - case "aginfra": - Assertions.assertEquals("Agricultural and Food Sciences", context.getName()); - Assertions.assertTrue(context.getDescription().length() > 0); - Assertions - .assertTrue( - context - .getDescription() - .startsWith( - "The scope of this community is to provide access to publications, research data, projects and software")); - Assertions - .assertFalse( - Optional - .ofNullable(context.getSubject()) - .map(value -> false) - .orElse(true)); - Assertions.assertEquals(18, context.getSubject().size()); - Assertions.assertEquals("oac_aginfra", context.getZenodocommunity()); - Assertions.assertEquals("community", context.getType()); - Assertions.assertTrue(context.getSubject().contains("food distribution")); - break; - case "dariah": - Assertions.assertEquals("DARIAH EU", context.getName()); - Assertions.assertTrue(context.getDescription().length() > 0); - Assertions - .assertTrue( - context - .getDescription() - .startsWith( - "The Digital Research Infrastructure for the Arts and Humanities (DARIAH) aims to enhance and support ")); - Assertions - .assertTrue( - Optional - .ofNullable(context.getSubject()) - .map(value -> false) - .orElse(true)); - - Assertions.assertEquals("dariah", context.getZenodocommunity()); - Assertions.assertEquals("ri", context.getType()); - - break; - case "epos": - Assertions.assertEquals("European Plate Observing System", context.getName()); - Assertions.assertTrue(context.getDescription().length() > 0); - Assertions - .assertTrue( - context - .getDescription() - .startsWith( - "EPOS, the European Plate Observing System, is a long-term plan to facilitate integrated use of ")); - Assertions - .assertTrue( - Optional - .ofNullable(context.getSubject()) - .map(value -> false) - .orElse(true)); - - Assertions.assertEquals("", context.getZenodocommunity()); - Assertions.assertEquals("ri", context.getType()); - - break; - case "covid-19": - Assertions.assertEquals("Corona Virus Disease", context.getName()); - Assertions.assertTrue(context.getDescription().length() > 0); - Assertions - .assertTrue( - context - .getDescription() - .startsWith( - "This portal provides access to publications, research data, projects and ")); - Assertions - .assertFalse( - Optional - .ofNullable(context.getSubject()) - .map(value -> false) - .orElse(true)); - Assertions.assertEquals(25, context.getSubject().size()); - Assertions.assertEquals("covid-19", context.getZenodocommunity()); - Assertions.assertEquals("community", context.getType()); - Assertions.assertTrue(context.getSubject().contains("coronavirus disease 2019")); - break; - - } - }); - - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/RelationFromOrganizationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/RelationFromOrganizationTest.java deleted file mode 100644 index 50a9f26b4..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/RelationFromOrganizationTest.java +++ /dev/null @@ -1,121 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.HashMap; - -import org.apache.commons.io.FileUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SparkSession; -import org.junit.jupiter.api.AfterAll; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.Test; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.schema.dump.oaf.graph.Relation; - -public class RelationFromOrganizationTest { - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private static SparkSession spark; - - private static Path workingDir; - - private static final Logger log = LoggerFactory - .getLogger(RelationFromOrganizationTest.class); - - private static final HashMap map = new HashMap<>(); - - String organizationCommunityMap = "{\"20|grid________::afaa39865943381c51f76c08725ffa75\":[\"mes\",\"euromarine\"], \"20|corda__h2020::e8dbe14cca9bf6fce09d468872f813f8\":[\"mes\",\"euromarine\"], \"20|snsf________::9b253f265e3bef5cae6d881fdf61aceb\":[\"mes\",\"euromarine\"],\"20|rcuk________::e054eea0a47665af8c3656b5785ccf76\":[\"mes\",\"euromarine\"],\"20|corda__h2020::edc18d67c9b11fb616ca9f6e1db1b151\":[\"mes\",\"euromarine\"],\"20|rcuk________::d5736d9da90521ddcdc7828a05a85e9a\":[\"mes\",\"euromarine\"],\"20|corda__h2020::f5d418d3aa1cf817ddefcc3fdc039f27\":[\"mes\",\"euromarine\"],\"20|snsf________::8fa091f8f25a846779acb4ea97b50aef\":[\"mes\",\"euromarine\"],\"20|corda__h2020::81e020977211c2c40fae2e1a50bffd71\":[\"mes\",\"euromarine\"],\"20|corda_______::81e020977211c2c40fae2e1a50bffd71\":[\"mes\",\"euromarine\"],\"20|snsf________::31d0a100e54e3cdb3c6f52d91e638c78\":[\"mes\",\"euromarine\"],\"20|corda__h2020::ea379ef91b8cc86f9ac5edc4169292db\":[\"mes\",\"euromarine\"],\"20|corda__h2020::f75ee2ee48e5cb0ec8c8d30aaa8fef70\":[\"mes\",\"euromarine\"],\"20|rcuk________::e16010089551a1a9182a94604fc0ea59\":[\"mes\",\"euromarine\"],\"20|corda__h2020::38531a2cce7c5c347ffc439b07c1f43b\":[\"mes\",\"euromarine\"],\"20|corda_______::38531a2cce7c5c347ffc439b07c1f43b\":[\"mes\",\"euromarine\"],\"20|grid________::b2cbbf5eadbbf87d534b022bad3191d7\":[\"mes\",\"euromarine\"],\"20|snsf________::74730ef1439d7f7636a8be58a6b471b8\":[\"mes\",\"euromarine\"],\"20|nsf_________::ad72e19043a5a467e35f9b444d11563e\":[\"mes\",\"euromarine\"],\"20|rcuk________::0fc3e92500290902a2d38ec2445e74c3\":[\"mes\",\"euromarine\"],\"20|grid________::ad2c29905da0eb3c06b3fa80cacd89ea\":[\"mes\",\"euromarine\"],\"20|corda__h2020::30b53e4d63d3724f00acb9cbaca40860\":[\"mes\",\"euromarine\"],\"20|corda__h2020::f60f84bee14ad93f0db0e49af1d5c317\":[\"mes\",\"euromarine\"], \"20|corda__h2020::7bf251ac3765b5e89d82270a1763d09f\":[\"mes\",\"euromarine\"], \"20|corda__h2020::65531bd11be9935948c7f2f4db1c1832\":[\"mes\",\"euromarine\"], \"20|corda__h2020::e0e98f86bbc76638bbb72a8fe2302946\":[\"mes\",\"euromarine\"], \"20|snsf________::3eb43582ac27601459a8d8b3e195724b\":[\"mes\",\"euromarine\"], \"20|corda__h2020::af2481dab65d06c8ea0ae02b5517b9b6\":[\"mes\",\"euromarine\"], \"20|corda__h2020::c19d05cfde69a50d3ebc89bd0ee49929\":[\"mes\",\"euromarine\"], \"20|corda__h2020::af0bfd9fc09f80d9488f56d71a9832f0\":[\"mes\",\"euromarine\"], \"20|rcuk________::f33c02afb0dc66c49d0ed97ca5dd5cb0\":[\"beopen\"], " - + - "\"20|grid________::a867f78acdc5041b34acfe4f9a349157\":[\"beopen\"], \"20|grid________::7bb116a1a9f95ab812bf9d2dea2be1ff\":[\"beopen\"], \"20|corda__h2020::6ab0e0739dbe625b99a2ae45842164ad\":[\"beopen\"], \"20|corda__h2020::8ba50792bc5f4d51d79fca47d860c602\":[\"beopen\"], \"20|corda_______::8ba50792bc5f4d51d79fca47d860c602\":[\"beopen\"], \"20|corda__h2020::e70e9114979e963eef24666657b807c3\":[\"beopen\"], \"20|corda_______::e70e9114979e963eef24666657b807c3\":[\"beopen\"], \"20|corda_______::15911e01e9744d57205825d77c218737\":[\"beopen\"], \"20|opendoar____::056a41e24e2a9a67215e87bbee6a80ab\":[\"beopen\"], \"20|opendoar____::7f67f2e6c6fbb0628f8160fcd3d92ae3\":[\"beopen\"], \"20|grid________::a8ecfd7c084e561168bcbe6bf0daf3e3\":[\"beopen\"], \"20|corda_______::7bbe6cc5d8ec1864739a04b0d020c9e9\":[\"beopen\"], \"20|corda_______::3ff558e30c2e434d688539548300b050\":[\"beopen\"], \"20|corda__h2020::5ffee5b3b83b33a8cf0e046877bd3a39\":[\"beopen\"], \"20|corda__h2020::5187217e2e806a6df3579c46f82401bc\":[\"beopen\"], \"20|grid________::5fa7e2709bcd945e26bfa18689adeec1\":[\"beopen\"], \"20|corda_______::d8696683c53027438031a96ad27c3c07\":[\"beopen\"], \"20|corda__h2020::d8696683c53027438031a96ad27c3c07\":[\"beopen\"], \"20|rcuk________::23a79ebdfa59790864e4a485881568c1\":[\"beopen\"], \"20|corda__h2020::b76cf8fe49590a966953c37e18608af9\":[\"beopen\"], \"20|grid________::d2f0204126ee709244a488a4cd3b91c2\":[\"beopen\"], \"20|corda__h2020::05aba9d2ed17533d15221e5655ac11e6\":[\"beopen\"], \"20|grid________::802401579481dc32062bdee69f5e6a34\":[\"beopen\"], \"20|corda__h2020::3f6d9d54cac975a517ba6b252c81582d\":[\"beopen\"]}"; - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory(RelationFromOrganizationTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - - SparkConf conf = new SparkConf(); - conf.setAppName(RelationFromOrganizationTest.class.getSimpleName()); - - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - - spark = SparkSession - .builder() - .appName(RelationFromOrganizationTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Test - void test1() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/relation") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymapservices.json") - .getPath(); - - SparkOrganizationRelation.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/relation", - "-sourcePath", sourcePath, - "-organizationCommunityMap", organizationCommunityMap, - "-communityMapPath", communityMapPath - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/relation") - .map(item -> OBJECT_MAPPER.readValue(item, Relation.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Relation.class)); - - verificationDataset.createOrReplaceTempView("table"); - - // Assertions.assertEquals(170, verificationDataset.count()); - Assertions.assertEquals(0, verificationDataset.count()); - -// Dataset checkDs = spark -// .sql( -// "Select source.id, source.type " + -// "from table "); -// -// Assertions.assertEquals(2, checkDs.filter("substr(id, 4, 5) = 'dedup' ").count()); -// -// Assertions.assertEquals(0, checkDs.filter("id = '20|grid________::afaa39865943381c51f76c08725ffa75'").count()); -// -// Assertions.assertEquals(25, checkDs.filter("id = '00|context_____::" + DHPUtils.md5("beopen") + "'").count()); -// -// Assertions -// .assertEquals(30, checkDs.filter("id = '00|context_____::" + DHPUtils.md5("euromarine") + "'").count()); -// -// Assertions.assertEquals(30, checkDs.filter("id = '00|context_____::" + DHPUtils.md5("mes") + "'").count()); - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/SelectRelationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/SelectRelationTest.java deleted file mode 100644 index 3e4ab93c5..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/SelectRelationTest.java +++ /dev/null @@ -1,100 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.HashMap; - -import org.apache.commons.io.FileUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.api.java.function.ForeachFunction; -import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.Row; -import org.apache.spark.sql.SparkSession; -import org.junit.jupiter.api.AfterAll; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.Test; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.schema.oaf.Relation; -import net.sf.saxon.expr.instruct.ForEach; - -public class SelectRelationTest { - - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private static SparkSession spark; - - private static Path workingDir; - - private static final Logger log = LoggerFactory - .getLogger(SelectRelationTest.class); - - private static HashMap map = new HashMap<>(); - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory(SelectRelationTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - - SparkConf conf = new SparkConf(); - conf.setAppName(SelectRelationTest.class.getSimpleName()); - - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - - spark = SparkSession - .builder() - .appName(SelectRelationTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Test - public void test1() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/selectrelations") - .getPath(); - - SparkSelectValidRelationsJob.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/relation", - "-sourcePath", sourcePath - }); - -// dumpCommunityProducts.exec(MOCK_IS_LOOK_UP_URL,Boolean.FALSE, workingDir.toString()+"/dataset",sourcePath,"eu.dnetlib.dhp.schema.oaf.Dataset","eu.dnetlib.dhp.schema.dump.oaf.Dataset"); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/relation") - .map(item -> OBJECT_MAPPER.readValue(item, eu.dnetlib.dhp.schema.oaf.Relation.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(eu.dnetlib.dhp.schema.oaf.Relation.class)); - - Assertions.assertTrue(verificationDataset.count() == 7); - - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java deleted file mode 100644 index 7046b02c2..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java +++ /dev/null @@ -1,142 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.funderresult; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.HashMap; - -import org.apache.commons.io.FileUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SparkSession; -import org.junit.jupiter.api.AfterAll; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.Test; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject; -import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.Result; - -public class ResultLinkedToProjectTest { - - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private static SparkSession spark; - - private static Path workingDir; - - private static final Logger log = LoggerFactory - .getLogger(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class); - - private static final HashMap map = new HashMap<>(); - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory( - eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - - SparkConf conf = new SparkConf(); - conf.setAppName(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()); - - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - - spark = SparkSession - .builder() - .appName(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Test - void testNoMatch() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json") - .getPath(); - - final String graphPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/communityMapPath") - .getPath(); - - SparkResultLinkedToProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-graphPath", graphPath, - "-communityMapPath", communityMapPath - - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - Assertions.assertEquals(0, tmp.count()); - - } - - @Test - void testMatchOne() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/papers.json") - .getPath(); - - final String graphPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/communityMapPath") - .getPath(); - - SparkResultLinkedToProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-graphPath", graphPath, - "-communityMapPath", communityMapPath - - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - Assertions.assertEquals(1, tmp.count()); - - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java deleted file mode 100644 index e9d739db2..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java +++ /dev/null @@ -1,151 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.funderresult; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; - -// import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkDumpFunderResults2; -// import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkGetFunderList; -import org.apache.commons.io.FileUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.api.java.function.ForeachFunction; -import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SparkSession; -import org.junit.jupiter.api.AfterAll; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.Test; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.oa.graph.dump.DumpJobTest; -import eu.dnetlib.dhp.oa.graph.dump.SplitForCommunityTest; -import eu.dnetlib.dhp.oa.graph.dump.community.CommunitySplit; -import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkDumpFunderResults; -import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; - -public class SplitPerFunderTest { - - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private static SparkSession spark; - - private static Path workingDir; - - private static final Logger log = LoggerFactory.getLogger(SplitPerFunderTest.class); - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files.createTempDirectory(SplitPerFunderTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - - SparkConf conf = new SparkConf(); - conf.setAppName(SplitPerFunderTest.class.getSimpleName()); - - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - - spark = SparkSession - .builder() - .appName(SplitPerFunderTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Test - void test1() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext") - .getPath(); - - SparkDumpFunderResults.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/split", - "-sourcePath", sourcePath - - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - // FP7 3 and H2020 3 - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/split/EC_FP7") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - Assertions.assertEquals(3, verificationDataset.count()); - - Assertions - .assertEquals( - 1, verificationDataset.filter("id = '50|dedup_wf_001::0d16b1714ab3077df73893a8ea57d776'").count()); - - // CIHR 2 - tmp = sc - .textFile(workingDir.toString() + "/split/CIHR") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - Assertions.assertEquals(2, tmp.count()); - - // NWO 1 - tmp = sc - .textFile(workingDir.toString() + "/split/NWO") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - Assertions.assertEquals(1, tmp.count()); - - // NIH 3 - tmp = sc - .textFile(workingDir.toString() + "/split/NIH") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - Assertions.assertEquals(2, tmp.count()); - - // NSF 1 - tmp = sc - .textFile(workingDir.toString() + "/split/NSF") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - Assertions.assertEquals(1, tmp.count()); - - // SNSF 1 - tmp = sc - .textFile(workingDir.toString() + "/split/SNSF") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - Assertions.assertEquals(1, tmp.count()); - - // NHMRC 1 - tmp = sc - .textFile(workingDir.toString() + "/split/NHMRC") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - Assertions.assertEquals(1, tmp.count()); - - // H2020 3 - tmp = sc - .textFile(workingDir.toString() + "/split/EC_H2020") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - Assertions.assertEquals(3, tmp.count()); - - // MZOS 1 - tmp = sc - .textFile(workingDir.toString() + "/split/MZOS") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - Assertions.assertEquals(1, tmp.count()); - - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java deleted file mode 100644 index 8cdb285e4..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java +++ /dev/null @@ -1,125 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.projectssubset; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.HashMap; - -import org.apache.commons.io.FileUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.sql.SaveMode; -import org.apache.spark.sql.SparkSession; -import org.junit.jupiter.api.AfterAll; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.Test; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.schema.dump.oaf.graph.Project; - -public class ProjectSubsetTest { - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - private static SparkSession spark; - private static Path workingDir; - private static final Logger log = LoggerFactory - .getLogger(eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class); - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory( - eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - SparkConf conf = new SparkConf(); - conf.setAppName(eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class.getSimpleName()); - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - spark = SparkSession - .builder() - .appName(eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Test - void testAllNew() throws Exception { - final String projectListPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/projectId") - .getPath(); - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/allnew/projects") - .getPath(); - spark - .read() - .textFile(projectListPath) - .write() - .mode(SaveMode.Overwrite) - .text(workingDir.toString() + "/projectIds"); - ProjectsSubsetSparkJob.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/projects", - "-sourcePath", sourcePath, - "-projectListPath", workingDir.toString() + "/projectIds" - }); - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/projects") - .map(item -> OBJECT_MAPPER.readValue(item, Project.class)); - Assertions.assertEquals(12, tmp.count()); - Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("aka_________")).count()); - Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("anr_________")).count()); - Assertions.assertEquals(4, tmp.filter(p -> p.getId().substring(3, 15).equals("arc_________")).count()); - Assertions.assertEquals(3, tmp.filter(p -> p.getId().substring(3, 15).equals("conicytf____")).count()); - Assertions.assertEquals(1, tmp.filter(p -> p.getId().substring(3, 15).equals("corda_______")).count()); - Assertions.assertEquals(40, sc.textFile(workingDir.toString() + "/projectIds").count()); - } - - @Test - void testMatchOne() throws Exception { - final String projectListPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/projectId") - .getPath(); - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/matchOne/projects") - .getPath(); - spark - .read() - .textFile(projectListPath) - .write() - .mode(SaveMode.Overwrite) - .text(workingDir.toString() + "/projectIds"); - ProjectsSubsetSparkJob.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/projects", - "-sourcePath", sourcePath, - "-projectListPath", workingDir.toString() + "/projectIds" - }); - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/projects") - .map(item -> OBJECT_MAPPER.readValue(item, Project.class)); - Assertions.assertEquals(11, tmp.count()); - Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("aka_________")).count()); - Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("anr_________")).count()); - Assertions.assertEquals(4, tmp.filter(p -> p.getId().substring(3, 15).equals("arc_________")).count()); - Assertions.assertEquals(3, tmp.filter(p -> p.getId().substring(3, 15).equals("conicytf____")).count()); - Assertions.assertEquals(0, tmp.filter(p -> p.getId().substring(3, 15).equals("corda__h2020")).count()); - Assertions.assertEquals(39, sc.textFile(workingDir.toString() + "/projectIds").count()); - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/addProjectInfo/preparedInfo b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/addProjectInfo/preparedInfo deleted file mode 100644 index 7f35634f5..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/addProjectInfo/preparedInfo +++ /dev/null @@ -1,2 +0,0 @@ -{"projectsList":[{"code":"123455","funder":{"jurisdiction":"FI","name":"Academy of Finland","shortName":"AKA"},"id":"40|aka_________::0f7d119de1f656b5763a16acf876fed6","provenance":{"provenance":"sysimport:crosswalk:entityregistry","trust":"0.900000000000000022"},"title":"Business services for rural bioenergy entrepreneurship in Finland: a network analysis approach"},{"code":"119027","funder":{"fundingStream":"H2020","jurisdiction":"EU","name":"European Commission","shortName":"EC"},"id":"40|aka_________::03376222b28a3aebf2730ac514818d04","provenance":{"provenance":"sysimport:crosswalk:entityregistry","trust":"0.900000000000000022"},"title":"EGFR Tyrosine Kinase Inhibitors and LKB1 Tumor Suppressor in Non-Small-Cell Lung Cancer"}],"resultId":"50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb"} -{"projectsList":[{"code":"123455","funder":{"jurisdiction":"FI","name":"Academy of Finland","shortName":"AKA"},"id":"40|aka_________::0f7d119de1f656b5763a16acf876fed6","provenance":{"provenance":"sysimport:crosswalk:entityregistry","trust":"0.900000000000000022"},"title":"Business services for rural bioenergy entrepreneurship in Finland: a network analysis approach"}],"resultId":"50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80"} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/addProjectInfo/preparedInfoValidated b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/addProjectInfo/preparedInfoValidated deleted file mode 100644 index 588bec804..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/addProjectInfo/preparedInfoValidated +++ /dev/null @@ -1,2 +0,0 @@ -{"resultId":"50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2","projectsList":[{"id":"40|aka_________::0f7d119de1f656b5763a16acf876fed6","code":"123455","acronym":null,"title":"Business services for rural bioenergy entrepreneurship in Finland: a network analysis approach","funder":{"shortName":"AKA","name":"Academy of Finland","jurisdiction":"FI","fundingStream":null},"provenance":{"provenance":"sysimport:crosswalk:entityregistry","trust":"0.900000000000000022"},"validated":{"validationDate":"2021-08-06","validatedByFunder":true}},{"id":"40|aka_________::03376222b28a3aebf2730ac514818d04","code":"119027","acronym":null,"title":"EGFR Tyrosine Kinase Inhibitors and LKB1 Tumor Suppressor in Non-Small-Cell Lung Cancer","funder":{"shortName":"EC","name":"European Commission","jurisdiction":"EU","fundingStream":"H2020"},"provenance":{"provenance":"sysimport:crosswalk:entityregistry","trust":"0.900000000000000022"},"validated":null}]} 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KNAW","name":"NIOO-KNAW","pid":{"id":{"scheme":"orcid","value":"0000-0002-3835-159X"}},"rank":1,"surname":"KNAW"}],"bestaccessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":[{"key":"10|opendoar____::e820a45f1dfc7b95282d10b6087e11c0","value":"Repositorio Institucional de la Universidad de Alicante"},{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"},{"key":"10|openaire____::fdb035c8b3e0540a8d9a561a6c44f4de","value":"NARCIS"},{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"},{"key":"10|openaire____::8ac8380272269217cb09a928c8caa993","value":"UnpayWall"},{"key":"10|openaire____::806360c771262b4d6770e7cdf04b5c5a","value":"ORCID"},{"key":"10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a","value":"Microsoft Academic 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Departamento de Ciencias Ambientales y Recursos Naturales","Universidad de Alicante. Centro Iberoamericano de la Biodiversidad","Biodiversidad y Biotecnología aplicadas a la Biología de la Conservación","Terrestrial Ecology (TE)"],"country":[{"code":"NL","label":"Netherlands","provenance":{"provenance":"Propagation of country to result collected from datasources of type institutional repositories","trust":"0.85"}},{"code":"ES","label":"Spain","provenance":{"provenance":"Propagation of country to result collected from datasources of type institutional repositories","trust":"0.85"}}],"coverage":[],"dateofcollection":"2018-10-03T06:57:46.116Z","description":["Herbivory affects subsequent herbivores, mainly regulated by the phytohormones jasmonic (JA) and salicylic acid (SA). Additionally, organisms such as soil microbes belowground or parasitoids that develop inside their herbivorous hosts aboveground, can change plant responses to herbivory. However, it is not yet well known how organisms of trophic levels other than herbivores, below- and above-ground, alter the interactions between insect species sharing a host plant. Here, we investigated whether the parasitoid Aphidius colemani and different soil microbial communities (created through plant-soil feedbacks) affect the JA and SA signalling pathways in response to the aphid Myzus persicae and the thrips Frankliniella occidentalis, as well as subsequent thrips performance. Our results show that the expression of the JA-responsive gene CaPINII in sweet pepper was more suppressed by aphids than by parasitised aphids. However, parasitism did not affect the expression of CaPAL1, a biosynthetic gene of SA. Furthermore, aphid feeding enhanced thrips performance compared with uninfested plants, but this was not observed when aphids were parasitised. Soils where different plant species were previously grown, did not affect plant responses or the interaction between herbivores. Our study shows that members of the third trophic level can modify herbivore interactions by altering plant physiology.\nThis work and T.V.’s activities were supported by Spanish Ministry of Science and Innovation, (CGL2016-79054), the Open Technology Program of NWO (TTW-13848), and the STSM Cost Action FA1405 funded by the European Union. A.P. research activities were supported by the Netherlands Organisation for Scientific Research (NWO, project no. 870.15.080)."],"format":["application/pdf","application/octet-stream"],"id":"50|dedup_wf_001::01644aebfe64e809f593492e515bc070","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::e820a45f1dfc7b95282d10b6087e11c0","value":"Repositorio Institucional de la Universidad de Alicante"},"hostedby":{"key":"10|opendoar____::e820a45f1dfc7b95282d10b6087e11c0","value":"Repositorio Institucional de la Universidad de Alicante"},"license":"Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.","publicationdate":"2018-09-26","refereed":"UNKNOWN","type":"Article","url":["http://hdl.handle.net/10045/80968"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"},"hostedby":{"key":"10|doajarticles::70703810b20723fe33cba6ffd7128212","value":"Scientific 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(NWO)","shortName":"NWO"},"id":"40|nwo_________::dc69ada721bf21ed51055b6421850d73","provenance":{"provenance":"Harvested","trust":"0.900000000000000022"},"title":"Exploring and exploiting phytochemicals to lure hyperparasitoids away from beneficial biocontrol agents"},{"code":"2300189714","funder":{"jurisdiction":"NL","name":"Netherlands Organisation for Scientific Research (NWO)","shortName":"NWO"},"id":"40|nwo_________::39d892199c3b3d3b5ae9869a79e5bba8","provenance":{"provenance":"Harvested","trust":"0.900000000000000022"},"title":"Linking aboveground-belowground interactions and plant-soil feedback to improve pest control and sustainability in greenhouse cut-flowers"}],"publicationdate":"2018-09-26","publisher":"Springer Nature","subjects":[{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Plant-mediated interactions"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Herbivores"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Feeding guilds"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Parasitism"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Belowground interactions"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Zoología"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Medicine"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"R"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Science"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Q"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"international"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Laboratorium voor Entomologie"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"PE&RC"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Laboratory of Entomology"}},{"subject":{"scheme":"keywords","value":"Multidisciplinary"}}],"type":"publication"} -{"author":[{"fullname":"Bonnie Berger","name":"Bonnie","pid":{"id":{"scheme":"orcid","value":"0000-0002-2724-7228"}},"rank":1,"surname":"Berger"}],"bestaccessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":[{"key":"10|opendoar____::958adb57686c2fdec5796398de5f317a","value":"MPG.PuRe"},{"key":"10|share_______::bbd802baad85d1fd440f32a7a3a2c2b1","value":"bioRxiv"},{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"},{"key":"10|openaire____::8ac8380272269217cb09a928c8caa993","value":"UnpayWall"},{"key":"10|openaire____::806360c771262b4d6770e7cdf04b5c5a","value":"ORCID"},{"key":"10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a","value":"Microsoft Academic Graph"},{"key":"10|opendoar____::89f0fd5c927d466d6ec9a21b9ac34ffa","value":"eScholarship - University of California"},{"key":"10|openaire____::9e3be59865b2c1c335d32dae2fe7b254","value":"Datacite"},{"key":"10|opendoar____::eda80a3d5b344bc40f3bc04f65b7a357","value":"PubMed Central"},{"key":"10|opendoar____::8f19793b2671094e63a15ab883d50137","value":"Digital Access to Scholarship at Harvard"},{"key":"10|opendoar____::2a38a4a9316c49e5a833517c45d31070","value":"DSpace@MIT"}],"context":[{"code":"dh-ch","label":"Digital Humanities and Cultural Heritage","provenance":[{"provenance":"Inferred by OpenAIRE","trust":"0.8"}]}],"contributor":["Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory","Massachusetts Institute of Technology. Department of Mathematics","Lipson, Mark","Loh, Po-Ru","Berger, Bonnie"],"country":[{"code":"DZ","label":"Algeria","provenance":{"provenance":"Propagation of country to result collected from datasources of type institutional repositories","trust":"0.85"}},{"code":"US","label":"United States","provenance":{"provenance":"Propagation of country to result collected from datasources of type institutional repositories","trust":"0.85"}}],"coverage":[],"dateofcollection":"2020-09-12T07:56:34.334Z","description":["Austronesian languages are spread across half the globe, from Easter Island to Madagascar. Evidence from linguistics and archaeology indicates that the ‘Austronesian expansion,’ which began 4,000–5,000 years ago, likely had roots in Taiwan, but the ancestry of present-day Austronesian-speaking populations remains controversial. Here, we analyse genome-wide data from 56 populations using new methods for tracing ancestral gene flow, focusing primarily on Island Southeast Asia. We show that all sampled Austronesian groups harbour ancestry that is more closely related to aboriginal Taiwanese than to any present-day mainland population. Surprisingly, western Island Southeast Asian populations have also inherited ancestry from a source nested within the variation of present-day populations speaking Austro-Asiatic languages, which have historically been nearly exclusive to the mainland. Thus, either there was once a substantial Austro-Asiatic presence in Island Southeast Asia, or Austronesian speakers migrated to and through the mainland, admixing there before continuing to western Indonesia.","National Science Foundation (U.S.). Graduate Research Fellowship Program","Simons Foundation","National Institutes of Health (U.S.) (Grant R01GM108348)","National Institutes of Health (U.S.) (Training Grant 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In this paper the first results from the proton–lead collision data taken in early 2013 are presented. The Z boson production cross section is measured in the muon decay channel in bins of transverse momentum and rapidity together with the forward–backward ratio. The W production is studied in the muon and electron decay channels and the differential cross sections, lepton-charge and forward–backward asymmetries are computed as a function of the lepton pseudorapidity. All results are compared with theory predictions with and without nuclear modification of the parton distribution functions showing hints of nuclear effects."],"format":[],"id":"50|dedup_wf_001::02cb7e7397a1f775e53ed38b38aba680","instance":[{"accessright":{"code":"c_14cb","label":"CLOSED","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::666894f04637d4dd1861ad117e1c4a66","value":"SNSF P3 Database"},"hostedby":{"key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c","value":"Unknown Repository"},"publicationdate":"2014-01-01","refereed":"peerReviewed","type":"Conference object","url":["http://dx.doi.org/doi:10.1016/j.nuclphysa.2014.07.039"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::fc490ca45c00b1249bbe3554a4fdf6fb","value":"CERN Document 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prognostic accuracy in patients with disorders of consciousness. Due to the portability and relative inexpensiveness of electroencephalography, the N400 event-related potential component has been proposed as a clinically valid means to identify preserved linguistic function in non-communicative patients. Across three experiments, we show that changes in both stimuli and task demands significantly influence the probability of detecting statistically significant N400 effects — that is, the difference in N400 amplitudes caused by the experimental manipulation. In terms of task demands, passively heard linguistic stimuli were significantly less likely to elicit N400 effects than task-relevant stimuli. Due to the inability of the majority of patients with disorders of consciousness to follow task commands, the insensitivity of passive listening would impede the identification of residual language abilities even when such abilities exist. In terms of stimuli, passively heard normatively associated word pairs produced the highest detection rate of N400 effects (50% of the participants), compared with semantically-similar word pairs (0%) and high-cloze sentences (17%). This result is consistent with a prediction error account of N400 magnitude, with highly predictable targets leading to smaller N400 waves, and therefore larger N400 effects. Overall, our data indicate that non-repeating normatively associated word pairs provide the highest probability of detecting single-subject N400s during passive listening, and may thereby provide a clinically viable means of assessing residual linguistic function. We also show that more liberal analyses may further increase the detection-rate, but at the potential cost of increased false alarms.","Highlights • The N400 is a candidate marker of linguistic function after severe brain injury. • The probability of detecting N400s is dependent on task demands. • Passive listening is less sensitive than command-following. • The probability of detecting N400s is dependent on stimuli choices. • Word-pairs generated from association norms provide the highest sensitivity."],"format":["application/pdf"],"id":"50|dedup_wf_001::03d1b1b04480058e646b34c174e61082","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"},"hostedby":{"key":"10|doajarticles::0c0e74daa5d95504eade9c81ebbd5b8a","value":"NeuroImage: 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New polyethers, such as iubol (2), 22-hydroxy-15(28)- dehydrovenustatriol (3), 1,2-dehydropseudodehydrothyrsiferol (4), and secodehydrothyrsiferol (5) have been isolated and characterized from this alga. The structures were determined through the interpretation of NMR spectroscopic data and the relative configuration was proposed on the basis of NOESY spectrum and biogenetic considerations. All new compounds exhibited significant cytotoxic activity against a panel of cancer cell lines. © 2011 by the authors.","Financial support was provided by the grants MAREX (FP 7; KBBE-3-245137) (EU), CTQ2008-06754-C04-01 and SAF2008-02251 (MICINN); C2008000145 and EXMAR (ACISII); RD06/0020/1037 from Red Temática de Investigación Cooperativa en Cáncer, Instituto de Salud Carlos III, co-funded by the Fondo Europeo de Desarrollo Regional of the European Union, and Junta de Castilla y León (CSI052A11-2, and GR15-Experimental Therapeutics and Translational Oncology Program). F.C.P. is the recipient of a SEGAI-ULL fellowship.","Peer Reviewed"],"format":["application/pdf"],"id":"50|dedup_wf_001::06496bbae2934f9443037f3df7293791","instance":[{"accessright":{"code":"c_14cb","label":"CLOSED","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::4e99a7004945b3f6298b66c2b8dd4fc6","value":"SESAM Publication Database - FP7 KBBE"},"hostedby":{"key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c","value":"Unknown 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The validity and utility of standard measures of childhood maltreatment requires clarification in order to inform the design of future studies investigating the mental health consequences of maltreatment. The present study assessed agreement between prospective informant-reports and retrospective self-reports of childhood maltreatment, as well as the comparative utility of both reports for predicting a range of psychiatric problems at age 18. Data were obtained from the Environmental Risk (E-Risk) Longitudinal Twin Study, a nationally-representative birth cohort of 2232 children followed to 18 years of age (with 93% retention). Childhood maltreatment was assessed in two ways: (i) prospective informant-reports from caregivers, researchers, and clinicians when children were aged 5, 7, 10 and 12; and (ii) retrospective self-reports of maltreatment experiences occurring up to age 12, obtained at age 18 using the Childhood Trauma Questionnaire. Participants were privately interviewed at age 18 concerning several psychiatric problems including depression, anxiety, self-injury, alcohol/cannabis dependence, and conduct disorder. There was only slight to fair agreement between prospective and retrospective reports of childhood maltreatment (all Kappa's ≤ 0.31). Both prospective and retrospective reports of maltreatment were associated with age-18 psychiatric problems, though the strongest associations were found when maltreatment was retrospectively self-reported. These findings indicate that prospective and retrospective reports of childhood maltreatment capture largely non-overlapping groups of individuals. Young adults who recall being maltreated have a particularly elevated risk for psychopathology."],"format":["application/pdf","text"],"id":"50|dedup_wf_001::085f9efc74e1192abca87031fb573d70","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::566a9968b43628588e76be5a85a0f9e8","value":"King's Research Portal"},"hostedby":{"key":"10|opendoar____::566a9968b43628588e76be5a85a0f9e8","value":"King's Research 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Here, we focused on tomato (Solanum lycopersicum), testing the hypothesis that plants grown on native soils display different responses to soil microbiotas.\r\nUsing transcriptomics, proteomics, and biochemistry, we describe the responses of two tomato genotypes (susceptible or resistant to Fusarium oxysporum f. sp. lycopersici) grown on an artificial growth substrate and two native soils (conducive and suppressive to Fusarium).\r\nNative soils affected tomato responses by modulating pathways involved in responses to oxidative stress, phenol biosynthesis, lignin deposition, and innate immunity, particularly in the suppressive soil. In tomato plants grown on steam-disinfected soils, total phenols and lignin decreased significantly. The inoculation of a mycorrhizal fungus partly rescued this response locally and systemically. Plants inoculated with the fungal pathogen showed reduced disease symptoms in the resistant genotype in both soils, but the susceptible genotype was partially protected from the pathogen only when grown on the suppressive soil.\r\nThe ‘state of alert’ detected in tomatoes reveals novel mechanisms operating in plants in native soils and the soil microbiota appears to be one of the drivers of these plant responses."],"format":[],"id":"50|dedup_wf_001::09e54cbad6670d8f40a7de2704e2d2a4","instance":[{"accessright":{"code":"c_16ec","label":"RESTRICTED","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"},"hostedby":{"key":"10|issn___print::35ee75a5ad42581d604be113a8f56427","value":"New Phytologist"},"license":"http://doi.wiley.com/10.1002/tdm_license_1.1","publicationdate":"2018-02-09","refereed":"UNKNOWN","type":"Article","url":["https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2Fnph.15014","http://onlinelibrary.wiley.com/wol1/doi/10.1111/nph.15014/fullpdf","http://dx.doi.org/10.1111/nph.15014"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::8ac8380272269217cb09a928c8caa993","value":"UnpayWall"},"hostedby":{"key":"10|issn___print::35ee75a5ad42581d604be113a8f56427","value":"New Phytologist"},"refereed":"UNKNOWN","type":"Article","url":["https://nph.onlinelibrary.wiley.com/doi/pdfdirect/10.1111/nph.15014"]},{"collectedfrom":{"key":"10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a","value":"Microsoft Academic Graph"},"hostedby":{"key":"10|issn___print::35ee75a5ad42581d604be113a8f56427","value":"New Phytologist"},"refereed":"UNKNOWN","type":"Article","url":["https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.15014","https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.15014","http://onlinelibrary.wiley.com/doi/10.1111/nph.15014/abstract","https://aperto.unito.it/handle/2318/1660820","https://academic.microsoft.com/#/detail/2793208206"]},{"accessright":{"code":"c_16ec","label":"RESTRICTED","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::89fcd07f20b6785b92134bd6c1d0fa42","value":"Archivio Istituzionale"},"hostedby":{"key":"10|opendoar____::89fcd07f20b6785b92134bd6c1d0fa42","value":"Archivio Istituzionale"},"publicationdate":"2018-01-01","refereed":"UNKNOWN","type":"Article","url":["http://hdl.handle.net/2318/1660820"]},{"collectedfrom":{"key":"10|openaire____::9e3be59865b2c1c335d32dae2fe7b254","value":"Datacite"},"hostedby":{"key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c","value":"Unknown Repository"},"publicationdate":"2018-12-01","refereed":"UNKNOWN","type":"Other literature type","url":["http://dx.doi.org/10.1111/nph.15014"]}],"language":{"code":"und","label":"Undetermined"},"lastupdatetimestamp":1603727328518,"maintitle":"Native soils with their microbiotas elicit a state of alert in tomato plants","originalId":["10.1111/nph.15014","2793208206","oai:iris.unito.it:2318/1660820"],"pid":[{"scheme":"doi","value":"10.1111/nph.15014"},{"scheme":"pmid","value":"29424928"}],"projects":[{"acronym":"TomRes","code":"727929","funder":{"fundingStream":"H2020","jurisdiction":"EU","name":"European Commission","shortName":"EC"},"id":"40|corda__h2020::94c4a066401e22002c4811a301bb4655","provenance":{"provenance":"Harvested","trust":"0.900000000000000022"},"title":"A NOVEL AND INTEGRATED APPROACH TO INCREASE MULTIPLE AND COMBINED STRESS TOLERANCE IN PLANTS USING TOMATO AS A MODEL"}],"publicationdate":"2018-12-01","publisher":"Wiley","subjects":[{"subject":{"scheme":"keywords","value":"Plant Science"}},{"subject":{"scheme":"keywords","value":"Physiology"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Arbuscular mycorrhizal fungi; Defence responses; Lignin biosynthesis; Microbiota; Suppressive and conducive soils; Susceptible and resistant genotypes; Tomato; Physiology; Plant Science"}},{"provenance":{"provenance":"Inferred by OpenAIRE","trust":"0.891"},"subject":{"scheme":"mesheuropmc","value":"food and beverages"}},{"provenance":{"provenance":"Inferred by OpenAIRE","trust":"0.891"},"subject":{"scheme":"mesheuropmc","value":"fungi"}},{"provenance":{"provenance":"Inferred by OpenAIRE","trust":"0.8739"},"subject":{"scheme":"mesheuropmc","value":"complex mixtures"}}],"type":"publication"} -{"author":[{"fullname":"K.P. 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To this end, the main objective of this work is the prognosis of the mean, maximum and minimum hourly wind power (WP) 8hours ahead. For this purpose, Artificial Neural Networks (ANN) modeling is applied. For the appropriate training of the developed ANN models hourly meteorological data are used. These data have been recorded by a meteorological mast in Tilos Island, Greece.\n\nFor the evaluation of the developed ANN forecasting models proper statistical evaluation indices are used. According to the results, the coefficient of the determination ranges from 0.285 up to 0.768 (mean hourly WP), from 0.227 up to 0.798 (maximum hourly WP) and from 0.025 up to 0.398 (minimum hourly WP). Furthermore, the proposed forecasting methodology shows that is able to give sufficient and adequate prognosis of WP by a wind turbine in a specific location 8 hours ahead. This will be a useful tool for the operator of a RES system in order to achieve a better monitoring and a better management of the whole system."],"format":[],"id":"50|dedup_wf_001::0a6525f420fd1f922125c3a1a280c8df","instance":[{"accessright":{"code":"c_16ec","label":"RESTRICTED","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"},"hostedby":{"key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c","value":"Unknown Repository"},"publicationdate":"2017-02-23T20:11:53Z","refereed":"UNKNOWN","type":"Conference object","url":["http://digital-library.theiet.org/content/conferences/10.1049/cp.2016.1094?crawler=true","http://dx.doi.org/10.1049/cp.2016.1094"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::8ac8380272269217cb09a928c8caa993","value":"UnpayWall"},"hostedby":{"key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c","value":"Unknown Repository"},"license":"cc-by","refereed":"UNKNOWN","type":"Conference object","url":["https://zenodo.org/record/887339/files/Wind%20power%20forecasting%20using%20historical%20data%20and%20artificial%20neural%20networks%20modeling.pdf"]},{"collectedfrom":{"key":"10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a","value":"Microsoft Academic Graph"},"hostedby":{"key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c","value":"Unknown Repository"},"refereed":"UNKNOWN","type":"Conference object","url":["http://digital-library.theiet.org/content/conferences/10.1049/cp.2016.1094","https://core.ac.uk/display/144851191","http://jglobal.jst.go.jp/public/20090422/201702260673071390","https://academic.microsoft.com/#/detail/2590295725"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::358aee4cc897452c00244351e4d91f69","value":"ZENODO"},"hostedby":{"key":"10|opendoar____::358aee4cc897452c00244351e4d91f69","value":"ZENODO"},"license":"http://creativecommons.org/licenses/by/4.0/legalcode","publicationdate":"2016-11-07","refereed":"UNKNOWN","type":"Conference object","url":["https://zenodo.org/record/887339"]}],"language":{"code":"und","label":"Undetermined"},"lastupdatetimestamp":1603727328518,"maintitle":"Wind power forecasting using historical data and artificial neural networks modeling","originalId":["10.1049/cp.2016.1094","2590295725","oai:zenodo.org:887339"],"pid":[{"scheme":"doi","value":"10.1049/cp.2016.1094"}],"projects":[{"acronym":"TILOS","code":"646529","funder":{"fundingStream":"H2020","jurisdiction":"EU","name":"European Commission","shortName":"EC"},"id":"40|corda__h2020::64c901e621f90b9a38badb1d78902205","provenance":{"provenance":"Harvested","trust":"0.900000000000000022"},"title":"Technology Innovation for the Local Scale, Optimum Integration of Battery Energy Storage"}],"publicationdate":"2016-11-07","publisher":"Institution of Engineering and Technology","subjects":[{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Wind Power, Forecasting, Artificial Neural Networks"}}],"type":"publication"} -{"author":[{"fullname":"Juan M. 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Vertical velocities can be estimated indirectly from in situ observations by theoretical frameworks like the-equation. Direct measures of vertical exchanges are challenging due to their typically ephemeral spatiotemporal scales. In this study we address this problem with an adaptive sampling strategy coupling various biophysical instruments. We analyze the 3-D organization of a cyclonic mesoscale structure finely sampled during the Observing Submesoscale Coupling At High Resolution cruise in the Ligurian Sea during fall 2015. The observations, acquired with a moving vessel profiler, highlight a subsurface low-salinity layer (≃50 m), as well as rising isopycnals, generated by geostrophic cyclonic circulation, in the structure's center. Reconstructed 3-D fields of density and horizontal velocities are used to estimate the vertical velocity field down to 250 m by applying the adiabatic QG-equation, for the first time in this region. The vertical motions are characterized by multipolar patterns of downward and upward velocities on the edges of the structure and significantly smaller vertical velocities in its center. Both the 3-D distribution of particles (size ≥100 μm), measured with a laser optical plankton counter, and the Synechococcus and Prochlorococcus abundances (cell per cubic meter) measured by flow cytometry are consistent with the 3-D velocity field. In particular, a secondary vertical recirculation is identified that upwells particles (from 250 to 100 m) along isohalines to the structure's center. Besides demonstrating the effect of vertical patterns on biogeochemical distributions, this case study suggests to use particle matter as a tracer to assess physical dynamics."],"format":["application/pdf"],"id":"50|dedup_wf_001::0d16b1714ab3077df73893a8ea57d776","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::7e7757b1e12abcb736ab9a754ffb617a","value":"Hyper Article en Ligne"},"hostedby":{"key":"10|opendoar____::7e7757b1e12abcb736ab9a754ffb617a","value":"Hyper Article en 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Personality traits, affective status and stress are some of the relevant factors contributing to lower quality of life and symptom exacerbation in IBS patients. In order to examine the role of stress in IBS symptom exacerbation, the aims of this study were to explore the relationship of daily stressful events and symptom severity in a prospective manner and to explore the roles of neuroticism, anxiety, depression and stress in the vicious circle of symptom perpetuation. A total of 49 patients with IBS reported their symptom severity and daily stressful events intensity each day for 14 consecutive days. They also completed the Big five personality inventory, the Beck Depression Inventory and the State-trait anxiety inventory. Cross-correlation analyses were performed on the time series data for daily stress and symptom severity for each participant separately. Four different patterns of relationships were found in different subgroups of participants: positive cross-correlations of symptom severity and stress intensity on the same day; higher symptom severity on days following stressful days; lower symptom severity on days following stressful days; and lower stress intensity on days following severe symptoms. Using average scores for daily stress and symptom severity, as well as scores for neuroticism, anxiety and depression, we performed a path analysis to test a model of symptom exacerbation. It showed that, on the group level, average stress intensity predicts average symptom severity. Neuroticism and anxiety were not significant predictors of symptom severity, while depression showed a marginally significant relationship with symptom severity, mediated by stress intensity. In conclusion, depression and daily stress seem to be important contributors to the vicious circle of IBS symptom perpetuation.","Síndrome del intestino irritable se considera un trastorno biopsicosocial, el resultado de la combinación compleja de factores predisponentes, precipitantes y perpetuos. Rasgos de personalidad, estado afectivo y estrés son algunos de los factores relevantes que contribuyen a la calidad de vida más baja y la exacerbación sintomática de los pacientes con SII. Para examinar el papel del estrés en la exacerbación sintomática de SII, el objetivo de este estudio era explorar la relación entre los acontecimientos cotidianos estresantes y la intensidad de los síntomas de forma prospectiva, tanto como explorar los papeles del neuroticismo, ansiedad, depresión y estrés en el círculo vicioso de perpetuación de los síntomas. Todos los 49 pacientes con SII informaron sobre la intensidad de los síntomas y la intensidad de los acontecimientos cotidianos estresantes cada día durante 14 días consecutivos. Además, completaron el Test de personalidad de los cinco grandes, Inventario de depresión de Beck e Inventario de ansiedad estado-rasgo. En los datos de series temporales se hizo el análisis de correlación cruzada para la intensidad del estrés diario y de los síntomas para cada participante por separado. Se encontraron cuatro patrones de relación diferentes en diferentes subgrupos de participantes: correlación cruzada positiva de la intensidad de los síntomas y del estrés el mismo día; intensidad de los síntomas más alta en los días después de los días estresantes; intensidad de los síntomas más baja en los días después de los días estresantes e intensidad del estrés más baja en los días después de los síntomas graves. Usando resultados promedios para el estrés diario y la intensidad de los síntomas, tanto como resultados para el neuroticismo, ansiedad y depresión, realizamos un análisis del camino para examinar el modelo de la exacerbación de los síntomas. Mostró que, al nivel de grupo, la intensidad del estrés promedia predice la intensidad de los síntomas promedia. Neuroticismo y ansiedad no eran predictores significativos de la intensidad de los síntomas, mientras que la depresión demostró una relación marginalmente significante con la intensidad de los síntomas, mediada por la intensidad del estrés. En conclusión, la depresión y el estrés diario parecen ser contribuidores importantes al círculo vicioso de la perpetuación de los síntomas SII."],"format":["application/pdf"],"id":"50|dedup_wf_001::054ea3bc3ccc386d150d900776e1070d","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::2e3d2c4f33a7a1f58bc6c81cacd21e9c","value":"Repository of the University of Rijeka, Faculty of Humanities and Social Sciences"},"hostedby":{"key":"10|opendoar____::2e3d2c4f33a7a1f58bc6c81cacd21e9c","value":"Repository of the University of Rijeka, Faculty of Humanities and Social Sciences"},"license":"http://creativecommons.org/licenses/by/4.0/","publicationdate":"2016-04-01","refereed":"UNKNOWN","type":"Article","url":["https://repository.ffri.uniri.hr/islandora/object/ffri:1182","https://urn.nsk.hr/urn:nbn:hr:186:701987","https://repository.ffri.uniri.hr/islandora/object/ffri:1182/datastream/FILE0"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::1c1d4df596d01da60385f0bb17a4a9e0","value":"HRČAK - Portal of scientific journals of Croatia"},"hostedby":{"key":"10|opendoar____::1c1d4df596d01da60385f0bb17a4a9e0","value":"HRČAK - Portal of scientific journals of Croatia"},"publicationdate":"2016-01-01","refereed":"UNKNOWN","type":"Other literature type","url":["https://hrcak.srce.hr/156331","https://hrcak.srce.hr/file/230444"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"},"hostedby":{"key":"10|doajarticles::23738aeeb586d9f9b652c75aaff54dd4","value":"Psychological Topics"},"publicationdate":"2016-04-01","refereed":"UNKNOWN","type":"Article","url":["http://pt.ffri.hr/index.php/pt/article/view/317","https://doaj.org/toc/1332-0742"]}],"language":{"code":"eng","label":"English"},"lastupdatetimestamp":1603727328518,"maintitle":"The role of stress in IBS symptom severity","originalId":["oai:repository.ffri.uniri.hr:ffri_1182","oai:hrcak.srce.hr:156331","oai:doaj.org/article:4394c5a4f62849ffac7ea485a91540a3"],"pid":[],"projects":[{"code":"009-0092660-2655","funder":{"jurisdiction":"HR","name":"Ministry of Science, Education and Sports of the Republic of Croatia (MSES)","shortName":"MZOS"},"id":"40|irb_hr______::ad496254144c27606e4058841e060fa0","provenance":{"provenance":"Harvested","trust":"0.900000000000000022"},"title":"Psychosomatic aspects of chronic functional and inflammatory bowel diseases"}],"publicationdate":"2016-04-01","subjects":[{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"irritable bowel syndrome"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"symptom severity"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"daily stress"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"depression"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"DRUŠTVENE ZNANOSTI. 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dependence of the recovery of the transition temperature shift after annealing (475 °C, 100 h) on copper and phosphorus contents has been studied on irradiated reactor pressure vessel (RPV) materials. A set of model alloys with low nickel content, lower than 0.2 mass%, was used for the study. Copper and phosphorus contents were varied in a wide range: 0.005–0.99 and 0.002–0.039 mass%, respectively. Recovery efficiency has been estimated by the value of residual embrittlement after annealing, measured in terms of a shift in transition temperature (ΔTKres). A comparison of the results obtained on model alloys with data for VVER-440 RPV materials has also been carried out. Comparative analysis has confirmed the conclusion that ΔTKres is independent of phosphorus content while the effect of copper on ΔTKres is not significant for typical VVER-440 RPV materials with a typical range of Cu contents between 0.10 and 0.24 mass%. 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The bi-functionality of the protein also allowed the binding of hydrophobic solid drug nanoparticles to cellulose nanofibrils and thereby improving their long-term stability under physiological conditions."}],"externalReference":[],"extraInfo":[],"format":[],"fulltext":[],"id":"50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb","instance":[{"accessright":{"classid":"CLOSED","classname":"Closed Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"collectedfrom":{"key":"10|openaire____::4692342f0992d91f9e705c26959f09e0","value":"VTT Research Information 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Ce qui nous frappe en premier lieu dans le roman de Melchior Mbonimpa, Le Totem des Baranda, c'est l'efficacité de sa fonction didactique. Le livre est porteur d'un message, d'une vision sur l'histoire de l'Afrique des Grands Lacs qu'on rencontre rarement dans l'actualité ou l'histoire immédiate que nous livrent les médias.

Cette thèse se penchera sur un aspect de ce roman qui a particulièrement attiré notre attention: la représentation de la résistance à travers l'affirmation identitaire des personnages féminins. Dans notre analyse de ce thème, nous accordons une grande importance au contexte socioculturel et à l'imaginaire collectif qui nourrissent l'auteur et dans lesquels s'inscrivent ses personnages. L'étude soulignera la fonction sociale de l'écrivain et relèvera la contribution de la fiction à la culture africaine. Nous mettrons en évidence les positions idéologiques de l'auteur et le message de sensibilisation qu'il adresse à diverses catégories de lecteurs: ceux qui se trouvent en Afrique, les Africains de la diaspora, et les lecteurs non-Africains qui s'intéressent à son œuvre. Cette orientation idéologique affecte évidemment la manière dont s'exprime la résistance des pnncIpaux personnages féminins du roman. Elle détermine la place que cette fiction accorde à la femme, et qui correspond sans doute à la place que, selon les souhaits de l'auteur, la femme devrait occuper dans le contexte culturel africain. Notre étude insiste aussi sur le fait que dans ce roman, la modernité se nourrit de la culture traditionnelle et ne renie pas les valeurs du passé.

Ainsi, le parcours narratif montre que dans leur résistance, les héroïnes de la généalogie vivent à leur époque, mais chacune porte plus loin une mission transmise par les précédentes.

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The superconducting transition in the magnetic resistance of members of the family of bismuth based high temperature superconductors was investigated. Measurements were performed in magnetic fields up to 1.7 T. Small current densities ranging from 0.03 A/cm² to 3.0 A/cm² were applied. The resistivity of Bi₂Sr₂CaCu₂Ox single crystals was analyzed in terms of the thermally activated flux flow expression, ρ =ρ₀U/T exp(-U/T) where T is the temperature. It was found that the activation energy was given by Uα(Hsinθ)^(⁻α) where α≈1/3 and that the prefactor had the form, ρ₀Hsinθ, where H was the applied field and θ the angle of the field with respect to the CuO₂ planes. Results demonstrated that dissipation could be accounted for by the motion of two-dimensional vortices whose density is given by the field, Hsinθ, projected on the CuO₂ planes. Measurements of the resistivity and current dependent resistivity were performed with two Sn-doped and two Sb-doped polycrystalline Bi(1.7)Pb(0.3)Sr₂Ca₂Cu₃O(y) samples. Features in the temperature derivative of the resistivity curves were associated with the presence of a superconducting transition between superconducting grains, coupled by weak links with a distribution of critical currents and critical temperatures, and the superconducting transition within grains. The transition between grains was more strongly suppressed in temperature with the application of a magnetic field in samples with weaker coupling between grains. The presence of a transition in a magnetic field due to weak links between grains was verified at 77 K by the observation of a current dependent resistivity in a magnetic field. Measurements of a Bi₂Sr₂CaCu₂Ox diffusion grown thick film ring were done. The transverse voltage, the voltage at the centre of a 120 μm thick branch with respect to the centre of a 76 μm thick branch, was measured. A higher critical temperature from the presence of more texturing in the 76 μm branch as determined by separate resistivity, x-ray and scanning electron microscopy measurements was consistent with the measurement of a crossover from a negative to positive transverse voltage as the temperature of the sample went through its superconducting transition.

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This study examines Leonard Cohen's novel Beautiful Losers through the lenses of allegorical and authorial theories to appreciate how the novel uses allegorical techniques to code into symbolic terms an exploration of the polysemous nature of the word ''translation.'' The first chapter studies the stylistic and conceptual dimensions of allegory as a literary genre - as critics like Northrop Frye, Angus Fletchet, and Maureen Quilligan help to define it - while arguing that Cohen's novel is consciously allegorical, challenging readers to interpret what it \"means,\" or may mean. The second chapter performs an intensive re-reading of Beautiful Losers, examining how the novel uses complex systems of verbal play (particularly puns) to coordinate a reunification of various dichotomies historical \"reality\"/imaginative myth, secularity/spirituality, enslavement/sanctification, among others - employed throughout the text. The thesis concludes that the novel is perpetually playing with various types of translation (spiritual, linguistic, physical, and so forth), affirming the need for emotionally-charged, devotional forms of expression (like song and prayer) over more clinical attempts to reorder or recreate the world and its inhabitants. Ultimately, this discussion argues that an understanding of the allegorical dimensions of Beautiful Losers may illuminate how Cohen's other works (particularly his songs) may be studied as attempts to associate word with voice, to emphasize the process of expression (translation) rather than just the finished product.

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La NDI a été étudiée dans le cas de diverses applications, y compris en aéronautique et en aérospatiale. Elle permet de calculer des lois de contrôle capables de linéariser et de découpler un modèle non-linéaire à tout point de fonctionnement de son enveloppe d'état. Cependant cette méthode est intrinsèquement non-robuste aux erreurs de modélisation et aux saturations en entrée. En outre, dans un contexte non-linéaire, l'obtention d'une garantie quantifiable du domaine de stabilité atteint reste à l'heure actuelle complexe. Contrairement aux approches classiques de la NDI, notre méthodologie peut être considérée comme un cadre de compensation non-linéaire généralisé qui permet d'intégrer les incertitudes et les saturations en entrée dans le processus de conception. En utilisant des stratégies de contrôle antiwindup, la loi de pilotage peut être calculée grâce à un simple processus en deux phases. Dans ce cadre de travail généralisé des transformations linéaires fractionnaires (LFT - Linear Fractional Transformations) de la boucle fermée non-linéaire peuvent être facilement déduites pour l'analyse de la stabilité robuste en utilisant des outils standards pour de systèmes linéaires. La méthode proposée est testée pour le pilotage d'un véhicule de rentrée atmosphérique de type aile delta lors de ses phases hypersonique, transsonique et subsonique. Pour cette thèse, un simulateur du vol incluant divers facteurs externes ainsi que des erreurs de modélisation a été développé dans Simulink.\n\nThis thesis work is devoted to extending Nonlinear Dynamic Inversion (NDI) for a large scale of\nnonlinear systems while guaranteeing sufficient stability conditions. NDI has been studied in a wide range of applications, including aeronautics and aerospace. It allows to compute nonlinear control laws able to decouple and linearize a model at any operating point of its state envelope. 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Departamento de Ciencias Ambientales y Recursos Naturales","Universidad de Alicante. Centro Iberoamericano de la Biodiversidad","Biodiversidad y Biotecnología aplicadas a la Biología de la Conservación","Terrestrial Ecology (TE)"],"country":[{"code":"NL","label":"Netherlands","provenance":{"provenance":"Propagation of country to result collected from datasources of type institutional repositories","trust":"0.85"}},{"code":"ES","label":"Spain","provenance":{"provenance":"Propagation of country to result collected from datasources of type institutional repositories","trust":"0.85"}}],"coverage":[],"dateofcollection":"2018-10-03T06:57:46.116Z","description":["Herbivory affects subsequent herbivores, mainly regulated by the phytohormones jasmonic (JA) and salicylic acid (SA). Additionally, organisms such as soil microbes belowground or parasitoids that develop inside their herbivorous hosts aboveground, can change plant responses to herbivory. However, it is not yet well known how organisms of trophic levels other than herbivores, below- and above-ground, alter the interactions between insect species sharing a host plant. Here, we investigated whether the parasitoid Aphidius colemani and different soil microbial communities (created through plant-soil feedbacks) affect the JA and SA signalling pathways in response to the aphid Myzus persicae and the thrips Frankliniella occidentalis, as well as subsequent thrips performance. Our results show that the expression of the JA-responsive gene CaPINII in sweet pepper was more suppressed by aphids than by parasitised aphids. However, parasitism did not affect the expression of CaPAL1, a biosynthetic gene of SA. Furthermore, aphid feeding enhanced thrips performance compared with uninfested plants, but this was not observed when aphids were parasitised. Soils where different plant species were previously grown, did not affect plant responses or the interaction between herbivores. Our study shows that members of the third trophic level can modify herbivore interactions by altering plant physiology.\nThis work and T.V.’s activities were supported by Spanish Ministry of Science and Innovation, (CGL2016-79054), the Open Technology Program of NWO (TTW-13848), and the STSM Cost Action FA1405 funded by the European Union. A.P. research activities were supported by the Netherlands Organisation for Scientific Research (NWO, project no. 870.15.080)."],"format":["application/pdf","application/octet-stream"],"id":"50|dedup_wf_001::01644aebfe64e809f593492e515bc070","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::e820a45f1dfc7b95282d10b6087e11c0","value":"Repositorio Institucional de la Universidad de Alicante"},"hostedby":{"key":"10|opendoar____::e820a45f1dfc7b95282d10b6087e11c0","value":"Repositorio Institucional de la Universidad de Alicante"},"license":"Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.","publicationdate":"2018-09-26","refereed":"UNKNOWN","type":"Article","url":["http://hdl.handle.net/10045/80968"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"},"hostedby":{"key":"10|doajarticles::70703810b20723fe33cba6ffd7128212","value":"Scientific 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(NWO)","shortName":"NWO"},"id":"40|nwo_________::dc69ada721bf21ed51055b6421850d73","provenance":{"provenance":"Harvested","trust":"0.900000000000000022"},"title":"Exploring and exploiting phytochemicals to lure hyperparasitoids away from beneficial biocontrol agents"},{"code":"2300189714","funder":{"jurisdiction":"NL","name":"Netherlands Organisation for Scientific Research (NWO)","shortName":"NWO"},"id":"40|nwo_________::39d892199c3b3d3b5ae9869a79e5bba8","provenance":{"provenance":"Harvested","trust":"0.900000000000000022"},"title":"Linking aboveground-belowground interactions and plant-soil feedback to improve pest control and sustainability in greenhouse cut-flowers"}],"publicationdate":"2018-09-26","publisher":"Springer Nature","subjects":[{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Plant-mediated interactions"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Herbivores"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Feeding guilds"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Parasitism"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Belowground interactions"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Zoología"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Medicine"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"R"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Science"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Q"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"international"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Laboratorium voor Entomologie"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"PE&RC"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Laboratory of Entomology"}},{"subject":{"scheme":"keywords","value":"Multidisciplinary"}}],"type":"publication"} -{"author":[{"fullname":"Bonnie Berger","name":"Bonnie","pid":{"id":{"scheme":"orcid","value":"0000-0002-2724-7228"}},"rank":1,"surname":"Berger"}],"bestaccessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":[{"key":"10|opendoar____::958adb57686c2fdec5796398de5f317a","value":"MPG.PuRe"},{"key":"10|share_______::bbd802baad85d1fd440f32a7a3a2c2b1","value":"bioRxiv"},{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"},{"key":"10|openaire____::8ac8380272269217cb09a928c8caa993","value":"UnpayWall"},{"key":"10|openaire____::806360c771262b4d6770e7cdf04b5c5a","value":"ORCID"},{"key":"10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a","value":"Microsoft Academic Graph"},{"key":"10|opendoar____::89f0fd5c927d466d6ec9a21b9ac34ffa","value":"eScholarship - University of 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Computer Science and Artificial Intelligence Laboratory","Massachusetts Institute of Technology. Department of Mathematics","Lipson, Mark","Loh, Po-Ru","Berger, Bonnie"],"country":[{"code":"DZ","label":"Algeria","provenance":{"provenance":"Propagation of country to result collected from datasources of type institutional repositories","trust":"0.85"}},{"code":"US","label":"United States","provenance":{"provenance":"Propagation of country to result collected from datasources of type institutional repositories","trust":"0.85"}}],"coverage":[],"dateofcollection":"2020-09-12T07:56:34.334Z","description":["Austronesian languages are spread across half the globe, from Easter Island to Madagascar. Evidence from linguistics and archaeology indicates that the ‘Austronesian expansion,’ which began 4,000–5,000 years ago, likely had roots in Taiwan, but the ancestry of present-day Austronesian-speaking populations remains controversial. Here, we analyse genome-wide data from 56 populations using new methods for tracing ancestral gene flow, focusing primarily on Island Southeast Asia. We show that all sampled Austronesian groups harbour ancestry that is more closely related to aboriginal Taiwanese than to any present-day mainland population. Surprisingly, western Island Southeast Asian populations have also inherited ancestry from a source nested within the variation of present-day populations speaking Austro-Asiatic languages, which have historically been nearly exclusive to the mainland. Thus, either there was once a substantial Austro-Asiatic presence in Island Southeast Asia, or Austronesian speakers migrated to and through the mainland, admixing there before continuing to western Indonesia.","National Science Foundation (U.S.). Graduate Research Fellowship Program","Simons Foundation","National Institutes of Health (U.S.) (Grant R01GM108348)","National Institutes of Health (U.S.) (Training Grant 5T32HG004947-04)"],"format":["application/pdf"],"id":"50|dedup_wf_001::025dff86cc73c1c865ed35e5b7646e73","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::958adb57686c2fdec5796398de5f317a","value":"MPG.PuRe"},"hostedby":{"key":"10|opendoar____::958adb57686c2fdec5796398de5f317a","value":"MPG.PuRe"},"license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","publicationdate":"2014-01-01","refereed":"UNKNOWN","type":"Article","url":["http://hdl.handle.net/11858/00-001M-0000-0024-1F46-B","http://hdl.handle.net/11858/00-001M-0000-0024-1F8F-7","http://hdl.handle.net/11858/00-001M-0000-0024-1F90-1"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|share_______::bbd802baad85d1fd440f32a7a3a2c2b1","value":"bioRxiv"},"hostedby":{"key":"10|share_______::bbd802baad85d1fd440f32a7a3a2c2b1","value":"bioRxiv"},"publicationdate":"2014-05-27","refereed":"nonPeerReviewed","type":"Preprint","url":["http://dx.doi.org/10.1101/005603"]},{"accessright":{"code":"c_16ec","label":"RESTRICTED","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"},"hostedby":{"key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c","value":"Unknown 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Due to the portability and relative inexpensiveness of electroencephalography, the N400 event-related potential component has been proposed as a clinically valid means to identify preserved linguistic function in non-communicative patients. Across three experiments, we show that changes in both stimuli and task demands significantly influence the probability of detecting statistically significant N400 effects — that is, the difference in N400 amplitudes caused by the experimental manipulation. In terms of task demands, passively heard linguistic stimuli were significantly less likely to elicit N400 effects than task-relevant stimuli. Due to the inability of the majority of patients with disorders of consciousness to follow task commands, the insensitivity of passive listening would impede the identification of residual language abilities even when such abilities exist. In terms of stimuli, passively heard normatively associated word pairs produced the highest detection rate of N400 effects (50% of the participants), compared with semantically-similar word pairs (0%) and high-cloze sentences (17%). This result is consistent with a prediction error account of N400 magnitude, with highly predictable targets leading to smaller N400 waves, and therefore larger N400 effects. Overall, our data indicate that non-repeating normatively associated word pairs provide the highest probability of detecting single-subject N400s during passive listening, and may thereby provide a clinically viable means of assessing residual linguistic function. 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New polyethers, such as iubol (2), 22-hydroxy-15(28)- dehydrovenustatriol (3), 1,2-dehydropseudodehydrothyrsiferol (4), and secodehydrothyrsiferol (5) have been isolated and characterized from this alga. The structures were determined through the interpretation of NMR spectroscopic data and the relative configuration was proposed on the basis of NOESY spectrum and biogenetic considerations. All new compounds exhibited significant cytotoxic activity against a panel of cancer cell lines. © 2011 by the authors.","Financial support was provided by the grants MAREX (FP 7; KBBE-3-245137) (EU), CTQ2008-06754-C04-01 and SAF2008-02251 (MICINN); C2008000145 and EXMAR (ACISII); RD06/0020/1037 from Red Temática de Investigación Cooperativa en Cáncer, Instituto de Salud Carlos III, co-funded by the Fondo Europeo de Desarrollo Regional of the European Union, and Junta de Castilla y León (CSI052A11-2, and GR15-Experimental Therapeutics and Translational Oncology Program). 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The validity and utility of standard measures of childhood maltreatment requires clarification in order to inform the design of future studies investigating the mental health consequences of maltreatment. The present study assessed agreement between prospective informant-reports and retrospective self-reports of childhood maltreatment, as well as the comparative utility of both reports for predicting a range of psychiatric problems at age 18. Data were obtained from the Environmental Risk (E-Risk) Longitudinal Twin Study, a nationally-representative birth cohort of 2232 children followed to 18 years of age (with 93% retention). Childhood maltreatment was assessed in two ways: (i) prospective informant-reports from caregivers, researchers, and clinicians when children were aged 5, 7, 10 and 12; and (ii) retrospective self-reports of maltreatment experiences occurring up to age 12, obtained at age 18 using the Childhood Trauma Questionnaire. Participants were privately interviewed at age 18 concerning several psychiatric problems including depression, anxiety, self-injury, alcohol/cannabis dependence, and conduct disorder. There was only slight to fair agreement between prospective and retrospective reports of childhood maltreatment (all Kappa's ≤ 0.31). Both prospective and retrospective reports of maltreatment were associated with age-18 psychiatric problems, though the strongest associations were found when maltreatment was retrospectively self-reported. These findings indicate that prospective and retrospective reports of childhood maltreatment capture largely non-overlapping groups of individuals. Young adults who recall being maltreated have a particularly elevated risk for psychopathology."],"format":["application/pdf","text"],"id":"50|dedup_wf_001::085f9efc74e1192abca87031fb573d70","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::566a9968b43628588e76be5a85a0f9e8","value":"King's Research Portal"},"hostedby":{"key":"10|opendoar____::566a9968b43628588e76be5a85a0f9e8","value":"King's Research 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Plants inoculated with the fungal pathogen showed reduced disease symptoms in the resistant genotype in both soils, but the susceptible genotype was partially protected from the pathogen only when grown on the suppressive soil.\r\nThe ‘state of alert’ detected in tomatoes reveals novel mechanisms operating in plants in native soils and the soil microbiota appears to be one of the drivers of these plant responses."],"format":[],"id":"50|dedup_wf_001::09e54cbad6670d8f40a7de2704e2d2a4","instance":[{"accessright":{"code":"c_16ec","label":"RESTRICTED","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"},"hostedby":{"key":"10|issn___print::35ee75a5ad42581d604be113a8f56427","value":"New Phytologist"},"license":"http://doi.wiley.com/10.1002/tdm_license_1.1","publicationdate":"2018-02-09","refereed":"UNKNOWN","type":"Article","url":["https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2Fnph.15014","http://onlinelibrary.wiley.com/wol1/doi/10.1111/nph.15014/fullpdf","http://dx.doi.org/10.1111/nph.15014"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::8ac8380272269217cb09a928c8caa993","value":"UnpayWall"},"hostedby":{"key":"10|issn___print::35ee75a5ad42581d604be113a8f56427","value":"New Phytologist"},"refereed":"UNKNOWN","type":"Article","url":["https://nph.onlinelibrary.wiley.com/doi/pdfdirect/10.1111/nph.15014"]},{"collectedfrom":{"key":"10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a","value":"Microsoft Academic Graph"},"hostedby":{"key":"10|issn___print::35ee75a5ad42581d604be113a8f56427","value":"New Phytologist"},"refereed":"UNKNOWN","type":"Article","url":["https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.15014","https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.15014","http://onlinelibrary.wiley.com/doi/10.1111/nph.15014/abstract","https://aperto.unito.it/handle/2318/1660820","https://academic.microsoft.com/#/detail/2793208206"]},{"accessright":{"code":"c_16ec","label":"RESTRICTED","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::89fcd07f20b6785b92134bd6c1d0fa42","value":"Archivio Istituzionale"},"hostedby":{"key":"10|opendoar____::89fcd07f20b6785b92134bd6c1d0fa42","value":"Archivio Istituzionale"},"publicationdate":"2018-01-01","refereed":"UNKNOWN","type":"Article","url":["http://hdl.handle.net/2318/1660820"]},{"collectedfrom":{"key":"10|openaire____::9e3be59865b2c1c335d32dae2fe7b254","value":"Datacite"},"hostedby":{"key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c","value":"Unknown Repository"},"publicationdate":"2018-12-01","refereed":"UNKNOWN","type":"Other literature type","url":["http://dx.doi.org/10.1111/nph.15014"]}],"language":{"code":"und","label":"Undetermined"},"lastupdatetimestamp":1603727328518,"maintitle":"Native soils with their microbiotas elicit a state of alert in tomato plants","originalId":["10.1111/nph.15014","2793208206","oai:iris.unito.it:2318/1660820"],"pid":[{"scheme":"doi","value":"10.1111/nph.15014"},{"scheme":"pmid","value":"29424928"}],"projects":[{"acronym":"TomRes","code":"727929","funder":{"fundingStream":"H2020","jurisdiction":"EU","name":"European Commission","shortName":"EC"},"id":"40|corda__h2020::94c4a066401e22002c4811a301bb4655","provenance":{"provenance":"Harvested","trust":"0.900000000000000022"},"title":"A NOVEL AND INTEGRATED APPROACH TO INCREASE MULTIPLE AND COMBINED STRESS TOLERANCE IN PLANTS USING TOMATO AS A MODEL"}],"publicationdate":"2018-12-01","publisher":"Wiley","subjects":[{"subject":{"scheme":"keywords","value":"Plant Science"}},{"subject":{"scheme":"keywords","value":"Physiology"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Arbuscular mycorrhizal fungi; Defence responses; Lignin biosynthesis; Microbiota; Suppressive and conducive soils; Susceptible and resistant genotypes; Tomato; Physiology; Plant Science"}},{"provenance":{"provenance":"Inferred by OpenAIRE","trust":"0.891"},"subject":{"scheme":"mesheuropmc","value":"food and beverages"}},{"provenance":{"provenance":"Inferred by OpenAIRE","trust":"0.891"},"subject":{"scheme":"mesheuropmc","value":"fungi"}},{"provenance":{"provenance":"Inferred by OpenAIRE","trust":"0.8739"},"subject":{"scheme":"mesheuropmc","value":"complex mixtures"}}],"type":"publication"} -{"author":[{"fullname":"K.P. 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This study focuses on estimating the evapotranspiration and crop coefficients of table grapes vineyards trained on overhead “tendone” systems in the Apulia region (Italy). Maximum vineyard transpiration was estimated by adopting the “direct” methodology for ETp proposed by the Food and Agriculture Organization in Irrigation and Drainage Paper No. 56, with crop parameters estimated from Landsat 8 and RapidEye satellite data in combination with ground-based meteorological data. The modeling results of two growing seasons (2013 and 2014) indicated that canopy growth, seasonal and 10-day sums evapotranspiration values were strictly related to thermal requirements and rainfall events. The estimated values of mean seasonal daily evapotranspiration ranged between 4.2 and 4.1 mm·d−1, while midseason estimated values of crop coefficients ranged from 0.88 to 0.93 in 2013, and 1.02 to 1.04 in 2014, respectively. The experimental evapotranspiration values calculated represent the maximum value in absence of stress, so the resulting crop coefficients should be used with some caution. It is concluded that the retrieval of crop parameters and evapotranspiration derived from remotely-sensed data could be helpful for downscaling to the field the local weather conditions and agronomic practices and thus may be the basis for supporting grape growers and irrigation managers."],"format":["application/pdf"],"id":"50|dedup_wf_001::0bc332de35b4eb0cc3d0c54b3ff22dd3","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::a8db6f6b2ce4fe72e8b2314a9a93e7d9","value":"Sygma"},"hostedby":{"key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c","value":"Unknown Repository"},"license":"https://creativecommons.org/licenses/by/4.0/","refereed":"UNKNOWN","type":"Article","url":["http://dx.doi.org/10.3390/rs71114708"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"},"hostedby":{"key":"10|doajarticles::f7180a75ef642fcf5309759e0d2c431a","value":"Remote Sensing"},"license":"https://creativecommons.org/licenses/by/4.0/","publicationdate":"2015-11-05","refereed":"UNKNOWN","type":"Article","url":["http://www.mdpi.com/2072-4292/7/11/14708/pdf","http://dx.doi.org/10.3390/rs71114708"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::8ac8380272269217cb09a928c8caa993","value":"UnpayWall"},"hostedby":{"key":"10|doajarticles::f7180a75ef642fcf5309759e0d2c431a","value":"Remote Sensing"},"license":"cc-by","refereed":"UNKNOWN","type":"Article","url":["https://www.mdpi.com/2072-4292/7/11/14708/pdf"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a","value":"Microsoft Academic Graph"},"hostedby":{"key":"10|doajarticles::f7180a75ef642fcf5309759e0d2c431a","value":"Remote Sensing"},"refereed":"UNKNOWN","type":"Article","url":["https://dblp.uni-trier.de/db/journals/remotesensing/remotesensing7.html#VaninoPNMBD15","https://doi.org/10.3390/rs71114708","https://core.ac.uk/display/55147144","http://doi.org/10.3390/rs71114708","https://academic.microsoft.com/#/detail/2149946514"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::c2cdfa5866e03cdd07d313cbc8fb8311","value":"Multidisciplinary Digital Publishing Institute"},"hostedby":{"key":"10|doajarticles::f7180a75ef642fcf5309759e0d2c431a","value":"Remote Sensing"},"license":"http://creativecommons.org/licenses/by/3.0/","publicationdate":"2015-11-05","refereed":"UNKNOWN","type":"Other literature type","url":["http://dx.doi.org/10.3390/rs71114708"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"},"hostedby":{"key":"10|doajarticles::f7180a75ef642fcf5309759e0d2c431a","value":"Remote Sensing"},"publicationdate":"2015-11-01","refereed":"UNKNOWN","type":"Article","url":["http://www.mdpi.com/2072-4292/7/11/14708","https://doaj.org/toc/2072-4292"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::d8c24ca8f23c562a5600876ca2a550ce","value":"Archivio della ricerca - 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Vertical velocities can be estimated indirectly from in situ observations by theoretical frameworks like the-equation. Direct measures of vertical exchanges are challenging due to their typically ephemeral spatiotemporal scales. In this study we address this problem with an adaptive sampling strategy coupling various biophysical instruments. We analyze the 3-D organization of a cyclonic mesoscale structure finely sampled during the Observing Submesoscale Coupling At High Resolution cruise in the Ligurian Sea during fall 2015. The observations, acquired with a moving vessel profiler, highlight a subsurface low-salinity layer (≃50 m), as well as rising isopycnals, generated by geostrophic cyclonic circulation, in the structure's center. Reconstructed 3-D fields of density and horizontal velocities are used to estimate the vertical velocity field down to 250 m by applying the adiabatic QG-equation, for the first time in this region. The vertical motions are characterized by multipolar patterns of downward and upward velocities on the edges of the structure and significantly smaller vertical velocities in its center. Both the 3-D distribution of particles (size ≥100 μm), measured with a laser optical plankton counter, and the Synechococcus and Prochlorococcus abundances (cell per cubic meter) measured by flow cytometry are consistent with the 3-D velocity field. In particular, a secondary vertical recirculation is identified that upwells particles (from 250 to 100 m) along isohalines to the structure's center. Besides demonstrating the effect of vertical patterns on biogeochemical distributions, this case study suggests to use particle matter as a tracer to assess physical dynamics."],"format":["application/pdf"],"id":"50|dedup_wf_001::0d16b1714ab3077df73893a8ea57d776","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::7e7757b1e12abcb736ab9a754ffb617a","value":"Hyper Article en Ligne"},"hostedby":{"key":"10|opendoar____::7e7757b1e12abcb736ab9a754ffb617a","value":"Hyper Article en 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Personality traits, affective status and stress are some of the relevant factors contributing to lower quality of life and symptom exacerbation in IBS patients. In order to examine the role of stress in IBS symptom exacerbation, the aims of this study were to explore the relationship of daily stressful events and symptom severity in a prospective manner and to explore the roles of neuroticism, anxiety, depression and stress in the vicious circle of symptom perpetuation. A total of 49 patients with IBS reported their symptom severity and daily stressful events intensity each day for 14 consecutive days. They also completed the Big five personality inventory, the Beck Depression Inventory and the State-trait anxiety inventory. Cross-correlation analyses were performed on the time series data for daily stress and symptom severity for each participant separately. Four different patterns of relationships were found in different subgroups of participants: positive cross-correlations of symptom severity and stress intensity on the same day; higher symptom severity on days following stressful days; lower symptom severity on days following stressful days; and lower stress intensity on days following severe symptoms. Using average scores for daily stress and symptom severity, as well as scores for neuroticism, anxiety and depression, we performed a path analysis to test a model of symptom exacerbation. It showed that, on the group level, average stress intensity predicts average symptom severity. Neuroticism and anxiety were not significant predictors of symptom severity, while depression showed a marginally significant relationship with symptom severity, mediated by stress intensity. In conclusion, depression and daily stress seem to be important contributors to the vicious circle of IBS symptom perpetuation.","Síndrome del intestino irritable se considera un trastorno biopsicosocial, el resultado de la combinación compleja de factores predisponentes, precipitantes y perpetuos. Rasgos de personalidad, estado afectivo y estrés son algunos de los factores relevantes que contribuyen a la calidad de vida más baja y la exacerbación sintomática de los pacientes con SII. Para examinar el papel del estrés en la exacerbación sintomática de SII, el objetivo de este estudio era explorar la relación entre los acontecimientos cotidianos estresantes y la intensidad de los síntomas de forma prospectiva, tanto como explorar los papeles del neuroticismo, ansiedad, depresión y estrés en el círculo vicioso de perpetuación de los síntomas. Todos los 49 pacientes con SII informaron sobre la intensidad de los síntomas y la intensidad de los acontecimientos cotidianos estresantes cada día durante 14 días consecutivos. Además, completaron el Test de personalidad de los cinco grandes, Inventario de depresión de Beck e Inventario de ansiedad estado-rasgo. En los datos de series temporales se hizo el análisis de correlación cruzada para la intensidad del estrés diario y de los síntomas para cada participante por separado. Se encontraron cuatro patrones de relación diferentes en diferentes subgrupos de participantes: correlación cruzada positiva de la intensidad de los síntomas y del estrés el mismo día; intensidad de los síntomas más alta en los días después de los días estresantes; intensidad de los síntomas más baja en los días después de los días estresantes e intensidad del estrés más baja en los días después de los síntomas graves. Usando resultados promedios para el estrés diario y la intensidad de los síntomas, tanto como resultados para el neuroticismo, ansiedad y depresión, realizamos un análisis del camino para examinar el modelo de la exacerbación de los síntomas. Mostró que, al nivel de grupo, la intensidad del estrés promedia predice la intensidad de los síntomas promedia. Neuroticismo y ansiedad no eran predictores significativos de la intensidad de los síntomas, mientras que la depresión demostró una relación marginalmente significante con la intensidad de los síntomas, mediada por la intensidad del estrés. En conclusión, la depresión y el estrés diario parecen ser contribuidores importantes al círculo vicioso de la perpetuación de los síntomas SII."],"format":["application/pdf"],"id":"50|dedup_wf_001::054ea3bc3ccc386d150d900776e1070d","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::2e3d2c4f33a7a1f58bc6c81cacd21e9c","value":"Repository of the University of Rijeka, Faculty of Humanities and Social Sciences"},"hostedby":{"key":"10|opendoar____::2e3d2c4f33a7a1f58bc6c81cacd21e9c","value":"Repository of the University of Rijeka, Faculty of Humanities and Social Sciences"},"license":"http://creativecommons.org/licenses/by/4.0/","publicationdate":"2016-04-01","refereed":"UNKNOWN","type":"Article","url":["https://repository.ffri.uniri.hr/islandora/object/ffri:1182","https://urn.nsk.hr/urn:nbn:hr:186:701987","https://repository.ffri.uniri.hr/islandora/object/ffri:1182/datastream/FILE0"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::1c1d4df596d01da60385f0bb17a4a9e0","value":"HRČAK - Portal of scientific journals of Croatia"},"hostedby":{"key":"10|opendoar____::1c1d4df596d01da60385f0bb17a4a9e0","value":"HRČAK - Portal of scientific journals of Croatia"},"publicationdate":"2016-01-01","refereed":"UNKNOWN","type":"Other literature type","url":["https://hrcak.srce.hr/156331","https://hrcak.srce.hr/file/230444"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"},"hostedby":{"key":"10|doajarticles::23738aeeb586d9f9b652c75aaff54dd4","value":"Psychological Topics"},"publicationdate":"2016-04-01","refereed":"UNKNOWN","type":"Article","url":["http://pt.ffri.hr/index.php/pt/article/view/317","https://doaj.org/toc/1332-0742"]}],"language":{"code":"eng","label":"English"},"lastupdatetimestamp":1603727328518,"maintitle":"The role of stress in IBS symptom severity","originalId":["oai:repository.ffri.uniri.hr:ffri_1182","oai:hrcak.srce.hr:156331","oai:doaj.org/article:4394c5a4f62849ffac7ea485a91540a3"],"pid":[],"projects":[{"code":"009-0092660-2655","funder":{"jurisdiction":"HR","name":"Ministry of Science, Education and Sports of the Republic of Croatia (MSES)","shortName":"MZOS"},"id":"40|irb_hr______::ad496254144c27606e4058841e060fa0","provenance":{"provenance":"Harvested","trust":"0.900000000000000022"},"title":"Psychosomatic aspects of chronic functional and inflammatory bowel diseases"}],"publicationdate":"2016-04-01","subjects":[{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"irritable bowel syndrome"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"symptom severity"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"daily stress"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"depression"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"DRUŠTVENE ZNANOSTI. 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A set of model alloys with low nickel content, lower than 0.2 mass%, was used for the study. Copper and phosphorus contents were varied in a wide range: 0.005–0.99 and 0.002–0.039 mass%, respectively. Recovery efficiency has been estimated by the value of residual embrittlement after annealing, measured in terms of a shift in transition temperature (ΔTKres). A comparison of the results obtained on model alloys with data for VVER-440 RPV materials has also been carried out. Comparative analysis has confirmed the conclusion that ΔTKres is independent of phosphorus content while the effect of copper on ΔTKres is not significant for typical VVER-440 RPV materials with a typical range of Cu contents between 0.10 and 0.24 mass%. 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central problem for the function and manufacture of materials where performance relies on nanoscale structure is to control the compatibility and interactions of the building blocks. In natural materials, such as nacre, there are examples of multifunctional macromolecules that have combined binding affinities for different materials within the same molecule, thereby bridging these materials and acting as a molecular glue. Here, we describe the use of a designed multifunctional protein that is used for self-assembly of nanofibrillar cellulose. Recent advances in the production of cellulose nanofibrils have given inspiration for new uses of cellulosic materials. Cellulose nanofibrils have mechanical and structural features that open new possibilities for performance in composites and other nanoscale materials. Functionalisation was realised through a bi-functional fusion protein having both an ability to bind to cellulose and a second functionality of surface activity. The cellulose-binding function was obtained using cellulose-binding domains from cellulolytic enzymes and the surface activity through the use of a surface active protein called hydrophobin. Using the bi-functional protein, cellulose nanofibrils could be assembled into tightly packed thin films at the air/water interface and at the oil/water interface. It was shown that the combination of protein and cellulose nanofibrils resulted in a synergistic improvement in the formation and stability of oil-in-water emulsions resulting in emulsions that were stable for several months. The bi-functionality of the protein also allowed the binding of hydrophobic solid drug nanoparticles to cellulose nanofibrils and thereby improving their long-term stability under physiological conditions."}],"externalReference":[],"extraInfo":[],"format":[],"fulltext":[],"id":"50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb","instance":[{"accessright":{"classid":"CLOSED","classname":"Closed Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"collectedfrom":{"key":"10|openaire____::4692342f0992d91f9e705c26959f09e0","value":"VTT Research Information 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Ce qui nous frappe en premier lieu dans le roman de Melchior Mbonimpa, Le Totem des Baranda, c'est l'efficacité de sa fonction didactique. Le livre est porteur d'un message, d'une vision sur l'histoire de l'Afrique des Grands Lacs qu'on rencontre rarement dans l'actualité ou l'histoire immédiate que nous livrent les médias.

Cette thèse se penchera sur un aspect de ce roman qui a particulièrement attiré notre attention: la représentation de la résistance à travers l'affirmation identitaire des personnages féminins. Dans notre analyse de ce thème, nous accordons une grande importance au contexte socioculturel et à l'imaginaire collectif qui nourrissent l'auteur et dans lesquels s'inscrivent ses personnages. L'étude soulignera la fonction sociale de l'écrivain et relèvera la contribution de la fiction à la culture africaine. Nous mettrons en évidence les positions idéologiques de l'auteur et le message de sensibilisation qu'il adresse à diverses catégories de lecteurs: ceux qui se trouvent en Afrique, les Africains de la diaspora, et les lecteurs non-Africains qui s'intéressent à son œuvre. Cette orientation idéologique affecte évidemment la manière dont s'exprime la résistance des pnncIpaux personnages féminins du roman. Elle détermine la place que cette fiction accorde à la femme, et qui correspond sans doute à la place que, selon les souhaits de l'auteur, la femme devrait occuper dans le contexte culturel africain. Notre étude insiste aussi sur le fait que dans ce roman, la modernité se nourrit de la culture traditionnelle et ne renie pas les valeurs du passé.

Ainsi, le parcours narratif montre que dans leur résistance, les héroïnes de la généalogie vivent à leur époque, mais chacune porte plus loin une mission transmise par les précédentes.

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The superconducting transition in the magnetic resistance of members of the family of bismuth based high temperature superconductors was investigated. Measurements were performed in magnetic fields up to 1.7 T. Small current densities ranging from 0.03 A/cm² to 3.0 A/cm² were applied. The resistivity of Bi₂Sr₂CaCu₂Ox single crystals was analyzed in terms of the thermally activated flux flow expression, ρ =ρ₀U/T exp(-U/T) where T is the temperature. It was found that the activation energy was given by Uα(Hsinθ)^(⁻α) where α≈1/3 and that the prefactor had the form, ρ₀Hsinθ, where H was the applied field and θ the angle of the field with respect to the CuO₂ planes. Results demonstrated that dissipation could be accounted for by the motion of two-dimensional vortices whose density is given by the field, Hsinθ, projected on the CuO₂ planes. Measurements of the resistivity and current dependent resistivity were performed with two Sn-doped and two Sb-doped polycrystalline Bi(1.7)Pb(0.3)Sr₂Ca₂Cu₃O(y) samples. Features in the temperature derivative of the resistivity curves were associated with the presence of a superconducting transition between superconducting grains, coupled by weak links with a distribution of critical currents and critical temperatures, and the superconducting transition within grains. The transition between grains was more strongly suppressed in temperature with the application of a magnetic field in samples with weaker coupling between grains. The presence of a transition in a magnetic field due to weak links between grains was verified at 77 K by the observation of a current dependent resistivity in a magnetic field. Measurements of a Bi₂Sr₂CaCu₂Ox diffusion grown thick film ring were done. The transverse voltage, the voltage at the centre of a 120 μm thick branch with respect to the centre of a 76 μm thick branch, was measured. A higher critical temperature from the presence of more texturing in the 76 μm branch as determined by separate resistivity, x-ray and scanning electron microscopy measurements was consistent with the measurement of a crossover from a negative to positive transverse voltage as the temperature of the sample went through its superconducting transition.

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This study examines Leonard Cohen's novel Beautiful Losers through the lenses of allegorical and authorial theories to appreciate how the novel uses allegorical techniques to code into symbolic terms an exploration of the polysemous nature of the word ''translation.'' The first chapter studies the stylistic and conceptual dimensions of allegory as a literary genre - as critics like Northrop Frye, Angus Fletchet, and Maureen Quilligan help to define it - while arguing that Cohen's novel is consciously allegorical, challenging readers to interpret what it \"means,\" or may mean. The second chapter performs an intensive re-reading of Beautiful Losers, examining how the novel uses complex systems of verbal play (particularly puns) to coordinate a reunification of various dichotomies historical \"reality\"/imaginative myth, secularity/spirituality, enslavement/sanctification, among others - employed throughout the text. The thesis concludes that the novel is perpetually playing with various types of translation (spiritual, linguistic, physical, and so forth), affirming the need for emotionally-charged, devotional forms of expression (like song and prayer) over more clinical attempts to reorder or recreate the world and its inhabitants. Ultimately, this discussion argues that an understanding of the allegorical dimensions of Beautiful Losers may illuminate how Cohen's other works (particularly his songs) may be studied as attempts to associate word with voice, to emphasize the process of expression (translation) rather than just the finished product.

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dependence of the recovery of the transition temperature shift after annealing (475 °C, 100 h) on copper and phosphorus contents has been studied on irradiated reactor pressure vessel (RPV) materials. A set of model alloys with low nickel content, lower than 0.2 mass%, was used for the study. Copper and phosphorus contents were varied in a wide range: 0.005–0.99 and 0.002–0.039 mass%, respectively. Recovery efficiency has been estimated by the value of residual embrittlement after annealing, measured in terms of a shift in transition temperature (ΔTKres). A comparison of the results obtained on model alloys with data for VVER-440 RPV materials has also been carried out. Comparative analysis has confirmed the conclusion that ΔTKres is independent of phosphorus content while the effect of copper on ΔTKres is not significant for typical VVER-440 RPV materials with a typical range of Cu contents between 0.10 and 0.24 mass%. 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The bi-functionality of the protein also allowed the binding of hydrophobic solid drug nanoparticles to cellulose nanofibrils and thereby improving their long-term stability under physiological conditions."}],"externalReference":[],"extraInfo":[],"format":[],"fulltext":[],"id":"50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb","instance":[{"accessright":{"classid":"CLOSED","classname":"Closed Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"collectedfrom":{"key":"10|openaire____::4692342f0992d91f9e705c26959f09e0","value":"VTT Research Information 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Ce qui nous frappe en premier lieu dans le roman de Melchior Mbonimpa, Le Totem des Baranda, c'est l'efficacité de sa fonction didactique. Le livre est porteur d'un message, d'une vision sur l'histoire de l'Afrique des Grands Lacs qu'on rencontre rarement dans l'actualité ou l'histoire immédiate que nous livrent les médias.

Cette thèse se penchera sur un aspect de ce roman qui a particulièrement attiré notre attention: la représentation de la résistance à travers l'affirmation identitaire des personnages féminins. Dans notre analyse de ce thème, nous accordons une grande importance au contexte socioculturel et à l'imaginaire collectif qui nourrissent l'auteur et dans lesquels s'inscrivent ses personnages. L'étude soulignera la fonction sociale de l'écrivain et relèvera la contribution de la fiction à la culture africaine. Nous mettrons en évidence les positions idéologiques de l'auteur et le message de sensibilisation qu'il adresse à diverses catégories de lecteurs: ceux qui se trouvent en Afrique, les Africains de la diaspora, et les lecteurs non-Africains qui s'intéressent à son œuvre. Cette orientation idéologique affecte évidemment la manière dont s'exprime la résistance des pnncIpaux personnages féminins du roman. Elle détermine la place que cette fiction accorde à la femme, et qui correspond sans doute à la place que, selon les souhaits de l'auteur, la femme devrait occuper dans le contexte culturel africain. Notre étude insiste aussi sur le fait que dans ce roman, la modernité se nourrit de la culture traditionnelle et ne renie pas les valeurs du passé.

Ainsi, le parcours narratif montre que dans leur résistance, les héroïnes de la généalogie vivent à leur époque, mais chacune porte plus loin une mission transmise par les précédentes.

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The superconducting transition in the magnetic resistance of members of the family of bismuth based high temperature superconductors was investigated. Measurements were performed in magnetic fields up to 1.7 T. Small current densities ranging from 0.03 A/cm² to 3.0 A/cm² were applied. The resistivity of Bi₂Sr₂CaCu₂Ox single crystals was analyzed in terms of the thermally activated flux flow expression, ρ =ρ₀U/T exp(-U/T) where T is the temperature. It was found that the activation energy was given by Uα(Hsinθ)^(⁻α) where α≈1/3 and that the prefactor had the form, ρ₀Hsinθ, where H was the applied field and θ the angle of the field with respect to the CuO₂ planes. Results demonstrated that dissipation could be accounted for by the motion of two-dimensional vortices whose density is given by the field, Hsinθ, projected on the CuO₂ planes. Measurements of the resistivity and current dependent resistivity were performed with two Sn-doped and two Sb-doped polycrystalline Bi(1.7)Pb(0.3)Sr₂Ca₂Cu₃O(y) samples. Features in the temperature derivative of the resistivity curves were associated with the presence of a superconducting transition between superconducting grains, coupled by weak links with a distribution of critical currents and critical temperatures, and the superconducting transition within grains. The transition between grains was more strongly suppressed in temperature with the application of a magnetic field in samples with weaker coupling between grains. The presence of a transition in a magnetic field due to weak links between grains was verified at 77 K by the observation of a current dependent resistivity in a magnetic field. Measurements of a Bi₂Sr₂CaCu₂Ox diffusion grown thick film ring were done. The transverse voltage, the voltage at the centre of a 120 μm thick branch with respect to the centre of a 76 μm thick branch, was measured. A higher critical temperature from the presence of more texturing in the 76 μm branch as determined by separate resistivity, x-ray and scanning electron microscopy measurements was consistent with the measurement of a crossover from a negative to positive transverse voltage as the temperature of the sample went through its superconducting transition.

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This study examines Leonard Cohen's novel Beautiful Losers through the lenses of allegorical and authorial theories to appreciate how the novel uses allegorical techniques to code into symbolic terms an exploration of the polysemous nature of the word ''translation.'' The first chapter studies the stylistic and conceptual dimensions of allegory as a literary genre - as critics like Northrop Frye, Angus Fletchet, and Maureen Quilligan help to define it - while arguing that Cohen's novel is consciously allegorical, challenging readers to interpret what it \"means,\" or may mean. The second chapter performs an intensive re-reading of Beautiful Losers, examining how the novel uses complex systems of verbal play (particularly puns) to coordinate a reunification of various dichotomies historical \"reality\"/imaginative myth, secularity/spirituality, enslavement/sanctification, among others - employed throughout the text. The thesis concludes that the novel is perpetually playing with various types of translation (spiritual, linguistic, physical, and so forth), affirming the need for emotionally-charged, devotional forms of expression (like song and prayer) over more clinical attempts to reorder or recreate the world and its inhabitants. Ultimately, this discussion argues that an understanding of the allegorical dimensions of Beautiful Losers may illuminate how Cohen's other works (particularly his songs) may be studied as attempts to associate word with voice, to emphasize the process of expression (translation) rather than just the finished product.

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La NDI a été étudiée dans le cas de diverses applications, y compris en aéronautique et en aérospatiale. Elle permet de calculer des lois de contrôle capables de linéariser et de découpler un modèle non-linéaire à tout point de fonctionnement de son enveloppe d'état. Cependant cette méthode est intrinsèquement non-robuste aux erreurs de modélisation et aux saturations en entrée. En outre, dans un contexte non-linéaire, l'obtention d'une garantie quantifiable du domaine de stabilité atteint reste à l'heure actuelle complexe. Contrairement aux approches classiques de la NDI, notre méthodologie peut être considérée comme un cadre de compensation non-linéaire généralisé qui permet d'intégrer les incertitudes et les saturations en entrée dans le processus de conception. En utilisant des stratégies de contrôle antiwindup, la loi de pilotage peut être calculée grâce à un simple processus en deux phases. Dans ce cadre de travail généralisé des transformations linéaires fractionnaires (LFT - Linear Fractional Transformations) de la boucle fermée non-linéaire peuvent être facilement déduites pour l'analyse de la stabilité robuste en utilisant des outils standards pour de systèmes linéaires. La méthode proposée est testée pour le pilotage d'un véhicule de rentrée atmosphérique de type aile delta lors de ses phases hypersonique, transsonique et subsonique. Pour cette thèse, un simulateur du vol incluant divers facteurs externes ainsi que des erreurs de modélisation a été développé dans Simulink.\n\nThis thesis work is devoted to extending Nonlinear Dynamic Inversion (NDI) for a large scale of\nnonlinear systems while guaranteeing sufficient stability conditions. NDI has been studied in a wide range of applications, including aeronautics and aerospace. It allows to compute nonlinear control laws able to decouple and linearize a model at any operating point of its state envelope. 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Among them the Habitat (92/43/EC) and Bird Directives (79/409/EC), the Water Framework Directive (2000/60/EC), and the Noise Directive (2002/49/EC) have led to the evaluation/designation of areas in Europe with different criteria. In this study our goal was to understand how the ES capacity of an area is related to its designation and if areas with multiple designations have higher capacity in providing ES. We selected four catchments in Greece with a great variety of characteristics covering over 25% of the national territory. Inside the catchments we assessed the ES capacity (following the methodology of Burkhard et al. 2009) of areas designated as Natura 2000 sites, Quiet areas and Wetlands or Water bodies and found those areas that have multiple designations. Data were analyzed by GLM to reveal differences regarding the ES capacity among the different types of areas. We also investigated by PCA synergies and trade-offs among different kinds of ES and tested for correlations among landscape properties, such as elevation, aspect and slope and the ES potential. Our results show that areas with different types or multiple designations have a different capacity in providing ES. Areas of one designation type (Protected or Quiet Areas) had in general intermediate scores in most ES but scores were higher compared to areas with no designation, which displayed stronger capacity in provisioning services. Among Protected Areas and Quiet Areas the latter scored better in general. Areas that combined both designation types (Protected and Quiet Areas) showed the highest capacity in 13 out of 29 ES, that were mostly linked with natural and forest ecosystems. We found significant synergies among most regulating, supporting and cultural ES which in turn display trade-offs with provisioning services. The different ES are spatially related and display strong correlation with landscape properties, such as elevation and slope. We suggest that the designation status of an area can be used as an alternative tool for environmental policy, indicating the capacity for ES provision. Multiple designations of areas can be used as proxies for locating ES “hotspots”. 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Whereas there are several different web-based predictors for \u03b1-helical membrane proteins, currently there is no freely available prediction method for \u03b2-barrel membrane proteins, at least with an acceptable level of accuracy. We present here a web server (PRED-TMBB, http://bioinformatics.biol.uoa.gr/PRED-TMBB) which is capable of predicting the transmembrane strands and the topology of \u03b2-barrel outer membrane proteins of Gram-negative bacteria. The method is based on a Hidden Markov Model, trained according to the Conditional Maximum Likelihood criterion. The model was retrained and the training set now includes 16 non-homologous outer membrane proteins with structures known at atomic resolution. The user may submit one sequence at a time and has the option of choosing between three different decoding methods. 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tight-binding parameters via Slatet-Koster method with a very little effort. TBFIT is a scientific Fortran program for numerical tight-binding parameter fitting mainly based on Slater-Koster scheme and tight-binding calculations for the electronic band structures of given atomic and electronic configurations with a simple input interfaces. Basically TBFIT fits Slater-Koster parameters including scaling factors to your target first-principles band structure. For the fitting algorithm, Levenberg–Marquardt algorithm is used (implemented by modifying MINPACK library). You can taste how TBFIT works and its performance in Example section. Once you get proper tight-binding parameters, you can also calculate various Berry phase related quantities, such as Berry curvature, Zak phase, Wilson's loop (Z2 index, Wannier charge center), first Chern number, and so on. In addition, density of states, eigenstate charge density or wavefunction plot, STM simulations (integerated eigenstate density within certain energy window), band structures for edge/surface geometries, E-field effects, etc. You do not need to specify all the bond connections, instead, just provide hopping classes (whether it is 1st-, 2nd-, or 3rd-nearest-neighbor hopping) between atomic species and corresponding hopping parameter names in your input file. Then TBFIT automatically set up tight-binding hamiltonian based on your input geometry and tight-binding parameter setup as defined in input interfaces. In the future release, I will add some routines for the Green function approach to get the surface state (or edge spectrum as well) and the routines for the spin/mirror Chern number evaluation within the given tight-binding parameter and model hamiltonian. 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The result has largely been an unhappy marriage with uncertainties blamed more on the data than the process, although the data collection generally is detailed and comprehensive on catch and effort parameters. An extensive literature review of primary and grey literature on ecosystem drivers, exploitation pressures, and fish population and community states shows that Malawi has the necessary knowledge base for expanding their assessment into multi-causal and exploratory indicator-based methods that can assist in better understanding and more disciplined use of existing data and monitoring systems. Selection and ranking of a suite of indicators focusing on the major fisheries in the Southeast arm of Lake Malawi and Lake Malombe were done by a group of Malawian fisheries researchers and management advisers, thereby testing a framework of scoring criteria assessing an indicator's acceptability, observability, and relatedness to management. 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A visualization project that researches trends in military, healthcare, and education expenditures by government. This project uses the Google Charts API.

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classified"},{"scheme":"","value":"trend"},{"scheme":"","value":"healthcare"},{"scheme":"","value":"Education Visualization Project"},{"scheme":"","value":"Google Charts API"},{"scheme":"","value":"education expenditures"},{"scheme":"","value":"Military"},{"scheme":"","value":"visualization project"},{"scheme":"acm","value":"ComputingMilieux_LEGALASPECTSOFCOMPUTING"}],"type":"software"} From b78889a0ce27a79c7ab2d8da05b118ee4f1bcb36 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 5 Aug 2022 09:11:37 +0200 Subject: [PATCH 145/214] WIP: cleaning of subjects --- .../dhp/common/vocabulary/Vocabulary.java | 6 ++++ .../common/vocabulary/VocabularyGroup.java | 7 +++++ .../dhp/oa/graph/clean/CleaningRuleMap.java | 29 +++++++++++++++---- 3 files changed, 37 insertions(+), 5 deletions(-) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/Vocabulary.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/Vocabulary.java index b3eb98d4f..24a30500d 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/Vocabulary.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/Vocabulary.java @@ -83,4 +83,10 @@ public class Vocabulary implements Serializable { .orElse(null); } + public Qualifier lookup(String id) { + return Optional + .ofNullable(getSynonymAsQualifier(id)) + .orElse(getTermAsQualifier(id)); + } + } diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/VocabularyGroup.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/VocabularyGroup.java index 1c129ff9c..8435b8bf3 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/VocabularyGroup.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/VocabularyGroup.java @@ -81,6 +81,13 @@ public class VocabularyGroup implements Serializable { vocs.put(id.toLowerCase(), new Vocabulary(id, name)); } + public Optional find(final String vocId) { + return Optional + .ofNullable(vocId) + .map(String::toLowerCase) + .map(vocs::get); + } + public void addTerm(final String vocId, final String id, final String name) { if (vocabularyExists(vocId)) { vocs.get(vocId.toLowerCase()).addTerm(id, name); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleMap.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleMap.java index 6c156edb7..2a4183f1b 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleMap.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleMap.java @@ -4,15 +4,15 @@ package eu.dnetlib.dhp.oa.graph.clean; import java.io.Serializable; import java.util.HashMap; +import eu.dnetlib.dhp.common.vocabulary.Vocabulary; +import eu.dnetlib.dhp.schema.oaf.*; import org.apache.commons.lang3.StringUtils; import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableConsumer; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.oaf.AccessRight; -import eu.dnetlib.dhp.schema.oaf.Country; -import eu.dnetlib.dhp.schema.oaf.Qualifier; -import eu.dnetlib.dhp.schema.oaf.Relation; + +import javax.jws.WebParam; public class CleaningRuleMap extends HashMap, SerializableConsumer> implements Serializable { @@ -27,10 +27,29 @@ public class CleaningRuleMap extends HashMap, SerializableConsumer cleanQualifier(vocabularies, (AccessRight) o)); mapping.put(Country.class, o -> cleanCountry(vocabularies, (Country) o)); mapping.put(Relation.class, o -> cleanRelation(vocabularies, (Relation) o)); - + mapping.put(Subject.class, o -> cleanSubject(vocabularies, (Subject) o)); return mapping; } + private static void cleanSubject(VocabularyGroup vocabularies, Subject s) { + // TODO cleaning based on different subject vocabs can be added here + cleanSubjectForVocabulary(ModelConstants.DNET_SUBJECT_FOS_CLASSID, vocabularies, s); + } + + private static void cleanSubjectForVocabulary(String vocabularyId, VocabularyGroup vocabularies, Subject s) { + vocabularies.find(vocabularyId).ifPresent(vocabulary -> { + if (!ModelConstants.DNET_SUBJECT_KEYWORD.equalsIgnoreCase(s.getQualifier().getClassid())) { + return; + } + Qualifier newValue = vocabulary.lookup(s.getValue()); + if (!s.getValue().equals(newValue.getClassid())) { + s.setValue(newValue.getClassid()); + s.getQualifier().setClassid(vocabularyId); + s.getQualifier().setClassname(vocabulary.getName()); + } + }); + } + private static void cleanRelation(VocabularyGroup vocabularies, Relation r) { if (vocabularies.vocabularyExists(ModelConstants.DNET_RELATION_SUBRELTYPE)) { Qualifier newValue = vocabularies.lookup(ModelConstants.DNET_RELATION_SUBRELTYPE, r.getSubRelType()); From 227e10f4b3ae28cb531b8b8863536e7484ae2c58 Mon Sep 17 00:00:00 2001 From: Antonis Lempesis Date: Fri, 5 Aug 2022 12:54:36 +0300 Subject: [PATCH 146/214] commenting out the collab indicators because they still fail --- .../scripts/step16-createIndicatorsTables.sql | 162 +++++++++--------- .../scripts/step20-createMonitorDB.sql | 2 +- 2 files changed, 82 insertions(+), 82 deletions(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql index 25776316b..da344d132 100755 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql @@ -84,87 +84,87 @@ from project_results r compute stats indi_funded_result_with_fundref; -create table indi_result_org_collab stored as parquet as -select o1.organization org1, o2.organization org2, count(distinct o1.id) as collaborations -from result_organization as o1 - join result_organization as o2 on o1.id=o2.id and o1.organization!=o2.organization -group by o1.organization, o2.organization; - -compute stats indi_result_org_collab; - -create table indi_result_org_country_collab stored as parquet as - with tmp as - (select o.id as id, o.country , ro.id as result,r.type from organization o - join result_organization ro on o.id=ro.organization - join result r on r.id=ro.id where o.country <> 'UNKNOWN') -select o1.id org1,o2.country country2, o1.type, count(distinct o1.result) as collaborations -from tmp as o1 - join tmp as o2 on o1.result=o2.result -where o1.id<>o2.id and o1.country<>o2.country -group by o1.id, o1.type,o2.country; - -compute stats indi_result_org_country_collab; - -create table indi_result_org_collab stored as parquet as - with tmp as - (select o.id, ro.id as result,r.type from organization o - join result_organization ro on o.id=ro.organization - join result r on r.id=ro.id) -select o1.id org1,o2.id org2, o1.type, count(distinct o1.result) as collaborations -from tmp as o1 - join tmp as o2 on o1.result=o2.result -where o1.id<>o2.id -group by o1.id, o2.id, o1.type; - -compute stats indi_result_org_collab; - -create table indi_project_collab_org stored as parquet as -select o1.id org1,o2.id org2, count(distinct o1.project) as collaborations -from organization_projects as o1 - join organization_projects as o2 on o1.project=o2.project -where o1.id!=o2.id -group by o1.id, o2.id; - -compute stats indi_project_collab_org; - -create table indi_project_collab_org_country stored as parquet as - with tmp as - (select o.id organization, o.country , ro.project as project from organization o - join organization_projects ro on o.id=ro.id - and o.country <> 'UNKNOWN') -select o1.organization org1,o2.country country2, count(distinct o1.project) as collaborations -from tmp as o1 - join tmp as o2 on o1.project=o2.project -where o1.organization<>o2.organization and o1.country<>o2.country -group by o1.organization, o2.country; - -compute stats indi_project_collab_org_country; - -create table indi_funder_country_collab stored as parquet as - with tmp as (select funder, project, country from organization_projects op - join organization o on o.id=op.id - join project p on p.id=op.project - where country <> 'UNKNOWN') -select f1.funder, f1.country as country1, f2.country as country2, count(distinct f1.project) as collaborations -from tmp as f1 - join tmp as f2 on f1.project=f2.project -where f1.country<>f2.country -group by f1.funder, f2.country, f1.country; - -compute stats indi_funder_country_collab; - -create table indi_result_country_collab stored as parquet as - with tmp as - (select country, ro.id as result,r.type from organization o - join result_organization ro on o.id=ro.organization - join result r on r.id=ro.id where country <> 'UNKNOWN') -select o1.country country1, o2.country country2, o1.type, count(distinct o1.result) as collaborations -from tmp as o1 - join tmp as o2 on o1.result=o2.result -where o1.country<>o2.country -group by o1.country, o2.country, o1.type; - -compute stats indi_result_country_collab; +-- create table indi_result_org_collab stored as parquet as +-- select o1.organization org1, o2.organization org2, count(distinct o1.id) as collaborations +-- from result_organization as o1 +-- join result_organization as o2 on o1.id=o2.id and o1.organization!=o2.organization +-- group by o1.organization, o2.organization; +-- +-- compute stats indi_result_org_collab; +-- +-- create table indi_result_org_country_collab stored as parquet as +-- with tmp as +-- (select o.id as id, o.country , ro.id as result,r.type from organization o +-- join result_organization ro on o.id=ro.organization +-- join result r on r.id=ro.id where o.country <> 'UNKNOWN') +-- select o1.id org1,o2.country country2, o1.type, count(distinct o1.result) as collaborations +-- from tmp as o1 +-- join tmp as o2 on o1.result=o2.result +-- where o1.id<>o2.id and o1.country<>o2.country +-- group by o1.id, o1.type,o2.country; +-- +-- compute stats indi_result_org_country_collab; +-- +-- create table indi_result_org_collab stored as parquet as +-- with tmp as +-- (select o.id, ro.id as result,r.type from organization o +-- join result_organization ro on o.id=ro.organization +-- join result r on r.id=ro.id) +-- select o1.id org1,o2.id org2, o1.type, count(distinct o1.result) as collaborations +-- from tmp as o1 +-- join tmp as o2 on o1.result=o2.result +-- where o1.id<>o2.id +-- group by o1.id, o2.id, o1.type; +-- +-- compute stats indi_result_org_collab; +-- +-- create table indi_project_collab_org stored as parquet as +-- select o1.id org1,o2.id org2, count(distinct o1.project) as collaborations +-- from organization_projects as o1 +-- join organization_projects as o2 on o1.project=o2.project +-- where o1.id!=o2.id +-- group by o1.id, o2.id; +-- +-- compute stats indi_project_collab_org; +-- +-- create table indi_project_collab_org_country stored as parquet as +-- with tmp as +-- (select o.id organization, o.country , ro.project as project from organization o +-- join organization_projects ro on o.id=ro.id +-- and o.country <> 'UNKNOWN') +-- select o1.organization org1,o2.country country2, count(distinct o1.project) as collaborations +-- from tmp as o1 +-- join tmp as o2 on o1.project=o2.project +-- where o1.organization<>o2.organization and o1.country<>o2.country +-- group by o1.organization, o2.country; +-- +-- compute stats indi_project_collab_org_country; +-- +-- create table indi_funder_country_collab stored as parquet as +-- with tmp as (select funder, project, country from organization_projects op +-- join organization o on o.id=op.id +-- join project p on p.id=op.project +-- where country <> 'UNKNOWN') +-- select f1.funder, f1.country as country1, f2.country as country2, count(distinct f1.project) as collaborations +-- from tmp as f1 +-- join tmp as f2 on f1.project=f2.project +-- where f1.country<>f2.country +-- group by f1.funder, f2.country, f1.country; +-- +-- compute stats indi_funder_country_collab; +-- +-- create table indi_result_country_collab stored as parquet as +-- with tmp as +-- (select country, ro.id as result,r.type from organization o +-- join result_organization ro on o.id=ro.organization +-- join result r on r.id=ro.id where country <> 'UNKNOWN') +-- select o1.country country1, o2.country country2, o1.type, count(distinct o1.result) as collaborations +-- from tmp as o1 +-- join tmp as o2 on o1.result=o2.result +-- where o1.country<>o2.country +-- group by o1.country, o2.country, o1.type; +-- +-- compute stats indi_result_country_collab; ---- Sprint 4 ---- create table indi_pub_diamond stored as parquet as diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql index cc6b69e34..5aca19f6e 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql @@ -170,7 +170,7 @@ compute stats TARGET.indi_result_has_cc_licence; create table TARGET.indi_result_has_cc_licence_url stored as parquet as select * from SOURCE.indi_result_has_cc_licence_url orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_result_has_cc_licence_url; -create view TARGET.indi_funder_country_collab as select * from SOURCE.indi_funder_country_collab; +-- create view TARGET.indi_funder_country_collab as select * from SOURCE.indi_funder_country_collab; create table TARGET.indi_result_with_orcid stored as parquet as select * from SOURCE.indi_result_with_orcid orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_result_with_orcid; From 32cee1f619eb30d2e2ac6083435b76b1aba7db09 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 5 Aug 2022 12:32:08 +0200 Subject: [PATCH 147/214] WIP: cleaning of subjects --- .../dhp/common/vocabulary/Vocabulary.java | 4 ++-- .../common/vocabulary/VocabularyGroup.java | 6 +++--- .../dhp/oa/graph/clean/CleaningRuleMap.java | 8 ++++---- .../clean/GraphCleaningFunctionsTest.java | 11 ++++++++++ .../eu/dnetlib/dhp/oa/graph/clean/result.json | 20 +++++++++---------- .../dnetlib/dhp/oa/graph/clean/synonyms.txt | 4 +++- .../eu/dnetlib/dhp/oa/graph/clean/terms.txt | 5 ++++- 7 files changed, 37 insertions(+), 21 deletions(-) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/Vocabulary.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/Vocabulary.java index 24a30500d..3a8df5c9e 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/Vocabulary.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/Vocabulary.java @@ -85,8 +85,8 @@ public class Vocabulary implements Serializable { public Qualifier lookup(String id) { return Optional - .ofNullable(getSynonymAsQualifier(id)) - .orElse(getTermAsQualifier(id)); + .ofNullable(getSynonymAsQualifier(id)) + .orElse(getTermAsQualifier(id)); } } diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/VocabularyGroup.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/VocabularyGroup.java index 8435b8bf3..fc7175270 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/VocabularyGroup.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/VocabularyGroup.java @@ -83,9 +83,9 @@ public class VocabularyGroup implements Serializable { public Optional find(final String vocId) { return Optional - .ofNullable(vocId) - .map(String::toLowerCase) - .map(vocs::get); + .ofNullable(vocId) + .map(String::toLowerCase) + .map(vocs::get); } public void addTerm(final String vocId, final String id, final String name) { diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleMap.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleMap.java index 2a4183f1b..894d5d059 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleMap.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleMap.java @@ -4,15 +4,15 @@ package eu.dnetlib.dhp.oa.graph.clean; import java.io.Serializable; import java.util.HashMap; -import eu.dnetlib.dhp.common.vocabulary.Vocabulary; -import eu.dnetlib.dhp.schema.oaf.*; +import javax.jws.WebParam; + import org.apache.commons.lang3.StringUtils; import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableConsumer; +import eu.dnetlib.dhp.common.vocabulary.Vocabulary; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; import eu.dnetlib.dhp.schema.common.ModelConstants; - -import javax.jws.WebParam; +import eu.dnetlib.dhp.schema.oaf.*; public class CleaningRuleMap extends HashMap, SerializableConsumer> implements Serializable { diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java index 7c39efb40..f4c4581b1 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java @@ -251,6 +251,17 @@ public class GraphCleaningFunctionsTest { pid.getQualifier().getClassname())); }); + assertNotNull(p_cleaned.getSubject()); + + List fos_subjects = p_cleaned + .getSubject() + .stream() + .filter(s -> ModelConstants.DNET_SUBJECT_FOS_CLASSID.equals(s.getQualifier().getClassid())) + .collect(Collectors.toList()); + + assertNotNull(fos_subjects); + assertEquals(2, fos_subjects.size()); + // TODO add more assertions to verity the cleaned values System.out.println(MAPPER.writeValueAsString(p_cleaned)); } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json index 78fdc4c9d..ea63bba28 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json @@ -743,12 +743,12 @@ "trust": "0.9" }, "qualifier": { - "classid": "", - "classname": "", - "schemeid": "", - "schemename": "" + "classid": "keyword", + "classname": "keyword", + "schemeid": "dnet:subject_classification_typologies", + "schemename": "dnet:subject_classification_typologies" }, - "value": "infrared detectors" + "value": "FOS: Mathematics" }, { "dataInfo": { @@ -765,12 +765,12 @@ "trust": "0.9" }, "qualifier": { - "classid": "", - "classname": "", - "schemeid": "", - "schemename": "" + "classid": "keyword", + "classname": "keyword", + "schemeid": "dnet:subject_classification_typologies", + "schemename": "dnet:subject_classification_typologies" }, - "value": "lens antennas" + "value": "FOS: Computer and information sciences" }, { "dataInfo": { diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt index 39ed0cef1..409dfd5dc 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt @@ -1243,4 +1243,6 @@ dnet:relation_relClass @=@ IsSupplementTo @=@ isSupplementTo dnet:relation_relClass @=@ IsSupplementedBy @=@ isSupplementedBy dnet:relation_relClass @=@ IsRelatedTo @=@ isRelatedTo dnet:relation_subRelType @=@ relationship @=@ publicationDataset -dnet:provenanceActions @=@ iis @=@ erroneous label to be cleaned \ No newline at end of file +dnet:provenanceActions @=@ iis @=@ erroneous label to be cleaned +FOS @=@ 0101 mathematics @=@ FOS: Mathematics +FOS @=@ 0102 computer and information sciences @=@ FOS: Computer and information sciences \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt index 59311d5a7..83ca81670 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt @@ -1117,4 +1117,7 @@ dnet:relation_subRelType @=@ dnet:relation_subRelType @=@ relationship @=@ relat dnet:relation_subRelType @=@ dnet:relation_subRelType @=@ review @=@ review dnet:relation_subRelType @=@ dnet:relation_subRelType @=@ similarity @=@ similarity dnet:relation_subRelType @=@ dnet:relation_subRelType @=@ supplement @=@ supplement -dnet:relation_subRelType @=@ dnet:relation_subRelType @=@ version @=@ version \ No newline at end of file +dnet:relation_subRelType @=@ dnet:relation_subRelType @=@ version @=@ version +FOS @=@ Fields of Science and Technology classification @=@ 0101 mathematics @=@ 0101 mathematics +FOS @=@ Fields of Science and Technology classification @=@ 0102 computer and information sciences @=@ 0102 computer and information sciences +FOS @=@ Fields of Science and Technology classification @=@ 0103 physical sciences @=@ 0103 physical sciences \ No newline at end of file From fcef5294e21c8a0c5ba4afcae03a460f8e1ea6fb Mon Sep 17 00:00:00 2001 From: Antonis Lempesis Date: Fri, 5 Aug 2022 13:45:01 +0300 Subject: [PATCH 148/214] restored some collab indicators --- .../scripts/step16-createIndicatorsTables.sql | 68 +++++++++---------- .../scripts/step20-createMonitorDB.sql | 4 +- 2 files changed, 37 insertions(+), 35 deletions(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql index da344d132..2581f1d64 100755 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql @@ -118,40 +118,40 @@ compute stats indi_funded_result_with_fundref; -- -- compute stats indi_result_org_collab; -- --- create table indi_project_collab_org stored as parquet as --- select o1.id org1,o2.id org2, count(distinct o1.project) as collaborations --- from organization_projects as o1 --- join organization_projects as o2 on o1.project=o2.project --- where o1.id!=o2.id --- group by o1.id, o2.id; --- --- compute stats indi_project_collab_org; --- --- create table indi_project_collab_org_country stored as parquet as --- with tmp as --- (select o.id organization, o.country , ro.project as project from organization o --- join organization_projects ro on o.id=ro.id --- and o.country <> 'UNKNOWN') --- select o1.organization org1,o2.country country2, count(distinct o1.project) as collaborations --- from tmp as o1 --- join tmp as o2 on o1.project=o2.project --- where o1.organization<>o2.organization and o1.country<>o2.country --- group by o1.organization, o2.country; --- --- compute stats indi_project_collab_org_country; --- --- create table indi_funder_country_collab stored as parquet as --- with tmp as (select funder, project, country from organization_projects op --- join organization o on o.id=op.id --- join project p on p.id=op.project --- where country <> 'UNKNOWN') --- select f1.funder, f1.country as country1, f2.country as country2, count(distinct f1.project) as collaborations --- from tmp as f1 --- join tmp as f2 on f1.project=f2.project --- where f1.country<>f2.country --- group by f1.funder, f2.country, f1.country; --- --- compute stats indi_funder_country_collab; +create table indi_project_collab_org stored as parquet as +select o1.id org1,o2.id org2, count(distinct o1.project) as collaborations +from organization_projects as o1 + join organization_projects as o2 on o1.project=o2.project +where o1.id!=o2.id +group by o1.id, o2.id; + +compute stats indi_project_collab_org; + +create table indi_project_collab_org_country stored as parquet as + with tmp as + (select o.id organization, o.country , ro.project as project from organization o + join organization_projects ro on o.id=ro.id + and o.country <> 'UNKNOWN') +select o1.organization org1,o2.country country2, count(distinct o1.project) as collaborations +from tmp as o1 + join tmp as o2 on o1.project=o2.project +where o1.organization<>o2.organization and o1.country<>o2.country +group by o1.organization, o2.country; + +compute stats indi_project_collab_org_country; + +create table indi_funder_country_collab stored as parquet as + with tmp as (select funder, project, country from organization_projects op + join organization o on o.id=op.id + join project p on p.id=op.project + where country <> 'UNKNOWN') +select f1.funder, f1.country as country1, f2.country as country2, count(distinct f1.project) as collaborations +from tmp as f1 + join tmp as f2 on f1.project=f2.project +where f1.country<>f2.country +group by f1.funder, f2.country, f1.country; + +compute stats indi_funder_country_collab; -- -- create table indi_result_country_collab stored as parquet as -- with tmp as diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql index 5aca19f6e..d78895198 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql @@ -170,7 +170,9 @@ compute stats TARGET.indi_result_has_cc_licence; create table TARGET.indi_result_has_cc_licence_url stored as parquet as select * from SOURCE.indi_result_has_cc_licence_url orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_result_has_cc_licence_url; --- create view TARGET.indi_funder_country_collab as select * from SOURCE.indi_funder_country_collab; +create view TARGET.indi_funder_country_collab as select * from SOURCE.indi_funder_country_collab; +create view TARGET.indi_project_collab_org as select * from SOURCE.indi_project_collab_org; +create view TARGET.indi_project_collab_org_country as select * from SOURCE.indi_project_collab_org_country; create table TARGET.indi_result_with_orcid stored as parquet as select * from SOURCE.indi_result_with_orcid orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_result_with_orcid; From 4eaa063b1f03f3b855ddc6687c905f6b269b1756 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 5 Aug 2022 16:56:09 +0200 Subject: [PATCH 149/214] cleaning of subjects --- .../dhp/oa/graph/clean/CleaningRuleMap.java | 32 +++++++++++-------- .../clean/GraphCleaningFunctionsTest.java | 14 ++++++++ 2 files changed, 33 insertions(+), 13 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleMap.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleMap.java index 894d5d059..c650400af 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleMap.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleMap.java @@ -3,13 +3,12 @@ package eu.dnetlib.dhp.oa.graph.clean; import java.io.Serializable; import java.util.HashMap; +import java.util.concurrent.atomic.AtomicReference; -import javax.jws.WebParam; - +import org.apache.commons.lang3.SerializationUtils; import org.apache.commons.lang3.StringUtils; import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableConsumer; -import eu.dnetlib.dhp.common.vocabulary.Vocabulary; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.*; @@ -31,23 +30,30 @@ public class CleaningRuleMap extends HashMap, SerializableConsumer modified = new AtomicReference<>(false); vocabularies.find(vocabularyId).ifPresent(vocabulary -> { - if (!ModelConstants.DNET_SUBJECT_KEYWORD.equalsIgnoreCase(s.getQualifier().getClassid())) { + if (!ModelConstants.DNET_SUBJECT_KEYWORD.equalsIgnoreCase(subject.getQualifier().getClassid())) { return; } - Qualifier newValue = vocabulary.lookup(s.getValue()); - if (!s.getValue().equals(newValue.getClassid())) { - s.setValue(newValue.getClassid()); - s.getQualifier().setClassid(vocabularyId); - s.getQualifier().setClassname(vocabulary.getName()); + Qualifier newValue = vocabulary.lookup(subject.getValue()); + if (!subject.getValue().equals(newValue.getClassid())) { + subject.setValue(newValue.getClassid()); + subject.getQualifier().setClassid(vocabularyId); + subject.getQualifier().setClassname(vocabulary.getName()); + modified.set(true); } }); + return modified.get(); } private static void cleanRelation(VocabularyGroup vocabularies, Relation r) { diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java index f4c4581b1..0bfee1151 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java @@ -262,6 +262,20 @@ public class GraphCleaningFunctionsTest { assertNotNull(fos_subjects); assertEquals(2, fos_subjects.size()); + assertTrue( + fos_subjects + .stream() + .anyMatch( + s -> "0101 mathematics".equals(s.getValue()) & + ModelConstants.DNET_SUBJECT_FOS_CLASSID.equals(s.getQualifier().getClassid()))); + + assertTrue( + fos_subjects + .stream() + .anyMatch( + s -> "0102 computer and information sciences".equals(s.getValue()) & + ModelConstants.DNET_SUBJECT_FOS_CLASSID.equals(s.getQualifier().getClassid()))); + // TODO add more assertions to verity the cleaned values System.out.println(MAPPER.writeValueAsString(p_cleaned)); } From 3418ce50ac9b28fed4fa949919e6c8208738cdcf Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 8 Aug 2022 12:48:47 +0200 Subject: [PATCH 150/214] cleaning of subjects: perform the cleaning when the given value is equivalent to one of the terms in the vocabulary --- .../dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java | 3 ++- .../eu/dnetlib/dhp/oa/graph/clean/CleaningRuleMap.java | 2 +- .../dhp/oa/graph/clean/GraphCleaningFunctionsTest.java | 2 +- .../eu/dnetlib/dhp/oa/graph/clean/result.json | 10 +++++----- 4 files changed, 9 insertions(+), 8 deletions(-) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java index d58b354ab..6ba7d70f1 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java @@ -11,6 +11,7 @@ import java.util.function.Function; import java.util.function.Predicate; import java.util.stream.Collectors; +import eu.dnetlib.dhp.schema.common.ModelConstants; import org.apache.commons.lang3.StringUtils; import eu.dnetlib.dhp.schema.common.AccessRightComparator; @@ -141,7 +142,7 @@ public class OafMapperUtils { } public static Qualifier unknown(final String schemeid, final String schemename) { - return qualifier("UNKNOWN", "Unknown", schemeid, schemename); + return qualifier(UNKNOWN, "Unknown", schemeid, schemename); } public static AccessRight accessRight( diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleMap.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleMap.java index c650400af..147e26699 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleMap.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleMap.java @@ -46,7 +46,7 @@ public class CleaningRuleMap extends HashMap, SerializableConsumer Date: Mon, 8 Aug 2022 14:10:47 +0200 Subject: [PATCH 151/214] [Clean Context] changed a bit the logic. Added the check not to have result hosted by a datasource of type institutional repository from NL. Added also the check that the country should have been included in the result via propagation for it to be removed --- .../clean/country/CleanCountrySparkJob.java | 231 ++++++++++-------- .../country/GetDatasourceFromCountry.java | 139 ++++++----- .../dhp/oa/graph/clean/CleanCountryTest.java | 212 ++++++++-------- .../eu/dnetlib/dhp/oa/graph/clean/hostedBy | 0 .../clean/publication_clean_country.json | 3 +- 5 files changed, 315 insertions(+), 270 deletions(-) create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/hostedBy diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java index 1af1aafc0..3ba84a317 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java @@ -1,15 +1,15 @@ + package eu.dnetlib.dhp.oa.graph.clean.country; -/** - * @author miriam.baglioni - * @Date 20/07/22 - */ +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.Serializable; +import java.util.List; +import java.util.Optional; +import java.util.stream.Collectors; + +import javax.swing.text.html.Option; -import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob; -import eu.dnetlib.dhp.schema.oaf.Result; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.FilterFunction; @@ -21,128 +21,147 @@ import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import java.io.Serializable; -import java.util.List; -import java.util.Optional; -import java.util.stream.Collectors; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; +/** + * @author miriam.baglioni + * @Date 20/07/22 + */ +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob; +import eu.dnetlib.dhp.schema.oaf.Country; +import eu.dnetlib.dhp.schema.oaf.Result; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; public class CleanCountrySparkJob implements Serializable { - private static final Logger log = LoggerFactory.getLogger(CleanCountrySparkJob.class); + private static final Logger log = LoggerFactory.getLogger(CleanCountrySparkJob.class); - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - public static void main(String[] args) throws Exception { + public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - CleanContextSparkJob.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/input_clean_country_parameters.json")); - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); + String jsonConfiguration = IOUtils + .toString( + CleanContextSparkJob.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/input_clean_country_parameters.json")); + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - String inputPath = parser.get("inputPath"); - log.info("inputPath: {}", inputPath); + String inputPath = parser.get("inputPath"); + log.info("inputPath: {}", inputPath); - String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + String workingPath = parser.get("workingPath"); + log.info("workingPath: {}", workingPath); - String datasourcePath = parser.get("datasourcePath"); - log.info("datasourcePath: {}", datasourcePath); + String datasourcePath = parser.get("hostedBy"); + log.info("datasourcePath: {}", datasourcePath); - String country = parser.get("country"); - log.info("country: {}", country); + String country = parser.get("country"); + log.info("country: {}", country); - String[] verifyParam = parser.get("verifyParam").split(";"); - log.info("verifyParam: {}", verifyParam); + String[] verifyParam = parser.get("verifyParam").split(";"); + log.info("verifyParam: {}", verifyParam); - String collectedfrom = parser.get("collectedfrom"); - log.info("collectedfrom: {}", collectedfrom); + String collectedfrom = parser.get("collectedfrom"); + log.info("collectedfrom: {}", collectedfrom); - String graphTableClassName = parser.get("graphTableClassName"); - log.info("graphTableClassName: {}", graphTableClassName); + String graphTableClassName = parser.get("graphTableClassName"); + log.info("graphTableClassName: {}", graphTableClassName); - Class entityClazz = (Class) Class.forName(graphTableClassName); + Class entityClazz = (Class) Class.forName(graphTableClassName); - SparkConf conf = new SparkConf(); - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { + SparkConf conf = new SparkConf(); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { - cleanCountry(spark, country, verifyParam, inputPath, entityClazz, workingPath,collectedfrom, datasourcePath); - }); - } + cleanCountry( + spark, country, verifyParam, inputPath, entityClazz, workingPath, collectedfrom, datasourcePath); + }); + } - private static void cleanCountry(SparkSession spark, String country, String[] verifyParam, - String inputPath, Class entityClazz, String workingPath, String collectedfrom, String datasourcePath) { + private static void cleanCountry(SparkSession spark, String country, String[] verifyParam, + String inputPath, Class entityClazz, String workingPath, String collectedfrom, String datasourcePath) { - List hostedBy = spark.read().textFile(datasourcePath) - // .filter((FilterFunction) ds -> !ds.equals(collectedfrom)) - .collectAsList(); + List hostedBy = spark + .read() + .textFile(datasourcePath) + // .filter((FilterFunction) ds -> !ds.equals(collectedfrom)) + .collectAsList(); - Dataset res = spark - .read() - .textFile(inputPath) - .map( - (MapFunction) value -> OBJECT_MAPPER.readValue(value, entityClazz), - Encoders.bean(entityClazz)) - ; + Dataset res = spark + .read() + .textFile(inputPath) + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, entityClazz), + Encoders.bean(entityClazz)); - res.map((MapFunction) r -> { - if(r.getInstance().stream().anyMatch(i -> hostedBy.contains(i.getHostedby().getKey())) || - !r.getCollectedfrom().stream().anyMatch(cf -> cf.getValue().equals(collectedfrom))){ - return r; - } + res.map((MapFunction) r -> { + if (r.getInstance().stream().anyMatch(i -> hostedBy.contains(i.getHostedby().getKey())) || + !r.getCollectedfrom().stream().anyMatch(cf -> cf.getValue().equals(collectedfrom))) { + return r; + } - if(r.getPid().stream().anyMatch(p -> p.getQualifier().getClassid().equals("doi") && pidInParam(p.getValue(), verifyParam)) - && r.getCountry().stream().anyMatch(c -> c.getClassid().equals(country) && c.getDataInfo().getInferenceprovenance().equals("propagation"))) - { r - .setCountry( - r - .getCountry() - .stream() - .filter( - c -> !c.getClassid() - .equalsIgnoreCase(country)) - .collect(Collectors.toList())); + if (r + .getPid() + .stream() + .anyMatch(p -> p.getQualifier().getClassid().equals("doi") && pidInParam(p.getValue(), verifyParam))) { + r + .setCountry( + r + .getCountry() + .stream() + .filter( + c -> toTakeCountry(c, country)) + .collect(Collectors.toList())); - } + } - return r; - }, Encoders.bean(entityClazz)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(workingPath); + return r; + }, Encoders.bean(entityClazz)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingPath); - spark - .read() - .textFile(workingPath) - .map( - (MapFunction) value -> OBJECT_MAPPER.readValue(value, entityClazz), - Encoders.bean(entityClazz)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(inputPath); - } + spark + .read() + .textFile(workingPath) + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, entityClazz), + Encoders.bean(entityClazz)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(inputPath); + } - private static boolean pidInParam(String value, String[] verifyParam) { - for (String s : verifyParam ) - if (value.startsWith(s)) - return true; - return false; - } + private static boolean pidInParam(String value, String[] verifyParam) { + for (String s : verifyParam) + if (value.startsWith(s)) + return true; + return false; + } + + private static boolean toTakeCountry(Country c, String country) { + // If dataInfo is not set, or dataInfo.inferenceprovenance is not set or not present then it cannot be + // inserted via propagation + if (!Optional.ofNullable(c.getDataInfo()).isPresent()) + return true; + if (!Optional.ofNullable(c.getDataInfo().getInferenceprovenance()).isPresent()) + return true; + return !(c + .getClassid() + .equalsIgnoreCase(country) && + c.getDataInfo().getInferenceprovenance().equals("propagation")); + } } - diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/GetDatasourceFromCountry.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/GetDatasourceFromCountry.java index c255c445f..dd5af6998 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/GetDatasourceFromCountry.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/GetDatasourceFromCountry.java @@ -1,10 +1,12 @@ + package eu.dnetlib.dhp.oa.graph.clean.country; -import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.oaf.*; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.Serializable; +import java.util.List; +import java.util.Optional; + import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.FilterFunction; @@ -15,85 +17,92 @@ import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.*; import scala.Tuple2; -import java.io.Serializable; -import java.util.List; -import java.util.Optional; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - /** * @author miriam.baglioni * @Date 22/07/22 */ public class GetDatasourceFromCountry implements Serializable { - private static final Logger log = LoggerFactory.getLogger(GetDatasourceFromCountry.class); + private static final Logger log = LoggerFactory.getLogger(GetDatasourceFromCountry.class); - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - public static void main(String[] args) throws Exception { + public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - GetDatasourceFromCountry.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/input_datasource_country_parameters.json")); - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); + String jsonConfiguration = IOUtils + .toString( + GetDatasourceFromCountry.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/input_datasource_country_parameters.json")); + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - String inputPath = parser.get("inputPath"); - log.info("inputPath: {}", inputPath); + String inputPath = parser.get("inputPath"); + log.info("inputPath: {}", inputPath); - String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + String workingPath = parser.get("workingPath"); + log.info("workingPath: {}", workingPath); - String country = parser.get("country"); - log.info("country: {}", country); + String country = parser.get("country"); + log.info("country: {}", country); - SparkConf conf = new SparkConf(); - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { + SparkConf conf = new SparkConf(); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { - getDatasourceFromCountry(spark, country, inputPath, workingPath); - }); - } + getDatasourceFromCountry(spark, country, inputPath, workingPath); + }); + } - private static void getDatasourceFromCountry(SparkSession spark, String country, String inputPath, String workingPath) { + private static void getDatasourceFromCountry(SparkSession spark, String country, String inputPath, + String workingPath) { - Dataset organization = spark.read().textFile(inputPath + "/organization") - .map( - (MapFunction) value -> OBJECT_MAPPER.readValue(value, Organization.class), - Encoders.bean(Organization.class)) - .filter( - (FilterFunction) o -> !o.getDataInfo().getDeletedbyinference() && - o.getCountry().getClassid().length() > 0 && - o.getCountry().getClassid().equals(country));; + Dataset organization = spark + .read() + .textFile(inputPath + "/organization") + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, Organization.class), + Encoders.bean(Organization.class)) + .filter( + (FilterFunction) o -> !o.getDataInfo().getDeletedbyinference() && + o.getCountry().getClassid().length() > 0 && + o.getCountry().getClassid().equals(country)); + ; + // filtering of the relations taking the non deleted by inference and those with IsProvidedBy as relclass + Dataset relation = spark + .read() + .textFile(inputPath + "/relation") + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, Relation.class), + Encoders.bean(Relation.class)) + .filter( + (FilterFunction) rel -> rel.getRelClass().equalsIgnoreCase(ModelConstants.IS_PROVIDED_BY) && + !rel.getDataInfo().getDeletedbyinference()); - // filtering of the relations taking the non deleted by inference and those with IsProvidedBy as relclass - Dataset relation = spark.read().textFile( inputPath + "/relation") - .map( - (MapFunction) value -> OBJECT_MAPPER.readValue(value, Relation.class), - Encoders.bean(Relation.class)) - .filter( - (FilterFunction) rel -> rel.getRelClass().equalsIgnoreCase(ModelConstants.IS_PROVIDED_BY) && - !rel.getDataInfo().getDeletedbyinference()); + organization + .joinWith(relation, organization.col("id").equalTo(relation.col("target")), "left") + .map((MapFunction, String>) t2 -> t2._2().getSource(), Encoders.STRING()) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingPath); - organization.joinWith(relation, organization.col("id").equalTo(relation.col("target")), "left") - .map((MapFunction, String>) t2 -> t2._2().getSource(), Encoders.STRING() ) - .write() - .mode(SaveMode.Overwrite) - .option("compression","gzip") - .json(workingPath); - - } + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountryTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountryTest.java index a72093156..c9f846570 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountryTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountryTest.java @@ -1,13 +1,10 @@ -package eu.dnetlib.dhp.oa.graph.clean; -/** - * @author miriam.baglioni - * @Date 20/07/22 - */ -import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob; -import eu.dnetlib.dhp.oa.graph.dump.DumpJobTest; -import eu.dnetlib.dhp.schema.oaf.Publication; +package eu.dnetlib.dhp.oa.graph.clean; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; + import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; @@ -22,113 +19,132 @@ import org.junit.jupiter.api.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; +/** + * @author miriam.baglioni + * @Date 20/07/22 + */ +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob; +import eu.dnetlib.dhp.schema.oaf.Publication; public class CleanCountryTest { - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - private static SparkSession spark; + private static SparkSession spark; - private static Path workingDir; + private static Path workingDir; - private static final Logger log = LoggerFactory.getLogger(CleanContextTest.class); + private static final Logger log = LoggerFactory.getLogger(CleanContextTest.class); - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files.createTempDirectory(DumpJobTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files.createTempDirectory(CleanCountryTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); - SparkConf conf = new SparkConf(); - conf.setAppName(DumpJobTest.class.getSimpleName()); + SparkConf conf = new SparkConf(); + conf.setAppName(CleanCountryTest.class.getSimpleName()); - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - spark = SparkSession - .builder() - .appName(DumpJobTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } + spark = SparkSession + .builder() + .appName(CleanCountryTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } - @Test - public void testResultClean() throws Exception { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/clean/publication_clean_country.json") - .getPath(); - final String prefix = "gcube "; + @Test + public void testResultClean() throws Exception { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/clean/publication_clean_country.json") + .getPath(); - spark - .read() - .textFile(sourcePath) - .map( - (MapFunction) r -> OBJECT_MAPPER.readValue(r, Publication.class), - Encoders.bean(Publication.class)) - .write() - .json(workingDir.toString() + "/publication"); + spark + .read() + .textFile(sourcePath) + .map( + (MapFunction) r -> OBJECT_MAPPER.readValue(r, Publication.class), + Encoders.bean(Publication.class)) + .write() + .json(workingDir.toString() + "/publication"); - CleanCountrySparkJob.main(new String[] { - "--isSparkSessionManaged", Boolean.FALSE.toString(), - "--inputPath", workingDir.toString() + "/publication", - "-graphTableClassName", Publication.class.getCanonicalName(), - "-workingPath", workingDir.toString() + "/working", - "-country", "NL", - "-verifyParam", "10.17632", - "-collectedfrom", "NARCIS" - }); + CleanCountrySparkJob.main(new String[] { + "--isSparkSessionManaged", Boolean.FALSE.toString(), + "--inputPath", workingDir.toString() + "/publication", + "-graphTableClassName", Publication.class.getCanonicalName(), + "-workingPath", workingDir.toString() + "/working", + "-country", "NL", + "-verifyParam", "10.17632", + "-collectedfrom", "NARCIS", + "-hostedBy", getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/clean/hostedBy") + .getPath() + }); - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/publication") - .map(item -> OBJECT_MAPPER.readValue(item, Publication.class)); + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/publication") + .map(item -> OBJECT_MAPPER.readValue(item, Publication.class)); - Assertions.assertEquals(7, tmp.count()); + Assertions.assertEquals(8, tmp.count()); - // original result with NL country and doi starting with Mendely prefix, but not collectedfrom NARCIS - Assertions - .assertEquals( - 1, - tmp - .filter(p -> p.getId().equals("50|DansKnawCris::0224aae28af558f21768dbc6439c7a95")) - .collect() - .get(0) - .getCountry() - .size()); + // original result with NL country and doi starting with Mendely prefix, but not collectedfrom NARCIS + Assertions + .assertEquals( + 1, + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::0224aae28af558f21768dbc6439c7a95")) + .collect() + .get(0) + .getCountry() + .size()); - // original result with NL country and pid not starting with Mendely prefix - Assertions - .assertEquals( - 1, - tmp - .filter(p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")) - .collect() - .get(0) - .getCountry() - .size()); + // original result with NL country and pid not starting with Mendely prefix + Assertions + .assertEquals( + 1, + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")) + .collect() + .get(0) + .getCountry() + .size()); - // original result with NL country and doi starting with Mendely prefix and collectedfrom NARCIS - Assertions - .assertEquals( - 0, - tmp - .filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")) - .collect() - .get(0) - .getCountry() - .size()); - } + // original result with NL country and doi starting with Mendely prefix and collectedfrom NARCIS but not + // inserted with propagation + Assertions + .assertEquals( + 1, + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")) + .collect() + .get(0) + .getCountry() + .size()); + + // original result with NL country and doi starting with Mendely prefix and collectedfrom NARCIS inserted with + // propagation + Assertions + .assertEquals( + 0, + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6ag")) + .collect() + .get(0) + .getCountry() + .size()); + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/hostedBy b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/hostedBy new file mode 100644 index 000000000..e69de29bb diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/publication_clean_country.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/publication_clean_country.json index ebceecff9..4916eee73 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/publication_clean_country.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/publication_clean_country.json @@ -4,4 +4,5 @@ {"author":[],"bestaccessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"collectedfrom":[{"dataInfo":null,"key":"10|openaire____::c6df70599aa984f16ee52b4b86d2e89f","value":"DANS (Data Archiving and Networked Services)"}],"context":[{"dataInfo":[{"deletedbyinference":false,"inferenceprovenance":"bulktagging","inferred":true,"invisible":false,"provenanceaction":{"classid":"community:subject","classname":"Bulktagging for 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communicatie"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","classname":"sysimport:crosswalk:datasetarchive","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"","classname":"","schemeid":"","schemename":""},"value":"Professional practice & society"}],"title":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","classname":"sysimport:crosswalk:datasetarchive","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"subtitle","classname":"subtitle","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"value":"GCUBE opwek"}],"journal":null} From 51ad93e545367100ee02e2542beb64f609959020 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 10 Aug 2022 11:57:56 +0200 Subject: [PATCH 152/214] [scholix] fixed OpenCitation dump procedure --- .../sx/graph/SparkConvertRDDtoDataset.scala | 59 ++++++++----------- 1 file changed, 24 insertions(+), 35 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala index 0073afff5..a54acf1d3 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala @@ -2,6 +2,7 @@ package eu.dnetlib.dhp.sx.graph import com.fasterxml.jackson.databind.ObjectMapper import eu.dnetlib.dhp.application.ArgumentApplicationParser +import eu.dnetlib.dhp.schema.common.ModelConstants import eu.dnetlib.dhp.schema.oaf.{OtherResearchProduct, Publication, Relation, Result, Software, Dataset => OafDataset} import org.apache.commons.io.IOUtils import org.apache.commons.lang3.StringUtils @@ -99,44 +100,32 @@ object SparkConvertRDDtoDataset { log.info("Converting Relation") - if (filterRelation != null && StringUtils.isNoneBlank(filterRelation)) { + val relationSemanticFilter = List( + ModelConstants.MERGES, + ModelConstants.IS_MERGED_IN, + ModelConstants.HAS_AMONG_TOP_N_SIMILAR_DOCS, + ModelConstants.IS_AMONG_TOP_N_SIMILAR_DOCS + ) - val rddRelation = spark.sparkContext - .textFile(s"$sourcePath/relation") - .map(s => mapper.readValue(s, classOf[Relation])) - .filter(r => r.getDataInfo != null && r.getDataInfo.getDeletedbyinference == false) - .filter(r => r.getSource.startsWith("50") && r.getTarget.startsWith("50")) - //filter OpenCitations relations - .filter(r => - r.getCollectedfrom != null && r.getCollectedfrom.size() > 0 && !r.getCollectedfrom.asScala.exists(k => - "opencitations".equalsIgnoreCase(k.getValue) - ) - ) - .filter(r => r.getSubRelType != null && r.getSubRelType.equalsIgnoreCase(filterRelation)) - spark.createDataset(rddRelation).as[Relation].write.mode(SaveMode.Overwrite).save(s"$relPath") - } else { - - val relationSemanticFilter = List( - "merges", - "ismergedin", - "HasAmongTopNSimilarDocuments", - "IsAmongTopNSimilarDocuments" + val rddRelation = spark.sparkContext + .textFile(s"$sourcePath/relation") + .map(s => mapper.readValue(s, classOf[Relation])) + .filter(r => r.getDataInfo != null && r.getDataInfo.getDeletedbyinference == false) + .filter(r => r.getSource.startsWith("50") && r.getTarget.startsWith("50")) + //filter OpenCitations relations + .filter(r => + r.getDataInfo.getProvenanceaction != null && + !"sysimport:crosswalk:opencitations".equals(r.getDataInfo.getProvenanceaction.getClassid) ) + .filter(r => filterRelations(filterRelation, relationSemanticFilter, r)) + spark.createDataset(rddRelation).as[Relation].write.mode(SaveMode.Overwrite).save(s"$relPath") + } - val rddRelation = spark.sparkContext - .textFile(s"$sourcePath/relation") - .map(s => mapper.readValue(s, classOf[Relation])) - .filter(r => r.getDataInfo != null && r.getDataInfo.getDeletedbyinference == false) - .filter(r => r.getSource.startsWith("50") && r.getTarget.startsWith("50")) - //filter OpenCitations relations - .filter(r => - r.getCollectedfrom != null && r.getCollectedfrom.size() > 0 && !r.getCollectedfrom.asScala.exists(k => - "opencitations".equalsIgnoreCase(k.getValue) - ) - ) - .filter(r => !relationSemanticFilter.exists(k => k.equalsIgnoreCase(r.getRelClass))) - spark.createDataset(rddRelation).as[Relation].write.mode(SaveMode.Overwrite).save(s"$relPath") + private def filterRelations(filterRelation: String, relationSemanticFilter: List[String], r: Relation): Boolean = { + if (filterRelation != null && StringUtils.isNoneBlank(filterRelation)) { + r.getSubRelType != null && r.getSubRelType.equalsIgnoreCase(filterRelation) + } else { + !relationSemanticFilter.exists(k => k.equalsIgnoreCase(r.getRelClass)) } - } } From 7dbdd4a0fe9832273790a777b7bc54895b35df93 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 10 Aug 2022 15:13:10 +0200 Subject: [PATCH 153/214] [Clean Country]changes related to https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/241#issuecomment-6766 --- .../dhp/oa/graph/clean/country/CleanCountrySparkJob.java | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java index 3ba84a317..30991e9d7 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java @@ -10,6 +10,7 @@ import java.util.stream.Collectors; import javax.swing.text.html.Option; +import eu.dnetlib.dhp.schema.oaf.utils.PidType; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.FilterFunction; @@ -94,7 +95,6 @@ public class CleanCountrySparkJob implements Serializable { List hostedBy = spark .read() .textFile(datasourcePath) - // .filter((FilterFunction) ds -> !ds.equals(collectedfrom)) .collectAsList(); Dataset res = spark @@ -113,7 +113,8 @@ public class CleanCountrySparkJob implements Serializable { if (r .getPid() .stream() - .anyMatch(p -> p.getQualifier().getClassid().equals("doi") && pidInParam(p.getValue(), verifyParam))) { + .anyMatch(p -> p.getQualifier().getClassid() + .equals(PidType.doi) && pidInParam(p.getValue(), verifyParam))) { r .setCountry( r From 2aa16d04326b1f219a578b44d1b0e853b23f2250 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 10 Aug 2022 17:39:29 +0200 Subject: [PATCH 154/214] [scholix] fixed OpenCitation dump procedure --- .../dhp/sx/graph/create_scholix_params.json | 3 +- .../graph/dumpScholix/oozie_app/workflow.xml | 7 ++- .../sx/graph/SparkConvertRDDtoDataset.scala | 58 +++++++++++++++---- .../dhp/sx/graph/SparkCreateScholix.scala | 6 +- 4 files changed, 61 insertions(+), 13 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/create_scholix_params.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/create_scholix_params.json index 336181e0a..c56e130c0 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/create_scholix_params.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/create_scholix_params.json @@ -2,5 +2,6 @@ {"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true}, {"paramName":"r", "paramLongName":"relationPath", "paramDescription": "the relation resolved Path", "paramRequired": true}, {"paramName":"s", "paramLongName":"summaryPath", "paramDescription": "the summary Path", "paramRequired": true}, - {"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the target base path of the scholix", "paramRequired": true} + {"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the target base path of the scholix", "paramRequired": true}, + {"paramName":"dc", "paramLongName":"dumpCitations", "paramDescription": "should dump citation relations", "paramRequired": false} ] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/dumpScholix/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/dumpScholix/oozie_app/workflow.xml index a37d85ad4..8135c9815 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/dumpScholix/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/dumpScholix/oozie_app/workflow.xml @@ -16,7 +16,11 @@ maxNumberOfPid filter relation with at least #maxNumberOfPid - + + dumpCitations + false + should dump citation relations + @@ -98,6 +102,7 @@ --summaryPath${targetPath}/provision/summaries --targetPath${targetPath}/provision/scholix --relationPath${targetPath}/relation + --dumpCitations${dumpCitations} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala index a54acf1d3..556106180 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala @@ -1,6 +1,8 @@ package eu.dnetlib.dhp.sx.graph import com.fasterxml.jackson.databind.ObjectMapper +import com.fasterxml.jackson.module.scala.DefaultScalaModule +import com.fasterxml.jackson.module.scala.experimental.ScalaObjectMapper import eu.dnetlib.dhp.application.ArgumentApplicationParser import eu.dnetlib.dhp.schema.common.ModelConstants import eu.dnetlib.dhp.schema.oaf.{OtherResearchProduct, Publication, Relation, Result, Software, Dataset => OafDataset} @@ -10,7 +12,8 @@ import org.apache.spark.SparkConf import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession} import org.slf4j.{Logger, LoggerFactory} -import scala.collection.JavaConverters._ +import scala.reflect.ClassTag +import scala.util.Try object SparkConvertRDDtoDataset { @@ -37,11 +40,12 @@ object SparkConvertRDDtoDataset { val t = parser.get("targetPath") log.info(s"targetPath -> $t") - val filterRelation = parser.get("filterRelation") - log.info(s"filterRelation -> $filterRelation") + val subRelTypeFilter = parser.get("filterRelation") + log.info(s"filterRelation -> $subRelTypeFilter") val entityPath = s"$t/entities" val relPath = s"$t/relation" + val mapper = new ObjectMapper() implicit val datasetEncoder: Encoder[OafDataset] = Encoders.kryo(classOf[OafDataset]) implicit val publicationEncoder: Encoder[Publication] = Encoders.kryo(classOf[Publication]) @@ -100,7 +104,7 @@ object SparkConvertRDDtoDataset { log.info("Converting Relation") - val relationSemanticFilter = List( + val relClassFilter = List( ModelConstants.MERGES, ModelConstants.IS_MERGED_IN, ModelConstants.HAS_AMONG_TOP_N_SIMILAR_DOCS, @@ -110,22 +114,56 @@ object SparkConvertRDDtoDataset { val rddRelation = spark.sparkContext .textFile(s"$sourcePath/relation") .map(s => mapper.readValue(s, classOf[Relation])) - .filter(r => r.getDataInfo != null && r.getDataInfo.getDeletedbyinference == false) + .filter(r => r.getDataInfo != null && !r.getDataInfo.getDeletedbyinference) .filter(r => r.getSource.startsWith("50") && r.getTarget.startsWith("50")) + .filter(r => filterRelations(subRelTypeFilter, relClassFilter, r)) //filter OpenCitations relations .filter(r => r.getDataInfo.getProvenanceaction != null && !"sysimport:crosswalk:opencitations".equals(r.getDataInfo.getProvenanceaction.getClassid) ) - .filter(r => filterRelations(filterRelation, relationSemanticFilter, r)) + spark.createDataset(rddRelation).as[Relation].write.mode(SaveMode.Overwrite).save(s"$relPath") } - private def filterRelations(filterRelation: String, relationSemanticFilter: List[String], r: Relation): Boolean = { - if (filterRelation != null && StringUtils.isNoneBlank(filterRelation)) { - r.getSubRelType != null && r.getSubRelType.equalsIgnoreCase(filterRelation) + private def filterRelations(subRelTypeFilter: String, relClassFilter: List[String], r: Relation): Boolean = { + if (StringUtils.isNotBlank(subRelTypeFilter)) { + subRelTypeFilter.equalsIgnoreCase(r.getSubRelType) } else { - !relationSemanticFilter.exists(k => k.equalsIgnoreCase(r.getRelClass)) + !relClassFilter.exists(k => k.equalsIgnoreCase(r.getRelClass)) } } + + /* + //TODO: finalise implementation + private def processResult[T<: Result]( + implicit ct: ClassTag[T], + log: Logger, + spark: SparkSession, + sourcePath: String, + entityPath: String, + clazz: Class[T] + ): Unit = { + val entityType = clazz.getSimpleName.toLowerCase + + log.info(s"Converting $entityType") + + val mapper = new ObjectMapper() with ScalaObjectMapper + mapper.registerModule(DefaultScalaModule) + + val rdd = spark.sparkContext + .textFile(s"$sourcePath/$entityType") + .map(s => mapper.readValue(s, clazz)) + .filter(r => r.getDataInfo != null && !r.getDataInfo.getDeletedbyinference); + + implicit val encoder: Encoder[T] = Encoders.kryo(clazz) + spark + .createDataset(rdd) + .as[T] + .write + .mode(SaveMode.Overwrite) + .save(s"$entityPath/$entityType") + } + */ + } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkCreateScholix.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkCreateScholix.scala index af19b9698..fd06e7dea 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkCreateScholix.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkCreateScholix.scala @@ -12,6 +12,8 @@ import org.apache.spark.sql.functions.count import org.apache.spark.sql._ import org.slf4j.{Logger, LoggerFactory} +import scala.util.Try + object SparkCreateScholix { def main(args: Array[String]): Unit = { @@ -37,6 +39,8 @@ object SparkCreateScholix { log.info(s"summaryPath -> $summaryPath") val targetPath = parser.get("targetPath") log.info(s"targetPath -> $targetPath") + val dumpCitations = Try(parser.get("dumpCitations").toBoolean).getOrElse(false) + log.info(s"dumpCitations -> $dumpCitations") implicit val relEncoder: Encoder[Relation] = Encoders.kryo[Relation] implicit val summaryEncoder: Encoder[ScholixSummary] = Encoders.kryo[ScholixSummary] @@ -138,7 +142,7 @@ object SparkCreateScholix { val relatedEntitiesDS: Dataset[RelatedEntities] = spark.read .load(s"$targetPath/related_entities") .as[RelatedEntities] - .filter(r => r.relatedPublication > 0 || r.relatedDataset > 0) + .filter(r => dumpCitations || r.relatedPublication > 0 || r.relatedDataset > 0) relatedEntitiesDS .joinWith(summaryDS, relatedEntitiesDS("id").equalTo(summaryDS("_1")), "inner") From cb7c07c54e59675e8dffe42b7f2a13f16c956068 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 11 Aug 2022 11:25:24 +0200 Subject: [PATCH 155/214] [scholix] added step to create tar archive --- .../eu/dnetlib/dhp/common/MakeTarArchive.java | 96 +++++++++++++++---- .../dhp/common/input_maketar_parameters.json | 30 ++++++ .../graph/dumpScholix/oozie_app/workflow.xml | 14 ++- 3 files changed, 118 insertions(+), 22 deletions(-) create mode 100644 dhp-common/src/main/resources/eu/dnetlib/dhp/common/input_maketar_parameters.json diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/MakeTarArchive.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/MakeTarArchive.java index abb9dc148..eca433e9e 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/MakeTarArchive.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/MakeTarArchive.java @@ -5,13 +5,71 @@ import java.io.BufferedInputStream; import java.io.IOException; import java.io.InputStream; import java.io.Serializable; +import java.util.Optional; import org.apache.commons.compress.archivers.tar.TarArchiveEntry; import org.apache.commons.compress.archivers.tar.TarArchiveOutputStream; +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.fs.*; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; public class MakeTarArchive implements Serializable { + private static final Logger log = LoggerFactory.getLogger(MakeTarArchive.class); + + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + MakeTarArchive.class + .getResourceAsStream( + "/eu/dnetlib/dhp/common/input_maketar_parameters.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + + final String outputPath = parser.get("hdfsPath"); + log.info("hdfsPath: {}", outputPath); + + final String hdfsNameNode = parser.get("nameNode"); + log.info("nameNode: {}", hdfsNameNode); + + final String inputPath = parser.get("sourcePath"); + log.info("input path : {}", inputPath); + + final int gBperSplit = Optional + .ofNullable(parser.get("splitSize")) + .map(Integer::valueOf) + .orElse(10); + + Configuration conf = new Configuration(); + conf.set("fs.defaultFS", hdfsNameNode); + + FileSystem fileSystem = FileSystem.get(conf); + + makeTArArchive(fileSystem, inputPath, outputPath, gBperSplit); + + } + + public static void makeTArArchive(FileSystem fileSystem, String inputPath, String outputPath, int gBperSplit) + throws IOException { + + RemoteIterator dirIterator = fileSystem.listLocatedStatus(new Path(inputPath)); + + while (dirIterator.hasNext()) { + LocatedFileStatus fileStatus = dirIterator.next(); + + Path p = fileStatus.getPath(); + String pathString = p.toString(); + String entity = pathString.substring(pathString.lastIndexOf("/") + 1); + + MakeTarArchive.tarMaxSize(fileSystem, pathString, outputPath + "/" + entity, entity, gBperSplit); + } + } + private static TarArchiveOutputStream getTar(FileSystem fileSystem, String outputPath) throws IOException { Path hdfsWritePath = new Path(outputPath); if (fileSystem.exists(hdfsWritePath)) { @@ -21,7 +79,7 @@ public class MakeTarArchive implements Serializable { return new TarArchiveOutputStream(fileSystem.create(hdfsWritePath).getWrappedStream()); } - private static void write(FileSystem fileSystem, String inputPath, String outputPath, String dir_name) + private static void write(FileSystem fileSystem, String inputPath, String outputPath, String dirName) throws IOException { Path hdfsWritePath = new Path(outputPath); @@ -37,7 +95,7 @@ public class MakeTarArchive implements Serializable { new Path(inputPath), true); while (iterator.hasNext()) { - writeCurrentFile(fileSystem, dir_name, iterator, ar, 0); + writeCurrentFile(fileSystem, dirName, iterator, ar, 0); } } @@ -59,32 +117,30 @@ public class MakeTarArchive implements Serializable { new Path(inputPath), true); boolean next = fileStatusListIterator.hasNext(); while (next) { - TarArchiveOutputStream ar = getTar(fileSystem, outputPath + "_" + (partNum + 1) + ".tar"); + try (TarArchiveOutputStream ar = getTar(fileSystem, outputPath + "_" + (partNum + 1) + ".tar")) { - long current_size = 0; - while (next && current_size < bytesPerSplit) { - current_size = writeCurrentFile(fileSystem, dir_name, fileStatusListIterator, ar, current_size); - next = fileStatusListIterator.hasNext(); + long currentSize = 0; + while (next && currentSize < bytesPerSplit) { + currentSize = writeCurrentFile(fileSystem, dir_name, fileStatusListIterator, ar, currentSize); + next = fileStatusListIterator.hasNext(); + } + + partNum += 1; } - - partNum += 1; - ar.close(); } - } - } - private static long writeCurrentFile(FileSystem fileSystem, String dir_name, + private static long writeCurrentFile(FileSystem fileSystem, String dirName, RemoteIterator fileStatusListIterator, - TarArchiveOutputStream ar, long current_size) throws IOException { + TarArchiveOutputStream ar, long currentSize) throws IOException { LocatedFileStatus fileStatus = fileStatusListIterator.next(); Path p = fileStatus.getPath(); - String p_string = p.toString(); - if (!p_string.endsWith("_SUCCESS")) { - String name = p_string.substring(p_string.lastIndexOf("/") + 1); + String pString = p.toString(); + if (!pString.endsWith("_SUCCESS")) { + String name = pString.substring(pString.lastIndexOf("/") + 1); if (name.startsWith("part-") & name.length() > 10) { String tmp = name.substring(0, 10); if (name.contains(".")) { @@ -92,9 +148,9 @@ public class MakeTarArchive implements Serializable { } name = tmp; } - TarArchiveEntry entry = new TarArchiveEntry(dir_name + "/" + name); + TarArchiveEntry entry = new TarArchiveEntry(dirName + "/" + name); entry.setSize(fileStatus.getLen()); - current_size += fileStatus.getLen(); + currentSize += fileStatus.getLen(); ar.putArchiveEntry(entry); InputStream is = fileSystem.open(fileStatus.getPath()); @@ -110,7 +166,7 @@ public class MakeTarArchive implements Serializable { ar.closeArchiveEntry(); } - return current_size; + return currentSize; } } diff --git a/dhp-common/src/main/resources/eu/dnetlib/dhp/common/input_maketar_parameters.json b/dhp-common/src/main/resources/eu/dnetlib/dhp/common/input_maketar_parameters.json new file mode 100644 index 000000000..a15318865 --- /dev/null +++ b/dhp-common/src/main/resources/eu/dnetlib/dhp/common/input_maketar_parameters.json @@ -0,0 +1,30 @@ +[ + + { + "paramName":"s", + "paramLongName":"sourcePath", + "paramDescription": "the path of the sequencial file to read", + "paramRequired": true + }, + { + "paramName": "hdp", + "paramLongName": "hdfsPath", + "paramDescription": "the path used to store the output archive", + "paramRequired": true + }, + { + "paramName":"nn", + "paramLongName":"nameNode", + "paramDescription": "the name node", + "paramRequired": true + }, + { + "paramName":"ss", + "paramLongName":"splitSize", + "paramDescription": "the maximum size of the archive", + "paramRequired": false + } +] + + + diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/dumpScholix/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/dumpScholix/oozie_app/workflow.xml index 8135c9815..d47ebb0be 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/dumpScholix/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/dumpScholix/oozie_app/workflow.xml @@ -140,11 +140,21 @@ --objectTypescholix --maxPidNumberFiltermaxNumberOfPid + + + + + + + eu.dnetlib.dhp.common.MakeTarArchive + --nameNode${nameNode} + --hdfsPath${targetPath}/tar + --sourcePath${targetPath}/json + - - + \ No newline at end of file From b7c387c21f946adbc9da90ded95166205195edb0 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 12 Aug 2022 15:09:16 +0200 Subject: [PATCH 156/214] cleaning of subjects: avoid duplicated subjects, prioritise collected vs inferred or other sources --- .../oaf/utils/GraphCleaningFunctions.java | 29 +++++++----- .../dhp/schema/oaf/utils/OafMapperUtils.java | 13 +++++- .../utils/SubjectProvenanceComparator.java | 46 +++++++++++++++++++ .../clean/GraphCleaningFunctionsTest.java | 6 ++- .../eu/dnetlib/dhp/oa/graph/clean/result.json | 22 +++++++++ 5 files changed, 101 insertions(+), 15 deletions(-) create mode 100644 dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/SubjectProvenanceComparator.java diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java index 151c53685..775f228eb 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java @@ -1,6 +1,8 @@ package eu.dnetlib.dhp.schema.oaf.utils; +import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.getProvenance; + import java.time.LocalDate; import java.time.ZoneId; import java.time.format.DateTimeFormatter; @@ -16,7 +18,6 @@ import com.github.sisyphsu.dateparser.DateParserUtils; import com.google.common.collect.Lists; import com.google.common.collect.Sets; -import eu.dnetlib.dhp.common.vocabulary.Vocabulary; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelSupport; @@ -191,8 +192,8 @@ public class GraphCleaningFunctions extends CleaningFunctions { qualifier("und", "Undetermined", ModelConstants.DNET_LANGUAGES)); } if (Objects.nonNull(r.getSubject())) { - r - .setSubject( + List subjects = Lists + .newArrayList( r .getSubject() .stream() @@ -201,7 +202,18 @@ public class GraphCleaningFunctions extends CleaningFunctions { .filter(sp -> Objects.nonNull(sp.getQualifier())) .filter(sp -> StringUtils.isNotBlank(sp.getQualifier().getClassid())) .map(GraphCleaningFunctions::cleanValue) - .collect(Collectors.toList())); + .collect( + Collectors + .toMap( + s -> Optional + .ofNullable(s.getQualifier()) + .map(q -> q.getClassid() + s.getValue()) + .orElse(s.getValue()), + Function.identity(), + (s1, s2) -> Collections + .min(Lists.newArrayList(s1, s1), new SubjectProvenanceComparator()))) + .values()); + r.setSubject(subjects); } if (Objects.nonNull(r.getTitle())) { r @@ -382,14 +394,7 @@ public class GraphCleaningFunctions extends CleaningFunctions { .filter(p -> StringUtils.isNotBlank(p.getValue())) .map(p -> { // hack to distinguish orcid from orcid_pending - String pidProvenance = Optional - .ofNullable(p.getDataInfo()) - .map( - d -> Optional - .ofNullable(d.getProvenanceaction()) - .map(Qualifier::getClassid) - .orElse("")) - .orElse(""); + String pidProvenance = getProvenance(p.getDataInfo()); if (p .getQualifier() .getClassid() diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java index 6ba7d70f1..c58096d35 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java @@ -11,10 +11,10 @@ import java.util.function.Function; import java.util.function.Predicate; import java.util.stream.Collectors; -import eu.dnetlib.dhp.schema.common.ModelConstants; import org.apache.commons.lang3.StringUtils; import eu.dnetlib.dhp.schema.common.AccessRightComparator; +import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.*; @@ -503,4 +503,15 @@ public class OafMapperUtils { rel.setProperties(properties); return rel; } + + public static String getProvenance(DataInfo dataInfo) { + return Optional + .ofNullable(dataInfo) + .map( + d -> Optional + .ofNullable(d.getProvenanceaction()) + .map(Qualifier::getClassid) + .orElse("")) + .orElse(""); + } } diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/SubjectProvenanceComparator.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/SubjectProvenanceComparator.java new file mode 100644 index 000000000..f4e3c8841 --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/SubjectProvenanceComparator.java @@ -0,0 +1,46 @@ + +package eu.dnetlib.dhp.schema.oaf.utils; + +import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.getProvenance; +import static org.apache.commons.lang3.StringUtils.isBlank; + +import java.util.Comparator; + +import eu.dnetlib.dhp.schema.oaf.Subject; + +public class SubjectProvenanceComparator implements Comparator { + + @Override + public int compare(Subject left, Subject right) { + + String lProv = getProvenance(left.getDataInfo()); + String rProv = getProvenance(right.getDataInfo()); + + if (isBlank(lProv) && isBlank(rProv)) + return 0; + if (isBlank(lProv)) + return 1; + if (isBlank(rProv)) + return -1; + if (lProv.equals(rProv)) + return 0; + if (lProv.toLowerCase().contains("crosswalk")) + return -1; + if (rProv.toLowerCase().contains("crosswalk")) + return 1; + if (lProv.toLowerCase().contains("user")) + return -1; + if (rProv.toLowerCase().contains("user")) + return 1; + if (lProv.toLowerCase().contains("propagation")) + return -1; + if (rProv.toLowerCase().contains("propagation")) + return 1; + if (lProv.toLowerCase().contains("iis")) + return -1; + if (rProv.toLowerCase().contains("iis")) + return 1; + + return 0; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java index 0289d62b4..c6222af14 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java @@ -260,14 +260,16 @@ public class GraphCleaningFunctionsTest { .collect(Collectors.toList()); assertNotNull(fos_subjects); - assertEquals(3, fos_subjects.size()); + assertEquals(2, fos_subjects.size()); assertTrue( fos_subjects .stream() .anyMatch( s -> "0101 mathematics".equals(s.getValue()) & - ModelConstants.DNET_SUBJECT_FOS_CLASSID.equals(s.getQualifier().getClassid()))); + ModelConstants.DNET_SUBJECT_FOS_CLASSID.equals(s.getQualifier().getClassid()) & + "sysimport:crosswalk:datasetarchive".equals(s.getDataInfo().getProvenanceaction().getClassid()) + )); assertTrue( fos_subjects diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json index a5ba747c4..8e4fc4545 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json @@ -794,6 +794,28 @@ }, "value": "0101 mathematics" }, + { + "dataInfo": { + "deletedbyinference": false, + "inferenceprovenance": "", + "inferred": false, + "invisible": false, + "provenanceaction": { + "classid": "subject:fos", + "classname": "subject:fos", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + }, + "trust": "0.9" + }, + "qualifier": { + "classid": "keyword", + "classname": "keyword", + "schemeid": "dnet:subject_classification_typologies", + "schemename": "dnet:subject_classification_typologies" + }, + "value": "0101 mathematics" + }, { "dataInfo": { "deletedbyinference": false, From 27445ccdaafd88270746d375f26784deb5f67cdd Mon Sep 17 00:00:00 2001 From: Enrico Ottonello Date: Thu, 25 Aug 2022 11:56:14 +0200 Subject: [PATCH 157/214] cleaned log --- .../doiboost/orcid/util/MultiAttemptsHttpConnector.java | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/util/MultiAttemptsHttpConnector.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/util/MultiAttemptsHttpConnector.java index 5ef6efa26..fc8f62bca 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/util/MultiAttemptsHttpConnector.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/util/MultiAttemptsHttpConnector.java @@ -83,8 +83,6 @@ public class MultiAttemptsHttpConnector { throw new CollectorException(msg); } - log.info("Request attempt {} [{}]", retryNumber, requestUrl); - InputStream input = null; try { @@ -104,9 +102,9 @@ public class MultiAttemptsHttpConnector { urlConn.addRequestProperty(HttpHeaders.AUTHORIZATION, String.format("Bearer %s", getAuthToken())); } - if (log.isDebugEnabled()) { - logHeaderFields(urlConn); - } +// if (log.isDebugEnabled()) { +// logHeaderFields(urlConn); +// } int retryAfter = obtainRetryAfter(urlConn.getHeaderFields()); if (is2xx(urlConn.getResponseCode())) { From da1cf561e6b89da40d4d147b6de4103fd84a475c Mon Sep 17 00:00:00 2001 From: Enrico Ottonello Date: Thu, 25 Aug 2022 11:57:20 +0200 Subject: [PATCH 158/214] alignment with beta --- .../eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala | 3 --- 1 file changed, 3 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala b/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala index 30928fdd0..98b5b708e 100644 --- a/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala +++ b/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala @@ -498,9 +498,6 @@ class CrossrefMappingTest { assertNotNull(pub.getJournal.getIssnOnline) assertNotNull(pub.getJournal.getName) - - - } @Test From a11eb380654f4337359b697b37b6a6281b027d13 Mon Sep 17 00:00:00 2001 From: Alessia Bardi Date: Fri, 2 Sep 2022 16:07:36 +0200 Subject: [PATCH 159/214] testing for RO-Hub --- .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 9 ++ .../eu/dnetlib/dhp/oa/graph/clean/terms.txt | 1 + .../dhp/oa/graph/raw/rohub-modified.xml | 85 +++++++++++++ .../eu/dnetlib/dhp/oa/graph/raw/rohub.xml | 116 ++++++++---------- 4 files changed, 144 insertions(+), 67 deletions(-) create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/rohub-modified.xml diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index b75f626d6..1ae08bf90 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -926,6 +926,15 @@ class MappersTest { // assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue())); } + @Test + void testROHub2() throws IOException, DocumentException { + final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("rohub-modified.xml"))); + final List list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml); + System.out.println("***************"); + System.out.println(new ObjectMapper().writeValueAsString(list)); + System.out.println("***************"); + } + private void assertValidId(final String id) { // System.out.println(id); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt index 59311d5a7..33c32a9c7 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt @@ -1049,6 +1049,7 @@ dnet:pid_types @=@ dnet:pid_types @=@ who @=@ WHO Identifier dnet:pid_types @=@ dnet:pid_types @=@ drks @=@ DRKS Identifier dnet:pid_types @=@ dnet:pid_types @=@ handle @=@ Handle dnet:pid_types @=@ dnet:pid_types @=@ data.europa.eu @=@ EU Persistent URL +dnet:pid_types @=@ dnet:pid_types @=@ w3id @=@ w3id.org dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/SUBJECT/ACM @=@ An ACM classification term that can be associated to your publications dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/SUBJECT/ARXIV @=@ An ARXIV classification term that can be associated to your publications dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/SUBJECT/DDC @=@ A Dewey Decimal classification term (DDC) that can be associated to your publications diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/rohub-modified.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/rohub-modified.xml new file mode 100644 index 000000000..95d65ac8d --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/rohub-modified.xml @@ -0,0 +1,85 @@ + + +
+ https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca + 2022-09-02T09:55:35Z + rohub_data + ro-crate_data + fsh_____4119::afc7592914ae190a50570db90f55f9c2 + https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca + 2019-03-27T15:15:22.22Z + fsh_____4119 + 2019-04-17T16:04:20.586Z +
+ + + https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca + + + + https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca/resources/24fae96f-f986-46e1-bfd0-a21ca20ff0ce + + + https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca/resources/6d3427a8-352e-49f4-9796-f618c44dc16d + + + RO-crate + + open access + + + Using biological effects tools to define Good Environmental Status under the European Union Marine Strategy Framework Directive + + + The use of biological effects tools offer enormous potential to meet the challenges outlined by the European Union Marine Strategy Framework Directive (MSFD) whereby Member States are required to develop a robust set of tools for defining 11 qualitative descriptors of Good Environmental Status (GES), such as demonstrating that "Concentrations of contaminants are at levels not giving rise to pollution effects" (GES Descriptor 8). This paper discusses the combined approach of monitoring chemical contaminant levels, along side biological effect measurements relating to the effect of pollutants, for undertaking assessments of GES across European marine regions. We outline the minimum standards that biological effects tools should meet if they are to be used for defining GES in relation to Descriptor 8 and describe the current international initiatives underway to develop assessment criteria for these biological effects techniques. Crown Copyright (C) 2010 Published by Elsevier Ltd. All rights reserved. + + Poznań Supercomputing and Networking Center + + + + Generation Service + + + + + + + CNR-ISMAR + + + + + 2018-06-20T11:21:46Z + + + The use of biological effects tools offer enormous potential to meet the challenges outlined by the European Union Marine Strategy Framework Directive (MSFD) whereby Member States are required to develop a robust set of tools for defining 11 qualitative descriptors of Good Environmental Status (GES), such as demonstrating that "Concentrations of contaminants are at levels not giving rise to pollution effects" (GES Descriptor 8). This paper discusses the combined approach of monitoring chemical contaminant levels, along side biological effect measurements relating to the effect of pollutants, for undertaking assessments of GES across European marine regions. We outline the minimum standards that biological effects tools should meet if they are to be used for defining GES in relation to Descriptor 8 and describe the current international initiatives underway to develop assessment criteria for these biological effects techniques. Crown Copyright (C) 2010 Published by Elsevier Ltd. All rights reserved. + + 2018 + + open access + + + 3.866 KB + + + Ecology + EOSC::RO-crate + + + https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca + other research product + + OPEN + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/rohub.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/rohub.xml index ca3ebe6c2..c85b55786 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/rohub.xml +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/rohub.xml @@ -1,103 +1,85 @@ - + xmlns:oai="http://www.openarchives.org/OAI/2.0/" + xmlns:dri="http://www.driver-repository.eu/namespace/dri" + xmlns:xs="http://www.w3.org/2001/XMLSchema" + xmlns:dc="http://purl.org/dc/elements/1.1/">
- eosca5322f5f::4dd1aaf93ae136b65dc9ee4e6f76eac9 - 53aa90bf-c593-4e6d-923f-d4711ac4b0e1 - 2022-05-25T15:35:48.262Z - eosca5322f5f - 53aa90bf-c593-4e6d-923f-d4711ac4b0e1 - 2022-05-25T15:35:38Z + https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca + 2022-09-02T09:55:35Z rohub_data ro-crate_data - 2022-05-25T15:36:11.094Z + fsh_____4119::afc7592914ae190a50570db90f55f9c2 + https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca + 2019-03-27T15:15:22.22Z + fsh_____4119 + 2019-04-17T16:04:20.586Z
- - https://w3id.org/ro-id/53aa90bf-c593-4e6d-923f-d4711ac4b0e1 - - http://api.rohub.org/api/ros/53aa90bf-c593-4e6d-923f-d4711ac4b0e1/ - + + https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca + - https://github.com/NordicESMhub/RELIANCE/blob/main/content/science/notebooks/air_quality_lockdown.ipynb + https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca/resources/24fae96f-f986-46e1-bfd0-a21ca20ff0ce - https://github.com/NordicESMhub/RELIANCE/blob/main/content/science/notebooks/air_quality_lockdown.ipynb - https://nordicesmhub.github.io/RELIANCE/science/notebooks/air_quality_lockdown.html + https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca/resources/6d3427a8-352e-49f4-9796-f618c44dc16d - https://nordicesmhub.github.io/RELIANCE/science/notebooks/air_quality_lockdown.html + RO-crate + + open access + + + Using biological effects tools to define Good Environmental Status under the European Union Marine Strategy Framework Directive + + + The use of biological effects tools offer enormous potential to meet the challenges outlined by the European Union Marine Strategy Framework Directive (MSFD) whereby Member States are required to develop a robust set of tools for defining 11 qualitative descriptors of Good Environmental Status (GES), such as demonstrating that "Concentrations of contaminants are at levels not giving rise to pollution effects" (GES Descriptor 8). This paper discusses the combined approach of monitoring chemical contaminant levels, along side biological effect measurements relating to the effect of pollutants, for undertaking assessments of GES across European marine regions. We outline the minimum standards that biological effects tools should meet if they are to be used for defining GES in relation to Descriptor 8 and describe the current international initiatives underway to develop assessment criteria for these biological effects techniques. Crown Copyright (C) 2010 Published by Elsevier Ltd. All rights reserved. + + Poznań Supercomputing and Networking Center + + + + Generation Service + + + - Anne Fouilloux + CNR-ISMAR - 2021-12-19T21:18:33Z + 2018-06-20T11:21:46Z - The COVID-19 pandemic has led to significant reductions in economic activity, especially during lockdowns. Several studies has shown that the concentration of nitrogen dioxyde and particulate matter levels have reduced during lockdown events. Reductions in transportation sector emissions are most likely largely responsible for the NO2 anomalies. In this study, we analyze the impact of lockdown events on the air quality using data from Copernicus Atmosphere Monitoring Service over Europe and at selected locations. + The use of biological effects tools offer enormous potential to meet the challenges outlined by the European Union Marine Strategy Framework Directive (MSFD) whereby Member States are required to develop a robust set of tools for defining 11 qualitative descriptors of Good Environmental Status (GES), such as demonstrating that "Concentrations of contaminants are at levels not giving rise to pollution effects" (GES Descriptor 8). This paper discusses the combined approach of monitoring chemical contaminant levels, along side biological effect measurements relating to the effect of pollutants, for undertaking assessments of GES across European marine regions. We outline the minimum standards that biological effects tools should meet if they are to be used for defining GES in relation to Descriptor 8 and describe the current international initiatives underway to develop assessment criteria for these biological effects techniques. Crown Copyright (C) 2010 Published by Elsevier Ltd. All rights reserved. - - - European Commission - 10.13039/501100000781 - 101017502 - Research Lifecycle Management for Earth Science Communities and Copernicus Users - - - MIT License - University of Oslo - 2021 - RO-crate + 2018 open access - 11.971 MB + 3.866 KB - Applied sciences - Meteorology + Ecology EOSC::RO-crate - - Impact of the Covid-19 Lockdown on Air quality over Europe - - - https://w3id.org/ro-id/53aa90bf-c593-4e6d-923f-d4711ac4b0e1 - 0048 + + https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca + other research product OPEN - https://opensource.org/licenses/MIT - und - - + + + - - - - https%3A%2F%2Fapi.rohub.org%2Fapi%2Foai2d%2F - 53aa90bf-c593-4e6d-923f-d4711ac4b0e1 - 2022-05-25T15:35:38Z - - - - - false - false - 0.9 - - - - \ No newline at end of file From 2b5f8c9c9a3611c57ee5febfe262a455a39ad801 Mon Sep 17 00:00:00 2001 From: dimitrispie Date: Tue, 6 Sep 2022 12:27:53 +0300 Subject: [PATCH 160/214] comment out duplicate table creation --- .../scripts/step16-createIndicatorsTables.sql | 22 +++++++++---------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql index 2581f1d64..b13eae0aa 100755 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql @@ -179,17 +179,17 @@ from publication_datasources pd compute stats indi_pub_diamond; -create table indi_pub_hybrid stored as parquet as -select distinct pd.id, coalesce(is_hybrid, 0) as is_hybrid -from publication_datasources pd - left outer join ( - select pd.id, 1 as is_hybrid from publication_datasources pd - join datasource d on d.id=pd.datasource - join stats_ext.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_online=d.issn_online) - and (ps.journal_is_in_doaj=false and ps.journal_is_oa=false)) tmp - on pd.id=tmp.id; - -compute stats indi_pub_hybrid; +--create table indi_pub_hybrid stored as parquet as +--select distinct pd.id, coalesce(is_hybrid, 0) as is_hybrid +--from publication_datasources pd +-- left outer join ( +-- select pd.id, 1 as is_hybrid from publication_datasources pd +-- join datasource d on d.id=pd.datasource +-- join stats_ext.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_online=d.issn_online) +-- and (ps.journal_is_in_doaj=false and ps.journal_is_oa=false)) tmp +-- on pd.id=tmp.id; +-- +--compute stats indi_pub_hybrid; create table indi_pub_in_transformative stored as parquet as select distinct pd.id, coalesce(is_transformative, 0) as is_transformative From 5c45d52af3ed925adc9750c113457a5d4db11c7f Mon Sep 17 00:00:00 2001 From: Alessia Bardi Date: Wed, 7 Sep 2022 15:40:57 +0300 Subject: [PATCH 161/214] testing for RiuNet --- .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 9 + .../eu/dnetlib/dhp/oa/graph/raw/riunet.xml | 93 ++++ .../provision/IndexRecordTransformerTest.java | 17 + .../eu/dnetlib/dhp/oa/provision/riunet.json | 470 ++++++++++++++++++ 4 files changed, 589 insertions(+) create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/riunet.xml create mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/riunet.json diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index 1ae08bf90..b4ee7e740 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -935,6 +935,15 @@ class MappersTest { System.out.println("***************"); } + @Test + void testRiunet() throws IOException, DocumentException { + final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("riunet.xml"))); + final List list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml); + System.out.println("***************"); + System.out.println(new ObjectMapper().writeValueAsString(list)); + System.out.println("***************"); + } + private void assertValidId(final String id) { // System.out.println(id); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/riunet.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/riunet.xml new file mode 100644 index 000000000..57c1c51b5 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/riunet.xml @@ -0,0 +1,93 @@ + + +
+ oai:riunet.upv.es:10251/178464 + 2022-05-10T09:12:14Z + com_10251_3822 + col_10251_169956 + 2022-09-01T07:51:12.657Z + od______1560::8f7a139735f493882bb0f4abceb6e200 + od______1560::8f7a139735f493882bb0f4abceb6e200 + 2019-03-27T15:15:22.22Z + riunet________ +
+ + + 10.4995/ijpme.2020.12944 + + 10251/148537 + + + journal article + VoR + + http://creativecommons.org/licenses/by-nc-nd/4.0/ + open access + + + Production planning in 3D printing factories + + + [EN] Production planning in 3D printing factories brings new challenges among which the scheduling of parts to be produced stands out. A main issue is to increase the efficiency of the plant and 3D printers productivity. Planning, scheduling, and nesting in 3D printing are recurrent problems in the search for new techniques to promote the development of this technology. In this work, we address the problem for the suppliers that have to schedule their daily production. This problem is part of the LONJA3D model, a managed 3D printing market where the parts ordered by the customers are reorganized into new batches so that suppliers can optimize their production capacity. In this paper, we propose a method derived from the design of combinatorial auctions to solve the nesting problem in 3D printing. First, we propose the use of a heuristic to create potential manufacturing batches. Then, we compute the expected return for each batch. The selected batch should generate the highest income. Several experiments have been tested to validate the process. This method is a first approach to the planning problem in 3D printing and further research is proposed to improve the procedure. + This research has been partially financed by the project: “Lonja de Impresión 3D para la Industria 4.0 y la Empresa Digital (LONJA3D)” funded by the Regional Government of Castile and Leon and the European Regional Development Fund (ERDF, FEDER) with grant VA049P17. + + eng + Universitat Politècnica de València + + application/pdf + 716912 + + + + Junta de Castilla y León + http://dx.doi.org/10.13039/501100014180 + VA049P17 + + + + + De Antón, J. + + + Senovilla, J. + + + González, J.M. + + + Acebes, F. + + + Pajares, J. + + + + + 2020-07-18 + + + Additive manufacturing + Production planning + Packing problem + Optimization + Nesting + + + 10.4995/ijpme.2020.12944 + 10251/148537 + 0038 + 2020-07-18 + OPEN + eng + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java index 86a155292..be5dda411 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java @@ -81,6 +81,21 @@ public class IndexRecordTransformerTest { testRecordTransformation(record); } + @Test + public void testRiunet() throws IOException, TransformerException { + + final XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false, + XmlConverterJob.schemaLocation); + + final Publication p = load("riunet.json", Publication.class); + + final JoinedEntity je = new JoinedEntity<>(p); + final String record = xmlRecordFactory.build(je); + assertNotNull(record); + testRecordTransformation(record); + } + + @Test public void testForEOSCFutureDataTransferPilot() throws IOException, TransformerException { final String record = IOUtils.toString(getClass().getResourceAsStream("eosc-future/data-transfer-pilot.xml")); @@ -114,6 +129,8 @@ public class IndexRecordTransformerTest { testRecordTransformation(record); } + + @Test void testDoiUrlNormalization() throws MalformedURLException { diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/riunet.json b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/riunet.json new file mode 100644 index 000000000..62f00a503 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/riunet.json @@ -0,0 +1,470 @@ +{ + "collectedfrom": [ + { + "key": "10|opendoar____::3a20f62a0af1aa152670bab3c602feed", + "value": "RiuNet", + "dataInfo": null + } + ], + "dataInfo": { + "invisible": false, + "inferred": false, + 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"dnet:provenanceActions" + } + } + } + ], + "dateofcollection": "2019-03-27T15:15:22.22Z", + "dateoftransformation": "2022-09-01T07:51:12.657Z", + "extraInfo": [], + "oaiprovenance": null, + "processingchargeamount": null, + "processingchargecurrency": null, + "measures": null, + "author": [ + { + "fullname": "Nieto Nieto, Justo", + "name": "Justo", + "surname": "Nieto Nieto", + "rank": 1, + "pid": [], + "affiliation": [] + } + ], + "resulttype": { + "classid": "publication", + "classname": "publication", + "schemeid": "dnet:result_typologies", + "schemename": "dnet:result_typologies" + }, + "language": { + "classid": "spa", + "classname": "Spanish; Castilian", + "schemeid": "dnet:languages", + "schemename": "dnet:languages" + }, + "country": [], + "subject": [ + { + "value": "Justo Nieto Nieto (Discursos)", + "qualifier": { + "classid": "", + "classname": "", + "schemeid": "", + "schemename": "" + }, + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.9", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:repository", + "classname": "sysimport:crosswalk:repository", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + { + "value": "Universitat Politècnica de València (UPV)", + "qualifier": { + "classid": "", + "classname": "", + "schemeid": "", + "schemename": "" + }, + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.9", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:repository", + "classname": "sysimport:crosswalk:repository", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + { + "value": "Presentación inaugural", + "qualifier": { + "classid": "", + "classname": "", + "schemeid": "", + "schemename": "" + }, + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": 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+ "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:repository", + "classname": "sysimport:crosswalk:repository", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + { + "value": "Inaugural speech", + "qualifier": { + "classid": "", + "classname": "", + "schemeid": "", + "schemename": "" + }, + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.9", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:repository", + "classname": "sysimport:crosswalk:repository", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + { + "value": "Inaugural presentation", + "qualifier": { + "classid": "", + "classname": "", + "schemeid": "", + "schemename": "" + }, + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.9", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:repository", + "classname": "sysimport:crosswalk:repository", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + } + ], + "title": [ + { + "value": "Discurso de inauguración del curso academico 1990-1991 de la Universitat Politècnica de València", + "qualifier": { + "classid": "main title", + "classname": "main title", + "schemeid": "dnet:dataCite_title", + "schemename": "dnet:dataCite_title" + }, + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.9", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:repository", + "classname": "sysimport:crosswalk:repository", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + } + ], + "relevantdate": [ + { + "value": "1991", + "qualifier": { + "classid": "Issued", + "classname": "Issued", + "schemeid": "dnet:dataCite_date", + "schemename": "dnet:dataCite_date" + }, + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.9", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:repository", + "classname": "sysimport:crosswalk:repository", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + } + ], + "description": [ + { + "value": "[ES] Discurso de Justo Nieto en el acto de inauguración del curso académico 1990-1991", + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.9", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:repository", + "classname": "sysimport:crosswalk:repository", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + { + "value": "[EN] Inaugural speech by Justo Nieto at the opening ceremony of the 1990-1991 academic year", + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.9", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:repository", + "classname": "sysimport:crosswalk:repository", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + } + ], + "dateofacceptance": { + "value": "1991-01-01", + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.9", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:repository", + "classname": "sysimport:crosswalk:repository", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + "publisher": null, + "embargoenddate": null, + "source": [], + "fulltext": [], + "format": [ + { + "value": "application/pdf", + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.9", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:repository", + "classname": "sysimport:crosswalk:repository", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + { + "value": "5055377", + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.9", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:repository", + "classname": "sysimport:crosswalk:repository", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + } + ], + "contributor": [], + "resourcetype": { + "classid": "lecture", + "classname": "lecture", + "schemeid": "dnet:dataCite_resource", + "schemename": "dnet:dataCite_resource" + }, + "coverage": [], + "bestaccessright": { + "classid": "OPEN", + "classname": "Open Access", + "schemeid": "dnet:access_modes", + "schemename": "dnet:access_modes" + }, + "context": [], + "externalReference": [], + "instance": [ + { + "license": null, + "accessright": { + "classid": "OPEN", + "classname": "Open Access", + "schemeid": "dnet:access_modes", + "schemename": "dnet:access_modes", + "openAccessRoute": null + }, + "instancetype": { + "classid": "0038", + "classname": "Other literature type", + "schemeid": "dnet:publication_resource", + "schemename": "dnet:publication_resource" + }, + "hostedby": { + "key": "10|opendoar____::3a20f62a0af1aa152670bab3c602feed", + "value": "RiuNet", + "dataInfo": null + }, + "url": null, + "distributionlocation": null, + "collectedfrom": { + "key": "10|opendoar____::3a20f62a0af1aa152670bab3c602feed", + "value": "RiuNet", + "dataInfo": null + }, + "pid": [ + { + "value": "10251/178464", + "qualifier": { + "classid": "handle", + "classname": "Handle", + "schemeid": "dnet:pid_types", + "schemename": "dnet:pid_types" + }, + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.9", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:repository", + "classname": "sysimport:crosswalk:repository", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + } + ], + "alternateIdentifier": [], + "dateofacceptance": { + "value": "1991-01-01", + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.9", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:repository", + "classname": "sysimport:crosswalk:repository", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + "processingchargeamount": null, + "processingchargecurrency": null, + "refereed": { + "classid": "UNKNOWN", + "classname": "Unknown", + "schemeid": "dnet:review_levels", + "schemename": "dnet:review_levels" + }, + "measures": null + } +] +} \ No newline at end of file From 9ef063d502f352cc1143b5117d22debe36abf6e8 Mon Sep 17 00:00:00 2001 From: Alessia Bardi Date: Wed, 7 Sep 2022 17:29:54 +0300 Subject: [PATCH 162/214] #7861#note-8 instance url from handle --- .../dhp/oa/graph/raw/OdfToOafMapper.java | 14 +++- .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 3 + .../eu/dnetlib/dhp/oa/graph/raw/riunet.xml | 64 ++++++------------- 3 files changed, 35 insertions(+), 46 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java index 1bbeac9fb..3dc510423 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java @@ -25,7 +25,8 @@ import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; public class OdfToOafMapper extends AbstractMdRecordToOafMapper { - public static final String HTTP_DX_DOI_PREIFX = "https://dx.doi.org/"; + public static final String HTTP_DOI_PREIFX = "https://doi.org/"; + public static final String HTTP_HANDLE_PREIFX = "http://hdl.handle.net/"; public OdfToOafMapper(final VocabularyGroup vocs, final boolean invisible, final boolean shouldHashId, final boolean forceOrginalId) { @@ -172,10 +173,17 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { } for (final Object o : doc .selectNodes("//*[local-name()='alternateIdentifier' and ./@alternateIdentifierType='DOI']")) { - url.add(HTTP_DX_DOI_PREIFX + ((Node) o).getText().trim()); + url.add(HTTP_DOI_PREIFX + ((Node) o).getText().trim()); } for (final Object o : doc.selectNodes("//*[local-name()='identifier' and ./@identifierType='DOI']")) { - url.add(HTTP_DX_DOI_PREIFX + ((Node) o).getText().trim()); + url.add(HTTP_DOI_PREIFX + ((Node) o).getText().trim()); + } + for (final Object o : doc + .selectNodes("//*[local-name()='alternateIdentifier' and ./@alternateIdentifierType='Handle']")) { + url.add(HTTP_HANDLE_PREIFX + ((Node) o).getText().trim()); + } + for (final Object o : doc.selectNodes("//*[local-name()='identifier' and ./@identifierType='Handle']")) { + url.add(HTTP_HANDLE_PREIFX + ((Node) o).getText().trim()); } if (!url.isEmpty()) { instance.setUrl(new ArrayList<>()); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index b4ee7e740..955ef1d42 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -942,6 +942,9 @@ class MappersTest { System.out.println("***************"); System.out.println(new ObjectMapper().writeValueAsString(list)); System.out.println("***************"); + final Publication p = (Publication) list.get(0); + assertNotNull(p.getInstance().get(0).getUrl().get(0)); + } private void assertValidId(final String id) { diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/riunet.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/riunet.xml index 57c1c51b5..ed195ba7b 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/riunet.xml +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/riunet.xml @@ -21,72 +21,50 @@ - 10.4995/ijpme.2020.12944 - - 10251/148537 - + 10251/178464 + - journal article - VoR + lecture - http://creativecommons.org/licenses/by-nc-nd/4.0/ + http://creativecommons.org/licenses/by-nc/4.0/ open access - Production planning in 3D printing factories + Discurso de inauguración del curso academico 1990-1991 de la Universitat Politècnica de València - [EN] Production planning in 3D printing factories brings new challenges among which the scheduling of parts to be produced stands out. A main issue is to increase the efficiency of the plant and 3D printers productivity. Planning, scheduling, and nesting in 3D printing are recurrent problems in the search for new techniques to promote the development of this technology. In this work, we address the problem for the suppliers that have to schedule their daily production. This problem is part of the LONJA3D model, a managed 3D printing market where the parts ordered by the customers are reorganized into new batches so that suppliers can optimize their production capacity. In this paper, we propose a method derived from the design of combinatorial auctions to solve the nesting problem in 3D printing. First, we propose the use of a heuristic to create potential manufacturing batches. Then, we compute the expected return for each batch. The selected batch should generate the highest income. Several experiments have been tested to validate the process. This method is a first approach to the planning problem in 3D printing and further research is proposed to improve the procedure. - This research has been partially financed by the project: “Lonja de Impresión 3D para la Industria 4.0 y la Empresa Digital (LONJA3D)” funded by the Regional Government of Castile and Leon and the European Regional Development Fund (ERDF, FEDER) with grant VA049P17. + [ES] Discurso de Justo Nieto en el acto de inauguración del curso académico 1990-1991 + [EN] Inaugural speech by Justo Nieto at the opening ceremony of the 1990-1991 academic year - eng - Universitat Politècnica de València + spa application/pdf - 716912 + 5055377 - - - Junta de Castilla y León - http://dx.doi.org/10.13039/501100014180 - VA049P17 - - - De Antón, J. - - - Senovilla, J. - - - González, J.M. - - - Acebes, F. - - - Pajares, J. + Nieto Nieto, Justo - 2020-07-18 + 1991 - Additive manufacturing - Production planning - Packing problem - Optimization - Nesting + Justo Nieto Nieto (Discursos) + Universitat Politècnica de València (UPV) + Presentación inaugural + Curso académico 1990-91 + Discurso inaugural + Inaugural speech + Inaugural presentation - 10.4995/ijpme.2020.12944 - 10251/148537 + 10251/178464 0038 - 2020-07-18 + 1991-01-01 OPEN - eng + spa From 71b069ca90a2f7ec09d64241c60917d3636fc81e Mon Sep 17 00:00:00 2001 From: dimitrispie Date: Fri, 9 Sep 2022 13:15:58 +0300 Subject: [PATCH 163/214] Changes to indicator and monitor scripts --- .../scripts/step16-createIndicatorsTables.sql | 16 ++++++++-------- .../oozie_app/scripts/step20-createMonitorDB.sql | 5 ++++- 2 files changed, 12 insertions(+), 9 deletions(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql index b13eae0aa..0f294145c 100755 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql @@ -564,12 +564,12 @@ create table indi_org_fairness stored as parquet as (select ro.organization organization, count(distinct ro.id) no_result_fair from result_organization ro join result r on r.id=ro.id --join result_pids rp on r.id=rp.id - where (title is not null) and (publisher is not null) and (abstract is true) and (year is not null) and (authors>0) and year>2003 + where (title is not null) and (publisher is not null) and (abstract is true) and (year is not null) and (authors>0) and cast(year as int)>2003 group by ro.organization), --return all results group by organization allresults as (select organization, count(distinct ro.id) no_allresults from result_organization ro join result r on r.id=ro.id - where year>2003 + where cast(year as int)>2003 group by organization) --return results_fair/all_results select allresults.organization, result_fair.no_result_fair/allresults.no_allresults org_fairness @@ -638,11 +638,11 @@ create table indi_org_fairness_year stored as parquet as (select year, ro.organization organization, count(distinct ro.id) no_result_fair from result_organization ro join result r on r.id=ro.id join result_pids rp on r.id=rp.id - where (title is not null) and (publisher is not null) and (abstract is true) and (year is not null) and (authors>0) and year>2003 + where (title is not null) and (publisher is not null) and (abstract is true) and (year is not null) and (authors>0) and cast(year as int)>2003 group by ro.organization, year), allresults as (select year, organization, count(distinct ro.id) no_allresults from result_organization ro join result r on r.id=ro.id - where year>2003 + where cast(year as int)>2003 group by organization, year) --return results_fair/all_results select allresults.year, allresults.organization, result_fair.no_result_fair/allresults.no_allresults org_fairness @@ -657,12 +657,12 @@ create table indi_org_findable_year stored as parquet as (select year, ro.organization organization, count(distinct rp.id) no_result_with_pid from result_organization ro join result_pids rp on rp.id=ro.id join result r on r.id=rp.id - where year >2003 + where cast(year as int) >2003 group by ro.organization, year), --return all results group by organization,year allresults as (select year, organization, count(distinct ro.id) no_allresults from result_organization ro join result r on r.id=ro.id - where year >2003 + where cast(year as int) >2003 group by organization, year) --return results_with_pid/all_results select allresults.year, allresults.organization, result_with_pid.no_result_with_pid/allresults.no_allresults org_findable @@ -677,12 +677,12 @@ create table indi_org_findable stored as parquet as (select ro.organization organization, count(distinct rp.id) no_result_with_pid from result_organization ro join result_pids rp on rp.id=ro.id join result r on r.id=rp.id - where year >2003 + where cast(year as int) >2003 group by ro.organization), --return all results group by organization allresults as (select organization, count(distinct ro.id) no_allresults from result_organization ro join result r on r.id=ro.id - where year >2003 + where cast(year as int) >2003 group by organization) --return results_with_pid/all_results select allresults.organization, result_with_pid.no_result_with_pid/allresults.no_allresults org_findable diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql index d78895198..572b70ef7 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql @@ -45,7 +45,10 @@ create table TARGET.result stored as parquet as 'openorgs____::15e7921fc50d9aa1229a82a84429419e', -- University Of Thessaly 'openorgs____::11f7919dadc8f8a7251af54bba60c956', -- Technical University of Crete 'openorgs____::84f0c5f5dbb6daf42748485924efde4b', -- University of Piraeus - 'openorgs____::4ac562f0376fce3539504567649cb373' -- University of Patras + 'openorgs____::4ac562f0376fce3539504567649cb373', -- University of Patras + 'openorgs____::3e8d1f8c3f6cd7f418b09f1f58b4873b', -- Aristotle University of Thessaloniki + 'openorgs____::3fcef6e1c469c10f2a84b281372c9814', -- World Bank + 'openorgs____::1698a2eb1885ef8adb5a4a969e745ad3' -- École des Ponts ParisTech ) )) foo; compute stats TARGET.result; From a539c6ccaf96a5577933a6f159465ba385002be3 Mon Sep 17 00:00:00 2001 From: Alessia Bardi Date: Fri, 9 Sep 2022 12:16:28 +0200 Subject: [PATCH 164/214] https for handle URLs --- .../main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java index 3dc510423..6f1236fff 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java @@ -26,7 +26,7 @@ import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; public class OdfToOafMapper extends AbstractMdRecordToOafMapper { public static final String HTTP_DOI_PREIFX = "https://doi.org/"; - public static final String HTTP_HANDLE_PREIFX = "http://hdl.handle.net/"; + public static final String HTTP_HANDLE_PREIFX = "https://hdl.handle.net/"; public OdfToOafMapper(final VocabularyGroup vocs, final boolean invisible, final boolean shouldHashId, final boolean forceOrginalId) { From ff6f789b6d9be0567b6ad72f8a0e75fe3f52726a Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 9 Sep 2022 15:16:31 +0200 Subject: [PATCH 165/214] code formatting --- .../java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java | 2 +- .../dhp/oa/graph/clean/GraphCleaningFunctionsTest.java | 4 ++-- .../test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java | 3 ++- .../dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java | 5 +---- pom.xml | 2 +- 5 files changed, 7 insertions(+), 9 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java index 24ec5d0ef..d6bfe6714 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java @@ -179,7 +179,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { url.add(HTTP_DOI_PREIFX + ((Node) o).getText().trim()); } for (final Object o : doc - .selectNodes("//*[local-name()='alternateIdentifier' and ./@alternateIdentifierType='Handle']")) { + .selectNodes("//*[local-name()='alternateIdentifier' and ./@alternateIdentifierType='Handle']")) { url.add(HTTP_HANDLE_PREIFX + ((Node) o).getText().trim()); } for (final Object o : doc.selectNodes("//*[local-name()='identifier' and ./@identifierType='Handle']")) { diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java index c6222af14..6c43da832 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java @@ -268,8 +268,8 @@ public class GraphCleaningFunctionsTest { .anyMatch( s -> "0101 mathematics".equals(s.getValue()) & ModelConstants.DNET_SUBJECT_FOS_CLASSID.equals(s.getQualifier().getClassid()) & - "sysimport:crosswalk:datasetarchive".equals(s.getDataInfo().getProvenanceaction().getClassid()) - )); + "sysimport:crosswalk:datasetarchive" + .equals(s.getDataInfo().getProvenanceaction().getClassid()))); assertTrue( fos_subjects diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index 955ef1d42..67406e794 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -928,7 +928,8 @@ class MappersTest { @Test void testROHub2() throws IOException, DocumentException { - final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("rohub-modified.xml"))); + final String xml = IOUtils + .toString(Objects.requireNonNull(getClass().getResourceAsStream("rohub-modified.xml"))); final List list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml); System.out.println("***************"); System.out.println(new ObjectMapper().writeValueAsString(list)); diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java index be5dda411..e0fbb2a2f 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java @@ -85,7 +85,7 @@ public class IndexRecordTransformerTest { public void testRiunet() throws IOException, TransformerException { final XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false, - XmlConverterJob.schemaLocation); + XmlConverterJob.schemaLocation); final Publication p = load("riunet.json", Publication.class); @@ -95,7 +95,6 @@ public class IndexRecordTransformerTest { testRecordTransformation(record); } - @Test public void testForEOSCFutureDataTransferPilot() throws IOException, TransformerException { final String record = IOUtils.toString(getClass().getResourceAsStream("eosc-future/data-transfer-pilot.xml")); @@ -129,8 +128,6 @@ public class IndexRecordTransformerTest { testRecordTransformation(record); } - - @Test void testDoiUrlNormalization() throws MalformedURLException { diff --git a/pom.xml b/pom.xml index 632ca99b8..ab59e7be3 100644 --- a/pom.xml +++ b/pom.xml @@ -801,7 +801,7 @@ 3.3.3 3.4.2 [2.12,3.0) - [2.13.2-SNAPSHOT] + [3.14.0] [4.0.3] [6.0.5] [3.1.6] From 27af5122d2d7f7d6d549dc23a5bf79a0c0030d1c Mon Sep 17 00:00:00 2001 From: Alessia Bardi Date: Mon, 12 Sep 2022 14:25:23 +0200 Subject: [PATCH 166/214] logs for non well formed XML files --- .../raw/AbstractMdRecordToOafMapper.java | 62 +++++++++------- .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 12 ++++ .../dhp/oa/graph/raw/oaf_notwellformed.xml | 70 +++++++++++++++++++ .../src/test/resources/log4j.properties | 8 +++ 4 files changed, 125 insertions(+), 27 deletions(-) create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_notwellformed.xml create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/log4j.properties diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index a05faab80..e263cffa8 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -22,6 +22,8 @@ import java.util.*; import org.apache.commons.lang3.StringUtils; import org.dom4j.*; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import com.google.common.collect.Lists; import com.google.common.collect.Sets; @@ -77,6 +79,8 @@ public abstract class AbstractMdRecordToOafMapper { protected static final Map nsContext = new HashMap<>(); + private static final Logger log = LoggerFactory.getLogger(AbstractMdRecordToOafMapper.class); + static { nsContext.put("dr", "http://www.driver-repository.eu/namespace/dr"); nsContext.put("dri", "http://www.driver-repository.eu/namespace/dri"); @@ -106,37 +110,41 @@ public abstract class AbstractMdRecordToOafMapper { public List processMdRecord(final String xml) throws DocumentException { DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext); + try { + final Document doc = DocumentHelper + .parseText( + xml + .replaceAll(DATACITE_SCHEMA_KERNEL_4, DATACITE_SCHEMA_KERNEL_3) + .replaceAll(DATACITE_SCHEMA_KERNEL_4_SLASH, DATACITE_SCHEMA_KERNEL_3) + .replaceAll(DATACITE_SCHEMA_KERNEL_3_SLASH, DATACITE_SCHEMA_KERNEL_3)); - final Document doc = DocumentHelper - .parseText( - xml - .replaceAll(DATACITE_SCHEMA_KERNEL_4, DATACITE_SCHEMA_KERNEL_3) - .replaceAll(DATACITE_SCHEMA_KERNEL_4_SLASH, DATACITE_SCHEMA_KERNEL_3) - .replaceAll(DATACITE_SCHEMA_KERNEL_3_SLASH, DATACITE_SCHEMA_KERNEL_3)); + final KeyValue collectedFrom = getProvenanceDatasource( + doc, "//oaf:collectedFrom/@id", "//oaf:collectedFrom/@name"); - final KeyValue collectedFrom = getProvenanceDatasource( - doc, "//oaf:collectedFrom/@id", "//oaf:collectedFrom/@name"); + if (collectedFrom == null) { + return Lists.newArrayList(); + } - if (collectedFrom == null) { - return Lists.newArrayList(); + final KeyValue hostedBy = StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id")) + ? collectedFrom + : getProvenanceDatasource(doc, "//oaf:hostedBy/@id", "//oaf:hostedBy/@name"); + + if (hostedBy == null) { + return Lists.newArrayList(); + } + + final DataInfo info = prepareDataInfo(doc, invisible); + final long lastUpdateTimestamp = new Date().getTime(); + + final List instances = prepareInstances(doc, info, collectedFrom, hostedBy); + + final String type = getResultType(doc, instances); + + return createOafs(doc, type, instances, collectedFrom, info, lastUpdateTimestamp); + } catch (DocumentException e) { + log.error("Error with record:\n" + xml); + throw e; } - - final KeyValue hostedBy = StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id")) - ? collectedFrom - : getProvenanceDatasource(doc, "//oaf:hostedBy/@id", "//oaf:hostedBy/@name"); - - if (hostedBy == null) { - return Lists.newArrayList(); - } - - final DataInfo info = prepareDataInfo(doc, invisible); - final long lastUpdateTimestamp = new Date().getTime(); - - final List instances = prepareInstances(doc, info, collectedFrom, hostedBy); - - final String type = getResultType(doc, instances); - - return createOafs(doc, type, instances, collectedFrom, info, lastUpdateTimestamp); } protected String getResultType(final Document doc, final List instances) { diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index b75f626d6..c4e34a9a8 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -12,6 +12,7 @@ import java.util.Objects; import java.util.Optional; import java.util.stream.Collectors; +import kotlin.jvm.Throws; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; import org.dom4j.DocumentException; @@ -926,6 +927,17 @@ class MappersTest { // assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue())); } + @Test + void testNotWellFormed() throws IOException, DocumentException { + final String xml = IOUtils + .toString(Objects.requireNonNull(getClass().getResourceAsStream("oaf_notwellformed.xml"))); + final DocumentException generalEx = new DocumentException(); + + DocumentException exception = assertThrows(DocumentException.class, () -> { + new OafToOafMapper(vocs, false, true).processMdRecord(xml); + }); + } + private void assertValidId(final String id) { // System.out.println(id); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_notwellformed.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_notwellformed.xml new file mode 100644 index 000000000..09384054e --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_notwellformed.xml @@ -0,0 +1,70 @@ + + +
+ jairo_______::000012e58ed836576ef2a0d38b0f726f + oai:irdb.nii.ac.jp:01221:0000010198 + + + + + + 2021-05-10T11:31:09.424Z + 2021-06-03T01:45:42.536Z + jairo_______ +
+ + 多項式GCDを用いた復号法に関する研究 + 上原, 剛 + 甲斐, 博 + 野田, 松太郎 + application/pdf + http://hdl.handle.net/2433/25934 + jpn + 京都大学数理解析研究所 + 410 + Departmental Bulletin Paper + 0014 + 2004-10-01 + + openaire____::554c7c2873 + OPEN + + + 2433/25934 + AN00061013 + http://hdl.handle.net/2433/25934 + http://repository.kulib.kyoto-u.ac.jp/dspace/bitstream/2433/25934/1/1395-16.pdf + 数理解析研究所講究録 + + + + + https%3A%2F%2Firdb.nii.ac.jp%2Foai + oai:irdb.nii.ac.jp:01221:0000010198 + 2021-04-13T13:36:29Z + + + http://repository.kulib.kyoto-u.ac.jp/dspace-oai/request + oai:repository.kulib.kyoto-u.ac.jp:2433/25934 + 2012-07-12T14:15:41Z + http://irdb.nii.ac.jp/oai + + + + + false + false + 0.9 + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/log4j.properties b/dhp-workflows/dhp-graph-mapper/src/test/resources/log4j.properties new file mode 100644 index 000000000..71255bb77 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/log4j.properties @@ -0,0 +1,8 @@ +# Root logger option +log4j.rootLogger=DEBUG, stdout + +# Direct log messages to stdout +log4j.appender.stdout=org.apache.log4j.ConsoleAppender +log4j.appender.stdout.Target=System.out +log4j.appender.stdout.layout=org.apache.log4j.PatternLayout +log4j.appender.stdout.layout.ConversionPattern=%d{yyyy-MM-dd HH:mm:ss} %-5p %c{1}:%L - %m%n \ No newline at end of file From b99a01134545beb75cf3a4114575be61c9c75486 Mon Sep 17 00:00:00 2001 From: Alessia Bardi Date: Tue, 13 Sep 2022 11:51:55 +0200 Subject: [PATCH 167/214] return empty Oaf list if record cannot be parsed --- .../dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java | 2 +- .../test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java | 5 +---- 2 files changed, 2 insertions(+), 5 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index e263cffa8..984254665 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -143,7 +143,7 @@ public abstract class AbstractMdRecordToOafMapper { return createOafs(doc, type, instances, collectedFrom, info, lastUpdateTimestamp); } catch (DocumentException e) { log.error("Error with record:\n" + xml); - throw e; + return Lists.newArrayList(); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index c4e34a9a8..8165ad757 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -931,11 +931,8 @@ class MappersTest { void testNotWellFormed() throws IOException, DocumentException { final String xml = IOUtils .toString(Objects.requireNonNull(getClass().getResourceAsStream("oaf_notwellformed.xml"))); - final DocumentException generalEx = new DocumentException(); + assertEquals(0, new OafToOafMapper(vocs, false, true).processMdRecord(xml).size()); - DocumentException exception = assertThrows(DocumentException.class, () -> { - new OafToOafMapper(vocs, false, true).processMdRecord(xml); - }); } private void assertValidId(final String id) { From a0919ed495c61da8d4cecbfa4c322d8f9c95176a Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 14 Sep 2022 13:27:39 +0200 Subject: [PATCH 168/214] [aggregator graph] save invalid records aside for further inspection --- .../raw/AbstractMdRecordToOafMapper.java | 2 +- .../raw/GenerateEntitiesApplication.java | 37 ++++++++++++++++++- .../graph/generate_entities_parameters.json | 6 +++ .../oa/graph/raw_all/oozie_app/workflow.xml | 2 + .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 2 - .../raw/MigrateDbEntitiesApplicationTest.java | 2 +- 6 files changed, 45 insertions(+), 6 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index 984254665..cdc707084 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -107,7 +107,7 @@ public abstract class AbstractMdRecordToOafMapper { this.forceOriginalId = false; } - public List processMdRecord(final String xml) throws DocumentException { + public List processMdRecord(final String xml) { DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext); try { diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java index 6bb18c375..e9de43f7f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java @@ -16,6 +16,9 @@ import org.apache.hadoop.io.compress.GzipCodec; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.rdd.RDD; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; import org.dom4j.DocumentException; import org.slf4j.Logger; @@ -76,6 +79,9 @@ public class GenerateEntitiesApplication { final String targetPath = parser.get("targetPath"); log.info("targetPath: {}", targetPath); + final String invalidPath = parser.get("invalidPath"); + log.info("invalidPath: {}", invalidPath); + final String isLookupUrl = parser.get("isLookupUrl"); log.info("isLookupUrl: {}", isLookupUrl); @@ -97,7 +103,8 @@ public class GenerateEntitiesApplication { final SparkConf conf = new SparkConf(); runWithSparkSession(conf, isSparkSessionManaged, spark -> { HdfsSupport.remove(targetPath, spark.sparkContext().hadoopConfiguration()); - generateEntities(spark, vocs, sourcePaths, targetPath, shouldHashId, mode); + HdfsSupport.remove(invalidPath, spark.sparkContext().hadoopConfiguration()); + generateEntities(spark, vocs, sourcePaths, targetPath, invalidPath, shouldHashId, mode); }); } @@ -106,6 +113,7 @@ public class GenerateEntitiesApplication { final VocabularyGroup vocs, final String sourcePaths, final String targetPath, + final String invalidPath, final boolean shouldHashId, final Mode mode) { @@ -121,6 +129,19 @@ public class GenerateEntitiesApplication { JavaRDD inputRdd = sc.emptyRDD(); for (final String sp : existingSourcePaths) { + RDD invalidRecords = sc + .sequenceFile(sp, Text.class, Text.class) + .map(k -> new Tuple2<>(k._1().toString(), k._2().toString())) + .map(k -> tryApplyMapping(k._1(), k._2(), shouldHashId, vocs)) + .filter(Objects::nonNull) + .rdd(); + spark + .createDataset(invalidRecords, Encoders.STRING()) + .write() + .mode(SaveMode.Append) + .option("compression", "gzip") + .text(invalidPath); + inputRdd = inputRdd .union( sc @@ -159,7 +180,7 @@ public class GenerateEntitiesApplication { final String id, final String s, final boolean shouldHashId, - final VocabularyGroup vocs) throws DocumentException { + final VocabularyGroup vocs) { final String type = StringUtils.substringAfter(id, ":"); switch (type.toLowerCase()) { @@ -196,6 +217,18 @@ public class GenerateEntitiesApplication { } } + private static String tryApplyMapping( + final String id, + final String s, + final boolean shouldHashId, + final VocabularyGroup vocs) { + + if (convertToListOaf(id, s, shouldHashId, vocs).isEmpty()) { + return s; + } + return null; + } + private static Oaf convertFromJson(final String s, final Class clazz) { try { return OBJECT_MAPPER.readValue(s, clazz); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/generate_entities_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/generate_entities_parameters.json index 52cbbf45f..da6730fbb 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/generate_entities_parameters.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/generate_entities_parameters.json @@ -17,6 +17,12 @@ "paramDescription": "the path of the target file", "paramRequired": true }, + { + "paramName": "i", + "paramLongName": "invalidPath", + "paramDescription": "the path of the invalid records file", + "paramRequired": false + }, { "paramName": "isu", "paramLongName": "isLookupUrl", diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml index c6cc46c0f..d00232e9a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml @@ -468,6 +468,7 @@ --sourcePaths${contentPath}/db_claims,${contentPath}/oaf_claims,${contentPath}/odf_claims --targetPath${workingDir}/entities_claim + --invalidPath${workingDir}/invalid_records_claim --isLookupUrl${isLookupUrl} --shouldHashId${shouldHashId} --modeclaim @@ -517,6 +518,7 @@ --sourcePaths${contentPath}/db_openaire,${contentPath}/db_openorgs,${contentPath}/oaf_records,${contentPath}/odf_records,${contentPath}/oaf_records_hdfs,${contentPath}/odf_records_hdfs,${contentPath}/oaf_records_invisible --targetPath${workingDir}/entities + --invalidPath${workingDir}/invalid_records --isLookupUrl${isLookupUrl} --shouldHashId${shouldHashId} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index 8165ad757..204649633 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -12,7 +12,6 @@ import java.util.Objects; import java.util.Optional; import java.util.stream.Collectors; -import kotlin.jvm.Throws; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; import org.dom4j.DocumentException; @@ -22,7 +21,6 @@ import org.junit.jupiter.api.extension.ExtendWith; import org.mockito.Mock; import org.mockito.junit.jupiter.MockitoExtension; -import com.fasterxml.jackson.core.JsonProcessingException; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java index 408196665..11947dbe7 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java @@ -18,7 +18,6 @@ import java.util.Objects; import java.util.Optional; import java.util.stream.Collectors; -import eu.dnetlib.dhp.schema.common.ModelConstants; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; import org.junit.jupiter.api.BeforeEach; @@ -32,6 +31,7 @@ import com.fasterxml.jackson.core.type.TypeReference; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; +import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; From 3bf3127251477ea0a1ea5a3d422c55403aaf28b5 Mon Sep 17 00:00:00 2001 From: dimitrispie Date: Wed, 14 Sep 2022 16:36:19 +0300 Subject: [PATCH 169/214] Changes to monitor and indicator scripts --- .../oozie_app/scripts/step16-createIndicatorsTables.sql | 6 +++--- .../stats/oozie_app/scripts/step16_1-definitions.sql | 6 +++--- .../stats/oozie_app/scripts/step20-createMonitorDB.sql | 8 ++++---- 3 files changed, 10 insertions(+), 10 deletions(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql index 0f294145c..b8792ae61 100755 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql @@ -76,11 +76,11 @@ compute stats indi_result_with_orcid; ---- Sprint 3 ---- create table indi_funded_result_with_fundref stored as parquet as -select distinct r.id, coalesce(fundref, 0) as fundref +select distinct r.result as id, coalesce(fundref, 0) as fundref from project_results r - left outer join (select distinct id, 1 as fundref from project_results + left outer join (select distinct result, 1 as fundref from project_results where provenance='Harvested') tmp - on r.id= tmp.id; + on r.result= tmp.result; compute stats indi_funded_result_with_fundref; diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_1-definitions.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_1-definitions.sql index 88c1ece78..41c95758c 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_1-definitions.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_1-definitions.sql @@ -3,20 +3,20 @@ ---------------------------------------------------- -- Peer reviewed: -create table ${stats_db_name}.result_peerreviewed STORED AS PARQUET as +create table IF NOT EXISTS ${stats_db_name}.result_peerreviewed STORED AS PARQUET as select r.id as id, case when doi.doi_from_crossref=1 and grey.grey_lit=0 then true else false end as peer_reviewed from ${stats_db_name}.result r left outer join ${stats_db_name}.indi_pub_doi_from_crossref doi on doi.id=r.id left outer join ${stats_db_name}.indi_pub_grey_lit grey on grey.id=r.id; -- Green OA: -create table ${stats_db_name}.result_greenoa STORED AS PARQUET as +create table IF NOT EXISTS ${stats_db_name}.result_greenoa STORED AS PARQUET as select r.id, case when green.green_oa=1 then true else false end as green from ${stats_db_name}.result r left outer join ${stats_db_name}.indi_pub_green_oa green on green.id=r.id; -- GOLD OA: -create table ${stats_db_name}.result_gold STORED AS PARQUET as +create table IF NOT EXISTS ${stats_db_name}.result_gold STORED AS PARQUET as select r.id, case when gold.is_gold=1 then true else false end as gold from ${stats_db_name}.result r left outer join ${stats_db_name}.indi_pub_gold_oa gold on gold.id=r.id; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql index 572b70ef7..5af2e9edd 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql @@ -162,10 +162,10 @@ create table TARGET.indi_pub_doi_from_crossref stored as parquet as select * fro compute stats TARGET.indi_pub_doi_from_crossref; create table TARGET.indi_pub_gold_oa stored as parquet as select * from SOURCE.indi_pub_gold_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_pub_gold_oa; -create table TARGET.indi_datasets_gold_oa stored as parquet as select * from SOURCE.indi_datasets_gold_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id); -compute stats TARGET.indi_datasets_gold_oa; -create table TARGET.indi_software_gold_oa stored as parquet as select * from SOURCE.indi_software_gold_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id); -compute stats TARGET.indi_software_gold_oa; +--create table TARGET.indi_datasets_gold_oa stored as parquet as select * from SOURCE.indi_datasets_gold_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id); +--compute stats TARGET.indi_datasets_gold_oa; +--create table TARGET.indi_software_gold_oa stored as parquet as select * from SOURCE.indi_software_gold_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id); +--compute stats TARGET.indi_software_gold_oa; create table TARGET.indi_pub_has_abstract stored as parquet as select * from SOURCE.indi_pub_has_abstract orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_pub_has_abstract; create table TARGET.indi_result_has_cc_licence stored as parquet as select * from SOURCE.indi_result_has_cc_licence orig where exists (select 1 from TARGET.result r where r.id=orig.id); From c48f6e9c57c6b1fe549d59e032bc0cad6fa01f66 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 14 Sep 2022 17:11:26 +0200 Subject: [PATCH 170/214] [aggregator graph] save invalid records aside for further inspection --- .../dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java | 2 +- .../dhp/oa/graph/raw/GenerateEntitiesApplication.java | 8 +++++--- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index cdc707084..0a32766c9 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -143,7 +143,7 @@ public abstract class AbstractMdRecordToOafMapper { return createOafs(doc, type, instances, collectedFrom, info, lastUpdateTimestamp); } catch (DocumentException e) { log.error("Error with record:\n" + xml); - return Lists.newArrayList(); + return null; } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java index e9de43f7f..290a22656 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java @@ -126,8 +126,6 @@ public class GenerateEntitiesApplication { log.info("Generate entities from files:"); existingSourcePaths.forEach(log::info); - JavaRDD inputRdd = sc.emptyRDD(); - for (final String sp : existingSourcePaths) { RDD invalidRecords = sc .sequenceFile(sp, Text.class, Text.class) @@ -141,7 +139,11 @@ public class GenerateEntitiesApplication { .mode(SaveMode.Append) .option("compression", "gzip") .text(invalidPath); + } + JavaRDD inputRdd = sc.emptyRDD(); + + for (final String sp : existingSourcePaths) { inputRdd = inputRdd .union( sc @@ -223,7 +225,7 @@ public class GenerateEntitiesApplication { final boolean shouldHashId, final VocabularyGroup vocs) { - if (convertToListOaf(id, s, shouldHashId, vocs).isEmpty()) { + if (Objects.isNull(convertToListOaf(id, s, shouldHashId, vocs))) { return s; } return null; From 9e7ec4198fb99514b2f5e5f1c7817ffa7d0c1f8e Mon Sep 17 00:00:00 2001 From: Alessia Bardi Date: Wed, 14 Sep 2022 18:08:56 +0200 Subject: [PATCH 171/214] fixed test --- .../src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index 204649633..390920027 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -929,7 +929,7 @@ class MappersTest { void testNotWellFormed() throws IOException, DocumentException { final String xml = IOUtils .toString(Objects.requireNonNull(getClass().getResourceAsStream("oaf_notwellformed.xml"))); - assertEquals(0, new OafToOafMapper(vocs, false, true).processMdRecord(xml).size()); + assertEquals(null, new OafToOafMapper(vocs, false, true).processMdRecord(xml)); } From 1e42d984e1ead5e1e7519d69f8150f44060f9565 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 15 Sep 2022 10:49:42 +0200 Subject: [PATCH 172/214] [aggregator graph] save invalid records aside for further inspection --- .../dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java | 2 +- .../dhp/oa/graph/raw/GenerateEntitiesApplication.java | 10 +++++----- .../java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java | 7 ++++--- 3 files changed, 10 insertions(+), 9 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index 0a32766c9..cdc707084 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -143,7 +143,7 @@ public abstract class AbstractMdRecordToOafMapper { return createOafs(doc, type, instances, collectedFrom, info, lastUpdateTimestamp); } catch (DocumentException e) { log.error("Error with record:\n" + xml); - return null; + return Lists.newArrayList(); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java index 290a22656..06d5e9acb 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java @@ -150,8 +150,8 @@ public class GenerateEntitiesApplication { .sequenceFile(sp, Text.class, Text.class) .map(k -> new Tuple2<>(k._1().toString(), k._2().toString())) .map(k -> convertToListOaf(k._1(), k._2(), shouldHashId, vocs)) - .filter(Objects::nonNull) - .flatMap(List::iterator)); + .flatMap(List::iterator) + .filter(Objects::nonNull)); } switch (mode) { @@ -225,7 +225,8 @@ public class GenerateEntitiesApplication { final boolean shouldHashId, final VocabularyGroup vocs) { - if (Objects.isNull(convertToListOaf(id, s, shouldHashId, vocs))) { + final List oaf = convertToListOaf(id, s, shouldHashId, vocs); + if (Optional.ofNullable(oaf).map(List::isEmpty).orElse(false)) { return s; } return null; @@ -235,8 +236,7 @@ public class GenerateEntitiesApplication { try { return OBJECT_MAPPER.readValue(s, clazz); } catch (final Exception e) { - log.error("Error parsing object of class: {}", clazz); - log.error(s); + log.error("Error parsing object of class: {}:\n{}", clazz, s); throw new IllegalArgumentException(e); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index 390920027..506a69012 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -926,11 +926,12 @@ class MappersTest { } @Test - void testNotWellFormed() throws IOException, DocumentException { + void testNotWellFormed() throws IOException { final String xml = IOUtils .toString(Objects.requireNonNull(getClass().getResourceAsStream("oaf_notwellformed.xml"))); - assertEquals(null, new OafToOafMapper(vocs, false, true).processMdRecord(xml)); - + final List actual = new OafToOafMapper(vocs, false, true).processMdRecord(xml); + assertNotNull(actual); + assertTrue(actual.isEmpty()); } private void assertValidId(final String id) { From e370e940d871b5b9772eff48300ad8d9074641c3 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 16 Sep 2022 14:06:28 +0200 Subject: [PATCH 173/214] [aggregator graph] save invalid records aside for further inspection --- .../raw/GenerateEntitiesApplication.java | 37 +----- .../graph/raw/VerifyRecordsApplication.java | 108 ++++++++++++++++++ .../common/AbstractMigrationApplication.java | 6 +- .../graph/generate_entities_parameters.json | 6 - .../oa/graph/raw_all/oozie_app/workflow.xml | 54 ++++++++- .../oa/graph/verify_records_parameters.json | 26 +++++ 6 files changed, 191 insertions(+), 46 deletions(-) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/VerifyRecordsApplication.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/verify_records_parameters.json diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java index 06d5e9acb..5f9d98073 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java @@ -79,9 +79,6 @@ public class GenerateEntitiesApplication { final String targetPath = parser.get("targetPath"); log.info("targetPath: {}", targetPath); - final String invalidPath = parser.get("invalidPath"); - log.info("invalidPath: {}", invalidPath); - final String isLookupUrl = parser.get("isLookupUrl"); log.info("isLookupUrl: {}", isLookupUrl); @@ -103,8 +100,7 @@ public class GenerateEntitiesApplication { final SparkConf conf = new SparkConf(); runWithSparkSession(conf, isSparkSessionManaged, spark -> { HdfsSupport.remove(targetPath, spark.sparkContext().hadoopConfiguration()); - HdfsSupport.remove(invalidPath, spark.sparkContext().hadoopConfiguration()); - generateEntities(spark, vocs, sourcePaths, targetPath, invalidPath, shouldHashId, mode); + generateEntities(spark, vocs, sourcePaths, targetPath, shouldHashId, mode); }); } @@ -113,7 +109,6 @@ public class GenerateEntitiesApplication { final VocabularyGroup vocs, final String sourcePaths, final String targetPath, - final String invalidPath, final boolean shouldHashId, final Mode mode) { @@ -126,21 +121,6 @@ public class GenerateEntitiesApplication { log.info("Generate entities from files:"); existingSourcePaths.forEach(log::info); - for (final String sp : existingSourcePaths) { - RDD invalidRecords = sc - .sequenceFile(sp, Text.class, Text.class) - .map(k -> new Tuple2<>(k._1().toString(), k._2().toString())) - .map(k -> tryApplyMapping(k._1(), k._2(), shouldHashId, vocs)) - .filter(Objects::nonNull) - .rdd(); - spark - .createDataset(invalidRecords, Encoders.STRING()) - .write() - .mode(SaveMode.Append) - .option("compression", "gzip") - .text(invalidPath); - } - JavaRDD inputRdd = sc.emptyRDD(); for (final String sp : existingSourcePaths) { @@ -178,7 +158,7 @@ public class GenerateEntitiesApplication { .saveAsTextFile(targetPath, GzipCodec.class); } - private static List convertToListOaf( + public static List convertToListOaf( final String id, final String s, final boolean shouldHashId, @@ -219,19 +199,6 @@ public class GenerateEntitiesApplication { } } - private static String tryApplyMapping( - final String id, - final String s, - final boolean shouldHashId, - final VocabularyGroup vocs) { - - final List oaf = convertToListOaf(id, s, shouldHashId, vocs); - if (Optional.ofNullable(oaf).map(List::isEmpty).orElse(false)) { - return s; - } - return null; - } - private static Oaf convertFromJson(final String s, final Class clazz) { try { return OBJECT_MAPPER.readValue(s, clazz); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/VerifyRecordsApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/VerifyRecordsApplication.java new file mode 100644 index 000000000..a8eb871c8 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/VerifyRecordsApplication.java @@ -0,0 +1,108 @@ + +package eu.dnetlib.dhp.oa.graph.raw; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.util.Arrays; +import java.util.List; +import java.util.Objects; +import java.util.Optional; +import java.util.stream.Collectors; + +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.io.Text; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.rdd.RDD; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; +import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.utils.ISLookupClientFactory; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; +import scala.Tuple2; + +public class VerifyRecordsApplication { + + private static final Logger log = LoggerFactory.getLogger(VerifyRecordsApplication.class); + + public static void main(final String[] args) throws Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + VerifyRecordsApplication.class + .getResourceAsStream("/eu/dnetlib/dhp/oa/graph/verify_records_parameters.json"))); + + parser.parseArgument(args); + + final Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String sourcePaths = parser.get("sourcePaths"); + log.info("sourcePaths: {}", sourcePaths); + + final String invalidPath = parser.get("invalidPath"); + log.info("invalidPath: {}", invalidPath); + + final String isLookupUrl = parser.get("isLookupUrl"); + log.info("isLookupUrl: {}", isLookupUrl); + + final ISLookUpService isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl); + final VocabularyGroup vocs = VocabularyGroup.loadVocsFromIS(isLookupService); + + final SparkConf conf = new SparkConf(); + runWithSparkSession(conf, isSparkSessionManaged, spark -> { + HdfsSupport.remove(invalidPath, spark.sparkContext().hadoopConfiguration()); + validateRecords(spark, sourcePaths, invalidPath, vocs); + }); + } + + private static void validateRecords(SparkSession spark, String sourcePaths, String invalidPath, + VocabularyGroup vocs) { + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + final List existingSourcePaths = Arrays + .stream(sourcePaths.split(",")) + .filter(p -> HdfsSupport.exists(p, sc.hadoopConfiguration())) + .collect(Collectors.toList()); + + log.info("Verify records in files:"); + existingSourcePaths.forEach(log::info); + + for (final String sp : existingSourcePaths) { + RDD invalidRecords = sc + .sequenceFile(sp, Text.class, Text.class) + .map(k -> tryApplyMapping(k._1().toString(), k._2().toString(), true, vocs)) + .filter(Objects::nonNull) + .rdd(); + spark + .createDataset(invalidRecords, Encoders.STRING()) + .write() + .mode(SaveMode.Append) + .option("compression", "gzip") + .text(invalidPath); + } + } + + private static String tryApplyMapping( + final String id, + final String xmlRecord, + final boolean shouldHashId, + final VocabularyGroup vocs) { + + final List oaf = GenerateEntitiesApplication.convertToListOaf(id, xmlRecord, shouldHashId, vocs); + if (Optional.ofNullable(oaf).map(List::isEmpty).orElse(false)) { + return xmlRecord; + } + return null; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/AbstractMigrationApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/AbstractMigrationApplication.java index cba64899b..6f63e9327 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/AbstractMigrationApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/AbstractMigrationApplication.java @@ -4,6 +4,7 @@ package eu.dnetlib.dhp.oa.graph.raw.common; import java.io.Closeable; import java.io.IOException; import java.util.Arrays; +import java.util.List; import java.util.Set; import java.util.concurrent.atomic.AtomicInteger; import java.util.stream.Collectors; @@ -24,8 +25,11 @@ import org.apache.http.impl.client.HttpClients; import com.fasterxml.jackson.core.JsonProcessingException; import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; +import eu.dnetlib.dhp.oa.graph.raw.OafToOafMapper; +import eu.dnetlib.dhp.oa.graph.raw.OdfToOafMapper; import eu.dnetlib.dhp.schema.mdstore.MDStoreWithInfo; -import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.utils.DHPUtils; public class AbstractMigrationApplication implements Closeable { diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/generate_entities_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/generate_entities_parameters.json index da6730fbb..52cbbf45f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/generate_entities_parameters.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/generate_entities_parameters.json @@ -17,12 +17,6 @@ "paramDescription": "the path of the target file", "paramRequired": true }, - { - "paramName": "i", - "paramLongName": "invalidPath", - "paramDescription": "the path of the invalid records file", - "paramRequired": false - }, { "paramName": "isu", "paramLongName": "isLookupUrl", diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml index d00232e9a..8262c6923 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml @@ -446,10 +446,34 @@ - - + + + + + yarn + cluster + VerifyRecords_claim + eu.dnetlib.dhp.oa.graph.raw.VerifyRecordsApplication + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory ${sparkExecutorMemory} + --executor-cores ${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --sourcePaths${contentPath}/db_claims,${contentPath}/oaf_claims,${contentPath}/odf_claims + --invalidPath${workingDir}/invalid_records_claim + --isLookupUrl${isLookupUrl} + + + + + yarn @@ -468,7 +492,6 @@ --sourcePaths${contentPath}/db_claims,${contentPath}/oaf_claims,${contentPath}/odf_claims --targetPath${workingDir}/entities_claim - --invalidPath${workingDir}/invalid_records_claim --isLookupUrl${isLookupUrl} --shouldHashId${shouldHashId} --modeclaim @@ -500,6 +523,30 @@ + + + yarn + cluster + VerifyRecords + eu.dnetlib.dhp.oa.graph.raw.VerifyRecordsApplication + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory ${sparkExecutorMemory} + --executor-cores ${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --sourcePaths${contentPath}/db_openaire,${contentPath}/db_openorgs,${contentPath}/oaf_records,${contentPath}/odf_records,${contentPath}/oaf_records_hdfs,${contentPath}/odf_records_hdfs,${contentPath}/oaf_records_invisible + --invalidPath${workingDir}/invalid_records + --isLookupUrl${isLookupUrl} + + + + + yarn @@ -518,7 +565,6 @@ --sourcePaths${contentPath}/db_openaire,${contentPath}/db_openorgs,${contentPath}/oaf_records,${contentPath}/odf_records,${contentPath}/oaf_records_hdfs,${contentPath}/odf_records_hdfs,${contentPath}/oaf_records_invisible --targetPath${workingDir}/entities - --invalidPath${workingDir}/invalid_records --isLookupUrl${isLookupUrl} --shouldHashId${shouldHashId} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/verify_records_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/verify_records_parameters.json new file mode 100644 index 000000000..eb00e7609 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/verify_records_parameters.json @@ -0,0 +1,26 @@ +[ + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "when true will stop SparkSession after job execution", + "paramRequired": false + }, + { + "paramName": "s", + "paramLongName": "sourcePaths", + "paramDescription": "the HDFS source paths which contains the sequential file (comma separated)", + "paramRequired": true + }, + { + "paramName": "i", + "paramLongName": "invalidPath", + "paramDescription": "the path of the invalid records file", + "paramRequired": false + }, + { + "paramName": "isu", + "paramLongName": "isLookupUrl", + "paramDescription": "the url of the ISLookupService", + "paramRequired": true + } +] \ No newline at end of file From 5240ac3d7bdfeba3ce7f5bb2bbacab7fa8c84641 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 19 Sep 2022 11:02:18 +0200 Subject: [PATCH 174/214] [EOSC Tag] remove addition of eosc context for result with eosc if guidelines set --- .../java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java index 66e0c8af4..ed2d19253 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java @@ -121,8 +121,7 @@ public class SparkEoscBulkTag implements Serializable { .getInstance() .stream() .anyMatch( - i -> (hostedByList.contains(i.getHostedby().getKey())) || - (value.getEoscifguidelines() != null && value.getEoscifguidelines().size() > 0)) + i -> (hostedByList.contains(i.getHostedby().getKey())) ) && !value.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))) { Context context = new Context(); From 26e1baddedc95ee93ba7577ef34b29e9b09940ed Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 19 Sep 2022 11:19:10 +0200 Subject: [PATCH 175/214] added instance.url syntactical validation, avoid creating multiple duplicated URLs --- dhp-workflows/dhp-graph-mapper/pom.xml | 5 +++ .../raw/AbstractMdRecordToOafMapper.java | 15 +++++++ .../dhp/oa/graph/raw/OafToOafMapper.java | 35 +++++++++-------- .../dhp/oa/graph/raw/OdfToOafMapper.java | 39 ++++++++++++------- .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 2 +- pom.xml | 6 +++ 6 files changed, 71 insertions(+), 31 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/pom.xml b/dhp-workflows/dhp-graph-mapper/pom.xml index 687f0de66..f579a7d2b 100644 --- a/dhp-workflows/dhp-graph-mapper/pom.xml +++ b/dhp-workflows/dhp-graph-mapper/pom.xml @@ -57,6 +57,11 @@ commons-io + + commons-validator + commons-validator + + org.apache.spark spark-core_2.11 diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index 5cfb22cb9..a8d09e4a7 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -10,9 +10,13 @@ import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_PROJECT; import static eu.dnetlib.dhp.schema.common.ModelConstants.UNKNOWN; import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.*; +import java.net.MalformedURLException; +import java.net.URL; import java.util.*; +import java.util.stream.Collectors; import org.apache.commons.lang3.StringUtils; +import org.apache.commons.validator.routines.UrlValidator; import org.dom4j.*; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -617,4 +621,15 @@ public abstract class AbstractMdRecordToOafMapper { return res; } + protected Set validateUrl(Collection url) { + UrlValidator urlValidator = UrlValidator.getInstance(); + if (Objects.isNull(url)) { + return new HashSet<>(); + } + return url + .stream() + .filter(u -> urlValidator.isValid(u)) + .collect(Collectors.toCollection(HashSet::new)); + } + } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java index 9225e174d..30f3935f5 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java @@ -159,22 +159,25 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper { .setProcessingchargecurrency(field(doc.valueOf("//oaf:processingchargeamount/@currency"), info)); final List nodes = Lists.newArrayList(doc.selectNodes("//dc:identifier")); - instance - .setUrl( - nodes - .stream() - .filter(n -> StringUtils.isNotBlank(n.getText())) - .map(n -> n.getText().trim()) - .filter(u -> u.startsWith("http")) - .map(s -> { - try { - return URLDecoder.decode(s, "UTF-8"); - } catch (Throwable t) { - return s; - } - }) - .distinct() - .collect(Collectors.toCollection(ArrayList::new))); + final List url = nodes + .stream() + .filter(n -> StringUtils.isNotBlank(n.getText())) + .map(n -> n.getText().trim()) + .filter(u -> u.startsWith("http")) + .map(s -> { + try { + return URLDecoder.decode(s, "UTF-8"); + } catch (Throwable t) { + return s; + } + }) + .distinct() + .collect(Collectors.toCollection(ArrayList::new)); + final Set validUrl = validateUrl(url); + if (!validUrl.isEmpty()) { + instance.setUrl(new ArrayList<>()); + instance.getUrl().addAll(validUrl); + } return Lists.newArrayList(instance); } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java index d6bfe6714..5781988e6 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java @@ -6,11 +6,14 @@ import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.*; import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.structuredProperty; import java.io.UnsupportedEncodingException; +import java.net.MalformedURLException; +import java.net.URL; import java.net.URLDecoder; import java.util.*; import java.util.stream.Collectors; import org.apache.commons.lang3.StringUtils; +import org.apache.commons.validator.routines.UrlValidator; import org.dom4j.Document; import org.dom4j.Element; import org.dom4j.Node; @@ -171,23 +174,31 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { for (final Object o : doc.selectNodes("//*[local-name()='identifier' and ./@identifierType='landingPage']")) { url.add(trimAndDecodeUrl(((Node) o).getText().trim())); } - for (final Object o : doc - .selectNodes("//*[local-name()='alternateIdentifier' and ./@alternateIdentifierType='DOI']")) { - url.add(HTTP_DOI_PREIFX + ((Node) o).getText().trim()); + + Set validUrl = validateUrl(url); + + if (validUrl.stream().noneMatch(s -> s.contains("doi.org"))) { + for (final Object o : doc + .selectNodes("//*[local-name()='alternateIdentifier' and ./@alternateIdentifierType='DOI']")) { + validUrl.add(HTTP_DOI_PREIFX + ((Node) o).getText().trim()); + } + for (final Object o : doc.selectNodes("//*[local-name()='identifier' and ./@identifierType='DOI']")) { + validUrl.add(HTTP_DOI_PREIFX + ((Node) o).getText().trim()); + } } - for (final Object o : doc.selectNodes("//*[local-name()='identifier' and ./@identifierType='DOI']")) { - url.add(HTTP_DOI_PREIFX + ((Node) o).getText().trim()); + if (validUrl.stream().noneMatch(s -> s.contains("hdl.handle.net"))) { + for (final Object o : doc + .selectNodes("//*[local-name()='alternateIdentifier' and ./@alternateIdentifierType='Handle']")) { + validUrl.add(HTTP_HANDLE_PREIFX + ((Node) o).getText().trim()); + } + for (final Object o : doc.selectNodes("//*[local-name()='identifier' and ./@identifierType='Handle']")) { + validUrl.add(HTTP_HANDLE_PREIFX + ((Node) o).getText().trim()); + } } - for (final Object o : doc - .selectNodes("//*[local-name()='alternateIdentifier' and ./@alternateIdentifierType='Handle']")) { - url.add(HTTP_HANDLE_PREIFX + ((Node) o).getText().trim()); - } - for (final Object o : doc.selectNodes("//*[local-name()='identifier' and ./@identifierType='Handle']")) { - url.add(HTTP_HANDLE_PREIFX + ((Node) o).getText().trim()); - } - if (!url.isEmpty()) { + + if (!validUrl.isEmpty()) { instance.setUrl(new ArrayList<>()); - instance.getUrl().addAll(url); + instance.getUrl().addAll(validUrl); } return Arrays.asList(instance); } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index 231d5b0ac..64b68e6af 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -950,7 +950,7 @@ class MappersTest { @Test void testNotWellFormed() throws IOException { final String xml = IOUtils - .toString(Objects.requireNonNull(getClass().getResourceAsStream("oaf_notwellformed.xml"))); + .toString(Objects.requireNonNull(getClass().getResourceAsStream("oaf_notwellformed.xml"))); final List actual = new OafToOafMapper(vocs, false, true).processMdRecord(xml); assertNotNull(actual); assertTrue(actual.isEmpty()); diff --git a/pom.xml b/pom.xml index ab59e7be3..a1b26966e 100644 --- a/pom.xml +++ b/pom.xml @@ -200,6 +200,12 @@ ${dhp.commons.lang.version} + + commons-validator + commons-validator + 1.7 + + com.github.sisyphsu dateparser From dcd85f8cd79ab8342e03eca6ef9530f35dd242ab Mon Sep 17 00:00:00 2001 From: dimitrispie Date: Thu, 22 Sep 2022 13:33:07 +0300 Subject: [PATCH 176/214] - Synchronize indicators in stats-db with monitor-db - added new openorg id for Nanyang Technological University - changed openorg id for University of Helsinki #8088 ticket --- .../scripts/step16-createIndicatorsTables.sql | 35 +++++++++++ .../scripts/step20-createMonitorDB.sql | 61 ++++++++++++------- 2 files changed, 74 insertions(+), 22 deletions(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql index b8792ae61..417ed6e4e 100755 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql @@ -92,6 +92,17 @@ compute stats indi_funded_result_with_fundref; -- -- compute stats indi_result_org_collab; -- +create table indi_result_org_collab stored as parquet as +with tmp as ( +select distinct ro.organization organization, ro.id from result_organization ro +join organization o on o.id=ro.organization where o.name is not null) +select o1.organization org1, o2.organization org2, count(o1.id) as collaborations +from tmp as o1 +join tmp as o2 on o1.id=o2.id and o1.organization!=o2.organization +group by org1, org2; + +compute stats indi_result_org_collab; + -- create table indi_result_org_country_collab stored as parquet as -- with tmp as -- (select o.id as id, o.country , ro.id as result,r.type from organization o @@ -105,6 +116,17 @@ compute stats indi_funded_result_with_fundref; -- -- compute stats indi_result_org_country_collab; -- +create table indi_result_org_country_collab stored as parquet as +with tmp as +(select distinct ro.organization organization, ro.id, o.country from result_organization ro +join organization o on o.id=ro.organization where country <> 'UNKNOWN' and o.name is not null) +select o1.organization org1,o2.country country2, count(o1.id) as collaborations +from tmp as o1 join tmp as o2 on o1.id=o2.id +where o1.id=o2.id and o1.country!=o2.country +group by o1.organization, o1.id, o2.country; + +compute stats indi_result_org_country_collab; + -- create table indi_result_org_collab stored as parquet as -- with tmp as -- (select o.id, ro.id as result,r.type from organization o @@ -166,6 +188,19 @@ compute stats indi_funder_country_collab; -- -- compute stats indi_result_country_collab; +create table indi_result_country_collab stored as parquet as +with tmp as + (select distinct country, ro.id as result from organization o + join result_organization ro on o.id=ro.organization + where country <> 'UNKNOWN' and o.name is not null) +select o1.country country1, o2.country country2, count(o1.result) as collaborations +from tmp as o1 + join tmp as o2 on o1.result=o2.result +where o1.country<>o2.country +group by o1.country, o2.country; + +compute stats indi_result_country_collab; + ---- Sprint 4 ---- create table indi_pub_diamond stored as parquet as select distinct pd.id, coalesce(in_diamond_journal, 0) as in_diamond_journal diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql index 5af2e9edd..290acbf9f 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql @@ -23,7 +23,7 @@ create table TARGET.result stored as parquet as 'openorgs____::d2a09b9d5eabb10c95f9470e172d05d2', --??? Not exists ?? 'openorgs____::d169c7407dd417152596908d48c11460', --Masaryk University 'openorgs____::1ec924b1759bb16d0a02f2dad8689b21', --University of Belgrade - 'openorgs____::2fb1e47b4612688d9de9169d579939a7', --University of Helsinki + 'openorgs____::0ae431b820e4c33db8967fbb2b919150', --University of Helsinki 'openorgs____::759d59f05d77188faee99b7493b46805', --University of Minho 'openorgs____::cad284878801b9465fa51a95b1d779db', --Universidad Politécnica de Madrid 'openorgs____::eadc8da90a546e98c03f896661a2e4d4', --University of Göttingen @@ -48,7 +48,8 @@ create table TARGET.result stored as parquet as 'openorgs____::4ac562f0376fce3539504567649cb373', -- University of Patras 'openorgs____::3e8d1f8c3f6cd7f418b09f1f58b4873b', -- Aristotle University of Thessaloniki 'openorgs____::3fcef6e1c469c10f2a84b281372c9814', -- World Bank - 'openorgs____::1698a2eb1885ef8adb5a4a969e745ad3' -- École des Ponts ParisTech + 'openorgs____::1698a2eb1885ef8adb5a4a969e745ad3', -- École des Ponts ParisTech + 'openorgs____::e15adb13c4dadd49de4d35c39b5da93a' -- Nanyang Technological University ) )) foo; compute stats TARGET.result; @@ -154,50 +155,44 @@ create table TARGET.project_results stored as parquet as select id as result, pr compute stats TARGET.project_results; -- indicators +-- Sprint 1 ---- create table TARGET.indi_pub_green_oa stored as parquet as select * from SOURCE.indi_pub_green_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_pub_green_oa; create table TARGET.indi_pub_grey_lit stored as parquet as select * from SOURCE.indi_pub_grey_lit orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_pub_grey_lit; create table TARGET.indi_pub_doi_from_crossref stored as parquet as select * from SOURCE.indi_pub_doi_from_crossref orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_pub_doi_from_crossref; -create table TARGET.indi_pub_gold_oa stored as parquet as select * from SOURCE.indi_pub_gold_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id); -compute stats TARGET.indi_pub_gold_oa; ---create table TARGET.indi_datasets_gold_oa stored as parquet as select * from SOURCE.indi_datasets_gold_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---compute stats TARGET.indi_datasets_gold_oa; ---create table TARGET.indi_software_gold_oa stored as parquet as select * from SOURCE.indi_software_gold_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id); ---compute stats TARGET.indi_software_gold_oa; -create table TARGET.indi_pub_has_abstract stored as parquet as select * from SOURCE.indi_pub_has_abstract orig where exists (select 1 from TARGET.result r where r.id=orig.id); -compute stats TARGET.indi_pub_has_abstract; +-- Sprint 2 ---- create table TARGET.indi_result_has_cc_licence stored as parquet as select * from SOURCE.indi_result_has_cc_licence orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_result_has_cc_licence; create table TARGET.indi_result_has_cc_licence_url stored as parquet as select * from SOURCE.indi_result_has_cc_licence_url orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_result_has_cc_licence_url; - -create view TARGET.indi_funder_country_collab as select * from SOURCE.indi_funder_country_collab; -create view TARGET.indi_project_collab_org as select * from SOURCE.indi_project_collab_org; -create view TARGET.indi_project_collab_org_country as select * from SOURCE.indi_project_collab_org_country; - +create table TARGET.indi_pub_has_abstract stored as parquet as select * from SOURCE.indi_pub_has_abstract orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.indi_pub_has_abstract; create table TARGET.indi_result_with_orcid stored as parquet as select * from SOURCE.indi_result_with_orcid orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_result_with_orcid; +---- Sprint 3 ---- create table TARGET.indi_funded_result_with_fundref stored as parquet as select * from SOURCE.indi_funded_result_with_fundref orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_funded_result_with_fundref; +create view TARGET.indi_result_org_collab as select * from SOURCE.indi_result_org_collab; +create view TARGET.indi_result_org_country_collab as select * from SOURCE.indi_result_org_country_collab; +create view TARGET.indi_project_collab_org as select * from SOURCE.indi_project_collab_org; +create view TARGET.indi_project_collab_org_country as select * from SOURCE.indi_project_collab_org_country; +create view TARGET.indi_funder_country_collab as select * from SOURCE.indi_funder_country_collab; +create view TARGET.indi_result_country_collab as select * from SOURCE.indi_result_country_collab; +---- Sprint 4 ---- create table TARGET.indi_pub_diamond stored as parquet as select * from SOURCE.indi_pub_diamond orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_pub_diamond; -create table TARGET.indi_pub_hybrid stored as parquet as select * from SOURCE.indi_pub_hybrid orig where exists (select 1 from TARGET.result r where r.id=orig.id); -compute stats TARGET.indi_pub_hybrid; create table TARGET.indi_pub_in_transformative stored as parquet as select * from SOURCE.indi_pub_in_transformative orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_pub_in_transformative; create table TARGET.indi_pub_closed_other_open stored as parquet as select * from SOURCE.indi_pub_closed_other_open orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_pub_closed_other_open; - +---- Sprint 5 ---- create table TARGET.indi_result_no_of_copies stored as parquet as select * from SOURCE.indi_result_no_of_copies orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_result_no_of_copies; - -create view TARGET.indi_org_findable as select * from SOURCE.indi_org_findable; -create view TARGET.indi_org_openess as select * from SOURCE.indi_org_openess; +---- Sprint 6 ---- create table TARGET.indi_pub_hybrid_oa_with_cc stored as parquet as select * from SOURCE.indi_pub_hybrid_oa_with_cc orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_pub_hybrid_oa_with_cc; - create table TARGET.indi_pub_downloads stored as parquet as select * from SOURCE.indi_pub_downloads orig where exists (select 1 from TARGET.result r where r.id=orig.result_id); compute stats TARGET.indi_pub_downloads; create table TARGET.indi_pub_downloads_datasource stored as parquet as select * from SOURCE.indi_pub_downloads_datasource orig where exists (select 1 from TARGET.result r where r.id=orig.result_id); @@ -206,6 +201,28 @@ create table TARGET.indi_pub_downloads_year stored as parquet as select * from S compute stats TARGET.indi_pub_downloads_year; create table TARGET.indi_pub_downloads_datasource_year stored as parquet as select * from SOURCE.indi_pub_downloads_datasource_year orig where exists (select 1 from TARGET.result r where r.id=orig.result_id); compute stats TARGET.indi_pub_downloads_datasource_year; +---- Sprint 7 ---- +create table TARGET.indi_pub_gold_oa stored as parquet as select * from SOURCE.indi_pub_gold_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.indi_pub_gold_oa; +create table TARGET.indi_pub_hybrid stored as parquet as select * from SOURCE.indi_pub_hybrid orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.indi_pub_hybrid; +create view TARGET.indi_org_fairness as select * from SOURCE.indi_org_fairness; +create view TARGET.indi_org_fairness_pub_pr as select * from SOURCE.indi_org_fairness_pub_pr; +create view TARGET.indi_org_fairness_pub_year as select * from SOURCE.indi_org_fairness_pub_year; +create view TARGET.indi_org_fairness_pub as select * from SOURCE.indi_org_fairness_pub; +create view TARGET.indi_org_fairness_year as select * from SOURCE.indi_org_fairness_year; +create view TARGET.indi_org_findable_year as select * from SOURCE.indi_org_findable_year; +create view TARGET.indi_org_findable as select * from SOURCE.indi_org_findable; +create view TARGET.indi_org_openess as select * from SOURCE.indi_org_openess; +create view TARGET.indi_org_openess_year as select * from SOURCE.indi_org_openess_year; +create table TARGET.indi_pub_has_preprint stored as parquet as select * from SOURCE.indi_pub_has_preprint orig where exists (select 1 from TARGET.result r where r.id=orig.id); +create table TARGET.indi_pub_in_subscribed stored as parquet as select * from SOURCE.indi_pub_in_subscribed orig where exists (select 1 from TARGET.result r where r.id=orig.id); +create table TARGET.indi_result_with_pid stored as parquet as select * from SOURCE.indi_result_with_pid orig where exists (select 1 from TARGET.result r where r.id=orig.id); + +--create table TARGET.indi_datasets_gold_oa stored as parquet as select * from SOURCE.indi_datasets_gold_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id); +--compute stats TARGET.indi_datasets_gold_oa; +--create table TARGET.indi_software_gold_oa stored as parquet as select * from SOURCE.indi_software_gold_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id); +--compute stats TARGET.indi_software_gold_oa; --denorm alter table TARGET.result rename to TARGET.res_tmp; From c42850328e602bc59fa7f76bcdf452215404d7a2 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 22 Sep 2022 16:23:25 +0200 Subject: [PATCH 177/214] fixed semantic (subreltype) for ServiceOrganization relations --- .../dhp/oa/graph/raw/MigrateDbEntitiesApplication.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java index f40d3d19b..2b1c257ad 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java @@ -417,12 +417,12 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i final Relation r1 = OafMapperUtils .getRelation( - dsId, orgId, DATASOURCE_ORGANIZATION, PRODUCES, IS_PROVIDED_BY, collectedFrom, info, + dsId, orgId, DATASOURCE_ORGANIZATION, PROVISION, IS_PROVIDED_BY, collectedFrom, info, lastUpdateTimestamp); final Relation r2 = OafMapperUtils .getRelation( - orgId, dsId, DATASOURCE_ORGANIZATION, PRODUCES, PROVIDES, collectedFrom, info, lastUpdateTimestamp); + orgId, dsId, DATASOURCE_ORGANIZATION, PROVISION, PROVIDES, collectedFrom, info, lastUpdateTimestamp); return Arrays.asList(r1, r2); } catch (final Exception e) { From 960cb861a0ace5556213016942ca0b05039632ca Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 23 Sep 2022 11:14:04 +0200 Subject: [PATCH 178/214] refactoring --- .../main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java index ed2d19253..c4b2122b4 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java @@ -121,7 +121,7 @@ public class SparkEoscBulkTag implements Serializable { .getInstance() .stream() .anyMatch( - i -> (hostedByList.contains(i.getHostedby().getKey())) ) + i -> (hostedByList.contains(i.getHostedby().getKey()))) && !value.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))) { Context context = new Context(); From 982bcc1e3535e15dcaeca2cd14551d216e9356c8 Mon Sep 17 00:00:00 2001 From: Alessia Bardi Date: Fri, 23 Sep 2022 12:06:06 +0200 Subject: [PATCH 179/214] test wrid pid and record identifier --- .../dhp/oa/graph/raw/OdfToOafMapper.java | 33 +++++++++++++++++++ .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 13 ++++++-- pom.xml | 2 +- 3 files changed, 44 insertions(+), 4 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java index 5781988e6..7d615a1f0 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java @@ -391,6 +391,39 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { final String docId = entity.getId(); final List res = new ArrayList<>(); + /* + /* + + https://w3id.org/ro-id/13c54585-362e-4925-a785-08afb591fa0d/resources/b4be0f3e-41d7-471f-b34e-f0bd54ff5698 + https://w3id.org/ro-id/13c54585-362e-4925-a785-08afb591fa0d/resources/5d6e575b-ef84-417a-9d76-61c6702f7cb2 + https://w3id.org/ro-id/13c54585-362e-4925-a785-08afb591fa0d/resources/35e01545-8c6d-49bd-ab98-5c152df69934 + + We could extend it to create the relationships targeting w3id, dois, pmcids and other pid types for which we know how to build the target openaire identifier "blindly". + + + + for (final Object o : doc + .selectNodes("//*[local-name()='relatedIdentifier']")) { + + final String originalId = ((Node) o).getText(); + + if (StringUtils.isNotBlank(originalId)) { + final String otherId = createOpenaireId(50, originalId, false); + final String type = ((Node) o).valueOf("@relationType"); + switch(type){ + case IS_SUPPLEMENT_TO: + break; + case SUPPLEMENT: + break; + case IS_PART_OF: + break; + case HAS_PART: + break; + + + } + + */ for (final Object o : doc .selectNodes("//*[local-name()='relatedIdentifier' and ./@relatedIdentifierType='OPENAIRE']")) { diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index 64b68e6af..b163ecff3 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -912,13 +912,13 @@ class MappersTest { } @Test - void testROHub() throws IOException, DocumentException { + void testROHub() throws IOException { final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("rohub.xml"))); final List list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml); System.out.println("***************"); System.out.println(new ObjectMapper().writeValueAsString(list)); System.out.println("***************"); -// final Dataset p = (Dataset) list.get(0); +// final OtherResearchProduct p = (OtherResearchProduct) list.get(0); // assertValidId(p.getId()); // assertValidId(p.getCollectedfrom().get(0).getKey()); // System.out.println(p.getTitle().get(0).getValue()); @@ -926,13 +926,20 @@ class MappersTest { } @Test - void testROHub2() throws IOException, DocumentException { + void testROHub2() throws IOException { final String xml = IOUtils .toString(Objects.requireNonNull(getClass().getResourceAsStream("rohub-modified.xml"))); final List list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml); System.out.println("***************"); System.out.println(new ObjectMapper().writeValueAsString(list)); System.out.println("***************"); + final OtherResearchProduct p = (OtherResearchProduct) list.get(0); + assertValidId(p.getId()); + assertValidId(p.getCollectedfrom().get(0).getKey()); + assertEquals("50|w3id________::afc7592914ae190a50570db90f55f9c2", p.getId()); + assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue())); + assertEquals("w3id", (p.getPid().get(0).getQualifier().getClassid())); + assertEquals("https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca", (p.getPid().get(0).getValue())); } @Test diff --git a/pom.xml b/pom.xml index a1b26966e..55265bf55 100644 --- a/pom.xml +++ b/pom.xml @@ -807,7 +807,7 @@ 3.3.3 3.4.2 [2.12,3.0) - [3.14.0] + [3.14.0-SNAPSHOT] [4.0.3] [6.0.5] [3.1.6] From ba33ff71fdc9eaf142d329ae5430e6ef8f81474b Mon Sep 17 00:00:00 2001 From: Alessia Bardi Date: Fri, 23 Sep 2022 15:17:13 +0200 Subject: [PATCH 180/214] refactoring for the generation of relationships from related identifier of type 'OPENAIRE' --- .../raw/MigrateDbEntitiesApplication.java | 3 +- .../dhp/oa/graph/raw/OdfToOafMapper.java | 117 +++++++++--------- .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 1 + .../dhp/oa/graph/raw/rohub-modified.xml | 3 + 4 files changed, 66 insertions(+), 58 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java index 2b1c257ad..c69a7a6ff 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java @@ -422,7 +422,8 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i final Relation r2 = OafMapperUtils .getRelation( - orgId, dsId, DATASOURCE_ORGANIZATION, PROVISION, PROVIDES, collectedFrom, info, lastUpdateTimestamp); + orgId, dsId, DATASOURCE_ORGANIZATION, PROVISION, PROVIDES, collectedFrom, info, + lastUpdateTimestamp); return Arrays.asList(r1, r2); } catch (final Exception e) { diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java index 7d615a1f0..fc063a242 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java @@ -25,6 +25,7 @@ import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions; import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; +import eu.dnetlib.dhp.schema.oaf.utils.PidType; public class OdfToOafMapper extends AbstractMdRecordToOafMapper { @@ -391,75 +392,77 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { final String docId = entity.getId(); final List res = new ArrayList<>(); - /* - /* - - https://w3id.org/ro-id/13c54585-362e-4925-a785-08afb591fa0d/resources/b4be0f3e-41d7-471f-b34e-f0bd54ff5698 - https://w3id.org/ro-id/13c54585-362e-4925-a785-08afb591fa0d/resources/5d6e575b-ef84-417a-9d76-61c6702f7cb2 - https://w3id.org/ro-id/13c54585-362e-4925-a785-08afb591fa0d/resources/35e01545-8c6d-49bd-ab98-5c152df69934 - - We could extend it to create the relationships targeting w3id, dois, pmcids and other pid types for which we know how to build the target openaire identifier "blindly". - - for (final Object o : doc - .selectNodes("//*[local-name()='relatedIdentifier']")) { + .selectNodes("//*[local-name()='relatedIdentifier']")) { - final String originalId = ((Node) o).getText(); + final String originalId = ((Node) o).getText().trim(); if (StringUtils.isNotBlank(originalId)) { - final String otherId = createOpenaireId(50, originalId, false); - final String type = ((Node) o).valueOf("@relationType"); - switch(type){ - case IS_SUPPLEMENT_TO: - break; - case SUPPLEMENT: - break; - case IS_PART_OF: - break; - case HAS_PART: - break; + final String idType = ((Node) o).valueOf("@relatedIdentifierType"); + final String reltype = ((Node) o).valueOf("@relationType"); + String otherId = guessRelatedIdentifier(idType, originalId); + if (StringUtils.isNotBlank(otherId)) { + if (reltype.equalsIgnoreCase(IS_SUPPLEMENT_TO)) { + res + .add( + getRelation( + docId, otherId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENT_TO, entity)); + res + .add( + getRelation( + otherId, docId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENTED_BY, entity)); + } else { + if (reltype.equalsIgnoreCase(IS_SUPPLEMENTED_BY)) { + res + .add( + getRelation( + otherId, docId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENT_TO, entity)); + res + .add( + getRelation( + docId, otherId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENTED_BY, entity)); + } else { + if (reltype.equalsIgnoreCase(IS_PART_OF)) { + res + .add( + getRelation( + docId, otherId, RESULT_RESULT, PART, IS_PART_OF, entity)); + res + .add( + getRelation( + otherId, docId, RESULT_RESULT, PART, HAS_PART, entity)); + } else { + if (reltype.equalsIgnoreCase(HAS_PART)) { + res + .add( + getRelation( + otherId, docId, RESULT_RESULT, PART, IS_PART_OF, entity)); + res + .add( + getRelation( + docId, otherId, RESULT_RESULT, PART, HAS_PART, entity)); + } + // else TODO catch more semantics + } + } + } - - } - - */ - - for (final Object o : doc - .selectNodes("//*[local-name()='relatedIdentifier' and ./@relatedIdentifierType='OPENAIRE']")) { - - final String originalId = ((Node) o).getText(); - - if (StringUtils.isNotBlank(originalId)) { - final String otherId = createOpenaireId(50, originalId, false); - final String type = ((Node) o).valueOf("@relationType"); - - if (type.equalsIgnoreCase(IS_SUPPLEMENT_TO)) { - res - .add( - getRelation( - docId, otherId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENT_TO, entity)); - res - .add( - getRelation( - otherId, docId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENTED_BY, entity)); - } else if (type.equalsIgnoreCase(IS_PART_OF)) { - res - .add( - getRelation( - docId, otherId, RESULT_RESULT, PART, IS_PART_OF, entity)); - res - .add( - getRelation( - otherId, docId, RESULT_RESULT, PART, HAS_PART, entity)); - } else { - // TODO catch more semantics } } } return res; } + protected String guessRelatedIdentifier(final String idType, final String value) { + if (StringUtils.isBlank(idType) || StringUtils.isBlank(value)) + return null; + if (idType.equalsIgnoreCase("OPENAIRE")) { + return createOpenaireId(50, value, false); + } else + return null; + } + @Override protected Qualifier prepareResourceType(final Document doc, final DataInfo info) { return prepareQualifier( diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index b163ecff3..fbfbf5af8 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -933,6 +933,7 @@ class MappersTest { System.out.println("***************"); System.out.println(new ObjectMapper().writeValueAsString(list)); System.out.println("***************"); + assertEquals(3, list.size()); final OtherResearchProduct p = (OtherResearchProduct) list.get(0); assertValidId(p.getId()); assertValidId(p.getCollectedfrom().get(0).getKey()); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/rohub-modified.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/rohub-modified.xml index 95d65ac8d..ce846a2cf 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/rohub-modified.xml +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/rohub-modified.xml @@ -30,6 +30,9 @@ https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca/resources/6d3427a8-352e-49f4-9796-f618c44dc16d + + fsh_____4119::afc7592914ae190a50570db90f55f9c3 + RO-crate From c86cc53520216a7890cdfa0574187ce488ac27f6 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 23 Sep 2022 15:19:50 +0200 Subject: [PATCH 181/214] suppressing hyper verbose spark logs during unit test execution --- .../dhp-graph-mapper/src/test/resources/log4j.properties | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/log4j.properties b/dhp-workflows/dhp-graph-mapper/src/test/resources/log4j.properties index 71255bb77..d5604dc45 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/log4j.properties +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/log4j.properties @@ -5,4 +5,11 @@ log4j.rootLogger=DEBUG, stdout log4j.appender.stdout=org.apache.log4j.ConsoleAppender log4j.appender.stdout.Target=System.out log4j.appender.stdout.layout=org.apache.log4j.PatternLayout -log4j.appender.stdout.layout.ConversionPattern=%d{yyyy-MM-dd HH:mm:ss} %-5p %c{1}:%L - %m%n \ No newline at end of file +log4j.appender.stdout.layout.ConversionPattern=%d{yyyy-MM-dd HH:mm:ss} %-5p %c{1}:%L - %m%n + +# Change this to set Spark log level +log4j.logger.org.apache.spark=WARN +# Silence akka remoting +log4j.logger.Remoting=WARN +# Ignore messages below warning level from Jetty, because it's a bit verbose +log4j.logger.org.eclipse.jetty=WARN \ No newline at end of file From c5eb72217047e15fea0b8d9f0c46fb4acdae45bc Mon Sep 17 00:00:00 2001 From: Alessia Bardi Date: Fri, 23 Sep 2022 15:47:05 +0200 Subject: [PATCH 182/214] relationships from relatedIdentifier whose target id type is one of the pid type with an authority --- .../raw/AbstractMdRecordToOafMapper.java | 1206 +++++++++-------- .../dhp/oa/graph/raw/OdfToOafMapper.java | 10 +- .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 17 +- 3 files changed, 630 insertions(+), 603 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index a8d09e4a7..bb5472a88 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -15,6 +15,7 @@ import java.net.URL; import java.util.*; import java.util.stream.Collectors; +import eu.dnetlib.dhp.schema.oaf.utils.PidType; import org.apache.commons.lang3.StringUtils; import org.apache.commons.validator.routines.UrlValidator; import org.dom4j.*; @@ -33,603 +34,612 @@ import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; public abstract class AbstractMdRecordToOafMapper { - protected final VocabularyGroup vocs; - - private final boolean invisible; - - private final boolean shouldHashId; - - private final boolean forceOriginalId; - - protected static final String DATACITE_SCHEMA_KERNEL_4 = "http://datacite.org/schema/kernel-4"; - protected static final String DATACITE_SCHEMA_KERNEL_4_SLASH = "http://datacite.org/schema/kernel-4/"; - protected static final String DATACITE_SCHEMA_KERNEL_3 = "http://datacite.org/schema/kernel-3"; - protected static final String DATACITE_SCHEMA_KERNEL_3_SLASH = "http://datacite.org/schema/kernel-3/"; - protected static final Qualifier ORCID_PID_TYPE = qualifier( - ModelConstants.ORCID_PENDING, - ModelConstants.ORCID_CLASSNAME, - DNET_PID_TYPES, DNET_PID_TYPES); - protected static final Qualifier MAG_PID_TYPE = qualifier( - "MAGIdentifier", "Microsoft Academic Graph Identifier", DNET_PID_TYPES, DNET_PID_TYPES); - - protected static final String DEFAULT_TRUST_FOR_VALIDATED_RELS = "0.999"; - - protected static final Map nsContext = new HashMap<>(); - - private static final Logger log = LoggerFactory.getLogger(AbstractMdRecordToOafMapper.class); - - static { - nsContext.put("dr", "http://www.driver-repository.eu/namespace/dr"); - nsContext.put("dri", "http://www.driver-repository.eu/namespace/dri"); - nsContext.put("oaf", "http://namespace.openaire.eu/oaf"); - nsContext.put("oai", "http://www.openarchives.org/OAI/2.0/"); - nsContext.put("prov", "http://www.openarchives.org/OAI/2.0/provenance"); - nsContext.put("dc", "http://purl.org/dc/elements/1.1/"); - nsContext.put("datacite", DATACITE_SCHEMA_KERNEL_3); - } - - protected AbstractMdRecordToOafMapper(final VocabularyGroup vocs, final boolean invisible, - final boolean shouldHashId, final boolean forceOriginalId) { - this.vocs = vocs; - this.invisible = invisible; - this.shouldHashId = shouldHashId; - this.forceOriginalId = forceOriginalId; - } - - protected AbstractMdRecordToOafMapper(final VocabularyGroup vocs, final boolean invisible, - final boolean shouldHashId) { - this.vocs = vocs; - this.invisible = invisible; - this.shouldHashId = shouldHashId; - this.forceOriginalId = false; - } - - public List processMdRecord(final String xml) { - - DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext); - try { - final Document doc = DocumentHelper - .parseText( - xml - .replaceAll(DATACITE_SCHEMA_KERNEL_4, DATACITE_SCHEMA_KERNEL_3) - .replaceAll(DATACITE_SCHEMA_KERNEL_4_SLASH, DATACITE_SCHEMA_KERNEL_3) - .replaceAll(DATACITE_SCHEMA_KERNEL_3_SLASH, DATACITE_SCHEMA_KERNEL_3)); - - final KeyValue collectedFrom = getProvenanceDatasource( - doc, "//oaf:collectedFrom/@id", "//oaf:collectedFrom/@name"); - - if (collectedFrom == null) { - return Lists.newArrayList(); - } - - final KeyValue hostedBy = StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id")) - ? collectedFrom - : getProvenanceDatasource(doc, "//oaf:hostedBy/@id", "//oaf:hostedBy/@name"); - - if (hostedBy == null) { - return Lists.newArrayList(); - } - - final DataInfo info = prepareDataInfo(doc, invisible); - final long lastUpdateTimestamp = new Date().getTime(); - - final List instances = prepareInstances(doc, info, collectedFrom, hostedBy); - - final String type = getResultType(doc, instances); - - return createOafs(doc, type, instances, collectedFrom, info, lastUpdateTimestamp); - } catch (DocumentException e) { - log.error("Error with record:\n" + xml); - return Lists.newArrayList(); - } - } - - protected String getResultType(final Document doc, final List instances) { - final String type = doc.valueOf("//dr:CobjCategory/@type"); - - if (StringUtils.isBlank(type) && vocs.vocabularyExists(ModelConstants.DNET_RESULT_TYPOLOGIES)) { - final String instanceType = instances - .stream() - .map(i -> i.getInstancetype().getClassid()) - .findFirst() - .filter(s -> !UNKNOWN.equalsIgnoreCase(s)) - .orElse("0000"); // Unknown - return Optional - .ofNullable(vocs.getSynonymAsQualifier(ModelConstants.DNET_RESULT_TYPOLOGIES, instanceType)) - .map(Qualifier::getClassid) - .orElse("0000"); - } - - return type; - } - - private KeyValue getProvenanceDatasource(final Document doc, final String xpathId, final String xpathName) { - final String dsId = doc.valueOf(xpathId); - final String dsName = doc.valueOf(xpathName); - - if (StringUtils.isBlank(dsId) || StringUtils.isBlank(dsName)) { - return null; - } - - return keyValue(createOpenaireId(10, dsId, true), dsName); - } - - protected List createOafs( - final Document doc, - final String type, - final List instances, - final KeyValue collectedFrom, - final DataInfo info, - final long lastUpdateTimestamp) { - - final OafEntity entity = createEntity(doc, type, instances, collectedFrom, info, lastUpdateTimestamp); - - final Set originalId = Sets.newHashSet(entity.getOriginalId()); - originalId.add(entity.getId()); - entity.setOriginalId(Lists.newArrayList(originalId)); - - if (!forceOriginalId) { - final String id = IdentifierFactory.createIdentifier(entity, shouldHashId); - if (!id.equals(entity.getId())) { - entity.setId(id); - } - } - - final List oafs = Lists.newArrayList(entity); - - if (!oafs.isEmpty()) { - Set rels = Sets.newHashSet(); - - rels.addAll(addProjectRels(doc, entity)); - rels.addAll(addOtherResultRels(doc, entity)); - rels.addAll(addRelations(doc, entity)); - - oafs.addAll(rels); - } - - return oafs; - } - - private OafEntity createEntity(final Document doc, - final String type, - final List instances, - final KeyValue collectedFrom, - final DataInfo info, - final long lastUpdateTimestamp) { - switch (type.toLowerCase()) { - case "publication": - final Publication p = new Publication(); - populateResultFields(p, doc, instances, collectedFrom, info, lastUpdateTimestamp); - p.setJournal(prepareJournal(doc, info)); - return p; - case "dataset": - final Dataset d = new Dataset(); - populateResultFields(d, doc, instances, collectedFrom, info, lastUpdateTimestamp); - d.setStoragedate(prepareDatasetStorageDate(doc, info)); - d.setDevice(prepareDatasetDevice(doc, info)); - d.setSize(prepareDatasetSize(doc, info)); - d.setVersion(prepareDatasetVersion(doc, info)); - d.setLastmetadataupdate(prepareDatasetLastMetadataUpdate(doc, info)); - d.setMetadataversionnumber(prepareDatasetMetadataVersionNumber(doc, info)); - d.setGeolocation(prepareDatasetGeoLocations(doc, info)); - return d; - case "software": - final Software s = new Software(); - populateResultFields(s, doc, instances, collectedFrom, info, lastUpdateTimestamp); - s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info)); - s.setLicense(prepareSoftwareLicenses(doc, info)); - s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info)); - s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info)); - return s; - case "": - case "otherresearchproducts": - default: - final OtherResearchProduct o = new OtherResearchProduct(); - populateResultFields(o, doc, instances, collectedFrom, info, lastUpdateTimestamp); - o.setContactperson(prepareOtherResearchProductContactPersons(doc, info)); - o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info)); - o.setTool(prepareOtherResearchProductTools(doc, info)); - return o; - } - } - - private List addProjectRels( - final Document doc, - final OafEntity entity) { - - final List res = new ArrayList<>(); - - final String docId = entity.getId(); - - for (final Object o : doc.selectNodes("//oaf:projectid")) { - - final String originalId = ((Node) o).getText(); - - final String validationdDate = ((Node) o).valueOf("@validationDate"); - - if (StringUtils.isNotBlank(originalId)) { - final String projectId = createOpenaireId(40, originalId, true); - - res - .add( - OafMapperUtils - .getRelation( - docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, entity, validationdDate)); - res - .add( - OafMapperUtils - .getRelation(projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, entity, validationdDate)); - } - } - - return res; - } - - private List addRelations(Document doc, OafEntity entity) { - - final List rels = Lists.newArrayList(); - - for (Object o : doc.selectNodes("//oaf:relation")) { - Element element = (Element) o; - - final String target = StringUtils.trim(element.getText()); - final String relType = element.attributeValue("relType"); - final String subRelType = element.attributeValue("subRelType"); - final String relClass = element.attributeValue("relClass"); - - if (StringUtils.isNotBlank(target) && StringUtils.isNotBlank(relType) && StringUtils.isNotBlank(subRelType) - && StringUtils.isNotBlank(relClass)) { - - final String relClassInverse = ModelSupport - .findInverse(ModelSupport.rel(relType, subRelType, relClass)) - .getInverseRelClass(); - final String validationdDate = ((Node) o).valueOf("@validationDate"); - - if (StringUtils.isNotBlank(target)) { - final String targetType = element.attributeValue("targetType"); - if (StringUtils.isNotBlank(targetType)) { - final String targetId = createOpenaireId(targetType, target, true); - rels - .add( - OafMapperUtils - .getRelation( - entity.getId(), targetId, relType, subRelType, relClass, entity, - validationdDate)); - rels - .add( - OafMapperUtils - .getRelation( - targetId, entity.getId(), relType, subRelType, relClassInverse, entity, - validationdDate)); - } - } - } - } - return rels; - } - - protected abstract List addOtherResultRels( - final Document doc, - final OafEntity entity); - - private void populateResultFields( - final Result r, - final Document doc, - final List instances, - final KeyValue collectedFrom, - final DataInfo info, - final long lastUpdateTimestamp) { - r.setDataInfo(info); - r.setLastupdatetimestamp(lastUpdateTimestamp); - r.setId(createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false)); - r.setOriginalId(findOriginalId(doc)); - r.setCollectedfrom(Arrays.asList(collectedFrom)); - r.setPid(IdentifierFactory.getPids(prepareResultPids(doc, info), collectedFrom)); - r.setDateofcollection(doc.valueOf("//dr:dateOfCollection/text()|//dri:dateOfCollection/text()")); - r.setDateoftransformation(doc.valueOf("//dr:dateOfTransformation/text()|//dri:dateOfTransformation/text()")); - r.setExtraInfo(new ArrayList<>()); // NOT PRESENT IN MDSTORES - r.setOaiprovenance(prepareOAIprovenance(doc)); - r.setAuthor(prepareAuthors(doc, info)); - r.setLanguage(prepareLanguages(doc)); - r.setCountry(new ArrayList<>()); // NOT PRESENT IN MDSTORES - r.setSubject(prepareSubjects(doc, info)); - r.setTitle(prepareTitles(doc, info)); - r.setRelevantdate(prepareRelevantDates(doc, info)); - r.setDescription(prepareDescriptions(doc, info)); - r.setDateofacceptance(prepareField(doc, "//oaf:dateAccepted", info)); - r.setPublisher(preparePublisher(doc, info)); - r.setEmbargoenddate(prepareField(doc, "//oaf:embargoenddate", info)); - r.setSource(prepareSources(doc, info)); - r.setFulltext(prepareListFields(doc, "//oaf:fulltext", info)); - r.setFormat(prepareFormats(doc, info)); - r.setContributor(prepareContributors(doc, info)); - r.setResourcetype(prepareResourceType(doc, info)); - r.setCoverage(prepareCoverages(doc, info)); - r.setContext(prepareContexts(doc, info)); - r.setExternalReference(new ArrayList<>()); // NOT PRESENT IN MDSTORES - r - .setProcessingchargeamount(field(doc.valueOf("//oaf:processingchargeamount"), info)); - r - .setProcessingchargecurrency(field(doc.valueOf("//oaf:processingchargeamount/@currency"), info)); - - r.setInstance(instances); - r.setBestaccessright(OafMapperUtils.createBestAccessRights(instances)); - } - - protected abstract List prepareResultPids(Document doc, DataInfo info); - - private List prepareContexts(final Document doc, final DataInfo info) { - final List list = new ArrayList<>(); - for (final Object o : doc.selectNodes("//oaf:concept")) { - final String cid = ((Node) o).valueOf("@id"); - if (StringUtils.isNotBlank(cid)) { - final Context c = new Context(); - c.setId(cid); - c.setDataInfo(Arrays.asList(info)); - list.add(c); - } - } - return list; - } - - protected abstract Qualifier prepareResourceType(Document doc, DataInfo info); - - protected abstract List prepareInstances( - Document doc, - DataInfo info, - KeyValue collectedfrom, - KeyValue hostedby); - - protected abstract List> prepareSources(Document doc, DataInfo info); - - protected abstract List prepareRelevantDates(Document doc, DataInfo info); - - protected abstract List> prepareCoverages(Document doc, DataInfo info); - - protected abstract List> prepareContributors(Document doc, DataInfo info); - - protected abstract List> prepareFormats(Document doc, DataInfo info); - - protected abstract Field preparePublisher(Document doc, DataInfo info); - - protected abstract List> prepareDescriptions(Document doc, DataInfo info); - - protected abstract List prepareTitles(Document doc, DataInfo info); - - protected abstract List prepareSubjects(Document doc, DataInfo info); - - protected abstract Qualifier prepareLanguages(Document doc); - - protected abstract List prepareAuthors(Document doc, DataInfo info); - - protected abstract List> prepareOtherResearchProductTools( - Document doc, - DataInfo info); - - protected abstract List> prepareOtherResearchProductContactGroups( - Document doc, - DataInfo info); - - protected abstract List> prepareOtherResearchProductContactPersons( - Document doc, - DataInfo info); - - protected abstract Qualifier prepareSoftwareProgrammingLanguage(Document doc, DataInfo info); - - protected abstract Field prepareSoftwareCodeRepositoryUrl(Document doc, DataInfo info); - - protected abstract List prepareSoftwareLicenses(Document doc, DataInfo info); - - protected abstract List> prepareSoftwareDocumentationUrls( - Document doc, - DataInfo info); - - protected abstract List prepareDatasetGeoLocations(Document doc, DataInfo info); - - protected abstract Field prepareDatasetMetadataVersionNumber(Document doc, DataInfo info); - - protected abstract Field prepareDatasetLastMetadataUpdate(Document doc, DataInfo info); - - protected abstract Field prepareDatasetVersion(Document doc, DataInfo info); - - protected abstract Field prepareDatasetSize(Document doc, DataInfo info); - - protected abstract Field prepareDatasetDevice(Document doc, DataInfo info); - - protected abstract Field prepareDatasetStorageDate(Document doc, DataInfo info); - - private Journal prepareJournal(final Document doc, final DataInfo info) { - final Node n = doc.selectSingleNode("//oaf:journal"); - if (n != null) { - final String name = n.getText(); - final String issnPrinted = n.valueOf("@issn"); - final String issnOnline = n.valueOf("@eissn"); - final String issnLinking = n.valueOf("@lissn"); - final String ep = n.valueOf("@ep"); - final String iss = n.valueOf("@iss"); - final String sp = n.valueOf("@sp"); - final String vol = n.valueOf("@vol"); - final String edition = n.valueOf("@edition"); - if (StringUtils.isNotBlank(name)) { - return journal(name, issnPrinted, issnOnline, issnLinking, ep, iss, sp, vol, edition, null, null, info); - } - } - return null; - } - - private List findOriginalId(final Document doc) { - final Node n = doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']"); - if (n != null) { - final String id = n.valueOf("./*[local-name()='identifier']"); - if (StringUtils.isNotBlank(id)) { - return Lists.newArrayList(id); - } - } - final List idList = doc - .selectNodes( - "normalize-space(//*[local-name()='header']/*[local-name()='identifier' or local-name()='recordIdentifier']/text())"); - final Set originalIds = Sets.newHashSet(idList); - - if (originalIds.isEmpty()) { - throw new IllegalStateException("missing originalID on " + doc.asXML()); - } - return Lists.newArrayList(originalIds); - } - - protected AccessRight prepareAccessRight(final Node node, final String xpath, final String schemeId) { - final Qualifier qualifier = prepareQualifier(node.valueOf(xpath).trim(), schemeId); - final AccessRight accessRight = new AccessRight(); - accessRight.setClassid(qualifier.getClassid()); - accessRight.setClassname(qualifier.getClassname()); - accessRight.setSchemeid(qualifier.getSchemeid()); - accessRight.setSchemename(qualifier.getSchemename()); - - // TODO set the OAStatus - - return accessRight; - } - - protected Qualifier prepareQualifier(final Node node, final String xpath, final String schemeId) { - return prepareQualifier(node.valueOf(xpath).trim(), schemeId); - } - - protected Qualifier prepareQualifier(final String classId, final String schemeId) { - return vocs.getTermAsQualifier(schemeId, classId); - } - - protected List prepareListStructPropsWithValidQualifier( - final Node node, - final String xpath, - final String xpathClassId, - final String schemeId, - final DataInfo info) { - final List res = new ArrayList<>(); - - for (final Object o : node.selectNodes(xpath)) { - final Node n = (Node) o; - final String classId = n.valueOf(xpathClassId).trim(); - if (vocs.termExists(schemeId, classId)) { - res.add(structuredProperty(n.getText(), vocs.getTermAsQualifier(schemeId, classId), info)); - } - } - return res; - } - - protected List prepareListStructProps( - final Node node, - final String xpath, - final Qualifier qualifier, - final DataInfo info) { - final List res = new ArrayList<>(); - for (final Object o : node.selectNodes(xpath)) { - final Node n = (Node) o; - res.add(structuredProperty(n.getText(), qualifier, info)); - } - return res; - } - - protected List prepareListStructProps( - final Node node, - final String xpath, - final DataInfo info) { - final List res = new ArrayList<>(); - for (final Object o : node.selectNodes(xpath)) { - final Node n = (Node) o; - res - .add( - structuredProperty( - n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"), - n.valueOf("@schemename"), info)); - } - return res; - } - - protected List prepareSubjectList( - final Node node, - final String xpath, - final DataInfo info) { - final List res = new ArrayList<>(); - for (final Object o : node.selectNodes(xpath)) { - final Node n = (Node) o; - res - .add( - subject( - n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"), - n.valueOf("@schemename"), info)); - } - return res; - } - - protected OAIProvenance prepareOAIprovenance(final Document doc) { - final Node n = doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']"); - - if (n == null) { - return null; - } - - final String identifier = n.valueOf("./*[local-name()='identifier']"); - final String baseURL = n.valueOf("./*[local-name()='baseURL']"); - final String metadataNamespace = n.valueOf("./*[local-name()='metadataNamespace']"); - final boolean altered = n.valueOf("@altered").equalsIgnoreCase("true"); - final String datestamp = n.valueOf("./*[local-name()='datestamp']"); - final String harvestDate = n.valueOf("@harvestDate"); - - return oaiIProvenance(identifier, baseURL, metadataNamespace, altered, datestamp, harvestDate); - } - - protected DataInfo prepareDataInfo(final Document doc, final boolean invisible) { - final Node n = doc.selectSingleNode("//oaf:datainfo"); - - if (n == null) { - return dataInfo(false, null, false, invisible, REPOSITORY_PROVENANCE_ACTIONS, "0.9"); - } - - final String paClassId = n.valueOf("./oaf:provenanceaction/@classid"); - final String paClassName = n.valueOf("./oaf:provenanceaction/@classname"); - final String paSchemeId = n.valueOf("./oaf:provenanceaction/@schemeid"); - final String paSchemeName = n.valueOf("./oaf:provenanceaction/@schemename"); - - final boolean deletedbyinference = Boolean.parseBoolean(n.valueOf("./oaf:deletedbyinference")); - final String inferenceprovenance = n.valueOf("./oaf:inferenceprovenance"); - final Boolean inferred = Boolean.parseBoolean(n.valueOf("./oaf:inferred")); - final String trust = n.valueOf("./oaf:trust"); - - return dataInfo( - deletedbyinference, inferenceprovenance, inferred, invisible, - qualifier(paClassId, paClassName, paSchemeId, paSchemeName), trust); - } - - protected Field prepareField(final Node node, final String xpath, final DataInfo info) { - return field(node.valueOf(xpath), info); - } - - protected List> prepareListFields( - final Node node, - final String xpath, - final DataInfo info) { - return listFields(info, prepareListString(node, xpath)); - } - - protected List prepareListString(final Node node, final String xpath) { - final List res = new ArrayList<>(); - for (final Object o : node.selectNodes(xpath)) { - final String s = ((Node) o).getText().trim(); - if (StringUtils.isNotBlank(s)) { - res.add(s); - } - } - return res; - } - - protected Set validateUrl(Collection url) { - UrlValidator urlValidator = UrlValidator.getInstance(); - if (Objects.isNull(url)) { - return new HashSet<>(); - } - return url - .stream() - .filter(u -> urlValidator.isValid(u)) - .collect(Collectors.toCollection(HashSet::new)); - } + protected final VocabularyGroup vocs; + + private final boolean invisible; + + private final boolean shouldHashId; + + private final boolean forceOriginalId; + + protected static final String DATACITE_SCHEMA_KERNEL_4 = "http://datacite.org/schema/kernel-4"; + protected static final String DATACITE_SCHEMA_KERNEL_4_SLASH = "http://datacite.org/schema/kernel-4/"; + protected static final String DATACITE_SCHEMA_KERNEL_3 = "http://datacite.org/schema/kernel-3"; + protected static final String DATACITE_SCHEMA_KERNEL_3_SLASH = "http://datacite.org/schema/kernel-3/"; + protected static final Qualifier ORCID_PID_TYPE = qualifier( + ModelConstants.ORCID_PENDING, + ModelConstants.ORCID_CLASSNAME, + DNET_PID_TYPES, DNET_PID_TYPES); + protected static final Qualifier MAG_PID_TYPE = qualifier( + "MAGIdentifier", "Microsoft Academic Graph Identifier", DNET_PID_TYPES, DNET_PID_TYPES); + + protected static final String DEFAULT_TRUST_FOR_VALIDATED_RELS = "0.999"; + + protected static final Map nsContext = new HashMap<>(); + + private static final Logger log = LoggerFactory.getLogger(AbstractMdRecordToOafMapper.class); + + static { + nsContext.put("dr", "http://www.driver-repository.eu/namespace/dr"); + nsContext.put("dri", "http://www.driver-repository.eu/namespace/dri"); + nsContext.put("oaf", "http://namespace.openaire.eu/oaf"); + nsContext.put("oai", "http://www.openarchives.org/OAI/2.0/"); + nsContext.put("prov", "http://www.openarchives.org/OAI/2.0/provenance"); + nsContext.put("dc", "http://purl.org/dc/elements/1.1/"); + nsContext.put("datacite", DATACITE_SCHEMA_KERNEL_3); + } + + protected static final Set pidTypeWithAuthority = new HashSet<>(); + + static { + pidTypeWithAuthority.addAll(IdentifierFactory.PID_AUTHORITY.keySet().stream() + .map(PidType::toString) + .map(String::toLowerCase) + .collect(Collectors.toCollection(HashSet::new))); + } + + protected AbstractMdRecordToOafMapper(final VocabularyGroup vocs, final boolean invisible, + final boolean shouldHashId, final boolean forceOriginalId) { + this.vocs = vocs; + this.invisible = invisible; + this.shouldHashId = shouldHashId; + this.forceOriginalId = forceOriginalId; + } + + protected AbstractMdRecordToOafMapper(final VocabularyGroup vocs, final boolean invisible, + final boolean shouldHashId) { + this.vocs = vocs; + this.invisible = invisible; + this.shouldHashId = shouldHashId; + this.forceOriginalId = false; + } + + public List processMdRecord(final String xml) { + + DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext); + try { + final Document doc = DocumentHelper + .parseText( + xml + .replaceAll(DATACITE_SCHEMA_KERNEL_4, DATACITE_SCHEMA_KERNEL_3) + .replaceAll(DATACITE_SCHEMA_KERNEL_4_SLASH, DATACITE_SCHEMA_KERNEL_3) + .replaceAll(DATACITE_SCHEMA_KERNEL_3_SLASH, DATACITE_SCHEMA_KERNEL_3)); + + final KeyValue collectedFrom = getProvenanceDatasource( + doc, "//oaf:collectedFrom/@id", "//oaf:collectedFrom/@name"); + + if (collectedFrom == null) { + return Lists.newArrayList(); + } + + final KeyValue hostedBy = StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id")) + ? collectedFrom + : getProvenanceDatasource(doc, "//oaf:hostedBy/@id", "//oaf:hostedBy/@name"); + + if (hostedBy == null) { + return Lists.newArrayList(); + } + + final DataInfo info = prepareDataInfo(doc, invisible); + final long lastUpdateTimestamp = new Date().getTime(); + + final List instances = prepareInstances(doc, info, collectedFrom, hostedBy); + + final String type = getResultType(doc, instances); + + return createOafs(doc, type, instances, collectedFrom, info, lastUpdateTimestamp); + } catch (DocumentException e) { + log.error("Error with record:\n" + xml); + return Lists.newArrayList(); + } + } + + protected String getResultType(final Document doc, final List instances) { + final String type = doc.valueOf("//dr:CobjCategory/@type"); + + if (StringUtils.isBlank(type) && vocs.vocabularyExists(ModelConstants.DNET_RESULT_TYPOLOGIES)) { + final String instanceType = instances + .stream() + .map(i -> i.getInstancetype().getClassid()) + .findFirst() + .filter(s -> !UNKNOWN.equalsIgnoreCase(s)) + .orElse("0000"); // Unknown + return Optional + .ofNullable(vocs.getSynonymAsQualifier(ModelConstants.DNET_RESULT_TYPOLOGIES, instanceType)) + .map(Qualifier::getClassid) + .orElse("0000"); + } + + return type; + } + + private KeyValue getProvenanceDatasource(final Document doc, final String xpathId, final String xpathName) { + final String dsId = doc.valueOf(xpathId); + final String dsName = doc.valueOf(xpathName); + + if (StringUtils.isBlank(dsId) || StringUtils.isBlank(dsName)) { + return null; + } + + return keyValue(createOpenaireId(10, dsId, true), dsName); + } + + protected List createOafs( + final Document doc, + final String type, + final List instances, + final KeyValue collectedFrom, + final DataInfo info, + final long lastUpdateTimestamp) { + + final OafEntity entity = createEntity(doc, type, instances, collectedFrom, info, lastUpdateTimestamp); + + final Set originalId = Sets.newHashSet(entity.getOriginalId()); + originalId.add(entity.getId()); + entity.setOriginalId(Lists.newArrayList(originalId)); + + if (!forceOriginalId) { + final String id = IdentifierFactory.createIdentifier(entity, shouldHashId); + if (!id.equals(entity.getId())) { + entity.setId(id); + } + } + + final List oafs = Lists.newArrayList(entity); + + if (!oafs.isEmpty()) { + Set rels = Sets.newHashSet(); + + rels.addAll(addProjectRels(doc, entity)); + rels.addAll(addOtherResultRels(doc, entity)); + rels.addAll(addRelations(doc, entity)); + + oafs.addAll(rels); + } + + return oafs; + } + + private OafEntity createEntity(final Document doc, + final String type, + final List instances, + final KeyValue collectedFrom, + final DataInfo info, + final long lastUpdateTimestamp) { + switch (type.toLowerCase()) { + case "publication": + final Publication p = new Publication(); + populateResultFields(p, doc, instances, collectedFrom, info, lastUpdateTimestamp); + p.setJournal(prepareJournal(doc, info)); + return p; + case "dataset": + final Dataset d = new Dataset(); + populateResultFields(d, doc, instances, collectedFrom, info, lastUpdateTimestamp); + d.setStoragedate(prepareDatasetStorageDate(doc, info)); + d.setDevice(prepareDatasetDevice(doc, info)); + d.setSize(prepareDatasetSize(doc, info)); + d.setVersion(prepareDatasetVersion(doc, info)); + d.setLastmetadataupdate(prepareDatasetLastMetadataUpdate(doc, info)); + d.setMetadataversionnumber(prepareDatasetMetadataVersionNumber(doc, info)); + d.setGeolocation(prepareDatasetGeoLocations(doc, info)); + return d; + case "software": + final Software s = new Software(); + populateResultFields(s, doc, instances, collectedFrom, info, lastUpdateTimestamp); + s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info)); + s.setLicense(prepareSoftwareLicenses(doc, info)); + s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info)); + s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info)); + return s; + case "": + case "otherresearchproducts": + default: + final OtherResearchProduct o = new OtherResearchProduct(); + populateResultFields(o, doc, instances, collectedFrom, info, lastUpdateTimestamp); + o.setContactperson(prepareOtherResearchProductContactPersons(doc, info)); + o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info)); + o.setTool(prepareOtherResearchProductTools(doc, info)); + return o; + } + } + + private List addProjectRels( + final Document doc, + final OafEntity entity) { + + final List res = new ArrayList<>(); + + final String docId = entity.getId(); + + for (final Object o : doc.selectNodes("//oaf:projectid")) { + + final String originalId = ((Node) o).getText(); + + final String validationdDate = ((Node) o).valueOf("@validationDate"); + + if (StringUtils.isNotBlank(originalId)) { + final String projectId = createOpenaireId(40, originalId, true); + + res + .add( + OafMapperUtils + .getRelation( + docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, entity, validationdDate)); + res + .add( + OafMapperUtils + .getRelation(projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, entity, validationdDate)); + } + } + + return res; + } + + private List addRelations(Document doc, OafEntity entity) { + + final List rels = Lists.newArrayList(); + + for (Object o : doc.selectNodes("//oaf:relation")) { + Element element = (Element) o; + + final String target = StringUtils.trim(element.getText()); + final String relType = element.attributeValue("relType"); + final String subRelType = element.attributeValue("subRelType"); + final String relClass = element.attributeValue("relClass"); + + if (StringUtils.isNotBlank(target) && StringUtils.isNotBlank(relType) && StringUtils.isNotBlank(subRelType) + && StringUtils.isNotBlank(relClass)) { + + final String relClassInverse = ModelSupport + .findInverse(ModelSupport.rel(relType, subRelType, relClass)) + .getInverseRelClass(); + final String validationdDate = ((Node) o).valueOf("@validationDate"); + + if (StringUtils.isNotBlank(target)) { + final String targetType = element.attributeValue("targetType"); + if (StringUtils.isNotBlank(targetType)) { + final String targetId = createOpenaireId(targetType, target, true); + rels + .add( + OafMapperUtils + .getRelation( + entity.getId(), targetId, relType, subRelType, relClass, entity, + validationdDate)); + rels + .add( + OafMapperUtils + .getRelation( + targetId, entity.getId(), relType, subRelType, relClassInverse, entity, + validationdDate)); + } + } + } + } + return rels; + } + + protected abstract List addOtherResultRels( + final Document doc, + final OafEntity entity); + + private void populateResultFields( + final Result r, + final Document doc, + final List instances, + final KeyValue collectedFrom, + final DataInfo info, + final long lastUpdateTimestamp) { + r.setDataInfo(info); + r.setLastupdatetimestamp(lastUpdateTimestamp); + r.setId(createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false)); + r.setOriginalId(findOriginalId(doc)); + r.setCollectedfrom(Arrays.asList(collectedFrom)); + r.setPid(IdentifierFactory.getPids(prepareResultPids(doc, info), collectedFrom)); + r.setDateofcollection(doc.valueOf("//dr:dateOfCollection/text()|//dri:dateOfCollection/text()")); + r.setDateoftransformation(doc.valueOf("//dr:dateOfTransformation/text()|//dri:dateOfTransformation/text()")); + r.setExtraInfo(new ArrayList<>()); // NOT PRESENT IN MDSTORES + r.setOaiprovenance(prepareOAIprovenance(doc)); + r.setAuthor(prepareAuthors(doc, info)); + r.setLanguage(prepareLanguages(doc)); + r.setCountry(new ArrayList<>()); // NOT PRESENT IN MDSTORES + r.setSubject(prepareSubjects(doc, info)); + r.setTitle(prepareTitles(doc, info)); + r.setRelevantdate(prepareRelevantDates(doc, info)); + r.setDescription(prepareDescriptions(doc, info)); + r.setDateofacceptance(prepareField(doc, "//oaf:dateAccepted", info)); + r.setPublisher(preparePublisher(doc, info)); + r.setEmbargoenddate(prepareField(doc, "//oaf:embargoenddate", info)); + r.setSource(prepareSources(doc, info)); + r.setFulltext(prepareListFields(doc, "//oaf:fulltext", info)); + r.setFormat(prepareFormats(doc, info)); + r.setContributor(prepareContributors(doc, info)); + r.setResourcetype(prepareResourceType(doc, info)); + r.setCoverage(prepareCoverages(doc, info)); + r.setContext(prepareContexts(doc, info)); + r.setExternalReference(new ArrayList<>()); // NOT PRESENT IN MDSTORES + r + .setProcessingchargeamount(field(doc.valueOf("//oaf:processingchargeamount"), info)); + r + .setProcessingchargecurrency(field(doc.valueOf("//oaf:processingchargeamount/@currency"), info)); + + r.setInstance(instances); + r.setBestaccessright(OafMapperUtils.createBestAccessRights(instances)); + } + + protected abstract List prepareResultPids(Document doc, DataInfo info); + + private List prepareContexts(final Document doc, final DataInfo info) { + final List list = new ArrayList<>(); + for (final Object o : doc.selectNodes("//oaf:concept")) { + final String cid = ((Node) o).valueOf("@id"); + if (StringUtils.isNotBlank(cid)) { + final Context c = new Context(); + c.setId(cid); + c.setDataInfo(Arrays.asList(info)); + list.add(c); + } + } + return list; + } + + protected abstract Qualifier prepareResourceType(Document doc, DataInfo info); + + protected abstract List prepareInstances( + Document doc, + DataInfo info, + KeyValue collectedfrom, + KeyValue hostedby); + + protected abstract List> prepareSources(Document doc, DataInfo info); + + protected abstract List prepareRelevantDates(Document doc, DataInfo info); + + protected abstract List> prepareCoverages(Document doc, DataInfo info); + + protected abstract List> prepareContributors(Document doc, DataInfo info); + + protected abstract List> prepareFormats(Document doc, DataInfo info); + + protected abstract Field preparePublisher(Document doc, DataInfo info); + + protected abstract List> prepareDescriptions(Document doc, DataInfo info); + + protected abstract List prepareTitles(Document doc, DataInfo info); + + protected abstract List prepareSubjects(Document doc, DataInfo info); + + protected abstract Qualifier prepareLanguages(Document doc); + + protected abstract List prepareAuthors(Document doc, DataInfo info); + + protected abstract List> prepareOtherResearchProductTools( + Document doc, + DataInfo info); + + protected abstract List> prepareOtherResearchProductContactGroups( + Document doc, + DataInfo info); + + protected abstract List> prepareOtherResearchProductContactPersons( + Document doc, + DataInfo info); + + protected abstract Qualifier prepareSoftwareProgrammingLanguage(Document doc, DataInfo info); + + protected abstract Field prepareSoftwareCodeRepositoryUrl(Document doc, DataInfo info); + + protected abstract List prepareSoftwareLicenses(Document doc, DataInfo info); + + protected abstract List> prepareSoftwareDocumentationUrls( + Document doc, + DataInfo info); + + protected abstract List prepareDatasetGeoLocations(Document doc, DataInfo info); + + protected abstract Field prepareDatasetMetadataVersionNumber(Document doc, DataInfo info); + + protected abstract Field prepareDatasetLastMetadataUpdate(Document doc, DataInfo info); + + protected abstract Field prepareDatasetVersion(Document doc, DataInfo info); + + protected abstract Field prepareDatasetSize(Document doc, DataInfo info); + + protected abstract Field prepareDatasetDevice(Document doc, DataInfo info); + + protected abstract Field prepareDatasetStorageDate(Document doc, DataInfo info); + + private Journal prepareJournal(final Document doc, final DataInfo info) { + final Node n = doc.selectSingleNode("//oaf:journal"); + if (n != null) { + final String name = n.getText(); + final String issnPrinted = n.valueOf("@issn"); + final String issnOnline = n.valueOf("@eissn"); + final String issnLinking = n.valueOf("@lissn"); + final String ep = n.valueOf("@ep"); + final String iss = n.valueOf("@iss"); + final String sp = n.valueOf("@sp"); + final String vol = n.valueOf("@vol"); + final String edition = n.valueOf("@edition"); + if (StringUtils.isNotBlank(name)) { + return journal(name, issnPrinted, issnOnline, issnLinking, ep, iss, sp, vol, edition, null, null, info); + } + } + return null; + } + + private List findOriginalId(final Document doc) { + final Node n = doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']"); + if (n != null) { + final String id = n.valueOf("./*[local-name()='identifier']"); + if (StringUtils.isNotBlank(id)) { + return Lists.newArrayList(id); + } + } + final List idList = doc + .selectNodes( + "normalize-space(//*[local-name()='header']/*[local-name()='identifier' or local-name()='recordIdentifier']/text())"); + final Set originalIds = Sets.newHashSet(idList); + + if (originalIds.isEmpty()) { + throw new IllegalStateException("missing originalID on " + doc.asXML()); + } + return Lists.newArrayList(originalIds); + } + + protected AccessRight prepareAccessRight(final Node node, final String xpath, final String schemeId) { + final Qualifier qualifier = prepareQualifier(node.valueOf(xpath).trim(), schemeId); + final AccessRight accessRight = new AccessRight(); + accessRight.setClassid(qualifier.getClassid()); + accessRight.setClassname(qualifier.getClassname()); + accessRight.setSchemeid(qualifier.getSchemeid()); + accessRight.setSchemename(qualifier.getSchemename()); + + // TODO set the OAStatus + + return accessRight; + } + + protected Qualifier prepareQualifier(final Node node, final String xpath, final String schemeId) { + return prepareQualifier(node.valueOf(xpath).trim(), schemeId); + } + + protected Qualifier prepareQualifier(final String classId, final String schemeId) { + return vocs.getTermAsQualifier(schemeId, classId); + } + + protected List prepareListStructPropsWithValidQualifier( + final Node node, + final String xpath, + final String xpathClassId, + final String schemeId, + final DataInfo info) { + final List res = new ArrayList<>(); + + for (final Object o : node.selectNodes(xpath)) { + final Node n = (Node) o; + final String classId = n.valueOf(xpathClassId).trim(); + if (vocs.termExists(schemeId, classId)) { + res.add(structuredProperty(n.getText(), vocs.getTermAsQualifier(schemeId, classId), info)); + } + } + return res; + } + + protected List prepareListStructProps( + final Node node, + final String xpath, + final Qualifier qualifier, + final DataInfo info) { + final List res = new ArrayList<>(); + for (final Object o : node.selectNodes(xpath)) { + final Node n = (Node) o; + res.add(structuredProperty(n.getText(), qualifier, info)); + } + return res; + } + + protected List prepareListStructProps( + final Node node, + final String xpath, + final DataInfo info) { + final List res = new ArrayList<>(); + for (final Object o : node.selectNodes(xpath)) { + final Node n = (Node) o; + res + .add( + structuredProperty( + n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"), + n.valueOf("@schemename"), info)); + } + return res; + } + + protected List prepareSubjectList( + final Node node, + final String xpath, + final DataInfo info) { + final List res = new ArrayList<>(); + for (final Object o : node.selectNodes(xpath)) { + final Node n = (Node) o; + res + .add( + subject( + n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"), + n.valueOf("@schemename"), info)); + } + return res; + } + + protected OAIProvenance prepareOAIprovenance(final Document doc) { + final Node n = doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']"); + + if (n == null) { + return null; + } + + final String identifier = n.valueOf("./*[local-name()='identifier']"); + final String baseURL = n.valueOf("./*[local-name()='baseURL']"); + final String metadataNamespace = n.valueOf("./*[local-name()='metadataNamespace']"); + final boolean altered = n.valueOf("@altered").equalsIgnoreCase("true"); + final String datestamp = n.valueOf("./*[local-name()='datestamp']"); + final String harvestDate = n.valueOf("@harvestDate"); + + return oaiIProvenance(identifier, baseURL, metadataNamespace, altered, datestamp, harvestDate); + } + + protected DataInfo prepareDataInfo(final Document doc, final boolean invisible) { + final Node n = doc.selectSingleNode("//oaf:datainfo"); + + if (n == null) { + return dataInfo(false, null, false, invisible, REPOSITORY_PROVENANCE_ACTIONS, "0.9"); + } + + final String paClassId = n.valueOf("./oaf:provenanceaction/@classid"); + final String paClassName = n.valueOf("./oaf:provenanceaction/@classname"); + final String paSchemeId = n.valueOf("./oaf:provenanceaction/@schemeid"); + final String paSchemeName = n.valueOf("./oaf:provenanceaction/@schemename"); + + final boolean deletedbyinference = Boolean.parseBoolean(n.valueOf("./oaf:deletedbyinference")); + final String inferenceprovenance = n.valueOf("./oaf:inferenceprovenance"); + final Boolean inferred = Boolean.parseBoolean(n.valueOf("./oaf:inferred")); + final String trust = n.valueOf("./oaf:trust"); + + return dataInfo( + deletedbyinference, inferenceprovenance, inferred, invisible, + qualifier(paClassId, paClassName, paSchemeId, paSchemeName), trust); + } + + protected Field prepareField(final Node node, final String xpath, final DataInfo info) { + return field(node.valueOf(xpath), info); + } + + protected List> prepareListFields( + final Node node, + final String xpath, + final DataInfo info) { + return listFields(info, prepareListString(node, xpath)); + } + + protected List prepareListString(final Node node, final String xpath) { + final List res = new ArrayList<>(); + for (final Object o : node.selectNodes(xpath)) { + final String s = ((Node) o).getText().trim(); + if (StringUtils.isNotBlank(s)) { + res.add(s); + } + } + return res; + } + + protected Set validateUrl(Collection url) { + UrlValidator urlValidator = UrlValidator.getInstance(); + if (Objects.isNull(url)) { + return new HashSet<>(); + } + return url + .stream() + .filter(u -> urlValidator.isValid(u)) + .collect(Collectors.toCollection(HashSet::new)); + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java index fc063a242..304ec8f99 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java @@ -457,10 +457,12 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { protected String guessRelatedIdentifier(final String idType, final String value) { if (StringUtils.isBlank(idType) || StringUtils.isBlank(value)) return null; - if (idType.equalsIgnoreCase("OPENAIRE")) { - return createOpenaireId(50, value, false); - } else - return null; + if (idType.equalsIgnoreCase("OPENAIRE")) return createOpenaireId(50, value, false); + if(pidTypeWithAuthority.contains(idType.toLowerCase())){ + return IdentifierFactory.idFromPid("50", idType, value, true); + } + return null; + } @Override diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index fbfbf5af8..32b23e42f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -933,7 +933,7 @@ class MappersTest { System.out.println("***************"); System.out.println(new ObjectMapper().writeValueAsString(list)); System.out.println("***************"); - assertEquals(3, list.size()); + assertEquals(7, list.size()); final OtherResearchProduct p = (OtherResearchProduct) list.get(0); assertValidId(p.getId()); assertValidId(p.getCollectedfrom().get(0).getKey()); @@ -941,6 +941,21 @@ class MappersTest { assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue())); assertEquals("w3id", (p.getPid().get(0).getQualifier().getClassid())); assertEquals("https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca", (p.getPid().get(0).getValue())); + + assertEquals(1, list.stream().filter(o -> o instanceof OtherResearchProduct).count()); + assertEquals(6, list.stream().filter(o -> o instanceof Relation).count()); + + for(Oaf oaf : list){ + if(oaf instanceof Relation){ + String source = ((Relation) oaf).getSource(); + String target = ((Relation) oaf).getTarget(); + assertNotEquals(source, target); + assertTrue(source.equals(p.getId()) || target.equals(p.getId())); + assertNotNull(((Relation) oaf).getSubRelType()); + assertNotNull( ((Relation) oaf).getRelClass()); + assertNotNull(((Relation) oaf).getRelType()); + } + } } @Test From 55da4d871509f5f1e71c5939298d49eac9d9d92b Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 23 Sep 2022 16:02:19 +0200 Subject: [PATCH 183/214] [BulkTagging] modifying code to represent constraints horizontally on all the results. Added subject to the set of field used to express the constraint. Modified resorces to test the new approach. Modified test calss --- .../dhp/bulktag/community/Community.java | 10 ++ .../community/CommunityConfiguration.java | 14 +++ .../CommunityConfigurationFactory.java | 12 ++ .../dhp/bulktag/community/Constraint.java | 9 ++ .../dhp/bulktag/community/ResultTagger.java | 107 +++++++----------- .../bulktag/community/TaggingConstants.java | 2 + .../dnetlib/dhp/bulktag/BulkTagJobTest.java | 37 ++++-- .../communityconfiguration/tagging_conf.xml | 5 +- .../dataset_10.json | 10 ++ .../dataset_10.json.gz | Bin 6883 -> 0 bytes 10 files changed, 134 insertions(+), 72 deletions(-) create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/update_datasourcewithconstraints/dataset_10.json delete mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/update_datasourcewithconstraints/dataset_10.json.gz diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Community.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Community.java index 8e76b5778..c5feb8d3f 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Community.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Community.java @@ -6,6 +6,7 @@ import java.util.ArrayList; import java.util.List; import com.google.gson.Gson; +import org.apache.avro.generic.GenericData; /** Created by miriam on 01/08/2018. */ public class Community implements Serializable { @@ -14,6 +15,7 @@ public class Community implements Serializable { private List subjects = new ArrayList<>(); private List providers = new ArrayList<>(); private List zenodoCommunities = new ArrayList<>(); + private SelectionConstraints constraints = new SelectionConstraints(); public String toJson() { final Gson g = new Gson(); @@ -57,4 +59,12 @@ public class Community implements Serializable { public void setZenodoCommunities(List zenodoCommunities) { this.zenodoCommunities = zenodoCommunities; } + + public SelectionConstraints getConstraints() { + return constraints; + } + + public void setConstraints(SelectionConstraints constraints) { + this.constraints = constraints; + } } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfiguration.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfiguration.java index 5d92f5ab6..8e34ccebf 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfiguration.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfiguration.java @@ -24,6 +24,8 @@ public class CommunityConfiguration implements Serializable { private Map>> datasourceMap = new HashMap<>(); // map zenodocommunityid -> communityid private Map>> zenodocommunityMap = new HashMap<>(); + // map communityid -> selectionconstraints + private Map selectionConstraintsMap = new HashMap<>(); public Map>> getSubjectMap() { return subjectMap; @@ -51,6 +53,14 @@ public class CommunityConfiguration implements Serializable { this.zenodocommunityMap = zenodocommunityMap; } + public Map getSelectionConstraintsMap() { + return selectionConstraintsMap; + } + + public void setSelectionConstraintsMap(Map selectionConstraintsMap) { + this.selectionConstraintsMap = selectionConstraintsMap; + } + CommunityConfiguration(final Map communities) { this.communities = communities; init(); @@ -67,6 +77,9 @@ public class CommunityConfiguration implements Serializable { if (zenodocommunityMap == null) { zenodocommunityMap = Maps.newHashMap(); } + if(selectionConstraintsMap == null){ + selectionConstraintsMap = Maps.newHashMap(); + } for (Community c : getCommunities().values()) { // get subjects @@ -87,6 +100,7 @@ public class CommunityConfiguration implements Serializable { new Pair<>(id, zc.getSelCriteria()), zenodocommunityMap); } + selectionConstraintsMap.put(id, c.getConstraints()); } } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfigurationFactory.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfigurationFactory.java index 822d35078..7a43ca476 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfigurationFactory.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfigurationFactory.java @@ -85,9 +85,21 @@ public class CommunityConfigurationFactory { c.setSubjects(parseSubjects(node)); c.setProviders(parseDatasources(node)); c.setZenodoCommunities(parseZenodoCommunities(node)); + c.setConstraints(parseConstrains(node)); return c; } + private static SelectionConstraints parseConstrains(Node node) { + Node aconstraints = node.selectSingleNode("./advancedConstraints"); + if(aconstraints == null){ + return null; + } + SelectionConstraints selectionConstraints = new Gson().fromJson(aconstraints.getText(), SelectionConstraints.class); + + selectionConstraints.setSelection(resolver); + return selectionConstraints; + } + private static List parseSubjects(final Node node) { final List subjects = Lists.newArrayList(); diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Constraint.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Constraint.java index 9002e718f..ed58cc14d 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Constraint.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Constraint.java @@ -11,6 +11,7 @@ public class Constraint implements Serializable { private String verb; private String field; private String value; +// private String element; private Selection selection; public String getVerb() { @@ -50,4 +51,12 @@ public class Constraint implements Serializable { public boolean verifyCriteria(String metadata) { return selection.apply(metadata); } + +// public String getElement() { +// return element; +// } +// +// public void setElement(String element) { +// this.element = element; +// } } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java index 71a2b3525..ccb69a97d 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java @@ -9,6 +9,9 @@ import java.util.*; import java.util.stream.Collectors; import java.util.stream.Stream; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; import org.apache.commons.lang3.StringUtils; import com.google.gson.Gson; @@ -95,13 +98,6 @@ public class ResultTagger implements Serializable { } -// result -// .getInstance() -// .stream() -// .map(i -> new Pair<>(i.getCollectedfrom().getKey(), i.getHostedby().getKey())) -// .flatMap(p -> Stream.of(p.getFst(), p.getSnd())) -// .map(s -> StringUtils.substringAfter(s, "|")) -// .collect(Collectors.toCollection(HashSet::new)) tmp .forEach( dsId -> datasources @@ -135,6 +131,19 @@ public class ResultTagger implements Serializable { communities.addAll(czenodo); + /* Tagging for Advanced Constraints */ + final Set aconstraints = new HashSet<>(); + + conf.getSelectionConstraintsMap().keySet() + .forEach(communityId -> { + if(conf.getSelectionConstraintsMap().get(communityId) != null && + conf.getSelectionConstraintsMap().get(communityId) + .getCriteria().stream().anyMatch(crit -> crit.verifyCriteria(param))) + aconstraints.add(communityId); + }); + + communities.addAll(aconstraints); + clearContext(result); /* Verify if there is something to bulktag */ @@ -152,30 +161,24 @@ public class ResultTagger implements Serializable { dataInfoList = new ArrayList<>(); c.setDataInfo(dataInfoList); } - if (subjects.contains(c.getId())) + if (subjects.contains(c)) dataInfoList - .add( - getDataInfo( - BULKTAG_DATA_INFO_TYPE, - CLASS_ID_SUBJECT, - CLASS_NAME_BULKTAG_SUBJECT, - TAGGING_TRUST)); - if (datasources.contains(c.getId())) + .add(OafMapperUtils.dataInfo(false, BULKTAG_DATA_INFO_TYPE, true, false, + OafMapperUtils.qualifier(CLASS_ID_SUBJECT, CLASS_NAME_BULKTAG_SUBJECT, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), TAGGING_TRUST)); + if (datasources.contains(c)) dataInfoList - .add( - getDataInfo( - BULKTAG_DATA_INFO_TYPE, - CLASS_ID_DATASOURCE, - CLASS_NAME_BULKTAG_DATASOURCE, - TAGGING_TRUST)); - if (czenodo.contains(c.getId())) + .add(OafMapperUtils.dataInfo(false, BULKTAG_DATA_INFO_TYPE, true, false, + OafMapperUtils.qualifier(CLASS_ID_DATASOURCE, CLASS_NAME_BULKTAG_DATASOURCE, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), TAGGING_TRUST)); + if (czenodo.contains(c)) dataInfoList - .add( - getDataInfo( - BULKTAG_DATA_INFO_TYPE, - CLASS_ID_CZENODO, - CLASS_NAME_BULKTAG_ZENODO, - TAGGING_TRUST)); + .add(OafMapperUtils.dataInfo(false, BULKTAG_DATA_INFO_TYPE, true, false, + OafMapperUtils.qualifier(CLASS_ID_CZENODO, CLASS_NAME_BULKTAG_ZENODO, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), TAGGING_TRUST)); + if (aconstraints.contains(c)) + dataInfoList + .add( + OafMapperUtils.dataInfo(false, BULKTAG_DATA_INFO_TYPE, true, false, + OafMapperUtils.qualifier(CLASS_ID_ADVANCED_CONSTRAINT, CLASS_NAME_BULKTAG_ADVANCED_CONSTRAINT, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), TAGGING_TRUST)); + } }); @@ -195,28 +198,22 @@ public class ResultTagger implements Serializable { List dataInfoList = new ArrayList<>(); if (subjects.contains(c)) dataInfoList - .add( - getDataInfo( - BULKTAG_DATA_INFO_TYPE, - CLASS_ID_SUBJECT, - CLASS_NAME_BULKTAG_SUBJECT, - TAGGING_TRUST)); + .add(OafMapperUtils.dataInfo(false, BULKTAG_DATA_INFO_TYPE, true, false, + OafMapperUtils.qualifier(CLASS_ID_SUBJECT, CLASS_NAME_BULKTAG_SUBJECT, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), TAGGING_TRUST)); if (datasources.contains(c)) dataInfoList - .add( - getDataInfo( - BULKTAG_DATA_INFO_TYPE, - CLASS_ID_DATASOURCE, - CLASS_NAME_BULKTAG_DATASOURCE, - TAGGING_TRUST)); + .add(OafMapperUtils.dataInfo(false, BULKTAG_DATA_INFO_TYPE, true, false, + OafMapperUtils.qualifier(CLASS_ID_DATASOURCE, CLASS_NAME_BULKTAG_DATASOURCE, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), TAGGING_TRUST)); if (czenodo.contains(c)) dataInfoList - .add( - getDataInfo( - BULKTAG_DATA_INFO_TYPE, - CLASS_ID_CZENODO, - CLASS_NAME_BULKTAG_ZENODO, - TAGGING_TRUST)); + .add(OafMapperUtils.dataInfo(false, BULKTAG_DATA_INFO_TYPE, true, false, + OafMapperUtils.qualifier(CLASS_ID_CZENODO, CLASS_NAME_BULKTAG_ZENODO, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), TAGGING_TRUST)); + if (aconstraints.contains(c)) + dataInfoList + .add( + OafMapperUtils.dataInfo(false, BULKTAG_DATA_INFO_TYPE, true, false, + OafMapperUtils.qualifier(CLASS_ID_ADVANCED_CONSTRAINT, CLASS_NAME_BULKTAG_ADVANCED_CONSTRAINT, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), TAGGING_TRUST)); + context.setDataInfo(dataInfoList); return context; }) @@ -226,22 +223,4 @@ public class ResultTagger implements Serializable { return result; } - public static DataInfo getDataInfo( - String inference_provenance, String inference_class_id, String inference_class_name, String trust) { - DataInfo di = new DataInfo(); - di.setInferred(true); - di.setInferenceprovenance(inference_provenance); - di.setProvenanceaction(getQualifier(inference_class_id, inference_class_name)); - di.setTrust(trust); - return di; - } - - public static Qualifier getQualifier(String inference_class_id, String inference_class_name) { - Qualifier pa = new Qualifier(); - pa.setClassid(inference_class_id); - pa.setClassname(inference_class_name); - pa.setSchemeid(DNET_PROVENANCE_ACTIONS); - pa.setSchemename(DNET_PROVENANCE_ACTIONS); - return pa; - } } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/TaggingConstants.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/TaggingConstants.java index 8274e26c9..aea21f8e5 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/TaggingConstants.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/TaggingConstants.java @@ -11,12 +11,14 @@ public class TaggingConstants { public static final String CLASS_ID_SUBJECT = "community:subject"; public static final String CLASS_ID_DATASOURCE = "community:datasource"; public static final String CLASS_ID_CZENODO = "community:zenodocommunity"; + public static final String CLASS_ID_ADVANCED_CONSTRAINT = "community:advconstraint"; public static final String ZENODO_COMMUNITY_INDICATOR = "zenodo.org/communities/"; public static final String CLASS_NAME_BULKTAG_SUBJECT = "Bulktagging for Community - Subject"; public static final String CLASS_NAME_BULKTAG_DATASOURCE = "Bulktagging for Community - Datasource"; public static final String CLASS_NAME_BULKTAG_ZENODO = "Bulktagging for Community - Zenodo"; + public static final String CLASS_NAME_BULKTAG_ADVANCED_CONSTRAINT = "Bulktagging for Community - Advanced Constraints"; public static final String TAGGING_TRUST = "0.8"; } diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java index 07299f01a..0212f4a49 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java @@ -6,7 +6,16 @@ import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.ZENODO_COMMUNITY import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; +import java.util.ArrayList; +import java.util.HashMap; +import java.util.List; +import java.util.Map; +import com.google.gson.Gson; +import com.jayway.jsonpath.DocumentContext; +import com.jayway.jsonpath.JsonPath; +import eu.dnetlib.dhp.bulktag.community.ProtoMap; +import eu.dnetlib.dhp.schema.oaf.*; import org.apache.commons.io.FileUtils; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; @@ -24,11 +33,6 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.schema.oaf.Dataset; -import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.Software; - public class BulkTagJobTest { private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); @@ -39,7 +43,8 @@ public class BulkTagJobTest { + " \"title\" : \"$['title'][*]['value']\"," + " \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\"," + " \"contributor\" : \"$['contributor'][*]['value']\"," - + " \"description\" : \"$['description'][*]['value']\"}"; + + " \"description\" : \"$['description'][*]['value']\", " + +" \"subject\" :\"$['subject'][*]['value']\" }"; private static SparkSession spark; @@ -763,10 +768,28 @@ public class BulkTagJobTest { org.apache.spark.sql.Dataset idExplodeCommunity = spark.sql(query); idExplodeCommunity.show(false); - Assertions.assertEquals(3, idExplodeCommunity.count()); + Assertions.assertEquals(4, idExplodeCommunity.count()); Assertions .assertEquals( 3, idExplodeCommunity.filter("provenance = 'community:datasource'").count()); + Assertions + .assertEquals( + 1, idExplodeCommunity.filter("provenance = 'community:advconstraint'").count()); } + +// @Test +// void test1(){ +// ProtoMap params = new Gson().fromJson(pathMap, ProtoMap.class); +// HashMap param = new HashMap<>(); +// for (String key : params.keySet()) { +// try { +// param.put(key, jsonContext.read(params.get(key))); +// } catch (com.jayway.jsonpath.PathNotFoundException e) { +// param.put(key, new ArrayList<>()); +// } +// } +// return param; +// } +// } } diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf.xml b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf.xml index d4c83438b..06c57511d 100644 --- a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf.xml +++ b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf.xml @@ -1193,6 +1193,9 @@ + {"criteria":[{"constraint":[{"verb":"equals_ignorecase","field":"subject","value":"ciencias de la comunicación"}, + {"verb":"equals","field":"subject","value":"Miriam"}]}, + {"constraint":[{"verb":"equals","field":"subject","value":"miriam"}]}]} Sustainability-oriented science policy STI policies @@ -1316,7 +1319,7 @@ opendoar____::358aee4cc897452c00244351e4d91f69 {"criteria":[{"constraint":[{"verb":"contains_ignorecase","field":"title","value":"COVID-19"}]}, {"constraint":[{"verb":"contains_ignorecase","field":"title","value":"SARS-CoV-2"}]}, - {"constraint":[{"verb":"contains_ignorecase","field":"title","value":"2019-nCoV"}]}]} + {"constraint":[{"verb":"contains_ignorecase","field":"title","value":"2019-nCoV"}}]} diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/update_datasourcewithconstraints/dataset_10.json b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/update_datasourcewithconstraints/dataset_10.json new file mode 100644 index 000000000..168343401 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/update_datasourcewithconstraints/dataset_10.json @@ -0,0 +1,10 @@ +{"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1585055868909,"id":"50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529","originalId":["od______3989::02dd5d2c222191b0b9bd4f33c8e96529"],"collectedfrom":[{"key":"opendoar____::3989","value":"Depósito Digital e-UCJC","dataInfo":null}],"pid":[{"value":"10.4185/RLCS-2018-1243","qualifier":{"classid":"doi","classname":"doi","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofcollection":"2020-03-03T13:05:26.091Z","dateoftransformation":"2020-03-03T13:06:53.161Z","extraInfo":[],"oaiprovenance":{"originDescription":{"harvestDate":"2020-03-03T13:05:26.091Z","altered":true,"baseURL":"http%3A%2F%2Frepositorio.ucjc.edu%2Foai%2Frequest","identifier":"oai:repositorio.ucjc.edu:20.500.12020/562","datestamp":"2018-01-23T15:06:07Z","metadataNamespace":"http://www.openarchives.org/OAI/2.0/oai_dc/"}},"author":[{"fullname":"Gallardo-Camacho, Jorge","name":"Jorge","surname":"Gallardo-Camacho","rank":1,"pid":null,"affiliation":null},{"fullname":"Trujillo Fernández, José Ramón","name":"José Ramón","surname":"Trujillo Fernández","rank":2,"pid":null,"affiliation":null},{"fullname":"Jorge Alonso, Ana","name":"Ana","surname":"Jorge Alonso","rank":3,"pid":null,"affiliation":null}],"resulttype":{"classid":"dataset","classname":"dataset","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"esl/spa","classname":"Spanish","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Ciencias de la 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El formato es al estilo inglés, similar al de la Oxford Union, donde algunos jóvenes se reunían a debatir sobre temas de la más candente actualidad y polemizaban con la intención de formarse en tan valoradas habilidades.\n\nLa Liga de Debate CICAE-UCJC es una ocasión única para los alumnos de ponerse en contacto con herramientas tan útiles como la oratoria y la comunicación efectiva. Pero, sobre todo, una oportunidad de fomentar el pensamiento crítico y la socialización entre alumnos con espíritu emprendedor. La Liga de Debate CICAE - Universidad Camilo José Cela se diferencia del resto de torneos en que potenciamos que sea eminentemente formativa. 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Masas","qualifier":{"classid":"","classname":"","schemeid":"","schemename":""},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"Ramón Luis Varcárcel - La Unión Europea ante el reto de la desinformación","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[],"description":[{"value":"Conferencia de Ramón Luis Valcárcel, vicepresidente del Parlamento Europeo, en el Campus de Almagro de la Universidad Camilo José Cela (UCJC) bajo el título \"La Unión Europea ante el reto de la desinformación\", en la que ha alertado sobre el alcance de la desinformación en las democracias y sobre cómo pone en peligro los derechos de los ciudadanos europeos. 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"miriam.baglioni" Date: Fri, 23 Sep 2022 16:47:19 +0200 Subject: [PATCH 184/214] [BulkTagging] changed the query to the IS to get also the information for the advancedConstraint from the profile --- .../dnetlib/dhp/bulktag/community/QueryInformationSystem.java | 3 +++ 1 file changed, 3 insertions(+) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/QueryInformationSystem.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/QueryInformationSystem.java index 89cf5beff..cde8d7d11 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/QueryInformationSystem.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/QueryInformationSystem.java @@ -61,6 +61,9 @@ public class QueryInformationSystem { + " " + " } " + " " + + "" + +"{$x//CONFIGURATION/context/param[./@name='advancedConstaint']/text()} " + + "" + " "; public static CommunityConfiguration getCommunityConfiguration(final String isLookupUrl) From ca216a92ad8db5bd658e45c72f93ed861f27a7cb Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 23 Sep 2022 17:06:07 +0200 Subject: [PATCH 185/214] [BulkTagging] changed the query to the IS to insert values for FOS and SDG as subject in the configuration used for the tagging --- .../dhp/bulktag/community/QueryInformationSystem.java | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/QueryInformationSystem.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/QueryInformationSystem.java index cde8d7d11..9803c5e63 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/QueryInformationSystem.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/QueryInformationSystem.java @@ -18,6 +18,8 @@ public class QueryInformationSystem { + " let $datasources := $x//CONFIGURATION/context/category[./@id=concat($x//CONFIGURATION/context/@id,'::contentproviders')]/concept " + " let $organizations := $x//CONFIGURATION/context/category[./@id=concat($x//CONFIGURATION/context/@id,'::resultorganizations')]/concept " + " let $communities := $x//CONFIGURATION/context/category[./@id=concat($x//CONFIGURATION/context/@id,'::zenodocommunities')]/concept " + + " let $fos := $x//CONFIGURATION/context/param[./@name='fos']/text() " + + " let $sdg := $x//CONFIGURATION/context/param[./@name='sdg']/text() " + "let $zenodo := $x//param[./@name='zenodoCommunity']/text() " + " where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] and $x//context/param[./@name = 'status']/text() != 'hidden' " @@ -28,6 +30,12 @@ public class QueryInformationSystem { + " {for $y in tokenize($subj,',') " + " return " + " {$y}} " + + " {for $y in tokenize($fos,',') " + + " return " + + " {$y}} " + + " {for $y in tokenize($sdg,',') " + + " return " + + " {$y}} " + " " + " " + " {for $d in $datasources " @@ -62,7 +70,7 @@ public class QueryInformationSystem { + " } " + " " + "" - +"{$x//CONFIGURATION/context/param[./@name='advancedConstaint']/text()} " + +"{$x//CONFIGURATION/context/param[./@name='advancedConstraint']/text()} " + "" + " "; From fd63e9bfac41a4ec508dd9cb66880db46a1cb1b5 Mon Sep 17 00:00:00 2001 From: Alessia Bardi Date: Mon, 26 Sep 2022 11:24:13 +0200 Subject: [PATCH 186/214] Mapping all relationships supported in ModelConstants and ModelSupport --- .../raw/AbstractMdRecordToOafMapper.java | 14 ++-- .../dhp/oa/graph/raw/OdfToOafMapper.java | 78 +++++++------------ .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 26 ++++++- .../dnetlib/dhp/oa/graph/raw/odf_dataset.xml | 1 - .../dnetlib/dhp/oa/graph/raw/odf_software.xml | 2 +- 5 files changed, 59 insertions(+), 62 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index bb5472a88..5f185444f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -69,14 +69,16 @@ public abstract class AbstractMdRecordToOafMapper { nsContext.put("datacite", DATACITE_SCHEMA_KERNEL_3); } - protected static final Set pidTypeWithAuthority = new HashSet<>(); + // lowercase pidTypes as keys, normal casing for the values + protected static final Map pidTypeWithAuthority = new HashMap<>(); static { - pidTypeWithAuthority.addAll(IdentifierFactory.PID_AUTHORITY.keySet().stream() - .map(PidType::toString) - .map(String::toLowerCase) - .collect(Collectors.toCollection(HashSet::new))); - } + IdentifierFactory.PID_AUTHORITY + .keySet() + .stream() + .forEach(entry -> pidTypeWithAuthority.put(entry.toString().toLowerCase(), entry.toString())); + + } protected AbstractMdRecordToOafMapper(final VocabularyGroup vocs, final boolean invisible, final boolean shouldHashId, final boolean forceOriginalId) { diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java index 304ec8f99..a25bcd47e 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java @@ -22,6 +22,8 @@ import com.google.common.collect.Lists; import eu.dnetlib.dhp.common.PacePerson; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.common.RelationInverse; import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions; import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; @@ -400,55 +402,12 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { if (StringUtils.isNotBlank(originalId)) { final String idType = ((Node) o).valueOf("@relatedIdentifierType"); - final String reltype = ((Node) o).valueOf("@relationType"); + final String relType = ((Node) o).valueOf("@relationType"); String otherId = guessRelatedIdentifier(idType, originalId); if (StringUtils.isNotBlank(otherId)) { - if (reltype.equalsIgnoreCase(IS_SUPPLEMENT_TO)) { - res - .add( - getRelation( - docId, otherId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENT_TO, entity)); - res - .add( - getRelation( - otherId, docId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENTED_BY, entity)); - } else { - if (reltype.equalsIgnoreCase(IS_SUPPLEMENTED_BY)) { - res - .add( - getRelation( - otherId, docId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENT_TO, entity)); - res - .add( - getRelation( - docId, otherId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENTED_BY, entity)); - } else { - if (reltype.equalsIgnoreCase(IS_PART_OF)) { - res - .add( - getRelation( - docId, otherId, RESULT_RESULT, PART, IS_PART_OF, entity)); - res - .add( - getRelation( - otherId, docId, RESULT_RESULT, PART, HAS_PART, entity)); - } else { - if (reltype.equalsIgnoreCase(HAS_PART)) { - res - .add( - getRelation( - otherId, docId, RESULT_RESULT, PART, IS_PART_OF, entity)); - res - .add( - getRelation( - docId, otherId, RESULT_RESULT, PART, HAS_PART, entity)); - } - // else TODO catch more semantics - } - } - } - + res.addAll(getRelations(relType, docId, otherId, entity)); } + } } return res; @@ -457,14 +416,33 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { protected String guessRelatedIdentifier(final String idType, final String value) { if (StringUtils.isBlank(idType) || StringUtils.isBlank(value)) return null; - if (idType.equalsIgnoreCase("OPENAIRE")) return createOpenaireId(50, value, false); - if(pidTypeWithAuthority.contains(idType.toLowerCase())){ - return IdentifierFactory.idFromPid("50", idType, value, true); - } + if (idType.equalsIgnoreCase("OPENAIRE")) + return createOpenaireId(50, value, false); + if (pidTypeWithAuthority.containsKey(idType.toLowerCase())) { + return IdentifierFactory.idFromPid("50", pidTypeWithAuthority.get(idType.toLowerCase()), value, true); + } return null; } + protected List getRelations(final String reltype, final String entityId, final String otherId, + final OafEntity entity) { + final List res = new ArrayList<>(); + RelationInverse rel = ModelSupport.findRelation(reltype); + if (rel != null) { + res + .add( + getRelation( + entityId, otherId, rel.getRelType(), rel.getSubReltype(), rel.getRelClass(), entity)); + res + .add( + getRelation( + otherId, entityId, rel.getRelType(), rel.getSubReltype(), rel.getInverseRelClass(), entity)); + + } + return res; + } + @Override protected Qualifier prepareResourceType(final Document doc, final DataInfo info) { return prepareQualifier( diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index 32b23e42f..7552d1789 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -579,8 +579,10 @@ class MappersTest { final List list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml); - assertEquals(1, list.size()); + assertEquals(3, list.size()); assertTrue(list.get(0) instanceof Software); + assertTrue(list.get(1) instanceof Relation); + assertTrue(list.get(2) instanceof Relation); final Software s = (Software) list.get(0); @@ -590,6 +592,22 @@ class MappersTest { assertTrue(s.getAuthor().size() > 0); assertTrue(s.getSubject().size() > 0); assertTrue(s.getInstance().size() > 0); + + final Relation r1 = (Relation) list.get(1); + final Relation r2 = (Relation) list.get(2); + + assertEquals(s.getId(), r1.getSource()); + assertEquals("50|doi_________::b453e7b4b2130ace57ff0c3db470a982", r1.getTarget()); + assertEquals(ModelConstants.RESULT_RESULT, r1.getRelType()); + assertEquals(ModelConstants.RELATIONSHIP, r1.getSubRelType()); + assertEquals(ModelConstants.IS_REFERENCED_BY, r1.getRelClass()); + + assertEquals(s.getId(), r2.getTarget()); + assertEquals("50|doi_________::b453e7b4b2130ace57ff0c3db470a982", r2.getSource()); + assertEquals(ModelConstants.RESULT_RESULT, r2.getRelType()); + assertEquals(ModelConstants.RELATIONSHIP, r2.getSubRelType()); + assertEquals(ModelConstants.REFERENCES, r2.getRelClass()); + } @Test @@ -945,14 +963,14 @@ class MappersTest { assertEquals(1, list.stream().filter(o -> o instanceof OtherResearchProduct).count()); assertEquals(6, list.stream().filter(o -> o instanceof Relation).count()); - for(Oaf oaf : list){ - if(oaf instanceof Relation){ + for (Oaf oaf : list) { + if (oaf instanceof Relation) { String source = ((Relation) oaf).getSource(); String target = ((Relation) oaf).getTarget(); assertNotEquals(source, target); assertTrue(source.equals(p.getId()) || target.equals(p.getId())); assertNotNull(((Relation) oaf).getSubRelType()); - assertNotNull( ((Relation) oaf).getRelClass()); + assertNotNull(((Relation) oaf).getRelClass()); assertNotNull(((Relation) oaf).getRelType()); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_dataset.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_dataset.xml index 4f41ee6ea..4633d62c3 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_dataset.xml +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_dataset.xml @@ -69,7 +69,6 @@ - 10.5281/zenodo.3234525 https://zenodo.org/communities/epfl 1.0.0 diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_software.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_software.xml index 6a9170ce1..387b1ee86 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_software.xml +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_software.xml @@ -20,7 +20,7 @@ bio.tools http://maplab.imppc.org/chainy/ - 10.1093/bioinformatics/btw839 + 10.1093/bioinformatics/btw839 https://bio.tools/ From 57dbeb08d2e07bacd2ba7c559e2f8fc9dace0ee1 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 27 Sep 2022 14:55:10 +0200 Subject: [PATCH 187/214] code formatting --- .../dhp/bulktag/community/Community.java | 3 +- .../community/CommunityConfiguration.java | 2 +- .../CommunityConfigurationFactory.java | 5 +- .../community/QueryInformationSystem.java | 22 ++-- .../dhp/bulktag/community/ResultTagger.java | 116 +++++++++++++----- .../dnetlib/dhp/bulktag/BulkTagJobTest.java | 17 +-- .../clean/country/CleanCountrySparkJob.java | 7 +- .../raw/MigrateDbEntitiesApplication.java | 3 +- 8 files changed, 121 insertions(+), 54 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Community.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Community.java index c5feb8d3f..3db584c76 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Community.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Community.java @@ -5,9 +5,10 @@ import java.io.Serializable; import java.util.ArrayList; import java.util.List; -import com.google.gson.Gson; import org.apache.avro.generic.GenericData; +import com.google.gson.Gson; + /** Created by miriam on 01/08/2018. */ public class Community implements Serializable { diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfiguration.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfiguration.java index 8e34ccebf..66407a4b3 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfiguration.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfiguration.java @@ -77,7 +77,7 @@ public class CommunityConfiguration implements Serializable { if (zenodocommunityMap == null) { zenodocommunityMap = Maps.newHashMap(); } - if(selectionConstraintsMap == null){ + if (selectionConstraintsMap == null) { selectionConstraintsMap = Maps.newHashMap(); } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfigurationFactory.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfigurationFactory.java index 7a43ca476..52ca606fc 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfigurationFactory.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfigurationFactory.java @@ -91,10 +91,11 @@ public class CommunityConfigurationFactory { private static SelectionConstraints parseConstrains(Node node) { Node aconstraints = node.selectSingleNode("./advancedConstraints"); - if(aconstraints == null){ + if (aconstraints == null) { return null; } - SelectionConstraints selectionConstraints = new Gson().fromJson(aconstraints.getText(), SelectionConstraints.class); + SelectionConstraints selectionConstraints = new Gson() + .fromJson(aconstraints.getText(), SelectionConstraints.class); selectionConstraints.setSelection(resolver); return selectionConstraints; diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/QueryInformationSystem.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/QueryInformationSystem.java index 9803c5e63..f06c0d47a 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/QueryInformationSystem.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/QueryInformationSystem.java @@ -18,8 +18,8 @@ public class QueryInformationSystem { + " let $datasources := $x//CONFIGURATION/context/category[./@id=concat($x//CONFIGURATION/context/@id,'::contentproviders')]/concept " + " let $organizations := $x//CONFIGURATION/context/category[./@id=concat($x//CONFIGURATION/context/@id,'::resultorganizations')]/concept " + " let $communities := $x//CONFIGURATION/context/category[./@id=concat($x//CONFIGURATION/context/@id,'::zenodocommunities')]/concept " - + " let $fos := $x//CONFIGURATION/context/param[./@name='fos']/text() " - + " let $sdg := $x//CONFIGURATION/context/param[./@name='sdg']/text() " + + " let $fos := $x//CONFIGURATION/context/param[./@name='fos']/text() " + + " let $sdg := $x//CONFIGURATION/context/param[./@name='sdg']/text() " + "let $zenodo := $x//param[./@name='zenodoCommunity']/text() " + " where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] and $x//context/param[./@name = 'status']/text() != 'hidden' " @@ -30,12 +30,12 @@ public class QueryInformationSystem { + " {for $y in tokenize($subj,',') " + " return " + " {$y}} " - + " {for $y in tokenize($fos,',') " - + " return " - + " {$y}} " - + " {for $y in tokenize($sdg,',') " - + " return " - + " {$y}} " + + " {for $y in tokenize($fos,',') " + + " return " + + " {$y}} " + + " {for $y in tokenize($sdg,',') " + + " return " + + " {$y}} " + " " + " " + " {for $d in $datasources " @@ -69,9 +69,9 @@ public class QueryInformationSystem { + " " + " } " + " " - + "" - +"{$x//CONFIGURATION/context/param[./@name='advancedConstraint']/text()} " - + "" + + "" + + "{$x//CONFIGURATION/context/param[./@name='advancedConstraint']/text()} " + + "" + " "; public static CommunityConfiguration getCommunityConfiguration(final String isLookupUrl) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java index ccb69a97d..ee75bf955 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java @@ -9,16 +9,16 @@ import java.util.*; import java.util.stream.Collectors; import java.util.stream.Stream; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; import org.apache.commons.lang3.StringUtils; import com.google.gson.Gson; import com.jayway.jsonpath.DocumentContext; import com.jayway.jsonpath.JsonPath; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; /** Created by miriam on 02/08/2018. */ public class ResultTagger implements Serializable { @@ -134,13 +134,19 @@ public class ResultTagger implements Serializable { /* Tagging for Advanced Constraints */ final Set aconstraints = new HashSet<>(); - conf.getSelectionConstraintsMap().keySet() - .forEach(communityId -> { - if(conf.getSelectionConstraintsMap().get(communityId) != null && - conf.getSelectionConstraintsMap().get(communityId) - .getCriteria().stream().anyMatch(crit -> crit.verifyCriteria(param))) - aconstraints.add(communityId); - }); + conf + .getSelectionConstraintsMap() + .keySet() + .forEach(communityId -> { + if (conf.getSelectionConstraintsMap().get(communityId) != null && + conf + .getSelectionConstraintsMap() + .get(communityId) + .getCriteria() + .stream() + .anyMatch(crit -> crit.verifyCriteria(param))) + aconstraints.add(communityId); + }); communities.addAll(aconstraints); @@ -163,21 +169,48 @@ public class ResultTagger implements Serializable { } if (subjects.contains(c)) dataInfoList - .add(OafMapperUtils.dataInfo(false, BULKTAG_DATA_INFO_TYPE, true, false, - OafMapperUtils.qualifier(CLASS_ID_SUBJECT, CLASS_NAME_BULKTAG_SUBJECT, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), TAGGING_TRUST)); + .add( + OafMapperUtils + .dataInfo( + false, BULKTAG_DATA_INFO_TYPE, true, false, + OafMapperUtils + .qualifier( + CLASS_ID_SUBJECT, CLASS_NAME_BULKTAG_SUBJECT, DNET_PROVENANCE_ACTIONS, + DNET_PROVENANCE_ACTIONS), + TAGGING_TRUST)); if (datasources.contains(c)) dataInfoList - .add(OafMapperUtils.dataInfo(false, BULKTAG_DATA_INFO_TYPE, true, false, - OafMapperUtils.qualifier(CLASS_ID_DATASOURCE, CLASS_NAME_BULKTAG_DATASOURCE, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), TAGGING_TRUST)); + .add( + OafMapperUtils + .dataInfo( + false, BULKTAG_DATA_INFO_TYPE, true, false, + OafMapperUtils + .qualifier( + CLASS_ID_DATASOURCE, CLASS_NAME_BULKTAG_DATASOURCE, DNET_PROVENANCE_ACTIONS, + DNET_PROVENANCE_ACTIONS), + TAGGING_TRUST)); if (czenodo.contains(c)) dataInfoList - .add(OafMapperUtils.dataInfo(false, BULKTAG_DATA_INFO_TYPE, true, false, - OafMapperUtils.qualifier(CLASS_ID_CZENODO, CLASS_NAME_BULKTAG_ZENODO, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), TAGGING_TRUST)); + .add( + OafMapperUtils + .dataInfo( + false, BULKTAG_DATA_INFO_TYPE, true, false, + OafMapperUtils + .qualifier( + CLASS_ID_CZENODO, CLASS_NAME_BULKTAG_ZENODO, DNET_PROVENANCE_ACTIONS, + DNET_PROVENANCE_ACTIONS), + TAGGING_TRUST)); if (aconstraints.contains(c)) dataInfoList - .add( - OafMapperUtils.dataInfo(false, BULKTAG_DATA_INFO_TYPE, true, false, - OafMapperUtils.qualifier(CLASS_ID_ADVANCED_CONSTRAINT, CLASS_NAME_BULKTAG_ADVANCED_CONSTRAINT, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), TAGGING_TRUST)); + .add( + OafMapperUtils + .dataInfo( + false, BULKTAG_DATA_INFO_TYPE, true, false, + OafMapperUtils + .qualifier( + CLASS_ID_ADVANCED_CONSTRAINT, CLASS_NAME_BULKTAG_ADVANCED_CONSTRAINT, + DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), + TAGGING_TRUST)); } }); @@ -198,21 +231,48 @@ public class ResultTagger implements Serializable { List dataInfoList = new ArrayList<>(); if (subjects.contains(c)) dataInfoList - .add(OafMapperUtils.dataInfo(false, BULKTAG_DATA_INFO_TYPE, true, false, - OafMapperUtils.qualifier(CLASS_ID_SUBJECT, CLASS_NAME_BULKTAG_SUBJECT, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), TAGGING_TRUST)); + .add( + OafMapperUtils + .dataInfo( + false, BULKTAG_DATA_INFO_TYPE, true, false, + OafMapperUtils + .qualifier( + CLASS_ID_SUBJECT, CLASS_NAME_BULKTAG_SUBJECT, DNET_PROVENANCE_ACTIONS, + DNET_PROVENANCE_ACTIONS), + TAGGING_TRUST)); if (datasources.contains(c)) dataInfoList - .add(OafMapperUtils.dataInfo(false, BULKTAG_DATA_INFO_TYPE, true, false, - OafMapperUtils.qualifier(CLASS_ID_DATASOURCE, CLASS_NAME_BULKTAG_DATASOURCE, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), TAGGING_TRUST)); + .add( + OafMapperUtils + .dataInfo( + false, BULKTAG_DATA_INFO_TYPE, true, false, + OafMapperUtils + .qualifier( + CLASS_ID_DATASOURCE, CLASS_NAME_BULKTAG_DATASOURCE, + DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), + TAGGING_TRUST)); if (czenodo.contains(c)) dataInfoList - .add(OafMapperUtils.dataInfo(false, BULKTAG_DATA_INFO_TYPE, true, false, - OafMapperUtils.qualifier(CLASS_ID_CZENODO, CLASS_NAME_BULKTAG_ZENODO, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), TAGGING_TRUST)); + .add( + OafMapperUtils + .dataInfo( + false, BULKTAG_DATA_INFO_TYPE, true, false, + OafMapperUtils + .qualifier( + CLASS_ID_CZENODO, CLASS_NAME_BULKTAG_ZENODO, DNET_PROVENANCE_ACTIONS, + DNET_PROVENANCE_ACTIONS), + TAGGING_TRUST)); if (aconstraints.contains(c)) dataInfoList - .add( - OafMapperUtils.dataInfo(false, BULKTAG_DATA_INFO_TYPE, true, false, - OafMapperUtils.qualifier(CLASS_ID_ADVANCED_CONSTRAINT, CLASS_NAME_BULKTAG_ADVANCED_CONSTRAINT, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), TAGGING_TRUST)); + .add( + OafMapperUtils + .dataInfo( + false, BULKTAG_DATA_INFO_TYPE, true, false, + OafMapperUtils + .qualifier( + CLASS_ID_ADVANCED_CONSTRAINT, CLASS_NAME_BULKTAG_ADVANCED_CONSTRAINT, + DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), + TAGGING_TRUST)); context.setDataInfo(dataInfoList); return context; diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java index 0212f4a49..def524156 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java @@ -11,11 +11,6 @@ import java.util.HashMap; import java.util.List; import java.util.Map; -import com.google.gson.Gson; -import com.jayway.jsonpath.DocumentContext; -import com.jayway.jsonpath.JsonPath; -import eu.dnetlib.dhp.bulktag.community.ProtoMap; -import eu.dnetlib.dhp.schema.oaf.*; import org.apache.commons.io.FileUtils; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; @@ -32,6 +27,12 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; +import com.google.gson.Gson; +import com.jayway.jsonpath.DocumentContext; +import com.jayway.jsonpath.JsonPath; + +import eu.dnetlib.dhp.bulktag.community.ProtoMap; +import eu.dnetlib.dhp.schema.oaf.*; public class BulkTagJobTest { @@ -44,7 +45,7 @@ public class BulkTagJobTest { + " \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\"," + " \"contributor\" : \"$['contributor'][*]['value']\"," + " \"description\" : \"$['description'][*]['value']\", " - +" \"subject\" :\"$['subject'][*]['value']\" }"; + + " \"subject\" :\"$['subject'][*]['value']\" }"; private static SparkSession spark; @@ -774,8 +775,8 @@ public class BulkTagJobTest { .assertEquals( 3, idExplodeCommunity.filter("provenance = 'community:datasource'").count()); Assertions - .assertEquals( - 1, idExplodeCommunity.filter("provenance = 'community:advconstraint'").count()); + .assertEquals( + 1, idExplodeCommunity.filter("provenance = 'community:advconstraint'").count()); } // @Test diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java index 30991e9d7..c150c63df 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java @@ -10,7 +10,6 @@ import java.util.stream.Collectors; import javax.swing.text.html.Option; -import eu.dnetlib.dhp.schema.oaf.utils.PidType; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.FilterFunction; @@ -33,6 +32,7 @@ import eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob; import eu.dnetlib.dhp.schema.oaf.Country; import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import eu.dnetlib.dhp.schema.oaf.utils.PidType; public class CleanCountrySparkJob implements Serializable { private static final Logger log = LoggerFactory.getLogger(CleanCountrySparkJob.class); @@ -113,7 +113,10 @@ public class CleanCountrySparkJob implements Serializable { if (r .getPid() .stream() - .anyMatch(p -> p.getQualifier().getClassid() + .anyMatch( + p -> p + .getQualifier() + .getClassid() .equals(PidType.doi) && pidInParam(p.getValue(), verifyParam))) { r .setCountry( diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java index 2b1c257ad..c69a7a6ff 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java @@ -422,7 +422,8 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i final Relation r2 = OafMapperUtils .getRelation( - orgId, dsId, DATASOURCE_ORGANIZATION, PROVISION, PROVIDES, collectedFrom, info, lastUpdateTimestamp); + orgId, dsId, DATASOURCE_ORGANIZATION, PROVISION, PROVIDES, collectedFrom, info, + lastUpdateTimestamp); return Arrays.asList(r1, r2); } catch (final Exception e) { From 3f90d159e3efc63529f5a51ae03c2410230869b4 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 27 Sep 2022 15:08:00 +0200 Subject: [PATCH 188/214] code formatting --- .../raw/AbstractMdRecordToOafMapper.java | 1188 ++++++++--------- pom.xml | 2 +- 2 files changed, 595 insertions(+), 595 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index 5f185444f..c157be51a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -15,7 +15,6 @@ import java.net.URL; import java.util.*; import java.util.stream.Collectors; -import eu.dnetlib.dhp.schema.oaf.utils.PidType; import org.apache.commons.lang3.StringUtils; import org.apache.commons.validator.routines.UrlValidator; import org.dom4j.*; @@ -31,617 +30,618 @@ import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; +import eu.dnetlib.dhp.schema.oaf.utils.PidType; public abstract class AbstractMdRecordToOafMapper { - protected final VocabularyGroup vocs; + protected final VocabularyGroup vocs; - private final boolean invisible; + private final boolean invisible; - private final boolean shouldHashId; + private final boolean shouldHashId; - private final boolean forceOriginalId; + private final boolean forceOriginalId; - protected static final String DATACITE_SCHEMA_KERNEL_4 = "http://datacite.org/schema/kernel-4"; - protected static final String DATACITE_SCHEMA_KERNEL_4_SLASH = "http://datacite.org/schema/kernel-4/"; - protected static final String DATACITE_SCHEMA_KERNEL_3 = "http://datacite.org/schema/kernel-3"; - protected static final String DATACITE_SCHEMA_KERNEL_3_SLASH = "http://datacite.org/schema/kernel-3/"; - protected static final Qualifier ORCID_PID_TYPE = qualifier( - ModelConstants.ORCID_PENDING, - ModelConstants.ORCID_CLASSNAME, - DNET_PID_TYPES, DNET_PID_TYPES); - protected static final Qualifier MAG_PID_TYPE = qualifier( - "MAGIdentifier", "Microsoft Academic Graph Identifier", DNET_PID_TYPES, DNET_PID_TYPES); + protected static final String DATACITE_SCHEMA_KERNEL_4 = "http://datacite.org/schema/kernel-4"; + protected static final String DATACITE_SCHEMA_KERNEL_4_SLASH = "http://datacite.org/schema/kernel-4/"; + protected static final String DATACITE_SCHEMA_KERNEL_3 = "http://datacite.org/schema/kernel-3"; + protected static final String DATACITE_SCHEMA_KERNEL_3_SLASH = "http://datacite.org/schema/kernel-3/"; + protected static final Qualifier ORCID_PID_TYPE = qualifier( + ModelConstants.ORCID_PENDING, + ModelConstants.ORCID_CLASSNAME, + DNET_PID_TYPES, DNET_PID_TYPES); + protected static final Qualifier MAG_PID_TYPE = qualifier( + "MAGIdentifier", "Microsoft Academic Graph Identifier", DNET_PID_TYPES, DNET_PID_TYPES); - protected static final String DEFAULT_TRUST_FOR_VALIDATED_RELS = "0.999"; + protected static final String DEFAULT_TRUST_FOR_VALIDATED_RELS = "0.999"; - protected static final Map nsContext = new HashMap<>(); + protected static final Map nsContext = new HashMap<>(); - private static final Logger log = LoggerFactory.getLogger(AbstractMdRecordToOafMapper.class); + private static final Logger log = LoggerFactory.getLogger(AbstractMdRecordToOafMapper.class); - static { - nsContext.put("dr", "http://www.driver-repository.eu/namespace/dr"); - nsContext.put("dri", "http://www.driver-repository.eu/namespace/dri"); - nsContext.put("oaf", "http://namespace.openaire.eu/oaf"); - nsContext.put("oai", "http://www.openarchives.org/OAI/2.0/"); - nsContext.put("prov", "http://www.openarchives.org/OAI/2.0/provenance"); - nsContext.put("dc", "http://purl.org/dc/elements/1.1/"); - nsContext.put("datacite", DATACITE_SCHEMA_KERNEL_3); - } + static { + nsContext.put("dr", "http://www.driver-repository.eu/namespace/dr"); + nsContext.put("dri", "http://www.driver-repository.eu/namespace/dri"); + nsContext.put("oaf", "http://namespace.openaire.eu/oaf"); + nsContext.put("oai", "http://www.openarchives.org/OAI/2.0/"); + nsContext.put("prov", "http://www.openarchives.org/OAI/2.0/provenance"); + nsContext.put("dc", "http://purl.org/dc/elements/1.1/"); + nsContext.put("datacite", DATACITE_SCHEMA_KERNEL_3); + } // lowercase pidTypes as keys, normal casing for the values protected static final Map pidTypeWithAuthority = new HashMap<>(); - static { + static { IdentifierFactory.PID_AUTHORITY - .keySet() - .stream() - .forEach(entry -> pidTypeWithAuthority.put(entry.toString().toLowerCase(), entry.toString())); + .keySet() + .stream() + .forEach(entry -> pidTypeWithAuthority.put(entry.toString().toLowerCase(), entry.toString())); } - protected AbstractMdRecordToOafMapper(final VocabularyGroup vocs, final boolean invisible, - final boolean shouldHashId, final boolean forceOriginalId) { - this.vocs = vocs; - this.invisible = invisible; - this.shouldHashId = shouldHashId; - this.forceOriginalId = forceOriginalId; - } - - protected AbstractMdRecordToOafMapper(final VocabularyGroup vocs, final boolean invisible, - final boolean shouldHashId) { - this.vocs = vocs; - this.invisible = invisible; - this.shouldHashId = shouldHashId; - this.forceOriginalId = false; - } - - public List processMdRecord(final String xml) { - - DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext); - try { - final Document doc = DocumentHelper - .parseText( - xml - .replaceAll(DATACITE_SCHEMA_KERNEL_4, DATACITE_SCHEMA_KERNEL_3) - .replaceAll(DATACITE_SCHEMA_KERNEL_4_SLASH, DATACITE_SCHEMA_KERNEL_3) - .replaceAll(DATACITE_SCHEMA_KERNEL_3_SLASH, DATACITE_SCHEMA_KERNEL_3)); - - final KeyValue collectedFrom = getProvenanceDatasource( - doc, "//oaf:collectedFrom/@id", "//oaf:collectedFrom/@name"); - - if (collectedFrom == null) { - return Lists.newArrayList(); - } - - final KeyValue hostedBy = StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id")) - ? collectedFrom - : getProvenanceDatasource(doc, "//oaf:hostedBy/@id", "//oaf:hostedBy/@name"); - - if (hostedBy == null) { - return Lists.newArrayList(); - } - - final DataInfo info = prepareDataInfo(doc, invisible); - final long lastUpdateTimestamp = new Date().getTime(); - - final List instances = prepareInstances(doc, info, collectedFrom, hostedBy); - - final String type = getResultType(doc, instances); - - return createOafs(doc, type, instances, collectedFrom, info, lastUpdateTimestamp); - } catch (DocumentException e) { - log.error("Error with record:\n" + xml); - return Lists.newArrayList(); - } - } - - protected String getResultType(final Document doc, final List instances) { - final String type = doc.valueOf("//dr:CobjCategory/@type"); - - if (StringUtils.isBlank(type) && vocs.vocabularyExists(ModelConstants.DNET_RESULT_TYPOLOGIES)) { - final String instanceType = instances - .stream() - .map(i -> i.getInstancetype().getClassid()) - .findFirst() - .filter(s -> !UNKNOWN.equalsIgnoreCase(s)) - .orElse("0000"); // Unknown - return Optional - .ofNullable(vocs.getSynonymAsQualifier(ModelConstants.DNET_RESULT_TYPOLOGIES, instanceType)) - .map(Qualifier::getClassid) - .orElse("0000"); - } - - return type; - } - - private KeyValue getProvenanceDatasource(final Document doc, final String xpathId, final String xpathName) { - final String dsId = doc.valueOf(xpathId); - final String dsName = doc.valueOf(xpathName); - - if (StringUtils.isBlank(dsId) || StringUtils.isBlank(dsName)) { - return null; - } - - return keyValue(createOpenaireId(10, dsId, true), dsName); - } - - protected List createOafs( - final Document doc, - final String type, - final List instances, - final KeyValue collectedFrom, - final DataInfo info, - final long lastUpdateTimestamp) { - - final OafEntity entity = createEntity(doc, type, instances, collectedFrom, info, lastUpdateTimestamp); - - final Set originalId = Sets.newHashSet(entity.getOriginalId()); - originalId.add(entity.getId()); - entity.setOriginalId(Lists.newArrayList(originalId)); - - if (!forceOriginalId) { - final String id = IdentifierFactory.createIdentifier(entity, shouldHashId); - if (!id.equals(entity.getId())) { - entity.setId(id); - } - } - - final List oafs = Lists.newArrayList(entity); - - if (!oafs.isEmpty()) { - Set rels = Sets.newHashSet(); - - rels.addAll(addProjectRels(doc, entity)); - rels.addAll(addOtherResultRels(doc, entity)); - rels.addAll(addRelations(doc, entity)); - - oafs.addAll(rels); - } - - return oafs; - } - - private OafEntity createEntity(final Document doc, - final String type, - final List instances, - final KeyValue collectedFrom, - final DataInfo info, - final long lastUpdateTimestamp) { - switch (type.toLowerCase()) { - case "publication": - final Publication p = new Publication(); - populateResultFields(p, doc, instances, collectedFrom, info, lastUpdateTimestamp); - p.setJournal(prepareJournal(doc, info)); - return p; - case "dataset": - final Dataset d = new Dataset(); - populateResultFields(d, doc, instances, collectedFrom, info, lastUpdateTimestamp); - d.setStoragedate(prepareDatasetStorageDate(doc, info)); - d.setDevice(prepareDatasetDevice(doc, info)); - d.setSize(prepareDatasetSize(doc, info)); - d.setVersion(prepareDatasetVersion(doc, info)); - d.setLastmetadataupdate(prepareDatasetLastMetadataUpdate(doc, info)); - d.setMetadataversionnumber(prepareDatasetMetadataVersionNumber(doc, info)); - d.setGeolocation(prepareDatasetGeoLocations(doc, info)); - return d; - case "software": - final Software s = new Software(); - populateResultFields(s, doc, instances, collectedFrom, info, lastUpdateTimestamp); - s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info)); - s.setLicense(prepareSoftwareLicenses(doc, info)); - s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info)); - s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info)); - return s; - case "": - case "otherresearchproducts": - default: - final OtherResearchProduct o = new OtherResearchProduct(); - populateResultFields(o, doc, instances, collectedFrom, info, lastUpdateTimestamp); - o.setContactperson(prepareOtherResearchProductContactPersons(doc, info)); - o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info)); - o.setTool(prepareOtherResearchProductTools(doc, info)); - return o; - } - } - - private List addProjectRels( - final Document doc, - final OafEntity entity) { - - final List res = new ArrayList<>(); - - final String docId = entity.getId(); - - for (final Object o : doc.selectNodes("//oaf:projectid")) { - - final String originalId = ((Node) o).getText(); - - final String validationdDate = ((Node) o).valueOf("@validationDate"); - - if (StringUtils.isNotBlank(originalId)) { - final String projectId = createOpenaireId(40, originalId, true); - - res - .add( - OafMapperUtils - .getRelation( - docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, entity, validationdDate)); - res - .add( - OafMapperUtils - .getRelation(projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, entity, validationdDate)); - } - } - - return res; - } - - private List addRelations(Document doc, OafEntity entity) { - - final List rels = Lists.newArrayList(); - - for (Object o : doc.selectNodes("//oaf:relation")) { - Element element = (Element) o; - - final String target = StringUtils.trim(element.getText()); - final String relType = element.attributeValue("relType"); - final String subRelType = element.attributeValue("subRelType"); - final String relClass = element.attributeValue("relClass"); - - if (StringUtils.isNotBlank(target) && StringUtils.isNotBlank(relType) && StringUtils.isNotBlank(subRelType) - && StringUtils.isNotBlank(relClass)) { - - final String relClassInverse = ModelSupport - .findInverse(ModelSupport.rel(relType, subRelType, relClass)) - .getInverseRelClass(); - final String validationdDate = ((Node) o).valueOf("@validationDate"); - - if (StringUtils.isNotBlank(target)) { - final String targetType = element.attributeValue("targetType"); - if (StringUtils.isNotBlank(targetType)) { - final String targetId = createOpenaireId(targetType, target, true); - rels - .add( - OafMapperUtils - .getRelation( - entity.getId(), targetId, relType, subRelType, relClass, entity, - validationdDate)); - rels - .add( - OafMapperUtils - .getRelation( - targetId, entity.getId(), relType, subRelType, relClassInverse, entity, - validationdDate)); - } - } - } - } - return rels; - } - - protected abstract List addOtherResultRels( - final Document doc, - final OafEntity entity); - - private void populateResultFields( - final Result r, - final Document doc, - final List instances, - final KeyValue collectedFrom, - final DataInfo info, - final long lastUpdateTimestamp) { - r.setDataInfo(info); - r.setLastupdatetimestamp(lastUpdateTimestamp); - r.setId(createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false)); - r.setOriginalId(findOriginalId(doc)); - r.setCollectedfrom(Arrays.asList(collectedFrom)); - r.setPid(IdentifierFactory.getPids(prepareResultPids(doc, info), collectedFrom)); - r.setDateofcollection(doc.valueOf("//dr:dateOfCollection/text()|//dri:dateOfCollection/text()")); - r.setDateoftransformation(doc.valueOf("//dr:dateOfTransformation/text()|//dri:dateOfTransformation/text()")); - r.setExtraInfo(new ArrayList<>()); // NOT PRESENT IN MDSTORES - r.setOaiprovenance(prepareOAIprovenance(doc)); - r.setAuthor(prepareAuthors(doc, info)); - r.setLanguage(prepareLanguages(doc)); - r.setCountry(new ArrayList<>()); // NOT PRESENT IN MDSTORES - r.setSubject(prepareSubjects(doc, info)); - r.setTitle(prepareTitles(doc, info)); - r.setRelevantdate(prepareRelevantDates(doc, info)); - r.setDescription(prepareDescriptions(doc, info)); - r.setDateofacceptance(prepareField(doc, "//oaf:dateAccepted", info)); - r.setPublisher(preparePublisher(doc, info)); - r.setEmbargoenddate(prepareField(doc, "//oaf:embargoenddate", info)); - r.setSource(prepareSources(doc, info)); - r.setFulltext(prepareListFields(doc, "//oaf:fulltext", info)); - r.setFormat(prepareFormats(doc, info)); - r.setContributor(prepareContributors(doc, info)); - r.setResourcetype(prepareResourceType(doc, info)); - r.setCoverage(prepareCoverages(doc, info)); - r.setContext(prepareContexts(doc, info)); - r.setExternalReference(new ArrayList<>()); // NOT PRESENT IN MDSTORES - r - .setProcessingchargeamount(field(doc.valueOf("//oaf:processingchargeamount"), info)); - r - .setProcessingchargecurrency(field(doc.valueOf("//oaf:processingchargeamount/@currency"), info)); - - r.setInstance(instances); - r.setBestaccessright(OafMapperUtils.createBestAccessRights(instances)); - } - - protected abstract List prepareResultPids(Document doc, DataInfo info); - - private List prepareContexts(final Document doc, final DataInfo info) { - final List list = new ArrayList<>(); - for (final Object o : doc.selectNodes("//oaf:concept")) { - final String cid = ((Node) o).valueOf("@id"); - if (StringUtils.isNotBlank(cid)) { - final Context c = new Context(); - c.setId(cid); - c.setDataInfo(Arrays.asList(info)); - list.add(c); - } - } - return list; - } - - protected abstract Qualifier prepareResourceType(Document doc, DataInfo info); - - protected abstract List prepareInstances( - Document doc, - DataInfo info, - KeyValue collectedfrom, - KeyValue hostedby); - - protected abstract List> prepareSources(Document doc, DataInfo info); - - protected abstract List prepareRelevantDates(Document doc, DataInfo info); - - protected abstract List> prepareCoverages(Document doc, DataInfo info); - - protected abstract List> prepareContributors(Document doc, DataInfo info); - - protected abstract List> prepareFormats(Document doc, DataInfo info); - - protected abstract Field preparePublisher(Document doc, DataInfo info); - - protected abstract List> prepareDescriptions(Document doc, DataInfo info); - - protected abstract List prepareTitles(Document doc, DataInfo info); - - protected abstract List prepareSubjects(Document doc, DataInfo info); - - protected abstract Qualifier prepareLanguages(Document doc); - - protected abstract List prepareAuthors(Document doc, DataInfo info); - - protected abstract List> prepareOtherResearchProductTools( - Document doc, - DataInfo info); - - protected abstract List> prepareOtherResearchProductContactGroups( - Document doc, - DataInfo info); - - protected abstract List> prepareOtherResearchProductContactPersons( - Document doc, - DataInfo info); - - protected abstract Qualifier prepareSoftwareProgrammingLanguage(Document doc, DataInfo info); - - protected abstract Field prepareSoftwareCodeRepositoryUrl(Document doc, DataInfo info); - - protected abstract List prepareSoftwareLicenses(Document doc, DataInfo info); - - protected abstract List> prepareSoftwareDocumentationUrls( - Document doc, - DataInfo info); - - protected abstract List prepareDatasetGeoLocations(Document doc, DataInfo info); - - protected abstract Field prepareDatasetMetadataVersionNumber(Document doc, DataInfo info); - - protected abstract Field prepareDatasetLastMetadataUpdate(Document doc, DataInfo info); - - protected abstract Field prepareDatasetVersion(Document doc, DataInfo info); - - protected abstract Field prepareDatasetSize(Document doc, DataInfo info); - - protected abstract Field prepareDatasetDevice(Document doc, DataInfo info); - - protected abstract Field prepareDatasetStorageDate(Document doc, DataInfo info); - - private Journal prepareJournal(final Document doc, final DataInfo info) { - final Node n = doc.selectSingleNode("//oaf:journal"); - if (n != null) { - final String name = n.getText(); - final String issnPrinted = n.valueOf("@issn"); - final String issnOnline = n.valueOf("@eissn"); - final String issnLinking = n.valueOf("@lissn"); - final String ep = n.valueOf("@ep"); - final String iss = n.valueOf("@iss"); - final String sp = n.valueOf("@sp"); - final String vol = n.valueOf("@vol"); - final String edition = n.valueOf("@edition"); - if (StringUtils.isNotBlank(name)) { - return journal(name, issnPrinted, issnOnline, issnLinking, ep, iss, sp, vol, edition, null, null, info); - } - } - return null; - } - - private List findOriginalId(final Document doc) { - final Node n = doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']"); - if (n != null) { - final String id = n.valueOf("./*[local-name()='identifier']"); - if (StringUtils.isNotBlank(id)) { - return Lists.newArrayList(id); - } - } - final List idList = doc - .selectNodes( - "normalize-space(//*[local-name()='header']/*[local-name()='identifier' or local-name()='recordIdentifier']/text())"); - final Set originalIds = Sets.newHashSet(idList); - - if (originalIds.isEmpty()) { - throw new IllegalStateException("missing originalID on " + doc.asXML()); - } - return Lists.newArrayList(originalIds); - } - - protected AccessRight prepareAccessRight(final Node node, final String xpath, final String schemeId) { - final Qualifier qualifier = prepareQualifier(node.valueOf(xpath).trim(), schemeId); - final AccessRight accessRight = new AccessRight(); - accessRight.setClassid(qualifier.getClassid()); - accessRight.setClassname(qualifier.getClassname()); - accessRight.setSchemeid(qualifier.getSchemeid()); - accessRight.setSchemename(qualifier.getSchemename()); - - // TODO set the OAStatus - - return accessRight; - } - - protected Qualifier prepareQualifier(final Node node, final String xpath, final String schemeId) { - return prepareQualifier(node.valueOf(xpath).trim(), schemeId); - } - - protected Qualifier prepareQualifier(final String classId, final String schemeId) { - return vocs.getTermAsQualifier(schemeId, classId); - } - - protected List prepareListStructPropsWithValidQualifier( - final Node node, - final String xpath, - final String xpathClassId, - final String schemeId, - final DataInfo info) { - final List res = new ArrayList<>(); - - for (final Object o : node.selectNodes(xpath)) { - final Node n = (Node) o; - final String classId = n.valueOf(xpathClassId).trim(); - if (vocs.termExists(schemeId, classId)) { - res.add(structuredProperty(n.getText(), vocs.getTermAsQualifier(schemeId, classId), info)); - } - } - return res; - } - - protected List prepareListStructProps( - final Node node, - final String xpath, - final Qualifier qualifier, - final DataInfo info) { - final List res = new ArrayList<>(); - for (final Object o : node.selectNodes(xpath)) { - final Node n = (Node) o; - res.add(structuredProperty(n.getText(), qualifier, info)); - } - return res; - } - - protected List prepareListStructProps( - final Node node, - final String xpath, - final DataInfo info) { - final List res = new ArrayList<>(); - for (final Object o : node.selectNodes(xpath)) { - final Node n = (Node) o; - res - .add( - structuredProperty( - n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"), - n.valueOf("@schemename"), info)); - } - return res; - } - - protected List prepareSubjectList( - final Node node, - final String xpath, - final DataInfo info) { - final List res = new ArrayList<>(); - for (final Object o : node.selectNodes(xpath)) { - final Node n = (Node) o; - res - .add( - subject( - n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"), - n.valueOf("@schemename"), info)); - } - return res; - } - - protected OAIProvenance prepareOAIprovenance(final Document doc) { - final Node n = doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']"); - - if (n == null) { - return null; - } - - final String identifier = n.valueOf("./*[local-name()='identifier']"); - final String baseURL = n.valueOf("./*[local-name()='baseURL']"); - final String metadataNamespace = n.valueOf("./*[local-name()='metadataNamespace']"); - final boolean altered = n.valueOf("@altered").equalsIgnoreCase("true"); - final String datestamp = n.valueOf("./*[local-name()='datestamp']"); - final String harvestDate = n.valueOf("@harvestDate"); - - return oaiIProvenance(identifier, baseURL, metadataNamespace, altered, datestamp, harvestDate); - } - - protected DataInfo prepareDataInfo(final Document doc, final boolean invisible) { - final Node n = doc.selectSingleNode("//oaf:datainfo"); - - if (n == null) { - return dataInfo(false, null, false, invisible, REPOSITORY_PROVENANCE_ACTIONS, "0.9"); - } - - final String paClassId = n.valueOf("./oaf:provenanceaction/@classid"); - final String paClassName = n.valueOf("./oaf:provenanceaction/@classname"); - final String paSchemeId = n.valueOf("./oaf:provenanceaction/@schemeid"); - final String paSchemeName = n.valueOf("./oaf:provenanceaction/@schemename"); - - final boolean deletedbyinference = Boolean.parseBoolean(n.valueOf("./oaf:deletedbyinference")); - final String inferenceprovenance = n.valueOf("./oaf:inferenceprovenance"); - final Boolean inferred = Boolean.parseBoolean(n.valueOf("./oaf:inferred")); - final String trust = n.valueOf("./oaf:trust"); - - return dataInfo( - deletedbyinference, inferenceprovenance, inferred, invisible, - qualifier(paClassId, paClassName, paSchemeId, paSchemeName), trust); - } - - protected Field prepareField(final Node node, final String xpath, final DataInfo info) { - return field(node.valueOf(xpath), info); - } - - protected List> prepareListFields( - final Node node, - final String xpath, - final DataInfo info) { - return listFields(info, prepareListString(node, xpath)); - } - - protected List prepareListString(final Node node, final String xpath) { - final List res = new ArrayList<>(); - for (final Object o : node.selectNodes(xpath)) { - final String s = ((Node) o).getText().trim(); - if (StringUtils.isNotBlank(s)) { - res.add(s); - } - } - return res; - } - - protected Set validateUrl(Collection url) { - UrlValidator urlValidator = UrlValidator.getInstance(); - if (Objects.isNull(url)) { - return new HashSet<>(); - } - return url - .stream() - .filter(u -> urlValidator.isValid(u)) - .collect(Collectors.toCollection(HashSet::new)); - } + protected AbstractMdRecordToOafMapper(final VocabularyGroup vocs, final boolean invisible, + final boolean shouldHashId, final boolean forceOriginalId) { + this.vocs = vocs; + this.invisible = invisible; + this.shouldHashId = shouldHashId; + this.forceOriginalId = forceOriginalId; + } + + protected AbstractMdRecordToOafMapper(final VocabularyGroup vocs, final boolean invisible, + final boolean shouldHashId) { + this.vocs = vocs; + this.invisible = invisible; + this.shouldHashId = shouldHashId; + this.forceOriginalId = false; + } + + public List processMdRecord(final String xml) { + + DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext); + try { + final Document doc = DocumentHelper + .parseText( + xml + .replaceAll(DATACITE_SCHEMA_KERNEL_4, DATACITE_SCHEMA_KERNEL_3) + .replaceAll(DATACITE_SCHEMA_KERNEL_4_SLASH, DATACITE_SCHEMA_KERNEL_3) + .replaceAll(DATACITE_SCHEMA_KERNEL_3_SLASH, DATACITE_SCHEMA_KERNEL_3)); + + final KeyValue collectedFrom = getProvenanceDatasource( + doc, "//oaf:collectedFrom/@id", "//oaf:collectedFrom/@name"); + + if (collectedFrom == null) { + return Lists.newArrayList(); + } + + final KeyValue hostedBy = StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id")) + ? collectedFrom + : getProvenanceDatasource(doc, "//oaf:hostedBy/@id", "//oaf:hostedBy/@name"); + + if (hostedBy == null) { + return Lists.newArrayList(); + } + + final DataInfo info = prepareDataInfo(doc, invisible); + final long lastUpdateTimestamp = new Date().getTime(); + + final List instances = prepareInstances(doc, info, collectedFrom, hostedBy); + + final String type = getResultType(doc, instances); + + return createOafs(doc, type, instances, collectedFrom, info, lastUpdateTimestamp); + } catch (DocumentException e) { + log.error("Error with record:\n" + xml); + return Lists.newArrayList(); + } + } + + protected String getResultType(final Document doc, final List instances) { + final String type = doc.valueOf("//dr:CobjCategory/@type"); + + if (StringUtils.isBlank(type) && vocs.vocabularyExists(ModelConstants.DNET_RESULT_TYPOLOGIES)) { + final String instanceType = instances + .stream() + .map(i -> i.getInstancetype().getClassid()) + .findFirst() + .filter(s -> !UNKNOWN.equalsIgnoreCase(s)) + .orElse("0000"); // Unknown + return Optional + .ofNullable(vocs.getSynonymAsQualifier(ModelConstants.DNET_RESULT_TYPOLOGIES, instanceType)) + .map(Qualifier::getClassid) + .orElse("0000"); + } + + return type; + } + + private KeyValue getProvenanceDatasource(final Document doc, final String xpathId, final String xpathName) { + final String dsId = doc.valueOf(xpathId); + final String dsName = doc.valueOf(xpathName); + + if (StringUtils.isBlank(dsId) || StringUtils.isBlank(dsName)) { + return null; + } + + return keyValue(createOpenaireId(10, dsId, true), dsName); + } + + protected List createOafs( + final Document doc, + final String type, + final List instances, + final KeyValue collectedFrom, + final DataInfo info, + final long lastUpdateTimestamp) { + + final OafEntity entity = createEntity(doc, type, instances, collectedFrom, info, lastUpdateTimestamp); + + final Set originalId = Sets.newHashSet(entity.getOriginalId()); + originalId.add(entity.getId()); + entity.setOriginalId(Lists.newArrayList(originalId)); + + if (!forceOriginalId) { + final String id = IdentifierFactory.createIdentifier(entity, shouldHashId); + if (!id.equals(entity.getId())) { + entity.setId(id); + } + } + + final List oafs = Lists.newArrayList(entity); + + if (!oafs.isEmpty()) { + Set rels = Sets.newHashSet(); + + rels.addAll(addProjectRels(doc, entity)); + rels.addAll(addOtherResultRels(doc, entity)); + rels.addAll(addRelations(doc, entity)); + + oafs.addAll(rels); + } + + return oafs; + } + + private OafEntity createEntity(final Document doc, + final String type, + final List instances, + final KeyValue collectedFrom, + final DataInfo info, + final long lastUpdateTimestamp) { + switch (type.toLowerCase()) { + case "publication": + final Publication p = new Publication(); + populateResultFields(p, doc, instances, collectedFrom, info, lastUpdateTimestamp); + p.setJournal(prepareJournal(doc, info)); + return p; + case "dataset": + final Dataset d = new Dataset(); + populateResultFields(d, doc, instances, collectedFrom, info, lastUpdateTimestamp); + d.setStoragedate(prepareDatasetStorageDate(doc, info)); + d.setDevice(prepareDatasetDevice(doc, info)); + d.setSize(prepareDatasetSize(doc, info)); + d.setVersion(prepareDatasetVersion(doc, info)); + d.setLastmetadataupdate(prepareDatasetLastMetadataUpdate(doc, info)); + d.setMetadataversionnumber(prepareDatasetMetadataVersionNumber(doc, info)); + d.setGeolocation(prepareDatasetGeoLocations(doc, info)); + return d; + case "software": + final Software s = new Software(); + populateResultFields(s, doc, instances, collectedFrom, info, lastUpdateTimestamp); + s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info)); + s.setLicense(prepareSoftwareLicenses(doc, info)); + s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info)); + s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info)); + return s; + case "": + case "otherresearchproducts": + default: + final OtherResearchProduct o = new OtherResearchProduct(); + populateResultFields(o, doc, instances, collectedFrom, info, lastUpdateTimestamp); + o.setContactperson(prepareOtherResearchProductContactPersons(doc, info)); + o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info)); + o.setTool(prepareOtherResearchProductTools(doc, info)); + return o; + } + } + + private List addProjectRels( + final Document doc, + final OafEntity entity) { + + final List res = new ArrayList<>(); + + final String docId = entity.getId(); + + for (final Object o : doc.selectNodes("//oaf:projectid")) { + + final String originalId = ((Node) o).getText(); + + final String validationdDate = ((Node) o).valueOf("@validationDate"); + + if (StringUtils.isNotBlank(originalId)) { + final String projectId = createOpenaireId(40, originalId, true); + + res + .add( + OafMapperUtils + .getRelation( + docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, entity, validationdDate)); + res + .add( + OafMapperUtils + .getRelation(projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, entity, validationdDate)); + } + } + + return res; + } + + private List addRelations(Document doc, OafEntity entity) { + + final List rels = Lists.newArrayList(); + + for (Object o : doc.selectNodes("//oaf:relation")) { + Element element = (Element) o; + + final String target = StringUtils.trim(element.getText()); + final String relType = element.attributeValue("relType"); + final String subRelType = element.attributeValue("subRelType"); + final String relClass = element.attributeValue("relClass"); + + if (StringUtils.isNotBlank(target) && StringUtils.isNotBlank(relType) && StringUtils.isNotBlank(subRelType) + && StringUtils.isNotBlank(relClass)) { + + final String relClassInverse = ModelSupport + .findInverse(ModelSupport.rel(relType, subRelType, relClass)) + .getInverseRelClass(); + final String validationdDate = ((Node) o).valueOf("@validationDate"); + + if (StringUtils.isNotBlank(target)) { + final String targetType = element.attributeValue("targetType"); + if (StringUtils.isNotBlank(targetType)) { + final String targetId = createOpenaireId(targetType, target, true); + rels + .add( + OafMapperUtils + .getRelation( + entity.getId(), targetId, relType, subRelType, relClass, entity, + validationdDate)); + rels + .add( + OafMapperUtils + .getRelation( + targetId, entity.getId(), relType, subRelType, relClassInverse, entity, + validationdDate)); + } + } + } + } + return rels; + } + + protected abstract List addOtherResultRels( + final Document doc, + final OafEntity entity); + + private void populateResultFields( + final Result r, + final Document doc, + final List instances, + final KeyValue collectedFrom, + final DataInfo info, + final long lastUpdateTimestamp) { + r.setDataInfo(info); + r.setLastupdatetimestamp(lastUpdateTimestamp); + r.setId(createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false)); + r.setOriginalId(findOriginalId(doc)); + r.setCollectedfrom(Arrays.asList(collectedFrom)); + r.setPid(IdentifierFactory.getPids(prepareResultPids(doc, info), collectedFrom)); + r.setDateofcollection(doc.valueOf("//dr:dateOfCollection/text()|//dri:dateOfCollection/text()")); + r.setDateoftransformation(doc.valueOf("//dr:dateOfTransformation/text()|//dri:dateOfTransformation/text()")); + r.setExtraInfo(new ArrayList<>()); // NOT PRESENT IN MDSTORES + r.setOaiprovenance(prepareOAIprovenance(doc)); + r.setAuthor(prepareAuthors(doc, info)); + r.setLanguage(prepareLanguages(doc)); + r.setCountry(new ArrayList<>()); // NOT PRESENT IN MDSTORES + r.setSubject(prepareSubjects(doc, info)); + r.setTitle(prepareTitles(doc, info)); + r.setRelevantdate(prepareRelevantDates(doc, info)); + r.setDescription(prepareDescriptions(doc, info)); + r.setDateofacceptance(prepareField(doc, "//oaf:dateAccepted", info)); + r.setPublisher(preparePublisher(doc, info)); + r.setEmbargoenddate(prepareField(doc, "//oaf:embargoenddate", info)); + r.setSource(prepareSources(doc, info)); + r.setFulltext(prepareListFields(doc, "//oaf:fulltext", info)); + r.setFormat(prepareFormats(doc, info)); + r.setContributor(prepareContributors(doc, info)); + r.setResourcetype(prepareResourceType(doc, info)); + r.setCoverage(prepareCoverages(doc, info)); + r.setContext(prepareContexts(doc, info)); + r.setExternalReference(new ArrayList<>()); // NOT PRESENT IN MDSTORES + r + .setProcessingchargeamount(field(doc.valueOf("//oaf:processingchargeamount"), info)); + r + .setProcessingchargecurrency(field(doc.valueOf("//oaf:processingchargeamount/@currency"), info)); + + r.setInstance(instances); + r.setBestaccessright(OafMapperUtils.createBestAccessRights(instances)); + } + + protected abstract List prepareResultPids(Document doc, DataInfo info); + + private List prepareContexts(final Document doc, final DataInfo info) { + final List list = new ArrayList<>(); + for (final Object o : doc.selectNodes("//oaf:concept")) { + final String cid = ((Node) o).valueOf("@id"); + if (StringUtils.isNotBlank(cid)) { + final Context c = new Context(); + c.setId(cid); + c.setDataInfo(Arrays.asList(info)); + list.add(c); + } + } + return list; + } + + protected abstract Qualifier prepareResourceType(Document doc, DataInfo info); + + protected abstract List prepareInstances( + Document doc, + DataInfo info, + KeyValue collectedfrom, + KeyValue hostedby); + + protected abstract List> prepareSources(Document doc, DataInfo info); + + protected abstract List prepareRelevantDates(Document doc, DataInfo info); + + protected abstract List> prepareCoverages(Document doc, DataInfo info); + + protected abstract List> prepareContributors(Document doc, DataInfo info); + + protected abstract List> prepareFormats(Document doc, DataInfo info); + + protected abstract Field preparePublisher(Document doc, DataInfo info); + + protected abstract List> prepareDescriptions(Document doc, DataInfo info); + + protected abstract List prepareTitles(Document doc, DataInfo info); + + protected abstract List prepareSubjects(Document doc, DataInfo info); + + protected abstract Qualifier prepareLanguages(Document doc); + + protected abstract List prepareAuthors(Document doc, DataInfo info); + + protected abstract List> prepareOtherResearchProductTools( + Document doc, + DataInfo info); + + protected abstract List> prepareOtherResearchProductContactGroups( + Document doc, + DataInfo info); + + protected abstract List> prepareOtherResearchProductContactPersons( + Document doc, + DataInfo info); + + protected abstract Qualifier prepareSoftwareProgrammingLanguage(Document doc, DataInfo info); + + protected abstract Field prepareSoftwareCodeRepositoryUrl(Document doc, DataInfo info); + + protected abstract List prepareSoftwareLicenses(Document doc, DataInfo info); + + protected abstract List> prepareSoftwareDocumentationUrls( + Document doc, + DataInfo info); + + protected abstract List prepareDatasetGeoLocations(Document doc, DataInfo info); + + protected abstract Field prepareDatasetMetadataVersionNumber(Document doc, DataInfo info); + + protected abstract Field prepareDatasetLastMetadataUpdate(Document doc, DataInfo info); + + protected abstract Field prepareDatasetVersion(Document doc, DataInfo info); + + protected abstract Field prepareDatasetSize(Document doc, DataInfo info); + + protected abstract Field prepareDatasetDevice(Document doc, DataInfo info); + + protected abstract Field prepareDatasetStorageDate(Document doc, DataInfo info); + + private Journal prepareJournal(final Document doc, final DataInfo info) { + final Node n = doc.selectSingleNode("//oaf:journal"); + if (n != null) { + final String name = n.getText(); + final String issnPrinted = n.valueOf("@issn"); + final String issnOnline = n.valueOf("@eissn"); + final String issnLinking = n.valueOf("@lissn"); + final String ep = n.valueOf("@ep"); + final String iss = n.valueOf("@iss"); + final String sp = n.valueOf("@sp"); + final String vol = n.valueOf("@vol"); + final String edition = n.valueOf("@edition"); + if (StringUtils.isNotBlank(name)) { + return journal(name, issnPrinted, issnOnline, issnLinking, ep, iss, sp, vol, edition, null, null, info); + } + } + return null; + } + + private List findOriginalId(final Document doc) { + final Node n = doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']"); + if (n != null) { + final String id = n.valueOf("./*[local-name()='identifier']"); + if (StringUtils.isNotBlank(id)) { + return Lists.newArrayList(id); + } + } + final List idList = doc + .selectNodes( + "normalize-space(//*[local-name()='header']/*[local-name()='identifier' or local-name()='recordIdentifier']/text())"); + final Set originalIds = Sets.newHashSet(idList); + + if (originalIds.isEmpty()) { + throw new IllegalStateException("missing originalID on " + doc.asXML()); + } + return Lists.newArrayList(originalIds); + } + + protected AccessRight prepareAccessRight(final Node node, final String xpath, final String schemeId) { + final Qualifier qualifier = prepareQualifier(node.valueOf(xpath).trim(), schemeId); + final AccessRight accessRight = new AccessRight(); + accessRight.setClassid(qualifier.getClassid()); + accessRight.setClassname(qualifier.getClassname()); + accessRight.setSchemeid(qualifier.getSchemeid()); + accessRight.setSchemename(qualifier.getSchemename()); + + // TODO set the OAStatus + + return accessRight; + } + + protected Qualifier prepareQualifier(final Node node, final String xpath, final String schemeId) { + return prepareQualifier(node.valueOf(xpath).trim(), schemeId); + } + + protected Qualifier prepareQualifier(final String classId, final String schemeId) { + return vocs.getTermAsQualifier(schemeId, classId); + } + + protected List prepareListStructPropsWithValidQualifier( + final Node node, + final String xpath, + final String xpathClassId, + final String schemeId, + final DataInfo info) { + final List res = new ArrayList<>(); + + for (final Object o : node.selectNodes(xpath)) { + final Node n = (Node) o; + final String classId = n.valueOf(xpathClassId).trim(); + if (vocs.termExists(schemeId, classId)) { + res.add(structuredProperty(n.getText(), vocs.getTermAsQualifier(schemeId, classId), info)); + } + } + return res; + } + + protected List prepareListStructProps( + final Node node, + final String xpath, + final Qualifier qualifier, + final DataInfo info) { + final List res = new ArrayList<>(); + for (final Object o : node.selectNodes(xpath)) { + final Node n = (Node) o; + res.add(structuredProperty(n.getText(), qualifier, info)); + } + return res; + } + + protected List prepareListStructProps( + final Node node, + final String xpath, + final DataInfo info) { + final List res = new ArrayList<>(); + for (final Object o : node.selectNodes(xpath)) { + final Node n = (Node) o; + res + .add( + structuredProperty( + n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"), + n.valueOf("@schemename"), info)); + } + return res; + } + + protected List prepareSubjectList( + final Node node, + final String xpath, + final DataInfo info) { + final List res = new ArrayList<>(); + for (final Object o : node.selectNodes(xpath)) { + final Node n = (Node) o; + res + .add( + subject( + n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"), + n.valueOf("@schemename"), info)); + } + return res; + } + + protected OAIProvenance prepareOAIprovenance(final Document doc) { + final Node n = doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']"); + + if (n == null) { + return null; + } + + final String identifier = n.valueOf("./*[local-name()='identifier']"); + final String baseURL = n.valueOf("./*[local-name()='baseURL']"); + final String metadataNamespace = n.valueOf("./*[local-name()='metadataNamespace']"); + final boolean altered = n.valueOf("@altered").equalsIgnoreCase("true"); + final String datestamp = n.valueOf("./*[local-name()='datestamp']"); + final String harvestDate = n.valueOf("@harvestDate"); + + return oaiIProvenance(identifier, baseURL, metadataNamespace, altered, datestamp, harvestDate); + } + + protected DataInfo prepareDataInfo(final Document doc, final boolean invisible) { + final Node n = doc.selectSingleNode("//oaf:datainfo"); + + if (n == null) { + return dataInfo(false, null, false, invisible, REPOSITORY_PROVENANCE_ACTIONS, "0.9"); + } + + final String paClassId = n.valueOf("./oaf:provenanceaction/@classid"); + final String paClassName = n.valueOf("./oaf:provenanceaction/@classname"); + final String paSchemeId = n.valueOf("./oaf:provenanceaction/@schemeid"); + final String paSchemeName = n.valueOf("./oaf:provenanceaction/@schemename"); + + final boolean deletedbyinference = Boolean.parseBoolean(n.valueOf("./oaf:deletedbyinference")); + final String inferenceprovenance = n.valueOf("./oaf:inferenceprovenance"); + final Boolean inferred = Boolean.parseBoolean(n.valueOf("./oaf:inferred")); + final String trust = n.valueOf("./oaf:trust"); + + return dataInfo( + deletedbyinference, inferenceprovenance, inferred, invisible, + qualifier(paClassId, paClassName, paSchemeId, paSchemeName), trust); + } + + protected Field prepareField(final Node node, final String xpath, final DataInfo info) { + return field(node.valueOf(xpath), info); + } + + protected List> prepareListFields( + final Node node, + final String xpath, + final DataInfo info) { + return listFields(info, prepareListString(node, xpath)); + } + + protected List prepareListString(final Node node, final String xpath) { + final List res = new ArrayList<>(); + for (final Object o : node.selectNodes(xpath)) { + final String s = ((Node) o).getText().trim(); + if (StringUtils.isNotBlank(s)) { + res.add(s); + } + } + return res; + } + + protected Set validateUrl(Collection url) { + UrlValidator urlValidator = UrlValidator.getInstance(); + if (Objects.isNull(url)) { + return new HashSet<>(); + } + return url + .stream() + .filter(u -> urlValidator.isValid(u)) + .collect(Collectors.toCollection(HashSet::new)); + } } diff --git a/pom.xml b/pom.xml index 55265bf55..9b60b9078 100644 --- a/pom.xml +++ b/pom.xml @@ -807,7 +807,7 @@ 3.3.3 3.4.2 [2.12,3.0) - [3.14.0-SNAPSHOT] + [3.15.0] [4.0.3] [6.0.5] [3.1.6] From f3f7604e6c342a4ec931ec5d1e5fb7370da029c3 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 27 Sep 2022 15:21:37 +0200 Subject: [PATCH 189/214] trying to fix a test that fails only on Jenkins --- .../test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala | 3 +++ 1 file changed, 3 insertions(+) diff --git a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala index 48da049da..01ef3ba54 100644 --- a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala +++ b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala @@ -54,6 +54,9 @@ class DataciteToOAFTest extends AbstractVocabularyTest { val path = getClass.getResource("/eu/dnetlib/dhp/actionmanager/datacite/dataset").getPath val conf = new SparkConf() + conf.set("spark.driver.host", "localhost") + conf.set("spark.ui.enabled", "false") + val spark: SparkSession = SparkSession .builder() .config(conf) From f1d7d45cf7b210c43d8af9635220bc710fce2341 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 28 Sep 2022 12:01:43 +0200 Subject: [PATCH 190/214] [BulkTag] fixed issue --- .../dnetlib/dhp/bulktag/community/ResultTagger.java | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java index ee75bf955..0452a6ebf 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java @@ -158,7 +158,8 @@ public class ResultTagger implements Serializable { } result.getContext().forEach(c -> { - if (communities.contains(c.getId())) { + final String cId = c.getId(); + if (communities.contains(cId)) { Optional> opt_dataInfoList = Optional.ofNullable(c.getDataInfo()); List dataInfoList; if (opt_dataInfoList.isPresent()) @@ -167,7 +168,7 @@ public class ResultTagger implements Serializable { dataInfoList = new ArrayList<>(); c.setDataInfo(dataInfoList); } - if (subjects.contains(c)) + if (subjects.contains(cId)) dataInfoList .add( OafMapperUtils @@ -178,7 +179,7 @@ public class ResultTagger implements Serializable { CLASS_ID_SUBJECT, CLASS_NAME_BULKTAG_SUBJECT, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), TAGGING_TRUST)); - if (datasources.contains(c)) + if (datasources.contains(cId)) dataInfoList .add( OafMapperUtils @@ -189,7 +190,7 @@ public class ResultTagger implements Serializable { CLASS_ID_DATASOURCE, CLASS_NAME_BULKTAG_DATASOURCE, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), TAGGING_TRUST)); - if (czenodo.contains(c)) + if (czenodo.contains(cId)) dataInfoList .add( OafMapperUtils @@ -200,7 +201,7 @@ public class ResultTagger implements Serializable { CLASS_ID_CZENODO, CLASS_NAME_BULKTAG_ZENODO, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), TAGGING_TRUST)); - if (aconstraints.contains(c)) + if (aconstraints.contains(cId)) dataInfoList .add( OafMapperUtils From b5b5a4c1928679ab308bcfe70d7969f0c1b99664 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 28 Sep 2022 12:42:51 +0200 Subject: [PATCH 191/214] [CleanCountry] fixed issue --- .../dhp/oa/graph/clean/country/CleanCountrySparkJob.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java index c150c63df..cd77f342e 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java @@ -117,7 +117,7 @@ public class CleanCountrySparkJob implements Serializable { p -> p .getQualifier() .getClassid() - .equals(PidType.doi) && pidInParam(p.getValue(), verifyParam))) { + .equals(PidType.doi.toString()) && pidInParam(p.getValue(), verifyParam))) { r .setCountry( r From 2ebb1459a9c01eeda8d81865c75585e361cc5426 Mon Sep 17 00:00:00 2001 From: dimitrispie Date: Wed, 28 Sep 2022 14:36:57 +0300 Subject: [PATCH 192/214] Fixed type in no_downloads --- .../scripts/step16-createIndicatorsTables.sql | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql index 417ed6e4e..1bda07629 100755 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql @@ -454,16 +454,16 @@ FROM publication_datasources pd compute stats indi_pub_hybrid_oa_with_cc; create table indi_pub_downloads stored as parquet as -SELECT result_id, sum(downloads) no_dowloads from openaire_prod_usage_stats.usage_stats +SELECT result_id, sum(downloads) no_downloads from openaire_prod_usage_stats.usage_stats join publication on result_id=id where downloads>0 GROUP BY result_id -order by no_dowloads desc; +order by no_downloads desc; compute stats indi_pub_downloads; create table indi_pub_downloads_datasource stored as parquet as -SELECT result_id, repository_id, sum(downloads) no_dowloads from openaire_prod_usage_stats.usage_stats +SELECT result_id, repository_id, sum(downloads) no_downloads from openaire_prod_usage_stats.usage_stats join publication on result_id=id where downloads>0 GROUP BY result_id, repository_id @@ -472,7 +472,7 @@ order by result_id; compute stats indi_pub_downloads_datasource; create table indi_pub_downloads_year stored as parquet as -SELECT result_id, substring(us.`date`, 1,4) as `year`, sum(downloads) no_dowloads from openaire_prod_usage_stats.usage_stats us +SELECT result_id, substring(us.`date`, 1,4) as `year`, sum(downloads) no_downloads from openaire_prod_usage_stats.usage_stats us join publication on result_id=id where downloads>0 GROUP BY result_id, `year` order by `year` asc; @@ -480,7 +480,7 @@ order by `year` asc; compute stats indi_pub_downloads_year; create table indi_pub_downloads_datasource_year stored as parquet as -SELECT result_id, substring(us.`date`, 1,4) as `year`, repository_id, sum(downloads) no_dowloads from openaire_prod_usage_stats.usage_stats us +SELECT result_id, substring(us.`date`, 1,4) as `year`, repository_id, sum(downloads) no_downloads from openaire_prod_usage_stats.usage_stats us join publication on result_id=id where downloads>0 GROUP BY result_id, repository_id, `year` From bdc46e3eaab57a926977d162131d78933566c08b Mon Sep 17 00:00:00 2001 From: dimitrispie Date: Wed, 28 Sep 2022 14:59:08 +0300 Subject: [PATCH 193/214] Remove denormalization of results to fix downloads numbers in monitor --- .../oozie_app/scripts/step20-createMonitorDB.sql | 16 ---------------- 1 file changed, 16 deletions(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql index 290acbf9f..2505c3a34 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql @@ -39,7 +39,6 @@ create table TARGET.result stored as parquet as 'openorgs____::5f31346d444a7f06a28c880fb170b0f6', --Ghent University 'openorgs____::2dbe47117fd5409f9c61620813456632', --University of Luxembourg 'openorgs____::6445d7758d3a40c4d997953b6632a368', --National Institute of Informatics (NII) - 'openorgs____::b77c01aa15de3675da34277d48de2ec1', -- Valencia Catholic University Saint Vincent Martyr 'openorgs____::7fe2f66cdc43983c6b24816bfe9cf6a0', -- Unviersity of Warsaw 'openorgs____::15e7921fc50d9aa1229a82a84429419e', -- University Of Thessaly @@ -224,18 +223,3 @@ create table TARGET.indi_result_with_pid stored as parquet as select * from SOUR --create table TARGET.indi_software_gold_oa stored as parquet as select * from SOURCE.indi_software_gold_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id); --compute stats TARGET.indi_software_gold_oa; ---denorm -alter table TARGET.result rename to TARGET.res_tmp; - -create table TARGET.result_denorm stored as parquet as - select distinct r.*, rp.project, p.acronym as pacronym, p.title as ptitle, p.funder as pfunder, p.funding_lvl0 as pfunding_lvl0, rd.datasource, d.name as dname, d.type as dtype - from TARGET.res_tmp r - left outer join TARGET.result_projects rp on rp.id=r.id - left outer join TARGET.result_datasources rd on rd.id=r.id - left outer join TARGET.project p on p.id=rp.project - left outer join TARGET.datasource d on d.id=rd.datasource; -compute stats TARGET.result_denorm; - -alter table TARGET.result_denorm rename to TARGET.result; -drop table TARGET.res_tmp; ---- done! \ No newline at end of file From 49360770d71d8930838240866a1cbc3ea06b465d Mon Sep 17 00:00:00 2001 From: Alessia Bardi Date: Wed, 28 Sep 2022 14:16:39 +0200 Subject: [PATCH 194/214] map w3id as instance url --- .../dhp/oa/graph/raw/OdfToOafMapper.java | 3 ++ .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 17 +++++++---- .../eu/dnetlib/dhp/oa/graph/raw/rohub.xml | 30 ++++++++----------- 3 files changed, 27 insertions(+), 23 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java index a25bcd47e..39c77bd37 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java @@ -177,6 +177,9 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { for (final Object o : doc.selectNodes("//*[local-name()='identifier' and ./@identifierType='landingPage']")) { url.add(trimAndDecodeUrl(((Node) o).getText().trim())); } + for (final Object o : doc.selectNodes("//*[local-name()='identifier' and ./@identifierType='w3id']")) { + url.add(trimAndDecodeUrl(((Node) o).getText().trim())); + } Set validUrl = validateUrl(url); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index 7552d1789..f0eadbd0d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -936,11 +936,18 @@ class MappersTest { System.out.println("***************"); System.out.println(new ObjectMapper().writeValueAsString(list)); System.out.println("***************"); -// final OtherResearchProduct p = (OtherResearchProduct) list.get(0); -// assertValidId(p.getId()); -// assertValidId(p.getCollectedfrom().get(0).getKey()); -// System.out.println(p.getTitle().get(0).getValue()); -// assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue())); + assertEquals(5, list.size()); + final OtherResearchProduct p = (OtherResearchProduct) list.get(0); + assertValidId(p.getId()); + assertTrue(p.getId().startsWith("50|w3id")); + assertValidId(p.getCollectedfrom().get(0).getKey()); + assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue())); + assertEquals(1, p.getInstance().size()); + assertEquals("https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca", p.getPid().get(0).getValue()); + Instance inst = p.getInstance().get(0); + assertEquals("https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca", inst.getPid().get(0).getValue()); + assertEquals("https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca", inst.getUrl().get(0)); + } @Test diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/rohub.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/rohub.xml index c85b55786..e1e30c3de 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/rohub.xml +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/rohub.xml @@ -21,15 +21,13 @@ - https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca - + https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca + + https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca + - - https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca/resources/24fae96f-f986-46e1-bfd0-a21ca20ff0ce - - - https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca/resources/6d3427a8-352e-49f4-9796-f618c44dc16d - + https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca/resources/24fae96f-f986-46e1-bfd0-a21ca20ff0ce + https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca/resources/6d3427a8-352e-49f4-9796-f618c44dc16d RO-crate @@ -43,21 +41,17 @@ Poznań Supercomputing and Networking Center - - - Generation Service - + + Generation Service - - CNR-ISMAR - + CNR-ISMAR - 2018-06-20T11:21:46Z + 2018-06-20T11:21:46Z The use of biological effects tools offer enormous potential to meet the challenges outlined by the European Union Marine Strategy Framework Directive (MSFD) whereby Member States are required to develop a robust set of tools for defining 11 qualitative descriptors of Good Environmental Status (GES), such as demonstrating that "Concentrations of contaminants are at levels not giving rise to pollution effects" (GES Descriptor 8). This paper discusses the combined approach of monitoring chemical contaminant levels, along side biological effect measurements relating to the effect of pollutants, for undertaking assessments of GES across European marine regions. We outline the minimum standards that biological effects tools should meet if they are to be used for defining GES in relation to Descriptor 8 and describe the current international initiatives underway to develop assessment criteria for these biological effects techniques. Crown Copyright (C) 2010 Published by Elsevier Ltd. All rights reserved. @@ -74,9 +68,9 @@ EOSC::RO-crate - https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca + https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca other research product - + 2018-06-20 OPEN From 2c0c3f18064da57d31f88639b41f94348a404b6e Mon Sep 17 00:00:00 2001 From: dimitrispie Date: Wed, 28 Sep 2022 19:33:24 +0300 Subject: [PATCH 195/214] Cast amount to float for table result_apcs --- .../dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15_5.sql | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15_5.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15_5.sql index 04c7f83b9..86ead4a2c 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15_5.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15_5.sql @@ -42,7 +42,7 @@ join ${stats_db_name}.result res on res.id=r.id; create table ${stats_db_name}.result_apc as select r.id, r.amount, r.currency from ( - select substr(r.id, 4) as id, inst.processingchargeamount.value as amount, inst.processingchargecurrency.value as currency + select substr(r.id, 4) as id, cast(inst.processingchargeamount.value as float) as amount, inst.processingchargecurrency.value as currency from ${openaire_db_name}.result r lateral view explode(r.instance) instances as inst) r join ${stats_db_name}.result res on res.id=r.id where r.amount is not null; From 188f25eefae15d23eb92dbd977d6e41fd78af157 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 3 Oct 2022 12:42:52 +0200 Subject: [PATCH 196/214] [BipFinder] Fixed issue for wrong escaped char in doi --- .../createunresolvedentities/PrepareBipFinder.java | 6 ++++-- .../actionmanager/createunresolvedentities/PrepareTest.java | 5 ++++- .../dhp/actionmanager/createunresolvedentities/bip/bip.json | 3 ++- 3 files changed, 10 insertions(+), 4 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareBipFinder.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareBipFinder.java index 80573c71a..a4f5c22bc 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareBipFinder.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareBipFinder.java @@ -11,6 +11,7 @@ import java.util.List; import java.util.Optional; import java.util.stream.Collectors; +import com.fasterxml.jackson.core.JsonParser; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; @@ -40,7 +41,6 @@ import eu.dnetlib.dhp.utils.DHPUtils; public class PrepareBipFinder implements Serializable { private static final Logger log = LoggerFactory.getLogger(PrepareBipFinder.class); - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); public static void main(String[] args) throws Exception { @@ -82,9 +82,11 @@ public class PrepareBipFinder implements Serializable { final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + ObjectMapper mapper = new ObjectMapper() + .configure(JsonParser.Feature.ALLOW_BACKSLASH_ESCAPING_ANY_CHARACTER, true); JavaRDD bipDeserializeJavaRDD = sc .textFile(inputPath) - .map(item -> OBJECT_MAPPER.readValue(item, BipDeserialize.class)); + .map(item -> mapper.readValue(item, BipDeserialize.class)); spark .createDataset(bipDeserializeJavaRDD.flatMap(entry -> entry.keySet().stream().map(key -> { diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareTest.java index cc8108bde..d0ce69043 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareTest.java @@ -88,7 +88,7 @@ public class PrepareTest { .textFile(workingDir.toString() + "/work/bip") .map(item -> OBJECT_MAPPER.readValue(item, Result.class)); - Assertions.assertEquals(86, tmp.count()); + Assertions.assertEquals(87, tmp.count()); String doi1 = "unresolved::10.0000/096020199389707::doi"; @@ -151,6 +151,9 @@ public class PrepareTest { Assertions.assertEquals(1, tmp.filter(r -> r.getId().equals(doi2)).count()); Assertions.assertEquals(1, tmp.filter(r -> r.getId().equals(doi2)).collect().get(0).getInstance().size()); + tmp.filter(r -> r.getId().startsWith("unresolved::10.2111/1551-5028(2004)057")) + .foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r))); + } @Test diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/bip/bip.json b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/bip/bip.json index 03cef4be1..3a077ab5c 100644 --- a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/bip/bip.json +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/bip/bip.json @@ -83,4 +83,5 @@ {"10.0000/hoplos.v4i7.41295": [{"id": "influence", "unit": [{"value": "5.91019644836e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.0", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "8.48190886761e-09", "key": "score"}]}]} {"10.0000/hoplos.v4i7.42830": [{"id": "influence", "unit": [{"value": "5.91019644836e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.0", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "8.48190886761e-09", "key": "score"}]}]} {"10.0000/hoplos.v4i7.42861": [{"id": "influence", "unit": [{"value": "5.91019644836e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.0", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "8.48190886761e-09", "key": "score"}]}]} -{"10.0000/hoplos.v4i7.43096": [{"id": "influence", "unit": [{"value": "5.91019644836e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.0", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "8.48190886761e-09", "key": "score"}]}]} \ No newline at end of file +{"10.0000/hoplos.v4i7.43096": [{"id": "influence", "unit": [{"value": "5.91019644836e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.0", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "8.48190886761e-09", "key": "score"}]}]} +{"10.2111/1551-5028(2004)057\[0539:sdsocg\]2.0.co;2": [{"id":"influence", "unit":[{"key":"score","value":"6.3290875E-9"},{"key":"class","value":"C"}]}, {"id":"popularity", "unit":[{"key":"score","value":"6.576763E-9"},{"key":"class","value":"C"}]}, {"id":"influence_alt", "unit":[{"key":"score","value":"11"},{"key":"class","value":"C"}]}, {"id":"popularity_alt", "unit":[{"key":"score","value":"1.0142108"},{"key":"class","value":"C"}]}, {"id":"impulse", "unit":[{"key":"score","value":"1"},{"key":"class","value":"C"}]}]} \ No newline at end of file From 28dc317350d792e75a843e8d4c9d6b2ea5735a2c Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 4 Oct 2022 09:47:27 +0200 Subject: [PATCH 197/214] [BipFinder] refactoring --- .../createunresolvedentities/PrepareBipFinder.java | 4 ++-- .../actionmanager/createunresolvedentities/PrepareTest.java | 5 +++-- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareBipFinder.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareBipFinder.java index a4f5c22bc..2d2633e0f 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareBipFinder.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareBipFinder.java @@ -11,7 +11,6 @@ import java.util.List; import java.util.Optional; import java.util.stream.Collectors; -import com.fasterxml.jackson.core.JsonParser; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; @@ -23,6 +22,7 @@ import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; import org.slf4j.LoggerFactory; +import com.fasterxml.jackson.core.JsonParser; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.actionmanager.bipmodel.BipDeserialize; @@ -83,7 +83,7 @@ public class PrepareBipFinder implements Serializable { final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); ObjectMapper mapper = new ObjectMapper() - .configure(JsonParser.Feature.ALLOW_BACKSLASH_ESCAPING_ANY_CHARACTER, true); + .configure(JsonParser.Feature.ALLOW_BACKSLASH_ESCAPING_ANY_CHARACTER, true); JavaRDD bipDeserializeJavaRDD = sc .textFile(inputPath) .map(item -> mapper.readValue(item, BipDeserialize.class)); diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareTest.java index d0ce69043..6ae1f246d 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareTest.java @@ -151,8 +151,9 @@ public class PrepareTest { Assertions.assertEquals(1, tmp.filter(r -> r.getId().equals(doi2)).count()); Assertions.assertEquals(1, tmp.filter(r -> r.getId().equals(doi2)).collect().get(0).getInstance().size()); - tmp.filter(r -> r.getId().startsWith("unresolved::10.2111/1551-5028(2004)057")) - .foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r))); + tmp + .filter(r -> r.getId().startsWith("unresolved::10.2111/1551-5028(2004)057")) + .foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r))); } From 7324853a1720821fc7d2ce4f1db94cd5f9892932 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 4 Oct 2022 14:29:39 +0200 Subject: [PATCH 198/214] Revert "[BipFinder] refactoring" This reverts commit 28dc317350d792e75a843e8d4c9d6b2ea5735a2c. --- .../createunresolvedentities/PrepareBipFinder.java | 4 ++-- .../actionmanager/createunresolvedentities/PrepareTest.java | 5 ++--- 2 files changed, 4 insertions(+), 5 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareBipFinder.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareBipFinder.java index 2d2633e0f..a4f5c22bc 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareBipFinder.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareBipFinder.java @@ -11,6 +11,7 @@ import java.util.List; import java.util.Optional; import java.util.stream.Collectors; +import com.fasterxml.jackson.core.JsonParser; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; @@ -22,7 +23,6 @@ import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import com.fasterxml.jackson.core.JsonParser; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.actionmanager.bipmodel.BipDeserialize; @@ -83,7 +83,7 @@ public class PrepareBipFinder implements Serializable { final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); ObjectMapper mapper = new ObjectMapper() - .configure(JsonParser.Feature.ALLOW_BACKSLASH_ESCAPING_ANY_CHARACTER, true); + .configure(JsonParser.Feature.ALLOW_BACKSLASH_ESCAPING_ANY_CHARACTER, true); JavaRDD bipDeserializeJavaRDD = sc .textFile(inputPath) .map(item -> mapper.readValue(item, BipDeserialize.class)); diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareTest.java index 6ae1f246d..d0ce69043 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareTest.java @@ -151,9 +151,8 @@ public class PrepareTest { Assertions.assertEquals(1, tmp.filter(r -> r.getId().equals(doi2)).count()); Assertions.assertEquals(1, tmp.filter(r -> r.getId().equals(doi2)).collect().get(0).getInstance().size()); - tmp - .filter(r -> r.getId().startsWith("unresolved::10.2111/1551-5028(2004)057")) - .foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r))); + tmp.filter(r -> r.getId().startsWith("unresolved::10.2111/1551-5028(2004)057")) + .foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r))); } From 4d8339614b5e1240243e4a139d494e1988f6746e Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 4 Oct 2022 14:29:47 +0200 Subject: [PATCH 199/214] Revert "[BipFinder] Fixed issue for wrong escaped char in doi" This reverts commit 188f25eefae15d23eb92dbd977d6e41fd78af157. --- .../createunresolvedentities/PrepareBipFinder.java | 6 ++---- .../actionmanager/createunresolvedentities/PrepareTest.java | 5 +---- .../dhp/actionmanager/createunresolvedentities/bip/bip.json | 3 +-- 3 files changed, 4 insertions(+), 10 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareBipFinder.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareBipFinder.java index a4f5c22bc..80573c71a 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareBipFinder.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareBipFinder.java @@ -11,7 +11,6 @@ import java.util.List; import java.util.Optional; import java.util.stream.Collectors; -import com.fasterxml.jackson.core.JsonParser; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; @@ -41,6 +40,7 @@ import eu.dnetlib.dhp.utils.DHPUtils; public class PrepareBipFinder implements Serializable { private static final Logger log = LoggerFactory.getLogger(PrepareBipFinder.class); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); public static void main(String[] args) throws Exception { @@ -82,11 +82,9 @@ public class PrepareBipFinder implements Serializable { final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - ObjectMapper mapper = new ObjectMapper() - .configure(JsonParser.Feature.ALLOW_BACKSLASH_ESCAPING_ANY_CHARACTER, true); JavaRDD bipDeserializeJavaRDD = sc .textFile(inputPath) - .map(item -> mapper.readValue(item, BipDeserialize.class)); + .map(item -> OBJECT_MAPPER.readValue(item, BipDeserialize.class)); spark .createDataset(bipDeserializeJavaRDD.flatMap(entry -> entry.keySet().stream().map(key -> { diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareTest.java index d0ce69043..cc8108bde 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareTest.java @@ -88,7 +88,7 @@ public class PrepareTest { .textFile(workingDir.toString() + "/work/bip") .map(item -> OBJECT_MAPPER.readValue(item, Result.class)); - Assertions.assertEquals(87, tmp.count()); + Assertions.assertEquals(86, tmp.count()); String doi1 = "unresolved::10.0000/096020199389707::doi"; @@ -151,9 +151,6 @@ public class PrepareTest { Assertions.assertEquals(1, tmp.filter(r -> r.getId().equals(doi2)).count()); Assertions.assertEquals(1, tmp.filter(r -> r.getId().equals(doi2)).collect().get(0).getInstance().size()); - tmp.filter(r -> r.getId().startsWith("unresolved::10.2111/1551-5028(2004)057")) - .foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r))); - } @Test diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/bip/bip.json b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/bip/bip.json index 3a077ab5c..03cef4be1 100644 --- a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/bip/bip.json +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/bip/bip.json @@ -83,5 +83,4 @@ {"10.0000/hoplos.v4i7.41295": [{"id": "influence", "unit": [{"value": "5.91019644836e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.0", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "8.48190886761e-09", "key": "score"}]}]} {"10.0000/hoplos.v4i7.42830": [{"id": "influence", "unit": [{"value": "5.91019644836e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.0", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "8.48190886761e-09", "key": "score"}]}]} {"10.0000/hoplos.v4i7.42861": [{"id": "influence", "unit": [{"value": "5.91019644836e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.0", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "8.48190886761e-09", "key": "score"}]}]} -{"10.0000/hoplos.v4i7.43096": [{"id": "influence", "unit": [{"value": "5.91019644836e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.0", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "8.48190886761e-09", "key": "score"}]}]} -{"10.2111/1551-5028(2004)057\[0539:sdsocg\]2.0.co;2": [{"id":"influence", "unit":[{"key":"score","value":"6.3290875E-9"},{"key":"class","value":"C"}]}, {"id":"popularity", "unit":[{"key":"score","value":"6.576763E-9"},{"key":"class","value":"C"}]}, {"id":"influence_alt", "unit":[{"key":"score","value":"11"},{"key":"class","value":"C"}]}, {"id":"popularity_alt", "unit":[{"key":"score","value":"1.0142108"},{"key":"class","value":"C"}]}, {"id":"impulse", "unit":[{"key":"score","value":"1"},{"key":"class","value":"C"}]}]} \ No newline at end of file +{"10.0000/hoplos.v4i7.43096": [{"id": "influence", "unit": [{"value": "5.91019644836e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.0", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "8.48190886761e-09", "key": "score"}]}]} \ No newline at end of file From 8d97949316a93884a123746cec0d60f6c34b2a2e Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 7 Oct 2022 09:52:45 +0200 Subject: [PATCH 200/214] [cleaning] fixed loop in wf nodes --- .../eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml index 2ba0a7ad7..08e74a5e5 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml @@ -492,7 +492,7 @@ --datasourcePath${workingDir}/working/hostedby --collectedfrom${collectedfrom} - + @@ -521,7 +521,7 @@ --datasourcePath${workingDir}/working/hostedby --collectedfrom${collectedfrom} - + @@ -550,7 +550,7 @@ --datasourcePath${workingDir}/working/hostedby --collectedfrom${collectedfrom} - + From ece40adc09b5124386fb4f28391f7b151ea0ceea Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 11 Oct 2022 10:10:20 +0200 Subject: [PATCH 201/214] [cleaning] fixing NPE in the country cleaning phase --- .../dhp/oa/graph/clean/country/GetDatasourceFromCountry.java | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/GetDatasourceFromCountry.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/GetDatasourceFromCountry.java index dd5af6998..d3741d3e8 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/GetDatasourceFromCountry.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/GetDatasourceFromCountry.java @@ -65,7 +65,6 @@ public class GetDatasourceFromCountry implements Serializable { conf, isSparkSessionManaged, spark -> { - getDatasourceFromCountry(spark, country, inputPath, workingPath); }); } @@ -83,7 +82,6 @@ public class GetDatasourceFromCountry implements Serializable { (FilterFunction) o -> !o.getDataInfo().getDeletedbyinference() && o.getCountry().getClassid().length() > 0 && o.getCountry().getClassid().equals(country)); - ; // filtering of the relations taking the non deleted by inference and those with IsProvidedBy as relclass Dataset relation = spark @@ -97,7 +95,7 @@ public class GetDatasourceFromCountry implements Serializable { !rel.getDataInfo().getDeletedbyinference()); organization - .joinWith(relation, organization.col("id").equalTo(relation.col("target")), "left") + .joinWith(relation, organization.col("id").equalTo(relation.col("target"))) .map((MapFunction, String>) t2 -> t2._2().getSource(), Encoders.STRING()) .write() .mode(SaveMode.Overwrite) From b301e9fdfffa4da0240981f97e0bd3bb5dbbfcdc Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 11 Oct 2022 11:08:52 +0200 Subject: [PATCH 202/214] [cleaning] renamed action name/description --- .../eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml index 08e74a5e5..19e1b2a02 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml @@ -432,14 +432,14 @@ - + - + yarn cluster - Clean publications context + Select datasource ID from country eu.dnetlib.dhp.oa.graph.clean.country.GetDatasourceFromCountry dhp-graph-mapper-${projectVersion}.jar From 6163ecbf63858f5a3b34cffa19b63fa59f851d9a Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 11 Oct 2022 11:20:03 +0200 Subject: [PATCH 203/214] [cleaning] renamed parameters in wf action --- .../dhp/oa/graph/clean/oozie_app/workflow.xml | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml index 19e1b2a02..6435d5131 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml @@ -471,7 +471,7 @@ yarn cluster - Clean publications counmtry + Clean publication country eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob dhp-graph-mapper-${projectVersion}.jar @@ -489,7 +489,7 @@ --workingPath${workingDir}/working/publication --country${country} --verifyParam${verifyCountryParam} - --datasourcePath${workingDir}/working/hostedby + --hostedBy${workingDir}/working/hostedby --collectedfrom${collectedfrom} @@ -500,7 +500,7 @@ yarn cluster - Clean datasets Country + Clean dataset country eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob dhp-graph-mapper-${projectVersion}.jar @@ -518,7 +518,7 @@ --workingPath${workingDir}/working/dataset --country${country} --verifyParam${verifyCountryParam} - --datasourcePath${workingDir}/working/hostedby + --hostedBy${workingDir}/working/hostedby --collectedfrom${collectedfrom} @@ -529,7 +529,7 @@ yarn cluster - Clean otherresearchproducts country + Clean otherresearchproduct country eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob dhp-graph-mapper-${projectVersion}.jar @@ -547,7 +547,7 @@ --workingPath${workingDir}/working/otherresearchproduct --country${country} --verifyParam${verifyCountryParam} - --datasourcePath${workingDir}/working/hostedby + --hostedBy${workingDir}/working/hostedby --collectedfrom${collectedfrom} @@ -558,7 +558,7 @@ yarn cluster - Clean softwares country + Clean software country eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob dhp-graph-mapper-${projectVersion}.jar @@ -576,7 +576,7 @@ --workingPath${workingDir}/working/software --country${country} --verifyParam${verifyCountryParam} - --datasourcePath${workingDir}/working/hostedby + --hostedBy${workingDir}/working/hostedby --collectedfrom${collectedfrom} From b47aaf4dd17b9446bd423637391fbe83aab80775 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 13 Oct 2022 11:23:43 +0200 Subject: [PATCH 204/214] [cleaning] subjects declared as belonging to specific vocabularies whose values are not found in the vocab are set to type keyword --- .../oaf/utils/GraphCleaningFunctions.java | 2 +- .../dhp/oa/graph/clean/CleaningRuleMap.java | 37 ++++++++++--------- .../clean/country/CleanCountrySparkJob.java | 2 +- .../clean/GraphCleaningFunctionsTest.java | 10 +++++ .../eu/dnetlib/dhp/oa/graph/clean/result.json | 22 +++++++++++ 5 files changed, 54 insertions(+), 19 deletions(-) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java index 775f228eb..363f95423 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java @@ -211,7 +211,7 @@ public class GraphCleaningFunctions extends CleaningFunctions { .orElse(s.getValue()), Function.identity(), (s1, s2) -> Collections - .min(Lists.newArrayList(s1, s1), new SubjectProvenanceComparator()))) + .min(Lists.newArrayList(s1, s2), new SubjectProvenanceComparator()))) .values()); r.setSubject(subjects); } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleMap.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleMap.java index 147e26699..5f3b4e1ca 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleMap.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleMap.java @@ -3,6 +3,7 @@ package eu.dnetlib.dhp.oa.graph.clean; import java.io.Serializable; import java.util.HashMap; +import java.util.Objects; import java.util.concurrent.atomic.AtomicReference; import org.apache.commons.lang3.SerializationUtils; @@ -10,6 +11,7 @@ import org.apache.commons.lang3.StringUtils; import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableConsumer; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; +import eu.dnetlib.dhp.common.vocabulary.VocabularyTerm; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.*; @@ -31,29 +33,30 @@ public class CleaningRuleMap extends HashMap, SerializableConsumer modified = new AtomicReference<>(false); + vocabularies.find(vocabularyId).ifPresent(vocabulary -> { - if (!ModelConstants.DNET_SUBJECT_KEYWORD.equalsIgnoreCase(subject.getQualifier().getClassid())) { - return; - } - Qualifier newValue = vocabulary.lookup(subject.getValue()); - if (!ModelConstants.UNKNOWN.equals(newValue.getClassid())) { - subject.setValue(newValue.getClassid()); - subject.getQualifier().setClassid(vocabularyId); - subject.getQualifier().setClassname(vocabulary.getName()); - modified.set(true); + if (ModelConstants.DNET_SUBJECT_KEYWORD.equalsIgnoreCase(subject.getQualifier().getClassid())) { + Qualifier newValue = vocabulary.lookup(subject.getValue()); + if (!ModelConstants.UNKNOWN.equals(newValue.getClassid())) { + subject.setValue(newValue.getClassid()); + subject.getQualifier().setClassid(vocabularyId); + subject.getQualifier().setClassname(vocabulary.getName()); + } + } else if (vocabularyId.equals(subject.getQualifier().getClassid())) { + Qualifier syn = vocabulary.getSynonymAsQualifier(subject.getValue()); + VocabularyTerm term = vocabulary.getTerm(subject.getValue()); + if (Objects.isNull(syn) && Objects.isNull(term)) { + subject.getQualifier().setClassid(ModelConstants.DNET_SUBJECT_KEYWORD); + subject.getQualifier().setClassname(ModelConstants.DNET_SUBJECT_KEYWORD); + } } }); - return modified.get(); } private static void cleanRelation(VocabularyGroup vocabularies, Relation r) { diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java index cd77f342e..45590f789 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java @@ -43,7 +43,7 @@ public class CleanCountrySparkJob implements Serializable { String jsonConfiguration = IOUtils .toString( - CleanContextSparkJob.class + CleanCountrySparkJob.class .getResourceAsStream( "/eu/dnetlib/dhp/oa/graph/input_clean_country_parameters.json")); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java index 6c43da832..4035307e5 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java @@ -278,6 +278,16 @@ public class GraphCleaningFunctionsTest { s -> "0102 computer and information sciences".equals(s.getValue()) & ModelConstants.DNET_SUBJECT_FOS_CLASSID.equals(s.getQualifier().getClassid()))); + List s1 = p_cleaned + .getSubject() + .stream() + .filter(s -> s.getValue().equals("In Situ Hybridization")) + .collect(Collectors.toList()); + assertNotNull(s1); + assertEquals(1, s1.size()); + assertEquals(ModelConstants.DNET_SUBJECT_KEYWORD, s1.get(0).getQualifier().getClassid()); + assertEquals(ModelConstants.DNET_SUBJECT_KEYWORD, s1.get(0).getQualifier().getClassname()); + // TODO add more assertions to verity the cleaned values System.out.println(MAPPER.writeValueAsString(p_cleaned)); } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json index 8e4fc4545..84ff35c08 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json @@ -706,6 +706,28 @@ "source": [ ], "subject": [ + { + "dataInfo": { + "provenanceaction": { + "classid": "sysimport:crosswalk:repository", + "classname": "sysimport:crosswalk:repository", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + }, + "deletedbyinference": false, + "inferred": false, + "inferenceprovenance": "", + "invisible": false, + "trust": "0.9" + }, + "qualifier": { + "classid": "FOS", + "classname": "Fields of Science and Technology classification", + "schemeid": "dnet:result_subject", + "schemename": "dnet:result_subject" + }, + "value": "In Situ Hybridization" + }, { "dataInfo": { "deletedbyinference": false, From a1f94530a3a170b8095de027660df0c2d4a35b09 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Thu, 13 Oct 2022 11:47:11 +0200 Subject: [PATCH 205/214] added documentation --- .../DataciteToOAFTransformation.scala | 122 +++++++++++------- 1 file changed, 74 insertions(+), 48 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala index c29614d33..29f5cb99c 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala @@ -24,11 +24,11 @@ import scala.io.Source object DataciteToOAFTransformation { case class HostedByMapType( - openaire_id: String, - datacite_name: String, - official_name: String, - similarity: Option[Float] - ) {} + openaire_id: String, + datacite_name: String, + official_name: String, + similarity: Option[Float] + ) {} val mapper = new ObjectMapper() @@ -47,12 +47,12 @@ object DataciteToOAFTransformation { } /** This method should skip record if json contains invalid text - * defined in file datacite_filter - * - * @param record : unparsed datacite record - * @param json : parsed record - * @return True if the record should be skipped - */ + * defined in file datacite_filter + * + * @param record : not parsed Datacite record + * @param json : parsed record + * @return True if the record should be skipped + */ def skip_record(record: String, json: org.json4s.JValue): Boolean = { implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats datacite_filter.exists(f => record.contains(f)) || (json \\ "publisher") @@ -98,6 +98,11 @@ object DataciteToOAFTransformation { } + /** + * This utility method indicates whether the embargo date has been reached + * @param embargo_end_date + * @return True if the embargo date has been reached, false otherwise + */ def embargo_end(embargo_end_date: String): Boolean = { val dt = LocalDate.parse(embargo_end_date, DateTimeFormatter.ofPattern("[yyyy-MM-dd]")) val td = LocalDate.now() @@ -142,12 +147,27 @@ object DataciteToOAFTransformation { } } + /*** + * Use the vocabulary dnet:publication_resource to find a synonym to one of these terms and get the instance.type. + * Using the dnet:result_typologies vocabulary, we look up the instance.type synonym + * to generate one of the following main entities: + * - publication + * - dataset + * - software + * - otherresearchproduct + + * @param resourceType + * @param resourceTypeGeneral + * @param schemaOrg + * @param vocabularies + * @return + */ def getTypeQualifier( - resourceType: String, - resourceTypeGeneral: String, - schemaOrg: String, - vocabularies: VocabularyGroup - ): (Qualifier, Qualifier) = { + resourceType: String, + resourceTypeGeneral: String, + schemaOrg: String, + vocabularies: VocabularyGroup + ): (Qualifier, Qualifier) = { if (resourceType != null && resourceType.nonEmpty) { val typeQualifier = vocabularies.getSynonymAsQualifier(ModelConstants.DNET_PUBLICATION_RESOURCE, resourceType) @@ -192,11 +212,11 @@ object DataciteToOAFTransformation { } def getResult( - resourceType: String, - resourceTypeGeneral: String, - schemaOrg: String, - vocabularies: VocabularyGroup - ): Result = { + resourceType: String, + resourceTypeGeneral: String, + schemaOrg: String, + vocabularies: VocabularyGroup + ): Result = { val typeQualifiers: (Qualifier, Qualifier) = getTypeQualifier(resourceType, resourceTypeGeneral, schemaOrg, vocabularies) if (typeQualifiers == null) @@ -238,11 +258,11 @@ object DataciteToOAFTransformation { } /** As describe in ticket #6377 - * when the result come from figshare we need to remove subject - * and set Access rights OPEN. - * - * @param r - */ + * when the result come from figshare we need to remove subject + * and set Access rights OPEN. + * + * @param r + */ def fix_figshare(r: Result): Unit = { if (r.getInstance() != null) { @@ -269,12 +289,12 @@ object DataciteToOAFTransformation { } def generateRelation( - sourceId: String, - targetId: String, - relClass: String, - cf: KeyValue, - di: DataInfo - ): Relation = { + sourceId: String, + targetId: String, + relClass: String, + cf: KeyValue, + di: DataInfo + ): Relation = { val r = new Relation r.setSource(sourceId) @@ -303,12 +323,12 @@ object DataciteToOAFTransformation { } def generateOAF( - input: String, - ts: Long, - dateOfCollection: Long, - vocabularies: VocabularyGroup, - exportLinks: Boolean - ): List[Oaf] = { + input: String, + ts: Long, + dateOfCollection: Long, + vocabularies: VocabularyGroup, + exportLinks: Boolean + ): List[Oaf] = { implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats lazy val json = parse(input) @@ -330,6 +350,7 @@ object DataciteToOAFTransformation { if (result == null) return List() + // DOI is mapped on a PID inside a Instance object val doi_q = OafMapperUtils.qualifier( "doi", "doi", @@ -338,6 +359,8 @@ object DataciteToOAFTransformation { ) val pid = OafMapperUtils.structuredProperty(doi, doi_q, dataInfo) result.setPid(List(pid).asJava) + + // This identifiere will be replaced in a second moment using the PID logic generation result.setId(OafMapperUtils.createOpenaireId(50, s"datacite____::$doi", true)) result.setOriginalId(List(doi).asJava) @@ -386,6 +409,11 @@ object DataciteToOAFTransformation { a } + if (authors == null || authors.isEmpty || !authors.exists(a => a != null)) + return List() + result.setAuthor(authors.asJava) + + val titles: List[TitleType] = (json \\ "titles").extractOrElse[List[TitleType]](List()) result.setTitle( @@ -409,9 +437,7 @@ object DataciteToOAFTransformation { .asJava ) - if (authors == null || authors.isEmpty || !authors.exists(a => a != null)) - return List() - result.setAuthor(authors.asJava) + val dates = (json \\ "dates").extract[List[DateType]] val publication_year = (json \\ "publicationYear").extractOrElse[String](null) @@ -619,16 +645,16 @@ object DataciteToOAFTransformation { } private def generateRelations( - rels: List[RelatedIdentifierType], - id: String, - date: String - ): List[Relation] = { + rels: List[RelatedIdentifierType], + id: String, + date: String + ): List[Relation] = { rels .filter(r => subRelTypeMapping .contains(r.relationType) && (r.relatedIdentifierType.equalsIgnoreCase("doi") || - r.relatedIdentifierType.equalsIgnoreCase("pmid") || - r.relatedIdentifierType.equalsIgnoreCase("arxiv")) + r.relatedIdentifierType.equalsIgnoreCase("pmid") || + r.relatedIdentifierType.equalsIgnoreCase("arxiv")) ) .map(r => { val rel = new Relation @@ -660,4 +686,4 @@ object DataciteToOAFTransformation { s"10|$b::${DHPUtils.md5(a)}" } -} +} \ No newline at end of file From ae7cd0735a8528cd419ce2863077d436bd34cd0d Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 14 Oct 2022 15:47:58 +0200 Subject: [PATCH 206/214] [graph2hive] more partitions --- .../eu/dnetlib/dhp/oa/graph/hive/oozie_app/workflow.xml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/workflow.xml index ba5f4f375..4468382be 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/workflow.xml @@ -126,6 +126,7 @@ --hiveDbName${hiveDbName} --classNameeu.dnetlib.dhp.schema.oaf.Publication --hiveMetastoreUris${hiveMetastoreUris} + --numPartitions8000 @@ -152,6 +153,7 @@ --hiveDbName${hiveDbName} --classNameeu.dnetlib.dhp.schema.oaf.Dataset --hiveMetastoreUris${hiveMetastoreUris} + --numPartitions4000 @@ -178,6 +180,7 @@ --hiveDbName${hiveDbName} --classNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct --hiveMetastoreUris${hiveMetastoreUris} + --numPartitions3000 @@ -204,6 +207,7 @@ --hiveDbName${hiveDbName} --classNameeu.dnetlib.dhp.schema.oaf.Software --hiveMetastoreUris${hiveMetastoreUris} + --numPartitions300 @@ -230,6 +234,7 @@ --hiveDbName${hiveDbName} --classNameeu.dnetlib.dhp.schema.oaf.Datasource --hiveMetastoreUris${hiveMetastoreUris} + --numPartitions100 @@ -256,6 +261,7 @@ --hiveDbName${hiveDbName} --classNameeu.dnetlib.dhp.schema.oaf.Organization --hiveMetastoreUris${hiveMetastoreUris} + --numPartitions400 @@ -309,6 +315,7 @@ --hiveDbName${hiveDbName} --classNameeu.dnetlib.dhp.schema.oaf.Relation --hiveMetastoreUris${hiveMetastoreUris} + --numPartitions10000 From 72f0d88d6ce9536a2577b24b8c5d7242b5dc6e39 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Wed, 19 Oct 2022 14:18:42 +0200 Subject: [PATCH 207/214] formatted code --- .../DataciteToOAFTransformation.scala | 132 +++++++++--------- 1 file changed, 64 insertions(+), 68 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala index 29f5cb99c..a7ad9e2d6 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala @@ -24,11 +24,11 @@ import scala.io.Source object DataciteToOAFTransformation { case class HostedByMapType( - openaire_id: String, - datacite_name: String, - official_name: String, - similarity: Option[Float] - ) {} + openaire_id: String, + datacite_name: String, + official_name: String, + similarity: Option[Float] + ) {} val mapper = new ObjectMapper() @@ -47,12 +47,12 @@ object DataciteToOAFTransformation { } /** This method should skip record if json contains invalid text - * defined in file datacite_filter - * - * @param record : not parsed Datacite record - * @param json : parsed record - * @return True if the record should be skipped - */ + * defined in file datacite_filter + * + * @param record : not parsed Datacite record + * @param json : parsed record + * @return True if the record should be skipped + */ def skip_record(record: String, json: org.json4s.JValue): Boolean = { implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats datacite_filter.exists(f => record.contains(f)) || (json \\ "publisher") @@ -98,11 +98,10 @@ object DataciteToOAFTransformation { } - /** - * This utility method indicates whether the embargo date has been reached - * @param embargo_end_date - * @return True if the embargo date has been reached, false otherwise - */ + /** This utility method indicates whether the embargo date has been reached + * @param embargo_end_date + * @return True if the embargo date has been reached, false otherwise + */ def embargo_end(embargo_end_date: String): Boolean = { val dt = LocalDate.parse(embargo_end_date, DateTimeFormatter.ofPattern("[yyyy-MM-dd]")) val td = LocalDate.now() @@ -147,27 +146,27 @@ object DataciteToOAFTransformation { } } - /*** - * Use the vocabulary dnet:publication_resource to find a synonym to one of these terms and get the instance.type. - * Using the dnet:result_typologies vocabulary, we look up the instance.type synonym - * to generate one of the following main entities: - * - publication - * - dataset - * - software - * - otherresearchproduct - - * @param resourceType - * @param resourceTypeGeneral - * @param schemaOrg - * @param vocabularies - * @return - */ + /** * + * Use the vocabulary dnet:publication_resource to find a synonym to one of these terms and get the instance.type. + * Using the dnet:result_typologies vocabulary, we look up the instance.type synonym + * to generate one of the following main entities: + * - publication + * - dataset + * - software + * - otherresearchproduct + * + * @param resourceType + * @param resourceTypeGeneral + * @param schemaOrg + * @param vocabularies + * @return + */ def getTypeQualifier( - resourceType: String, - resourceTypeGeneral: String, - schemaOrg: String, - vocabularies: VocabularyGroup - ): (Qualifier, Qualifier) = { + resourceType: String, + resourceTypeGeneral: String, + schemaOrg: String, + vocabularies: VocabularyGroup + ): (Qualifier, Qualifier) = { if (resourceType != null && resourceType.nonEmpty) { val typeQualifier = vocabularies.getSynonymAsQualifier(ModelConstants.DNET_PUBLICATION_RESOURCE, resourceType) @@ -212,11 +211,11 @@ object DataciteToOAFTransformation { } def getResult( - resourceType: String, - resourceTypeGeneral: String, - schemaOrg: String, - vocabularies: VocabularyGroup - ): Result = { + resourceType: String, + resourceTypeGeneral: String, + schemaOrg: String, + vocabularies: VocabularyGroup + ): Result = { val typeQualifiers: (Qualifier, Qualifier) = getTypeQualifier(resourceType, resourceTypeGeneral, schemaOrg, vocabularies) if (typeQualifiers == null) @@ -258,11 +257,11 @@ object DataciteToOAFTransformation { } /** As describe in ticket #6377 - * when the result come from figshare we need to remove subject - * and set Access rights OPEN. - * - * @param r - */ + * when the result come from figshare we need to remove subject + * and set Access rights OPEN. + * + * @param r + */ def fix_figshare(r: Result): Unit = { if (r.getInstance() != null) { @@ -289,12 +288,12 @@ object DataciteToOAFTransformation { } def generateRelation( - sourceId: String, - targetId: String, - relClass: String, - cf: KeyValue, - di: DataInfo - ): Relation = { + sourceId: String, + targetId: String, + relClass: String, + cf: KeyValue, + di: DataInfo + ): Relation = { val r = new Relation r.setSource(sourceId) @@ -323,12 +322,12 @@ object DataciteToOAFTransformation { } def generateOAF( - input: String, - ts: Long, - dateOfCollection: Long, - vocabularies: VocabularyGroup, - exportLinks: Boolean - ): List[Oaf] = { + input: String, + ts: Long, + dateOfCollection: Long, + vocabularies: VocabularyGroup, + exportLinks: Boolean + ): List[Oaf] = { implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats lazy val json = parse(input) @@ -413,7 +412,6 @@ object DataciteToOAFTransformation { return List() result.setAuthor(authors.asJava) - val titles: List[TitleType] = (json \\ "titles").extractOrElse[List[TitleType]](List()) result.setTitle( @@ -437,8 +435,6 @@ object DataciteToOAFTransformation { .asJava ) - - val dates = (json \\ "dates").extract[List[DateType]] val publication_year = (json \\ "publicationYear").extractOrElse[String](null) @@ -645,16 +641,16 @@ object DataciteToOAFTransformation { } private def generateRelations( - rels: List[RelatedIdentifierType], - id: String, - date: String - ): List[Relation] = { + rels: List[RelatedIdentifierType], + id: String, + date: String + ): List[Relation] = { rels .filter(r => subRelTypeMapping .contains(r.relationType) && (r.relatedIdentifierType.equalsIgnoreCase("doi") || - r.relatedIdentifierType.equalsIgnoreCase("pmid") || - r.relatedIdentifierType.equalsIgnoreCase("arxiv")) + r.relatedIdentifierType.equalsIgnoreCase("pmid") || + r.relatedIdentifierType.equalsIgnoreCase("arxiv")) ) .map(r => { val rel = new Relation @@ -686,4 +682,4 @@ object DataciteToOAFTransformation { s"10|$b::${DHPUtils.md5(a)}" } -} \ No newline at end of file +} From bca4a61710ed7d394937a28973f44018d99aa2be Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 19 Oct 2022 15:20:58 +0200 Subject: [PATCH 208/214] suppressing hyper verbose spark logs during unit test execution --- .../src/test/resources/log4j.properties | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/log4j.properties diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/log4j.properties b/dhp-workflows/dhp-enrichment/src/test/resources/log4j.properties new file mode 100644 index 000000000..ce37270c6 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/test/resources/log4j.properties @@ -0,0 +1,25 @@ +# Root logger option +log4j.rootLogger=DEBUG, stdout + +# Direct log messages to stdout +log4j.appender.stdout=org.apache.log4j.ConsoleAppender +log4j.appender.stdout.Target=System.out +log4j.appender.stdout.layout=org.apache.log4j.PatternLayout +log4j.appender.stdout.layout.ConversionPattern=%d{yyyy-MM-dd HH:mm:ss} %-5p %c{1}:%L - %m%n + +# Change this to set Spark log level +log4j.logger.org.apache.spark=ERROR +log4j.rootCategory=WARN + +# Silence akka remoting +log4j.logger.Remoting=WARN + +# Ignore messages below warning level from Jetty, because it's a bit verbose +log4j.logger.org.eclipse.jetty=WARN + +log4j.logger.org.apache.hadoop.mapreduce.lib.output.FileOutputCommitterFactory=WARN +log4j.logger.org.apache.hadoop.mapreduce.lib.output.FileOutputCommitter=WARN +log4j.logger.org.apache.parquet.hadoop.ParquetOutputFormat=WARN +log4j.logger.org.apache.parquet.hadoop.InternalParquetRecordWriter=WARN +log4j.logger.org.apache.hadoop.io.compress.CodecPool=WARN +log4j.logger.org.apache.parquet.hadoop.codec.CodecConfig=WARN \ No newline at end of file From 31a10f000b200d047ad50be1c0a376a7316d8be9 Mon Sep 17 00:00:00 2001 From: Alessia Bardi Date: Sun, 23 Oct 2022 18:05:37 +0200 Subject: [PATCH 209/214] Map the field oaf:eoscifguidelines from mdstores. Currently we can find it in ROHub metadata --- .../raw/AbstractMdRecordToOafMapper.java | 20 +++++++++++++++++++ .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 1 + .../eu/dnetlib/dhp/oa/graph/raw/rohub.xml | 5 ++++- 3 files changed, 25 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index c157be51a..a33a04be3 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -366,6 +366,7 @@ public abstract class AbstractMdRecordToOafMapper { r.setInstance(instances); r.setBestaccessright(OafMapperUtils.createBestAccessRights(instances)); + r.setEoscifguidelines(prepareEOSCIfGuidelines(doc, info)); } protected abstract List prepareResultPids(Document doc, DataInfo info); @@ -384,6 +385,25 @@ public abstract class AbstractMdRecordToOafMapper { return list; } + private List prepareEOSCIfGuidelines(Document doc, DataInfo info){ + final Set set = Sets.newHashSet(); + for (final Object o : doc.selectNodes("//oaf:eoscifguidelines")) { + final String code = ((Node) o).valueOf("@code"); + final String label = ((Node) o).valueOf("@label"); + final String url = ((Node) o).valueOf("@url"); + final String semrel = ((Node) o).valueOf("@semrel"); + if (StringUtils.isNotBlank(code)) { + final EoscIfGuidelines eig = new EoscIfGuidelines(); + eig.setCode(code); + eig.setLabel(label); + eig.setUrl(url); + eig.setSemanticRelation(semrel); + set.add(eig); + } + } + return Lists.newArrayList(set); + } + protected abstract Qualifier prepareResourceType(Document doc, DataInfo info); protected abstract List prepareInstances( diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index f0eadbd0d..8c9b3caba 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -947,6 +947,7 @@ class MappersTest { Instance inst = p.getInstance().get(0); assertEquals("https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca", inst.getPid().get(0).getValue()); assertEquals("https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca", inst.getUrl().get(0)); + assertEquals(1, p.getEoscifguidelines().size()); } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/rohub.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/rohub.xml index e1e30c3de..18f637ecc 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/rohub.xml +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/rohub.xml @@ -65,7 +65,6 @@ Ecology - EOSC::RO-crate https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca @@ -75,5 +74,9 @@ + \ No newline at end of file From ee759ac92da0116f2f6c0c8b11aacce98e5a55a3 Mon Sep 17 00:00:00 2001 From: Alessia Bardi Date: Sun, 23 Oct 2022 18:09:47 +0200 Subject: [PATCH 210/214] file format after mvn compile --- .../dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index a33a04be3..02b1e7e7c 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -385,7 +385,7 @@ public abstract class AbstractMdRecordToOafMapper { return list; } - private List prepareEOSCIfGuidelines(Document doc, DataInfo info){ + private List prepareEOSCIfGuidelines(Document doc, DataInfo info) { final Set set = Sets.newHashSet(); for (final Object o : doc.selectNodes("//oaf:eoscifguidelines")) { final String code = ((Node) o).valueOf("@code"); From 208ed323153a0b19189f6ddf65776f67a6df2e67 Mon Sep 17 00:00:00 2001 From: Alessia Bardi Date: Sun, 23 Oct 2022 18:18:13 +0200 Subject: [PATCH 211/214] fixed xpath for semantic relation --- .../dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java | 2 +- .../test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java | 4 ++++ 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index 02b1e7e7c..7aa40cb8a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -391,7 +391,7 @@ public abstract class AbstractMdRecordToOafMapper { final String code = ((Node) o).valueOf("@code"); final String label = ((Node) o).valueOf("@label"); final String url = ((Node) o).valueOf("@url"); - final String semrel = ((Node) o).valueOf("@semrel"); + final String semrel = ((Node) o).valueOf("@semanticrelation"); if (StringUtils.isNotBlank(code)) { final EoscIfGuidelines eig = new EoscIfGuidelines(); eig.setCode(code); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index 8c9b3caba..ad733bec0 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -948,6 +948,10 @@ class MappersTest { assertEquals("https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca", inst.getPid().get(0).getValue()); assertEquals("https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca", inst.getUrl().get(0)); assertEquals(1, p.getEoscifguidelines().size()); + assertEquals("EOSC::RO-crate", p.getEoscifguidelines().get(0).getCode()); + assertEquals("EOSC::RO-crate", p.getEoscifguidelines().get(0).getLabel()); + assertEquals("", p.getEoscifguidelines().get(0).getUrl()); + assertEquals("compliesWith", p.getEoscifguidelines().get(0).getSemanticRelation()); } From 2b9a20a4a378d887d801df3eb6958bd20b079276 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Mon, 24 Oct 2022 12:53:47 +0200 Subject: [PATCH 212/214] Changed the way Scholexplorer filter the relationships, I found that filter all relation coming from openCitation is wrong, because we loose a lot of relation than intersect OpenCitation, but they don't come only from there --- .../sx/graph/SparkConvertRDDtoDataset.scala | 77 ++++++++----------- 1 file changed, 34 insertions(+), 43 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala index 556106180..362cb2028 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala @@ -116,54 +116,45 @@ object SparkConvertRDDtoDataset { .map(s => mapper.readValue(s, classOf[Relation])) .filter(r => r.getDataInfo != null && !r.getDataInfo.getDeletedbyinference) .filter(r => r.getSource.startsWith("50") && r.getTarget.startsWith("50")) - .filter(r => filterRelations(subRelTypeFilter, relClassFilter, r)) - //filter OpenCitations relations - .filter(r => - r.getDataInfo.getProvenanceaction != null && - !"sysimport:crosswalk:opencitations".equals(r.getDataInfo.getProvenanceaction.getClassid) - ) + .filter(r => filterRelations(r)) + //filter OpenCitations relations +// .filter(r => +// r.getDataInfo.getProvenanceaction != null && +// !"sysimport:crosswalk:opencitations".equals(r.getDataInfo.getProvenanceaction.getClassid) +// ) spark.createDataset(rddRelation).as[Relation].write.mode(SaveMode.Overwrite).save(s"$relPath") } - private def filterRelations(subRelTypeFilter: String, relClassFilter: List[String], r: Relation): Boolean = { - if (StringUtils.isNotBlank(subRelTypeFilter)) { - subRelTypeFilter.equalsIgnoreCase(r.getSubRelType) - } else { - !relClassFilter.exists(k => k.equalsIgnoreCase(r.getRelClass)) + private def filterRelations(r: Relation): Boolean = { + + /** * + * We filter relation generated by dedups + * and all the relation that have one single collectedFrom OpenCitation + */ + + val relClassFilter = List( + ModelConstants.MERGES, + ModelConstants.IS_MERGED_IN, + ModelConstants.HAS_AMONG_TOP_N_SIMILAR_DOCS, + ModelConstants.IS_AMONG_TOP_N_SIMILAR_DOCS + ) + if (relClassFilter.exists(k => k.equalsIgnoreCase(r.getRelClass))) + false + else { + if (r.getCollectedfrom == null || r.getCollectedfrom.size() == 0) + false + else if (r.getCollectedfrom.size() > 1) + true + else if ( + r.getCollectedfrom.size() == 1 && r.getCollectedfrom.get(0) != null && "OpenCitations".equalsIgnoreCase( + r.getCollectedfrom.get(0).getValue + ) + ) + false + else + true } } - /* - //TODO: finalise implementation - private def processResult[T<: Result]( - implicit ct: ClassTag[T], - log: Logger, - spark: SparkSession, - sourcePath: String, - entityPath: String, - clazz: Class[T] - ): Unit = { - val entityType = clazz.getSimpleName.toLowerCase - - log.info(s"Converting $entityType") - - val mapper = new ObjectMapper() with ScalaObjectMapper - mapper.registerModule(DefaultScalaModule) - - val rdd = spark.sparkContext - .textFile(s"$sourcePath/$entityType") - .map(s => mapper.readValue(s, clazz)) - .filter(r => r.getDataInfo != null && !r.getDataInfo.getDeletedbyinference); - - implicit val encoder: Encoder[T] = Encoders.kryo(clazz) - spark - .createDataset(rdd) - .as[T] - .write - .mode(SaveMode.Overwrite) - .save(s"$entityPath/$entityType") - } - */ - } From 5df9c6396336e895708d00642ebb229825dc7665 Mon Sep 17 00:00:00 2001 From: dimitrispie Date: Thu, 27 Oct 2022 16:44:26 +0300 Subject: [PATCH 213/214] Added fields: totalcost, fundedamount, currency, in project table --- .../dhp/oa/graph/stats/oozie_app/scripts/step11.sql | 4 +++- .../dhp/oa/graph/stats/oozie_app/scripts/step13.sql | 8 ++++---- .../dhp/oa/graph/stats/oozie_app/scripts/step6.sql | 8 ++++++-- 3 files changed, 13 insertions(+), 7 deletions(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql index d699b68c3..41c3ed751 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql @@ -42,7 +42,9 @@ SELECT p.id, CASE WHEN prr2.id IS NULL THEN 0 ELSE prr2.dp END AS delayedpubs, p.callidentifier, p.code, - p.totalcost + p.totalcost, + p.fundedamount, + p.currency FROM ${stats_db_name}.project_tmp p LEFT JOIN (SELECT pr.id, count(distinct pr.result) AS np FROM ${stats_db_name}.project_results pr diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql index aee66fd5e..24e1a1355 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql @@ -59,7 +59,7 @@ UNION ALL SELECT * FROM ${stats_db_name}.otherresearchproduct_sources; -create table ${stats_db_name}.result_orcid STORED AS PARQUET as +CREATE TABLE IF NOT EXISTS ${stats_db_name}.result_orcid STORED AS PARQUET as select distinct res.id, regexp_replace(res.orcid, 'http://orcid.org/' ,'') as orcid from ( SELECT substr(res.id, 4) as id, auth_pid.value as orcid @@ -69,7 +69,7 @@ from ( LATERAL VIEW explode(auth.pid.qualifier.classid) apt as author_pid_type WHERE res.datainfo.deletedbyinference = FALSE and res.datainfo.invisible = FALSE and author_pid_type = 'orcid') as res; -create table ${stats_db_name}.result_result stored as parquet as +CREATE TABLE IF NOT EXISTS ${stats_db_name}.result_result stored as parquet as select substr(rel.source, 4) as source, substr(rel.target, 4) as target, relclass, subreltype from ${openaire_db_name}.relation rel join ${openaire_db_name}.result r1 on rel.source=r1.id @@ -82,7 +82,7 @@ where reltype='resultResult' and r2.resulttype.classname != 'other' and rel.datainfo.deletedbyinference=false and rel.datainfo.invisible = FALSE; -create table ${stats_db_name}.result_citations_oc stored as parquet as +CREATE TABLE IF NOT EXISTS ${stats_db_name}.result_citations_oc stored as parquet as select substr(target, 4) as id, count(distinct substr(source, 4)) as citations from ${openaire_db_name}.relation rel join ${openaire_db_name}.result r1 on rel.source=r1.id @@ -97,7 +97,7 @@ where relClass='Cites' and rel.datainfo.provenanceaction.classid = 'sysimport:cr and rel.datainfo.deletedbyinference=false and rel.datainfo.invisible = FALSE group by substr(target, 4); -create table ${stats_db_name}.result_references_oc stored as parquet as +CREATE TABLE IF NOT EXISTS ${stats_db_name}.result_references_oc stored as parquet as select substr(source, 4) as id, count(distinct substr(target, 4)) as references from ${openaire_db_name}.relation rel join ${openaire_db_name}.result r1 on rel.source=r1.id diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql index 5461afde6..c31180c14 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql @@ -48,7 +48,9 @@ CREATE TABLE ${stats_db_name}.project_tmp delayedpubs INT, callidentifier STRING, code STRING, - totalcost FLOAT + totalcost FLOAT, + fundedamount FLOAT, + currency STRING ) CLUSTERED BY (id) INTO 100 buckets stored AS orc tblproperties ('transactional' = 'true'); INSERT INTO ${stats_db_name}.project_tmp @@ -72,7 +74,9 @@ SELECT substr(p.id, 4) AS id, 0 AS delayedpubs, p.callidentifier.value AS callidentifier, p.code.value AS code, - p.totalcost AS totalcost + p.totalcost AS totalcost, + p.fundedamount AS fundedamount, + p.currency.value AS currency FROM ${openaire_db_name}.project p WHERE p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; From 7861c472e0c8e4c3084a04721dafc736111c4963 Mon Sep 17 00:00:00 2001 From: dimitrispie Date: Fri, 28 Oct 2022 19:00:32 +0300 Subject: [PATCH 214/214] Hive memory parameters --- .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/config-default.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/config-default.xml b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/config-default.xml index 9331d4ac5..63fc84d75 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/config-default.xml +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/config-default.xml @@ -21,7 +21,7 @@ hive_jdbc_url - jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000 + jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000/;UseNativeQuery=1;?spark.executor.memory=19166291558;spark.yarn.executor.memoryOverhead=3225;spark.driver.memory=11596411699;spark.yarn.driver.memoryOverhead=1228 oozie.wf.workflow.notification.url

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Apr 2022 14:31:22 +0300 Subject: [PATCH 003/214] Add AbstractSplittedRecordPlugin --- .../dhp/collection/CollectorWorker.java | 2 +- .../file/AbstractSplittedRecordPlugin.java | 54 ++++++ .../plugin/file/FileGZipCollectorPlugin.java | 29 +++ .../fileGZip/FileGZipCollectorPlugin.java | 49 ----- .../collection/plugin/oai/OaiIterator.java | 2 +- .../collection/plugin/rest/RestIterator.java | 2 +- .../{ => plugin/utils}/JsonUtils.java | 2 +- .../collection/plugin/utils/XMLIterator.java | 170 ++++++++++++++++++ .../{ => plugin/utils}/XmlCleaner.java | 2 +- .../FileGZipCollectorPluginTest.java | 7 +- .../{fileGZip => file/gzip}/opendoar.xml.gz | Bin 11 files changed, 260 insertions(+), 59 deletions(-) create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/file/AbstractSplittedRecordPlugin.java create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/file/FileGZipCollectorPlugin.java delete mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/fileGZip/FileGZipCollectorPlugin.java rename dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/{ => plugin/utils}/JsonUtils.java (98%) create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/utils/XMLIterator.java rename dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/{ => plugin/utils}/XmlCleaner.java (99%) rename dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/{fileGZip => file}/FileGZipCollectorPluginTest.java (87%) rename dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/plugin/{fileGZip => file/gzip}/opendoar.xml.gz (100%) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java index 03f592169..5de4eb84b 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java @@ -7,7 +7,7 @@ import java.io.IOException; import java.util.Optional; import java.util.concurrent.atomic.AtomicInteger; -import eu.dnetlib.dhp.collection.plugin.fileGZip.FileGZipCollectorPlugin; +import eu.dnetlib.dhp.collection.plugin.file.FileGZipCollectorPlugin; import org.apache.hadoop.fs.FileSystem; import org.apache.hadoop.fs.Path; import org.apache.hadoop.io.IntWritable; diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/file/AbstractSplittedRecordPlugin.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/file/AbstractSplittedRecordPlugin.java new file mode 100644 index 000000000..c569926c0 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/file/AbstractSplittedRecordPlugin.java @@ -0,0 +1,54 @@ +package eu.dnetlib.dhp.collection.plugin.file; + +import java.io.BufferedInputStream; +import java.util.Iterator; +import java.util.Optional; +import java.util.Spliterator; +import java.util.Spliterators; +import java.util.stream.Collectors; +import java.util.stream.Stream; +import java.util.stream.StreamSupport; + +import eu.dnetlib.dhp.collection.ApiDescriptor; +import eu.dnetlib.dhp.collection.plugin.CollectorPlugin; +import eu.dnetlib.dhp.collection.plugin.utils.XMLIterator; +import eu.dnetlib.dhp.common.aggregation.AggregatorReport; +import eu.dnetlib.dhp.common.collection.CollectorException; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +public abstract class AbstractSplittedRecordPlugin implements CollectorPlugin { + + private static final Logger log = LoggerFactory.getLogger(AbstractSplittedRecordPlugin.class); + + public static final String SPLIT_ON_ELEMENT = "splitOnElement"; + + @Override + public Stream collect(ApiDescriptor api, AggregatorReport report) throws CollectorException { + + final String baseUrl = Optional + .ofNullable(api.getBaseUrl()) + .orElseThrow( () -> new CollectorException("missing baseUrl, required by the AbstractSplittedRecordPlugin")); + + log.info("baseUrl: {}", baseUrl); + + final String splitOnElement = Optional + .ofNullable(api.getParams().get(SPLIT_ON_ELEMENT)) + .orElseThrow(() -> new CollectorException(String.format("missing parameter '%s', required by the AbstractSplittedRecordPlugin", SPLIT_ON_ELEMENT))); + + log.info("splitOnElement: {}", splitOnElement); + + final BufferedInputStream bis = getBufferedInputStream(baseUrl); + + Iterator xmlIterator = new XMLIterator(splitOnElement, bis); + + return StreamSupport.stream( + Spliterators.spliteratorUnknownSize(xmlIterator, Spliterator.ORDERED), + false + ); + } + + abstract protected BufferedInputStream getBufferedInputStream(final String baseUrl) throws CollectorException; + +} \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/file/FileGZipCollectorPlugin.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/file/FileGZipCollectorPlugin.java new file mode 100644 index 000000000..a4dd65d2a --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/file/FileGZipCollectorPlugin.java @@ -0,0 +1,29 @@ +package eu.dnetlib.dhp.collection.plugin.file; + +import eu.dnetlib.dhp.common.collection.CollectorException; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.*; +import java.net.MalformedURLException; +import java.net.URL; +import java.util.zip.GZIPInputStream; + +public class FileGZipCollectorPlugin extends AbstractSplittedRecordPlugin { + + private static final Logger log = LoggerFactory.getLogger(FileGZipCollectorPlugin.class); + + @Override + protected BufferedInputStream getBufferedInputStream(String baseUrl) throws CollectorException { + + log.info("baseUrl: {}", baseUrl); + + try { + GZIPInputStream stream = new GZIPInputStream(new FileInputStream(baseUrl)); + return new BufferedInputStream(stream); + } catch (Exception e) { + e.printStackTrace(); + throw new CollectorException(e); + } + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/fileGZip/FileGZipCollectorPlugin.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/fileGZip/FileGZipCollectorPlugin.java deleted file mode 100644 index 38f328890..000000000 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/fileGZip/FileGZipCollectorPlugin.java +++ /dev/null @@ -1,49 +0,0 @@ -package eu.dnetlib.dhp.collection.plugin.fileGZip; - -import eu.dnetlib.dhp.collection.ApiDescriptor; -import eu.dnetlib.dhp.collection.plugin.CollectorPlugin; -import eu.dnetlib.dhp.common.aggregation.AggregatorReport; -import eu.dnetlib.dhp.common.collection.CollectorException; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import java.io.*; -import java.net.URL; -import java.util.Optional; -import java.util.stream.Stream; -import java.util.zip.GZIPInputStream; - -public class FileGZipCollectorPlugin implements CollectorPlugin { - - private static final Logger log = LoggerFactory.getLogger(FileGZipCollectorPlugin.class); - - public static final String ENCODING = "encoding"; - - @Override - public Stream collect(ApiDescriptor api, AggregatorReport report) throws CollectorException { - - final String baseUrl = Optional - .ofNullable(api.getBaseUrl()) - .orElseThrow( () -> new CollectorException("missing baseUrl, required by the fileGZip collector plugin")); - - log.info("fileGZip.baseUrl: {}", baseUrl); - - final String encoding = Optional - .ofNullable(api.getParams().get(ENCODING)) - .orElseThrow(() -> new CollectorException(String.format("missing parameter '%s', required by the fileGZip collector plugin", ENCODING))); - - log.info("fileGZip.encoding: {}", encoding); - - try { - - InputStream gzipStream = new GZIPInputStream(new FileInputStream(baseUrl)); - Reader decoder = new InputStreamReader(gzipStream, encoding); - BufferedReader reader = new BufferedReader(decoder); - - return reader.lines(); - - } catch (Exception e) { - throw new CollectorException(e); - } - } -} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiIterator.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiIterator.java index 566c6b216..28b2572fb 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiIterator.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiIterator.java @@ -19,7 +19,7 @@ import org.dom4j.io.XMLWriter; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import eu.dnetlib.dhp.collection.XmlCleaner; +import eu.dnetlib.dhp.collection.plugin.utils.XmlCleaner; import eu.dnetlib.dhp.common.aggregation.AggregatorReport; import eu.dnetlib.dhp.common.collection.CollectorException; import eu.dnetlib.dhp.common.collection.HttpConnector2; diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/rest/RestIterator.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/rest/RestIterator.java index 64a041fd4..e4bad2f8d 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/rest/RestIterator.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/rest/RestIterator.java @@ -30,7 +30,7 @@ import org.w3c.dom.Node; import org.w3c.dom.NodeList; import org.xml.sax.InputSource; -import eu.dnetlib.dhp.collection.JsonUtils; +import eu.dnetlib.dhp.collection.plugin.utils.JsonUtils; import eu.dnetlib.dhp.common.collection.CollectorException; import eu.dnetlib.dhp.common.collection.HttpClientParams; diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/JsonUtils.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/utils/JsonUtils.java similarity index 98% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/JsonUtils.java rename to dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/utils/JsonUtils.java index da3768a4a..15401e223 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/JsonUtils.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/utils/JsonUtils.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.collection; +package eu.dnetlib.dhp.collection.plugin.utils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/utils/XMLIterator.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/utils/XMLIterator.java new file mode 100644 index 000000000..853973ebb --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/utils/XMLIterator.java @@ -0,0 +1,170 @@ +package eu.dnetlib.dhp.collection.plugin.utils; + +import java.io.InputStream; +import java.io.InputStreamReader; +import java.io.Reader; +import java.io.StringWriter; +import java.nio.charset.Charset; +import java.nio.charset.CharsetDecoder; +import java.nio.charset.CodingErrorAction; +import java.util.Iterator; + +import javax.xml.stream.XMLEventFactory; +import javax.xml.stream.XMLEventReader; +import javax.xml.stream.XMLEventWriter; +import javax.xml.stream.XMLInputFactory; +import javax.xml.stream.XMLOutputFactory; +import javax.xml.stream.XMLStreamException; +import javax.xml.stream.events.StartElement; +import javax.xml.stream.events.XMLEvent; + +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; + +public class XMLIterator implements Iterator { + + private static final Log log = LogFactory.getLog(XMLIterator.class); + + private ThreadLocal inputFactory = new ThreadLocal() { + + @Override + protected XMLInputFactory initialValue() { + return XMLInputFactory.newInstance(); + } + }; + + private ThreadLocal outputFactory = new ThreadLocal() { + + @Override + protected XMLOutputFactory initialValue() { + return XMLOutputFactory.newInstance(); + } + }; + + private ThreadLocal eventFactory = new ThreadLocal() { + + @Override + protected XMLEventFactory initialValue() { + return XMLEventFactory.newInstance(); + } + }; + + public static final String UTF_8 = "UTF-8"; + + final XMLEventReader parser; + + private XMLEvent current = null; + + private String element; + + private InputStream inputStream; + + public XMLIterator(final String element, final InputStream inputStream) { + super(); + this.element = element; + this.inputStream = inputStream; + this.parser = getParser(); + try { + this.current = findElement(parser); + } catch (XMLStreamException e) { + log.warn("cannot init parser position. No element found: " + element); + current = null; + } + } + + @Override + public boolean hasNext() { + return current != null; + } + + @Override + public String next() { + String result = null; + try { + result = copy(parser); + current = findElement(parser); + return result; + } catch (XMLStreamException e) { + throw new RuntimeException(String.format("error copying xml, built so far: '%s'", result), e); + } + } + + @Override + public void remove() { + throw new UnsupportedOperationException(); + } + + @SuppressWarnings("finally") + private String copy(final XMLEventReader parser) throws XMLStreamException { + final StringWriter result = new StringWriter(); + try { + final XMLEventWriter writer = outputFactory.get().createXMLEventWriter(result); + final StartElement start = current.asStartElement(); + final StartElement newRecord = eventFactory.get().createStartElement(start.getName(), start.getAttributes(), start.getNamespaces()); + + // new root record + writer.add(newRecord); + + // copy the rest as it is + while (parser.hasNext()) { + final XMLEvent event = parser.nextEvent(); + + // TODO: replace with depth tracking instead of close tag tracking. + if (event.isEndElement() && event.asEndElement().getName().getLocalPart().equals(element)) { + writer.add(event); + break; + } + + writer.add(event); + } + writer.close(); + } finally { + return result.toString(); + } + } + + /** + * Looks for the next occurrence of the splitter element. + * + * @param parser + * @return + * @throws XMLStreamException + */ + private XMLEvent findElement(final XMLEventReader parser) throws XMLStreamException { + + /* + * if (current != null && element.equals(current.asStartElement().getName().getLocalPart())) { return current; } + */ + + XMLEvent peek = parser.peek(); + if (peek != null && peek.isStartElement()) { + String name = peek.asStartElement().getName().getLocalPart(); + if (element.equals(name)) { return peek; } + } + + while (parser.hasNext()) { + final XMLEvent event = parser.nextEvent(); + if (event != null && event.isStartElement()) { + String name = event.asStartElement().getName().getLocalPart(); + if (element.equals(name)) { return event; } + } + } + return null; + } + + private XMLEventReader getParser() { + try { + return inputFactory.get().createXMLEventReader(sanitize(inputStream)); + } catch (XMLStreamException e) { + throw new RuntimeException(e); + } + } + + private Reader sanitize(final InputStream in) { + final CharsetDecoder charsetDecoder = Charset.forName(UTF_8).newDecoder(); + charsetDecoder.onMalformedInput(CodingErrorAction.REPLACE); + charsetDecoder.onUnmappableCharacter(CodingErrorAction.REPLACE); + return new InputStreamReader(in, charsetDecoder); + } + +} \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/XmlCleaner.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/utils/XmlCleaner.java similarity index 99% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/XmlCleaner.java rename to dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/utils/XmlCleaner.java index c674031f6..95d1d2402 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/XmlCleaner.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/utils/XmlCleaner.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.collection; +package eu.dnetlib.dhp.collection.plugin.utils; import java.util.HashMap; import java.util.HashSet; diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/fileGZip/FileGZipCollectorPluginTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/file/FileGZipCollectorPluginTest.java similarity index 87% rename from dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/fileGZip/FileGZipCollectorPluginTest.java rename to dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/file/FileGZipCollectorPluginTest.java index 793a5b04c..43f00928f 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/fileGZip/FileGZipCollectorPluginTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/file/FileGZipCollectorPluginTest.java @@ -1,4 +1,4 @@ -package eu.dnetlib.dhp.collection.plugin.fileGZip; +package eu.dnetlib.dhp.collection.plugin.file; import eu.dnetlib.dhp.collection.ApiDescriptor; import eu.dnetlib.dhp.common.aggregation.AggregatorReport; @@ -20,22 +20,19 @@ public class FileGZipCollectorPluginTest { private FileGZipCollectorPlugin plugin; private static final String SPLIT_ON_ELEMENT = "repository"; - private static final String ENCODING = "UTF-8"; @BeforeEach public void setUp() { final String gzipFile = this .getClass() - .getResource("/eu/dnetlib/dhp/collection/plugin/fileGZip/opendoar.xml.gz") + .getResource("/eu/dnetlib/dhp/collection/plugin/file/gzip/opendoar.xml.gz") .getFile(); - System.out.println(gzipFile); api.setBaseUrl(gzipFile); HashMap params = new HashMap<>(); params.put("splitOnElement", SPLIT_ON_ELEMENT); - params.put("encoding", ENCODING); api.setParams(params); diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/plugin/fileGZip/opendoar.xml.gz b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/plugin/file/gzip/opendoar.xml.gz similarity index 100% rename from dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/plugin/fileGZip/opendoar.xml.gz rename to dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/plugin/file/gzip/opendoar.xml.gz From d0b84d32970d757bb49cac3b824b9969f7b39101 Mon Sep 17 00:00:00 2001 From: Serafeim Chatzopoulos Date: Thu, 7 Apr 2022 15:06:38 +0300 Subject: [PATCH 004/214] Add FileCollectorPlugin and respective test --- .../dhp/collection/CollectorWorker.java | 3 + .../collection/plugin/CollectorPlugin.java | 2 +- .../plugin/file/FileCollectorPlugin.java | 25 + .../plugin/file/FileGZipCollectorPlugin.java | 3 +- .../plugin/file/FileCollectorPluginTest.java | 53 + .../file/FileGZipCollectorPluginTest.java | 2 +- .../dhp/collection/plugin/file/opendoar.xml | 1079 +++++++++++++++++ .../plugin/file/{gzip => }/opendoar.xml.gz | Bin 8 files changed, 1163 insertions(+), 4 deletions(-) create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/file/FileCollectorPlugin.java create mode 100644 dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/file/FileCollectorPluginTest.java create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/plugin/file/opendoar.xml rename dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/plugin/file/{gzip => }/opendoar.xml.gz (100%) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java index 5de4eb84b..a770af804 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java @@ -7,6 +7,7 @@ import java.io.IOException; import java.util.Optional; import java.util.concurrent.atomic.AtomicInteger; +import eu.dnetlib.dhp.collection.plugin.file.FileCollectorPlugin; import eu.dnetlib.dhp.collection.plugin.file.FileGZipCollectorPlugin; import org.apache.hadoop.fs.FileSystem; import org.apache.hadoop.fs.Path; @@ -115,6 +116,8 @@ public class CollectorWorker extends ReportingJob { return new OaiCollectorPlugin(clientParams); case rest_json2xml: return new RestCollectorPlugin(clientParams); + case file: + return new FileCollectorPlugin(); case fileGZip: return new FileGZipCollectorPlugin(); case other: diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java index 7d6aaaff8..08084e22a 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java @@ -10,7 +10,7 @@ import eu.dnetlib.dhp.common.collection.CollectorException; public interface CollectorPlugin { enum NAME { - oai, other, rest_json2xml, fileGZip; + oai, other, rest_json2xml, file, fileGZip; public enum OTHER_NAME { mdstore_mongodb_dump, mdstore_mongodb diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/file/FileCollectorPlugin.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/file/FileCollectorPlugin.java new file mode 100644 index 000000000..3a268eabb --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/file/FileCollectorPlugin.java @@ -0,0 +1,25 @@ +package eu.dnetlib.dhp.collection.plugin.file; + +import eu.dnetlib.dhp.common.collection.CollectorException; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.BufferedInputStream; +import java.io.FileInputStream; + +public class FileCollectorPlugin extends AbstractSplittedRecordPlugin { + + private static final Logger log = LoggerFactory.getLogger(FileCollectorPlugin.class); + + @Override + protected BufferedInputStream getBufferedInputStream(final String baseUrl) throws CollectorException { + + log.info("baseUrl: {}", baseUrl); + + try { + return new BufferedInputStream(new FileInputStream(baseUrl)); + } catch (Exception e) { + throw new CollectorException("Error reading file " + baseUrl, e); + } + } +} \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/file/FileGZipCollectorPlugin.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/file/FileGZipCollectorPlugin.java index a4dd65d2a..b2c77e8b6 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/file/FileGZipCollectorPlugin.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/file/FileGZipCollectorPlugin.java @@ -22,8 +22,7 @@ public class FileGZipCollectorPlugin extends AbstractSplittedRecordPlugin { GZIPInputStream stream = new GZIPInputStream(new FileInputStream(baseUrl)); return new BufferedInputStream(stream); } catch (Exception e) { - e.printStackTrace(); - throw new CollectorException(e); + throw new CollectorException("Error reading file " + baseUrl, e); } } } diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/file/FileCollectorPluginTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/file/FileCollectorPluginTest.java new file mode 100644 index 000000000..d9b5152fe --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/file/FileCollectorPluginTest.java @@ -0,0 +1,53 @@ +package eu.dnetlib.dhp.collection.plugin.file; + +import eu.dnetlib.dhp.collection.ApiDescriptor; +import eu.dnetlib.dhp.common.aggregation.AggregatorReport; +import eu.dnetlib.dhp.common.collection.CollectorException; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.util.HashMap; +import java.util.stream.Stream; + +public class FileCollectorPluginTest { + + private static final Logger log = LoggerFactory.getLogger(FileGZipCollectorPluginTest.class); + + private final ApiDescriptor api = new ApiDescriptor(); + private FileCollectorPlugin plugin; + + private static final String SPLIT_ON_ELEMENT = "repository"; + + @BeforeEach + public void setUp() { + + final String gzipFile = this + .getClass() + .getResource("/eu/dnetlib/dhp/collection/plugin/file/opendoar.xml") + .getFile(); + + api.setBaseUrl(gzipFile); + + HashMap params = new HashMap<>(); + params.put("splitOnElement", SPLIT_ON_ELEMENT); + + api.setParams(params); + + plugin = new FileCollectorPlugin(); + } + + @Test + void test() throws CollectorException { + + final Stream stream = plugin.collect(api, new AggregatorReport()); + + stream.limit(10).forEach(s -> { + Assertions.assertTrue(s.length() > 0); + log.info(s); + }); + } +} + diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/file/FileGZipCollectorPluginTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/file/FileGZipCollectorPluginTest.java index 43f00928f..18caf1c45 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/file/FileGZipCollectorPluginTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/file/FileGZipCollectorPluginTest.java @@ -26,7 +26,7 @@ public class FileGZipCollectorPluginTest { final String gzipFile = this .getClass() - .getResource("/eu/dnetlib/dhp/collection/plugin/file/gzip/opendoar.xml.gz") + .getResource("/eu/dnetlib/dhp/collection/plugin/file/opendoar.xml.gz") .getFile(); 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Interface is in German. + + 514 + 2012-02-13 + + Aggregating + Operational + + + + + C + Multidisciplinary + + + + + de + German + + + + Journal articles + Theses and dissertations + + + + Content + Content policies explicitly undefined + + No policy registered in OpenDOAR. + + + + Metadata + Metadata re-use policy explicitly undefined + + No policy registered in OpenDOAR. + + + + Data + Full data item policies explicitly undefined + + No policy registered in OpenDOAR. + + + + Submission + Submission policies explicitly undefined + + No policy registered in OpenDOAR. + + + + Preserve + Preservation policies explicitly undefined + + No policy registered in OpenDOAR. + + + + + + + Repository of Belarusian National Technical University (BNTU) + + Y + http://rep.bntu.by/ + + + + + + Belarusian National Technical University + + Y + http://www.bntu.by/ + + + BY + Belarus + + 53.922100 + 27.590700 + + + This site provides access to the research output of the institution. The interface is available in Russian and English. Users may set up RSS feeds to be alerted to new content. + + 286 + 2012-01-26 + + Institutional + Operational + DSpace + + + + C + Multidisciplinary + + + + + en + English + + + ru + Russian + + + + Journal articles + Books, chapters and sections + Learning Objects + + + + + Alexey Skalaban + Administrator + skalaban@gmail.com + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/plugin/file/gzip/opendoar.xml.gz b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/plugin/file/opendoar.xml.gz similarity index 100% rename from dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/plugin/file/gzip/opendoar.xml.gz rename to dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/plugin/file/opendoar.xml.gz From 21f32b83c68f75fcf7122454f0f66cd16a5e0f2f Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 11 Apr 2022 08:52:12 +0200 Subject: [PATCH 005/214] [graph enrichment] fixed country_propagation oozie workflow definition, parameter saveGraph is not needed anymore by the SparkCountryPropagationJob --- .../eu/dnetlib/dhp/countrypropagation/oozie_app/workflow.xml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/oozie_app/workflow.xml index 202c86a6d..271ccbf72 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/oozie_app/workflow.xml @@ -274,7 +274,6 @@ --sourcePath${sourcePath}/publication --preparedInfoPath${workingDir}/publication - --saveGraph${saveGraph} --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication --outputPath${outputPath}/publication @@ -304,7 +303,6 @@ --sourcePath${sourcePath}/dataset --preparedInfoPath${workingDir}/dataset - --saveGraph${saveGraph} --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset --outputPath${outputPath}/dataset @@ -334,7 +332,6 @@ --sourcePath${sourcePath}/otherresearchproduct --preparedInfoPath${workingDir}/otherresearchproduct - --saveGraph${saveGraph} --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct --outputPath${outputPath}/otherresearchproduct @@ -364,7 +361,6 @@ --sourcePath${sourcePath}/software --preparedInfoPath${workingDir}/software - --saveGraph${saveGraph} --resultTableNameeu.dnetlib.dhp.schema.oaf.Software --outputPath${outputPath}/software From b93a141d6c76aa4e89413868f87a9b6604046ba1 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 12 Apr 2022 10:25:42 +0200 Subject: [PATCH 006/214] [Doiboost] fixed fundingReference extraction from the Crossref records --- .../doiboost/crossref/Crossref2Oaf.scala | 39 +++++++------------ 1 file changed, 14 insertions(+), 25 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala index 0cb08ea94..b4d6d67e2 100644 --- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala +++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala @@ -446,16 +446,12 @@ case object Crossref2Oaf { case "10.13039/501100000781" => generateSimpleRelationFromAward(funder, "corda_______", extractECAward) generateSimpleRelationFromAward(funder, "corda__h2020", extractECAward) - case "10.13039/100000001" => - generateSimpleRelationFromAward(funder, "nsf_________", a => a) - case "10.13039/501100001665" => - generateSimpleRelationFromAward(funder, "anr_________", a => a) - case "10.13039/501100002341" => - generateSimpleRelationFromAward(funder, "aka_________", a => a) + case "10.13039/100000001" => generateSimpleRelationFromAward(funder, "nsf_________", a => a) + case "10.13039/501100001665" => generateSimpleRelationFromAward(funder, "anr_________", a => a) + case "10.13039/501100002341" => generateSimpleRelationFromAward(funder, "aka_________", a => a) case "10.13039/501100001602" => - generateSimpleRelationFromAward(funder, "aka_________", a => a.replace("SFI", "")) - case "10.13039/501100000923" => - generateSimpleRelationFromAward(funder, "arc_________", a => a) + generateSimpleRelationFromAward(funder, "sfi_________", a => a.replace("SFI", "")) + case "10.13039/501100000923" => generateSimpleRelationFromAward(funder, "arc_________", a => a) case "10.13039/501100000038" => val targetId = getProjectId("nserc_______", "1e5e62235d094afd01cd56e65112fc63") queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY) @@ -468,14 +464,10 @@ case object Crossref2Oaf { val targetId = getProjectId("cihr________", "1e5e62235d094afd01cd56e65112fc63") queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY) queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES) - case "10.13039/501100002848" => - generateSimpleRelationFromAward(funder, "conicytf____", a => a) - case "10.13039/501100003448" => - generateSimpleRelationFromAward(funder, "gsrt________", extractECAward) - case "10.13039/501100010198" => - generateSimpleRelationFromAward(funder, "sgov________", a => a) - case "10.13039/501100004564" => - generateSimpleRelationFromAward(funder, "mestd_______", extractECAward) + case "10.13039/501100002848" => generateSimpleRelationFromAward(funder, "conicytf____", a => a) + case "10.13039/501100003448" => generateSimpleRelationFromAward(funder, "gsrt________", extractECAward) + case "10.13039/501100010198" => generateSimpleRelationFromAward(funder, "sgov________", a => a) + case "10.13039/501100004564" => generateSimpleRelationFromAward(funder, "mestd_______", extractECAward) case "10.13039/501100003407" => generateSimpleRelationFromAward(funder, "miur________", a => a) val targetId = getProjectId("miur________", "1e5e62235d094afd01cd56e65112fc63") @@ -487,15 +479,11 @@ case object Crossref2Oaf { "irb_hr______", a => a.replaceAll("Project No.", "").replaceAll("HRZZ-", "") ) - case "10.13039/501100006769" => - generateSimpleRelationFromAward(funder, "rsf_________", a => a) - case "10.13039/501100001711" => - generateSimpleRelationFromAward(funder, "snsf________", snsfRule) - case "10.13039/501100004410" => - generateSimpleRelationFromAward(funder, "tubitakf____", a => a) - case "10.10.13039/100004440" => - generateSimpleRelationFromAward(funder, "wt__________", a => a) + case "10.13039/501100006769" => generateSimpleRelationFromAward(funder, "rsf_________", a => a) + case "10.13039/501100001711" => generateSimpleRelationFromAward(funder, "snsf________", snsfRule) + case "10.13039/501100004410" => generateSimpleRelationFromAward(funder, "tubitakf____", a => a) case "10.13039/100004440" => + generateSimpleRelationFromAward(funder, "wt__________", a => a) val targetId = getProjectId("wt__________", "1e5e62235d094afd01cd56e65112fc63") queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY) queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES) @@ -516,6 +504,7 @@ case object Crossref2Oaf { case "CONICYT, Programa de Formación de Capital Humano Avanzado" => generateSimpleRelationFromAward(funder, "conicytf____", extractECAward) case "Wellcome Trust Masters Fellowship" => + generateSimpleRelationFromAward(funder, "wt__________", a => a) val targetId = getProjectId("wt__________", "1e5e62235d094afd01cd56e65112fc63") queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY) queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES) From 8e8933d41abb871e49e20d7046f235afc6ed875b Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 14 Apr 2022 09:04:24 +0200 Subject: [PATCH 007/214] [BulkTagging] added fix if result.dataInfo is null --- .../main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java index 1a0afb981..6664d36ec 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java @@ -5,6 +5,7 @@ import static eu.dnetlib.dhp.PropagationConstant.removeOutputDir; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.util.ArrayList; +import java.util.Objects; import java.util.Optional; import org.apache.commons.io.IOUtils; @@ -102,6 +103,7 @@ public class SparkBulkTagJob { ResultTagger resultTagger = new ResultTagger(); readPath(spark, inputPath, resultClazz) .map(patchResult(), Encoders.bean(resultClazz)) + .filter(Objects::nonNull) .map( (MapFunction) value -> resultTagger .enrichContextCriteria( @@ -124,6 +126,9 @@ public class SparkBulkTagJob { // TODO remove this hack as soon as the values fixed by this method will be provided as NON null private static MapFunction patchResult() { return r -> { + if(r.getDataInfo() == null){ + return null; + } if (r.getDataInfo().getDeletedbyinference() == null) { r.getDataInfo().setDeletedbyinference(false); } From d5b29d96a7c7b8d77e2b31599a65e4bd48164382 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Thu, 14 Apr 2022 11:07:04 +0200 Subject: [PATCH 008/214] fix merging in crossrefAggregator which creates dataInfo null --- .../main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala | 2 ++ 1 file changed, 2 insertions(+) diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala index 9323c994c..79b9e8183 100644 --- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala +++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala @@ -71,6 +71,7 @@ object SparkGenerateDoiBoost { } } else { if (a != null && a._2 != null) { + b.mergeOAFDataInfo(a._2) b.mergeFrom(a._2) b.setId(a._1) val authors = AuthorMerger.mergeAuthor(b.getAuthor, a._2.getAuthor) @@ -87,6 +88,7 @@ object SparkGenerateDoiBoost { return b2 } else { if (b2 != null) { + b1.mergeOAFDataInfo(b2) b1.mergeFrom(b2) val authors = AuthorMerger.mergeAuthor(b1.getAuthor, b2.getAuthor) b1.setAuthor(authors) From c5a863132c124e25d1b75ca8d7c8546a7db33043 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 14 Apr 2022 14:14:13 +0200 Subject: [PATCH 009/214] [BulkTagging] revert it --- .../src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java | 3 --- 1 file changed, 3 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java index 6664d36ec..ad1e8721a 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java @@ -126,9 +126,6 @@ public class SparkBulkTagJob { // TODO remove this hack as soon as the values fixed by this method will be provided as NON null private static MapFunction patchResult() { return r -> { - if(r.getDataInfo() == null){ - return null; - } if (r.getDataInfo().getDeletedbyinference() == null) { r.getDataInfo().setDeletedbyinference(false); } From 4314db55c8bf94150cabe07d7b2342fc18ec1001 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Tue, 19 Apr 2022 15:05:02 +0200 Subject: [PATCH 010/214] migration to services: update sql queries --- ...eryDatasourceOrganization.sql => queryServiceOrganization.sql} | 0 .../dhp/oa/graph/sql/{queryDatasources.sql => queryServices.sql} | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/{queryDatasourceOrganization.sql => queryServiceOrganization.sql} (100%) rename dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/{queryDatasources.sql => queryServices.sql} (100%) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryDatasourceOrganization.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServiceOrganization.sql similarity index 100% rename from dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryDatasourceOrganization.sql rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServiceOrganization.sql diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryDatasources.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql similarity index 100% rename from dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryDatasources.sql rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql From c96a8613f8152311480aec93b65a627d4f6421f3 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Wed, 20 Apr 2022 12:07:49 +0200 Subject: [PATCH 011/214] update SQL queries --- .../dhp/oa/graph/sql/queryOrganizations.sql | 2 +- .../oa/graph/sql/queryProjectOrganization.sql | 2 +- .../dhp/oa/graph/sql/queryProjects.sql | 2 +- .../oa/graph/sql/queryProjects_production.sql | 2 +- .../oa/graph/sql/queryServiceOrganization.sql | 8 +-- .../dhp/oa/graph/sql/queryServices.sql | 57 +++++++++++-------- 6 files changed, 40 insertions(+), 33 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryOrganizations.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryOrganizations.sql index 11a8c50af..3451333c0 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryOrganizations.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryOrganizations.sql @@ -27,7 +27,7 @@ SELECT 'sysimport:crosswalk:entityregistry@@@dnet:provenance_actions' AS provenanceaction, array_remove(array_agg(DISTINCT i.pid || '###' || i.issuertype || '@@@' || i.issuertype), NULL) AS pid FROM dsm_organizations o - LEFT OUTER JOIN dsm_datasources d ON (d.id = o.collectedfrom) + LEFT OUTER JOIN dsm_services d ON (d.id = o.collectedfrom) LEFT OUTER JOIN dsm_organizationpids p ON (p.organization = o.id) LEFT OUTER JOIN dsm_identities i ON (i.pid = p.pid) GROUP BY diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjectOrganization.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjectOrganization.sql index bcdef8221..d9a77427d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjectOrganization.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjectOrganization.sql @@ -16,4 +16,4 @@ SELECT FROM project_organization po LEFT OUTER JOIN projects p ON (p.id = po.project) - LEFT OUTER JOIN dsm_datasources dc ON (dc.id = p.collectedfrom); \ No newline at end of file + LEFT OUTER JOIN dsm_services dc ON (dc.id = p.collectedfrom); \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjects.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjects.sql index db0da83f7..af5913e75 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjects.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjects.sql @@ -42,7 +42,7 @@ SELECT LEFT OUTER JOIN projectpids pp ON (pp.project = p.id) LEFT OUTER JOIN dsm_identities i ON (i.pid = pp.pid) - LEFT OUTER JOIN dsm_datasources dc ON (dc.id = p.collectedfrom) + LEFT OUTER JOIN dsm_services dc ON (dc.id = p.collectedfrom) LEFT OUTER JOIN project_fundingpath pf ON (pf.project = p.id) LEFT OUTER JOIN fundingpaths fp ON (fp.id = pf.funding) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjects_production.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjects_production.sql index 234bb7c3e..80cbda4b7 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjects_production.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjects_production.sql @@ -40,7 +40,7 @@ SELECT LEFT OUTER JOIN projectpids pp ON (pp.project = p.id) LEFT OUTER JOIN dsm_identities i ON (i.pid = pp.pid) - LEFT OUTER JOIN dsm_datasources dc ON (dc.id = p.collectedfrom) + LEFT OUTER JOIN dsm_services dc ON (dc.id = p.collectedfrom) LEFT OUTER JOIN project_fundingpath pf ON (pf.project = p.id) LEFT OUTER JOIN fundingpaths fp ON (fp.id = pf.funding) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServiceOrganization.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServiceOrganization.sql index f72e72105..02bed4b65 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServiceOrganization.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServiceOrganization.sql @@ -1,5 +1,5 @@ SELECT - dor.datasource AS datasource, + dor.service AS service, dor.organization AS organization, NULL AS startdate, NULL AS enddate, @@ -11,6 +11,6 @@ SELECT dc.officialname AS collectedfromname, 'providedBy@@@dnet:datasources_organizations_typologies' AS semantics, d.provenanceaction || '@@@dnet:provenanceActions' AS provenanceaction -FROM dsm_datasource_organization dor - LEFT OUTER JOIN dsm_datasources d ON (dor.datasource = d.id) - LEFT OUTER JOIN dsm_datasources dc ON (dc.id = d.collectedfrom); \ No newline at end of file +FROM dsm_service_organization dor + LEFT OUTER JOIN dsm_services d ON (dor.service = d.id) + LEFT OUTER JOIN dsm_services dc ON (dc.id = d.collectedfrom); \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql index 2623c65c4..81be79420 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql @@ -57,8 +57,12 @@ SELECT NULL AS odpolicies, ARRAY(SELECT trim(s) FROM unnest(string_to_array(d.languages, ',')) AS s) AS odlanguages, - ARRAY(SELECT trim(s) - FROM unnest(string_to_array(d.od_contenttypes, '-')) AS s) AS odcontenttypes, + + -- Term provided only by OpenDOAR: + -- probably updating the TR it could be replaced by research_entity_types[] + -- But a study on the vocabulary terms is needed + -- REMOVED: ARRAY(SELECT trim(s) FROM unnest(string_to_array(d.od_contenttypes, '-')) AS s) AS odcontenttypes, + false AS inferred, false AS deletedbyinference, 0.9 AS trust, @@ -69,22 +73,25 @@ SELECT d.releasestartdate AS releasestartdate, d.releaseenddate AS releaseenddate, d.missionstatementurl AS missionstatementurl, - d.dataprovider AS dataprovider, - d.serviceprovider AS serviceprovider, + -- the following 2 fields (provided by re3data) have been replaced by research_entity_types[] + -- VALUE 'Research Data' : d.dataprovider AS dataprovider, + -- VALUE 'Services' : d.serviceprovider AS serviceprovider, d.databaseaccesstype AS databaseaccesstype, d.datauploadtype AS datauploadtype, d.databaseaccessrestriction AS databaseaccessrestriction, d.datauploadrestriction AS datauploadrestriction, - d.versioning AS versioning, + -- REPLACED BY version_control : d.versioning AS versioning, + d.version_control AS versioning, d.citationguidelineurl AS citationguidelineurl, - d.qualitymanagementkind AS qualitymanagementkind, + -- REMOVED (it was provided only by re3data: yes, no, unknown): d.qualitymanagementkind AS qualitymanagementkind, d.pidsystems AS pidsystems, d.certificates AS certificates, ARRAY[]::text[] AS policies, dc.id AS collectedfromid, dc.officialname AS collectedfromname, - d.typology||'@@@dnet:datasource_typologies' AS datasourcetype, - d.typology||'@@@dnet:datasource_typologies_ui' AS datasourcetypeui, + d._typology_to_remove_||'@@@dnet:datasource_typologies' AS datasourcetype, + d.eosc_type||'@@@dnet:eosc_types' AS eosc_type, + d.eosc_datasource_type||'@@@dnet:eosc_datasource_types' AS eosc_datasoorce_type, 'sysimport:crosswalk:entityregistry@@@dnet:provenance_actions' AS provenanceaction, d.issn AS issnPrinted, d.eissn AS issnOnline, @@ -92,16 +99,15 @@ SELECT d.consenttermsofuse AS consenttermsofuse, d.fulltextdownload AS fulltextdownload, d.consenttermsofusedate AS consenttermsofusedate, - de.jurisdiction||'@@@eosc:jurisdictions' AS jurisdiction, - de.thematic AS thematic, - de.knowledge_graph AS knowledgegraph, - array(select unnest(de.content_policies)||'@@@eosc:contentpolicies') AS contentpolicies + d.jurisdiction||'@@@eosc:jurisdictions' AS jurisdiction, + d.thematic AS thematic, + -- REMOVED ???: d.knowledge_graph AS knowledgegraph, + array(select unnest(d.content_policies)||'@@@eosc:contentpolicies') AS contentpolicies -FROM dsm_datasources d -LEFT OUTER JOIN dsm_datasources_eosc de on (d.id = de.id) -LEFT OUTER JOIN dsm_datasources dc on (d.collectedfrom = dc.id) -LEFT OUTER JOIN dsm_api a ON (d.id = a.datasource) -LEFT OUTER JOIN dsm_datasourcepids di ON (d.id = di.datasource) +FROM dsm_services d +LEFT OUTER JOIN dsm_services dc on (d.collectedfrom = dc.id) +LEFT OUTER JOIN dsm_api a ON (d.id = a.service) +LEFT OUTER JOIN dsm_servicepids di ON (d.id = di.service) GROUP BY d.id, @@ -119,15 +125,16 @@ GROUP BY d.releasestartdate, d.releaseenddate, d.missionstatementurl, - d.dataprovider, - d.serviceprovider, + -- TODO REMOVED ???: d.dataprovider, + -- TODO REMOVED ???: d.serviceprovider, d.databaseaccesstype, d.datauploadtype, d.databaseaccessrestriction, d.datauploadrestriction, - d.versioning, + -- REPLACED BY version_control : d.versioning, + d.version_control d.citationguidelineurl, - d.qualitymanagementkind, + -- REMOVED: d.qualitymanagementkind, d.pidsystems, d.certificates, dc.id, @@ -135,7 +142,7 @@ GROUP BY d.issn, d.eissn, d.lissn, - de.jurisdiction, - de.thematic, - de.knowledge_graph, - de.content_policies + d.jurisdiction, + d.thematic, + -- REMOVED ???: de.knowledge_graph, + d.content_policies From b7cd2c6ca1a377097775d9dcc7ed6cfebdbd9728 Mon Sep 17 00:00:00 2001 From: Antonis Lempesis Date: Wed, 20 Apr 2022 14:46:55 +0300 Subject: [PATCH 012/214] added open citations --- .../graph/stats/oozie_app/scripts/step13.sql | 32 ++++++++++++++++++- 1 file changed, 31 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql index a5839da11..aee66fd5e 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql @@ -80,4 +80,34 @@ where reltype='resultResult' and r2.datainfo.deletedbyinference=false and r2.datainfo.invisible = FALSE and r1.resulttype.classname != 'other' and r2.resulttype.classname != 'other' - and rel.datainfo.deletedbyinference=false and rel.datainfo.invisible = FALSE; \ No newline at end of file + and rel.datainfo.deletedbyinference=false and rel.datainfo.invisible = FALSE; + +create table ${stats_db_name}.result_citations_oc stored as parquet as +select substr(target, 4) as id, count(distinct substr(source, 4)) as citations +from ${openaire_db_name}.relation rel +join ${openaire_db_name}.result r1 on rel.source=r1.id +join ${openaire_db_name}.result r2 on r2.id=rel.target +where relClass='Cites' and rel.datainfo.provenanceaction.classid = 'sysimport:crosswalk:opencitations' + and reltype='resultResult' + and r1.resulttype.classname!=r2.resulttype.classname + and r1.datainfo.deletedbyinference=false and r1.datainfo.invisible = FALSE + and r2.datainfo.deletedbyinference=false and r2.datainfo.invisible = FALSE + and r1.resulttype.classname != 'other' + and r2.resulttype.classname != 'other' + and rel.datainfo.deletedbyinference=false and rel.datainfo.invisible = FALSE +group by substr(target, 4); + +create table ${stats_db_name}.result_references_oc stored as parquet as +select substr(source, 4) as id, count(distinct substr(target, 4)) as references +from ${openaire_db_name}.relation rel + join ${openaire_db_name}.result r1 on rel.source=r1.id + join ${openaire_db_name}.result r2 on r2.id=rel.target +where relClass='Cites' and rel.datainfo.provenanceaction.classid = 'sysimport:crosswalk:opencitations' + and reltype='resultResult' + and r1.resulttype.classname!=r2.resulttype.classname + and r1.datainfo.deletedbyinference=false and r1.datainfo.invisible = FALSE + and r2.datainfo.deletedbyinference=false and r2.datainfo.invisible = FALSE + and r1.resulttype.classname != 'other' + and r2.resulttype.classname != 'other' + and rel.datainfo.deletedbyinference=false and rel.datainfo.invisible = FALSE +group by substr(source, 4); \ No newline at end of file From 869407c6e202e765ba26d15b684ad47c516eff12 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 20 Apr 2022 14:02:05 +0200 Subject: [PATCH 013/214] [Measures] added new measure (usagecounts) as action set. Measure added at the level of the result. Ref #7587 --- .../dnetlib/dhp/actionmanager/Constants.java | 2 + .../usagestats/SparkAtomicActionUsageJob.java | 165 ++++++++++++++++++ .../usagestats/UsageStatsModel.java | 34 ++++ .../usagestats/input_actionset_parameter.json | 26 +++ .../usagestats/oozie_app/config-default.xml | 30 ++++ .../usagestats/oozie_app/workflow.xml | 98 +++++++++++ .../SparkAtomicActionCountJobTest.java | 133 ++++++++++++++ .../dhp/actionmanager/usagestats/usagestatsdb | 12 ++ pom.xml | 2 +- 9 files changed, 501 insertions(+), 1 deletion(-) create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/UsageStatsModel.java create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/input_actionset_parameter.json create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/oozie_app/config-default.xml create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/oozie_app/workflow.xml create mode 100644 dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionCountJobTest.java create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/usagestats/usagestatsdb diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java index b790d90cb..aa25ca633 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java @@ -27,6 +27,8 @@ public class Constants { public static final String UPDATE_CLASS_NAME = "Inferred by OpenAIRE"; public static final String UPDATE_MEASURE_BIP_CLASS_ID = "measure:bip"; public static final String UPDATE_SUBJECT_SDG_CLASS_ID = "subject:sdg"; + public static final String UPDATE_MEASURE_USAGE_COUNTS_CLASS_ID = "measure:usage_counts"; + public static final String UPDATE_KEY_USAGE_COUNTS = "count"; public static final String FOS_CLASS_ID = "FOS"; public static final String FOS_CLASS_NAME = "Fields of Science and Technology classification"; diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java new file mode 100644 index 000000000..04f861df5 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java @@ -0,0 +1,165 @@ + +package eu.dnetlib.dhp.actionmanager.usagestats; + +import static eu.dnetlib.dhp.actionmanager.Constants.*; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.Serializable; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; +import java.util.Optional; +import java.util.stream.Collectors; + +import org.apache.commons.io.IOUtils; +import org.apache.cxf.wsdl.service.factory.MethodNameSoapActionServiceConfiguration; +import org.apache.hadoop.io.Text; +import org.apache.hadoop.mapred.SequenceFileOutputFormat; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.ForeachFunction; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.api.java.function.MapGroupsFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.actionmanager.bipmodel.BipDeserialize; +import eu.dnetlib.dhp.actionmanager.bipmodel.BipScore; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.schema.action.AtomicAction; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.DataInfo; +import eu.dnetlib.dhp.schema.oaf.KeyValue; +import eu.dnetlib.dhp.schema.oaf.Measure; +import eu.dnetlib.dhp.schema.oaf.Result; +import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; +import lombok.val; +import scala.Tuple2; + +/** + * created the Atomic Action for each tipe of results + */ +public class SparkAtomicActionUsageJob implements Serializable { + + private static final Logger log = LoggerFactory.getLogger(SparkAtomicActionUsageJob.class); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + public static void main(String[] args) throws Exception { + + String jsonConfiguration = IOUtils + .toString( + SparkAtomicActionUsageJob.class + .getResourceAsStream( + "/eu/dnetlib/dhp/actionmanager/usagestats/input_actionset_parameter.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath {}: ", outputPath); + + SparkConf conf = new SparkConf(); + conf.set("hive.metastore.uris", parser.get("hive_metastore_uris")); + + final String dbname = parser.get("statsdb"); + + final String workingPath = parser.get("workingPath"); + + runWithSparkHiveSession( + conf, + isSparkSessionManaged, + spark -> { + removeOutputDir(spark, outputPath); + prepareResults(dbname, spark, outputPath); + prepareActionSet(spark, workingPath, outputPath); + }); + } + + public static void prepareResults(String db, SparkSession spark, String workingPath) { + spark + .sql( + "Select result_id, downloads, views " + + "from " + db + ".usage_stats") + .as(Encoders.bean(UsageStatsModel.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingPath); + } + + public static void prepareActionSet(SparkSession spark, String inputPath, String outputPath){ + readPath(spark, inputPath, UsageStatsModel.class) + .groupByKey((MapFunction) us -> us.getResult_id(), Encoders.STRING()) + .mapGroups((MapGroupsFunction) (k, it) -> { + UsageStatsModel first = it.next(); + it.forEachRemaining(us -> { + first.setDownloads(first.getDownloads() + us.getDownloads()); + first.setViews(first.getViews() + us.getViews()); + }); + + Result res = new Result(); + res.setId("50|" + k); + + + res.setMeasures(getMeasure(first.getDownloads(), first.getViews())); + return res; + }, Encoders.bean(Result.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath); + } + + private static List getMeasure(Long downloads, Long views) { + DataInfo dataInfo = OafMapperUtils + .dataInfo( + false, + UPDATE_DATA_INFO_TYPE, + true, + false, + OafMapperUtils + .qualifier( + UPDATE_MEASURE_USAGE_COUNTS_CLASS_ID, + UPDATE_CLASS_NAME, + ModelConstants.DNET_PROVENANCE_ACTIONS, + ModelConstants.DNET_PROVENANCE_ACTIONS), + ""); + + return Arrays + .asList( + Measure + .newInstance("downloads", String.valueOf(downloads), UPDATE_KEY_USAGE_COUNTS, dataInfo), + Measure.newInstance("views", String.valueOf(views), UPDATE_KEY_USAGE_COUNTS, dataInfo)); + + } + + private static void removeOutputDir(SparkSession spark, String path) { + HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); + } + + public static Dataset readPath( + SparkSession spark, String inputPath, Class clazz) { + return spark + .read() + .textFile(inputPath) + .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz)); + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/UsageStatsModel.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/UsageStatsModel.java new file mode 100644 index 000000000..df8a77eb6 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/UsageStatsModel.java @@ -0,0 +1,34 @@ + +package eu.dnetlib.dhp.actionmanager.usagestats; + +import java.io.Serializable; + +public class UsageStatsModel implements Serializable { + private String result_id; + private Long downloads; + private Long views; + + public String getResult_id() { + return result_id; + } + + public void setResult_id(String result_id) { + this.result_id = result_id; + } + + public Long getDownloads() { + return downloads; + } + + public void setDownloads(Long downloads) { + this.downloads = downloads; + } + + public Long getViews() { + return views; + } + + public void setViews(Long views) { + this.views = views; + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/input_actionset_parameter.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/input_actionset_parameter.json new file mode 100644 index 000000000..b8ae24e12 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/input_actionset_parameter.json @@ -0,0 +1,26 @@ +[ + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "when true will stop SparkSession after job execution", + "paramRequired": false + }, + { + "paramName": "hmu", + "paramLongName": "hive_metastore_uris", + "paramDescription": "the URI for the hive metastore", + "paramRequired": true + }, + { + "paramName": "o", + "paramLongName": "outputPath", + "paramDescription": "the path of the new ActionSet", + "paramRequired": true + }, + { + "paramName": "sdb", + "paramLongName": "statsdb", + "paramDescription": "the name of the db to be used", + "paramRequired": true + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/oozie_app/config-default.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/oozie_app/config-default.xml new file mode 100644 index 000000000..d262cb6e0 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/oozie_app/config-default.xml @@ -0,0 +1,30 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + hiveMetastoreUris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + hiveJdbcUrl + jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000 + + + hiveDbName + openaire + + + oozie.launcher.mapreduce.user.classpath.first + true + + diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/oozie_app/workflow.xml new file mode 100644 index 000000000..781efb475 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/oozie_app/workflow.xml @@ -0,0 +1,98 @@ + + + + outputPath + the path where to store the actionset + + + statsdb + the path where to store the actionset + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + + + spark2YarnHistoryServerAddress + spark 2.* yarn history server address + + + spark2EventLogDir + spark 2.* event log dir location + + + + + ${jobTracker} + ${nameNode} + + + mapreduce.job.queuename + ${queueName} + + + oozie.launcher.mapred.job.queue.name + ${oozieLauncherQueueName} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + yarn + cluster + Produces the atomic action with the usage stats count for results + eu.dnetlib.dhp.actionmanager.usagestats.SparkAtomicActionUsageJob + dhp-aggregation-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --hive_metastore_uris${hiveMetastoreUris} + --outputPath${outputPath} + --statsdb${statsdb} + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionCountJobTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionCountJobTest.java new file mode 100644 index 000000000..33d76893d --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionCountJobTest.java @@ -0,0 +1,133 @@ + +package eu.dnetlib.dhp.actionmanager.usagestats; + +import static org.junit.jupiter.api.Assertions.assertEquals; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.stream.Collectors; + +import org.apache.commons.io.FileUtils; +import org.apache.hadoop.io.Text; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.Row; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob; +import eu.dnetlib.dhp.schema.action.AtomicAction; +import eu.dnetlib.dhp.schema.oaf.Result; + +public class SparkAtomicActionCountJobTest { + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path workingDir; + private static final Logger log = LoggerFactory + .getLogger(SparkAtomicActionCountJobTest.class); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files + .createTempDirectory(SparkAtomicActionCountJobTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(SparkAtomicActionCountJobTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(SparkAtomicActionCountJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + void testMatch() { + String usageScoresPath = getClass() + .getResource("/eu/dnetlib/dhp/actionmanager/usagestats/usagestatsdb") + .getPath(); + + SparkAtomicActionUsageJob.prepareActionSet(spark, usageScoresPath, workingDir.toString() + "/actionSet"); + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/actionSet") + .map(usm -> OBJECT_MAPPER.readValue(usm, Result.class)); + + Assertions.assertEquals(9, tmp.count()); + + tmp.foreach(r -> Assertions.assertEquals(2, r.getMeasures().size())); + tmp.foreach(r -> r.getMeasures().stream().forEach(m -> + m.getUnit().stream().forEach(u -> Assertions.assertFalse(u.getDataInfo().getDeletedbyinference())))); + tmp.foreach(r -> r.getMeasures().stream().forEach(m -> + m.getUnit().stream().forEach(u -> Assertions.assertTrue(u.getDataInfo().getInferred())))); + tmp.foreach(r -> r.getMeasures().stream().forEach(m -> + m.getUnit().stream().forEach(u -> Assertions.assertFalse(u.getDataInfo().getInvisible())))); + + tmp.foreach(r -> r.getMeasures().stream().forEach(m -> + m.getUnit().stream().forEach(u -> Assertions.assertEquals("measure:usage_counts", + u.getDataInfo().getProvenanceaction().getClassid())))); + tmp.foreach(r -> r.getMeasures().stream().forEach(m -> + m.getUnit().stream().forEach(u -> Assertions.assertEquals("Inferred by OpenAIRE", + u.getDataInfo().getProvenanceaction().getClassname())))); + + tmp.foreach(r -> r.getMeasures().stream().forEach(m -> + m.getUnit().stream().forEach(u -> Assertions.assertEquals("count", + u.getKey())))); + + Assertions.assertEquals(1, tmp.filter(r -> r.getId().equals("50|dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6")).count()); + + Assertions.assertEquals("0", tmp.filter(r -> r.getId().equals("50|dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6")).collect().get(0) + .getMeasures().stream().filter(m -> m.getId().equals("downloads")).collect(Collectors.toList()).get(0) + .getUnit().get(0).getValue()); + Assertions.assertEquals("5", tmp.filter(r -> r.getId().equals("50|dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6")).collect().get(0) + .getMeasures().stream().filter(m -> m.getId().equals("views")).collect(Collectors.toList()).get(0) + .getUnit().get(0).getValue()); + + Assertions.assertEquals("0", tmp.filter(r -> r.getId().equals("50|doi_________::17eda2ff77407538fbe5d3d719b9d1c0")).collect().get(0) + .getMeasures().stream().filter(m -> m.getId().equals("downloads")).collect(Collectors.toList()).get(0) + .getUnit().get(0).getValue()); + Assertions.assertEquals("1", tmp.filter(r -> r.getId().equals("50|doi_________::17eda2ff77407538fbe5d3d719b9d1c0")).collect().get(0) + .getMeasures().stream().filter(m -> m.getId().equals("views")).collect(Collectors.toList()).get(0) + .getUnit().get(0).getValue()); + + Assertions.assertEquals("2", tmp.filter(r -> r.getId().equals("50|doi_________::3085e4c6e051378ca6157fe7f0430c1f")).collect().get(0) + .getMeasures().stream().filter(m -> m.getId().equals("downloads")).collect(Collectors.toList()).get(0) + .getUnit().get(0).getValue()); + Assertions.assertEquals("6", tmp.filter(r -> r.getId().equals("50|doi_________::3085e4c6e051378ca6157fe7f0430c1f")).collect().get(0) + .getMeasures().stream().filter(m -> m.getId().equals("views")).collect(Collectors.toList()).get(0) + .getUnit().get(0).getValue()); + } + + + +} diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/usagestats/usagestatsdb b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/usagestats/usagestatsdb new file mode 100644 index 000000000..fee74f697 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/usagestats/usagestatsdb @@ -0,0 +1,12 @@ +{"result_id":"dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6","downloads":0,"views":4} +{"result_id":"dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6","downloads":0,"views":1} +{"result_id":"doi_________::17eda2ff77407538fbe5d3d719b9d1c0","downloads":0,"views":1} +{"result_id":"doi_________::1d4dc08605fd0a2be1105d30c63bfea1","downloads":1,"views":3} +{"result_id":"doi_________::2e3527822854ca9816f6dfea5bff61a8","downloads":1,"views":1} +{"result_id":"doi_________::3085e4c6e051378ca6157fe7f0430c1f","downloads":2,"views":3} +{"result_id":"doi_________::3085e4c6e051378ca6157fe7f0430c1f","downloads":0,"views":3} +{"result_id":"doi_________::33f710e6dd30cc5e67e35b371ddc33cf","downloads":0,"views":1} +{"result_id":"doi_________::39738ebf10654732dd3a7af9f24655f8","downloads":1,"views":3} +{"result_id":"doi_________::3c3b65f07c1a06c7894397eda1d11bbf","downloads":1,"views":8} +{"result_id":"doi_________::3c3b65f07c1a06c7894397eda1d11bbf","downloads":0,"views":2} +{"result_id":"doi_________::4938a71a884dd481d329657aa543b850","downloads":0,"views":3} \ No newline at end of file diff --git a/pom.xml b/pom.xml index 136b9b867..b0957393a 100644 --- a/pom.xml +++ b/pom.xml @@ -801,7 +801,7 @@ 3.3.3 3.4.2 [2.12,3.0) - [2.10.32] + [2.11.34-SNAPSHOT] [4.0.3] [6.0.5] [3.1.6] From 5feae77937df688e43f8c17988424dcf04259722 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 20 Apr 2022 15:13:09 +0200 Subject: [PATCH 014/214] [Measures] last changes to accomodate tests --- .../usagestats/SparkAtomicActionUsageJob.java | 23 +- .../usagestats/input_actionset_parameter.json | 6 + .../usagestats/oozie_app/workflow.xml | 1 + .../SparkAtomicActionCountJobTest.java | 200 ++++++++++++++---- 4 files changed, 181 insertions(+), 49 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java index 04f861df5..012261c39 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java @@ -94,19 +94,19 @@ public class SparkAtomicActionUsageJob implements Serializable { public static void prepareResults(String db, SparkSession spark, String workingPath) { spark - .sql( - "Select result_id, downloads, views " + - "from " + db + ".usage_stats") - .as(Encoders.bean(UsageStatsModel.class)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(workingPath); + .sql( + "Select result_id, downloads, views " + + "from " + db + ".usage_stats") + .as(Encoders.bean(UsageStatsModel.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingPath); } - public static void prepareActionSet(SparkSession spark, String inputPath, String outputPath){ - readPath(spark, inputPath, UsageStatsModel.class) - .groupByKey((MapFunction) us -> us.getResult_id(), Encoders.STRING()) + public static void prepareActionSet(SparkSession spark, String inputPath, String outputPath) { + readPath(spark, inputPath, UsageStatsModel.class) + .groupByKey((MapFunction) us -> us.getResult_id(), Encoders.STRING()) .mapGroups((MapGroupsFunction) (k, it) -> { UsageStatsModel first = it.next(); it.forEachRemaining(us -> { @@ -117,7 +117,6 @@ public class SparkAtomicActionUsageJob implements Serializable { Result res = new Result(); res.setId("50|" + k); - res.setMeasures(getMeasure(first.getDownloads(), first.getViews())); return res; }, Encoders.bean(Result.class)) diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/input_actionset_parameter.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/input_actionset_parameter.json index b8ae24e12..821905da4 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/input_actionset_parameter.json +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/input_actionset_parameter.json @@ -22,5 +22,11 @@ "paramLongName": "statsdb", "paramDescription": "the name of the db to be used", "paramRequired": true + }, + { + "paramName": "wp", + "paramLongName": "workingPath", + "paramDescription": "the workingPath where to save the content of the usage_stats table", + "paramRequired": true } ] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/oozie_app/workflow.xml index 781efb475..5b552ca4b 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/oozie_app/workflow.xml @@ -89,6 +89,7 @@ --hive_metastore_uris${hiveMetastoreUris} --outputPath${outputPath} --statsdb${statsdb} + --workingPath${workingDir}/usageDb diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionCountJobTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionCountJobTest.java index 33d76893d..7cc9eb326 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionCountJobTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionCountJobTest.java @@ -75,7 +75,7 @@ public class SparkAtomicActionCountJobTest { .getResource("/eu/dnetlib/dhp/actionmanager/usagestats/usagestatsdb") .getPath(); - SparkAtomicActionUsageJob.prepareActionSet(spark, usageScoresPath, workingDir.toString() + "/actionSet"); + SparkAtomicActionUsageJob.prepareActionSet(spark, usageScoresPath, workingDir.toString() + "/actionSet"); final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); @@ -86,48 +86,174 @@ public class SparkAtomicActionCountJobTest { Assertions.assertEquals(9, tmp.count()); tmp.foreach(r -> Assertions.assertEquals(2, r.getMeasures().size())); - tmp.foreach(r -> r.getMeasures().stream().forEach(m -> - m.getUnit().stream().forEach(u -> Assertions.assertFalse(u.getDataInfo().getDeletedbyinference())))); - tmp.foreach(r -> r.getMeasures().stream().forEach(m -> - m.getUnit().stream().forEach(u -> Assertions.assertTrue(u.getDataInfo().getInferred())))); - tmp.foreach(r -> r.getMeasures().stream().forEach(m -> - m.getUnit().stream().forEach(u -> Assertions.assertFalse(u.getDataInfo().getInvisible())))); + tmp + .foreach( + r -> r + .getMeasures() + .stream() + .forEach( + m -> m + .getUnit() + .stream() + .forEach(u -> Assertions.assertFalse(u.getDataInfo().getDeletedbyinference())))); + tmp + .foreach( + r -> r + .getMeasures() + .stream() + .forEach( + m -> m.getUnit().stream().forEach(u -> Assertions.assertTrue(u.getDataInfo().getInferred())))); + tmp + .foreach( + r -> r + .getMeasures() + .stream() + .forEach( + m -> m + .getUnit() + .stream() + .forEach(u -> Assertions.assertFalse(u.getDataInfo().getInvisible())))); - tmp.foreach(r -> r.getMeasures().stream().forEach(m -> - m.getUnit().stream().forEach(u -> Assertions.assertEquals("measure:usage_counts", - u.getDataInfo().getProvenanceaction().getClassid())))); - tmp.foreach(r -> r.getMeasures().stream().forEach(m -> - m.getUnit().stream().forEach(u -> Assertions.assertEquals("Inferred by OpenAIRE", - u.getDataInfo().getProvenanceaction().getClassname())))); + tmp + .foreach( + r -> r + .getMeasures() + .stream() + .forEach( + m -> m + .getUnit() + .stream() + .forEach( + u -> Assertions + .assertEquals( + "measure:usage_counts", + u.getDataInfo().getProvenanceaction().getClassid())))); + tmp + .foreach( + r -> r + .getMeasures() + .stream() + .forEach( + m -> m + .getUnit() + .stream() + .forEach( + u -> Assertions + .assertEquals( + "Inferred by OpenAIRE", + u.getDataInfo().getProvenanceaction().getClassname())))); - tmp.foreach(r -> r.getMeasures().stream().forEach(m -> - m.getUnit().stream().forEach(u -> Assertions.assertEquals("count", - u.getKey())))); + tmp + .foreach( + r -> r + .getMeasures() + .stream() + .forEach( + m -> m + .getUnit() + .stream() + .forEach( + u -> Assertions + .assertEquals( + "count", + u.getKey())))); - Assertions.assertEquals(1, tmp.filter(r -> r.getId().equals("50|dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6")).count()); + Assertions + .assertEquals( + 1, tmp.filter(r -> r.getId().equals("50|dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6")).count()); - Assertions.assertEquals("0", tmp.filter(r -> r.getId().equals("50|dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6")).collect().get(0) - .getMeasures().stream().filter(m -> m.getId().equals("downloads")).collect(Collectors.toList()).get(0) - .getUnit().get(0).getValue()); - Assertions.assertEquals("5", tmp.filter(r -> r.getId().equals("50|dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6")).collect().get(0) - .getMeasures().stream().filter(m -> m.getId().equals("views")).collect(Collectors.toList()).get(0) - .getUnit().get(0).getValue()); + Assertions + .assertEquals( + "0", + tmp + .filter(r -> r.getId().equals("50|dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6")) + .collect() + .get(0) + .getMeasures() + .stream() + .filter(m -> m.getId().equals("downloads")) + .collect(Collectors.toList()) + .get(0) + .getUnit() + .get(0) + .getValue()); + Assertions + .assertEquals( + "5", + tmp + .filter(r -> r.getId().equals("50|dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6")) + .collect() + .get(0) + .getMeasures() + .stream() + .filter(m -> m.getId().equals("views")) + .collect(Collectors.toList()) + .get(0) + .getUnit() + .get(0) + .getValue()); - Assertions.assertEquals("0", tmp.filter(r -> r.getId().equals("50|doi_________::17eda2ff77407538fbe5d3d719b9d1c0")).collect().get(0) - .getMeasures().stream().filter(m -> m.getId().equals("downloads")).collect(Collectors.toList()).get(0) - .getUnit().get(0).getValue()); - Assertions.assertEquals("1", tmp.filter(r -> r.getId().equals("50|doi_________::17eda2ff77407538fbe5d3d719b9d1c0")).collect().get(0) - .getMeasures().stream().filter(m -> m.getId().equals("views")).collect(Collectors.toList()).get(0) - .getUnit().get(0).getValue()); + Assertions + .assertEquals( + "0", + tmp + .filter(r -> r.getId().equals("50|doi_________::17eda2ff77407538fbe5d3d719b9d1c0")) + .collect() + .get(0) + .getMeasures() + .stream() + .filter(m -> m.getId().equals("downloads")) + .collect(Collectors.toList()) + .get(0) + .getUnit() + .get(0) + .getValue()); + Assertions + .assertEquals( + "1", + tmp + .filter(r -> r.getId().equals("50|doi_________::17eda2ff77407538fbe5d3d719b9d1c0")) + .collect() + .get(0) + .getMeasures() + .stream() + .filter(m -> m.getId().equals("views")) + .collect(Collectors.toList()) + .get(0) + .getUnit() + .get(0) + .getValue()); - Assertions.assertEquals("2", tmp.filter(r -> r.getId().equals("50|doi_________::3085e4c6e051378ca6157fe7f0430c1f")).collect().get(0) - .getMeasures().stream().filter(m -> m.getId().equals("downloads")).collect(Collectors.toList()).get(0) - .getUnit().get(0).getValue()); - Assertions.assertEquals("6", tmp.filter(r -> r.getId().equals("50|doi_________::3085e4c6e051378ca6157fe7f0430c1f")).collect().get(0) - .getMeasures().stream().filter(m -> m.getId().equals("views")).collect(Collectors.toList()).get(0) - .getUnit().get(0).getValue()); + Assertions + .assertEquals( + "2", + tmp + .filter(r -> r.getId().equals("50|doi_________::3085e4c6e051378ca6157fe7f0430c1f")) + .collect() + .get(0) + .getMeasures() + .stream() + .filter(m -> m.getId().equals("downloads")) + .collect(Collectors.toList()) + .get(0) + .getUnit() + .get(0) + .getValue()); + Assertions + .assertEquals( + "6", + tmp + .filter(r -> r.getId().equals("50|doi_________::3085e4c6e051378ca6157fe7f0430c1f")) + .collect() + .get(0) + .getMeasures() + .stream() + .filter(m -> m.getId().equals("views")) + .collect(Collectors.toList()) + .get(0) + .getUnit() + .get(0) + .getValue()); } - - } From dbfbe8841a8ec3335ed479111cc96b48f2a6b30b Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 20 Apr 2022 15:41:03 +0200 Subject: [PATCH 015/214] [Clean Context] changed the description in input parameters --- .../dnetlib/dhp/oa/graph/input_clean_context_parameters.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_context_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_context_parameters.json index 9b1588283..e3d31d69f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_context_parameters.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_context_parameters.json @@ -20,7 +20,7 @@ { "paramName": "ci", "paramLongName": "contextId", - "paramDescription": "url to the ISLookup Service", + "paramDescription": "the id of the context to be removed", "paramRequired": true }, { @@ -31,7 +31,7 @@ },{ "paramName": "vf", "paramLongName": "verifyParam", - "paramDescription": "url to the ISLookup Service", + "paramDescription": "the parameter to be verified to remove the context", "paramRequired": true } ] From 5295effc9664fea8f92e148019d36469091484fd Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 20 Apr 2022 16:20:40 +0200 Subject: [PATCH 016/214] [Measures] fixed issue --- .../dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java index 012261c39..261794598 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java @@ -87,7 +87,7 @@ public class SparkAtomicActionUsageJob implements Serializable { isSparkSessionManaged, spark -> { removeOutputDir(spark, outputPath); - prepareResults(dbname, spark, outputPath); + prepareResults(dbname, spark, workingPath); prepareActionSet(spark, workingPath, outputPath); }); } From d580e154424a8f211cf35ab1cae079f2624b8e44 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Thu, 21 Apr 2022 11:06:08 +0200 Subject: [PATCH 017/214] Modified last intersection since we lost many titles. this is my last resource, after that, I've to change my job --- .../doiboost/SparkGenerateDoiBoost.scala | 37 +++++++++++++++++-- 1 file changed, 34 insertions(+), 3 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala index 79b9e8183..bc26e44d6 100644 --- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala +++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala @@ -60,7 +60,7 @@ object SparkGenerateDoiBoost { val openaireOrganizationPath = parser.get("openaireOrganizationPath") val crossrefAggregator = new Aggregator[(String, Publication), Publication, Publication] with Serializable { - override def zero: Publication = new Publication + override def zero: Publication = null override def reduce(b: Publication, a: (String, Publication)): Publication = { @@ -177,12 +177,43 @@ object SparkGenerateDoiBoost { .map(DoiBoostMappingUtil.fixPublication) .map(p => (p.getId, p)) .groupByKey(_._1) - .agg(crossrefAggregator.toColumn) - .map(p => p._2) + .reduceGroups((left, right) => + { + //Check left is not null + if (left != null && left._1 != null) + { + //If right is null then return left + if (right == null || right._2 == null) + left + else { + // Here Left and Right are not null + // So we have to merge + val b1 = left._2 + val b2 = right._2 + b1.mergeFrom(b2) + b1.mergeOAFDataInfo(b2) + val authors = AuthorMerger.mergeAuthor(b1.getAuthor, b2.getAuthor) + b1.setAuthor(authors) + if (b2.getId != null && b2.getId.nonEmpty) + b1.setId(b2.getId) + //Return publication Merged + (b1.getId, b1) + } + } + else { + // Left is Null so we return right + right + } + } + + ) + .filter(s => s!= null && s._2!=null) + .map(s => s._2) .write .mode(SaveMode.Overwrite) .save(s"$workingDirPath/doiBoostPublicationFiltered") + val affiliationPath = parser.get("affiliationPath") val paperAffiliationPath = parser.get("paperAffiliationPath") From c304657d9195b334c44bce4a11649a68c60a3299 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 21 Apr 2022 11:27:26 +0200 Subject: [PATCH 018/214] [Measures] put the logic in common, no need to change the schema --- .../dhp/schema/oaf/utils/OafMapperUtils.java | 15 +++++++++++++ .../usagestats/SparkAtomicActionUsageJob.java | 22 ++++--------------- pom.xml | 2 +- 3 files changed, 20 insertions(+), 19 deletions(-) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java index 0a51e8600..8d67ce804 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java @@ -391,4 +391,19 @@ public class OafMapperUtils { } return null; } + + public static KeyValue newKeyValueInstance (String key, String value, DataInfo dataInfo){ + KeyValue kv = new KeyValue(); + kv.setDataInfo(dataInfo); + kv.setKey(key); + kv.setValue(value); + return kv; + } + + public static Measure newMeasureInstance(String id, String value, String key, DataInfo dataInfo) { + Measure m = new Measure(); + m.setId(id); + m.setUnit(Arrays.asList(newKeyValueInstance(key, value, dataInfo))); + return m; + } } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java index 261794598..790170ccc 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java @@ -3,23 +3,14 @@ package eu.dnetlib.dhp.actionmanager.usagestats; import static eu.dnetlib.dhp.actionmanager.Constants.*; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.io.Serializable; -import java.util.ArrayList; import java.util.Arrays; import java.util.List; import java.util.Optional; -import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; -import org.apache.cxf.wsdl.service.factory.MethodNameSoapActionServiceConfiguration; -import org.apache.hadoop.io.Text; -import org.apache.hadoop.mapred.SequenceFileOutputFormat; import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.api.java.function.ForeachFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.MapGroupsFunction; import org.apache.spark.sql.Dataset; @@ -31,19 +22,15 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.actionmanager.bipmodel.BipDeserialize; -import eu.dnetlib.dhp.actionmanager.bipmodel.BipScore; + import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; -import eu.dnetlib.dhp.schema.action.AtomicAction; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.DataInfo; -import eu.dnetlib.dhp.schema.oaf.KeyValue; import eu.dnetlib.dhp.schema.oaf.Measure; import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; -import lombok.val; -import scala.Tuple2; + /** * created the Atomic Action for each tipe of results @@ -143,9 +130,8 @@ public class SparkAtomicActionUsageJob implements Serializable { return Arrays .asList( - Measure - .newInstance("downloads", String.valueOf(downloads), UPDATE_KEY_USAGE_COUNTS, dataInfo), - Measure.newInstance("views", String.valueOf(views), UPDATE_KEY_USAGE_COUNTS, dataInfo)); + OafMapperUtils.newMeasureInstance("downloads", String.valueOf(downloads), UPDATE_KEY_USAGE_COUNTS, dataInfo), + OafMapperUtils.newMeasureInstance("views", String.valueOf(views), UPDATE_KEY_USAGE_COUNTS, dataInfo)); } diff --git a/pom.xml b/pom.xml index b0957393a..136b9b867 100644 --- a/pom.xml +++ b/pom.xml @@ -801,7 +801,7 @@ 3.3.3 3.4.2 [2.12,3.0) - [2.11.34-SNAPSHOT] + [2.10.32] [4.0.3] [6.0.5] [3.1.6] From d012d125d7b5c75a5d492353a0e387f05cf0934e Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 21 Apr 2022 12:02:09 +0200 Subject: [PATCH 019/214] [EOSCTag] - --- .../eu/dnetlib/dhp/bulktag/SparkEoscTag.java | 67 +++++++++++++++++++ 1 file changed, 67 insertions(+) create mode 100644 dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java new file mode 100644 index 000000000..2b44275cd --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java @@ -0,0 +1,67 @@ +package eu.dnetlib.dhp.bulktag; + +import com.fasterxml.jackson.databind.ObjectMapper; +import com.google.gson.Gson; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.bulktag.community.CommunityConfiguration; +import eu.dnetlib.dhp.bulktag.community.CommunityConfigurationFactory; +import eu.dnetlib.dhp.bulktag.community.ProtoMap; +import eu.dnetlib.dhp.bulktag.community.QueryInformationSystem; +import eu.dnetlib.dhp.schema.oaf.Result; +import eu.dnetlib.dhp.schema.oaf.Software; +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.util.Optional; + +import static eu.dnetlib.dhp.PropagationConstant.readPath; +import static eu.dnetlib.dhp.PropagationConstant.removeOutputDir; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +public class SparkEoscTag { + private static final Logger log = LoggerFactory.getLogger(SparkEoscTag.class); + public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + SparkEoscTag.class + .getResourceAsStream( + "/eu/dnetlib/dhp/bulktag/input_eosctag_parameters.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String inputPath = parser.get("sourcePath"); + log.info("inputPath: {}", inputPath); + + SparkConf conf = new SparkConf(); + + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + execEoscTag(spark, inputPath); + + }); + } + + private static void execEoscTag(SparkSession spark, String inputPath) { + //search for notebook + //subject contiene jupyter. + //esistono python e notebook nei subject non necessariamente nello stesso + //si cerca fra i prodotto di tipo software + Dataset sw = readPath(spark, inputPath + "/software", Software.class) + + } +} From b61efd613b5ba5e324f2a1e4a40f549baf52b4dc Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 21 Apr 2022 12:09:37 +0200 Subject: [PATCH 020/214] [Measures] addressed comments in the PR --- .../eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java | 2 +- .../usagestats/SparkAtomicActionUsageJob.java | 9 ++++----- .../usagestats/input_actionset_parameter.json | 2 +- .../dhp/actionmanager/usagestats/oozie_app/workflow.xml | 6 +++--- 4 files changed, 9 insertions(+), 10 deletions(-) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java index 8d67ce804..9ee359cd5 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java @@ -392,7 +392,7 @@ public class OafMapperUtils { return null; } - public static KeyValue newKeyValueInstance (String key, String value, DataInfo dataInfo){ + public static KeyValue newKeyValueInstance(String key, String value, DataInfo dataInfo) { KeyValue kv = new KeyValue(); kv.setDataInfo(dataInfo); kv.setKey(key); diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java index 790170ccc..04533aa53 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java @@ -22,7 +22,6 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; - import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.schema.common.ModelConstants; @@ -31,7 +30,6 @@ import eu.dnetlib.dhp.schema.oaf.Measure; import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; - /** * created the Atomic Action for each tipe of results */ @@ -65,7 +63,7 @@ public class SparkAtomicActionUsageJob implements Serializable { SparkConf conf = new SparkConf(); conf.set("hive.metastore.uris", parser.get("hive_metastore_uris")); - final String dbname = parser.get("statsdb"); + final String dbname = parser.get("usagestatsdb"); final String workingPath = parser.get("workingPath"); @@ -130,8 +128,9 @@ public class SparkAtomicActionUsageJob implements Serializable { return Arrays .asList( - OafMapperUtils.newMeasureInstance("downloads", String.valueOf(downloads), UPDATE_KEY_USAGE_COUNTS, dataInfo), - OafMapperUtils.newMeasureInstance("views", String.valueOf(views), UPDATE_KEY_USAGE_COUNTS, dataInfo)); + OafMapperUtils + .newMeasureInstance("downloads", String.valueOf(downloads), UPDATE_KEY_USAGE_COUNTS, dataInfo), + OafMapperUtils.newMeasureInstance("views", String.valueOf(views), UPDATE_KEY_USAGE_COUNTS, dataInfo)); } diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/input_actionset_parameter.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/input_actionset_parameter.json index 821905da4..e9200d3ad 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/input_actionset_parameter.json +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/input_actionset_parameter.json @@ -19,7 +19,7 @@ }, { "paramName": "sdb", - "paramLongName": "statsdb", + "paramLongName": "usagestatsdb", "paramDescription": "the name of the db to be used", "paramRequired": true }, diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/oozie_app/workflow.xml index 5b552ca4b..d94cf7d53 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/oozie_app/workflow.xml @@ -5,8 +5,8 @@ the path where to store the actionset - statsdb - the path where to store the actionset + usagestatsdb + the name of the db to be used sparkDriverMemory @@ -88,7 +88,7 @@ --hive_metastore_uris${hiveMetastoreUris} --outputPath${outputPath} - --statsdb${statsdb} + --usagestatsdb${usagestatsdb} --workingPath${workingDir}/usageDb From 20de75ca64cb0237dcc6a19caa0fc1308d60f7d5 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 21 Apr 2022 12:14:03 +0200 Subject: [PATCH 021/214] [Measures] removed typo --- .../dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java index 04533aa53..c284ad8bd 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java @@ -31,7 +31,7 @@ import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; /** - * created the Atomic Action for each tipe of results + * created the Atomic Action for each type of results */ public class SparkAtomicActionUsageJob implements Serializable { From ccba1a3db1f5dfd99743e4aee957a2e5553f4a83 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 21 Apr 2022 13:00:06 +0200 Subject: [PATCH 022/214] [Clean Context] added logic to cleaning workflow to accomodate also context cleaning --- .../dhp/oa/graph/clean/oozie_app/workflow.xml | 22 ++++++++++++++++++- 1 file changed, 21 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml index dc0529012..58ad6f1f5 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml @@ -13,6 +13,10 @@ isLookupUrl the address of the lookUp service + + shouldCleanContext + false + sparkDriverMemory @@ -275,7 +279,23 @@ - + + + + + ${wf:conf('shouldCleanContext') eq true} + + + + + + + + + + + + \ No newline at end of file From 5b7d9e741c2a77d408cc0db3ef9d357c4c27fe96 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 21 Apr 2022 13:02:14 +0200 Subject: [PATCH 023/214] [Clean Context] added logic to cleaning workflow to accomodate also context cleaning --- .../dhp/oa/graph/clean/oozie_app/workflow.xml | 108 ++++++++++++++++++ 1 file changed, 108 insertions(+) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml index 58ad6f1f5..12ba3e5a7 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml @@ -295,7 +295,115 @@ + + + yarn + cluster + Clean publications context + eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-cores=${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=7680 + + --inputPath${inputPath}/publication + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Publication + --workingPath${workingDir}/working + --contextId${contextId} + --verifyParam${verifyParam} + + + + + + + yarn + cluster + Clean datasets Context + eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-cores=${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=7680 + + --inputPath${graphInputPath}/dataset + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Dataset + --workingPath${workingDir}/working + --contextId${contextId} + --verifyParam${verifyParam} + + + + + + + yarn + cluster + Clean otherresearchproducts context + eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-cores=${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=7680 + + --inputPath${graphInputPath}/otherresearchproduct + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct + --workingPath${workingDir}/working + --contextId${contextId} + --verifyParam${verifyParam} + + + + + + + + yarn + cluster + Clean softwares context + eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-cores=${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=7680 + + --inputPath${graphInputPath}/software + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Software + --workingPath${workingDir}/working + --contextId${contextId} + --verifyParam${verifyParam} + + + + + + + \ No newline at end of file From 29150a5d0c69a540b546ffcfbc91114e68c40301 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 21 Apr 2022 13:31:56 +0200 Subject: [PATCH 024/214] code formatting --- .../oa/graph/clean/CleanContextSparkJob.java | 181 +++++---- .../dhp/oa/graph/clean/CleanContextTest.java | 375 ++++++++++++------ 2 files changed, 357 insertions(+), 199 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java index b20dcb67b..3e9b17f3f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java @@ -1,16 +1,13 @@ + package eu.dnetlib.dhp.oa.graph.clean; -import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.common.HdfsSupport; -import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.oaf.Context; -import eu.dnetlib.dhp.schema.oaf.Oaf; -import eu.dnetlib.dhp.schema.oaf.OafEntity; -import eu.dnetlib.dhp.schema.oaf.Result; -import eu.dnetlib.dhp.utils.ISLookupClientFactory; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.Serializable; +import java.util.List; +import java.util.Optional; +import java.util.stream.Collectors; + import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; @@ -21,93 +18,113 @@ import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import java.io.Serializable; -import java.util.List; -import java.util.Optional; -import java.util.stream.Collectors; +import com.fasterxml.jackson.databind.ObjectMapper; -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.Context; +import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.schema.oaf.OafEntity; +import eu.dnetlib.dhp.schema.oaf.Result; +import eu.dnetlib.dhp.utils.ISLookupClientFactory; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; public class CleanContextSparkJob implements Serializable { - private static final Logger log = LoggerFactory.getLogger(CleanContextSparkJob.class); + private static final Logger log = LoggerFactory.getLogger(CleanContextSparkJob.class); - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - public static void main(String[] args) throws Exception { + public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - CleanContextSparkJob.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/input_clean_context_parameters.json")); - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); + String jsonConfiguration = IOUtils + .toString( + CleanContextSparkJob.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/input_clean_context_parameters.json")); + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - String inputPath = parser.get("inputPath"); - log.info("inputPath: {}", inputPath); + String inputPath = parser.get("inputPath"); + log.info("inputPath: {}", inputPath); - String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + String workingPath = parser.get("workingPath"); + log.info("workingPath: {}", workingPath); - String contextId = parser.get("contextId"); - log.info("contextId: {}", contextId); + String contextId = parser.get("contextId"); + log.info("contextId: {}", contextId); - String verifyParam = parser.get("verifyParam"); - log.info("verifyParam: {}", verifyParam); + String verifyParam = parser.get("verifyParam"); + log.info("verifyParam: {}", verifyParam); + String graphTableClassName = parser.get("graphTableClassName"); + log.info("graphTableClassName: {}", graphTableClassName); - String graphTableClassName = parser.get("graphTableClassName"); - log.info("graphTableClassName: {}", graphTableClassName); + Class entityClazz = (Class) Class.forName(graphTableClassName); - Class entityClazz = (Class) Class.forName(graphTableClassName); + SparkConf conf = new SparkConf(); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + cleanContext(spark, contextId, verifyParam, inputPath, entityClazz, workingPath); + }); + } - SparkConf conf = new SparkConf(); - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { + private static void cleanContext(SparkSession spark, String contextId, String verifyParam, + String inputPath, Class entityClazz, String workingPath) { + Dataset res = spark + .read() + .textFile(inputPath) + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, entityClazz), + Encoders.bean(entityClazz)); - cleanContext(spark, contextId, verifyParam, inputPath, entityClazz, workingPath); - }); - } + res.map((MapFunction) r -> { + if (!r + .getTitle() + .stream() + .filter( + t -> t + .getQualifier() + .getClassid() + .equalsIgnoreCase(ModelConstants.MAIN_TITLE_QUALIFIER.getClassid())) + .anyMatch(t -> t.getValue().toLowerCase().startsWith(verifyParam.toLowerCase()))) { + return r; + } + r + .setContext( + r + .getContext() + .stream() + .filter( + c -> !c.getId().split("::")[0] + .equalsIgnoreCase(contextId)) + .collect(Collectors.toList())); + return r; + }, Encoders.bean(entityClazz)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingPath); - private static void cleanContext(SparkSession spark, String contextId, String verifyParam, String inputPath, Class entityClazz, String workingPath) { - Dataset res = spark - .read() - .textFile(inputPath) - .map( - (MapFunction) value -> OBJECT_MAPPER.readValue(value, entityClazz), - Encoders.bean(entityClazz)); - - res.map((MapFunction) r -> { - if(!r.getTitle() - .stream() - .filter(t -> t.getQualifier().getClassid() - .equalsIgnoreCase(ModelConstants.MAIN_TITLE_QUALIFIER.getClassid())) - .anyMatch(t -> t.getValue().toLowerCase().startsWith(verifyParam.toLowerCase()))){ - return r; - } - r.setContext(r.getContext().stream().filter(c -> !c.getId().split("::")[0] - .equalsIgnoreCase(contextId)).collect(Collectors.toList())); - return r; - } ,Encoders.bean(entityClazz)) - .write() - .mode(SaveMode.Overwrite) - .option("compression","gzip") - .json(workingPath); - - spark.read().textFile(workingPath).map((MapFunction) value -> OBJECT_MAPPER.readValue(value, entityClazz), - Encoders.bean(entityClazz)) - .write() - .mode(SaveMode.Overwrite) - .option("compression","gzip") - .json(inputPath); - } + spark + .read() + .textFile(workingPath) + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, entityClazz), + Encoders.bean(entityClazz)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(inputPath); + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java index bba814346..472d3781d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java @@ -1,18 +1,12 @@ + package eu.dnetlib.dhp.oa.graph.clean; -import com.fasterxml.jackson.core.JsonProcessingException; -import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.oa.graph.dump.Constants; -import eu.dnetlib.dhp.oa.graph.dump.DumpJobTest; -import eu.dnetlib.dhp.oa.graph.dump.DumpProducts; -import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.dump.oaf.Instance; -import eu.dnetlib.dhp.schema.dump.oaf.OpenAccessRoute; -import eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.Software; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.List; +import java.util.Locale; + import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; @@ -27,133 +21,280 @@ import org.junit.jupiter.api.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.List; -import java.util.Locale; +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.oa.graph.dump.Constants; +import eu.dnetlib.dhp.oa.graph.dump.DumpJobTest; +import eu.dnetlib.dhp.oa.graph.dump.DumpProducts; +import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.dump.oaf.Instance; +import eu.dnetlib.dhp.schema.dump.oaf.OpenAccessRoute; +import eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Software; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; public class CleanContextTest { - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - private static SparkSession spark; + private static SparkSession spark; - private static Path workingDir; + private static Path workingDir; - private static final Logger log = LoggerFactory.getLogger(CleanContextTest.class); + private static final Logger log = LoggerFactory.getLogger(CleanContextTest.class); - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files.createTempDirectory(DumpJobTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files.createTempDirectory(DumpJobTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); - SparkConf conf = new SparkConf(); - conf.setAppName(DumpJobTest.class.getSimpleName()); + SparkConf conf = new SparkConf(); + conf.setAppName(DumpJobTest.class.getSimpleName()); - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - spark = SparkSession - .builder() - .appName(DumpJobTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } + spark = SparkSession + .builder() + .appName(DumpJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } - @Test - public void testResultClean() throws Exception { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/clean/publication_clean_context.json") - .getPath(); - final String prefix = "gcube "; + @Test + public void testResultClean() throws Exception { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/clean/publication_clean_context.json") + .getPath(); + final String prefix = "gcube "; + spark + .read() + .textFile(sourcePath) + .map( + (MapFunction) r -> OBJECT_MAPPER.readValue(r, Publication.class), + Encoders.bean(Publication.class)) + .write() + .json(workingDir.toString() + "/publication"); - spark.read().textFile(sourcePath).map((MapFunction) r -> OBJECT_MAPPER.readValue(r, Publication.class), Encoders.bean(Publication.class)) - .write().json(workingDir.toString() + "/publication"); + CleanContextSparkJob.main(new String[] { + "--isSparkSessionManaged", Boolean.FALSE.toString(), + "--inputPath", workingDir.toString() + "/publication", + "-graphTableClassName", Publication.class.getCanonicalName(), + "-workingPath", workingDir.toString() + "/working", + "-contextId", "sobigdata", + "-verifyParam", "gCube " + }); + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/publication") + .map(item -> OBJECT_MAPPER.readValue(item, Publication.class)); - CleanContextSparkJob.main(new String[] { - "--isSparkSessionManaged", Boolean.FALSE.toString(), - "--inputPath", workingDir.toString() + "/publication", - "-graphTableClassName", Publication.class.getCanonicalName(), - "-workingPath", workingDir.toString() + "/working", - "-contextId","sobigdata", - "-verifyParam","gCube " - }); + Assertions.assertEquals(7, tmp.count()); - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/publication") - .map(item -> OBJECT_MAPPER.readValue(item, Publication.class)); + // original result with sobigdata context and gcube as starting string in the main title for the publication + Assertions + .assertEquals( + 0, + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::0224aae28af558f21768dbc6439c7a95")) + .collect() + .get(0) + .getContext() + .size()); - Assertions.assertEquals(7, tmp.count()); + // original result with sobigdata context without gcube as starting string in the main title for the publication + Assertions + .assertEquals( + 1, + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")) + .collect() + .get(0) + .getContext() + .size()); + Assertions + .assertEquals( + "sobigdata::projects::2", + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")) + .collect() + .get(0) + .getContext() + .get(0) + .getId()); - //original result with sobigdata context and gcube as starting string in the main title for the publication - Assertions.assertEquals(0, - tmp.filter(p->p.getId().equals("50|DansKnawCris::0224aae28af558f21768dbc6439c7a95")).collect().get(0).getContext().size()); + // original result with sobigdata context with gcube as starting string in the subtitle + Assertions + .assertEquals( + 1, + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")) + .collect() + .get(0) + .getContext() + .size()); + Assertions + .assertEquals( + "sobigdata::projects::2", + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")) + .collect() + .get(0) + .getContext() + .get(0) + .getId()); + List titles = tmp + .filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")) + .collect() + .get(0) + .getTitle(); + Assertions.assertEquals(1, titles.size()); + Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix)); + Assertions.assertEquals("subtitle", titles.get(0).getQualifier().getClassid()); - //original result with sobigdata context without gcube as starting string in the main title for the publication - Assertions.assertEquals(1, - tmp.filter(p->p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")).collect().get(0).getContext().size()); - Assertions.assertEquals("sobigdata::projects::2",tmp.filter(p->p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")).collect().get(0).getContext().get(0).getId() ); + // original result with sobigdata context with gcube not as starting string in the main title + Assertions + .assertEquals( + 1, + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")) + .collect() + .get(0) + .getContext() + .size()); + Assertions + .assertEquals( + "sobigdata::projects::1", + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")) + .collect() + .get(0) + .getContext() + .get(0) + .getId()); + titles = tmp + .filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")) + .collect() + .get(0) + .getTitle(); + Assertions.assertEquals(1, titles.size()); + Assertions.assertFalse(titles.get(0).getValue().toLowerCase().startsWith(prefix)); + Assertions.assertTrue(titles.get(0).getValue().toLowerCase().contains(prefix.trim())); + Assertions.assertEquals("main title", titles.get(0).getQualifier().getClassid()); - //original result with sobigdata context with gcube as starting string in the subtitle - Assertions.assertEquals(1, - tmp.filter(p->p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")).collect().get(0).getContext().size()); - Assertions.assertEquals("sobigdata::projects::2",tmp.filter(p->p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")).collect().get(0).getContext().get(0).getId() ); - List titles = tmp.filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")).collect().get(0).getTitle(); - Assertions.assertEquals(1, titles.size()); - Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix) ); - Assertions.assertEquals("subtitle", titles.get(0).getQualifier().getClassid()); + // original result with sobigdata in context and also other contexts with gcube as starting string for the main + // title + Assertions + .assertEquals( + 1, + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")) + .collect() + .get(0) + .getContext() + .size()); + Assertions + .assertEquals( + "dh-ch", + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")) + .collect() + .get(0) + .getContext() + .get(0) + .getId()); + titles = tmp + .filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")) + .collect() + .get(0) + .getTitle(); + Assertions.assertEquals(1, titles.size()); + Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix)); + Assertions.assertEquals("main title", titles.get(0).getQualifier().getClassid()); - //original result with sobigdata context with gcube not as starting string in the main title - Assertions.assertEquals(1, - tmp.filter(p->p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")).collect().get(0).getContext().size()); - Assertions.assertEquals("sobigdata::projects::1",tmp.filter(p->p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")).collect().get(0).getContext().get(0).getId() ); - titles = tmp.filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")).collect().get(0).getTitle(); - Assertions.assertEquals(1, titles.size()); - Assertions.assertFalse(titles.get(0).getValue().toLowerCase().startsWith(prefix) ); - Assertions.assertTrue(titles.get(0).getValue().toLowerCase().contains(prefix.trim()) ); - Assertions.assertEquals("main title", titles.get(0).getQualifier().getClassid()); + // original result with multiple main title one of which whith gcube as starting string and with 2 contextes + Assertions + .assertEquals( + 1, + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")) + .collect() + .get(0) + .getContext() + .size()); + Assertions + .assertEquals( + "dh-ch", + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")) + .collect() + .get(0) + .getContext() + .get(0) + .getId()); + titles = tmp + .filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")) + .collect() + .get(0) + .getTitle(); + Assertions.assertEquals(2, titles.size()); + Assertions + .assertTrue( + titles + .stream() + .anyMatch( + t -> t.getQualifier().getClassid().equals("main title") + && t.getValue().toLowerCase().startsWith(prefix))); - //original result with sobigdata in context and also other contexts with gcube as starting string for the main title - Assertions.assertEquals(1, - tmp.filter(p->p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")).collect().get(0).getContext().size()); - Assertions.assertEquals("dh-ch",tmp.filter(p->p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")).collect().get(0).getContext().get(0).getId() ); - titles = tmp.filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")).collect().get(0).getTitle(); - Assertions.assertEquals(1, titles.size()); - Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix) ); - Assertions.assertEquals("main title", titles.get(0).getQualifier().getClassid()); + // original result without sobigdata in context with gcube as starting string for the main title + Assertions + .assertEquals( + 1, + tmp + .filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")) + .collect() + .get(0) + .getContext() + .size()); + Assertions + .assertEquals( + "dh-ch", + tmp + .filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")) + .collect() + .get(0) + .getContext() + .get(0) + .getId()); + titles = tmp + .filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")) + .collect() + .get(0) + .getTitle(); + Assertions.assertEquals(2, titles.size()); - //original result with multiple main title one of which whith gcube as starting string and with 2 contextes - Assertions.assertEquals(1, - tmp.filter(p->p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")).collect().get(0).getContext().size()); - Assertions.assertEquals("dh-ch",tmp.filter(p->p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")).collect().get(0).getContext().get(0).getId() ); - titles = tmp.filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")).collect().get(0).getTitle(); - Assertions.assertEquals(2, titles.size()); - Assertions.assertTrue(titles.stream().anyMatch(t -> t.getQualifier().getClassid().equals("main title") && t.getValue().toLowerCase().startsWith(prefix)) ); + Assertions + .assertTrue( + titles + .stream() + .anyMatch( + t -> t.getQualifier().getClassid().equals("main title") + && t.getValue().toLowerCase().startsWith(prefix))); - - //original result without sobigdata in context with gcube as starting string for the main title - Assertions.assertEquals(1, - tmp.filter(p->p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")).collect().get(0).getContext().size()); - Assertions.assertEquals("dh-ch",tmp.filter(p->p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")).collect().get(0).getContext().get(0).getId() ); - titles = tmp.filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")).collect().get(0).getTitle(); - Assertions.assertEquals(2, titles.size()); - - Assertions.assertTrue(titles.stream().anyMatch(t -> t.getQualifier().getClassid().equals("main title") && t.getValue().toLowerCase().startsWith(prefix))); - - - } + } } From 9a961a0092d2de554c197934cb317beb5bb0335f Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 21 Apr 2022 15:12:24 +0200 Subject: [PATCH 025/214] [Clean Context] fixed issue in param name --- .../oa/graph/clean/CleanContextSparkJob.java | 181 +++++---- .../dhp/oa/graph/clean/oozie_app/workflow.xml | 20 +- .../dhp/oa/graph/clean/CleanContextTest.java | 375 ++++++++++++------ 3 files changed, 367 insertions(+), 209 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java index b20dcb67b..3e9b17f3f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java @@ -1,16 +1,13 @@ + package eu.dnetlib.dhp.oa.graph.clean; -import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.common.HdfsSupport; -import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.oaf.Context; -import eu.dnetlib.dhp.schema.oaf.Oaf; -import eu.dnetlib.dhp.schema.oaf.OafEntity; -import eu.dnetlib.dhp.schema.oaf.Result; -import eu.dnetlib.dhp.utils.ISLookupClientFactory; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.Serializable; +import java.util.List; +import java.util.Optional; +import java.util.stream.Collectors; + import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; @@ -21,93 +18,113 @@ import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import java.io.Serializable; -import java.util.List; -import java.util.Optional; -import java.util.stream.Collectors; +import com.fasterxml.jackson.databind.ObjectMapper; -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.Context; +import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.schema.oaf.OafEntity; +import eu.dnetlib.dhp.schema.oaf.Result; +import eu.dnetlib.dhp.utils.ISLookupClientFactory; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; public class CleanContextSparkJob implements Serializable { - private static final Logger log = LoggerFactory.getLogger(CleanContextSparkJob.class); + private static final Logger log = LoggerFactory.getLogger(CleanContextSparkJob.class); - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - public static void main(String[] args) throws Exception { + public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - CleanContextSparkJob.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/input_clean_context_parameters.json")); - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); + String jsonConfiguration = IOUtils + .toString( + CleanContextSparkJob.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/input_clean_context_parameters.json")); + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - String inputPath = parser.get("inputPath"); - log.info("inputPath: {}", inputPath); + String inputPath = parser.get("inputPath"); + log.info("inputPath: {}", inputPath); - String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + String workingPath = parser.get("workingPath"); + log.info("workingPath: {}", workingPath); - String contextId = parser.get("contextId"); - log.info("contextId: {}", contextId); + String contextId = parser.get("contextId"); + log.info("contextId: {}", contextId); - String verifyParam = parser.get("verifyParam"); - log.info("verifyParam: {}", verifyParam); + String verifyParam = parser.get("verifyParam"); + log.info("verifyParam: {}", verifyParam); + String graphTableClassName = parser.get("graphTableClassName"); + log.info("graphTableClassName: {}", graphTableClassName); - String graphTableClassName = parser.get("graphTableClassName"); - log.info("graphTableClassName: {}", graphTableClassName); + Class entityClazz = (Class) Class.forName(graphTableClassName); - Class entityClazz = (Class) Class.forName(graphTableClassName); + SparkConf conf = new SparkConf(); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + cleanContext(spark, contextId, verifyParam, inputPath, entityClazz, workingPath); + }); + } - SparkConf conf = new SparkConf(); - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { + private static void cleanContext(SparkSession spark, String contextId, String verifyParam, + String inputPath, Class entityClazz, String workingPath) { + Dataset res = spark + .read() + .textFile(inputPath) + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, entityClazz), + Encoders.bean(entityClazz)); - cleanContext(spark, contextId, verifyParam, inputPath, entityClazz, workingPath); - }); - } + res.map((MapFunction) r -> { + if (!r + .getTitle() + .stream() + .filter( + t -> t + .getQualifier() + .getClassid() + .equalsIgnoreCase(ModelConstants.MAIN_TITLE_QUALIFIER.getClassid())) + .anyMatch(t -> t.getValue().toLowerCase().startsWith(verifyParam.toLowerCase()))) { + return r; + } + r + .setContext( + r + .getContext() + .stream() + .filter( + c -> !c.getId().split("::")[0] + .equalsIgnoreCase(contextId)) + .collect(Collectors.toList())); + return r; + }, Encoders.bean(entityClazz)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingPath); - private static void cleanContext(SparkSession spark, String contextId, String verifyParam, String inputPath, Class entityClazz, String workingPath) { - Dataset res = spark - .read() - .textFile(inputPath) - .map( - (MapFunction) value -> OBJECT_MAPPER.readValue(value, entityClazz), - Encoders.bean(entityClazz)); - - res.map((MapFunction) r -> { - if(!r.getTitle() - .stream() - .filter(t -> t.getQualifier().getClassid() - .equalsIgnoreCase(ModelConstants.MAIN_TITLE_QUALIFIER.getClassid())) - .anyMatch(t -> t.getValue().toLowerCase().startsWith(verifyParam.toLowerCase()))){ - return r; - } - r.setContext(r.getContext().stream().filter(c -> !c.getId().split("::")[0] - .equalsIgnoreCase(contextId)).collect(Collectors.toList())); - return r; - } ,Encoders.bean(entityClazz)) - .write() - .mode(SaveMode.Overwrite) - .option("compression","gzip") - .json(workingPath); - - spark.read().textFile(workingPath).map((MapFunction) value -> OBJECT_MAPPER.readValue(value, entityClazz), - Encoders.bean(entityClazz)) - .write() - .mode(SaveMode.Overwrite) - .option("compression","gzip") - .json(inputPath); - } + spark + .read() + .textFile(workingPath) + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, entityClazz), + Encoders.bean(entityClazz)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(inputPath); + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml index 12ba3e5a7..3d4d60d73 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml @@ -15,7 +15,7 @@ shouldCleanContext - false + true if the context have to be cleaned @@ -312,9 +312,9 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.shuffle.partitions=7680 - --inputPath${inputPath}/publication + --inputPath${graphOutputPath}/publication --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Publication - --workingPath${workingDir}/working + --workingPath${workingDir}/working/publication --contextId${contextId} --verifyParam${verifyParam} @@ -339,9 +339,9 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.shuffle.partitions=7680 - --inputPath${graphInputPath}/dataset + --inputPath${graphOutputPath}/dataset --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Dataset - --workingPath${workingDir}/working + --workingPath${workingDir}/working/dataset --contextId${contextId} --verifyParam${verifyParam} @@ -366,9 +366,9 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.shuffle.partitions=7680 - --inputPath${graphInputPath}/otherresearchproduct + --inputPath${graphOutputPath}/otherresearchproduct --graphTableClassNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct - --workingPath${workingDir}/working + --workingPath${workingDir}/working/otherresearchproduct --contextId${contextId} --verifyParam${verifyParam} @@ -393,9 +393,9 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.shuffle.partitions=7680 - --inputPath${graphInputPath}/software + --inputPath${graphOutputPath}/software --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Software - --workingPath${workingDir}/working + --workingPath${workingDir}/working/software --contextId${contextId} --verifyParam${verifyParam} @@ -404,6 +404,6 @@ - + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java index bba814346..472d3781d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java @@ -1,18 +1,12 @@ + package eu.dnetlib.dhp.oa.graph.clean; -import com.fasterxml.jackson.core.JsonProcessingException; -import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.oa.graph.dump.Constants; -import eu.dnetlib.dhp.oa.graph.dump.DumpJobTest; -import eu.dnetlib.dhp.oa.graph.dump.DumpProducts; -import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.dump.oaf.Instance; -import eu.dnetlib.dhp.schema.dump.oaf.OpenAccessRoute; -import eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.Software; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.List; +import java.util.Locale; + import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; @@ -27,133 +21,280 @@ import org.junit.jupiter.api.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.List; -import java.util.Locale; +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.oa.graph.dump.Constants; +import eu.dnetlib.dhp.oa.graph.dump.DumpJobTest; +import eu.dnetlib.dhp.oa.graph.dump.DumpProducts; +import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.dump.oaf.Instance; +import eu.dnetlib.dhp.schema.dump.oaf.OpenAccessRoute; +import eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Software; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; public class CleanContextTest { - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - private static SparkSession spark; + private static SparkSession spark; - private static Path workingDir; + private static Path workingDir; - private static final Logger log = LoggerFactory.getLogger(CleanContextTest.class); + private static final Logger log = LoggerFactory.getLogger(CleanContextTest.class); - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files.createTempDirectory(DumpJobTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files.createTempDirectory(DumpJobTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); - SparkConf conf = new SparkConf(); - conf.setAppName(DumpJobTest.class.getSimpleName()); + SparkConf conf = new SparkConf(); + conf.setAppName(DumpJobTest.class.getSimpleName()); - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - spark = SparkSession - .builder() - .appName(DumpJobTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } + spark = SparkSession + .builder() + .appName(DumpJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } - @Test - public void testResultClean() throws Exception { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/clean/publication_clean_context.json") - .getPath(); - final String prefix = "gcube "; + @Test + public void testResultClean() throws Exception { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/clean/publication_clean_context.json") + .getPath(); + final String prefix = "gcube "; + spark + .read() + .textFile(sourcePath) + .map( + (MapFunction) r -> OBJECT_MAPPER.readValue(r, Publication.class), + Encoders.bean(Publication.class)) + .write() + .json(workingDir.toString() + "/publication"); - spark.read().textFile(sourcePath).map((MapFunction) r -> OBJECT_MAPPER.readValue(r, Publication.class), Encoders.bean(Publication.class)) - .write().json(workingDir.toString() + "/publication"); + CleanContextSparkJob.main(new String[] { + "--isSparkSessionManaged", Boolean.FALSE.toString(), + "--inputPath", workingDir.toString() + "/publication", + "-graphTableClassName", Publication.class.getCanonicalName(), + "-workingPath", workingDir.toString() + "/working", + "-contextId", "sobigdata", + "-verifyParam", "gCube " + }); + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/publication") + .map(item -> OBJECT_MAPPER.readValue(item, Publication.class)); - CleanContextSparkJob.main(new String[] { - "--isSparkSessionManaged", Boolean.FALSE.toString(), - "--inputPath", workingDir.toString() + "/publication", - "-graphTableClassName", Publication.class.getCanonicalName(), - "-workingPath", workingDir.toString() + "/working", - "-contextId","sobigdata", - "-verifyParam","gCube " - }); + Assertions.assertEquals(7, tmp.count()); - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/publication") - .map(item -> OBJECT_MAPPER.readValue(item, Publication.class)); + // original result with sobigdata context and gcube as starting string in the main title for the publication + Assertions + .assertEquals( + 0, + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::0224aae28af558f21768dbc6439c7a95")) + .collect() + .get(0) + .getContext() + .size()); - Assertions.assertEquals(7, tmp.count()); + // original result with sobigdata context without gcube as starting string in the main title for the publication + Assertions + .assertEquals( + 1, + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")) + .collect() + .get(0) + .getContext() + .size()); + Assertions + .assertEquals( + "sobigdata::projects::2", + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")) + .collect() + .get(0) + .getContext() + .get(0) + .getId()); - //original result with sobigdata context and gcube as starting string in the main title for the publication - Assertions.assertEquals(0, - tmp.filter(p->p.getId().equals("50|DansKnawCris::0224aae28af558f21768dbc6439c7a95")).collect().get(0).getContext().size()); + // original result with sobigdata context with gcube as starting string in the subtitle + Assertions + .assertEquals( + 1, + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")) + .collect() + .get(0) + .getContext() + .size()); + Assertions + .assertEquals( + "sobigdata::projects::2", + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")) + .collect() + .get(0) + .getContext() + .get(0) + .getId()); + List titles = tmp + .filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")) + .collect() + .get(0) + .getTitle(); + Assertions.assertEquals(1, titles.size()); + Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix)); + Assertions.assertEquals("subtitle", titles.get(0).getQualifier().getClassid()); - //original result with sobigdata context without gcube as starting string in the main title for the publication - Assertions.assertEquals(1, - tmp.filter(p->p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")).collect().get(0).getContext().size()); - Assertions.assertEquals("sobigdata::projects::2",tmp.filter(p->p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")).collect().get(0).getContext().get(0).getId() ); + // original result with sobigdata context with gcube not as starting string in the main title + Assertions + .assertEquals( + 1, + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")) + .collect() + .get(0) + .getContext() + .size()); + Assertions + .assertEquals( + "sobigdata::projects::1", + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")) + .collect() + .get(0) + .getContext() + .get(0) + .getId()); + titles = tmp + .filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")) + .collect() + .get(0) + .getTitle(); + Assertions.assertEquals(1, titles.size()); + Assertions.assertFalse(titles.get(0).getValue().toLowerCase().startsWith(prefix)); + Assertions.assertTrue(titles.get(0).getValue().toLowerCase().contains(prefix.trim())); + Assertions.assertEquals("main title", titles.get(0).getQualifier().getClassid()); - //original result with sobigdata context with gcube as starting string in the subtitle - Assertions.assertEquals(1, - tmp.filter(p->p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")).collect().get(0).getContext().size()); - Assertions.assertEquals("sobigdata::projects::2",tmp.filter(p->p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")).collect().get(0).getContext().get(0).getId() ); - List titles = tmp.filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")).collect().get(0).getTitle(); - Assertions.assertEquals(1, titles.size()); - Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix) ); - Assertions.assertEquals("subtitle", titles.get(0).getQualifier().getClassid()); + // original result with sobigdata in context and also other contexts with gcube as starting string for the main + // title + Assertions + .assertEquals( + 1, + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")) + .collect() + .get(0) + .getContext() + .size()); + Assertions + .assertEquals( + "dh-ch", + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")) + .collect() + .get(0) + .getContext() + .get(0) + .getId()); + titles = tmp + .filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")) + .collect() + .get(0) + .getTitle(); + Assertions.assertEquals(1, titles.size()); + Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix)); + Assertions.assertEquals("main title", titles.get(0).getQualifier().getClassid()); - //original result with sobigdata context with gcube not as starting string in the main title - Assertions.assertEquals(1, - tmp.filter(p->p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")).collect().get(0).getContext().size()); - Assertions.assertEquals("sobigdata::projects::1",tmp.filter(p->p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")).collect().get(0).getContext().get(0).getId() ); - titles = tmp.filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")).collect().get(0).getTitle(); - Assertions.assertEquals(1, titles.size()); - Assertions.assertFalse(titles.get(0).getValue().toLowerCase().startsWith(prefix) ); - Assertions.assertTrue(titles.get(0).getValue().toLowerCase().contains(prefix.trim()) ); - Assertions.assertEquals("main title", titles.get(0).getQualifier().getClassid()); + // original result with multiple main title one of which whith gcube as starting string and with 2 contextes + Assertions + .assertEquals( + 1, + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")) + .collect() + .get(0) + .getContext() + .size()); + Assertions + .assertEquals( + "dh-ch", + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")) + .collect() + .get(0) + .getContext() + .get(0) + .getId()); + titles = tmp + .filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")) + .collect() + .get(0) + .getTitle(); + Assertions.assertEquals(2, titles.size()); + Assertions + .assertTrue( + titles + .stream() + .anyMatch( + t -> t.getQualifier().getClassid().equals("main title") + && t.getValue().toLowerCase().startsWith(prefix))); - //original result with sobigdata in context and also other contexts with gcube as starting string for the main title - Assertions.assertEquals(1, - tmp.filter(p->p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")).collect().get(0).getContext().size()); - Assertions.assertEquals("dh-ch",tmp.filter(p->p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")).collect().get(0).getContext().get(0).getId() ); - titles = tmp.filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")).collect().get(0).getTitle(); - Assertions.assertEquals(1, titles.size()); - Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix) ); - Assertions.assertEquals("main title", titles.get(0).getQualifier().getClassid()); + // original result without sobigdata in context with gcube as starting string for the main title + Assertions + .assertEquals( + 1, + tmp + .filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")) + .collect() + .get(0) + .getContext() + .size()); + Assertions + .assertEquals( + "dh-ch", + tmp + .filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")) + .collect() + .get(0) + .getContext() + .get(0) + .getId()); + titles = tmp + .filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")) + .collect() + .get(0) + .getTitle(); + Assertions.assertEquals(2, titles.size()); - //original result with multiple main title one of which whith gcube as starting string and with 2 contextes - Assertions.assertEquals(1, - tmp.filter(p->p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")).collect().get(0).getContext().size()); - Assertions.assertEquals("dh-ch",tmp.filter(p->p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")).collect().get(0).getContext().get(0).getId() ); - titles = tmp.filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")).collect().get(0).getTitle(); - Assertions.assertEquals(2, titles.size()); - Assertions.assertTrue(titles.stream().anyMatch(t -> t.getQualifier().getClassid().equals("main title") && t.getValue().toLowerCase().startsWith(prefix)) ); + Assertions + .assertTrue( + titles + .stream() + .anyMatch( + t -> t.getQualifier().getClassid().equals("main title") + && t.getValue().toLowerCase().startsWith(prefix))); - - //original result without sobigdata in context with gcube as starting string for the main title - Assertions.assertEquals(1, - tmp.filter(p->p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")).collect().get(0).getContext().size()); - Assertions.assertEquals("dh-ch",tmp.filter(p->p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")).collect().get(0).getContext().get(0).getId() ); - titles = tmp.filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")).collect().get(0).getTitle(); - Assertions.assertEquals(2, titles.size()); - - Assertions.assertTrue(titles.stream().anyMatch(t -> t.getQualifier().getClassid().equals("main title") && t.getValue().toLowerCase().startsWith(prefix))); - - - } + } } From 6dc68c48e0d8720b875173692eab09d9e46e77cb Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 21 Apr 2022 16:19:04 +0200 Subject: [PATCH 026/214] [EOSCTag] - --- .../eu/dnetlib/dhp/bulktag/SparkEoscTag.java | 61 +++++++++++++++++-- 1 file changed, 57 insertions(+), 4 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java index 2b44275cd..7dc3b5878 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java @@ -7,11 +7,18 @@ import eu.dnetlib.dhp.bulktag.community.CommunityConfiguration; import eu.dnetlib.dhp.bulktag.community.CommunityConfigurationFactory; import eu.dnetlib.dhp.bulktag.community.ProtoMap; import eu.dnetlib.dhp.bulktag.community.QueryInformationSystem; +import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.Software; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.FilterFunction; +import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -25,6 +32,12 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; public class SparkEoscTag { private static final Logger log = LoggerFactory.getLogger(SparkEoscTag.class); public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + public final static StructuredProperty EOSC_NOTEBOOK = OafMapperUtils.structuredProperty( + "EOSC::Jupyter Notebook", OafMapperUtils.qualifier("eosc","European Open Science Cloud", + ModelConstants.DNET_SUBJECT_TYPOLOGIES,ModelConstants.DNET_SUBJECT_TYPOLOGIES) + ,OafMapperUtils.dataInfo(false, "propagation", true, false, + OafMapperUtils.qualifier("propagation:subject","Inferred by OpenAIRE", + ModelConstants.DNET_PROVENANCE_ACTIONS,ModelConstants.DNET_PROVENANCE_ACTIONS), "0.9")); public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils @@ -45,23 +58,63 @@ public class SparkEoscTag { final String inputPath = parser.get("sourcePath"); log.info("inputPath: {}", inputPath); + final String workingPath = parser.get("workingPath"); + log.info("workingPath: {}", workingPath); + SparkConf conf = new SparkConf(); runWithSparkSession( conf, isSparkSessionManaged, spark -> { - execEoscTag(spark, inputPath); + execEoscTag(spark, inputPath, workingPath); }); } - private static void execEoscTag(SparkSession spark, String inputPath) { + private static void execEoscTag(SparkSession spark, String inputPath, String workingPath) { //search for notebook //subject contiene jupyter. //esistono python e notebook nei subject non necessariamente nello stesso - //si cerca fra i prodotto di tipo software - Dataset sw = readPath(spark, inputPath + "/software", Software.class) + //si cerca fra i prodotti di tipo software + + + readPath(spark, inputPath + "/software", Software.class) + .map((MapFunction) s -> { + if(containsSubjectNotebook(s)){ + s.getSubject().add(EOSC_NOTEBOOK); + } + return s; + }, Encoders.bean(Software.class) ) + .write() + .mode(SaveMode.Overwrite) + .option("compression","gzip") + .json(workingPath + "/software"); + + readPath(spark, workingPath + "/software" , Software.class) + .write() + .mode(SaveMode.Overwrite) + .option("compression","gzip") + .json(inputPath + "/software"); } + + private static boolean containsSubjectNotebook(Software s) { + if(s.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("jupyter"))) + return true; + if(s.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("python") && + sbj.getValue().toLowerCase().contains("notebook"))) + return true; + if(s.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("python")) && + s.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("notebook"))) + return true; + return false; + } + + private static boolean containsTitleNotebook(Software s) { + if (s.getTitle().stream().anyMatch(t -> t.getValue().toLowerCase().contains("jupyter") && + t.getValue().toLowerCase().contains("notebook"))) + return true; + return false; + } } From e0915061c234447edbeb898a4cb726f62b89eb29 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 21 Apr 2022 16:32:40 +0200 Subject: [PATCH 027/214] [Clean Context] fixed issue in param name --- .../eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml index 3d4d60d73..45e492387 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml @@ -17,6 +17,14 @@ shouldCleanContext true if the context have to be cleaned + + contextId + sobigdata + + + verifyParam + gcube + sparkDriverMemory From d660895b309d185e84c4ea3d55d1c1351820f0b2 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Thu, 21 Apr 2022 20:41:13 +0200 Subject: [PATCH 028/214] fixed wrong mapping type of dataset --- .../main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala index bc26e44d6..fbe42ef7c 100644 --- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala +++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala @@ -208,7 +208,7 @@ object SparkGenerateDoiBoost { ) .filter(s => s!= null && s._2!=null) - .map(s => s._2) + .map(s => s._2._2) .write .mode(SaveMode.Overwrite) .save(s"$workingDirPath/doiBoostPublicationFiltered") From 7cb70664721e57c0bd9a8d9b0aaafaf87257b508 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 22 Apr 2022 10:44:17 +0200 Subject: [PATCH 029/214] [EoscTag] first "rough" implementation --- .../eu/dnetlib/dhp/bulktag/SparkEoscTag.java | 109 ++++++++++++++---- .../dhp/bulktag/input_eoscTag_parameters.json | 21 ++++ .../dhp/bulktag/oozie_app/workflow.xml | 26 ++++- 3 files changed, 131 insertions(+), 25 deletions(-) create mode 100644 dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/input_eoscTag_parameters.json diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java index 7dc3b5878..ea7e77e39 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java @@ -1,22 +1,13 @@ package eu.dnetlib.dhp.bulktag; import com.fasterxml.jackson.databind.ObjectMapper; -import com.google.gson.Gson; import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.bulktag.community.CommunityConfiguration; -import eu.dnetlib.dhp.bulktag.community.CommunityConfigurationFactory; -import eu.dnetlib.dhp.bulktag.community.ProtoMap; -import eu.dnetlib.dhp.bulktag.community.QueryInformationSystem; import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.oaf.Result; -import eu.dnetlib.dhp.schema.oaf.Software; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; @@ -26,25 +17,30 @@ import org.slf4j.LoggerFactory; import java.util.Optional; import static eu.dnetlib.dhp.PropagationConstant.readPath; -import static eu.dnetlib.dhp.PropagationConstant.removeOutputDir; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; public class SparkEoscTag { private static final Logger log = LoggerFactory.getLogger(SparkEoscTag.class); public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + public static final Qualifier EOSC_QUALIFIER = OafMapperUtils.qualifier("eosc", + "European Open Science Cloud", + ModelConstants.DNET_SUBJECT_TYPOLOGIES,ModelConstants.DNET_SUBJECT_TYPOLOGIES); + public static final DataInfo EOSC_DATAINFO = OafMapperUtils.dataInfo(false, "propagation", true, false, + OafMapperUtils.qualifier("propagation:subject","Inferred by OpenAIRE", + ModelConstants.DNET_PROVENANCE_ACTIONS,ModelConstants.DNET_PROVENANCE_ACTIONS), "0.9"); public final static StructuredProperty EOSC_NOTEBOOK = OafMapperUtils.structuredProperty( - "EOSC::Jupyter Notebook", OafMapperUtils.qualifier("eosc","European Open Science Cloud", - ModelConstants.DNET_SUBJECT_TYPOLOGIES,ModelConstants.DNET_SUBJECT_TYPOLOGIES) - ,OafMapperUtils.dataInfo(false, "propagation", true, false, - OafMapperUtils.qualifier("propagation:subject","Inferred by OpenAIRE", - ModelConstants.DNET_PROVENANCE_ACTIONS,ModelConstants.DNET_PROVENANCE_ACTIONS), "0.9")); + "EOSC::Jupyter Notebook", EOSC_QUALIFIER,EOSC_DATAINFO); + public final static StructuredProperty EOSC_GALAXY = OafMapperUtils.structuredProperty( + "EOSC::Galaxy Workflow", EOSC_QUALIFIER, EOSC_DATAINFO); + public final static StructuredProperty EOSC_TWITTER = OafMapperUtils.structuredProperty( + "EOSC::Twitter Data", EOSC_QUALIFIER,EOSC_DATAINFO); public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils .toString( SparkEoscTag.class .getResourceAsStream( - "/eu/dnetlib/dhp/bulktag/input_eosctag_parameters.json")); + "/eu/dnetlib/dhp/bulktag/input_eoscTag_parameters.json")); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); parser.parseArgument(args); @@ -73,17 +69,15 @@ public class SparkEoscTag { } private static void execEoscTag(SparkSession spark, String inputPath, String workingPath) { - //search for notebook - //subject contiene jupyter. - //esistono python e notebook nei subject non necessariamente nello stesso - //si cerca fra i prodotti di tipo software - readPath(spark, inputPath + "/software", Software.class) .map((MapFunction) s -> { - if(containsSubjectNotebook(s)){ + if(containsCriteriaNotebook(s)){ s.getSubject().add(EOSC_NOTEBOOK); } + if(containsCriteriaGalaxy(s)){ + s.getSubject().add(EOSC_GALAXY); + } return s; }, Encoders.bean(Software.class) ) .write() @@ -97,9 +91,75 @@ public class SparkEoscTag { .option("compression","gzip") .json(inputPath + "/software"); + readPath(spark, inputPath + "/otherresearchproduct", OtherResearchProduct.class) + .map((MapFunction) orp -> + { + if(containsCriteriaGalaxy(orp)){ + orp.getSubject().add(EOSC_GALAXY); + } + if(containscriteriaTwitter(orp)){ + orp.getSubject().add(EOSC_TWITTER); + } + return orp; + }, Encoders.bean(OtherResearchProduct.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression","gzip") + .json(workingPath + "/otherresearchproduct"); + + readPath(spark, workingPath + "/otherresearchproduct", OtherResearchProduct.class) + .write() + .mode(SaveMode.Overwrite) + .option("compression","gzip") + .json(inputPath + "/otherresearchproduct"); + + readPath(spark, inputPath + "/dataset", Dataset.class) + .map((MapFunction) d -> { + if(containscriteriaTwitter(d)){ + d.getSubject().add(EOSC_TWITTER); + } + return d; + } , Encoders.bean(Dataset.class) ) + .write() + .mode(SaveMode.Overwrite) + .option("compression","gzip") + .json(workingPath + "/dataset"); + + readPath(spark, workingPath + "/dataset" , Dataset.class) + .write() + .mode(SaveMode.Overwrite) + .option("compression","gzip") + .json(inputPath + "/dataset"); } - private static boolean containsSubjectNotebook(Software s) { + private static boolean containscriteriaTwitter(Result r) { + if (r.getTitle().stream().anyMatch(t -> t.getValue().toLowerCase().contains("twitter") && + t.getValue().toLowerCase().contains("data"))) + return true; + if(r.getDescription().stream().anyMatch(d -> d.getValue().toLowerCase().contains("twitter") && + d.getValue().toLowerCase().contains("data") )) + return true; + if(r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("twitter")) && + r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("data"))) + return true; + return false; + } + + private static boolean containsCriteriaGalaxy(Result r) { + if (r.getTitle().stream().anyMatch(t -> t.getValue().toLowerCase().contains("galaxy") && + (t.getValue().toLowerCase().contains("workflow") || t.getValue().toLowerCase().contains("software")))) + return true; + if(r.getDescription().stream().anyMatch(d -> d.getValue().toLowerCase().contains("galaxy") && + (d.getValue().toLowerCase().contains("workflow") || d.getValue().toLowerCase().contains("software")))) + return true; + if(r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("galaxy")) && + (r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("workflow"))) || + r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("software"))) + return true; + return false; + } + + private static boolean containsCriteriaNotebook(Software s) { if(s.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("jupyter"))) return true; if(s.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("python") && @@ -117,4 +177,5 @@ public class SparkEoscTag { return true; return false; } + } diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/input_eoscTag_parameters.json b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/input_eoscTag_parameters.json new file mode 100644 index 000000000..4c25fea01 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/input_eoscTag_parameters.json @@ -0,0 +1,21 @@ +[ + { + "paramName":"s", + "paramLongName":"sourcePath", + "paramDescription": "the path of the sequencial file to read", + "paramRequired": true + }, + { + "paramName": "wp", + "paramLongName": "workingPath", + "paramDescription": "the path used to store temporary output files", + "paramRequired": true + }, + { + "paramName": "ssm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "true if the spark session is managed, false otherwise", + "paramRequired": false + } + +] \ No newline at end of file diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml index f019f8413..91fca7d61 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml @@ -204,7 +204,31 @@ - + + + + + yarn-cluster + cluster + EOSC_tagging + eu.dnetlib.dhp.bulktag.SparkEoscTag + dhp-enrichment-${projectVersion}.jar + + --num-executors=${sparkExecutorNumber} + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --sourcePath${outputPath} + --workingPath${workingDir}/eoscTag + + + + From aa12429f500e563a114b39650b3d8c13c361d3fa Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Fri, 22 Apr 2022 11:05:08 +0200 Subject: [PATCH 030/214] Modified last intersection since we lost many titles. --- .../doiboost/SparkGenerateDoiBoost.scala | 83 ++++++++----------- 1 file changed, 34 insertions(+), 49 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala index 9323c994c..10a5be969 100644 --- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala +++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala @@ -59,52 +59,6 @@ object SparkGenerateDoiBoost { val workingDirPath = parser.get("workingPath") val openaireOrganizationPath = parser.get("openaireOrganizationPath") - val crossrefAggregator = new Aggregator[(String, Publication), Publication, Publication] with Serializable { - override def zero: Publication = new Publication - - override def reduce(b: Publication, a: (String, Publication)): Publication = { - - if (b == null) { - if (a != null && a._2 != null) { - a._2.setId(a._1) - return a._2 - } - } else { - if (a != null && a._2 != null) { - b.mergeFrom(a._2) - b.setId(a._1) - val authors = AuthorMerger.mergeAuthor(b.getAuthor, a._2.getAuthor) - b.setAuthor(authors) - return b - } - } - new Publication - } - - override def merge(b1: Publication, b2: Publication): Publication = { - if (b1 == null) { - if (b2 != null) - return b2 - } else { - if (b2 != null) { - b1.mergeFrom(b2) - val authors = AuthorMerger.mergeAuthor(b1.getAuthor, b2.getAuthor) - b1.setAuthor(authors) - if (b2.getId != null && b2.getId.nonEmpty) - b1.setId(b2.getId) - return b1 - } - } - new Publication - } - - override def finish(reduction: Publication): Publication = reduction - - override def bufferEncoder: Encoder[Publication] = Encoders.kryo[Publication] - - override def outputEncoder: Encoder[Publication] = Encoders.kryo[Publication] - } - implicit val mapEncoderPub: Encoder[Publication] = Encoders.kryo[Publication] implicit val mapEncoderOrg: Encoder[Organization] = Encoders.kryo[Organization] implicit val mapEncoderDataset: Encoder[OafDataset] = Encoders.kryo[OafDataset] @@ -175,12 +129,43 @@ object SparkGenerateDoiBoost { .map(DoiBoostMappingUtil.fixPublication) .map(p => (p.getId, p)) .groupByKey(_._1) - .agg(crossrefAggregator.toColumn) - .map(p => p._2) + .reduceGroups((left, right) => + { + //Check left is not null + if (left != null && left._1 != null) + { + //If right is null then return left + if (right == null || right._2 == null) + left + else { + // Here Left and Right are not null + // So we have to merge + val b1 = left._2 + val b2 = right._2 + b1.mergeFrom(b2) + b1.mergeOAFDataInfo(b2) + val authors = AuthorMerger.mergeAuthor(b1.getAuthor, b2.getAuthor) + b1.setAuthor(authors) + if (b2.getId != null && b2.getId.nonEmpty) + b1.setId(b2.getId) + //Return publication Merged + (b1.getId, b1) + } + } + else { + // Left is Null so we return right + right + } + } + + ) + .filter(s => s!= null && s._2!=null) + .map(s => s._2._2) .write .mode(SaveMode.Overwrite) .save(s"$workingDirPath/doiBoostPublicationFiltered") + val affiliationPath = parser.get("affiliationPath") val paperAffiliationPath = parser.get("paperAffiliationPath") @@ -305,4 +290,4 @@ object SparkGenerateDoiBoost { .save(s"$workingDirPath/doiBoostOrganization") } -} +} \ No newline at end of file From a82ec3aaaf60ea77918f3ff1cfab20538ef6fe7e Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Fri, 22 Apr 2022 11:08:13 +0200 Subject: [PATCH 031/214] code formatter --- .../doiboost/SparkGenerateDoiBoost.scala | 18 ++++++------------ 1 file changed, 6 insertions(+), 12 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala index 10a5be969..2cbd53097 100644 --- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala +++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala @@ -129,11 +129,9 @@ object SparkGenerateDoiBoost { .map(DoiBoostMappingUtil.fixPublication) .map(p => (p.getId, p)) .groupByKey(_._1) - .reduceGroups((left, right) => - { + .reduceGroups((left, right) => { //Check left is not null - if (left != null && left._1 != null) - { + if (left != null && left._1 != null) { //If right is null then return left if (right == null || right._2 == null) left @@ -151,21 +149,17 @@ object SparkGenerateDoiBoost { //Return publication Merged (b1.getId, b1) } - } - else { + } else { // Left is Null so we return right right } - } - - ) - .filter(s => s!= null && s._2!=null) + }) + .filter(s => s != null && s._2 != null) .map(s => s._2._2) .write .mode(SaveMode.Overwrite) .save(s"$workingDirPath/doiBoostPublicationFiltered") - val affiliationPath = parser.get("affiliationPath") val paperAffiliationPath = parser.get("paperAffiliationPath") @@ -290,4 +284,4 @@ object SparkGenerateDoiBoost { .save(s"$workingDirPath/doiBoostOrganization") } -} \ No newline at end of file +} From bbb77052d321498f1148ac7371036789b09146fd Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 22 Apr 2022 11:32:57 +0200 Subject: [PATCH 032/214] [EOSCTag] first test --- .../dnetlib/dhp/bulktag/EOSCTagJobTest.java | 770 ++++++++++++++++++ 1 file changed, 770 insertions(+) create mode 100644 dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java new file mode 100644 index 000000000..2141e1eac --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java @@ -0,0 +1,770 @@ + +package eu.dnetlib.dhp.bulktag; + +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.schema.oaf.Dataset; +import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Software; +import org.apache.commons.io.FileUtils; +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.Row; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; + +import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.ZENODO_COMMUNITY_INDICATOR; + +public class EOSCTagJobTest { + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + public static final String MOCK_IS_LOOK_UP_URL = "BASEURL:8280/is/services/isLookUp"; + + public static final String pathMap = "{ \"author\" : \"$['author'][*]['fullname']\"," + + " \"title\" : \"$['title'][*]['value']\"," + + " \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\"," + + " \"contributor\" : \"$['contributor'][*]['value']\"," + + " \"description\" : \"$['description'][*]['value']\"}"; + + private static SparkSession spark; + + private static Path workingDir; + + private static final Logger log = LoggerFactory.getLogger(EOSCTagJobTest.class); + + private static String taggingConf = ""; + + static { + try { + taggingConf = IOUtils + .toString( + EOSCTagJobTest.class + .getResourceAsStream( + "/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf.xml")); + } catch (IOException e) { + e.printStackTrace(); + } + } + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files.createTempDirectory(EOSCTagJobTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(EOSCTagJobTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(EOSCTagJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + void noUpdatesTest() throws Exception { + final String pathMap = EOSCTagJobTest.pathMap; + SparkBulkTagJob + .main( + new String[] { + "-isTest", Boolean.TRUE.toString(), + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", + getClass().getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/no_updates").getPath(), + "-taggingConf", taggingConf, + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", + "-outputPath", workingDir.toString() + "/dataset", + "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, + "-pathMap", pathMap + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); + + Assertions.assertEquals(10, tmp.count()); + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(Dataset.class)); + + verificationDataset.createOrReplaceTempView("dataset"); + + String query = "select id, MyT.id community " + + "from dataset " + + "lateral view explode(context) c as MyT " + + "lateral view explode(MyT.datainfo) d as MyD " + + "where MyD.inferenceprovenance = 'bulktagging'"; + + Assertions.assertEquals(0, spark.sql(query).count()); + } + + @Test + void bulktagBySubjectNoPreviousContextTest() throws Exception { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject/nocontext") + .getPath(); + final String pathMap = EOSCTagJobTest.pathMap; + SparkBulkTagJob + .main( + new String[] { + "-isTest", Boolean.TRUE.toString(), + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", sourcePath, + "-taggingConf", taggingConf, + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", + "-outputPath", workingDir.toString() + "/dataset", + "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, + "-pathMap", pathMap + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); + + Assertions.assertEquals(10, tmp.count()); + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(Dataset.class)); + + verificationDataset.createOrReplaceTempView("dataset"); + + String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name " + + "from dataset " + + "lateral view explode(context) c as MyT " + + "lateral view explode(MyT.datainfo) d as MyD " + + "where MyD.inferenceprovenance = 'bulktagging'"; + + Assertions.assertEquals(5, spark.sql(query).count()); + + org.apache.spark.sql.Dataset idExplodeCommunity = spark.sql(query); + Assertions + .assertEquals( + 5, idExplodeCommunity.filter("provenance = 'community:subject'").count()); + Assertions + .assertEquals( + 5, + idExplodeCommunity.filter("name = 'Bulktagging for Community - Subject'").count()); + + Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'covid-19'").count()); + Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'mes'").count()); + Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'fam'").count()); + Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'aginfra'").count()); + + Assertions + .assertEquals( + 1, + idExplodeCommunity + .filter("id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529'") + .count()); + Assertions + .assertEquals( + 1, + idExplodeCommunity + .filter( + "community = 'covid-19' and id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529'") + .count()); + + Assertions + .assertEquals( + 2, + idExplodeCommunity + .filter("id = '50|od______3989::05d8c751462f9bb8d2b06956dfbc5c7b'") + .count()); + Assertions + .assertEquals( + 2, + idExplodeCommunity + .filter( + "(community = 'covid-19' or community = 'aginfra') and id = '50|od______3989::05d8c751462f9bb8d2b06956dfbc5c7b'") + .count()); + + Assertions + .assertEquals( + 2, + idExplodeCommunity + .filter("id = '50|od______3989::0f89464c4ac4c398fe0c71433b175a62'") + .count()); + Assertions + .assertEquals( + 2, + idExplodeCommunity + .filter( + "(community = 'mes' or community = 'fam') and id = '50|od______3989::0f89464c4ac4c398fe0c71433b175a62'") + .count()); + } + + @Test + void bulktagBySubjectPreviousContextNoProvenanceTest() throws Exception { + final String sourcePath = getClass() + .getResource( + "/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject/contextnoprovenance") + .getPath(); + final String pathMap = EOSCTagJobTest.pathMap; + SparkBulkTagJob + .main( + new String[] { + "-isTest", Boolean.TRUE.toString(), + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", sourcePath, + "-taggingConf", taggingConf, + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", + "-outputPath", workingDir.toString() + "/dataset", + "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, + "-pathMap", pathMap + }); + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); + + Assertions.assertEquals(10, tmp.count()); + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(Dataset.class)); + + verificationDataset.createOrReplaceTempView("dataset"); + + String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance " + + "from dataset " + + "lateral view explode(context) c as MyT " + + "lateral view explode(MyT.datainfo) d as MyD " + + "where MyT.id = 'covid-19' "; + + Assertions.assertEquals(3, spark.sql(query).count()); + + org.apache.spark.sql.Dataset communityContext = spark.sql(query); + + Assertions + .assertEquals( + 2, + communityContext + .filter("id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529'") + .count()); + Assertions + .assertEquals( + 1, + communityContext + .filter( + "id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529' and provenance = 'community:subject'") + .count()); + Assertions + .assertEquals( + 1, + communityContext + .filter( + "id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529' and provenance = 'propagation:community:productsthroughsemrel'") + .count()); + + query = "select id, MyT.id community, size(MyT.datainfo) datainfosize " + + "from dataset " + + "lateral view explode (context) as MyT " + + "where size(MyT.datainfo) > 0"; + + Assertions + .assertEquals( + 2, + spark + .sql(query) + .select("datainfosize") + .where( + "id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529' a" + + "nd community = 'covid-19'") + .collectAsList() + .get(0) + .getInt(0)); + } + + @Test + void bulktagByDatasourceTest() throws Exception { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/bulktag/sample/publication/update_datasource") + .getPath(); + SparkBulkTagJob + .main( + new String[] { + "-isTest", Boolean.TRUE.toString(), + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", sourcePath, + "-taggingConf", taggingConf, + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", + "-outputPath", workingDir.toString() + "/publication", + "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, + "-pathMap", pathMap + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/publication") + .map(item -> OBJECT_MAPPER.readValue(item, Publication.class)); + + Assertions.assertEquals(10, tmp.count()); + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(Publication.class)); + + verificationDataset.createOrReplaceTempView("publication"); + + String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name " + + "from publication " + + "lateral view explode(context) c as MyT " + + "lateral view explode(MyT.datainfo) d as MyD " + + "where MyD.inferenceprovenance = 'bulktagging'"; + + org.apache.spark.sql.Dataset idExplodeCommunity = spark.sql(query); + + Assertions.assertEquals(5, idExplodeCommunity.count()); + Assertions + .assertEquals( + 5, idExplodeCommunity.filter("provenance = 'community:datasource'").count()); + Assertions + .assertEquals( + 5, + idExplodeCommunity + .filter("name = 'Bulktagging for Community - Datasource'") + .count()); + + Assertions.assertEquals(3, idExplodeCommunity.filter("community = 'fam'").count()); + Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'aginfra'").count()); + + Assertions + .assertEquals( + 3, + idExplodeCommunity + .filter( + "community = 'fam' and (id = '50|ec_fp7health::000085c89f4b96dc2269bd37edb35306' " + + "or id = '50|ec_fp7health::000b9e61f83f5a4b0c35777b7bccdf38' " + + "or id = '50|ec_fp7health::0010eb63e181e3e91b8b6dc6b3e1c798')") + .count()); + + Assertions + .assertEquals( + 2, + idExplodeCommunity + .filter( + "community = 'aginfra' and (id = '50|ec_fp7health::000c8195edd542e4e64ebb32172cbf89' " + + "or id = '50|ec_fp7health::0010eb63e181e3e91b8b6dc6b3e1c798')") + .count()); + } + + @Test + void bulktagByZenodoCommunityTest() throws Exception { + final String sourcePath = getClass() + .getResource( + "/eu/dnetlib/dhp/bulktag/sample/otherresearchproduct/update_zenodocommunity") + .getPath(); + SparkBulkTagJob + .main( + new String[] { + "-isTest", Boolean.TRUE.toString(), + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", sourcePath, + "-taggingConf", taggingConf, + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.OtherResearchProduct", + "-outputPath", workingDir.toString() + "/orp", + "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, + "-pathMap", pathMap + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/orp") + .map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)); + + Assertions.assertEquals(10, tmp.count()); + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(OtherResearchProduct.class)); + + verificationDataset.createOrReplaceTempView("orp"); + + String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name " + + "from orp " + + "lateral view explode(context) c as MyT " + + "lateral view explode(MyT.datainfo) d as MyD " + + "where MyD.inferenceprovenance = 'bulktagging'"; + + org.apache.spark.sql.Dataset idExplodeCommunity = spark.sql(query); + Assertions.assertEquals(8, idExplodeCommunity.count()); + + Assertions + .assertEquals( + 8, idExplodeCommunity.filter("provenance = 'community:zenodocommunity'").count()); + Assertions + .assertEquals( + 8, + idExplodeCommunity.filter("name = 'Bulktagging for Community - Zenodo'").count()); + + Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'covid-19'").count()); + Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'aginfra'").count()); + Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'beopen'").count()); + Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'fam'").count()); + Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'mes'").count()); + + Assertions + .assertEquals( + 1, + idExplodeCommunity + .filter( + "id = '50|od______2017::0750a4d0782265873d669520f5e33c07' " + + "and community = 'covid-19'") + .count()); + Assertions + .assertEquals( + 3, + idExplodeCommunity + .filter( + "id = '50|od______2017::1bd97baef19dbd2db3203b112bb83bc5' and " + + "(community = 'aginfra' or community = 'mes' or community = 'fam')") + .count()); + Assertions + .assertEquals( + 1, + idExplodeCommunity + .filter( + "id = '50|od______2017::1e400f1747487fd15998735c41a55c72' " + + "and community = 'beopen'") + .count()); + Assertions + .assertEquals( + 3, + idExplodeCommunity + .filter( + "id = '50|od______2017::210281c5bc1c739a11ccceeeca806396' and " + + "(community = 'beopen' or community = 'fam' or community = 'mes')") + .count()); + + query = "select id, MyT.id community, size(MyT.datainfo) datainfosize " + + "from orp " + + "lateral view explode (context) as MyT " + + "where size(MyT.datainfo) > 0"; + + Assertions + .assertEquals( + 2, + spark + .sql(query) + .select("datainfosize") + .where( + "id = '50|od______2017::210281c5bc1c739a11ccceeeca806396' a" + + "nd community = 'beopen'") + .collectAsList() + .get(0) + .getInt(0)); + + // verify the zenodo community context is not present anymore in the records + query = "select id, MyT.id community " + + "from orp " + + "lateral view explode(context) c as MyT " + + "lateral view explode(MyT.datainfo) d as MyD "; + + org.apache.spark.sql.Dataset tmp2 = spark.sql(query); + + Assertions + .assertEquals( + 0, + tmp2 + .select("community") + .where(tmp2.col("community").contains(ZENODO_COMMUNITY_INDICATOR)) + .count()); + } + + @Test + void bulktagBySubjectDatasourceTest() throws Exception { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject_datasource") + .getPath(); + SparkBulkTagJob + .main( + new String[] { + "-isTest", Boolean.TRUE.toString(), + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", sourcePath, + "-taggingConf", taggingConf, + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", + "-outputPath", workingDir.toString() + "/dataset", + "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, + "-pathMap", pathMap + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); + + Assertions.assertEquals(10, tmp.count()); + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(Dataset.class)); + + verificationDataset.createOrReplaceTempView("dataset"); + + String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name " + + "from dataset " + + "lateral view explode(context) c as MyT " + + "lateral view explode(MyT.datainfo) d as MyD " + + "where MyD.inferenceprovenance = 'bulktagging'"; + + org.apache.spark.sql.Dataset idExplodeCommunity = spark.sql(query); + Assertions.assertEquals(7, idExplodeCommunity.count()); + + Assertions + .assertEquals( + 5, idExplodeCommunity.filter("provenance = 'community:subject'").count()); + Assertions + .assertEquals( + 2, idExplodeCommunity.filter("provenance = 'community:datasource'").count()); + Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'covid-19'").count()); + Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'fam'").count()); + Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'aginfra'").count()); + Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'mes'").count()); + + query = "select id, MyT.id community, size(MyT.datainfo) datainfosize " + + "from dataset " + + "lateral view explode (context) as MyT " + + "where size(MyT.datainfo) > 0"; + + org.apache.spark.sql.Dataset tmp2 = spark.sql(query); + + Assertions + .assertEquals( + 2, + tmp2 + .select("datainfosize") + .where( + "id = '50|od______3989::05d8c751462f9bb8d2b06956dfbc5c7b' and " + + "community = 'aginfra'") + .collectAsList() + .get(0) + .getInt(0)); + + Assertions + .assertEquals( + 1, + tmp2 + .select("datainfosize") + .where( + "id = '50|od______3989::05d8c751462f9bb8d2b06956dfbc5c7b' and " + + "community = 'covid-19'") + .collectAsList() + .get(0) + .getInt(0)); + + Assertions + .assertEquals( + 2, + tmp2 + .select("datainfosize") + .where( + "id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529' and " + + "community = 'fam'") + .collectAsList() + .get(0) + .getInt(0)); + Assertions + .assertEquals( + 2, + tmp2 + .select("datainfosize") + .where( + "id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529' and " + + "community = 'covid-19'") + .collectAsList() + .get(0) + .getInt(0)); + + Assertions + .assertEquals( + 1, + tmp2 + .select("datainfosize") + .where( + "id = '50|od______3989::0f89464c4ac4c398fe0c71433b175a62' and " + + "community = 'fam'") + .collectAsList() + .get(0) + .getInt(0)); + Assertions + .assertEquals( + 1, + tmp2 + .select("datainfosize") + .where( + "id = '50|od______3989::0f89464c4ac4c398fe0c71433b175a62' and " + + "community = 'mes'") + .collectAsList() + .get(0) + .getInt(0)); + } + + @Test + void bulktagBySubjectDatasourceZenodoCommunityTest() throws Exception { + + SparkBulkTagJob + .main( + new String[] { + "-isTest", Boolean.TRUE.toString(), + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", getClass().getResource("/eu/dnetlib/dhp/bulktag/sample/software/").getPath(), + "-taggingConf", taggingConf, + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Software", + "-outputPath", workingDir.toString() + "/software", + "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, + "-pathMap", pathMap + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/software") + .map(item -> OBJECT_MAPPER.readValue(item, Software.class)); + + Assertions.assertEquals(10, tmp.count()); + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(Software.class)); + + verificationDataset.createOrReplaceTempView("software"); + + String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name " + + "from software " + + "lateral view explode(context) c as MyT " + + "lateral view explode(MyT.datainfo) d as MyD " + + "where MyD.inferenceprovenance = 'bulktagging'"; + + org.apache.spark.sql.Dataset idExplodeCommunity = spark.sql(query); + Assertions.assertEquals(10, idExplodeCommunity.count()); + + idExplodeCommunity.show(false); + Assertions + .assertEquals( + 3, idExplodeCommunity.filter("provenance = 'community:subject'").count()); + Assertions + .assertEquals( + 3, idExplodeCommunity.filter("provenance = 'community:datasource'").count()); + Assertions + .assertEquals( + 4, idExplodeCommunity.filter("provenance = 'community:zenodocommunity'").count()); + + Assertions.assertEquals(3, idExplodeCommunity.filter("community = 'covid-19'").count()); + Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'dh-ch'").count()); + Assertions.assertEquals(4, idExplodeCommunity.filter("community = 'aginfra'").count()); + Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'dariah'").count()); + Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'fam'").count()); + + Assertions + .assertEquals( + 2, + idExplodeCommunity + .filter( + "provenance = 'community:zenodocommunity' and " + + "id = '50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4' and (" + + "community = 'dh-ch' or community = 'dariah')") + .count()); + + query = "select id, MyT.id community, size(MyT.datainfo) datainfosize " + + "from software " + + "lateral view explode (context) as MyT " + + "where size(MyT.datainfo) > 0"; + + org.apache.spark.sql.Dataset tmp2 = spark.sql(query); + + Assertions + .assertEquals( + 2, + tmp2 + .select("datainfosize") + .where( + "id = '50|od______1582::501b25d420f808c8eddcd9b16e917f11' and " + + "community = 'covid-19'") + .collectAsList() + .get(0) + .getInt(0)); + + Assertions + .assertEquals( + 3, + tmp2 + .select("datainfosize") + .where( + "id = '50|od______1582::581621232a561b7e8b4952b18b8b0e56' and " + + "community = 'aginfra'") + .collectAsList() + .get(0) + .getInt(0)); + } + + @Test + void bulktagDatasourcewithConstraintsTest() throws Exception { + + final String sourcePath = getClass() + .getResource( + "/eu/dnetlib/dhp/bulktag/sample/dataset/update_datasourcewithconstraints") + .getPath(); + SparkBulkTagJob + .main( + new String[] { + "-isTest", Boolean.TRUE.toString(), + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", sourcePath, + "-taggingConf", taggingConf, + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", + "-outputPath", workingDir.toString() + "/dataset", + "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, + "-pathMap", pathMap + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); + + Assertions.assertEquals(10, tmp.count()); + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(Dataset.class)); + + verificationDataset.createOrReplaceTempView("dataset"); + String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name " + + "from dataset " + + "lateral view explode(context) c as MyT " + + "lateral view explode(MyT.datainfo) d as MyD " + + "where MyD.inferenceprovenance = 'bulktagging'"; + + org.apache.spark.sql.Dataset idExplodeCommunity = spark.sql(query); + + idExplodeCommunity.show(false); + Assertions.assertEquals(3, idExplodeCommunity.count()); + + Assertions + .assertEquals( + 3, idExplodeCommunity.filter("provenance = 'community:datasource'").count()); + } +} From 19d90658fc74006408d76269dc332d7205aaeedd Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 22 Apr 2022 15:41:23 +0200 Subject: [PATCH 033/214] [Clean Context] added description to parameters --- .../eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml index 45e492387..0cf6cdd05 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml @@ -20,10 +20,15 @@ contextId sobigdata + It is the context id that should be removed from the result if the condition is matched. + Now it is just sobigdata. In a futere implementation I plan to have the contextId as value in a json + where to specify also the constraints that should be verified to remove the context from the result verifyParam gcube + It is the constrint to be verified. This time is hardcoded as gcube and it is searched for in + the title. If title starts with gcube than the context sobigdata will be removed by the result if present From 27c85e901a9162a1c171f521f989f8f77c7c1395 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 22 Apr 2022 17:38:10 +0200 Subject: [PATCH 034/214] [EOSCTag] added resources and finalized test for Jupyter Notebook tagging --- .../dnetlib/dhp/bulktag/EOSCTagJobTest.java | 751 ++---------------- .../eosctag/galaxy/dataset/dataset_10.json | 10 + .../otherresearchproduct_10.json | 10 + .../eosctag/galaxy/software/software_10.json | 10 + .../eosctag/jupyter/dataset/dataset_10.json | 10 + .../otherresearchproduct_10.json | 10 + .../eosctag/jupyter/software/software_10.json | 10 + .../eosctag/twitter/dataset/dataset_10.json | 10 + .../otherresearchproduct_10.json | 10 + .../eosctag/twitter/software/software_10.json | 10 + 10 files changed, 165 insertions(+), 676 deletions(-) create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/galaxy/dataset/dataset_10.json create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/galaxy/otherresearchproduct/otherresearchproduct_10.json create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/galaxy/software/software_10.json create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/jupyter/dataset/dataset_10.json create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/jupyter/otherresearchproduct/otherresearchproduct_10.json create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/jupyter/software/software_10.json create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/twitter/dataset/dataset_10.json create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/twitter/otherresearchproduct/otherresearchproduct_10.json create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/twitter/software/software_10.json diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java index 2141e1eac..82ac9f751 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java @@ -2,15 +2,13 @@ package eu.dnetlib.dhp.bulktag; import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.schema.oaf.Dataset; -import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.Software; +import eu.dnetlib.dhp.schema.oaf.*; import org.apache.commons.io.FileUtils; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.Row; import org.apache.spark.sql.SparkSession; @@ -24,6 +22,7 @@ import org.slf4j.LoggerFactory; import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; +import java.util.List; import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.ZENODO_COMMUNITY_INDICATOR; @@ -31,13 +30,7 @@ public class EOSCTagJobTest { private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - public static final String MOCK_IS_LOOK_UP_URL = "BASEURL:8280/is/services/isLookUp"; - public static final String pathMap = "{ \"author\" : \"$['author'][*]['fullname']\"," - + " \"title\" : \"$['title'][*]['value']\"," - + " \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\"," - + " \"contributor\" : \"$['contributor'][*]['value']\"," - + " \"description\" : \"$['description'][*]['value']\"}"; private static SparkSession spark; @@ -45,19 +38,6 @@ public class EOSCTagJobTest { private static final Logger log = LoggerFactory.getLogger(EOSCTagJobTest.class); - private static String taggingConf = ""; - - static { - try { - taggingConf = IOUtils - .toString( - EOSCTagJobTest.class - .getResourceAsStream( - "/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf.xml")); - } catch (IOException e) { - e.printStackTrace(); - } - } @BeforeAll public static void beforeAll() throws IOException { @@ -88,683 +68,102 @@ public class EOSCTagJobTest { } @Test - void noUpdatesTest() throws Exception { - final String pathMap = EOSCTagJobTest.pathMap; - SparkBulkTagJob + void jupyterUpdatesTest() throws Exception { + + spark.read().textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/jupyter/software").getPath()) + .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, Software.class), Encoders.bean(Software.class)) + .write() + .option("compression","gzip") + .json(workingDir.toString() + "/input/software"); + + spark.read().textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/jupyter/dataset").getPath()) + .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, Dataset.class), Encoders.bean(Dataset.class)) + .write() + .option("compression","gzip") + .json(workingDir.toString() + "/input/dataset"); + + spark.read().textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/jupyter/otherresearchproduct").getPath()) + .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, OtherResearchProduct.class), Encoders.bean(OtherResearchProduct.class)) + .write() + .option("compression","gzip") + .json(workingDir.toString() + "/input/otherresearchproduct"); + + SparkEoscTag .main( new String[] { - "-isTest", Boolean.TRUE.toString(), "-isSparkSessionManaged", Boolean.FALSE.toString(), "-sourcePath", - getClass().getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/no_updates").getPath(), - "-taggingConf", taggingConf, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", - "-outputPath", workingDir.toString() + "/dataset", - "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, - "-pathMap", pathMap - }); + workingDir.toString() + "/input", + "-workingPath", workingDir.toString() + "/working" - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/dataset") - .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); - - Assertions.assertEquals(10, tmp.count()); - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Dataset.class)); - - verificationDataset.createOrReplaceTempView("dataset"); - - String query = "select id, MyT.id community " - + "from dataset " - + "lateral view explode(context) c as MyT " - + "lateral view explode(MyT.datainfo) d as MyD " - + "where MyD.inferenceprovenance = 'bulktagging'"; - - Assertions.assertEquals(0, spark.sql(query).count()); - } - - @Test - void bulktagBySubjectNoPreviousContextTest() throws Exception { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject/nocontext") - .getPath(); - final String pathMap = EOSCTagJobTest.pathMap; - SparkBulkTagJob - .main( - new String[] { - "-isTest", Boolean.TRUE.toString(), - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", sourcePath, - "-taggingConf", taggingConf, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", - "-outputPath", workingDir.toString() + "/dataset", - "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, - "-pathMap", pathMap - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/dataset") - .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); - - Assertions.assertEquals(10, tmp.count()); - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Dataset.class)); - - verificationDataset.createOrReplaceTempView("dataset"); - - String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name " - + "from dataset " - + "lateral view explode(context) c as MyT " - + "lateral view explode(MyT.datainfo) d as MyD " - + "where MyD.inferenceprovenance = 'bulktagging'"; - - Assertions.assertEquals(5, spark.sql(query).count()); - - org.apache.spark.sql.Dataset idExplodeCommunity = spark.sql(query); - Assertions - .assertEquals( - 5, idExplodeCommunity.filter("provenance = 'community:subject'").count()); - Assertions - .assertEquals( - 5, - idExplodeCommunity.filter("name = 'Bulktagging for Community - Subject'").count()); - - Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'covid-19'").count()); - Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'mes'").count()); - Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'fam'").count()); - Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'aginfra'").count()); - - Assertions - .assertEquals( - 1, - idExplodeCommunity - .filter("id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529'") - .count()); - Assertions - .assertEquals( - 1, - idExplodeCommunity - .filter( - "community = 'covid-19' and id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529'") - .count()); - - Assertions - .assertEquals( - 2, - idExplodeCommunity - .filter("id = '50|od______3989::05d8c751462f9bb8d2b06956dfbc5c7b'") - .count()); - Assertions - .assertEquals( - 2, - idExplodeCommunity - .filter( - "(community = 'covid-19' or community = 'aginfra') and id = '50|od______3989::05d8c751462f9bb8d2b06956dfbc5c7b'") - .count()); - - Assertions - .assertEquals( - 2, - idExplodeCommunity - .filter("id = '50|od______3989::0f89464c4ac4c398fe0c71433b175a62'") - .count()); - Assertions - .assertEquals( - 2, - idExplodeCommunity - .filter( - "(community = 'mes' or community = 'fam') and id = '50|od______3989::0f89464c4ac4c398fe0c71433b175a62'") - .count()); - } - - @Test - void bulktagBySubjectPreviousContextNoProvenanceTest() throws Exception { - final String sourcePath = getClass() - .getResource( - "/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject/contextnoprovenance") - .getPath(); - final String pathMap = EOSCTagJobTest.pathMap; - SparkBulkTagJob - .main( - new String[] { - "-isTest", Boolean.TRUE.toString(), - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", sourcePath, - "-taggingConf", taggingConf, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", - "-outputPath", workingDir.toString() + "/dataset", - "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, - "-pathMap", pathMap - }); - - final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/dataset") - .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); - - Assertions.assertEquals(10, tmp.count()); - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Dataset.class)); - - verificationDataset.createOrReplaceTempView("dataset"); - - String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance " - + "from dataset " - + "lateral view explode(context) c as MyT " - + "lateral view explode(MyT.datainfo) d as MyD " - + "where MyT.id = 'covid-19' "; - - Assertions.assertEquals(3, spark.sql(query).count()); - - org.apache.spark.sql.Dataset communityContext = spark.sql(query); - - Assertions - .assertEquals( - 2, - communityContext - .filter("id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529'") - .count()); - Assertions - .assertEquals( - 1, - communityContext - .filter( - "id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529' and provenance = 'community:subject'") - .count()); - Assertions - .assertEquals( - 1, - communityContext - .filter( - "id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529' and provenance = 'propagation:community:productsthroughsemrel'") - .count()); - - query = "select id, MyT.id community, size(MyT.datainfo) datainfosize " - + "from dataset " - + "lateral view explode (context) as MyT " - + "where size(MyT.datainfo) > 0"; - - Assertions - .assertEquals( - 2, - spark - .sql(query) - .select("datainfosize") - .where( - "id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529' a" - + "nd community = 'covid-19'") - .collectAsList() - .get(0) - .getInt(0)); - } - - @Test - void bulktagByDatasourceTest() throws Exception { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/bulktag/sample/publication/update_datasource") - .getPath(); - SparkBulkTagJob - .main( - new String[] { - "-isTest", Boolean.TRUE.toString(), - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", sourcePath, - "-taggingConf", taggingConf, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-outputPath", workingDir.toString() + "/publication", - "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, - "-pathMap", pathMap - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/publication") - .map(item -> OBJECT_MAPPER.readValue(item, Publication.class)); - - Assertions.assertEquals(10, tmp.count()); - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Publication.class)); - - verificationDataset.createOrReplaceTempView("publication"); - - String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name " - + "from publication " - + "lateral view explode(context) c as MyT " - + "lateral view explode(MyT.datainfo) d as MyD " - + "where MyD.inferenceprovenance = 'bulktagging'"; - - org.apache.spark.sql.Dataset idExplodeCommunity = spark.sql(query); - - Assertions.assertEquals(5, idExplodeCommunity.count()); - Assertions - .assertEquals( - 5, idExplodeCommunity.filter("provenance = 'community:datasource'").count()); - Assertions - .assertEquals( - 5, - idExplodeCommunity - .filter("name = 'Bulktagging for Community - Datasource'") - .count()); - - Assertions.assertEquals(3, idExplodeCommunity.filter("community = 'fam'").count()); - Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'aginfra'").count()); - - Assertions - .assertEquals( - 3, - idExplodeCommunity - .filter( - "community = 'fam' and (id = '50|ec_fp7health::000085c89f4b96dc2269bd37edb35306' " - + "or id = '50|ec_fp7health::000b9e61f83f5a4b0c35777b7bccdf38' " - + "or id = '50|ec_fp7health::0010eb63e181e3e91b8b6dc6b3e1c798')") - .count()); - - Assertions - .assertEquals( - 2, - idExplodeCommunity - .filter( - "community = 'aginfra' and (id = '50|ec_fp7health::000c8195edd542e4e64ebb32172cbf89' " - + "or id = '50|ec_fp7health::0010eb63e181e3e91b8b6dc6b3e1c798')") - .count()); - } - - @Test - void bulktagByZenodoCommunityTest() throws Exception { - final String sourcePath = getClass() - .getResource( - "/eu/dnetlib/dhp/bulktag/sample/otherresearchproduct/update_zenodocommunity") - .getPath(); - SparkBulkTagJob - .main( - new String[] { - "-isTest", Boolean.TRUE.toString(), - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", sourcePath, - "-taggingConf", taggingConf, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.OtherResearchProduct", - "-outputPath", workingDir.toString() + "/orp", - "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, - "-pathMap", pathMap - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/orp") - .map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)); - - Assertions.assertEquals(10, tmp.count()); - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(OtherResearchProduct.class)); - - verificationDataset.createOrReplaceTempView("orp"); - - String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name " - + "from orp " - + "lateral view explode(context) c as MyT " - + "lateral view explode(MyT.datainfo) d as MyD " - + "where MyD.inferenceprovenance = 'bulktagging'"; - - org.apache.spark.sql.Dataset idExplodeCommunity = spark.sql(query); - Assertions.assertEquals(8, idExplodeCommunity.count()); - - Assertions - .assertEquals( - 8, idExplodeCommunity.filter("provenance = 'community:zenodocommunity'").count()); - Assertions - .assertEquals( - 8, - idExplodeCommunity.filter("name = 'Bulktagging for Community - Zenodo'").count()); - - Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'covid-19'").count()); - Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'aginfra'").count()); - Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'beopen'").count()); - Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'fam'").count()); - Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'mes'").count()); - - Assertions - .assertEquals( - 1, - idExplodeCommunity - .filter( - "id = '50|od______2017::0750a4d0782265873d669520f5e33c07' " - + "and community = 'covid-19'") - .count()); - Assertions - .assertEquals( - 3, - idExplodeCommunity - .filter( - "id = '50|od______2017::1bd97baef19dbd2db3203b112bb83bc5' and " - + "(community = 'aginfra' or community = 'mes' or community = 'fam')") - .count()); - Assertions - .assertEquals( - 1, - idExplodeCommunity - .filter( - "id = '50|od______2017::1e400f1747487fd15998735c41a55c72' " - + "and community = 'beopen'") - .count()); - Assertions - .assertEquals( - 3, - idExplodeCommunity - .filter( - "id = '50|od______2017::210281c5bc1c739a11ccceeeca806396' and " - + "(community = 'beopen' or community = 'fam' or community = 'mes')") - .count()); - - query = "select id, MyT.id community, size(MyT.datainfo) datainfosize " - + "from orp " - + "lateral view explode (context) as MyT " - + "where size(MyT.datainfo) > 0"; - - Assertions - .assertEquals( - 2, - spark - .sql(query) - .select("datainfosize") - .where( - "id = '50|od______2017::210281c5bc1c739a11ccceeeca806396' a" - + "nd community = 'beopen'") - .collectAsList() - .get(0) - .getInt(0)); - - // verify the zenodo community context is not present anymore in the records - query = "select id, MyT.id community " - + "from orp " - + "lateral view explode(context) c as MyT " - + "lateral view explode(MyT.datainfo) d as MyD "; - - org.apache.spark.sql.Dataset tmp2 = spark.sql(query); - - Assertions - .assertEquals( - 0, - tmp2 - .select("community") - .where(tmp2.col("community").contains(ZENODO_COMMUNITY_INDICATOR)) - .count()); - } - - @Test - void bulktagBySubjectDatasourceTest() throws Exception { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject_datasource") - .getPath(); - SparkBulkTagJob - .main( - new String[] { - "-isTest", Boolean.TRUE.toString(), - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", sourcePath, - "-taggingConf", taggingConf, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", - "-outputPath", workingDir.toString() + "/dataset", - "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, - "-pathMap", pathMap - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/dataset") - .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); - - Assertions.assertEquals(10, tmp.count()); - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Dataset.class)); - - verificationDataset.createOrReplaceTempView("dataset"); - - String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name " - + "from dataset " - + "lateral view explode(context) c as MyT " - + "lateral view explode(MyT.datainfo) d as MyD " - + "where MyD.inferenceprovenance = 'bulktagging'"; - - org.apache.spark.sql.Dataset idExplodeCommunity = spark.sql(query); - Assertions.assertEquals(7, idExplodeCommunity.count()); - - Assertions - .assertEquals( - 5, idExplodeCommunity.filter("provenance = 'community:subject'").count()); - Assertions - .assertEquals( - 2, idExplodeCommunity.filter("provenance = 'community:datasource'").count()); - Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'covid-19'").count()); - Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'fam'").count()); - Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'aginfra'").count()); - Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'mes'").count()); - - query = "select id, MyT.id community, size(MyT.datainfo) datainfosize " - + "from dataset " - + "lateral view explode (context) as MyT " - + "where size(MyT.datainfo) > 0"; - - org.apache.spark.sql.Dataset tmp2 = spark.sql(query); - - Assertions - .assertEquals( - 2, - tmp2 - .select("datainfosize") - .where( - "id = '50|od______3989::05d8c751462f9bb8d2b06956dfbc5c7b' and " - + "community = 'aginfra'") - .collectAsList() - .get(0) - .getInt(0)); - - Assertions - .assertEquals( - 1, - tmp2 - .select("datainfosize") - .where( - "id = '50|od______3989::05d8c751462f9bb8d2b06956dfbc5c7b' and " - + "community = 'covid-19'") - .collectAsList() - .get(0) - .getInt(0)); - - Assertions - .assertEquals( - 2, - tmp2 - .select("datainfosize") - .where( - "id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529' and " - + "community = 'fam'") - .collectAsList() - .get(0) - .getInt(0)); - Assertions - .assertEquals( - 2, - tmp2 - .select("datainfosize") - .where( - "id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529' and " - + "community = 'covid-19'") - .collectAsList() - .get(0) - .getInt(0)); - - Assertions - .assertEquals( - 1, - tmp2 - .select("datainfosize") - .where( - "id = '50|od______3989::0f89464c4ac4c398fe0c71433b175a62' and " - + "community = 'fam'") - .collectAsList() - .get(0) - .getInt(0)); - Assertions - .assertEquals( - 1, - tmp2 - .select("datainfosize") - .where( - "id = '50|od______3989::0f89464c4ac4c398fe0c71433b175a62' and " - + "community = 'mes'") - .collectAsList() - .get(0) - .getInt(0)); - } - - @Test - void bulktagBySubjectDatasourceZenodoCommunityTest() throws Exception { - - SparkBulkTagJob - .main( - new String[] { - "-isTest", Boolean.TRUE.toString(), - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", getClass().getResource("/eu/dnetlib/dhp/bulktag/sample/software/").getPath(), - "-taggingConf", taggingConf, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Software", - "-outputPath", workingDir.toString() + "/software", - "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, - "-pathMap", pathMap }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/software") + .textFile(workingDir.toString() + "/input/software") .map(item -> OBJECT_MAPPER.readValue(item, Software.class)); Assertions.assertEquals(10, tmp.count()); - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Software.class)); - verificationDataset.createOrReplaceTempView("software"); + Assertions.assertEquals(4, tmp.filter(s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook"))).count()); - String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name " - + "from software " - + "lateral view explode(context) c as MyT " - + "lateral view explode(MyT.datainfo) d as MyD " - + "where MyD.inferenceprovenance = 'bulktagging'"; + Assertions.assertEquals(2, tmp.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")).collect() + .get(0).getSubject().size()); + Assertions.assertTrue(tmp.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")).collect() + .get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); - org.apache.spark.sql.Dataset idExplodeCommunity = spark.sql(query); - Assertions.assertEquals(10, idExplodeCommunity.count()); - idExplodeCommunity.show(false); - Assertions - .assertEquals( - 3, idExplodeCommunity.filter("provenance = 'community:subject'").count()); - Assertions - .assertEquals( - 3, idExplodeCommunity.filter("provenance = 'community:datasource'").count()); - Assertions - .assertEquals( - 4, idExplodeCommunity.filter("provenance = 'community:zenodocommunity'").count()); + Assertions.assertEquals(5, tmp.filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11")).collect() + .get(0).getSubject().size()); + Assertions.assertFalse(tmp.filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11")).collect() + .get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); - Assertions.assertEquals(3, idExplodeCommunity.filter("community = 'covid-19'").count()); - Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'dh-ch'").count()); - Assertions.assertEquals(4, idExplodeCommunity.filter("community = 'aginfra'").count()); - Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'dariah'").count()); - Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'fam'").count()); + Assertions.assertEquals(9, tmp.filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")).collect() + .get(0).getSubject().size()); + Assertions.assertTrue(tmp.filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")).collect() + .get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); - Assertions - .assertEquals( - 2, - idExplodeCommunity - .filter( - "provenance = 'community:zenodocommunity' and " - + "id = '50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4' and (" - + "community = 'dh-ch' or community = 'dariah')") - .count()); + Assertions.assertEquals(5, tmp.filter(sw -> sw.getId().equals("50|od______1582::5aec1186054301b66c0c5dc35972a589")).collect() + .get(0).getSubject().size()); + Assertions.assertFalse(tmp.filter(sw -> sw.getId().equals("50|od______1582::5aec1186054301b66c0c5dc35972a589")).collect() + .get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); - query = "select id, MyT.id community, size(MyT.datainfo) datainfosize " - + "from software " - + "lateral view explode (context) as MyT " - + "where size(MyT.datainfo) > 0"; + Assertions.assertEquals(9, tmp.filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0")).collect() + .get(0).getSubject().size()); + Assertions.assertTrue(tmp.filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0")).collect() + .get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); - org.apache.spark.sql.Dataset tmp2 = spark.sql(query); + List subjects = tmp.filter(sw -> sw.getId().equals("50|od______1582::6e7a9b21a2feef45673890432af34244")).collect() + .get(0).getSubject(); + Assertions.assertEquals(8, subjects.size()); + Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); + Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("jupyter"))); + Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("Modeling and Simulation"))); + Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("structure granulaire"))); + Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("algorithme"))); + Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("simulation numérique"))); + Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("flux de gaz"))); + Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("flux de liquide"))); - Assertions - .assertEquals( - 2, - tmp2 - .select("datainfosize") - .where( - "id = '50|od______1582::501b25d420f808c8eddcd9b16e917f11' and " - + "community = 'covid-19'") - .collectAsList() - .get(0) - .getInt(0)); - Assertions - .assertEquals( - 3, - tmp2 - .select("datainfosize") - .where( - "id = '50|od______1582::581621232a561b7e8b4952b18b8b0e56' and " - + "community = 'aginfra'") - .collectAsList() - .get(0) - .getInt(0)); + Assertions.assertEquals(10, sc + .textFile(workingDir.toString() + "/input/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)).count()); + + Assertions.assertEquals(0, sc + .textFile(workingDir.toString() + "/input/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)).filter(ds -> ds.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook"))).count()); + + + Assertions.assertEquals(10, sc + .textFile(workingDir.toString() + "/input/otherresearchproduct") + .map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)).count()); + + Assertions.assertEquals(0, sc + .textFile(workingDir.toString() + "/input/otherresearchproduct") + .map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)).filter(ds -> ds.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook"))).count()); } - @Test - void bulktagDatasourcewithConstraintsTest() throws Exception { - final String sourcePath = getClass() - .getResource( - "/eu/dnetlib/dhp/bulktag/sample/dataset/update_datasourcewithconstraints") - .getPath(); - SparkBulkTagJob - .main( - new String[] { - "-isTest", Boolean.TRUE.toString(), - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", sourcePath, - "-taggingConf", taggingConf, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", - "-outputPath", workingDir.toString() + "/dataset", - "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, - "-pathMap", pathMap - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/dataset") - .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); - - Assertions.assertEquals(10, tmp.count()); - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Dataset.class)); - - verificationDataset.createOrReplaceTempView("dataset"); - String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name " - + "from dataset " - + "lateral view explode(context) c as MyT " - + "lateral view explode(MyT.datainfo) d as MyD " - + "where MyD.inferenceprovenance = 'bulktagging'"; - - org.apache.spark.sql.Dataset idExplodeCommunity = spark.sql(query); - - idExplodeCommunity.show(false); - Assertions.assertEquals(3, idExplodeCommunity.count()); - - Assertions - .assertEquals( - 3, idExplodeCommunity.filter("provenance = 'community:datasource'").count()); - } } diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/galaxy/dataset/dataset_10.json b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/galaxy/dataset/dataset_10.json new file mode 100644 index 000000000..0243a4e3d --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/galaxy/dataset/dataset_10.json @@ -0,0 +1,10 @@ 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se están desarrollando en la Universidad Camilo José Cela (UCJC) sobre la cafeína y sus efectos cuando se realiza deporte. https://www.ucjc.edu/2016/08/la-bbc-s...\n\nJuan Del Coso, director del Laboratorio de Fisiología del Ejercicio de la Universidad Camilo José Cela, nos describe cómo está siendo la investigación que desarrolla con deportistas de alto rendimiento y el consumo de cafeína.\n\n\"Nuestra investigación se enmarca dentro del campo de la fisiología del ejercicio y el objetivo que tenemos es investigar los efectos que tiene la cafeína en los deportistas, principalmente saber si es una ayuda ergogénica en la mayor parte de los deportes, pero también conocer qué perjuicios existen para aquellos deportistas que la utilizan para incrementar el rendimiento deportivo\", explica Del Coso.\n\nY es que los datos son muy llamativos: tres de cada cuatro deportistas de alto rendimiento utilizan la cafeína antes de la competición y muchas veces se utiliza sin saber los perjuicios que 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Oscar","name":"Oscar","surname":"Ribeiro","rank":6,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Quality of life","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Centenarians","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"Centenarians´ quality of life and the role of health and living context","qualifier":{"classid":"main 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Evidences about their quality of life (QoL) are, nevertheless, still limited. Different conceptualizations of QoL, the overvaluation of the negative aspects of advanced age and the heterogeneity of the oldest old are some issues that could explain the dif􏰀culties in this assessment. Objectives: This study aims to analyze the perceived QoL in a sample of centenarians and analyze if there are significant life context (community vs institutional) and health (objective and subjective perception) differences.\nMethods: A subsample of 59 Portuguese centenarians who participated in the PT100_Oporto Centenarian Study, conducted in 2013 was considered. Descriptive and chi-square analysis were conducted.\nResults: Most centenarians perceived their QoL in a very positive manner (50.8% rated it as “good”, 6.8% as “very good” and 3.4% as “excellent”); 28.8% perceived it as “acceptable” and 10.2% as “bad”. No significant statistical differences were found for the considered variables.\nConclusions: Centenarians seem to present high levels of perceived QoL, which can be associated with a great ability to adapt to adverse situations that occur through their lives. Neither contextual and health aspects seem to in􏰂uence the perception of QoL in this particular sample study. Nonetheless, more research is \nneeded to understand the speci􏰀cities of the QoL in the centenarian population, namely the role of psychological and social variables.\ninfo:eu-repo/semantics/publishedVersion","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2014-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":null,"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":null,"context":[{"id":"http://zenodo.org/communities/edenis"},{"id":"http://zenodo.org/communities/aginfra"}, {"id":"http://zenodo.org/communities/primefish"}],"externalReference":[],"instance":[{"license":null,"accessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"instancetype":{"classid":"0020","classname":"Other ORP type","schemeid":"dnet:publication_resource","schemename":"dnet:publication_resource"},"hostedby":{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null},"url":["http://hdl.handle.net/10400.19/5415"],"distributionlocation":"","collectedfrom":{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null},"dateofacceptance":{"value":"2014-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"processingchargeamount":null,"processingchargecurrency":null,"refereed":null}],"contactperson":[],"contactgroup":[],"tool":[]} +{"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1585055423836,"id":"50|od______2017::1e400f1747487fd15998735c41a55c72","originalId":["od______2017::1e400f1747487fd15998735c41a55c72"],"collectedfrom":[{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null}],"pid":[],"dateofcollection":"2019-02-25T04:30:56.996Z","dateoftransformation":"2019-11-30T04:19:59.556Z","extraInfo":[],"oaiprovenance":{"originDescription":{"harvestDate":"2019-02-25T04:30:56.996Z","altered":true,"baseURL":"http://repositorio.ipv.pt/oai/openaire","identifier":"oai:repositorio.ipv.pt:10400.19/5422","datestamp":"2019-02-23T03:01:29Z","metadataNamespace":"http://www.openarchives.org/OAI/2.0/oai_dc/"}},"author":[{"fullname":"Brandão, Daniela","name":"Daniela","surname":"Brandão","rank":1,"pid":null,"affiliation":null},{"fullname":"Ribeiro, Oscar","name":"Oscar","surname":"Ribeiro","rank":2,"pid":null,"affiliation":null},{"fullname":"Araújo, Lia","name":"Lia","surname":"Araújo","rank":3,"pid":null,"affiliation":null},{"fullname":"Paul, Constança","name":"Constança","surname":"Paul","rank":4,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Oldest old","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Census","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"What about the Portuguese oldest old? A global overview using census data","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[],"description":[{"value":"Background\nThe older population is itself aging, and achieving an advanced age is becoming more common worldwide. In Portugal, individuals aged 80+ represent 5.6 % of the total population and 26.5 % of the popu- lation were aged 65 and over in 2011. Having a national profile on this population will give important information to develop interven- tion programs and identify the areas requiring most attention. Ob- jective: This study aims to provide a profile of the Portuguese oldest old, as given by the last national census data.\nMethods\nThe characteristics of all residents aged 80+ (N = 532,219) were ana- lysed considering socio-demographic information (gender, marital status, education, type of residence, place of birth, income) and the existence of difficulties in functional, sensorial and cognitive activities due to health problems or ageing.\nResults\nThe majority of the most aged are females (64.5 %), widowed (53.9 %), and present low educational levels (46.1 % never attended school and 31.6 % do not know how to read/write). Own pensions constitute the main source of income (96.3 %) and the majority live in private households (88.8 %), with 43.2 % currently living in the place where they were born. The majority (73.0 %) reported major difficulties in at least one functional activity – bathing/dressing, walk- ing/climbing stairs, seeing, hearing, memory/concentration, under- standing others/being understood.\nConclusions\nThe high percentage of oldest old living in private households and the presence of functional limitations point to the importance of in- formal care and community care services to support this population. Further studies paying attention to their needs and utilisation of ser- vices are 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Desportiva","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Metodologia","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Didática","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"Treino 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básico (1.º a 9.º anos), tendo como objetivo fornecer informação sobre as capacidades transversais que o novo Programa de Matemática português (2007) veio destacar.\nEscola Superior de Educação de 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in Europe","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[],"description":[{"value":"In the last decade, the number of centenarians world- wide has increased. Following this tendency, the number of centenarian studies has also exponentially augmented. Given the complexity to conduct research with centenarians, elementary information on this specific age group remains unknown at a European level. This paper compares basic characteristics of centenarians from 32 European coun- tries based on Census 2011. Results revealed that France is the country with higher ratio of centenarians, followed by Italy and Greece; on the other hand Croatia, Romania and Bulgaria present the lower ratio. The distribution accord- ing to gender is similar for all countries, with higher ratio of women reaching 100 years old. Different patterns of education level were found on countries where this infor- mation was reliable: Portugal and Greece are the countries with lower levels of education, with more than half without formal education; Finland, UK and Iceland are the countries with higher levels of education, with all centenarians having at least lower secondary education. Analysing the residence situation (living in the community or living in the institu- tion), Romania, Bulgaria, Lithuania, Greece and Latvia are the countries that present higher percentages of centenarians living in the community; Iceland is the country with lower percentage of centenarians living in the community. A posi- tive correlation between the number of centenarians and the percentage of Total Health Expenditure of GDP is observed. This study provides important information about the current profile of European centenarians, which is compared to gen- eral information on the centenarian population from EUA and 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individuals aged 80 and over is growing faster than other segment of the population, and within this group the number of centenarians has risen exponentially worldwide. This phenomena lead to an increasing number of centenarian studies, improving the knowledge about this population, validating the idea of heterogeneity that char- acterizes this group. However, the factors influencing their aging survival remains understudied. The present study aims to identify factors associated with survival after 100 years old in a sample of Portuguese centenarians. After being included in a population-based study on centenarians (PT100–Oporto Centenarian Study), each participant was assessed by a tel- ephone interview every 6 months in order to assess his/her health condition. Follow-up was considered as the time (in months) between 100th birthday and death or the last tel- ephone contact. Survival analysis was performed to iden- tify factors associated with survival after 100 years old. Sociological and medical factors were considered. 140 cen- tenarians were assessed and 115 (82.1%) died. The median survival time after 100 years old was 38 months. Survival after age 100 was associated with acute disease (last month), self-perception of physical condition and drinking status. This study intends do identify factors that predict longevity in long-lived individuals. Findings recognize the importance of factors related with health status, self-perception of physi- cal condition and life style (no alcohol consume) for survival. Further studies should explore the predictive value of these factors, as well as psychosocial aspects, considering living longer but also the quality of time beyond one hundred.\ninfo:eu-repo/semantics/publishedVersion","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2018-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":null,"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":null,"context":[],"externalReference":[],"instance":[{"license":null,"accessright":{"classid":"OPEN","classname":"Open 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João","surname":"Azevedo","rank":5,"pid":null,"affiliation":null},{"fullname":"Ribeiro, Oscar","name":"Oscar","surname":"Ribeiro","rank":6,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Cognition","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Survival","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Functional capacity","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"Cognition and functionality: how do they related to time lived after 100 years of age?","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[],"description":[{"value":"Introduction: The number of centenarians has greatly increased in Portugal in the last decades. Therefore, the analysis of survival time after becoming a centenarian and related factors constitute an import- ant issue for the quality of care provision. The objective of this study is to identify health related factors associated with the time lived after being 100 years of age. Methods: Data come from the population-based study PT100 (Oporto Centenarian Study) and considers information gathered through face-to-face interviews with centenarians and their proxies during 2013. Study eligibility criteria included being 100 and more years old and living in the Oporto Metropolitan Area. Survival analyses were performed in order to identify factors associated with survival after the 100. Functional status (e.g., walking, being bedrid- den) and specific health conditions (e.g. presence/absence of cognitive impairment) were considered as potential factors. Results: The sam- ple comprises 140 centenarians with approximately 14.5 months as median survival time after their 100th anniversary. Centenarians who were bedridden presented a higher probability to live after 100 years when compared with functionally independent centenarians. Presence of cognitive impairment was not associated with the time lived after 100 years old. Conclusions: Given the increasing number of centenarians in Portugal, different studies based on this population need to be consid- ered. The present study, focused on the life after 100 years old, provides new information about this topic contributing to the formulation of new scientific questions for this 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This contribution is splitted in two components: one due to the diversity of the population, the other due to its differentiation from the remaining populations. The program may also be used to obtain allelic richness after rarefaction (to a sample size chosen by the investigator) for a set of populations. It can be used in conjunction with the program haplodiv, based on the paper by Pons & Petit 1995, TAG 90, 462-470, which will provide standard errors for the diversity and differentiation parameters. The input file is a text file (see example: rartest.txt), where the first line indicates the number of haplotypes (here it is 18), the number of populations (here it is 4), and the rarefaction size (it should not be larger than the smallest population sample size; here the rarefaction size is 10, and the smallest sample size is 20). Then follows the data for each population (line), with the number of each haplotype in each population (don't use relative frequencies): 18 4 10 1 0 1 0 0 0 1 1 ...(18 columns) 0 1 2 1 1 0 13 0 ... 0 0 8 0 0 3 6 0 ... 1 0 9 0 0 3 7 1 Results can be seen in the output file (rartest.out here; to be printed horizontally). General measures are given first: within population diversity (Hs), total diversity (Ht), and Gst are given, followed by similar measures based on allelic richness. Then you get the results for each population : H, its standard error, allelic richness after rarefaction, the divergence from the other populations (DHs, DHt, DGst, see the paper in Conservation Biology), and the contributions Ct, Cs, Cd followed by the contributions for allelic richness measures. The program is written for an haploid gene but may be used for nuclear genes, assuming Hardy-Weinberg equilibrium. How to proceed when there are several loci? Do not take the mean across Gst or across Contributions. They are ratios, so you should take the mean of the numerator and the mean of the denominator separately. For the denominator: take the mean of hT and Rt-1 across loci. For the numerator: multiply the contributions by hT or Rt-1 (respectively for contributions to diversity or to allelic richness) and take the mean of these products across loci. 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into account the distances between haplotypes (ie, that consider all haplotypes equally divergent).[br/] The source file should be an ASCII file (its name should have 8 characters maximum: 12345678.txt) and should include the following information:[br/] First line :[br/] Number of cytotypes Number of populations Number of characters distinguishing the variants (for instance number of polymorphic fragments, or of polymorphic nucleotide sites). The program asks for the number of permutations to be made.[br/] see the example (\\ExamplePermut\\input.txt and \\ExamplePermut\\output.out).[br/] Then follows the number of individuals having a given cytotype (column) in a given population (row). Finally, and without interruption, provide the table of character states for all haplotypes, where each line corresponds to one haplotype, and each column to a character. No column should be empty (no missing haplotype) and each population (row) should be composed of AT LEAST 3 individuals![br/] The output file provides permutated values of Nst in a single row, and the value of the last 5% and last 1%. The mean of the permutated values is also given and should be close to the Gst value (by construction). To test if the observed Nst value is larger than the Gst, we count how many permutated values are larger than the observed Nst. If you have 5% of the permutated values greater than the observed value of Nst, then your test is not significant, otherwise it is and you know the P-value. This is akin to testing if Gst = Nst.[br/] [br/] README CpSSR :[br/] It computes measures of diversity and differenciation from haploid population genetic data, when the difference in number of repeats between alleles is available, and tests whether the differentiation and diversity measures differ from the equivalent measures when the distances between haplotypes is not considered (ie, when all haplotypes are considered equally divergent). The source file should be an ASCII file (its name should have 8 characters maximum: 12345678.txt) and should include the following information:[br/] First line :[br/] Number of cytotypes Number of populations Number of cpSSR loci. The program asks for the number of permutations to be made. See the example (\\ExampleCpSSR\\input.txt and \\ExamplePermut\\CpSSR.out).[br/] Then follows the number of individuals having a given haplotype (column) in a given population (row). Finally, and without interruption, provide the table of length variant states for all haplotypes, where each line corresponds to one haplotype, and each column to a character. No column should be empty (no missing haplotype) and each population (row) should be composed of AT LEAST 3 individuals![br/] The output file provides permutated values of Rst in a single row, and the value of the last 5% and last 1%. The mean of the permutated values is also given and should be close to the Gst value (by construction). To test if the observed Rst value is larger than the Gst, you count how many permutated values are larger than the observed Rst. If you have 5% of the permutated values greater than the observed value of Rst, then your test is not significant, otherwise it is and you know the P-value. 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se están desarrollando en la Universidad Camilo José Cela (UCJC) sobre la cafeína y sus efectos cuando se realiza deporte. https://www.ucjc.edu/2016/08/la-bbc-s...\n\nJuan Del Coso, director del Laboratorio de Fisiología del Ejercicio de la Universidad Camilo José Cela, nos describe cómo está siendo la investigación que desarrolla con deportistas de alto rendimiento y el consumo de cafeína.\n\n\"Nuestra investigación se enmarca dentro del campo de la fisiología del ejercicio y el objetivo que tenemos es investigar los efectos que tiene la cafeína en los deportistas, principalmente saber si es una ayuda ergogénica en la mayor parte de los deportes, pero también conocer qué perjuicios existen para aquellos deportistas que la utilizan para incrementar el rendimiento deportivo\", explica Del Coso.\n\nY es que los datos son muy llamativos: tres de cada cuatro deportistas de alto rendimiento utilizan la cafeína antes de la competición y muchas veces se utiliza sin saber los perjuicios que 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El formato es al estilo inglés, similar al de la Oxford Union, donde algunos jóvenes se reunían a debatir sobre temas de la más candente actualidad y polemizaban con la intención de formarse en tan valoradas habilidades.\n\nLa Liga de Debate CICAE-UCJC es una ocasión única para los alumnos de ponerse en contacto con herramientas tan útiles como la oratoria y la comunicación efectiva. Pero, sobre todo, una oportunidad de fomentar el pensamiento crítico y la socialización entre alumnos con espíritu emprendedor. La Liga de Debate CICAE - Universidad Camilo José Cela se diferencia del resto de torneos en que potenciamos que sea eminentemente formativa. Alumnos y profesores reciben formación en comunicación, oratoria y debate por parte de alguno de los expertos en debate españoles más reconocidos en la escena internacional.\n\nDatos de la III Liga de Debate CICAE - UCJC http://ligacicae.ucjc.edu/","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2018-10-23","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":null,"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[{"value":"Universidad 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Amaro","surname":"Costa","rank":2,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"por","classname":"Portuguese","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Pesticidas","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Proteção 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Que caminhos?","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[],"description":[{"value":"A agricultura está inevitavelmente associada a um conjunto de variáveis no ecossistema, onde estão incluídos as pragas e doenças nas culturas e presença de outras plantas que competem pelo alimento, água e luz. Estes agentes são responsáveis por perdas no rendimento que, normalmente, não são aceites pelo agricultor. E é, por isso, que se recorre aos pesticidas: é preciso proteger as culturas do ataque dos seus inimigos.\nTambém é verdade que a agricultura é a atividade desenvolvida pelo Homem que mais se aproxima dos sistemas naturais e tem, assim, um papel central na produção de diversos serviços do ecossistema, como a biodiversidade agrícola, qualidade do solo e água, estabilidade climática e manutenção da paisagem. Ora, o uso dos pesticidas introduz efeitos negativos em todo este sistema: degradam o solo, reduzem a qualidade e disponibilidade de água, causam poluição e perda de habitats selvagens e de biodiversidade. Aqui reside a encruzilhada na proteção das 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Evidences about their quality of life (QoL) are, nevertheless, still limited. Different conceptualizations of QoL, the overvaluation of the negative aspects of advanced age and the heterogeneity of the oldest old are some issues that could explain the dif􏰀culties in this assessment. Objectives: This study aims to analyze the perceived QoL in a sample of centenarians and analyze if there are significant life context (community vs institutional) and health (objective and subjective perception) differences.\nMethods: A subsample of 59 Portuguese centenarians who participated in the PT100_Oporto Centenarian Study, conducted in 2013 was considered. Descriptive and chi-square analysis were conducted.\nResults: Most centenarians perceived their QoL in a very positive manner (50.8% rated it as “good”, 6.8% as “very good” and 3.4% as “excellent”); 28.8% perceived it as “acceptable” and 10.2% as “bad”. No significant statistical differences were found for the considered variables.\nConclusions: Centenarians seem to present high levels of perceived QoL, which can be associated with a great ability to adapt to adverse situations that occur through their lives. Neither contextual and health aspects seem to in􏰂uence the perception of QoL in this particular sample study. Nonetheless, more research is \nneeded to understand the speci􏰀cities of the QoL in the centenarian population, namely the role of psychological and social variables.\ninfo:eu-repo/semantics/publishedVersion","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2014-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":null,"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":null,"context":[{"id":"http://zenodo.org/communities/edenis"},{"id":"http://zenodo.org/communities/aginfra"}, {"id":"http://zenodo.org/communities/primefish"}],"externalReference":[],"instance":[{"license":null,"accessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"instancetype":{"classid":"0020","classname":"Other ORP type","schemeid":"dnet:publication_resource","schemename":"dnet:publication_resource"},"hostedby":{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null},"url":["http://hdl.handle.net/10400.19/5415"],"distributionlocation":"","collectedfrom":{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null},"dateofacceptance":{"value":"2014-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"processingchargeamount":null,"processingchargecurrency":null,"refereed":null}],"contactperson":[],"contactgroup":[],"tool":[]} +{"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1585055423836,"id":"50|od______2017::1e400f1747487fd15998735c41a55c72","originalId":["od______2017::1e400f1747487fd15998735c41a55c72"],"collectedfrom":[{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null}],"pid":[],"dateofcollection":"2019-02-25T04:30:56.996Z","dateoftransformation":"2019-11-30T04:19:59.556Z","extraInfo":[],"oaiprovenance":{"originDescription":{"harvestDate":"2019-02-25T04:30:56.996Z","altered":true,"baseURL":"http://repositorio.ipv.pt/oai/openaire","identifier":"oai:repositorio.ipv.pt:10400.19/5422","datestamp":"2019-02-23T03:01:29Z","metadataNamespace":"http://www.openarchives.org/OAI/2.0/oai_dc/"}},"author":[{"fullname":"Brandão, Daniela","name":"Daniela","surname":"Brandão","rank":1,"pid":null,"affiliation":null},{"fullname":"Ribeiro, Oscar","name":"Oscar","surname":"Ribeiro","rank":2,"pid":null,"affiliation":null},{"fullname":"Araújo, Lia","name":"Lia","surname":"Araújo","rank":3,"pid":null,"affiliation":null},{"fullname":"Paul, Constança","name":"Constança","surname":"Paul","rank":4,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Oldest old","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Census","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"What about the Portuguese oldest old? A global overview using census data","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[],"description":[{"value":"Background\nThe older population is itself aging, and achieving an advanced age is becoming more common worldwide. In Portugal, individuals aged 80+ represent 5.6 % of the total population and 26.5 % of the popu- lation were aged 65 and over in 2011. Having a national profile on this population will give important information to develop interven- tion programs and identify the areas requiring most attention. Ob- jective: This study aims to provide a profile of the Portuguese oldest old, as given by the last national census data.\nMethods\nThe characteristics of all residents aged 80+ (N = 532,219) were ana- lysed considering socio-demographic information (gender, marital status, education, type of residence, place of birth, income) and the existence of difficulties in functional, sensorial and cognitive activities due to health problems or ageing.\nResults\nThe majority of the most aged are females (64.5 %), widowed (53.9 %), and present low educational levels (46.1 % never attended school and 31.6 % do not know how to read/write). Own pensions constitute the main source of income (96.3 %) and the majority live in private households (88.8 %), with 43.2 % currently living in the place where they were born. The majority (73.0 %) reported major difficulties in at least one functional activity – bathing/dressing, walk- ing/climbing stairs, seeing, hearing, memory/concentration, under- standing others/being understood.\nConclusions\nThe high percentage of oldest old living in private households and the presence of functional limitations point to the importance of in- formal care and community care services to support this population. Further studies paying attention to their needs and utilisation of ser- vices are 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Following this tendency, the number of centenarian studies has also exponentially augmented. Given the complexity to conduct research with centenarians, elementary information on this specific age group remains unknown at a European level. This paper compares basic characteristics of centenarians from 32 European coun- tries based on Census 2011. Results revealed that France is the country with higher ratio of centenarians, followed by Italy and Greece; on the other hand Croatia, Romania and Bulgaria present the lower ratio. The distribution accord- ing to gender is similar for all countries, with higher ratio of women reaching 100 years old. Different patterns of education level were found on countries where this infor- mation was reliable: Portugal and Greece are the countries with lower levels of education, with more than half without formal education; Finland, UK and Iceland are the countries with higher levels of education, with all centenarians having at least lower secondary education. Analysing the residence situation (living in the community or living in the institu- tion), Romania, Bulgaria, Lithuania, Greece and Latvia are the countries that present higher percentages of centenarians living in the community; Iceland is the country with lower percentage of centenarians living in the community. A posi- tive correlation between the number of centenarians and the percentage of Total Health Expenditure of GDP is observed. This study provides important information about the current profile of European centenarians, which is compared to gen- eral information on the centenarian population from EUA and 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individuals aged 80 and over is growing faster than other segment of the population, and within this group the number of centenarians has risen exponentially worldwide. This phenomena lead to an increasing number of centenarian studies, improving the knowledge about this population, validating the idea of heterogeneity that char- acterizes this group. However, the factors influencing their aging survival remains understudied. The present study aims to identify factors associated with survival after 100 years old in a sample of Portuguese centenarians. After being included in a population-based study on centenarians (PT100–Oporto Centenarian Study), each participant was assessed by a tel- ephone interview every 6 months in order to assess his/her health condition. Follow-up was considered as the time (in months) between 100th birthday and death or the last tel- ephone contact. Survival analysis was performed to iden- tify factors associated with survival after 100 years old. Sociological and medical factors were considered. 140 cen- tenarians were assessed and 115 (82.1%) died. The median survival time after 100 years old was 38 months. Survival after age 100 was associated with acute disease (last month), self-perception of physical condition and drinking status. This study intends do identify factors that predict longevity in long-lived individuals. Findings recognize the importance of factors related with health status, self-perception of physi- cal condition and life style (no alcohol consume) for survival. Further studies should explore the predictive value of these factors, as well as psychosocial aspects, considering living longer but also the quality of time beyond one 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Therefore, the analysis of survival time after becoming a centenarian and related factors constitute an import- ant issue for the quality of care provision. The objective of this study is to identify health related factors associated with the time lived after being 100 years of age. Methods: Data come from the population-based study PT100 (Oporto Centenarian Study) and considers information gathered through face-to-face interviews with centenarians and their proxies during 2013. Study eligibility criteria included being 100 and more years old and living in the Oporto Metropolitan Area. Survival analyses were performed in order to identify factors associated with survival after the 100. Functional status (e.g., walking, being bedrid- den) and specific health conditions (e.g. presence/absence of cognitive impairment) were considered as potential factors. Results: The sam- ple comprises 140 centenarians with approximately 14.5 months as median survival time after their 100th anniversary. Centenarians who were bedridden presented a higher probability to live after 100 years when compared with functionally independent centenarians. Presence of cognitive impairment was not associated with the time lived after 100 years old. Conclusions: Given the increasing number of centenarians in Portugal, different studies based on this population need to be consid- ered. The present study, focused on the life after 100 years old, provides new information about this topic contributing to the formulation of new scientific questions for this 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into account the distances between haplotypes (ie, that consider all haplotypes equally divergent).[br/] The source file should be an ASCII file (its name should have 8 characters maximum: 12345678.txt) and should include the following information:[br/] First line :[br/] Number of cytotypes Number of populations Number of characters distinguishing the variants (for instance number of polymorphic fragments, or of polymorphic nucleotide sites). The program asks for the number of permutations to be made.[br/] see the example (\\ExamplePermut\\input.txt and \\ExamplePermut\\output.out).[br/] Then follows the number of individuals having a given cytotype (column) in a given population (row). Finally, and without interruption, provide the table of character states for all haplotypes, where each line corresponds to one haplotype, and each column to a character. No column should be empty (no missing haplotype) and each population (row) should be composed of AT LEAST 3 individuals![br/] The output file provides permutated values of Nst in a single row, and the value of the last 5% and last 1%. The mean of the permutated values is also given and should be close to the Gst value (by construction). To test if the observed Nst value is larger than the Gst, we count how many permutated values are larger than the observed Nst. If you have 5% of the permutated values greater than the observed value of Nst, then your test is not significant, otherwise it is and you know the P-value. This is akin to testing if Gst = Nst.[br/] [br/] README CpSSR :[br/] It computes measures of diversity and differenciation from haploid population genetic data, when the difference in number of repeats between alleles is available, and tests whether the differentiation and diversity measures differ from the equivalent measures when the distances between haplotypes is not considered (ie, when all haplotypes are considered equally divergent). The source file should be an ASCII file (its name should have 8 characters maximum: 12345678.txt) and should include the following information:[br/] First line :[br/] Number of cytotypes Number of populations Number of cpSSR loci. The program asks for the number of permutations to be made. See the example (\\ExampleCpSSR\\input.txt and \\ExamplePermut\\CpSSR.out).[br/] Then follows the number of individuals having a given haplotype (column) in a given population (row). Finally, and without interruption, provide the table of length variant states for all haplotypes, where each line corresponds to one haplotype, and each column to a character. No column should be empty (no missing haplotype) and each population (row) should be composed of AT LEAST 3 individuals![br/] The output file provides permutated values of Rst in a single row, and the value of the last 5% and last 1%. The mean of the permutated values is also given and should be close to the Gst value (by construction). To test if the observed Rst value is larger than the Gst, you count how many permutated values are larger than the observed Rst. If you have 5% of the permutated values greater than the observed value of Rst, then your test is not significant, otherwise it is and you know the P-value. 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se están desarrollando en la Universidad Camilo José Cela (UCJC) sobre la cafeína y sus efectos cuando se realiza deporte. https://www.ucjc.edu/2016/08/la-bbc-s...\n\nJuan Del Coso, director del Laboratorio de Fisiología del Ejercicio de la Universidad Camilo José Cela, nos describe cómo está siendo la investigación que desarrolla con deportistas de alto rendimiento y el consumo de cafeína.\n\n\"Nuestra investigación se enmarca dentro del campo de la fisiología del ejercicio y el objetivo que tenemos es investigar los efectos que tiene la cafeína en los deportistas, principalmente saber si es una ayuda ergogénica en la mayor parte de los deportes, pero también conocer qué perjuicios existen para aquellos deportistas que la utilizan para incrementar el rendimiento deportivo\", explica Del Coso.\n\nY es que los datos son muy llamativos: tres de cada cuatro deportistas de alto rendimiento utilizan la cafeína antes de la competición y muchas veces se utiliza sin saber los perjuicios que 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Oscar","name":"Oscar","surname":"Ribeiro","rank":6,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Quality of life","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Centenarians","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"Centenarians´ quality of life and the role of health and living context","qualifier":{"classid":"main 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Evidences about their quality of life (QoL) are, nevertheless, still limited. Different conceptualizations of QoL, the overvaluation of the negative aspects of advanced age and the heterogeneity of the oldest old are some issues that could explain the dif􏰀culties in this assessment. Objectives: This study aims to analyze the perceived QoL in a sample of centenarians and analyze if there are significant life context (community vs institutional) and health (objective and subjective perception) differences.\nMethods: A subsample of 59 Portuguese centenarians who participated in the PT100_Oporto Centenarian Study, conducted in 2013 was considered. Descriptive and chi-square analysis were conducted.\nResults: Most centenarians perceived their QoL in a very positive manner (50.8% rated it as “good”, 6.8% as “very good” and 3.4% as “excellent”); 28.8% perceived it as “acceptable” and 10.2% as “bad”. No significant statistical differences were found for the considered variables.\nConclusions: Centenarians seem to present high levels of perceived QoL, which can be associated with a great ability to adapt to adverse situations that occur through their lives. Neither contextual and health aspects seem to in􏰂uence the perception of QoL in this particular sample study. Nonetheless, more research is \nneeded to understand the speci􏰀cities of the QoL in the centenarian population, namely the role of psychological and social variables.\ninfo:eu-repo/semantics/publishedVersion","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2014-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":null,"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":null,"context":[{"id":"http://zenodo.org/communities/edenis"},{"id":"http://zenodo.org/communities/aginfra"}, {"id":"http://zenodo.org/communities/primefish"}],"externalReference":[],"instance":[{"license":null,"accessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"instancetype":{"classid":"0020","classname":"Other ORP type","schemeid":"dnet:publication_resource","schemename":"dnet:publication_resource"},"hostedby":{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null},"url":["http://hdl.handle.net/10400.19/5415"],"distributionlocation":"","collectedfrom":{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null},"dateofacceptance":{"value":"2014-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"processingchargeamount":null,"processingchargecurrency":null,"refereed":null}],"contactperson":[],"contactgroup":[],"tool":[]} +{"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1585055423836,"id":"50|od______2017::1e400f1747487fd15998735c41a55c72","originalId":["od______2017::1e400f1747487fd15998735c41a55c72"],"collectedfrom":[{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null}],"pid":[],"dateofcollection":"2019-02-25T04:30:56.996Z","dateoftransformation":"2019-11-30T04:19:59.556Z","extraInfo":[],"oaiprovenance":{"originDescription":{"harvestDate":"2019-02-25T04:30:56.996Z","altered":true,"baseURL":"http://repositorio.ipv.pt/oai/openaire","identifier":"oai:repositorio.ipv.pt:10400.19/5422","datestamp":"2019-02-23T03:01:29Z","metadataNamespace":"http://www.openarchives.org/OAI/2.0/oai_dc/"}},"author":[{"fullname":"Brandão, Daniela","name":"Daniela","surname":"Brandão","rank":1,"pid":null,"affiliation":null},{"fullname":"Ribeiro, Oscar","name":"Oscar","surname":"Ribeiro","rank":2,"pid":null,"affiliation":null},{"fullname":"Araújo, Lia","name":"Lia","surname":"Araújo","rank":3,"pid":null,"affiliation":null},{"fullname":"Paul, Constança","name":"Constança","surname":"Paul","rank":4,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Oldest old","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Census","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"What about the Portuguese oldest old? A global overview using census data","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[],"description":[{"value":"Background\nThe older population is itself aging, and achieving an advanced age is becoming more common worldwide. In Portugal, individuals aged 80+ represent 5.6 % of the total population and 26.5 % of the popu- lation were aged 65 and over in 2011. Having a national profile on this population will give important information to develop interven- tion programs and identify the areas requiring most attention. Ob- jective: This study aims to provide a profile of the Portuguese oldest old, as given by the last national census data.\nMethods\nThe characteristics of all residents aged 80+ (N = 532,219) were ana- lysed considering socio-demographic information (gender, marital status, education, type of residence, place of birth, income) and the existence of difficulties in functional, sensorial and cognitive activities due to health problems or ageing.\nResults\nThe majority of the most aged are females (64.5 %), widowed (53.9 %), and present low educational levels (46.1 % never attended school and 31.6 % do not know how to read/write). Own pensions constitute the main source of income (96.3 %) and the majority live in private households (88.8 %), with 43.2 % currently living in the place where they were born. The majority (73.0 %) reported major difficulties in at least one functional activity – bathing/dressing, walk- ing/climbing stairs, seeing, hearing, memory/concentration, under- standing others/being understood.\nConclusions\nThe high percentage of oldest old living in private households and the presence of functional limitations point to the importance of in- formal care and community care services to support this population. Further studies paying attention to their needs and utilisation of ser- vices are 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Desportiva","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Metodologia","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Didática","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"Treino 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básico (1.º a 9.º anos), tendo como objetivo fornecer informação sobre as capacidades transversais que o novo Programa de Matemática português (2007) veio destacar.\nEscola Superior de Educação de 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in Europe","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[],"description":[{"value":"In the last decade, the number of centenarians world- wide has increased. Following this tendency, the number of centenarian studies has also exponentially augmented. Given the complexity to conduct research with centenarians, elementary information on this specific age group remains unknown at a European level. This paper compares basic characteristics of centenarians from 32 European coun- tries based on Census 2011. Results revealed that France is the country with higher ratio of centenarians, followed by Italy and Greece; on the other hand Croatia, Romania and Bulgaria present the lower ratio. The distribution accord- ing to gender is similar for all countries, with higher ratio of women reaching 100 years old. Different patterns of education level were found on countries where this infor- mation was reliable: Portugal and Greece are the countries with lower levels of education, with more than half without formal education; Finland, UK and Iceland are the countries with higher levels of education, with all centenarians having at least lower secondary education. Analysing the residence situation (living in the community or living in the institu- tion), Romania, Bulgaria, Lithuania, Greece and Latvia are the countries that present higher percentages of centenarians living in the community; Iceland is the country with lower percentage of centenarians living in the community. A posi- tive correlation between the number of centenarians and the percentage of Total Health Expenditure of GDP is observed. This study provides important information about the current profile of European centenarians, which is compared to gen- eral information on the centenarian population from EUA and 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individuals aged 80 and over is growing faster than other segment of the population, and within this group the number of centenarians has risen exponentially worldwide. This phenomena lead to an increasing number of centenarian studies, improving the knowledge about this population, validating the idea of heterogeneity that char- acterizes this group. However, the factors influencing their aging survival remains understudied. The present study aims to identify factors associated with survival after 100 years old in a sample of Portuguese centenarians. After being included in a population-based study on centenarians (PT100–Oporto Centenarian Study), each participant was assessed by a tel- ephone interview every 6 months in order to assess his/her health condition. Follow-up was considered as the time (in months) between 100th birthday and death or the last tel- ephone contact. Survival analysis was performed to iden- tify factors associated with survival after 100 years old. Sociological and medical factors were considered. 140 cen- tenarians were assessed and 115 (82.1%) died. The median survival time after 100 years old was 38 months. Survival after age 100 was associated with acute disease (last month), self-perception of physical condition and drinking status. This study intends do identify factors that predict longevity in long-lived individuals. Findings recognize the importance of factors related with health status, self-perception of physi- cal condition and life style (no alcohol consume) for survival. Further studies should explore the predictive value of these factors, as well as psychosocial aspects, considering living longer but also the quality of time beyond one hundred.\ninfo:eu-repo/semantics/publishedVersion","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2018-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":null,"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":null,"context":[],"externalReference":[],"instance":[{"license":null,"accessright":{"classid":"OPEN","classname":"Open 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João","surname":"Azevedo","rank":5,"pid":null,"affiliation":null},{"fullname":"Ribeiro, Oscar","name":"Oscar","surname":"Ribeiro","rank":6,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Cognition","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Survival","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Functional capacity","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"Cognition and functionality: how do they related to time lived after 100 years of age?","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[],"description":[{"value":"Introduction: The number of centenarians has greatly increased in Portugal in the last decades. Therefore, the analysis of survival time after becoming a centenarian and related factors constitute an import- ant issue for the quality of care provision. The objective of this study is to identify health related factors associated with the time lived after being 100 years of age. Methods: Data come from the population-based study PT100 (Oporto Centenarian Study) and considers information gathered through face-to-face interviews with centenarians and their proxies during 2013. Study eligibility criteria included being 100 and more years old and living in the Oporto Metropolitan Area. Survival analyses were performed in order to identify factors associated with survival after the 100. Functional status (e.g., walking, being bedrid- den) and specific health conditions (e.g. presence/absence of cognitive impairment) were considered as potential factors. Results: The sam- ple comprises 140 centenarians with approximately 14.5 months as median survival time after their 100th anniversary. Centenarians who were bedridden presented a higher probability to live after 100 years when compared with functionally independent centenarians. Presence of cognitive impairment was not associated with the time lived after 100 years old. Conclusions: Given the increasing number of centenarians in Portugal, different studies based on this population need to be consid- ered. The present study, focused on the life after 100 years old, provides new information about this topic contributing to the formulation of new scientific questions for this 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This contribution is splitted in two components: one due to the diversity of the population, the other due to its differentiation from the remaining populations. The program may also be used to obtain allelic richness after rarefaction (to a sample size chosen by the investigator) for a set of populations. It can be used in conjunction with the program haplodiv, based on the paper by Pons & Petit 1995, TAG 90, 462-470, which will provide standard errors for the diversity and differentiation parameters. The input file is a text file (see example: rartest.txt), where the first line indicates the number of haplotypes (here it is 18), the number of populations (here it is 4), and the rarefaction size (it should not be larger than the smallest population sample size; here the rarefaction size is 10, and the smallest sample size is 20). Then follows the data for each population (line), with the number of each haplotype in each population (don't use relative frequencies): 18 4 10 1 0 1 0 0 0 1 1 ...(18 columns) 0 1 2 1 1 0 13 0 ... 0 0 8 0 0 3 6 0 ... 1 0 9 0 0 3 7 1 Results can be seen in the output file (rartest.out here; to be printed horizontally). General measures are given first: within population diversity (Hs), total diversity (Ht), and Gst are given, followed by similar measures based on allelic richness. Then you get the results for each population : H, its standard error, allelic richness after rarefaction, the divergence from the other populations (DHs, DHt, DGst, see the paper in Conservation Biology), and the contributions Ct, Cs, Cd followed by the contributions for allelic richness measures. The program is written for an haploid gene but may be used for nuclear genes, assuming Hardy-Weinberg equilibrium. How to proceed when there are several loci? Do not take the mean across Gst or across Contributions. They are ratios, so you should take the mean of the numerator and the mean of the denominator separately. For the denominator: take the mean of hT and Rt-1 across loci. For the numerator: multiply the contributions by hT or Rt-1 (respectively for contributions to diversity or to allelic richness) and take the mean of these products across loci. Then compute the ratio of the two 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into account the distances between haplotypes (ie, that consider all haplotypes equally divergent).[br/] The source file should be an ASCII file (its name should have 8 characters maximum: 12345678.txt) and should include the following information:[br/] First line :[br/] Number of cytotypes Number of populations Number of characters distinguishing the variants (for instance number of polymorphic fragments, or of polymorphic nucleotide sites). The program asks for the number of permutations to be made.[br/] see the example (\\ExamplePermut\\input.txt and \\ExamplePermut\\output.out).[br/] Then follows the number of individuals having a given cytotype (column) in a given population (row). Finally, and without interruption, provide the table of character states for all haplotypes, where each line corresponds to one haplotype, and each column to a character. No column should be empty (no missing haplotype) and each population (row) should be composed of AT LEAST 3 individuals![br/] The output file provides permutated values of Nst in a single row, and the value of the last 5% and last 1%. The mean of the permutated values is also given and should be close to the Gst value (by construction). To test if the observed Nst value is larger than the Gst, we count how many permutated values are larger than the observed Nst. If you have 5% of the permutated values greater than the observed value of Nst, then your test is not significant, otherwise it is and you know the P-value. This is akin to testing if Gst = Nst.[br/] [br/] README CpSSR :[br/] It computes measures of diversity and differenciation from haploid population genetic data, when the difference in number of repeats between alleles is available, and tests whether the differentiation and diversity measures differ from the equivalent measures when the distances between haplotypes is not considered (ie, when all haplotypes are considered equally divergent). The source file should be an ASCII file (its name should have 8 characters maximum: 12345678.txt) and should include the following information:[br/] First line :[br/] Number of cytotypes Number of populations Number of cpSSR loci. The program asks for the number of permutations to be made. See the example (\\ExampleCpSSR\\input.txt and \\ExamplePermut\\CpSSR.out).[br/] Then follows the number of individuals having a given haplotype (column) in a given population (row). Finally, and without interruption, provide the table of length variant states for all haplotypes, where each line corresponds to one haplotype, and each column to a character. No column should be empty (no missing haplotype) and each population (row) should be composed of AT LEAST 3 individuals![br/] The output file provides permutated values of Rst in a single row, and the value of the last 5% and last 1%. The mean of the permutated values is also given and should be close to the Gst value (by construction). To test if the observed Rst value is larger than the Gst, you count how many permutated values are larger than the observed Rst. If you have 5% of the permutated values greater than the observed value of Rst, then your test is not significant, otherwise it is and you know the P-value. 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import org.slf4j.Logger; import org.slf4j.LoggerFactory; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; import java.util.Optional; import static eu.dnetlib.dhp.PropagationConstant.readPath; @@ -72,11 +75,17 @@ public class SparkEoscTag { readPath(spark, inputPath + "/software", Software.class) .map((MapFunction) s -> { + List sbject; + if (!Optional.ofNullable(s.getSubject()).isPresent()) + s.setSubject(new ArrayList<>()); + sbject = s.getSubject(); + if(containsCriteriaNotebook(s)){ - s.getSubject().add(EOSC_NOTEBOOK); + sbject.add(EOSC_NOTEBOOK); + } if(containsCriteriaGalaxy(s)){ - s.getSubject().add(EOSC_GALAXY); + sbject.add(EOSC_GALAXY); } return s; }, Encoders.bean(Software.class) ) @@ -94,11 +103,15 @@ public class SparkEoscTag { readPath(spark, inputPath + "/otherresearchproduct", OtherResearchProduct.class) .map((MapFunction) orp -> { + List sbject; + if (!Optional.ofNullable(orp.getSubject()).isPresent()) + orp.setSubject(new ArrayList<>()); + sbject = orp.getSubject(); if(containsCriteriaGalaxy(orp)){ - orp.getSubject().add(EOSC_GALAXY); + sbject.add(EOSC_GALAXY); } if(containscriteriaTwitter(orp)){ - orp.getSubject().add(EOSC_TWITTER); + sbject.add(EOSC_TWITTER); } return orp; }, Encoders.bean(OtherResearchProduct.class)) @@ -115,8 +128,12 @@ public class SparkEoscTag { readPath(spark, inputPath + "/dataset", Dataset.class) .map((MapFunction) d -> { + List sbject; + if (!Optional.ofNullable(d.getSubject()).isPresent()) + d.setSubject(new ArrayList<>()); + sbject = d.getSubject(); if(containscriteriaTwitter(d)){ - d.getSubject().add(EOSC_TWITTER); + sbject.add(EOSC_TWITTER); } return d; } , Encoders.bean(Dataset.class) ) From 88562c0930dd65eef55e026ae2a299b56eeddeb5 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 22 Apr 2022 18:35:03 +0200 Subject: [PATCH 036/214] [EOSC TAG] added test for galaxy for title and description criterias --- .../dnetlib/dhp/bulktag/EOSCTagJobTest.java | 80 +++++++++++++++++++ 1 file changed, 80 insertions(+) diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java index 82ac9f751..2c2334a6c 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java @@ -166,4 +166,84 @@ public class EOSCTagJobTest { } + @Test + void galaxyUpdatesTest() throws Exception { + spark.read().textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/galaxy/software").getPath()) + .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, Software.class), Encoders.bean(Software.class)) + .write() + .option("compression","gzip") + .json(workingDir.toString() + "/input/software"); + + spark.read().textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/galaxy/dataset").getPath()) + .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, Dataset.class), Encoders.bean(Dataset.class)) + .write() + .option("compression","gzip") + .json(workingDir.toString() + "/input/dataset"); + + spark.read().textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/galaxy/otherresearchproduct").getPath()) + .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, OtherResearchProduct.class), Encoders.bean(OtherResearchProduct.class)) + .write() + .option("compression","gzip") + .json(workingDir.toString() + "/input/otherresearchproduct"); + + SparkEoscTag + .main( + new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", + workingDir.toString() + "/input", + "-workingPath", workingDir.toString() + "/working" + + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/input/software") + .map(item -> OBJECT_MAPPER.readValue(item, Software.class)); + + Assertions.assertEquals(10, tmp.count()); + + Assertions.assertEquals(2, tmp.filter(s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Galaxy Workflow"))).count()); + + Assertions.assertEquals(2, tmp.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")).collect() + .get(0).getSubject().size()); + Assertions.assertTrue(tmp.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")).collect() + .get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); + + + Assertions.assertEquals(6, tmp.filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11")).collect() + .get(0).getSubject().size()); + Assertions.assertTrue(tmp.filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11")).collect() + .get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); + + Assertions.assertEquals(8, tmp.filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")).collect() + .get(0).getSubject().size()); + Assertions.assertFalse(tmp.filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")).collect() + .get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); + + JavaRDD orp = sc.textFile(workingDir.toString() + "/input/otherresearchproduct").map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)); + + Assertions.assertEquals(10, orp.count()); + + Assertions.assertEquals(2, orp.filter(s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Galaxy Workflow"))).count()); + + + Assertions.assertEquals(3, orp.filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07")).collect() + .get(0).getSubject().size()); + Assertions.assertTrue(orp.filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07")).collect() + .get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); + + Assertions.assertEquals(2, orp.filter(sw -> sw.getId().equals("50|od______2017::1bd97baef19dbd2db3203b112bb83bc5")).collect() + .get(0).getSubject().size()); + Assertions.assertFalse(orp.filter(sw -> sw.getId().equals("50|od______2017::1bd97baef19dbd2db3203b112bb83bc5")).collect() + .get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); + + Assertions.assertEquals(3, orp.filter(sw -> sw.getId().equals("50|od______2017::1e400f1747487fd15998735c41a55c72")).collect() + .get(0).getSubject().size()); + Assertions.assertTrue(orp.filter(sw -> sw.getId().equals("50|od______2017::1e400f1747487fd15998735c41a55c72")).collect() + .get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); + + } + } From e342ec93f00e7ff5a042c700ce6a5e20ec364c30 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 22 Apr 2022 18:35:37 +0200 Subject: [PATCH 037/214] [EOSCTag] prepared resources for test --- .../otherresearchproduct/otherresearchproduct_10.json | 6 +++--- .../dnetlib/dhp/eosctag/galaxy/software/software_10.json | 8 ++++---- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/galaxy/otherresearchproduct/otherresearchproduct_10.json b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/galaxy/otherresearchproduct/otherresearchproduct_10.json index ae580eab9..d6b4603d5 100644 --- a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/galaxy/otherresearchproduct/otherresearchproduct_10.json +++ b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/galaxy/otherresearchproduct/otherresearchproduct_10.json @@ -1,6 +1,6 @@ -{"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1585055422336,"id":"50|od______2017::0750a4d0782265873d669520f5e33c07","originalId":["od______2017::0750a4d0782265873d669520f5e33c07"],"collectedfrom":[{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null}],"pid":[],"dateofcollection":"2018-05-08T17:28:57.843Z","dateoftransformation":"2019-11-30T04:19:48.897Z","extraInfo":[],"oaiprovenance":{"originDescription":{"harvestDate":"2018-05-08T17:28:57.843Z","altered":true,"baseURL":"http://repositorio.ipv.pt/oai/openaire","identifier":"oai:repositorio.ipv.pt:10400.19/4572","datestamp":"2017-05-05T02:01:39Z","metadataNamespace":"http://www.openarchives.org/OAI/2.0/oai_dc/"}},"author":[{"fullname":"Godinho, Maria do Céu","name":"Maria Do Céu","surname":"Godinho","rank":1,"pid":null,"affiliation":null},{"fullname":"Costa, Cristina Amaro","name":"Cristina Amaro","surname":"Costa","rank":2,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"por","classname":"Portuguese","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Pesticidas","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Proteção integrada","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"O uso dos pesticidas em Portugal. Que caminhos?","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[],"description":[{"value":"A agricultura está inevitavelmente associada a um conjunto de variáveis no ecossistema, onde estão incluídos as pragas e doenças nas culturas e presença de outras plantas que competem pelo alimento, água e luz. Estes agentes são responsáveis por perdas no rendimento que, normalmente, não são aceites pelo agricultor. E é, por isso, que se recorre aos pesticidas: é preciso proteger as culturas do ataque dos seus inimigos.\nTambém é verdade que a agricultura é a atividade desenvolvida pelo Homem que mais se aproxima dos sistemas naturais e tem, assim, um papel central na produção de diversos serviços do ecossistema, como a biodiversidade agrícola, qualidade do solo e água, estabilidade climática e manutenção da paisagem. Ora, o uso dos pesticidas introduz efeitos negativos em todo este sistema: degradam o solo, reduzem a qualidade e disponibilidade de água, causam poluição e perda de habitats selvagens e de biodiversidade. Aqui reside a encruzilhada na proteção das culturas.\ninfo:eu-repo/semantics/publishedVersion","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2016-07-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":{"value":"Quercus","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":null,"context":[{"id":"http://zenodo.org/communities/chicago-covid-19"}],"externalReference":[],"instance":[{"license":null,"accessright":{"classid":"OPEN","classname":"Open 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-{"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1585055423621,"id":"50|od______2017::1bd97baef19dbd2db3203b112bb83bc5","originalId":["od______2017::1bd97baef19dbd2db3203b112bb83bc5"],"collectedfrom":[{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null}],"pid":[],"dateofcollection":"2019-02-25T04:30:56.994Z","dateoftransformation":"2019-11-30T04:19:58.463Z","extraInfo":[],"oaiprovenance":{"originDescription":{"harvestDate":"2019-02-25T04:30:56.994Z","altered":true,"baseURL":"http://repositorio.ipv.pt/oai/openaire","identifier":"oai:repositorio.ipv.pt:10400.19/5415","datestamp":"2019-02-23T03:01:23Z","metadataNamespace":"http://www.openarchives.org/OAI/2.0/oai_dc/"}},"author":[{"fullname":"Brandão, Daniela","name":"Daniela","surname":"Brandão","rank":1,"pid":null,"affiliation":null},{"fullname":"Duarte, Natália","name":"Natália","surname":"Duarte","rank":2,"pid":null,"affiliation":null},{"fullname":"Araújo, Lia","name":"Lia","surname":"Araújo","rank":3,"pid":null,"affiliation":null},{"fullname":"Alves, Sara","name":"Sara","surname":"Alves","rank":4,"pid":null,"affiliation":null},{"fullname":"Teixeira, Laetitia","name":"Laetitia","surname":"Teixeira","rank":5,"pid":null,"affiliation":null},{"fullname":"Ribeiro, Oscar","name":"Oscar","surname":"Ribeiro","rank":6,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Quality of life","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Centenarians","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"Centenarians´ quality of life and the role of health and living context","qualifier":{"classid":"main 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Evidences about their quality of life (QoL) are, nevertheless, still limited. Different conceptualizations of QoL, the overvaluation of the negative aspects of advanced age and the heterogeneity of the oldest old are some issues that could explain the dif􏰀culties in this assessment. Objectives: This study aims to analyze the perceived QoL in a sample of centenarians and analyze if there are significant life context (community vs institutional) and health (objective and subjective perception) differences.\nMethods: A subsample of 59 Portuguese centenarians who participated in the PT100_Oporto Centenarian Study, conducted in 2013 was considered. Descriptive and chi-square analysis were conducted.\nResults: Most centenarians perceived their QoL in a very positive manner (50.8% rated it as “good”, 6.8% as “very good” and 3.4% as “excellent”); 28.8% perceived it as “acceptable” and 10.2% as “bad”. No significant statistical differences were found for the considered variables.\nConclusions: Centenarians seem to present high levels of perceived QoL, which can be associated with a great ability to adapt to adverse situations that occur through their lives. Neither contextual and health aspects seem to in􏰂uence the perception of QoL in this particular sample study. Nonetheless, more research is \nneeded to understand the speci􏰀cities of the QoL in the centenarian population, namely the role of psychological and social variables.\ninfo:eu-repo/semantics/publishedVersion","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2014-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":null,"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":null,"context":[{"id":"http://zenodo.org/communities/edenis"},{"id":"http://zenodo.org/communities/aginfra"}, {"id":"http://zenodo.org/communities/primefish"}],"externalReference":[],"instance":[{"license":null,"accessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"instancetype":{"classid":"0020","classname":"Other ORP type","schemeid":"dnet:publication_resource","schemename":"dnet:publication_resource"},"hostedby":{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null},"url":["http://hdl.handle.net/10400.19/5415"],"distributionlocation":"","collectedfrom":{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null},"dateofacceptance":{"value":"2014-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"processingchargeamount":null,"processingchargecurrency":null,"refereed":null}],"contactperson":[],"contactgroup":[],"tool":[]} -{"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1585055423836,"id":"50|od______2017::1e400f1747487fd15998735c41a55c72","originalId":["od______2017::1e400f1747487fd15998735c41a55c72"],"collectedfrom":[{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null}],"pid":[],"dateofcollection":"2019-02-25T04:30:56.996Z","dateoftransformation":"2019-11-30T04:19:59.556Z","extraInfo":[],"oaiprovenance":{"originDescription":{"harvestDate":"2019-02-25T04:30:56.996Z","altered":true,"baseURL":"http://repositorio.ipv.pt/oai/openaire","identifier":"oai:repositorio.ipv.pt:10400.19/5422","datestamp":"2019-02-23T03:01:29Z","metadataNamespace":"http://www.openarchives.org/OAI/2.0/oai_dc/"}},"author":[{"fullname":"Brandão, Daniela","name":"Daniela","surname":"Brandão","rank":1,"pid":null,"affiliation":null},{"fullname":"Ribeiro, Oscar","name":"Oscar","surname":"Ribeiro","rank":2,"pid":null,"affiliation":null},{"fullname":"Araújo, Lia","name":"Lia","surname":"Araújo","rank":3,"pid":null,"affiliation":null},{"fullname":"Paul, Constança","name":"Constança","surname":"Paul","rank":4,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Oldest old","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Census","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"What about the Portuguese oldest old? A global overview using census data","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[],"description":[{"value":"Background\nThe older population is itself aging, and achieving an advanced age is becoming more common worldwide. In Portugal, individuals aged 80+ represent 5.6 % of the total population and 26.5 % of the popu- lation were aged 65 and over in 2011. Having a national profile on this population will give important information to develop interven- tion programs and identify the areas requiring most attention. Ob- jective: This study aims to provide a profile of the Portuguese oldest old, as given by the last national census data.\nMethods\nThe characteristics of all residents aged 80+ (N = 532,219) were ana- lysed considering socio-demographic information (gender, marital status, education, type of residence, place of birth, income) and the existence of difficulties in functional, sensorial and cognitive activities due to health problems or ageing.\nResults\nThe majority of the most aged are females (64.5 %), widowed (53.9 %), and present low educational levels (46.1 % never attended school and 31.6 % do not know how to read/write). Own pensions constitute the main source of income (96.3 %) and the majority live in private households (88.8 %), with 43.2 % currently living in the place where they were born. The majority (73.0 %) reported major difficulties in at least one functional activity – bathing/dressing, walk- ing/climbing stairs, seeing, hearing, memory/concentration, under- standing others/being understood.\nConclusions\nThe high percentage of oldest old living in private households and the presence of functional limitations point to the importance of in- formal care and community care services to support this population. Further studies paying attention to their needs and utilisation of ser- vices are 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Que caminhos?","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[],"description":[{"value":"This galaxy workflow is for , onde estão incluídos onde estão incluídos as pragas e doenças nas culturas e presença de outras plantas que competem pelo alimento, água e luz. Estes agentes são responsáveis por perdas no rendimento que, normalmente, não são aceites pelo agricultor. E é, por isso, que se recorre aos pesticidas: é preciso proteger as culturas do ataque dos seus inimigos.\nTambém é verdade que a agricultura é a atividade desenvolvida pelo Homem que mais se aproxima dos sistemas naturais e tem, assim, um papel central na produção de diversos serviços do ecossistema, como a biodiversidade agrícola, qualidade do solo e água, estabilidade climática e manutenção da paisagem. Ora, o uso dos pesticidas introduz efeitos negativos em todo este sistema: degradam o solo, reduzem a qualidade e disponibilidade de água, causam poluição e perda de habitats selvagens e de biodiversidade. Aqui reside a encruzilhada na proteção das 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Oscar","name":"Oscar","surname":"Ribeiro","rank":6,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Quality of life","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Centenarians","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"Centenarians´ quality of life and the role of health and living context","qualifier":{"classid":"main 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Evidences about their quality of life (QoL) are, nevertheless, still limited. Different conceptualizations of QoL, the overvaluation of the negative aspects of advanced age and the heterogeneity of the oldest old are some issues that could explain the dif􏰀culties in this assessment. Objectives: This study aims to analyze the perceived QoL in a sample of centenarians and analyze if there are significant life context (community vs institutional) and health (objective and subjective perception) differences.\nMethods: A subsample of 59 Portuguese centenarians who participated in the PT100_Oporto Centenarian Study, conducted in 2013 was considered. Descriptive and chi-square analysis were conducted.\nResults: Most centenarians perceived their QoL in a very positive manner (50.8% rated it as “good”, 6.8% as “very good” and 3.4% as “excellent”); 28.8% perceived it as “acceptable” and 10.2% as “bad”. No significant statistical differences were found for the considered variables.\nConclusions: Centenarians seem to present high levels of perceived QoL, which can be associated with a great ability to adapt to adverse situations that occur through their lives. Neither contextual and health aspects seem to in􏰂uence the perception of QoL in this particular sample study. Nonetheless, more research is \nneeded to understand the speci􏰀cities of the QoL in the centenarian population, namely the role of psychological and social variables.\ninfo:eu-repo/semantics/publishedVersion","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2014-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":null,"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":null,"context":[{"id":"http://zenodo.org/communities/edenis"},{"id":"http://zenodo.org/communities/aginfra"}, {"id":"http://zenodo.org/communities/primefish"}],"externalReference":[],"instance":[{"license":null,"accessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"instancetype":{"classid":"0020","classname":"Other ORP type","schemeid":"dnet:publication_resource","schemename":"dnet:publication_resource"},"hostedby":{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null},"url":["http://hdl.handle.net/10400.19/5415"],"distributionlocation":"","collectedfrom":{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null},"dateofacceptance":{"value":"2014-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"processingchargeamount":null,"processingchargecurrency":null,"refereed":null}],"contactperson":[],"contactgroup":[],"tool":[]} +{"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1585055423836,"id":"50|od______2017::1e400f1747487fd15998735c41a55c72","originalId":["od______2017::1e400f1747487fd15998735c41a55c72"],"collectedfrom":[{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null}],"pid":[],"dateofcollection":"2019-02-25T04:30:56.996Z","dateoftransformation":"2019-11-30T04:19:59.556Z","extraInfo":[],"oaiprovenance":{"originDescription":{"harvestDate":"2019-02-25T04:30:56.996Z","altered":true,"baseURL":"http://repositorio.ipv.pt/oai/openaire","identifier":"oai:repositorio.ipv.pt:10400.19/5422","datestamp":"2019-02-23T03:01:29Z","metadataNamespace":"http://www.openarchives.org/OAI/2.0/oai_dc/"}},"author":[{"fullname":"Brandão, Daniela","name":"Daniela","surname":"Brandão","rank":1,"pid":null,"affiliation":null},{"fullname":"Ribeiro, Oscar","name":"Oscar","surname":"Ribeiro","rank":2,"pid":null,"affiliation":null},{"fullname":"Araújo, Lia","name":"Lia","surname":"Araújo","rank":3,"pid":null,"affiliation":null},{"fullname":"Paul, Constança","name":"Constança","surname":"Paul","rank":4,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Oldest old","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Census","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"What about the Portuguese oldest old? A global overview using census data","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[],"description":[{"value":"galaxy framwork and software is itself aging, and achieving an adva an advanced age is becoming more common worldwide. In Portugal, individuals aged 80+ represent 5.6 % of the total population and 26.5 % of the popu- lation were aged 65 and over in 2011. Having a national profile on this population will give important information to develop interven- tion programs and identify the areas requiring most attention. Ob- jective: This study aims to provide a profile of the Portuguese oldest old, as given by the last national census data.\nMethods\nThe characteristics of all residents aged 80+ (N = 532,219) were ana- lysed considering socio-demographic information (gender, marital status, education, type of residence, place of birth, income) and the existence of difficulties in functional, sensorial and cognitive activities due to health problems or ageing.\nResults\nThe majority of the most aged are females (64.5 %), widowed (53.9 %), and present low educational levels (46.1 % never attended school and 31.6 % do not know how to read/write). Own pensions constitute the main source of income (96.3 %) and the majority live in private households (88.8 %), with 43.2 % currently living in the place where they were born. The majority (73.0 %) reported major difficulties in at least one functional activity – bathing/dressing, walk- ing/climbing stairs, seeing, hearing, memory/concentration, under- standing others/being understood.\nConclusions\nThe high percentage of oldest old living in private households and the presence of functional limitations point to the importance of in- formal care and community care services to support this population. Further studies paying attention to their needs and utilisation of ser- vices are 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Jovens","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Iniciação Desportiva","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Metodologia","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Didática","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"Treino de Jovens: Princípios Orientadores","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[],"description":[{"value":"Documento que recolhe os traços gerais da intervenção do treinador de jovens, considerando as possíveis orientações pedagógicas, os eixos de evolução do praticante, os diferentes modelos didáticos de iniciação, os momentos idóneos para a intervenção nas diferentes qualidades motoras e a relação entre o treinador de jovens e os restantes agentes implicados no processo (destacando-se, naturalmente, os 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into account the distances between haplotypes (ie, that consider all haplotypes equally divergent).[br/] The source file should be an ASCII file (its name should have 8 characters maximum: 12345678.txt) and should include the following information:[br/] First line :[br/] Number of cytotypes Number of populations Number of characters distinguishing the variants (for instance number of polymorphic fragments, or of polymorphic nucleotide sites). The program asks for the number of permutations to be made.[br/] see the example (\\ExamplePermut\\input.txt and \\ExamplePermut\\output.out).[br/] Then follows the number of individuals having a given cytotype (column) in a given population (row). Finally, and without interruption, provide the table of character states for all haplotypes, where each line corresponds to one haplotype, and each column to a character. No column should be empty (no missing haplotype) and each population (row) should be composed of AT LEAST 3 individuals![br/] The output file provides permutated values of Nst in a single row, and the value of the last 5% and last 1%. The mean of the permutated values is also given and should be close to the Gst value (by construction). To test if the observed Nst value is larger than the Gst, we count how many permutated values are larger than the observed Nst. If you have 5% of the permutated values greater than the observed value of Nst, then your test is not significant, otherwise it is and you know the P-value. This is akin to testing if Gst = Nst.[br/] [br/] README CpSSR :[br/] It computes measures of diversity and differenciation from haploid population genetic data, when the difference in number of repeats between alleles is available, and tests whether the differentiation and diversity measures differ from the equivalent measures when the distances between haplotypes is not considered (ie, when all haplotypes are considered equally divergent). The source file should be an ASCII file (its name should have 8 characters maximum: 12345678.txt) and should include the following information:[br/] First line :[br/] Number of cytotypes Number of populations Number of cpSSR loci. The program asks for the number of permutations to be made. See the example (\\ExampleCpSSR\\input.txt and \\ExamplePermut\\CpSSR.out).[br/] Then follows the number of individuals having a given haplotype (column) in a given population (row). Finally, and without interruption, provide the table of length variant states for all haplotypes, where each line corresponds to one haplotype, and each column to a character. No column should be empty (no missing haplotype) and each population (row) should be composed of AT LEAST 3 individuals![br/] The output file provides permutated values of Rst in a single row, and the value of the last 5% and last 1%. The mean of the permutated values is also given and should be close to the Gst value (by construction). To test if the observed Rst value is larger than the Gst, you count how many permutated values are larger than the observed Rst. If you have 5% of the permutated values greater than the observed value of Rst, then your test is not significant, otherwise it is and you know the P-value. This is akin to testing if Gst = Rst. I usually go for a one-sided test (i.e. I test if Rst>Gst, and not 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the expected heterozygosity, or by R, the allelic richness). This contribution is splitted in two components: one due to the diversity of the population, the other due to its differentiation from the remaining populations. The program may also be used to obtain allelic richness after rarefaction (to a sample size chosen by the investigator) for a set of populations. It can be used in conjunction with the program haplodiv, based on the paper by Pons & Petit 1995, TAG 90, 462-470, which will provide standard errors for the diversity and differentiation parameters. The input file is a text file (see example: rartest.txt), where the first line indicates the number of haplotypes (here it is 18), the number of populations (here it is 4), and the rarefaction size (it should not be larger than the smallest population sample size; here the rarefaction size is 10, and the smallest sample size is 20). Then follows the data for each population (line), with the number of each haplotype in each population (don't use relative frequencies): 18 4 10 1 0 1 0 0 0 1 1 ...(18 columns) 0 1 2 1 1 0 13 0 ... 0 0 8 0 0 3 6 0 ... 1 0 9 0 0 3 7 1 Results can be seen in the output file (rartest.out here; to be printed horizontally). General measures are given first: within population diversity (Hs), total diversity (Ht), and Gst are given, followed by similar measures based on allelic richness. Then you get the results for each population : H, its standard error, allelic richness after rarefaction, the divergence from the other populations (DHs, DHt, DGst, see the paper in Conservation Biology), and the contributions Ct, Cs, Cd followed by the contributions for allelic richness measures. The program is written for an haploid gene but may be used for nuclear genes, assuming Hardy-Weinberg equilibrium. How to proceed when there are several loci? Do not take the mean across Gst or across Contributions. They are ratios, so you should take the mean of the numerator and the mean of the denominator separately. For the denominator: take the mean of hT and Rt-1 across loci. For the numerator: multiply the contributions by hT or Rt-1 (respectively for contributions to diversity or to allelic richness) and take the mean of these products across loci. 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The program asks for the number of permutations to be made.[br/] see the example (\\ExamplePermut\\input.txt and \\ExamplePermut\\output.out).[br/] Then follows the number of individuals having a given cytotype (column) in a given population (row). Finally, and without interruption, provide the table of character states for all haplotypes, where each line corresponds to one haplotype, and each column to a character. No column should be empty (no missing haplotype) and each population (row) should be composed of AT LEAST 3 individuals![br/] The output file provides permutated values of Nst in a single row, and the value of the last 5% and last 1%. The mean of the permutated values is also given and should be close to the Gst value (by construction). To test if the observed Nst value is larger than the Gst, we count how many permutated values are larger than the observed Nst. If you have 5% of the permutated values greater than the observed value of Nst, then your test is not significant, otherwise it is and you know the P-value. This is akin to testing if Gst = Nst.[br/] [br/] README CpSSR :[br/] It computes measures of diversity and differenciation from haploid population genetic data, when the difference in number of repeats between alleles is available, and tests whether the differentiation and diversity measures differ from the equivalent measures when the distances between haplotypes is not considered (ie, when all haplotypes are considered equally divergent). The source file should be an ASCII file (its name should have 8 characters maximum: 12345678.txt) and should include the following information:[br/] First line :[br/] Number of cytotypes Number of populations Number of cpSSR loci. The program asks for the number of permutations to be made. See the example (\\ExampleCpSSR\\input.txt and \\ExamplePermut\\CpSSR.out).[br/] Then follows the number of individuals having a given haplotype (column) in a given population (row). Finally, and without interruption, provide the table of length variant states for all haplotypes, where each line corresponds to one haplotype, and each column to a character. No column should be empty (no missing haplotype) and each population (row) should be composed of AT LEAST 3 individuals![br/] The output file provides permutated values of Rst in a single row, and the value of the last 5% and last 1%. The mean of the permutated values is also given and should be close to the Gst value (by construction). To test if the observed Rst value is larger than the Gst, you count how many permutated values are larger than the observed Rst. If you have 5% of the permutated values greater than the observed value of Rst, then your test is not significant, otherwise it is and you know the P-value. 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(2017) to estimate a stochastic frontier with technical inefficiency effects when one input is endogenous.","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2017-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":null,"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":null,"context":[],"externalReference":[],"instance":[{"license":{"value":"https://creativecommons.org/licenses/by-sa/3.0/","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"accessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"instancetype":{"classid":"0029","classname":"Software","schemeid":"dnet:publication_resource","schemename":"dnet:publication_resource"},"hostedby":{"key":"opendoar____::1582","value":"ProdInra","dataInfo":null},"url":["http://prodinra.inra.fr/record/407676"],"distributionlocation":"","collectedfrom":{"key":"opendoar____::1582","value":"ProdInra","dataInfo":null},"dateofacceptance":{"value":"2017-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"processingchargeamount":null,"processingchargecurrency":null,"refereed":null}],"documentationUrl":[],"license":[],"codeRepositoryUrl":null,"programmingLanguage":null} +{"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1585055748883,"id":"50|od______1582::7a6ace3d7ad42ac813e4955f66a44435","originalId":["od______1582::7a6ace3d7ad42ac813e4955f66a44435"],"collectedfrom":[{"key":"opendoar____::1582","value":"ProdInra","dataInfo":null}],"pid":[],"dateofcollection":"2019-01-24T16:45:07Z","dateoftransformation":"","extraInfo":[],"oaiprovenance":{"originDescription":{"harvestDate":"2019-01-23T18:52:22.609Z","altered":true,"baseURL":"http://oai.prodinra.inra.fr/ft","identifier":"oai:prodinra.inra.fr:407676","datestamp":"2018-03-19T00:00:00Z","metadataNamespace":"http://www.openarchives.org/OAI/2.0/oai_dc/"}},"author":[{"fullname":"Desjeux, Yann","name":"Yann","surname":"Desjeux","rank":1,"pid":null,"affiliation":null},{"fullname":"Latruffe, Laure","name":"Laure","surname":"Latruffe","rank":2,"pid":null,"affiliation":null}],"resulttype":{"classid":"software","classname":"software","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Stochastic Frontier Analysis (SFA);R; R package","qualifier":{"classid":"","classname":"","schemeid":"","schemename":""},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"sfadv: Advanced Methods for Stochastic Frontier Analysis. R package version 1.0.1","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[],"description":[{"value":"Stochastic frontier analysis with advanced methods.\nIn particular, it applies the approach proposed by Latruffe et al. (2017) to estimate a stochastic frontier with technical inefficiency effects when one input is endogenous.","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2017-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":null,"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":null,"context":[],"externalReference":[],"instance":[{"license":{"value":"https://creativecommons.org/licenses/by-sa/3.0/","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"accessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"instancetype":{"classid":"0029","classname":"Software","schemeid":"dnet:publication_resource","schemename":"dnet:publication_resource"},"hostedby":{"key":"opendoar____::1582","value":"ProdInra","dataInfo":null},"url":["http://prodinra.inra.fr/record/407676"],"distributionlocation":"","collectedfrom":{"key":"opendoar____::1582","value":"ProdInra","dataInfo":null},"dateofacceptance":{"value":"2017-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"processingchargeamount":null,"processingchargecurrency":null,"refereed":null}],"documentationUrl":[],"license":[],"codeRepositoryUrl":null,"programmingLanguage":null} \ No newline at end of file From 8c22e5c30a45272196da8a15dc41e408bfd551e7 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Tue, 26 Apr 2022 09:56:27 +0200 Subject: [PATCH 038/214] added fix to include date array with only year or year and month --- .../doiboost/crossref/Crossref2Oaf.scala | 13 +- .../dnetlib/doiboost/crossref/issue_date.json | 330 ++++++++++++++++++ .../crossref/CrossrefMappingTest.scala | 16 +- 3 files changed, 355 insertions(+), 4 deletions(-) create mode 100644 dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/issue_date.json diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala index b4d6d67e2..0ba77ca84 100644 --- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala +++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala @@ -2,7 +2,7 @@ package eu.dnetlib.doiboost.crossref import eu.dnetlib.dhp.schema.common.ModelConstants import eu.dnetlib.dhp.schema.oaf._ -import eu.dnetlib.dhp.schema.oaf.utils.{IdentifierFactory, OafMapperUtils} +import eu.dnetlib.dhp.schema.oaf.utils.{GraphCleaningFunctions, IdentifierFactory, OafMapperUtils} import eu.dnetlib.dhp.utils.DHPUtils import eu.dnetlib.doiboost.DoiBoostMappingUtil import eu.dnetlib.doiboost.DoiBoostMappingUtil._ @@ -576,15 +576,22 @@ case object Crossref2Oaf { def extractDate(dt: String, datePart: List[List[Int]]): String = { if (StringUtils.isNotBlank(dt)) - return dt + return GraphCleaningFunctions.cleanDate(dt) if (datePart != null && datePart.size == 1) { val res = datePart.head if (res.size == 3) { val dp = f"${res.head}-${res(1)}%02d-${res(2)}%02d" if (dp.length == 10) { - return dp + return GraphCleaningFunctions.cleanDate(dp) } } + else if (res.size ==2) { + val dp = f"${res.head}-${res(1)}%02d-01" + return GraphCleaningFunctions.cleanDate(dp) + } + else if (res.size ==1) { + return GraphCleaningFunctions.cleanDate(s"${res.head}-01-01") + } } null diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/issue_date.json b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/issue_date.json new file mode 100644 index 000000000..d74b2c167 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/issue_date.json @@ -0,0 +1,330 @@ +{ + "indexed":{ + "date-parts":[ + [ + 2022, + 4, + 14 + ] + ], + "date-time":"2022-04-14T11:27:30Z", + "timestamp":1649935650109 + }, + "reference-count":22, + "publisher":"SAGE Publications", + "issue":"2", + "license":[ + { + "start":{ + "date-parts":[ + [ + 1980, + 4, + 1 + ] + ], + "date-time":"1980-04-01T00:00:00Z", + "timestamp":323395200000 + }, + "content-version":"tdm", + "delay-in-days":0, + "URL":"http:\/\/journals.sagepub.com\/page\/policies\/text-and-data-mining-license" + } + ], + "content-domain":{ + "domain":[ + + ], + "crossmark-restriction":false + }, + "short-container-title":[ + "Perception" + ], + "published-print":{ + "date-parts":[ + [ + 1980, + 4 + ] + ] + }, + "abstract":" To answer the question \u2018What is suppressed during binocular rivalry?\u2019 a series of three experiments was performed. In the first experiment observers viewed binocular rivalry between orthogonally oriented patterns. When the dominant and suppressed patterns were interchanged between the eyes observers continued seeing with the dominant eye, indicating that an eye, not a pattern, is suppressed during rivalry. In a second experiment it was found that a suppressed eye was able to contribute to stereopsis. A third experiment demonstrated that the predominance of an eye could be influenced by prior adaptation of the other eye, indicating that binocular mechanisms participate in the rivalry process. <\/jats:p>", + "DOI":"10.1068\/p090223", + "type":"journal-article", + "created":{ + "date-parts":[ + [ + 2007, + 1, + 23 + ] + ], + "date-time":"2007-01-23T15:21:36Z", + "timestamp":1169565696000 + }, + "page":"223-231", + "source":"Crossref", + "is-referenced-by-count":123, + "title":[ + "What is Suppressed during Binocular Rivalry?" + ], + "prefix":"10.1177", + "volume":"9", + "author":[ + { + "given":"Randolph", + "family":"Blake", + "sequence":"first", + "affiliation":[ + { + "name":"Cresap Neuroscience Laboratory, Northwestern University, Evanston, Illinois 60201, USA" + } + ] + }, + { + "given":"David H", + "family":"Westendorf", + "sequence":"additional", + "affiliation":[ + { + "name":"Department of Psychology, University of Arkansas, Fayetteville, Arkansas 72701, USA" + } + ] + }, + { + "given":"Randall", + "family":"Overton", + "sequence":"additional", + "affiliation":[ + { + "name":"Department of Psychology, Illinois State University, Normal, Illinois 61761, USA" + } + ] + } + ], + "member":"179", + "published-online":{ + "date-parts":[ + [ + 2016, + 6, + 25 + ] + ] + }, + "reference":[ + { + "key":"bibr1-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1136\/bjo.37.1.37" + }, + { + "key":"bibr2-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1037\/0096-1523.5.2.315" + }, + { + "key":"bibr3-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1016\/0042-6989(74)90065-0" + }, + { + "key":"bibr4-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1068\/p080143" + }, + { + "key":"bibr5-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1016\/0042-6989(70)90036-2" + }, + { + "key":"bibr6-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1113\/jphysiol.1969.sp008862" + }, + { + "key":"bibr7-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1113\/jphysiol.1972.sp010006" + }, + { + "key":"bibr8-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1146\/annurev.ps.23.020172.002213" + }, + { + "key":"bibr9-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1126\/science.166.3902.245" + }, + { + "key":"bibr10-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1037\/h0075805" + }, + { + "key":"bibr11-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1113\/jphysiol.1968.sp008552" + }, + { + "key":"bibr12-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1113\/jphysiol.1965.sp007784" + }, + { + "key":"bibr13-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1037\/h0032455" + }, + { + "key":"bibr14-p090223", + "volume-title":"Treatise on Physiological Optics", + "volume":"3", + "author":"von Helmholtz H", + "year":"1866", + "edition":"3" + }, + { + "key":"bibr15-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1068\/p040125" + }, + { + "key":"bibr16-p090223", + "volume-title":"On Binocular Rivalry", + "author":"Levelt W J M", + "year":"1965" + }, + { + "key":"bibr17-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1001\/archopht.1935.00840020011001" + }, + { + "key":"bibr18-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.3758\/BF03205796" + }, + { + "key":"bibr19-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.3758\/BF03210180" + }, + { + "key":"bibr20-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1037\/0033-2909.85.2.376" + }, + { + "key":"bibr21-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1016\/0042-6989(79)90169-X" + }, + { + "key":"bibr22-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.3758\/BF03210465" + } + ], + "container-title":[ + "Perception" + ], + "original-title":[ + + ], + "language":"en", + "link":[ + { + "URL":"http:\/\/journals.sagepub.com\/doi\/pdf\/10.1068\/p090223", + "content-type":"application\/pdf", + "content-version":"vor", + "intended-application":"text-mining" + }, + { + "URL":"http:\/\/journals.sagepub.com\/doi\/pdf\/10.1068\/p090223", + "content-type":"unspecified", + "content-version":"vor", + "intended-application":"similarity-checking" + } + ], + "deposited":{ + "date-parts":[ + [ + 2021, + 12, + 3 + ] + ], + "date-time":"2021-12-03T11:49:48Z", + "timestamp":1638532188000 + }, + "score":1, + "resource":{ + "primary":{ + "URL":"http:\/\/journals.sagepub.com\/doi\/10.1068\/p090223" + } + }, + "subtitle":[ + + ], + "short-title":[ + + ], + "issued":{ + "date-parts":[ + [ + 1980, + 4 + ] + ] + }, + "references-count":22, + "journal-issue":{ + "issue":"2", + "published-print":{ + "date-parts":[ + [ + 1980, + 4 + ] + ] + } + }, + "alternative-id":[ + "10.1068\/p090223" + ], + "URL":"http:\/\/dx.doi.org\/10.1068\/p090223", + "relation":{ + + }, + "ISSN":[ + "0301-0066", + "1468-4233" + ], + "issn-type":[ + { + "value":"0301-0066", + "type":"print" + }, + { + "value":"1468-4233", + "type":"electronic" + } + ], + "subject":[ + "Artificial Intelligence", + "Sensory Systems", + "Experimental and Cognitive Psychology", + "Ophthalmology" + ], + "published":{ + "date-parts":[ + [ + 1980, + 4 + ] + ] + } +} \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala b/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala index 8124a5aae..9025cd6d2 100644 --- a/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala +++ b/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala @@ -73,6 +73,20 @@ class CrossrefMappingTest { } + + @Test + def crossrefIssueDateTest(): Unit = { + val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/issue_date.json")).mkString + assertNotNull(json) + assertFalse(json.isEmpty) + val resultList: List[Oaf] = Crossref2Oaf.convert(json) + assertTrue(resultList.nonEmpty) + + val items = resultList.filter(p => p.isInstanceOf[Result]) + + println(mapper.writeValueAsString(items.head)) + } + @Test def testOrcidID(): Unit = { val json = Source @@ -82,7 +96,7 @@ class CrossrefMappingTest { .mkString assertNotNull(json) - assertFalse(json.isEmpty); + assertFalse(json.isEmpty) val resultList: List[Oaf] = Crossref2Oaf.convert(json) From 5ffc24d1baead98eea96bb50bcef12488fcda3f1 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 26 Apr 2022 16:18:41 +0200 Subject: [PATCH 039/214] EOSC Services - ongoing update --- .../raw/MigrateDbEntitiesApplication.java | 6 +-- .../dhp/oa/graph/sql/queryServices.sql | 51 +++++++++++++------ .../raw/MigrateDbEntitiesApplicationTest.java | 4 +- 3 files changed, 40 insertions(+), 21 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java index b5801ca5c..b1be7f10a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java @@ -143,8 +143,8 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i smdbe.execute("queryClaims.sql", smdbe::processClaims); break; case openaire: - log.info("Processing datasources..."); - smdbe.execute("queryDatasources.sql", smdbe::processDatasource, verifyNamespacePrefix); + log.info("Processing services..."); + smdbe.execute("queryServices.sql", smdbe::processService, verifyNamespacePrefix); log.info("Processing projects..."); if (dbSchema.equalsIgnoreCase("beta")) { @@ -235,7 +235,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i dbClient.processResults(sql, consumer); } - public List processDatasource(final ResultSet rs) { + public List processService(final ResultSet rs) { try { final DataInfo info = prepareDataInfo(rs); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql index 81be79420..603b1e9b2 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql @@ -1,6 +1,6 @@ SELECT d.id AS datasourceid, - d.id || array_agg(distinct di.pid) AS identities, + array_remove(d.id || array_agg(distinct di.pid) filter (where di.pid like 'piwik%') || array_agg(distinct dds.duplicate), NULL) AS identities, d.officialname AS officialname, d.englishname AS englishname, d.contactemail AS contactemail, @@ -57,7 +57,8 @@ SELECT NULL AS odpolicies, ARRAY(SELECT trim(s) FROM unnest(string_to_array(d.languages, ',')) AS s) AS odlanguages, - + ARRAY(SELECT trim(s) + FROM unnest(string_to_array(d.languages, ',')) AS s) AS languages, -- Term provided only by OpenDOAR: -- probably updating the TR it could be replaced by research_entity_types[] -- But a study on the vocabulary terms is needed @@ -74,40 +75,54 @@ SELECT d.releaseenddate AS releaseenddate, d.missionstatementurl AS missionstatementurl, -- the following 2 fields (provided by re3data) have been replaced by research_entity_types[] - -- VALUE 'Research Data' : d.dataprovider AS dataprovider, - -- VALUE 'Services' : d.serviceprovider AS serviceprovider, + -- VALUE 'Research Data' : d.dataprovider AS dataprovider, + -- VALUE 'Services' : d.serviceprovider AS serviceprovider, d.databaseaccesstype AS databaseaccesstype, d.datauploadtype AS datauploadtype, d.databaseaccessrestriction AS databaseaccessrestriction, d.datauploadrestriction AS datauploadrestriction, -- REPLACED BY version_control : d.versioning AS versioning, - d.version_control AS versioning, + d.version_control AS versioning, + d.version_control AS versioncontrol, d.citationguidelineurl AS citationguidelineurl, - -- REMOVED (it was provided only by re3data: yes, no, unknown): d.qualitymanagementkind AS qualitymanagementkind, + d.pidsystems AS pidsystems, d.certificates AS certificates, ARRAY[]::text[] AS policies, - dc.id AS collectedfromid, - dc.officialname AS collectedfromname, + array_remove(dc.id||'@@@'||dc.officialname || array_agg(distinct dds_cf.id||'@@@'||dds_cf.officialname), NULL) AS collectedfrom, + d._typology_to_remove_||'@@@dnet:datasource_typologies' AS datasourcetype, - d.eosc_type||'@@@dnet:eosc_types' AS eosc_type, - d.eosc_datasource_type||'@@@dnet:eosc_datasource_types' AS eosc_datasoorce_type, + d.eosc_type||'@@@dnet:eosc_types' AS eosctype, + d.eosc_datasource_type||'@@@dnet:eosc_datasource_types' AS eoscdatasourcetype, 'sysimport:crosswalk:entityregistry@@@dnet:provenance_actions' AS provenanceaction, d.issn AS issnPrinted, d.eissn AS issnOnline, d.lissn AS issnLinking, + d.research_entity_types AS researchentitytypes, d.consenttermsofuse AS consenttermsofuse, d.fulltextdownload AS fulltextdownload, d.consenttermsofusedate AS consenttermsofusedate, - d.jurisdiction||'@@@eosc:jurisdictions' AS jurisdiction, - d.thematic AS thematic, - -- REMOVED ???: d.knowledge_graph AS knowledgegraph, - array(select unnest(d.content_policies)||'@@@eosc:contentpolicies') AS contentpolicies + d.lastconsenttermsofusedate AS lastconsenttermsofusedate, + d.jurisdiction||'@@@eosc:jurisdictions' AS jurisdiction, + d.thematic AS thematic, + -- REMOVED ???: d.knowledge_graph AS knowledgegraph, + array(select unnest(d.content_policies)||'@@@eosc:contentpolicies') AS contentpolicies, + d.submission_policy_url AS submissionpolicyurl, + d.preservation_policy_url AS preservationpolicyurl, + d.research_product_access_policies AS researchproductaccesspolicies, + d.research_product_metadata_access_policies AS researchproductmetadataaccesspolicies FROM dsm_services d LEFT OUTER JOIN dsm_services dc on (d.collectedfrom = dc.id) LEFT OUTER JOIN dsm_api a ON (d.id = a.service) LEFT OUTER JOIN dsm_servicepids di ON (d.id = di.service) +LEFT OUTER JOIN dsm_dedup_services dds ON (d.id = dds.id) +LEFT OUTER JOIN dsm_services dds_dup ON (dds.duplicate = dds_dup.id) +LEFT OUTER JOIN dsm_services dds_cf ON (dds_dup.collectedfrom = dds_cf.id) + + +WHERE + d.dedup_main_service = true GROUP BY d.id, @@ -132,7 +147,7 @@ GROUP BY d.databaseaccessrestriction, d.datauploadrestriction, -- REPLACED BY version_control : d.versioning, - d.version_control + d.version_control, d.citationguidelineurl, -- REMOVED: d.qualitymanagementkind, d.pidsystems, @@ -145,4 +160,8 @@ GROUP BY d.jurisdiction, d.thematic, -- REMOVED ???: de.knowledge_graph, - d.content_policies + d.content_policies, + d.submission_policy_url, + d.preservation_policy_url, + d.research_product_access_policies, + d.research_product_metadata_access_policies \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java index 05ae5be74..488a1f70b 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java @@ -63,10 +63,10 @@ public class MigrateDbEntitiesApplicationTest { } @Test - public void testProcessDatasource() throws Exception { + public void testProcessService() throws Exception { final List fields = prepareMocks("datasources_resultset_entry.json"); - final List list = app.processDatasource(rs); + final List list = app.processService(rs); assertEquals(1, list.size()); verifyMocks(fields); From 623f7be26d53063c88dc3f4946bd1d2cd1648561 Mon Sep 17 00:00:00 2001 From: Serafeim Chatzopoulos Date: Thu, 28 Apr 2022 16:31:11 +0300 Subject: [PATCH 040/214] Fix reading files from HDFS in FileCollector & FileGZipCollector plugins --- .../dhp/collection/CollectorWorker.java | 4 +-- .../file/AbstractSplittedRecordPlugin.java | 35 +++++++++++++++---- .../plugin/file/FileCollectorPlugin.java | 18 ++++++---- .../plugin/file/FileGZipCollectorPlugin.java | 21 ++++++----- .../plugin/file/FileCollectorPluginTest.java | 11 ++++-- .../file/FileGZipCollectorPluginTest.java | 29 ++++++++++----- 6 files changed, 86 insertions(+), 32 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java index a770af804..f6cba6fb8 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java @@ -117,9 +117,9 @@ public class CollectorWorker extends ReportingJob { case rest_json2xml: return new RestCollectorPlugin(clientParams); case file: - return new FileCollectorPlugin(); + return new FileCollectorPlugin(fileSystem); case fileGZip: - return new FileGZipCollectorPlugin(); + return new FileGZipCollectorPlugin(fileSystem); case other: final CollectorPlugin.NAME.OTHER_NAME plugin = Optional .ofNullable(api.getParams().get("other_plugin_type")) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/file/AbstractSplittedRecordPlugin.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/file/AbstractSplittedRecordPlugin.java index c569926c0..97f61980a 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/file/AbstractSplittedRecordPlugin.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/file/AbstractSplittedRecordPlugin.java @@ -1,11 +1,11 @@ package eu.dnetlib.dhp.collection.plugin.file; import java.io.BufferedInputStream; +import java.io.IOException; import java.util.Iterator; import java.util.Optional; import java.util.Spliterator; import java.util.Spliterators; -import java.util.stream.Collectors; import java.util.stream.Stream; import java.util.stream.StreamSupport; @@ -15,6 +15,8 @@ import eu.dnetlib.dhp.collection.plugin.utils.XMLIterator; import eu.dnetlib.dhp.common.aggregation.AggregatorReport; import eu.dnetlib.dhp.common.collection.CollectorException; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -24,22 +26,40 @@ public abstract class AbstractSplittedRecordPlugin implements CollectorPlugin { public static final String SPLIT_ON_ELEMENT = "splitOnElement"; + private final FileSystem fileSystem; + + public AbstractSplittedRecordPlugin(FileSystem fileSystem) { + this.fileSystem = fileSystem; + } + @Override public Stream collect(ApiDescriptor api, AggregatorReport report) throws CollectorException { - final String baseUrl = Optional + // get path to file + final Path filePath = Optional .ofNullable(api.getBaseUrl()) - .orElseThrow( () -> new CollectorException("missing baseUrl, required by the AbstractSplittedRecordPlugin")); + .map(Path::new) + .orElseThrow( () -> new CollectorException("missing baseUrl")); - log.info("baseUrl: {}", baseUrl); + log.info("baseUrl: {}", filePath); + // check that path to file exists + try { + if (!fileSystem.exists(filePath)) { + throw new CollectorException("path does not exist: " + filePath); + } + } catch (IOException e) { + throw new CollectorException(e); + } + + // get split element final String splitOnElement = Optional .ofNullable(api.getParams().get(SPLIT_ON_ELEMENT)) .orElseThrow(() -> new CollectorException(String.format("missing parameter '%s', required by the AbstractSplittedRecordPlugin", SPLIT_ON_ELEMENT))); log.info("splitOnElement: {}", splitOnElement); - final BufferedInputStream bis = getBufferedInputStream(baseUrl); + final BufferedInputStream bis = getBufferedInputStream(filePath); Iterator xmlIterator = new XMLIterator(splitOnElement, bis); @@ -49,6 +69,9 @@ public abstract class AbstractSplittedRecordPlugin implements CollectorPlugin { ); } - abstract protected BufferedInputStream getBufferedInputStream(final String baseUrl) throws CollectorException; + abstract protected BufferedInputStream getBufferedInputStream(final Path filePath) throws CollectorException; + public FileSystem getFileSystem() { + return fileSystem; + } } \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/file/FileCollectorPlugin.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/file/FileCollectorPlugin.java index 3a268eabb..d7a992038 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/file/FileCollectorPlugin.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/file/FileCollectorPlugin.java @@ -1,25 +1,31 @@ package eu.dnetlib.dhp.collection.plugin.file; import eu.dnetlib.dhp.common.collection.CollectorException; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import java.io.BufferedInputStream; -import java.io.FileInputStream; public class FileCollectorPlugin extends AbstractSplittedRecordPlugin { private static final Logger log = LoggerFactory.getLogger(FileCollectorPlugin.class); - @Override - protected BufferedInputStream getBufferedInputStream(final String baseUrl) throws CollectorException { + public FileCollectorPlugin(FileSystem fileSystem) { + super(fileSystem); + } - log.info("baseUrl: {}", baseUrl); + @Override + protected BufferedInputStream getBufferedInputStream(final Path filePath) throws CollectorException { + + log.info("filePath: {}", filePath); try { - return new BufferedInputStream(new FileInputStream(baseUrl)); + FileSystem fs = super.getFileSystem(); + return new BufferedInputStream(fs.open(filePath)); } catch (Exception e) { - throw new CollectorException("Error reading file " + baseUrl, e); + throw new CollectorException("Error reading file " + filePath, e); } } } \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/file/FileGZipCollectorPlugin.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/file/FileGZipCollectorPlugin.java index b2c77e8b6..b724cfefd 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/file/FileGZipCollectorPlugin.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/file/FileGZipCollectorPlugin.java @@ -1,28 +1,33 @@ package eu.dnetlib.dhp.collection.plugin.file; import eu.dnetlib.dhp.common.collection.CollectorException; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import java.io.*; -import java.net.MalformedURLException; -import java.net.URL; +import java.io.BufferedInputStream; import java.util.zip.GZIPInputStream; public class FileGZipCollectorPlugin extends AbstractSplittedRecordPlugin { private static final Logger log = LoggerFactory.getLogger(FileGZipCollectorPlugin.class); - @Override - protected BufferedInputStream getBufferedInputStream(String baseUrl) throws CollectorException { + public FileGZipCollectorPlugin(FileSystem fileSystem) { + super(fileSystem); + } - log.info("baseUrl: {}", baseUrl); + @Override + protected BufferedInputStream getBufferedInputStream(final Path filePath) throws CollectorException { + + log.info("filePath: {}", filePath); try { - GZIPInputStream stream = new GZIPInputStream(new FileInputStream(baseUrl)); + FileSystem fs = super.getFileSystem(); + GZIPInputStream stream = new GZIPInputStream(fs.open(filePath)); return new BufferedInputStream(stream); } catch (Exception e) { - throw new CollectorException("Error reading file " + baseUrl, e); + throw new CollectorException("Error reading file " + filePath, e); } } } diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/file/FileCollectorPluginTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/file/FileCollectorPluginTest.java index d9b5152fe..ed0578059 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/file/FileCollectorPluginTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/file/FileCollectorPluginTest.java @@ -3,12 +3,17 @@ package eu.dnetlib.dhp.collection.plugin.file; import eu.dnetlib.dhp.collection.ApiDescriptor; import eu.dnetlib.dhp.common.aggregation.AggregatorReport; import eu.dnetlib.dhp.common.collection.CollectorException; +import net.bytebuddy.asm.Advice; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.LocalFileSystem; import org.junit.jupiter.api.Assertions; import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; +import java.io.IOException; import java.util.HashMap; import java.util.stream.Stream; @@ -17,12 +22,13 @@ public class FileCollectorPluginTest { private static final Logger log = LoggerFactory.getLogger(FileGZipCollectorPluginTest.class); private final ApiDescriptor api = new ApiDescriptor(); + private FileCollectorPlugin plugin; private static final String SPLIT_ON_ELEMENT = "repository"; @BeforeEach - public void setUp() { + public void setUp() throws IOException { final String gzipFile = this .getClass() @@ -36,7 +42,8 @@ public class FileCollectorPluginTest { api.setParams(params); - plugin = new FileCollectorPlugin(); + FileSystem fs = FileSystem.get(new Configuration()); + plugin = new FileCollectorPlugin(fs); } @Test diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/file/FileGZipCollectorPluginTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/file/FileGZipCollectorPluginTest.java index 18caf1c45..23f08e6ea 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/file/FileGZipCollectorPluginTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/file/FileGZipCollectorPluginTest.java @@ -3,30 +3,42 @@ package eu.dnetlib.dhp.collection.plugin.file; import eu.dnetlib.dhp.collection.ApiDescriptor; import eu.dnetlib.dhp.common.aggregation.AggregatorReport; import eu.dnetlib.dhp.common.collection.CollectorException; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeEach; -import org.junit.jupiter.api.Test; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.LocalFileSystem; +import org.junit.jupiter.api.*; +import org.junit.jupiter.api.extension.ExtendWith; +import org.mockito.Mockito; +import org.mockito.junit.jupiter.MockitoExtension; import org.slf4j.Logger; import org.slf4j.LoggerFactory; +import java.io.File; +import java.io.IOException; +import java.nio.file.Files; import java.util.HashMap; +import java.util.Objects; import java.util.stream.Stream; + +@TestMethodOrder(MethodOrderer.OrderAnnotation.class) +@ExtendWith(MockitoExtension.class) public class FileGZipCollectorPluginTest { private static final Logger log = LoggerFactory.getLogger(FileGZipCollectorPluginTest.class); private final ApiDescriptor api = new ApiDescriptor(); + private FileGZipCollectorPlugin plugin; private static final String SPLIT_ON_ELEMENT = "repository"; @BeforeEach - public void setUp() { + public void setUp() throws IOException { - final String gzipFile = this - .getClass() - .getResource("/eu/dnetlib/dhp/collection/plugin/file/opendoar.xml.gz") + final String gzipFile = Objects.requireNonNull(this + .getClass() + .getResource("/eu/dnetlib/dhp/collection/plugin/file/opendoar.xml.gz")) .getFile(); api.setBaseUrl(gzipFile); @@ -36,7 +48,8 @@ public class FileGZipCollectorPluginTest { api.setParams(params); - plugin = new FileGZipCollectorPlugin(); + FileSystem fs = FileSystem.get(new Configuration()); + plugin = new FileGZipCollectorPlugin(fs); } @Test From f5f532d134159c1e14f72811cef1aba36f80d980 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 29 Apr 2022 12:25:24 +0200 Subject: [PATCH 041/214] EOSC Services - ongoing update --- .../dhp/schema/oaf/utils/OafMapperUtils.java | 13 + .../schema/oaf/utils/OafMapperUtilsTest.java | 185 +++++++------- .../raw/MigrateDbEntitiesApplication.java | 75 ++++-- .../dhp/oa/graph/sql/queryServices.sql | 52 ++-- .../raw/MigrateDbEntitiesApplicationTest.java | 137 +++++++++-- ...try.json => services_resultset_entry.json} | 229 ++++++++++++------ .../oa/provision/utils/XmlRecordFactory.java | 6 - pom.xml | 2 +- 8 files changed, 459 insertions(+), 240 deletions(-) rename dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/{datasources_resultset_entry.json => services_resultset_entry.json} (68%) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java index 0a51e8600..aac2a7801 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java @@ -3,6 +3,8 @@ package eu.dnetlib.dhp.schema.oaf.utils; import static eu.dnetlib.dhp.schema.common.ModelConstants.*; +import java.sql.Array; +import java.sql.SQLException; import java.util.*; import java.util.concurrent.ConcurrentHashMap; import java.util.function.Function; @@ -118,6 +120,17 @@ public class OafMapperUtils { .collect(Collectors.toList()); } + public static List listValues(Array values) throws SQLException { + if (Objects.isNull(values)) { + return null; + } + return Arrays + .stream((T[]) values.getArray()) + .filter(Objects::nonNull) + .distinct() + .collect(Collectors.toList()); + } + public static List> listFields(final DataInfo info, final List values) { return values .stream() diff --git a/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtilsTest.java b/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtilsTest.java index 79629a171..9111ac2df 100644 --- a/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtilsTest.java +++ b/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtilsTest.java @@ -44,105 +44,104 @@ class OafMapperUtilsTest { @Test void testDateValidation() { - assertTrue(GraphCleaningFunctions.doCleanDate("2016-05-07T12:41:19.202Z ").isPresent()); - assertTrue(GraphCleaningFunctions.doCleanDate("2020-09-10 11:08:52 ").isPresent()); - assertTrue(GraphCleaningFunctions.doCleanDate(" 2016-04-05").isPresent()); + assertNotNull(GraphCleaningFunctions.cleanDate("2016-05-07T12:41:19.202Z ")); + assertNotNull(GraphCleaningFunctions.cleanDate("2020-09-10 11:08:52 ")); + assertNotNull(GraphCleaningFunctions.cleanDate(" 2016-04-05")); - assertEquals("2016-04-05", GraphCleaningFunctions.doCleanDate("2016 Apr 05").get()); + assertEquals("2016-04-05", GraphCleaningFunctions.cleanDate("2016 Apr 05")); - assertEquals("2009-05-08", GraphCleaningFunctions.doCleanDate("May 8, 2009 5:57:51 PM").get()); - assertEquals("1970-10-07", GraphCleaningFunctions.doCleanDate("oct 7, 1970").get()); - assertEquals("1970-10-07", GraphCleaningFunctions.doCleanDate("oct 7, '70").get()); - assertEquals("1970-10-07", GraphCleaningFunctions.doCleanDate("oct. 7, 1970").get()); - assertEquals("1970-10-07", GraphCleaningFunctions.doCleanDate("oct. 7, 70").get()); - assertEquals("2006-01-02", GraphCleaningFunctions.doCleanDate("Mon Jan 2 15:04:05 2006").get()); - assertEquals("2006-01-02", GraphCleaningFunctions.doCleanDate("Mon Jan 2 15:04:05 MST 2006").get()); - assertEquals("2006-01-02", GraphCleaningFunctions.doCleanDate("Mon Jan 02 15:04:05 -0700 2006").get()); - assertEquals("2006-01-02", GraphCleaningFunctions.doCleanDate("Monday, 02-Jan-06 15:04:05 MST").get()); - assertEquals("2006-01-02", GraphCleaningFunctions.doCleanDate("Mon, 02 Jan 2006 15:04:05 MST").get()); - assertEquals("2017-07-11", GraphCleaningFunctions.doCleanDate("Tue, 11 Jul 2017 16:28:13 +0200 (CEST)").get()); - assertEquals("2006-01-02", GraphCleaningFunctions.doCleanDate("Mon, 02 Jan 2006 15:04:05 -0700").get()); - assertEquals("2018-01-04", GraphCleaningFunctions.doCleanDate("Thu, 4 Jan 2018 17:53:36 +0000").get()); - assertEquals("2015-08-10", GraphCleaningFunctions.doCleanDate("Mon Aug 10 15:44:11 UTC+0100 2015").get()); + assertEquals("2009-05-08", GraphCleaningFunctions.cleanDate("May 8, 2009 5:57:51 PM")); + assertEquals("1970-10-07", GraphCleaningFunctions.cleanDate("oct 7, 1970")); + assertEquals("1970-10-07", GraphCleaningFunctions.cleanDate("oct 7, '70")); + assertEquals("1970-10-07", GraphCleaningFunctions.cleanDate("oct. 7, 1970")); + assertEquals("1970-10-07", GraphCleaningFunctions.cleanDate("oct. 7, 70")); + assertEquals("2006-01-02", GraphCleaningFunctions.cleanDate("Mon Jan 2 15:04:05 2006")); + assertEquals("2006-01-02", GraphCleaningFunctions.cleanDate("Mon Jan 2 15:04:05 MST 2006")); + assertEquals("2006-01-02", GraphCleaningFunctions.cleanDate("Mon Jan 02 15:04:05 -0700 2006")); + assertEquals("2006-01-02", GraphCleaningFunctions.cleanDate("Monday, 02-Jan-06 15:04:05 MST")); + assertEquals("2006-01-02", GraphCleaningFunctions.cleanDate("Mon, 02 Jan 2006 15:04:05 MST")); + assertEquals("2017-07-11", GraphCleaningFunctions.cleanDate("Tue, 11 Jul 2017 16:28:13 +0200 (CEST)")); + assertEquals("2006-01-02", GraphCleaningFunctions.cleanDate("Mon, 02 Jan 2006 15:04:05 -0700")); + assertEquals("2018-01-04", GraphCleaningFunctions.cleanDate("Thu, 4 Jan 2018 17:53:36 +0000")); + assertEquals("2015-08-10", GraphCleaningFunctions.cleanDate("Mon Aug 10 15:44:11 UTC+0100 2015")); assertEquals( "2015-07-03", - GraphCleaningFunctions.doCleanDate("Fri Jul 03 2015 18:04:07 GMT+0100 (GMT Daylight Time)").get()); - assertEquals("2012-09-17", GraphCleaningFunctions.doCleanDate("September 17, 2012 10:09am").get()); - assertEquals("2012-09-17", GraphCleaningFunctions.doCleanDate("September 17, 2012 at 10:09am PST-08").get()); - assertEquals("2012-09-17", GraphCleaningFunctions.doCleanDate("September 17, 2012, 10:10:09").get()); - assertEquals("1970-10-07", GraphCleaningFunctions.doCleanDate("October 7, 1970").get()); - assertEquals("1970-10-07", GraphCleaningFunctions.doCleanDate("October 7th, 1970").get()); - assertEquals("2006-02-12", GraphCleaningFunctions.doCleanDate("12 Feb 2006, 19:17").get()); - assertEquals("2006-02-12", GraphCleaningFunctions.doCleanDate("12 Feb 2006 19:17").get()); - assertEquals("1970-10-07", GraphCleaningFunctions.doCleanDate("7 oct 70").get()); - assertEquals("1970-10-07", GraphCleaningFunctions.doCleanDate("7 oct 1970").get()); - assertEquals("2013-02-03", GraphCleaningFunctions.doCleanDate("03 February 2013").get()); - assertEquals("2013-07-01", GraphCleaningFunctions.doCleanDate("1 July 2013").get()); - assertEquals("2013-02-03", GraphCleaningFunctions.doCleanDate("2013-Feb-03").get()); - assertEquals("2014-03-31", GraphCleaningFunctions.doCleanDate("3/31/2014").get()); - assertEquals("2014-03-31", GraphCleaningFunctions.doCleanDate("03/31/2014").get()); - assertEquals("1971-08-21", GraphCleaningFunctions.doCleanDate("08/21/71").get()); - assertEquals("1971-01-08", GraphCleaningFunctions.doCleanDate("8/1/71").get()); - assertEquals("2014-08-04", GraphCleaningFunctions.doCleanDate("4/8/2014 22:05").get()); - assertEquals("2014-08-04", GraphCleaningFunctions.doCleanDate("04/08/2014 22:05").get()); - assertEquals("2014-08-04", GraphCleaningFunctions.doCleanDate("4/8/14 22:05").get()); - assertEquals("2014-02-04", GraphCleaningFunctions.doCleanDate("04/2/2014 03:00:51").get()); - assertEquals("1965-08-08", GraphCleaningFunctions.doCleanDate("8/8/1965 12:00:00 AM").get()); - assertEquals("1965-08-08", GraphCleaningFunctions.doCleanDate("8/8/1965 01:00:01 PM").get()); - assertEquals("1965-08-08", GraphCleaningFunctions.doCleanDate("8/8/1965 01:00 PM").get()); - assertEquals("1965-08-08", GraphCleaningFunctions.doCleanDate("8/8/1965 1:00 PM").get()); - assertEquals("1965-08-08", GraphCleaningFunctions.doCleanDate("8/8/1965 12:00 AM").get()); - assertEquals("2014-02-04", GraphCleaningFunctions.doCleanDate("4/02/2014 03:00:51").get()); - assertEquals("2012-03-19", GraphCleaningFunctions.doCleanDate("03/19/2012 10:11:59").get()); - assertEquals("2012-03-19", GraphCleaningFunctions.doCleanDate("03/19/2012 10:11:59.3186369").get()); - assertEquals("2014-03-31", GraphCleaningFunctions.doCleanDate("2014/3/31").get()); - assertEquals("2014-03-31", GraphCleaningFunctions.doCleanDate("2014/03/31").get()); - assertEquals("2014-04-08", GraphCleaningFunctions.doCleanDate("2014/4/8 22:05").get()); - assertEquals("2014-04-08", GraphCleaningFunctions.doCleanDate("2014/04/08 22:05").get()); - assertEquals("2014-04-02", GraphCleaningFunctions.doCleanDate("2014/04/2 03:00:51").get()); - assertEquals("2014-04-02", GraphCleaningFunctions.doCleanDate("2014/4/02 03:00:51").get()); - assertEquals("2012-03-19", GraphCleaningFunctions.doCleanDate("2012/03/19 10:11:59").get()); - assertEquals("2012-03-19", GraphCleaningFunctions.doCleanDate("2012/03/19 10:11:59.3186369").get()); - assertEquals("2014-04-08", GraphCleaningFunctions.doCleanDate("2014年04月08日").get()); - assertEquals("2006-01-02", GraphCleaningFunctions.doCleanDate("2006-01-02T15:04:05+0000").get()); - assertEquals("2009-08-13", GraphCleaningFunctions.doCleanDate("2009-08-12T22:15:09-07:00").get()); - assertEquals("2009-08-12", GraphCleaningFunctions.doCleanDate("2009-08-12T22:15:09").get()); - assertEquals("2009-08-13", GraphCleaningFunctions.doCleanDate("2009-08-12T22:15:09Z").get()); - assertEquals("2014-04-26", GraphCleaningFunctions.doCleanDate("2014-04-26 17:24:37.3186369").get()); - assertEquals("2012-08-03", GraphCleaningFunctions.doCleanDate("2012-08-03 18:31:59.257000000").get()); - assertEquals("2014-04-26", GraphCleaningFunctions.doCleanDate("2014-04-26 17:24:37.123").get()); - assertEquals("2013-04-01", GraphCleaningFunctions.doCleanDate("2013-04-01 22:43").get()); - assertEquals("2013-04-01", GraphCleaningFunctions.doCleanDate("2013-04-01 22:43:22").get()); - assertEquals("2014-12-16", GraphCleaningFunctions.doCleanDate("2014-12-16 06:20:00 UTC").get()); - assertEquals("2014-12-16", GraphCleaningFunctions.doCleanDate("2014-12-16 06:20:00 GMT").get()); - assertEquals("2014-04-26", GraphCleaningFunctions.doCleanDate("2014-04-26 05:24:37 PM").get()); - assertEquals("2014-04-26", GraphCleaningFunctions.doCleanDate("2014-04-26 13:13:43 +0800").get()); - assertEquals("2014-04-26", GraphCleaningFunctions.doCleanDate("2014-04-26 13:13:43 +0800 +08").get()); - assertEquals("2014-04-26", GraphCleaningFunctions.doCleanDate("2014-04-26 13:13:44 +09:00").get()); - assertEquals("2012-08-03", GraphCleaningFunctions.doCleanDate("2012-08-03 18:31:59.257000000 +0000 UTC").get()); - assertEquals("2015-09-30", GraphCleaningFunctions.doCleanDate("2015-09-30 18:48:56.35272715 +0000 UTC").get()); - assertEquals("2015-02-18", GraphCleaningFunctions.doCleanDate("2015-02-18 00:12:00 +0000 GMT").get()); - assertEquals("2015-02-18", GraphCleaningFunctions.doCleanDate("2015-02-18 00:12:00 +0000 UTC").get()); + GraphCleaningFunctions.cleanDate("Fri Jul 03 2015 18:04:07 GMT+0100 (GMT Daylight Time)")); + assertEquals("2012-09-17", GraphCleaningFunctions.cleanDate("September 17, 2012 10:09am")); + assertEquals("2012-09-17", GraphCleaningFunctions.cleanDate("September 17, 2012 at 10:09am PST-08")); + assertEquals("2012-09-17", GraphCleaningFunctions.cleanDate("September 17, 2012, 10:10:09")); + assertEquals("1970-10-07", GraphCleaningFunctions.cleanDate("October 7, 1970")); + assertEquals("1970-10-07", GraphCleaningFunctions.cleanDate("October 7th, 1970")); + assertEquals("2006-02-12", GraphCleaningFunctions.cleanDate("12 Feb 2006, 19:17")); + assertEquals("2006-02-12", GraphCleaningFunctions.cleanDate("12 Feb 2006 19:17")); + assertEquals("1970-10-07", GraphCleaningFunctions.cleanDate("7 oct 70")); + assertEquals("1970-10-07", GraphCleaningFunctions.cleanDate("7 oct 1970")); + assertEquals("2013-02-03", GraphCleaningFunctions.cleanDate("03 February 2013")); + assertEquals("2013-07-01", GraphCleaningFunctions.cleanDate("1 July 2013")); + assertEquals("2013-02-03", GraphCleaningFunctions.cleanDate("2013-Feb-03")); + assertEquals("2014-03-31", GraphCleaningFunctions.cleanDate("3/31/2014")); + assertEquals("2014-03-31", GraphCleaningFunctions.cleanDate("03/31/2014")); + assertEquals("1971-08-21", GraphCleaningFunctions.cleanDate("08/21/71")); + assertEquals("1971-01-08", GraphCleaningFunctions.cleanDate("8/1/71")); + assertEquals("2014-08-04", GraphCleaningFunctions.cleanDate("4/8/2014 22:05")); + assertEquals("2014-08-04", GraphCleaningFunctions.cleanDate("04/08/2014 22:05")); + assertEquals("2014-08-04", GraphCleaningFunctions.cleanDate("4/8/14 22:05")); + assertEquals("2014-02-04", GraphCleaningFunctions.cleanDate("04/2/2014 03:00:51")); + assertEquals("1965-08-08", GraphCleaningFunctions.cleanDate("8/8/1965 12:00:00 AM")); + assertEquals("1965-08-08", GraphCleaningFunctions.cleanDate("8/8/1965 01:00:01 PM")); + assertEquals("1965-08-08", GraphCleaningFunctions.cleanDate("8/8/1965 01:00 PM")); + assertEquals("1965-08-08", GraphCleaningFunctions.cleanDate("8/8/1965 1:00 PM")); + assertEquals("1965-08-08", GraphCleaningFunctions.cleanDate("8/8/1965 12:00 AM")); + assertEquals("2014-02-04", GraphCleaningFunctions.cleanDate("4/02/2014 03:00:51")); + assertEquals("2012-03-19", GraphCleaningFunctions.cleanDate("03/19/2012 10:11:59")); + assertEquals("2012-03-19", GraphCleaningFunctions.cleanDate("03/19/2012 10:11:59.3186369")); + assertEquals("2014-03-31", GraphCleaningFunctions.cleanDate("2014/3/31")); + assertEquals("2014-03-31", GraphCleaningFunctions.cleanDate("2014/03/31")); + assertEquals("2014-04-08", GraphCleaningFunctions.cleanDate("2014/4/8 22:05")); + assertEquals("2014-04-08", GraphCleaningFunctions.cleanDate("2014/04/08 22:05")); + assertEquals("2014-04-02", GraphCleaningFunctions.cleanDate("2014/04/2 03:00:51")); + assertEquals("2014-04-02", GraphCleaningFunctions.cleanDate("2014/4/02 03:00:51")); + assertEquals("2012-03-19", GraphCleaningFunctions.cleanDate("2012/03/19 10:11:59")); + assertEquals("2012-03-19", GraphCleaningFunctions.cleanDate("2012/03/19 10:11:59.3186369")); + assertEquals("2014-04-08", GraphCleaningFunctions.cleanDate("2014年04月08日")); + assertEquals("2006-01-02", GraphCleaningFunctions.cleanDate("2006-01-02T15:04:05+0000")); + assertEquals("2009-08-13", GraphCleaningFunctions.cleanDate("2009-08-12T22:15:09-07:00")); + assertEquals("2009-08-12", GraphCleaningFunctions.cleanDate("2009-08-12T22:15:09")); + assertEquals("2014-04-26", GraphCleaningFunctions.cleanDate("2014-04-26 17:24:37.3186369")); + assertEquals("2012-08-03", GraphCleaningFunctions.cleanDate("2012-08-03 18:31:59.257000000")); + assertEquals("2014-04-26", GraphCleaningFunctions.cleanDate("2014-04-26 17:24:37.123")); + assertEquals("2013-04-01", GraphCleaningFunctions.cleanDate("2013-04-01 22:43")); + assertEquals("2013-04-01", GraphCleaningFunctions.cleanDate("2013-04-01 22:43:22")); + assertEquals("2014-12-16", GraphCleaningFunctions.cleanDate("2014-12-16 06:20:00 UTC")); + assertEquals("2014-12-16", GraphCleaningFunctions.cleanDate("2014-12-16 06:20:00 GMT")); + assertEquals("2014-04-26", GraphCleaningFunctions.cleanDate("2014-04-26 05:24:37 PM")); + assertEquals("2014-04-26", GraphCleaningFunctions.cleanDate("2014-04-26 13:13:43 +0800")); + assertEquals("2014-04-26", GraphCleaningFunctions.cleanDate("2014-04-26 13:13:43 +0800 +08")); + assertEquals("2014-04-26", GraphCleaningFunctions.cleanDate("2014-04-26 13:13:44 +09:00")); + assertEquals("2012-08-03", GraphCleaningFunctions.cleanDate("2012-08-03 18:31:59.257000000 +0000 UTC")); + assertEquals("2015-09-30", GraphCleaningFunctions.cleanDate("2015-09-30 18:48:56.35272715 +0000 UTC")); + assertEquals("2015-02-18", GraphCleaningFunctions.cleanDate("2015-02-18 00:12:00 +0000 GMT")); + assertEquals("2015-02-18", GraphCleaningFunctions.cleanDate("2015-02-18 00:12:00 +0000 UTC")); assertEquals( - "2015-02-08", GraphCleaningFunctions.doCleanDate("2015-02-08 03:02:00 +0300 MSK m=+0.000000001").get()); + "2015-02-08", GraphCleaningFunctions.cleanDate("2015-02-08 03:02:00 +0300 MSK m=+0.000000001")); assertEquals( - "2015-02-08", GraphCleaningFunctions.doCleanDate("2015-02-08 03:02:00.001 +0300 MSK m=+0.000000001").get()); - assertEquals("2017-07-19", GraphCleaningFunctions.doCleanDate("2017-07-19 03:21:51+00:00").get()); - assertEquals("2014-04-26", GraphCleaningFunctions.doCleanDate("2014-04-26").get()); - assertEquals("2014-04-01", GraphCleaningFunctions.doCleanDate("2014-04").get()); - assertEquals("2014-01-01", GraphCleaningFunctions.doCleanDate("2014").get()); - assertEquals("2014-05-11", GraphCleaningFunctions.doCleanDate("2014-05-11 08:20:13,787").get()); - assertEquals("2014-03-31", GraphCleaningFunctions.doCleanDate("3.31.2014").get()); - assertEquals("2014-03-31", GraphCleaningFunctions.doCleanDate("03.31.2014").get()); - assertEquals("1971-08-21", GraphCleaningFunctions.doCleanDate("08.21.71").get()); - assertEquals("2014-03-01", GraphCleaningFunctions.doCleanDate("2014.03").get()); - assertEquals("2014-03-30", GraphCleaningFunctions.doCleanDate("2014.03.30").get()); - assertEquals("2014-06-01", GraphCleaningFunctions.doCleanDate("20140601").get()); - assertEquals("2014-07-22", GraphCleaningFunctions.doCleanDate("20140722105203").get()); - assertEquals("2012-03-19", GraphCleaningFunctions.doCleanDate("1332151919").get()); - assertEquals("2013-11-12", GraphCleaningFunctions.doCleanDate("1384216367189").get()); - assertEquals("2013-11-12", GraphCleaningFunctions.doCleanDate("1384216367111222").get()); - assertEquals("2013-11-12", GraphCleaningFunctions.doCleanDate("1384216367111222333").get()); + "2015-02-08", GraphCleaningFunctions.cleanDate("2015-02-08 03:02:00.001 +0300 MSK m=+0.000000001")); + assertEquals("2017-07-19", GraphCleaningFunctions.cleanDate("2017-07-19 03:21:51+00:00")); + assertEquals("2014-04-26", GraphCleaningFunctions.cleanDate("2014-04-26")); + assertEquals("2014-04-01", GraphCleaningFunctions.cleanDate("2014-04")); + assertEquals("2014-01-01", GraphCleaningFunctions.cleanDate("2014")); + assertEquals("2014-05-11", GraphCleaningFunctions.cleanDate("2014-05-11 08:20:13,787")); + assertEquals("2014-03-31", GraphCleaningFunctions.cleanDate("3.31.2014")); + assertEquals("2014-03-31", GraphCleaningFunctions.cleanDate("03.31.2014")); + assertEquals("1971-08-21", GraphCleaningFunctions.cleanDate("08.21.71")); + assertEquals("2014-03-01", GraphCleaningFunctions.cleanDate("2014.03")); + assertEquals("2014-03-30", GraphCleaningFunctions.cleanDate("2014.03.30")); + assertEquals("2014-06-01", GraphCleaningFunctions.cleanDate("20140601")); + assertEquals("2014-07-22", GraphCleaningFunctions.cleanDate("20140722105203")); + assertEquals("2012-03-19", GraphCleaningFunctions.cleanDate("1332151919")); + assertEquals("2013-11-12", GraphCleaningFunctions.cleanDate("1384216367189")); + assertEquals("2013-11-12", GraphCleaningFunctions.cleanDate("1384216367111222")); + assertEquals("2013-11-12", GraphCleaningFunctions.cleanDate("1384216367111222333")); } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java index b1be7f10a..924d53593 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java @@ -27,15 +27,7 @@ import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_PROJECT; import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_RESULT; import static eu.dnetlib.dhp.schema.common.ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE; import static eu.dnetlib.dhp.schema.common.ModelConstants.USER_CLAIM; -import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.asString; -import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.createOpenaireId; -import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.dataInfo; -import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.field; -import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.journal; -import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.listFields; -import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.listKeyValues; -import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.qualifier; -import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.structuredProperty; +import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.*; import java.io.Closeable; import java.io.IOException; @@ -245,22 +237,20 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i ds .setOriginalId( Arrays - .asList((String[]) rs.getArray("identities").getArray()) + .asList((String[]) rs.getArray("originalid").getArray()) .stream() .filter(StringUtils::isNotBlank) .collect(Collectors.toList())); - ds - .setCollectedfrom( - listKeyValues( - createOpenaireId(10, rs.getString("collectedfromid"), true), - rs.getString("collectedfromname"))); - ds.setPid(new ArrayList<>()); + ds.setCollectedfrom(prepareCollectedfrom(rs.getArray("collectedfrom"))); + ds.setPid(prepareListOfStructProps(rs.getArray("pid"), info)); ds.setDateofcollection(asString(rs.getDate("dateofcollection"))); ds.setDateoftransformation(null); // Value not returned by the SQL query ds.setExtraInfo(new ArrayList<>()); // Values not present in the DB ds.setOaiprovenance(null); // Values not present in the DB ds.setDatasourcetype(prepareQualifierSplitting(rs.getString("datasourcetype"))); ds.setDatasourcetypeui(prepareQualifierSplitting(rs.getString("datasourcetypeui"))); + ds.setEosctype(prepareQualifierSplitting(rs.getString("eosctype"))); + ds.setEoscdatasourcetype(prepareQualifierSplitting(rs.getString("eoscdatasourcetype"))); ds.setOpenairecompatibility(prepareQualifierSplitting(rs.getString("openairecompatibility"))); ds.setOfficialname(field(rs.getString("officialname"), info)); ds.setEnglishname(field(rs.getString("englishname"), info)); @@ -277,6 +267,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i ds.setOdnumberofitemsdate(field(asString(rs.getDate("odnumberofitemsdate")), info)); ds.setOdpolicies(field(rs.getString("odpolicies"), info)); ds.setOdlanguages(prepareListFields(rs.getArray("odlanguages"), info)); + ds.setLanguages(listValues(rs.getArray("languages"))); ds.setOdcontenttypes(prepareListFields(rs.getArray("odcontenttypes"), info)); ds.setAccessinfopackage(prepareListFields(rs.getArray("accessinfopackage"), info)); ds.setReleasestartdate(field(asString(rs.getDate("releasestartdate")), info)); @@ -289,8 +280,9 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i ds.setDatabaseaccessrestriction(field(rs.getString("databaseaccessrestriction"), info)); ds.setDatauploadrestriction(field(rs.getString("datauploadrestriction"), info)); ds.setVersioning(field(rs.getBoolean("versioning"), info)); + ds.setVersioncontrol(rs.getBoolean("versioncontrol")); ds.setCitationguidelineurl(field(rs.getString("citationguidelineurl"), info)); - ds.setQualitymanagementkind(field(rs.getString("qualitymanagementkind"), info)); + ds.setPidsystems(field(rs.getString("pidsystems"), info)); ds.setCertificates(field(rs.getString("certificates"), info)); ds.setPolicies(new ArrayList<>()); // The sql query returns an empty array @@ -299,13 +291,20 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i journal( rs.getString("officialname"), rs.getString("issnPrinted"), rs.getString("issnOnline"), rs.getString("issnLinking"), info)); // Journal - ds.setDataInfo(info); - ds.setLastupdatetimestamp(lastUpdateTimestamp); + ds.setResearchentitytypes(listValues(rs.getArray("researchentitytypes"))); + ds.setProvidedproducttypes(listValues(rs.getArray("providedproducttypes"))); ds.setJurisdiction(prepareQualifierSplitting(rs.getString("jurisdiction"))); ds.setThematic(rs.getBoolean("thematic")); ds.setKnowledgegraph(rs.getBoolean("knowledgegraph")); ds.setContentpolicies(prepareListOfQualifiers(rs.getArray("contentpolicies"))); + ds.setSubmissionpolicyurl(rs.getString("submissionpolicyurl")); + ds.setPreservationpolicyurl(rs.getString("preservationpolicyurl")); + ds.setResearchproductaccesspolicies(listValues(rs.getArray("researchproductaccesspolicies"))); + ds + .setResearchproductmetadataaccesspolicies( + listValues(rs.getArray("researchproductmetadataaccesspolicies"))); + ds.setConsenttermsofuse(rs.getBoolean("consenttermsofuse")); ds.setFulltextdownload(rs.getBoolean("fulltextdownload")); ds @@ -313,8 +312,18 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i Optional .ofNullable( rs.getDate("consenttermsofusedate")) - .map(c -> c.toString()) + .map(java.sql.Date::toString) .orElse(null)); + ds + .setLastconsenttermsofusedate( + Optional + .ofNullable( + rs.getDate("lastconsenttermsofusedate")) + .map(java.sql.Date::toString) + .orElse(null)); + + ds.setDataInfo(info); + ds.setLastupdatetimestamp(lastUpdateTimestamp); return Arrays.asList(ds); } catch (final Exception e) { @@ -603,6 +612,32 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i String.format("%.3f", trust)); } + private List prepareCollectedfrom(Array values) throws SQLException { + if (Objects.isNull(values)) { + return null; + } + return Arrays + .stream((String[]) values.getArray()) + .filter(Objects::nonNull) + .distinct() + .map(s -> keyValueSplitting(s, "@@@")) + .collect(Collectors.toList()); + } + + public static KeyValue keyValueSplitting(final String s, String separator) { + if (StringUtils.isBlank(s)) { + return null; + } + final String[] arr = s.split(separator); + if (arr.length != 2) { + return null; + } + KeyValue kv = new KeyValue(); + kv.setKey(createOpenaireId(10, arr[0], true)); + kv.setValue(arr[1]); + return kv; + } + private Qualifier prepareQualifierSplitting(final String s) { if (StringUtils.isBlank(s)) { return null; diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql index 603b1e9b2..3dbb46eaa 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql @@ -1,6 +1,7 @@ SELECT d.id AS datasourceid, - array_remove(d.id || array_agg(distinct di.pid) filter (where di.pid like 'piwik%') || array_agg(distinct dds.duplicate), NULL) AS identities, + array_remove(d.id || array_agg(distinct CASE WHEN dp.pid like 'piwik%' THEN di.pid ELSE NULL END) || array_agg(distinct dds.duplicate), NULL) AS originalid, + array_remove(array_agg(distinct CASE WHEN di.pid NOT LIKE 'piwik%' THEN di.pid||'###'||di.issuertype||'@@@'||'dnet:pid_types' ELSE NULL END), NULL) as pid, d.officialname AS officialname, d.englishname AS englishname, d.contactemail AS contactemail, @@ -9,8 +10,8 @@ SELECT THEN 'openaire-cris_1.1@@@dnet:datasourceCompatibilityLevel' WHEN (array_agg(DISTINCT COALESCE (a.compatibility_override, a.compatibility):: TEXT) @> ARRAY ['openaire4.0']) - THEN - 'openaire4.0@@@dnet:datasourceCompatibilityLevel' + THEN + 'openaire4.0@@@dnet:datasourceCompatibilityLevel' WHEN (array_agg(DISTINCT COALESCE (a.compatibility_override, a.compatibility):: TEXT) @> ARRAY ['driver', 'openaire2.0']) THEN 'driver-openaire2.0@@@dnet:datasourceCompatibilityLevel' @@ -40,29 +41,28 @@ SELECT END AS openairecompatibility, d.websiteurl AS websiteurl, d.logourl AS logourl, - array_agg(DISTINCT CASE WHEN a.protocol = 'oai' and last_aggregation_date is not null THEN a.baseurl ELSE NULL END) AS accessinfopackage, + array_remove(array_agg(DISTINCT CASE WHEN a.protocol = 'oai' and last_aggregation_date is not null THEN a.baseurl ELSE NULL END), NULL) AS accessinfopackage, d.latitude AS latitude, d.longitude AS longitude, d.namespaceprefix AS namespaceprefix, NULL AS odnumberofitems, NULL AS odnumberofitemsdate, - (SELECT array_agg(s|| '###keywords@@@dnet:subject_classification_typologies') FROM UNNEST( ARRAY( SELECT trim(s) - FROM unnest(string_to_array(d.subjects, '@@')) AS s)) AS s) AS subjects, + FROM unnest(string_to_array(d.subjects, '@@')) AS s)) AS s) AS subjects, d.description AS description, NULL AS odpolicies, - ARRAY(SELECT trim(s) - FROM unnest(string_to_array(d.languages, ',')) AS s) AS odlanguages, - ARRAY(SELECT trim(s) - FROM unnest(string_to_array(d.languages, ',')) AS s) AS languages, + array_remove(ARRAY(SELECT trim(s) + FROM unnest(string_to_array(regexp_replace(d.languages, '{|}|"', '', 'g') ',')) AS s), '{}') AS odlanguages, + array_remove(ARRAY(SELECT trim(s) + FROM unnest(string_to_array(regexp_replace(d.languages, '{|}|"', '', 'g') ',')) AS s), '{}') AS languages, -- Term provided only by OpenDOAR: -- probably updating the TR it could be replaced by research_entity_types[] -- But a study on the vocabulary terms is needed - -- REMOVED: ARRAY(SELECT trim(s) FROM unnest(string_to_array(d.od_contenttypes, '-')) AS s) AS odcontenttypes, + -- REMOVED: ARRAY(SELECT trim(s) FROM unnest(string_to_array(d.od_contenttypes, '-')) AS s) AS odcontenttypes, false AS inferred, false AS deletedbyinference, @@ -81,20 +81,24 @@ SELECT d.datauploadtype AS datauploadtype, d.databaseaccessrestriction AS databaseaccessrestriction, d.datauploadrestriction AS datauploadrestriction, - -- REPLACED BY version_control : d.versioning AS versioning, + -- REPLACED BY version_control : d.versioning AS versioning, d.version_control AS versioning, d.version_control AS versioncontrol, d.citationguidelineurl AS citationguidelineurl, - - d.pidsystems AS pidsystems, + array_to_string(array_agg(distinct dps.scheme), ' ') AS pidsystems, d.certificates AS certificates, ARRAY[]::text[] AS policies, - array_remove(dc.id||'@@@'||dc.officialname || array_agg(distinct dds_cf.id||'@@@'||dds_cf.officialname), NULL) AS collectedfrom, - + array_remove( + array( + select distinct cf + from unnest( + dc.id||'@@@'||dc.officialname || array_agg(distinct dds_cf.id||'@@@'||dds_cf.officialname) + ) as cf), + NULL) AS collectedfrom, d._typology_to_remove_||'@@@dnet:datasource_typologies' AS datasourcetype, + d._typology_to_remove_||'@@@dnet:datasource_typologies_ui' AS datasourcetypeui, d.eosc_type||'@@@dnet:eosc_types' AS eosctype, d.eosc_datasource_type||'@@@dnet:eosc_datasource_types' AS eoscdatasourcetype, - 'sysimport:crosswalk:entityregistry@@@dnet:provenance_actions' AS provenanceaction, d.issn AS issnPrinted, d.eissn AS issnOnline, d.lissn AS issnLinking, @@ -107,19 +111,20 @@ SELECT d.thematic AS thematic, -- REMOVED ???: d.knowledge_graph AS knowledgegraph, array(select unnest(d.content_policies)||'@@@eosc:contentpolicies') AS contentpolicies, - d.submission_policy_url AS submissionpolicyurl, - d.preservation_policy_url AS preservationpolicyurl, - d.research_product_access_policies AS researchproductaccesspolicies, - d.research_product_metadata_access_policies AS researchproductmetadataaccesspolicies + nullif(trim(d.submission_policy_url), '') AS submissionpolicyurl, + nullif(trim(d.preservation_policy_url), '') AS preservationpolicyurl, + array_remove(d.research_product_access_policies, '') AS researchproductaccesspolicies, + array_remove(d.research_product_metadata_access_policies, '') AS researchproductmetadataaccesspolicies FROM dsm_services d LEFT OUTER JOIN dsm_services dc on (d.collectedfrom = dc.id) LEFT OUTER JOIN dsm_api a ON (d.id = a.service) -LEFT OUTER JOIN dsm_servicepids di ON (d.id = di.service) +LEFT OUTER JOIN dsm_servicepids dp ON (d.id = dp.service) +LEFT OUTER JOIN dsm_identities di ON (dp.pid = di.pid) LEFT OUTER JOIN dsm_dedup_services dds ON (d.id = dds.id) LEFT OUTER JOIN dsm_services dds_dup ON (dds.duplicate = dds_dup.id) LEFT OUTER JOIN dsm_services dds_cf ON (dds_dup.collectedfrom = dds_cf.id) - +LEFT OUTER JOIN dsm_pid_systems dps ON (d.id = dps.service) WHERE d.dedup_main_service = true @@ -150,7 +155,6 @@ GROUP BY d.version_control, d.citationguidelineurl, -- REMOVED: d.qualitymanagementkind, - d.pidsystems, d.certificates, dc.id, dc.officialname, diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java index 488a1f70b..390db0e4e 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java @@ -12,8 +12,11 @@ import java.sql.Array; import java.sql.Date; import java.sql.ResultSet; import java.sql.SQLException; +import java.util.HashSet; import java.util.List; import java.util.Objects; +import java.util.Optional; +import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; @@ -28,12 +31,7 @@ import com.fasterxml.jackson.core.type.TypeReference; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; -import eu.dnetlib.dhp.schema.oaf.Datasource; -import eu.dnetlib.dhp.schema.oaf.Oaf; -import eu.dnetlib.dhp.schema.oaf.Organization; -import eu.dnetlib.dhp.schema.oaf.Project; -import eu.dnetlib.dhp.schema.oaf.Relation; -import eu.dnetlib.dhp.schema.oaf.Result; +import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; @ExtendWith(MockitoExtension.class) @@ -64,7 +62,7 @@ public class MigrateDbEntitiesApplicationTest { @Test public void testProcessService() throws Exception { - final List fields = prepareMocks("datasources_resultset_entry.json"); + final List fields = prepareMocks("services_resultset_entry.json"); final List list = app.processService(rs); assertEquals(1, list.size()); @@ -72,13 +70,17 @@ public class MigrateDbEntitiesApplicationTest { final Datasource ds = (Datasource) list.get(0); assertValidId(ds.getId()); - assertValidId(ds.getCollectedfrom().get(0).getKey()); + ds + .getCollectedfrom() + .stream() + .map(KeyValue::getKey) + .forEach(dsId -> assertValidId(dsId)); assertEquals(getValueAsString("officialname", fields), ds.getOfficialname().getValue()); assertEquals(getValueAsString("englishname", fields), ds.getEnglishname().getValue()); - assertEquals(getValueAsString("contactemail", fields), ds.getContactemail().getValue()); assertEquals(getValueAsString("websiteurl", fields), ds.getWebsiteurl().getValue()); + assertEquals(getValueAsString("logourl", fields), ds.getLogourl()); + assertEquals(getValueAsString("contactemail", fields), ds.getContactemail().getValue()); assertEquals(getValueAsString("namespaceprefix", fields), ds.getNamespaceprefix().getValue()); - assertEquals(getValueAsString("collectedfromname", fields), ds.getCollectedfrom().get(0).getValue()); assertEquals(getValueAsString("officialname", fields), ds.getJournal().getName()); assertEquals(getValueAsString("issnPrinted", fields), ds.getJournal().getIssnPrinted()); assertEquals(getValueAsString("issnOnline", fields), ds.getJournal().getIssnOnline()); @@ -90,19 +92,103 @@ public class MigrateDbEntitiesApplicationTest { assertEquals("pubsrepository::journal", ds.getDatasourcetypeui().getClassid()); assertEquals("dnet:datasource_typologies_ui", ds.getDatasourcetypeui().getSchemeid()); + assertEquals("Data Source", ds.getEosctype().getClassid()); + assertEquals("Data Source", ds.getEosctype().getClassname()); + assertEquals("dnet:eosc_types", ds.getEosctype().getSchemeid()); + assertEquals("dnet:eosc_types", ds.getEosctype().getSchemename()); + + assertEquals("Journal archive", ds.getEoscdatasourcetype().getClassid()); + assertEquals("Journal archive", ds.getEoscdatasourcetype().getClassname()); + assertEquals("dnet:eosc_datasource_types", ds.getEoscdatasourcetype().getSchemeid()); + assertEquals("dnet:eosc_datasource_types", ds.getEoscdatasourcetype().getSchemename()); + + assertEquals("openaire4.0", ds.getOpenairecompatibility().getClassid()); + assertEquals("openaire4.0", ds.getOpenairecompatibility().getClassname()); + assertEquals("dnet:datasourceCompatibilityLevel", ds.getOpenairecompatibility().getSchemeid()); + assertEquals("dnet:datasourceCompatibilityLevel", ds.getOpenairecompatibility().getSchemename()); + + assertEquals(getValueAsDouble("latitude", fields).toString(), ds.getLatitude().getValue()); + assertEquals(getValueAsDouble("longitude", fields).toString(), ds.getLongitude().getValue()); + assertEquals(getValueAsString("dateofvalidation", fields), ds.getDateofvalidation()); + + assertEquals(getValueAsString("description", fields), ds.getDescription().getValue()); + + // TODO assertEquals(getValueAsString("subjects", fields), ds.getSubjects()); + + assertEquals("0.0", ds.getOdnumberofitems().getValue()); + assertEquals(getValueAsString("odnumberofitemsdate", fields), ds.getOdnumberofitemsdate()); + assertEquals(getValueAsString("odpolicies", fields), ds.getOdpolicies()); + + assertEquals( + getValueAsList("odlanguages", fields), + ds.getOdlanguages().stream().map(Field::getValue).collect(Collectors.toList())); + assertEquals(getValueAsList("languages", fields), ds.getLanguages()); + assertEquals( + getValueAsList("odcontenttypes", fields), + ds.getOdcontenttypes().stream().map(Field::getValue).collect(Collectors.toList())); + assertEquals( + getValueAsList("accessinfopackage", fields), + ds.getAccessinfopackage().stream().map(Field::getValue).collect(Collectors.toList())); + assertEquals(getValueAsString("releasestartdate", fields), ds.getReleasestartdate()); + assertEquals(getValueAsString("releaseenddate", fields), ds.getReleasestartdate()); + assertEquals(getValueAsString("missionstatementurl", fields), ds.getMissionstatementurl()); + + assertEquals(false, ds.getDataprovider().getValue()); + assertEquals(false, ds.getServiceprovider().getValue()); + + assertEquals(getValueAsString("databaseaccesstype", fields), ds.getDatabaseaccesstype()); + assertEquals(getValueAsString("datauploadtype", fields), ds.getDatauploadtype()); + assertEquals(getValueAsString("databaseaccessrestriction", fields), ds.getDatabaseaccessrestriction()); + assertEquals(getValueAsString("datauploadrestriction", fields), ds.getDatauploadrestriction()); + + assertEquals(false, ds.getVersioning().getValue()); + assertEquals(false, ds.getVersioncontrol()); + + assertEquals(getValueAsString("citationguidelineurl", fields), ds.getCitationguidelineurl()); + assertEquals(getValueAsString("pidsystems", fields), ds.getPidsystems()); + assertEquals(getValueAsString("certificates", fields), ds.getCertificates()); + + assertEquals(getValueAsList("researchentitytypes", fields), ds.getResearchentitytypes()); + assertEquals(getValueAsList("providedproducttypes", fields), ds.getProvidedproducttypes()); + assertEquals("National", ds.getJurisdiction().getClassid()); assertEquals("eosc:jurisdictions", ds.getJurisdiction().getSchemeid()); assertTrue(ds.getThematic()); assertTrue(ds.getKnowledgegraph()); - assertEquals(1, ds.getContentpolicies().size()); - assertEquals("Journal article", ds.getContentpolicies().get(0).getClassid()); - assertEquals("eosc:contentpolicies", ds.getContentpolicies().get(0).getSchemeid()); + HashSet cpSchemeId = ds + .getContentpolicies() + .stream() + .map(Qualifier::getSchemeid) + .collect(Collectors.toCollection(HashSet::new)); + assertTrue(cpSchemeId.size() == 1); + assertTrue(cpSchemeId.contains("eosc:contentpolicies")); + HashSet cpSchemeName = ds + .getContentpolicies() + .stream() + .map(Qualifier::getSchemename) + .collect(Collectors.toCollection(HashSet::new)); + assertTrue(cpSchemeName.size() == 1); + assertTrue(cpSchemeName.contains("eosc:contentpolicies")); + assertEquals(2, ds.getContentpolicies().size()); + assertEquals("Taxonomic classification", ds.getContentpolicies().get(0).getClassid()); + assertEquals("Resource collection", ds.getContentpolicies().get(1).getClassid()); + + assertEquals(getValueAsString("submissionpolicyurl", fields), ds.getSubmissionpolicyurl()); + assertEquals(getValueAsString("preservationpolicyurl", fields), ds.getPreservationpolicyurl()); + + assertEquals( + getValueAsList("researchproductaccesspolicies", fields), + ds.getResearchproductaccesspolicies()); + assertEquals( + getValueAsList("researchproductmetadataaccesspolicies", fields), + ds.getResearchproductmetadataaccesspolicies()); assertEquals(true, ds.getConsenttermsofuse()); assertEquals(true, ds.getFulltextdownload()); assertEquals("2022-03-11", ds.getConsenttermsofusedate()); + assertEquals("2022-03-11", ds.getLastconsenttermsofusedate()); } @Test @@ -356,18 +442,31 @@ public class MigrateDbEntitiesApplicationTest { } private Float getValueAsFloat(final String name, final List fields) { - return new Float(getValueAs(name, fields).toString()); + final Object value = getValueAs(name, fields); + return value != null ? new Float(value.toString()) : null; + } + + private Double getValueAsDouble(final String name, final List fields) { + final Object value = getValueAs(name, fields); + return value != null ? new Double(value.toString()) : null; + } + + private Integer getValueAsInt(final String name, final List fields) { + final Object value = getValueAs(name, fields); + return value != null ? new Integer(value.toString()) : null; } private T getValueAs(final String name, final List fields) { - return fields + final Optional field = fields .stream() .filter(f -> f.getField().equals(name)) - .map(TypedField::getValue) - .filter(Objects::nonNull) - .map(o -> (T) o) .findFirst() - .get(); + .map(TypedField::getValue) + .map(o -> (T) o); + if (!field.isPresent()) { + return null; + } + return field.get(); } private List getValueAsList(final String name, final List fields) { diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/datasources_resultset_entry.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/services_resultset_entry.json similarity index 68% rename from dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/datasources_resultset_entry.json rename to dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/services_resultset_entry.json index 11b884cde..70fad3323 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/datasources_resultset_entry.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/services_resultset_entry.json @@ -5,14 +5,47 @@ "value": "274269ac6f3b::2579-5449" }, { - "field": "identities", + "field": "originalid", "type": "array", "value": [ - "274269ac6f3b::2579-5449", + "fairsharing_::1562", "piwik:13", - null + null, + "re3data_____::r3d100010213" ] }, + { + "field": "pid", + "type": "array", + "value": [ + "r3d100010218###re3data@@@dnet:pid_types" + ] + }, + { + "field": "datasourcetype", + "type": "string", + "value": "pubsrepository::journal@@@dnet:datasource_typologies" + }, + { + "field": "datasourcetypeui", + "type": "string", + "value": "pubsrepository::journal@@@dnet:datasource_typologies_ui" + }, + { + "field": "eosctype", + "type": "string", + "value": "Data Source@@@dnet:eosc_types" + }, + { + "field": "eoscdatasourcetype", + "type": "string", + "value": "Journal archive@@@dnet:eosc_datasource_types" + }, + { + "field": "openairecompatibility", + "type": "string", + "value": "openaire4.0@@@dnet:datasourceCompatibilityLevel" + }, { "field": "officialname", "type": "string", @@ -23,16 +56,6 @@ "type": "string", "value": "Jurnal Ilmiah Pendidikan Scholastic" }, - { - "field": "contactemail", - "type": "string", - "value": "test@test.it" - }, - { - "field": "openairecompatibility", - "type": "string", - "value": "hostedBy@@@dnet:datasourceCompatibilityLevel" - }, { "field": "websiteurl", "type": "string", @@ -44,11 +67,14 @@ "value": null }, { - "field": "accessinfopackage", - "type": "array", - "value": [ - null - ] + "field": "contactemail", + "type": "string", + "value": "test@test.it" + }, + { + "field": "namespaceprefix", + "type": "string", + "value": "ojs_25795449" }, { "field": "latitude", @@ -61,9 +87,19 @@ "value": 0 }, { - "field": "namespaceprefix", + "field": "dateofvalidation", + "type": "date", + "value": null + }, + { + "field": "description", "type": "string", - "value": "ojs_25795449" + "value": "veterinary medicine" + }, + { + "field": "subjects", + "type": "array", + "value": [] }, { "field": "odnumberofitems", @@ -75,16 +111,6 @@ "type": "date", "value": null }, - { - "field": "subjects", - "type": "array", - "value": null - }, - { - "field": "description", - "type": "string", - "value": null - }, { "field": "odpolicies", "type": "string", @@ -93,7 +119,26 @@ { "field": "odlanguages", "type": "array", - "value": [] + "value": [ + "English", + "German", + "French", + "Danish", + "Norwegian", + "Swedish" + ] + }, + { + "field": "languages", + "type": "array", + "value": [ + "English", + "German", + "French", + "Danish", + "Norwegian", + "Swedish" + ] }, { "field": "odcontenttypes", @@ -103,34 +148,11 @@ ] }, { - "field": "inferred", - "type": "boolean", - "value": false - }, - { - "field": "deletedbyinference", - "type": "boolean", - "value": false - }, - { - "field": "trust", - "type": "double", - "value": 0.9 - }, - { - "field": "inferenceprovenance", - "type": "string", - "value": null - }, - { - "field": "dateofcollection", - "type": "date", - "value": "2020-01-21" - }, - { - "field": "dateofvalidation", - "type": "date", - "value": null + "field": "accessinfopackage", + "type": "array", + "value": [ + "http://www.revista.vocesdelaeducacion.com.mx/index.php/index/oai" + ] }, { "field": "releasestartdate", @@ -183,12 +205,12 @@ "value": null }, { - "field": "citationguidelineurl", - "type": "string", + "field": "versioncontrol", + "type": "boolean", "value": null }, { - "field": "qualitymanagementkind", + "field": "citationguidelineurl", "type": "string", "value": null }, @@ -208,29 +230,38 @@ "value": [] }, { - "field": "collectedfromid", - "type": "string", - "value": "openaire____::SnVybmFsIEZha3VsdGFzIFNhc3RyYSBVbml2ZXJzaXRhcyBFa2FzYWt0aQ==" + "field": "inferred", + "type": "boolean", + "value": false }, { - "field": "collectedfromname", - "type": "string", - "value": "Jurnal Fakultas Sastra Universitas Ekasakti" + "field": "deletedbyinference", + "type": "boolean", + "value": false }, { - "field": "datasourcetype", - "type": "string", - "value": "pubsrepository::journal@@@dnet:datasource_typologies" + "field": "trust", + "type": "double", + "value": 0.9 }, { - "field": "datasourcetypeui", + "field": "inferenceprovenance", "type": "string", - "value": "pubsrepository::journal@@@dnet:datasource_typologies_ui" + "value": null }, { - "field": "provenanceaction", - "type": "not_used", - "value": "sysimport:crosswalk:entityregistry@@@dnet:provenance_actions" + "field": "dateofcollection", + "type": "date", + "value": "2020-01-21" + }, + { + "field": "collectedfrom", + "type": "array", + "value": [ + "openaire____::fairsharing@@@FAIRsharing.org", + "openaire____::opendoar@@@OpenDOAR", + "openaire____::re3data@@@Registry of Research Data Repository" + ] }, { "field": "issnPrinted", @@ -247,6 +278,20 @@ "type": "string", "value": "2579-5447" }, + { + "field": "researchentitytypes", + "type": "array", + "value": [ + "Research Data" + ] + }, + { + "field": "providedproducttypes", + "type": "array", + "value": [ + + ] + }, { "field": "jurisdiction", "type": "string", @@ -266,7 +311,32 @@ "field": "contentpolicies", "type": "array", "value": [ - "Journal article@@@eosc:contentpolicies" + "Taxonomic classification@@@eosc:contentpolicies", + "Resource collection@@@eosc:contentpolicies" + ] + }, + { + "field": "submissionpolicyurl", + "type": "string", + "value": null + }, + { + "field": "preservationpolicyurl", + "type": "string", + "value": "Permanent Archiving https://datadryad.org/stash/faq" + }, + { + "field": "researchproductaccesspolicies", + "type": "array", + "value": [ + "https://100percentit.com/legal/" + ] + }, + { + "field": "researchproductmetadataaccesspolicies", + "type": "array", + "value": [ + "https://wenmr.science.uu.nl/conditions" ] }, { @@ -283,5 +353,10 @@ "field": "consenttermsofusedate", "type": "date", "value": "2022-03-11" + }, + { + "field": "lastconsenttermsofusedate", + "type": "date", + "value": "2022-03-11" } ] diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java index 5d4a831c0..0daf1c085 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java @@ -695,12 +695,6 @@ public class XmlRecordFactory implements Serializable { XmlSerializationUtils .asXmlElement("citationguidelineurl", ds.getCitationguidelineurl().getValue())); } - if (ds.getQualitymanagementkind() != null) { - metadata - .add( - XmlSerializationUtils - .asXmlElement("qualitymanagementkind", ds.getQualitymanagementkind().getValue())); - } if (ds.getPidsystems() != null) { metadata .add(XmlSerializationUtils.asXmlElement("pidsystems", ds.getPidsystems().getValue())); diff --git a/pom.xml b/pom.xml index 136b9b867..03a4496d7 100644 --- a/pom.xml +++ b/pom.xml @@ -801,7 +801,7 @@ 3.3.3 3.4.2 [2.12,3.0) - [2.10.32] + [2.11.34-eosc-SNAPSHOT] [4.0.3] [6.0.5] [3.1.6] From 05c1ea92e967185012087f3829aa11bb4a340d1e Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 29 Apr 2022 15:56:55 +0200 Subject: [PATCH 042/214] EOSC Services - added Service-specific fields in the XML record serialization --- .../raw/MigrateDbEntitiesApplicationTest.java | 6 + .../oa/provision/utils/XmlRecordFactory.java | 78 +++- .../oa/provision/XmlRecordFactoryTest.java | 11 +- .../dnetlib/dhp/oa/provision/datasource.json | 408 +++++++++++++++++- 4 files changed, 495 insertions(+), 8 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java index 390db0e4e..69552c4dc 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java @@ -75,6 +75,12 @@ public class MigrateDbEntitiesApplicationTest { .stream() .map(KeyValue::getKey) .forEach(dsId -> assertValidId(dsId)); + + assertEquals(1, ds.getPid().size()); + assertEquals("r3d100010218", ds.getPid().get(0).getValue()); + assertEquals("re3data", ds.getPid().get(0).getQualifier().getClassid()); + assertEquals("dnet:pid_types", ds.getPid().get(0).getQualifier().getSchemeid()); + assertEquals(getValueAsString("officialname", fields), ds.getOfficialname().getValue()); assertEquals(getValueAsString("englishname", fields), ds.getEnglishname().getValue()); assertEquals(getValueAsString("websiteurl", fields), ds.getWebsiteurl().getValue()); diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java index 0daf1c085..b811a7a0f 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java @@ -535,6 +535,12 @@ public class XmlRecordFactory implements Serializable { if (ds.getDatasourcetypeui() != null) { metadata.add(XmlSerializationUtils.mapQualifier("datasourcetypeui", ds.getDatasourcetypeui())); } + if (ds.getEosctype() != null) { + metadata.add(XmlSerializationUtils.mapQualifier("eosctype", ds.getEosctype())); + } + if (ds.getEoscdatasourcetype() != null) { + metadata.add(XmlSerializationUtils.mapQualifier("eoscdatasourcetype", ds.getEoscdatasourcetype())); + } if (ds.getOpenairecompatibility() != null) { metadata .add( @@ -583,6 +589,16 @@ public class XmlRecordFactory implements Serializable { metadata .add(XmlSerializationUtils.asXmlElement("description", ds.getDescription().getValue())); } + if (ds.getSubjects() != null) { + metadata + .addAll( + ds + .getSubjects() + .stream() + .filter(Objects::nonNull) + .map(sp -> XmlSerializationUtils.mapStructuredProperty("subjects", sp)) + .collect(Collectors.toList())); + } if (ds.getOdnumberofitems() != null) { metadata .add( @@ -609,6 +625,16 @@ public class XmlRecordFactory implements Serializable { .map(c -> XmlSerializationUtils.asXmlElement("odlanguages", c.getValue())) .collect(Collectors.toList())); } + if (ds.getLanguages() != null) { + metadata + .addAll( + ds + .getLanguages() + .stream() + .filter(Objects::nonNull) + .map(c -> XmlSerializationUtils.asXmlElement("languages", c)) + .collect(Collectors.toList())); + } if (ds.getOdcontenttypes() != null) { metadata .addAll( @@ -689,6 +715,12 @@ public class XmlRecordFactory implements Serializable { XmlSerializationUtils .asXmlElement("versioning", ds.getVersioning().getValue().toString())); } + if (ds.getVersioncontrol() != null) { + metadata + .add( + XmlSerializationUtils + .asXmlElement("versioncontrol", ds.getVersioncontrol().toString())); + } if (ds.getCitationguidelineurl() != null) { metadata .add( @@ -716,17 +748,24 @@ public class XmlRecordFactory implements Serializable { if (ds.getJournal() != null) { metadata.add(XmlSerializationUtils.mapJournal(ds.getJournal())); } - if (ds.getSubjects() != null) { + if (ds.getResearchentitytypes() != null) { metadata .addAll( ds - .getSubjects() + .getResearchentitytypes() .stream() - .filter(Objects::nonNull) - .map(sp -> XmlSerializationUtils.mapStructuredProperty("subjects", sp)) + .map(c -> XmlSerializationUtils.asXmlElement("researchentitytypes", c)) + .collect(Collectors.toList())); + } + if (ds.getProvidedproducttypes() != null) { + metadata + .addAll( + ds + .getProvidedproducttypes() + .stream() + .map(c -> XmlSerializationUtils.asXmlElement("providedproducttypes", c)) .collect(Collectors.toList())); } - if (ds.getJurisdiction() != null) { metadata.add(XmlSerializationUtils.mapQualifier("jurisdiction", ds.getJurisdiction())); } @@ -750,7 +789,34 @@ public class XmlRecordFactory implements Serializable { .map(q -> XmlSerializationUtils.mapQualifier("contentpolicy", q)) .collect(Collectors.toList())); } - + if (ds.getSubmissionpolicyurl() != null) { + metadata + .add(XmlSerializationUtils.asXmlElement("submissionpolicyurl", ds.getSubmissionpolicyurl())); + } + if (ds.getPreservationpolicyurl() != null) { + metadata + .add( + XmlSerializationUtils.asXmlElement("preservationpolicyurl", ds.getPreservationpolicyurl())); + } + if (ds.getResearchproductaccesspolicies() != null) { + metadata + .addAll( + ds + .getResearchproductaccesspolicies() + .stream() + .map(c -> XmlSerializationUtils.asXmlElement("researchproductaccesspolicies", c)) + .collect(Collectors.toList())); + } + if (ds.getResearchproductmetadataaccesspolicies() != null) { + metadata + .addAll( + ds + .getResearchproductmetadataaccesspolicies() + .stream() + .map( + c -> XmlSerializationUtils.asXmlElement("researchproductmetadataaccesspolicies", c)) + .collect(Collectors.toList())); + } break; case organization: final Organization o = (Organization) entity; diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java index c32d868e8..f4763618b 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java @@ -11,6 +11,7 @@ import java.util.List; import org.apache.commons.io.IOUtils; import org.dom4j.Document; import org.dom4j.DocumentException; +import org.dom4j.Element; import org.dom4j.io.SAXReader; import org.junit.jupiter.api.Test; @@ -142,7 +143,7 @@ public class XmlRecordFactoryTest { } @Test - public void testDatasource() throws IOException, DocumentException { + public void testService() throws IOException, DocumentException { final ContextMapper contextMapper = new ContextMapper(); final XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false, @@ -167,6 +168,14 @@ public class XmlRecordFactoryTest { assertEquals("true", doc.valueOf("//thematic")); assertEquals("Journal article", doc.valueOf("//contentpolicy/@classname")); assertEquals("Journal archive", doc.valueOf("//datasourcetypeui/@classname")); + assertEquals("Data Source", doc.valueOf("//eosctype/@classname")); + final List pids = doc.selectNodes("//pid"); + assertEquals(1, pids.size()); + assertEquals("re3data", ((Element) pids.get(0)).attribute("classid").getValue()); + assertEquals( + "Registry of research data repositories", ((Element) pids.get(0)).attribute("classname").getValue()); + assertEquals("dnet:pid_types", ((Element) pids.get(0)).attribute("schemeid").getValue()); + assertEquals("dnet:pid_types", ((Element) pids.get(0)).attribute("schemename").getValue()); } } diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/datasource.json b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/datasource.json index ae069b8b5..8a23b4e6a 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/datasource.json +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/datasource.json @@ -1 +1,407 @@ -{"collectedfrom":[{"key":"10|openaire____::13068d7823ea0bd86516ac2cb66e96ba","value":"Jurnal Fakultas Sastra Universitas Ekasakti","dataInfo":null}],"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1645012035118,"id":"10|274269ac6f3b::2a2e2793b500f3f7b47ef24b1a9277b7","originalId":["274269ac6f3b::2579-5449","piwik:13"],"pid":[],"dateofcollection":"2020-01-21","dateoftransformation":null,"extraInfo":[],"oaiprovenance":null,"datasourcetype":{"classid":"pubsrepository::journal","classname":"pubsrepository::journal","schemeid":"dnet:datasource_typologies","schemename":"dnet:datasource_typologies"},"datasourcetypeui":{"classid":"pubsrepository::journal","classname":"Journal archive","schemeid":"dnet:datasource_typologies_ui","schemename":"dnet:datasource_typologies_ui"},"openairecompatibility":{"classid":"hostedBy","classname":"hostedBy","schemeid":"dnet:datasourceCompatibilityLevel","schemename":"dnet:datasourceCompatibilityLevel"},"officialname":{"value":"Jurnal Ilmiah Pendidikan Scholastic","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"englishname":{"value":"Jurnal Ilmiah Pendidikan Scholastic","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"websiteurl":{"value":"http://e-journal.sastra-unes.com/index.php/JIPS/index","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"logourl":null,"contactemail":{"value":"test@test.it","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"namespaceprefix":{"value":"ojs_25795449","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"latitude":{"value":"0.0","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"longitude":{"value":"0.0","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"dateofvalidation":null,"description":null,"subjects":[],"odnumberofitems":{"value":"0.0","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"odnumberofitemsdate":null,"odpolicies":null,"odlanguages":[],"odcontenttypes":[{"value":"Journal articles","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"accessinfopackage":[],"releasestartdate":null,"releaseenddate":null,"missionstatementurl":null,"dataprovider":{"value":false,"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"serviceprovider":{"value":false,"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"databaseaccesstype":null,"datauploadtype":null,"databaseaccessrestriction":null,"datauploadrestriction":null,"versioning":{"value":false,"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"citationguidelineurl":null,"qualitymanagementkind":null,"pidsystems":null,"certificates":null,"policies":[],"journal":{"name":"Jurnal Ilmiah Pendidikan Scholastic","issnPrinted":"2579-5449","issnOnline":"2579-5448","issnLinking":"2579-5447","ep":null,"iss":null,"sp":null,"vol":null,"edition":null,"conferenceplace":null,"conferencedate":null,"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"providedentitytypes":null,"providedproducttypes":null,"jurisdiction":{"classid":"National","classname":"National","schemeid":"eosc:jurisdictions","schemename":"eosc:jurisdictions"},"thematic":true,"knowledgegraph":true,"contentpolicies":[{"classid":"Journal article","classname":"Journal article","schemeid":"eosc:contentpolicies","schemename":"eosc:contentpolicies"}]} +{ + "collectedfrom": [ + { + "key": "10|openaire____::13068d7823ea0bd86516ac2cb66e96ba", + "value": "Jurnal Fakultas Sastra Universitas Ekasakti", + "dataInfo": null + } + ], + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + }, + "lastupdatetimestamp": 1645012035118, + "id": "10|274269ac6f3b::2a2e2793b500f3f7b47ef24b1a9277b7", + "originalId": [ + "274269ac6f3b::2579-5449", + "piwik:13" + ], + "dateofcollection": "2020-01-21", + "dateoftransformation": null, + "extraInfo": [], + "oaiprovenance": null, + "datasourcetype": { + "classid": "pubsrepository::journal", + "classname": "Journal", + "schemeid": "dnet:datasource_typologies", + "schemename": "dnet:datasource_typologies" + }, + "datasourcetypeui": { + "classid": "pubsrepository::journal", + "classname": "Journal archive", + "schemeid": "dnet:datasource_typologies_ui", + "schemename": "dnet:datasource_typologies_ui" + }, + "pid": [ + { + "value": "r3d100010218", + "qualifier": { + "classid": "re3data", + "classname": "Registry of research data repositories", + "schemeid": "dnet:pid_types", + "schemename": "dnet:pid_types" + } + } + ], + "eosctype": { + "classid": "Data Source", + "classname": "Data Source", + "schemeid": "dnet:eosc_types", + "schemename": "dnet:eosc_types" + }, + "eoscdatasourcetype": { + "classid": "Journal archive", + "classname": "Journal archive", + "schemeid": "dnet:eosc_datasource_types", + "schemename": "dnet:eosc_datasource_types" + }, + "openairecompatibility": { + "classid": "hostedBy", + "classname": "hostedBy", + "schemeid": "dnet:datasourceCompatibilityLevel", + "schemename": "dnet:datasourceCompatibilityLevel" + }, + "officialname": { + "value": "Jurnal Ilmiah Pendidikan Scholastic", + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + "englishname": { + "value": "Jurnal Ilmiah Pendidikan Scholastic", + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + "websiteurl": { + "value": "http://e-journal.sastra-unes.com/index.php/JIPS/index", + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + "logourl": null, + "contactemail": { + "value": "test@test.it", + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + "namespaceprefix": { + "value": "ojs_25795449", + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + "latitude": { + "value": "0.0", + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + "longitude": { + "value": "0.0", + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + "dateofvalidation": null, + "description": { + "value": "veterinary medicine", + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + "subjects": [], + "odnumberofitems": { + "value": "0.0", + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + "odnumberofitemsdate": null, + "odpolicies": null, + "odlanguages": [ + { + "value": "English", + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + { + "value": "German", + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + } + ], + "languages" : [ "English", "German" ], + "odcontenttypes": [ + { + "value": "Journal articles", + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + } + ], + "accessinfopackage": [ + { + "value": "http://www.revista.vocesdelaeducacion.com.mx/index.php/index/oai", + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + } + ], + "releasestartdate": null, + "releaseenddate": null, + "missionstatementurl": null, + "dataprovider": { + "value": false, + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + "serviceprovider": { + "value": false, + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + "databaseaccesstype": null, + "datauploadtype": null, + "databaseaccessrestriction": null, + "datauploadrestriction": null, + "versioning": { + "value": false, + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + "versioncontrol": false, + "citationguidelineurl": null, + "qualitymanagementkind": null, + "pidsystems": null, + "certificates": null, + "policies": [], + "journal": { + "name": "Jurnal Ilmiah Pendidikan Scholastic", + "issnPrinted": "2579-5449", + "issnOnline": "2579-5448", + "issnLinking": "2579-5447", + "ep": null, + "iss": null, + "sp": null, + "vol": null, + "edition": null, + "conferenceplace": null, + "conferencedate": null, + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + "researchentitytypes":[ "Research Data" ], + "providedentitytypes": null, + "providedproducttypes": null, + "jurisdiction": { + "classid": "National", + "classname": "National", + "schemeid": "eosc:jurisdictions", + "schemename": "eosc:jurisdictions" + }, + "thematic": true, + "knowledgegraph": true, + "contentpolicies": [ + { + "classid": "Journal article", + "classname": "Journal article", + "schemeid": "eosc:contentpolicies", + "schemename": "eosc:contentpolicies" + } + ], + "submissionpolicyurl": null, + "preservationpolicyurl" : "Permanent Archiving https://datadryad.org/stash/faq", + "researchproductaccesspolicies": [ + "https://100percentit.com/legal/" + ], + "researchproductmetadataaccesspolicies": [ + "https://wenmr.science.uu.nl/conditions" + ] +} From a8c51f6f1627b357679a6f0a3efc396b2a82f2e0 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 2 May 2022 11:09:03 +0200 Subject: [PATCH 043/214] EOSC Services - fixed query and testing preparation --- .../eu/dnetlib/dhp/oa/graph/raw_db/oozie_app/workflow.xml | 1 + .../resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql | 6 +++--- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_db/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_db/oozie_app/workflow.xml index 29d4269ef..52462adb4 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_db/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_db/oozie_app/workflow.xml @@ -102,6 +102,7 @@ --postgresUser${postgresUser} --postgresPassword${postgresPassword} --isLookupUrl${isLookupUrl} + --actionopenaire --dbschema${dbSchema} --nsPrefixBlacklist${nsPrefixBlacklist} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql index 3dbb46eaa..f83e077a3 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql @@ -56,10 +56,10 @@ SELECT d.description AS description, NULL AS odpolicies, array_remove(ARRAY(SELECT trim(s) - FROM unnest(string_to_array(regexp_replace(d.languages, '{|}|"', '', 'g') ',')) AS s), '{}') AS odlanguages, + FROM unnest(string_to_array(regexp_replace(d.languages, '{|}|"', '', 'g'), ',')) AS s), '{}') AS odlanguages, array_remove(ARRAY(SELECT trim(s) - FROM unnest(string_to_array(regexp_replace(d.languages, '{|}|"', '', 'g') ',')) AS s), '{}') AS languages, - -- Term provided only by OpenDOAR: + FROM unnest(string_to_array(regexp_replace(d.languages, '{|}|"', '', 'g'), ',')) AS s), '{}') AS languages, + -- Term provided only by OpenDOAR: -- probably updating the TR it could be replaced by research_entity_types[] -- But a study on the vocabulary terms is needed -- REMOVED: ARRAY(SELECT trim(s) FROM unnest(string_to_array(d.od_contenttypes, '-')) AS s) AS odcontenttypes, From b6a7ff3a99e0688f64e24e5f69c887245cece7bb Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 2 May 2022 15:52:33 +0200 Subject: [PATCH 044/214] EOSC Services - removed fields from mapping, testing preparation --- .../raw/MigrateDbEntitiesApplication.java | 13 ++-- .../oa/graph/raw_db/oozie_app/workflow.xml | 64 ++++++++++++++++++- .../dhp/oa/graph/sql/queryServices.sql | 1 - .../raw/MigrateDbEntitiesApplicationTest.java | 7 +- .../graph/raw/services_resultset_entry.json | 17 ----- .../dnetlib/dhp/oa/provision/datasource.json | 19 ------ 6 files changed, 68 insertions(+), 53 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java index 924d53593..c40f9b392 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java @@ -148,10 +148,10 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i log.info("Processing Organizations..."); smdbe.execute("queryOrganizations.sql", smdbe::processOrganization, verifyNamespacePrefix); - log.info("Processing relationsNoRemoval ds <-> orgs ..."); + log.info("Processing relations services <-> orgs ..."); smdbe .execute( - "queryDatasourceOrganization.sql", smdbe::processDatasourceOrganization, + "queryServiceOrganization.sql", smdbe::processServiceOrganization, verifyNamespacePrefix); log.info("Processing projects <-> orgs ..."); @@ -268,13 +268,10 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i ds.setOdpolicies(field(rs.getString("odpolicies"), info)); ds.setOdlanguages(prepareListFields(rs.getArray("odlanguages"), info)); ds.setLanguages(listValues(rs.getArray("languages"))); - ds.setOdcontenttypes(prepareListFields(rs.getArray("odcontenttypes"), info)); ds.setAccessinfopackage(prepareListFields(rs.getArray("accessinfopackage"), info)); ds.setReleasestartdate(field(asString(rs.getDate("releasestartdate")), info)); ds.setReleaseenddate(field(asString(rs.getDate("releaseenddate")), info)); ds.setMissionstatementurl(field(rs.getString("missionstatementurl"), info)); - ds.setDataprovider(field(rs.getBoolean("dataprovider"), info)); - ds.setServiceprovider(field(rs.getBoolean("serviceprovider"), info)); ds.setDatabaseaccesstype(field(rs.getString("databaseaccesstype"), info)); ds.setDatauploadtype(field(rs.getString("datauploadtype"), info)); ds.setDatabaseaccessrestriction(field(rs.getString("databaseaccessrestriction"), info)); @@ -293,10 +290,8 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i rs.getString("issnLinking"), info)); // Journal ds.setResearchentitytypes(listValues(rs.getArray("researchentitytypes"))); - ds.setProvidedproducttypes(listValues(rs.getArray("providedproducttypes"))); ds.setJurisdiction(prepareQualifierSplitting(rs.getString("jurisdiction"))); ds.setThematic(rs.getBoolean("thematic")); - ds.setKnowledgegraph(rs.getBoolean("knowledgegraph")); ds.setContentpolicies(prepareListOfQualifiers(rs.getArray("contentpolicies"))); ds.setSubmissionpolicyurl(rs.getString("submissionpolicyurl")); ds.setPreservationpolicyurl(rs.getString("preservationpolicyurl")); @@ -434,11 +429,11 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i } } - public List processDatasourceOrganization(final ResultSet rs) { + public List processServiceOrganization(final ResultSet rs) { try { final DataInfo info = prepareDataInfo(rs); final String orgId = createOpenaireId(20, rs.getString("organization"), true); - final String dsId = createOpenaireId(10, rs.getString("datasource"), true); + final String dsId = createOpenaireId(10, rs.getString("service"), true); final List collectedFrom = listKeyValues( createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname")); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_db/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_db/oozie_app/workflow.xml index 52462adb4..31b726f39 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_db/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_db/oozie_app/workflow.xml @@ -30,6 +30,11 @@ a blacklist of nsprefixes (comma separeted) + + reuseContent + false + reuse content in the aggregator database + sparkDriverMemory memory for driver process @@ -85,12 +90,20 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + ${wf:conf('reuseContent') eq false} + ${wf:conf('reuseContent') eq true} + + + + @@ -125,6 +138,55 @@ --actionclaims --nsPrefixBlacklist${nsPrefixBlacklist} + + + + + + + yarn + cluster + GenerateEntities + eu.dnetlib.dhp.oa.graph.raw.GenerateEntitiesApplication + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory ${sparkExecutorMemory} + --executor-cores ${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --sourcePaths${contentPath}/db_records,${contentPath}/db_claims + --targetPath${workingDir}/entities + --isLookupUrl${isLookupUrl} + --shouldHashIdtrue + + + + + + + + yarn + cluster + GenerateGraph + eu.dnetlib.dhp.oa.graph.raw.DispatchEntitiesApplication + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory ${sparkExecutorMemory} + --executor-cores ${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=7680 + + --sourcePath${workingDir}/entities + --graphRawPath${workingDir}/graph_aggregator + diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql index f83e077a3..eb70d39e0 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql @@ -109,7 +109,6 @@ SELECT d.lastconsenttermsofusedate AS lastconsenttermsofusedate, d.jurisdiction||'@@@eosc:jurisdictions' AS jurisdiction, d.thematic AS thematic, - -- REMOVED ???: d.knowledge_graph AS knowledgegraph, array(select unnest(d.content_policies)||'@@@eosc:contentpolicies') AS contentpolicies, nullif(trim(d.submission_policy_url), '') AS submissionpolicyurl, nullif(trim(d.preservation_policy_url), '') AS preservationpolicyurl, diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java index 69552c4dc..948dbfa50 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java @@ -129,9 +129,6 @@ public class MigrateDbEntitiesApplicationTest { getValueAsList("odlanguages", fields), ds.getOdlanguages().stream().map(Field::getValue).collect(Collectors.toList())); assertEquals(getValueAsList("languages", fields), ds.getLanguages()); - assertEquals( - getValueAsList("odcontenttypes", fields), - ds.getOdcontenttypes().stream().map(Field::getValue).collect(Collectors.toList())); assertEquals( getValueAsList("accessinfopackage", fields), ds.getAccessinfopackage().stream().map(Field::getValue).collect(Collectors.toList())); @@ -155,13 +152,11 @@ public class MigrateDbEntitiesApplicationTest { assertEquals(getValueAsString("certificates", fields), ds.getCertificates()); assertEquals(getValueAsList("researchentitytypes", fields), ds.getResearchentitytypes()); - assertEquals(getValueAsList("providedproducttypes", fields), ds.getProvidedproducttypes()); assertEquals("National", ds.getJurisdiction().getClassid()); assertEquals("eosc:jurisdictions", ds.getJurisdiction().getSchemeid()); assertTrue(ds.getThematic()); - assertTrue(ds.getKnowledgegraph()); HashSet cpSchemeId = ds .getContentpolicies() @@ -246,7 +241,7 @@ public class MigrateDbEntitiesApplicationTest { public void testProcessDatasourceOrganization() throws Exception { final List fields = prepareMocks("datasourceorganization_resultset_entry.json"); - final List list = app.processDatasourceOrganization(rs); + final List list = app.processServiceOrganization(rs); assertEquals(2, list.size()); verifyMocks(fields); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/services_resultset_entry.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/services_resultset_entry.json index 70fad3323..445334de5 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/services_resultset_entry.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/services_resultset_entry.json @@ -140,13 +140,6 @@ "Swedish" ] }, - { - "field": "odcontenttypes", - "type": "array", - "value": [ - "Journal articles" - ] - }, { "field": "accessinfopackage", "type": "array", @@ -169,16 +162,6 @@ "type": "string", "value": null }, - { - "field": "dataprovider", - "type": "boolean", - "value": null - }, - { - "field": "serviceprovider", - "type": "boolean", - "value": null - }, { "field": "databaseaccesstype", "type": "string", diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/datasource.json b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/datasource.json index 8a23b4e6a..ce6b10826 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/datasource.json +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/datasource.json @@ -254,24 +254,6 @@ } ], "languages" : [ "English", "German" ], - "odcontenttypes": [ - { - "value": "Journal articles", - "dataInfo": { - "invisible": false, - "inferred": false, - "deletedbyinference": false, - "trust": "0.900", - "inferenceprovenance": null, - "provenanceaction": { - "classid": "sysimport:crosswalk:entityregistry", - "classname": "sysimport:crosswalk:entityregistry", - "schemeid": "dnet:provenanceActions", - "schemename": "dnet:provenanceActions" - } - } - } - ], "accessinfopackage": [ { "value": "http://www.revista.vocesdelaeducacion.com.mx/index.php/index/oai", @@ -387,7 +369,6 @@ "schemename": "eosc:jurisdictions" }, "thematic": true, - "knowledgegraph": true, "contentpolicies": [ { "classid": "Journal article", From 2ade69dea694a6d57ce51a5d7da53bc43ac8a22e Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 2 May 2022 17:03:31 +0200 Subject: [PATCH 045/214] EOSC Services - minor --- .../dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java | 2 +- .../resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java index c40f9b392..552125307 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java @@ -233,7 +233,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i final Datasource ds = new Datasource(); - ds.setId(createOpenaireId(10, rs.getString("datasourceid"), true)); + ds.setId(createOpenaireId(10, rs.getString("id"), true)); ds .setOriginalId( Arrays diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql index eb70d39e0..81eab8163 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql @@ -1,5 +1,5 @@ SELECT - d.id AS datasourceid, + d.id AS id, array_remove(d.id || array_agg(distinct CASE WHEN dp.pid like 'piwik%' THEN di.pid ELSE NULL END) || array_agg(distinct dds.duplicate), NULL) AS originalid, array_remove(array_agg(distinct CASE WHEN di.pid NOT LIKE 'piwik%' THEN di.pid||'###'||di.issuertype||'@@@'||'dnet:pid_types' ELSE NULL END), NULL) as pid, d.officialname AS officialname, From a21fe310e57c5463eafb50205e1b35ab29759cf5 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 2 May 2022 17:43:20 +0200 Subject: [PATCH 046/214] [EOSCTag] last test and change in the implementation to search in title and descriptio --- .../doiboost/crossref/Crossref2Oaf.scala | 6 +- .../crossref/CrossrefMappingTest.scala | 4 +- .../eu/dnetlib/dhp/bulktag/SparkEoscTag.java | 355 ++++++------ .../dnetlib/dhp/bulktag/EOSCTagJobTest.java | 530 ++++++++++++++---- .../eosctag/twitter/dataset/dataset_10.json | 4 +- .../otherresearchproduct_10.json | 10 +- .../eosctag/twitter/software/software_10.json | 2 +- 7 files changed, 620 insertions(+), 291 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala index 0ba77ca84..f2d1dde3d 100644 --- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala +++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala @@ -584,12 +584,10 @@ case object Crossref2Oaf { if (dp.length == 10) { return GraphCleaningFunctions.cleanDate(dp) } - } - else if (res.size ==2) { + } else if (res.size == 2) { val dp = f"${res.head}-${res(1)}%02d-01" return GraphCleaningFunctions.cleanDate(dp) - } - else if (res.size ==1) { + } else if (res.size == 1) { return GraphCleaningFunctions.cleanDate(s"${res.head}-01-01") } } diff --git a/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala b/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala index 9025cd6d2..78ed375c6 100644 --- a/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala +++ b/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala @@ -73,10 +73,10 @@ class CrossrefMappingTest { } - @Test def crossrefIssueDateTest(): Unit = { - val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/issue_date.json")).mkString + val json = + Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/issue_date.json")).mkString assertNotNull(json) assertFalse(json.isEmpty) val resultList: List[Oaf] = Crossref2Oaf.convert(json) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java index 16baf70a6..1d0aaa631 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java @@ -1,10 +1,14 @@ + package eu.dnetlib.dhp.bulktag; -import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.oaf.*; -import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; +import static eu.dnetlib.dhp.PropagationConstant.readPath; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.util.*; +import java.util.function.Function; +import java.util.stream.Collectors; +import java.util.stream.Stream; + import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; @@ -14,185 +18,214 @@ import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.List; -import java.util.Optional; +import com.fasterxml.jackson.databind.ObjectMapper; -import static eu.dnetlib.dhp.PropagationConstant.readPath; -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; public class SparkEoscTag { - private static final Logger log = LoggerFactory.getLogger(SparkEoscTag.class); - public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - public static final Qualifier EOSC_QUALIFIER = OafMapperUtils.qualifier("eosc", - "European Open Science Cloud", - ModelConstants.DNET_SUBJECT_TYPOLOGIES,ModelConstants.DNET_SUBJECT_TYPOLOGIES); - public static final DataInfo EOSC_DATAINFO = OafMapperUtils.dataInfo(false, "propagation", true, false, - OafMapperUtils.qualifier("propagation:subject","Inferred by OpenAIRE", - ModelConstants.DNET_PROVENANCE_ACTIONS,ModelConstants.DNET_PROVENANCE_ACTIONS), "0.9"); - public final static StructuredProperty EOSC_NOTEBOOK = OafMapperUtils.structuredProperty( - "EOSC::Jupyter Notebook", EOSC_QUALIFIER,EOSC_DATAINFO); - public final static StructuredProperty EOSC_GALAXY = OafMapperUtils.structuredProperty( - "EOSC::Galaxy Workflow", EOSC_QUALIFIER, EOSC_DATAINFO); - public final static StructuredProperty EOSC_TWITTER = OafMapperUtils.structuredProperty( - "EOSC::Twitter Data", EOSC_QUALIFIER,EOSC_DATAINFO); + private static final Logger log = LoggerFactory.getLogger(SparkEoscTag.class); + public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + public static final Qualifier EOSC_QUALIFIER = OafMapperUtils + .qualifier( + "eosc", + "European Open Science Cloud", + ModelConstants.DNET_SUBJECT_TYPOLOGIES, ModelConstants.DNET_SUBJECT_TYPOLOGIES); + public static final DataInfo EOSC_DATAINFO = OafMapperUtils + .dataInfo( + false, "propagation", true, false, + OafMapperUtils + .qualifier( + "propagation:subject", "Inferred by OpenAIRE", + ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS), + "0.9"); + public final static StructuredProperty EOSC_NOTEBOOK = OafMapperUtils + .structuredProperty( + "EOSC::Jupyter Notebook", EOSC_QUALIFIER, EOSC_DATAINFO); + public final static StructuredProperty EOSC_GALAXY = OafMapperUtils + .structuredProperty( + "EOSC::Galaxy Workflow", EOSC_QUALIFIER, EOSC_DATAINFO); + public final static StructuredProperty EOSC_TWITTER = OafMapperUtils + .structuredProperty( + "EOSC::Twitter Data", EOSC_QUALIFIER, EOSC_DATAINFO); - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkEoscTag.class - .getResourceAsStream( - "/eu/dnetlib/dhp/bulktag/input_eoscTag_parameters.json")); + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + SparkEoscTag.class + .getResourceAsStream( + "/eu/dnetlib/dhp/bulktag/input_eoscTag_parameters.json")); - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); + final String inputPath = parser.get("sourcePath"); + log.info("inputPath: {}", inputPath); - final String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + final String workingPath = parser.get("workingPath"); + log.info("workingPath: {}", workingPath); - SparkConf conf = new SparkConf(); + SparkConf conf = new SparkConf(); - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - execEoscTag(spark, inputPath, workingPath); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + execEoscTag(spark, inputPath, workingPath); - }); - } + }); + } - private static void execEoscTag(SparkSession spark, String inputPath, String workingPath) { + private static void execEoscTag(SparkSession spark, String inputPath, String workingPath) { - readPath(spark, inputPath + "/software", Software.class) - .map((MapFunction) s -> { - List sbject; - if (!Optional.ofNullable(s.getSubject()).isPresent()) - s.setSubject(new ArrayList<>()); - sbject = s.getSubject(); + readPath(spark, inputPath + "/software", Software.class) + .map((MapFunction) s -> { + List sbject; + if (!Optional.ofNullable(s.getSubject()).isPresent()) + s.setSubject(new ArrayList<>()); + sbject = s.getSubject(); - if(containsCriteriaNotebook(s)){ - sbject.add(EOSC_NOTEBOOK); + if (containsCriteriaNotebook(s)) { + sbject.add(EOSC_NOTEBOOK); - } - if(containsCriteriaGalaxy(s)){ - sbject.add(EOSC_GALAXY); - } - return s; - }, Encoders.bean(Software.class) ) - .write() - .mode(SaveMode.Overwrite) - .option("compression","gzip") - .json(workingPath + "/software"); + } + if (containsCriteriaGalaxy(s)) { + sbject.add(EOSC_GALAXY); + } + return s; + }, Encoders.bean(Software.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingPath + "/software"); - readPath(spark, workingPath + "/software" , Software.class) - .write() - .mode(SaveMode.Overwrite) - .option("compression","gzip") - .json(inputPath + "/software"); + readPath(spark, workingPath + "/software", Software.class) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(inputPath + "/software"); - readPath(spark, inputPath + "/otherresearchproduct", OtherResearchProduct.class) - .map((MapFunction) orp -> - { - List sbject; - if (!Optional.ofNullable(orp.getSubject()).isPresent()) - orp.setSubject(new ArrayList<>()); - sbject = orp.getSubject(); - if(containsCriteriaGalaxy(orp)){ - sbject.add(EOSC_GALAXY); - } - if(containscriteriaTwitter(orp)){ - sbject.add(EOSC_TWITTER); - } - return orp; - }, Encoders.bean(OtherResearchProduct.class)) - .write() - .mode(SaveMode.Overwrite) - .option("compression","gzip") - .json(workingPath + "/otherresearchproduct"); + readPath(spark, inputPath + "/otherresearchproduct", OtherResearchProduct.class) + .map((MapFunction) orp -> { + List sbject; + if (!Optional.ofNullable(orp.getSubject()).isPresent()) + orp.setSubject(new ArrayList<>()); + sbject = orp.getSubject(); + if (containsCriteriaGalaxy(orp)) { + sbject.add(EOSC_GALAXY); + } + if (containscriteriaTwitter(orp)) { + sbject.add(EOSC_TWITTER); + } + return orp; + }, Encoders.bean(OtherResearchProduct.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingPath + "/otherresearchproduct"); - readPath(spark, workingPath + "/otherresearchproduct", OtherResearchProduct.class) - .write() - .mode(SaveMode.Overwrite) - .option("compression","gzip") - .json(inputPath + "/otherresearchproduct"); + readPath(spark, workingPath + "/otherresearchproduct", OtherResearchProduct.class) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(inputPath + "/otherresearchproduct"); - readPath(spark, inputPath + "/dataset", Dataset.class) - .map((MapFunction) d -> { - List sbject; - if (!Optional.ofNullable(d.getSubject()).isPresent()) - d.setSubject(new ArrayList<>()); - sbject = d.getSubject(); - if(containscriteriaTwitter(d)){ - sbject.add(EOSC_TWITTER); - } - return d; - } , Encoders.bean(Dataset.class) ) - .write() - .mode(SaveMode.Overwrite) - .option("compression","gzip") - .json(workingPath + "/dataset"); + readPath(spark, inputPath + "/dataset", Dataset.class) + .map((MapFunction) d -> { + List sbject; + if (!Optional.ofNullable(d.getSubject()).isPresent()) + d.setSubject(new ArrayList<>()); + sbject = d.getSubject(); + if (containscriteriaTwitter(d)) { + sbject.add(EOSC_TWITTER); + } + return d; + }, Encoders.bean(Dataset.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingPath + "/dataset"); - readPath(spark, workingPath + "/dataset" , Dataset.class) - .write() - .mode(SaveMode.Overwrite) - .option("compression","gzip") - .json(inputPath + "/dataset"); - } + readPath(spark, workingPath + "/dataset", Dataset.class) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(inputPath + "/dataset"); + } - private static boolean containscriteriaTwitter(Result r) { - if (r.getTitle().stream().anyMatch(t -> t.getValue().toLowerCase().contains("twitter") && - t.getValue().toLowerCase().contains("data"))) - return true; - if(r.getDescription().stream().anyMatch(d -> d.getValue().toLowerCase().contains("twitter") && - d.getValue().toLowerCase().contains("data") )) - return true; - if(r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("twitter")) && - r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("data"))) - return true; - return false; - } + private static boolean containscriteriaTwitter(Result r) { + Set words = getWordsSP(r.getTitle()); + words.addAll(getWordsF(r.getDescription())); - private static boolean containsCriteriaGalaxy(Result r) { - if (r.getTitle().stream().anyMatch(t -> t.getValue().toLowerCase().contains("galaxy") && - (t.getValue().toLowerCase().contains("workflow") || t.getValue().toLowerCase().contains("software")))) - return true; - if(r.getDescription().stream().anyMatch(d -> d.getValue().toLowerCase().contains("galaxy") && - (d.getValue().toLowerCase().contains("workflow") || d.getValue().toLowerCase().contains("software")))) - return true; - if(r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("galaxy")) && - (r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("workflow"))) || - r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("software"))) - return true; - return false; - } + if (words.contains("twitter") && + (words.contains("data") || words.contains("dataset"))) + return true; - private static boolean containsCriteriaNotebook(Software s) { - if(s.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("jupyter"))) - return true; - if(s.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("python") && - sbj.getValue().toLowerCase().contains("notebook"))) - return true; - if(s.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("python")) && - s.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("notebook"))) - return true; - return false; - } + if (r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("twitter")) && + r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("data"))) + return true; + return false; + } - private static boolean containsTitleNotebook(Software s) { - if (s.getTitle().stream().anyMatch(t -> t.getValue().toLowerCase().contains("jupyter") && - t.getValue().toLowerCase().contains("notebook"))) - return true; - return false; - } + private static boolean containsCriteriaGalaxy(Result r) { + Set words = getWordsSP(r.getTitle()); + words.addAll(getWordsF(r.getDescription())); + if (words.contains("galaxy") && + (words.contains("workflow") || words.contains("software"))) + return true; + if (r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("galaxy")) && + (r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("workflow"))) || + r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("software"))) + return true; + return false; + } + + private static boolean containsCriteriaNotebook(Software s) { + if (s.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("jupyter"))) + return true; + if (s + .getSubject() + .stream() + .anyMatch( + sbj -> sbj.getValue().toLowerCase().contains("python") && + sbj.getValue().toLowerCase().contains("notebook"))) + return true; + if (s.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("python")) && + s.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("notebook"))) + return true; + return false; + } + + private static Set getSubjects(List s) { + Set subjects = new HashSet<>(); + s.stream().forEach(sbj -> subjects.addAll(Arrays.asList(sbj.getValue().toLowerCase().split(" ")))); + s.stream().forEach(sbj -> subjects.add(sbj.getValue().toLowerCase())); + return subjects; + } + + private static Set getWordsSP(List elem) { + Set words = new HashSet<>(); + elem + .forEach( + t -> words.addAll(Arrays.asList(t.getValue().toLowerCase().replaceAll("[^a-zA-Z ]", "").split(" ")))); + return words; + } + + private static Set getWordsF(List> elem) { + Set words = new HashSet<>(); + elem + .forEach( + t -> words.addAll(Arrays.asList(t.getValue().toLowerCase().replaceAll("[^a-zA-Z ]", "").split(" ")))); + return words; + + } } diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java index 2c2334a6c..d96dc7f6c 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java @@ -1,8 +1,13 @@ package eu.dnetlib.dhp.bulktag; -import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.schema.oaf.*; +import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.ZENODO_COMMUNITY_INDICATOR; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.List; + import org.apache.commons.io.FileUtils; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; @@ -11,6 +16,7 @@ import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.Row; +import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; import org.junit.jupiter.api.AfterAll; import org.junit.jupiter.api.Assertions; @@ -19,26 +25,20 @@ import org.junit.jupiter.api.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.List; +import com.fasterxml.jackson.databind.ObjectMapper; -import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.ZENODO_COMMUNITY_INDICATOR; +import eu.dnetlib.dhp.schema.oaf.*; public class EOSCTagJobTest { private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private static SparkSession spark; private static Path workingDir; private static final Logger log = LoggerFactory.getLogger(EOSCTagJobTest.class); - @BeforeAll public static void beforeAll() throws IOException { workingDir = Files.createTempDirectory(EOSCTagJobTest.class.getSimpleName()); @@ -70,23 +70,39 @@ public class EOSCTagJobTest { @Test void jupyterUpdatesTest() throws Exception { - spark.read().textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/jupyter/software").getPath()) - .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, Software.class), Encoders.bean(Software.class)) - .write() - .option("compression","gzip") - .json(workingDir.toString() + "/input/software"); + spark + .read() + .textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/jupyter/software").getPath()) + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, Software.class), + Encoders.bean(Software.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingDir.toString() + "/input/software"); - spark.read().textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/jupyter/dataset").getPath()) - .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, Dataset.class), Encoders.bean(Dataset.class)) - .write() - .option("compression","gzip") - .json(workingDir.toString() + "/input/dataset"); + spark + .read() + .textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/jupyter/dataset").getPath()) + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, Dataset.class), + Encoders.bean(Dataset.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingDir.toString() + "/input/dataset"); - spark.read().textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/jupyter/otherresearchproduct").getPath()) - .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, OtherResearchProduct.class), Encoders.bean(OtherResearchProduct.class)) - .write() - .option("compression","gzip") - .json(workingDir.toString() + "/input/otherresearchproduct"); + spark + .read() + .textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/jupyter/otherresearchproduct").getPath()) + .map( + (MapFunction) value -> OBJECT_MAPPER + .readValue(value, OtherResearchProduct.class), + Encoders.bean(OtherResearchProduct.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingDir.toString() + "/input/otherresearchproduct"); SparkEoscTag .main( @@ -106,36 +122,109 @@ public class EOSCTagJobTest { Assertions.assertEquals(10, tmp.count()); - Assertions.assertEquals(4, tmp.filter(s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook"))).count()); + Assertions + .assertEquals( + 4, + tmp + .filter( + s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook"))) + .count()); - Assertions.assertEquals(2, tmp.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")).collect() - .get(0).getSubject().size()); - Assertions.assertTrue(tmp.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")).collect() - .get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); + Assertions + .assertEquals( + 2, tmp + .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) + .collect() + .get(0) + .getSubject() + .size()); + Assertions + .assertTrue( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) + .collect() + .get(0) + .getSubject() + .stream() + .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); + Assertions + .assertEquals( + 5, tmp + .filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11")) + .collect() + .get(0) + .getSubject() + .size()); + Assertions + .assertFalse( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11")) + .collect() + .get(0) + .getSubject() + .stream() + .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); - Assertions.assertEquals(5, tmp.filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11")).collect() - .get(0).getSubject().size()); - Assertions.assertFalse(tmp.filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11")).collect() - .get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); + Assertions + .assertEquals( + 9, tmp + .filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")) + .collect() + .get(0) + .getSubject() + .size()); + Assertions + .assertTrue( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")) + .collect() + .get(0) + .getSubject() + .stream() + .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); - Assertions.assertEquals(9, tmp.filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")).collect() - .get(0).getSubject().size()); - Assertions.assertTrue(tmp.filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")).collect() - .get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); + Assertions + .assertEquals( + 5, tmp + .filter(sw -> sw.getId().equals("50|od______1582::5aec1186054301b66c0c5dc35972a589")) + .collect() + .get(0) + .getSubject() + .size()); + Assertions + .assertFalse( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::5aec1186054301b66c0c5dc35972a589")) + .collect() + .get(0) + .getSubject() + .stream() + .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); - Assertions.assertEquals(5, tmp.filter(sw -> sw.getId().equals("50|od______1582::5aec1186054301b66c0c5dc35972a589")).collect() - .get(0).getSubject().size()); - Assertions.assertFalse(tmp.filter(sw -> sw.getId().equals("50|od______1582::5aec1186054301b66c0c5dc35972a589")).collect() - .get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); + Assertions + .assertEquals( + 9, tmp + .filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0")) + .collect() + .get(0) + .getSubject() + .size()); + Assertions + .assertTrue( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0")) + .collect() + .get(0) + .getSubject() + .stream() + .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); - Assertions.assertEquals(9, tmp.filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0")).collect() - .get(0).getSubject().size()); - Assertions.assertTrue(tmp.filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0")).collect() - .get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); - - List subjects = tmp.filter(sw -> sw.getId().equals("50|od______1582::6e7a9b21a2feef45673890432af34244")).collect() - .get(0).getSubject(); + List subjects = tmp + .filter(sw -> sw.getId().equals("50|od______1582::6e7a9b21a2feef45673890432af34244")) + .collect() + .get(0) + .getSubject(); Assertions.assertEquals(8, subjects.size()); Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("jupyter"))); @@ -146,104 +235,313 @@ public class EOSCTagJobTest { Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("flux de gaz"))); Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("flux de liquide"))); + Assertions + .assertEquals( + 10, sc + .textFile(workingDir.toString() + "/input/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)) + .count()); - Assertions.assertEquals(10, sc - .textFile(workingDir.toString() + "/input/dataset") - .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)).count()); + Assertions + .assertEquals( + 0, sc + .textFile(workingDir.toString() + "/input/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)) + .filter( + ds -> ds.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook"))) + .count()); - Assertions.assertEquals(0, sc - .textFile(workingDir.toString() + "/input/dataset") - .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)).filter(ds -> ds.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook"))).count()); + Assertions + .assertEquals( + 10, sc + .textFile(workingDir.toString() + "/input/otherresearchproduct") + .map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)) + .count()); + Assertions + .assertEquals( + 0, sc + .textFile(workingDir.toString() + "/input/otherresearchproduct") + .map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)) + .filter( + ds -> ds.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook"))) + .count()); - Assertions.assertEquals(10, sc - .textFile(workingDir.toString() + "/input/otherresearchproduct") - .map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)).count()); - - Assertions.assertEquals(0, sc - .textFile(workingDir.toString() + "/input/otherresearchproduct") - .map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)).filter(ds -> ds.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook"))).count()); + // spark.stop(); } - @Test void galaxyUpdatesTest() throws Exception { - spark.read().textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/galaxy/software").getPath()) - .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, Software.class), Encoders.bean(Software.class)) - .write() - .option("compression","gzip") - .json(workingDir.toString() + "/input/software"); + spark + .read() + .textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/galaxy/software").getPath()) + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, Software.class), + Encoders.bean(Software.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingDir.toString() + "/input/software"); - spark.read().textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/galaxy/dataset").getPath()) - .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, Dataset.class), Encoders.bean(Dataset.class)) - .write() - .option("compression","gzip") - .json(workingDir.toString() + "/input/dataset"); + spark + .read() + .textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/galaxy/dataset").getPath()) + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, Dataset.class), + Encoders.bean(Dataset.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingDir.toString() + "/input/dataset"); - spark.read().textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/galaxy/otherresearchproduct").getPath()) - .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, OtherResearchProduct.class), Encoders.bean(OtherResearchProduct.class)) - .write() - .option("compression","gzip") - .json(workingDir.toString() + "/input/otherresearchproduct"); + spark + .read() + .textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/galaxy/otherresearchproduct").getPath()) + .map( + (MapFunction) value -> OBJECT_MAPPER + .readValue(value, OtherResearchProduct.class), + Encoders.bean(OtherResearchProduct.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingDir.toString() + "/input/otherresearchproduct"); SparkEoscTag - .main( - new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", - workingDir.toString() + "/input", - "-workingPath", workingDir.toString() + "/working" + .main( + new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", + workingDir.toString() + "/input", + "-workingPath", workingDir.toString() + "/working" - }); + }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/input/software") - .map(item -> OBJECT_MAPPER.readValue(item, Software.class)); + .textFile(workingDir.toString() + "/input/software") + .map(item -> OBJECT_MAPPER.readValue(item, Software.class)); Assertions.assertEquals(10, tmp.count()); - Assertions.assertEquals(2, tmp.filter(s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Galaxy Workflow"))).count()); + Assertions + .assertEquals( + 2, + tmp + .filter( + s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Galaxy Workflow"))) + .count()); - Assertions.assertEquals(2, tmp.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")).collect() - .get(0).getSubject().size()); - Assertions.assertTrue(tmp.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")).collect() - .get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); + Assertions + .assertEquals( + 2, tmp + .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) + .collect() + .get(0) + .getSubject() + .size()); + Assertions + .assertTrue( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) + .collect() + .get(0) + .getSubject() + .stream() + .anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); + Assertions + .assertEquals( + 6, tmp + .filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11")) + .collect() + .get(0) + .getSubject() + .size()); + Assertions + .assertTrue( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11")) + .collect() + .get(0) + .getSubject() + .stream() + .anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); - Assertions.assertEquals(6, tmp.filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11")).collect() - .get(0).getSubject().size()); - Assertions.assertTrue(tmp.filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11")).collect() - .get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); + Assertions + .assertEquals( + 8, tmp + .filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")) + .collect() + .get(0) + .getSubject() + .size()); + Assertions + .assertFalse( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")) + .collect() + .get(0) + .getSubject() + .stream() + .anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); - Assertions.assertEquals(8, tmp.filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")).collect() - .get(0).getSubject().size()); - Assertions.assertFalse(tmp.filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")).collect() - .get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); - - JavaRDD orp = sc.textFile(workingDir.toString() + "/input/otherresearchproduct").map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)); + JavaRDD orp = sc + .textFile(workingDir.toString() + "/input/otherresearchproduct") + .map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)); Assertions.assertEquals(10, orp.count()); - Assertions.assertEquals(2, orp.filter(s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Galaxy Workflow"))).count()); + Assertions + .assertEquals( + 2, + orp + .filter( + s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Galaxy Workflow"))) + .count()); + Assertions + .assertEquals( + 3, orp + .filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07")) + .collect() + .get(0) + .getSubject() + .size()); + Assertions + .assertTrue( + orp + .filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07")) + .collect() + .get(0) + .getSubject() + .stream() + .anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); - Assertions.assertEquals(3, orp.filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07")).collect() - .get(0).getSubject().size()); - Assertions.assertTrue(orp.filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07")).collect() - .get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); + Assertions + .assertEquals( + 2, orp + .filter(sw -> sw.getId().equals("50|od______2017::1bd97baef19dbd2db3203b112bb83bc5")) + .collect() + .get(0) + .getSubject() + .size()); + Assertions + .assertFalse( + orp + .filter(sw -> sw.getId().equals("50|od______2017::1bd97baef19dbd2db3203b112bb83bc5")) + .collect() + .get(0) + .getSubject() + .stream() + .anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); - Assertions.assertEquals(2, orp.filter(sw -> sw.getId().equals("50|od______2017::1bd97baef19dbd2db3203b112bb83bc5")).collect() - .get(0).getSubject().size()); - Assertions.assertFalse(orp.filter(sw -> sw.getId().equals("50|od______2017::1bd97baef19dbd2db3203b112bb83bc5")).collect() - .get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); - - Assertions.assertEquals(3, orp.filter(sw -> sw.getId().equals("50|od______2017::1e400f1747487fd15998735c41a55c72")).collect() - .get(0).getSubject().size()); - Assertions.assertTrue(orp.filter(sw -> sw.getId().equals("50|od______2017::1e400f1747487fd15998735c41a55c72")).collect() - .get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); + Assertions + .assertEquals( + 3, orp + .filter(sw -> sw.getId().equals("50|od______2017::1e400f1747487fd15998735c41a55c72")) + .collect() + .get(0) + .getSubject() + .size()); + Assertions + .assertTrue( + orp + .filter(sw -> sw.getId().equals("50|od______2017::1e400f1747487fd15998735c41a55c72")) + .collect() + .get(0) + .getSubject() + .stream() + .anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); } + @Test + void twitterUpdatesTest() throws Exception { + spark + .read() + .textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/twitter/software").getPath()) + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, Software.class), + Encoders.bean(Software.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingDir.toString() + "/input/software"); + + spark + .read() + .textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/twitter/dataset").getPath()) + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, Dataset.class), + Encoders.bean(Dataset.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingDir.toString() + "/input/dataset"); + + spark + .read() + .textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/twitter/otherresearchproduct").getPath()) + .map( + (MapFunction) value -> OBJECT_MAPPER + .readValue(value, OtherResearchProduct.class), + Encoders.bean(OtherResearchProduct.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingDir.toString() + "/input/otherresearchproduct"); + + SparkEoscTag + .main( + new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", + workingDir.toString() + "/input", + "-workingPath", workingDir.toString() + "/working" + + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/input/software") + .map(item -> OBJECT_MAPPER.readValue(item, Software.class)); + + Assertions.assertEquals(10, tmp.count()); + + Assertions + .assertEquals( + 0, + tmp + .filter(s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Twitter Data"))) + .count()); + + JavaRDD orp = sc + .textFile(workingDir.toString() + "/input/otherresearchproduct") + .map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)); + + Assertions.assertEquals(10, orp.count()); + + Assertions + .assertEquals( + 3, + orp + .filter(s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Twitter Data"))) + .count()); + + JavaRDD dats = sc + .textFile(workingDir.toString() + "/input/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); + + Assertions.assertEquals(10, dats.count()); + + Assertions + .assertEquals( + 2, + dats + .filter(s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Twitter Data"))) + .count()); + + } } diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/twitter/dataset/dataset_10.json b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/twitter/dataset/dataset_10.json index 0243a4e3d..b441bc423 100644 --- a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/twitter/dataset/dataset_10.json +++ b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/twitter/dataset/dataset_10.json @@ -1,5 +1,5 @@ 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se están desarrollando en la Universidad Camilo José Cela (UCJC) sobre la cafeína y sus efectos cuando se realiza deporte. https://www.ucjc.edu/2016/08/la-bbc-s...\n\nJuan Del Coso, director del Laboratorio de Fisiología del Ejercicio de la Universidad Camilo José Cela, nos describe cómo está siendo la investigación que desarrolla con deportistas de alto rendimiento y el consumo de cafeína.\n\n\"Nuestra investigación se enmarca dentro del campo de la fisiología del ejercicio y el objetivo que tenemos es investigar los efectos que tiene la cafeína en los deportistas, principalmente saber si es una ayuda ergogénica en la mayor parte de los deportes, pero también conocer qué perjuicios existen para aquellos deportistas que la utilizan para incrementar el rendimiento deportivo\", explica Del Coso.\n\nY es que los datos son muy llamativos: tres de cada cuatro deportistas de alto rendimiento utilizan la cafeína antes de la competición y muchas veces se utiliza sin saber los perjuicios que 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Amaro","surname":"Costa","rank":2,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"por","classname":"Portuguese","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Pesticidas","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Proteção 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Que caminhos?","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[],"description":[{"value":"A agricultura está inevitavelmente associada a um conjunto de variáveis no ecossistema, onde estão incluídos as pragas e doenças nas culturas e presença de outras plantas que competem pelo alimento, água e luz. Estes agentes são responsáveis por perdas no rendimento que, normalmente, não são aceites pelo agricultor. E é, por isso, que se recorre aos pesticidas: é preciso proteger as culturas do ataque dos seus inimigos.\nTambém é verdade que a agricultura é a atividade desenvolvida pelo Homem que mais se aproxima dos sistemas naturais e tem, assim, um papel central na produção de diversos serviços do ecossistema, como a biodiversidade agrícola, qualidade do solo e água, estabilidade climática e manutenção da paisagem. Ora, o uso dos pesticidas introduz efeitos negativos em todo este sistema: degradam o solo, reduzem a qualidade e disponibilidade de água, causam poluição e perda de habitats selvagens e de biodiversidade. Aqui reside a encruzilhada na proteção das 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Evidences about their quality of life (QoL) are, nevertheless, still limited. Different conceptualizations of QoL, the overvaluation of the negative aspects of advanced age and the heterogeneity of the oldest old are some issues that could explain the dif􏰀culties in this assessment. Objectives: This study aims to analyze the perceived QoL in a sample of centenarians and analyze if there are significant life context (community vs institutional) and health (objective and subjective perception) differences.\nMethods: A subsample of 59 Portuguese centenarians who participated in the PT100_Oporto Centenarian Study, conducted in 2013 was considered. Descriptive and chi-square analysis were conducted.\nResults: Most centenarians perceived their QoL in a very positive manner (50.8% rated it as “good”, 6.8% as “very good” and 3.4% as “excellent”); 28.8% perceived it as “acceptable” and 10.2% as “bad”. No significant statistical differences were found for the considered variables.\nConclusions: Centenarians seem to present high levels of perceived QoL, which can be associated with a great ability to adapt to adverse situations that occur through their lives. Neither contextual and health aspects seem to in􏰂uence the perception of QoL in this particular sample study. Nonetheless, more research is \nneeded to understand the speci􏰀cities of the QoL in the centenarian population, namely the role of psychological and social variables.\ninfo:eu-repo/semantics/publishedVersion","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2014-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":null,"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":null,"context":[{"id":"http://zenodo.org/communities/edenis"},{"id":"http://zenodo.org/communities/aginfra"}, {"id":"http://zenodo.org/communities/primefish"}],"externalReference":[],"instance":[{"license":null,"accessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"instancetype":{"classid":"0020","classname":"Other ORP type","schemeid":"dnet:publication_resource","schemename":"dnet:publication_resource"},"hostedby":{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null},"url":["http://hdl.handle.net/10400.19/5415"],"distributionlocation":"","collectedfrom":{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null},"dateofacceptance":{"value":"2014-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"processingchargeamount":null,"processingchargecurrency":null,"refereed":null}],"contactperson":[],"contactgroup":[],"tool":[]} -{"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1585055423836,"id":"50|od______2017::1e400f1747487fd15998735c41a55c72","originalId":["od______2017::1e400f1747487fd15998735c41a55c72"],"collectedfrom":[{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null}],"pid":[],"dateofcollection":"2019-02-25T04:30:56.996Z","dateoftransformation":"2019-11-30T04:19:59.556Z","extraInfo":[],"oaiprovenance":{"originDescription":{"harvestDate":"2019-02-25T04:30:56.996Z","altered":true,"baseURL":"http://repositorio.ipv.pt/oai/openaire","identifier":"oai:repositorio.ipv.pt:10400.19/5422","datestamp":"2019-02-23T03:01:29Z","metadataNamespace":"http://www.openarchives.org/OAI/2.0/oai_dc/"}},"author":[{"fullname":"Brandão, Daniela","name":"Daniela","surname":"Brandão","rank":1,"pid":null,"affiliation":null},{"fullname":"Ribeiro, Oscar","name":"Oscar","surname":"Ribeiro","rank":2,"pid":null,"affiliation":null},{"fullname":"Araújo, Lia","name":"Lia","surname":"Araújo","rank":3,"pid":null,"affiliation":null},{"fullname":"Paul, Constança","name":"Constança","surname":"Paul","rank":4,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Oldest old","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Census","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"What about the Portuguese oldest old? A global overview using census data","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[],"description":[{"value":"Background\nThe older population is itself aging, and achieving an advanced age is becoming more common worldwide. In Portugal, individuals aged 80+ represent 5.6 % of the total population and 26.5 % of the popu- lation were aged 65 and over in 2011. Having a national profile on this population will give important information to develop interven- tion programs and identify the areas requiring most attention. Ob- jective: This study aims to provide a profile of the Portuguese oldest old, as given by the last national census data.\nMethods\nThe characteristics of all residents aged 80+ (N = 532,219) were ana- lysed considering socio-demographic information (gender, marital status, education, type of residence, place of birth, income) and the existence of difficulties in functional, sensorial and cognitive activities due to health problems or ageing.\nResults\nThe majority of the most aged are females (64.5 %), widowed (53.9 %), and present low educational levels (46.1 % never attended school and 31.6 % do not know how to read/write). Own pensions constitute the main source of income (96.3 %) and the majority live in private households (88.8 %), with 43.2 % currently living in the place where they were born. The majority (73.0 %) reported major difficulties in at least one functional activity – bathing/dressing, walk- ing/climbing stairs, seeing, hearing, memory/concentration, under- standing others/being understood.\nConclusions\nThe high percentage of oldest old living in private households and the presence of functional limitations point to the importance of in- formal care and community care services to support this population. Further studies paying attention to their needs and utilisation of ser- vices are 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agricultura está inevitavelmente associada a um conjunto de variáveis no ecossistema, onde estão incluídos as pragas e doenças nas culturas e presença de outras plantas que competem pelo alimento, água e luz. Estes agentes são responsáveis por perdas no rendimento que, normalmente, não são aceites pelo agricultor. E é, por isso, que se recorre aos pesticidas: é preciso proteger as culturas do ataque dos seus inimigos.\nTambém é verdade que a agricultura é a atividade desenvolvida pelo Homem que mais se aproxima dos sistemas naturais e tem, assim, um papel central na produção de diversos serviços do ecossistema, como a biodiversidade agrícola, qualidade do solo e água, estabilidade climática e manutenção da paisagem. Ora, o uso dos pesticidas introduz efeitos negativos em todo este sistema: degradam o solo, reduzem a qualidade e disponibilidade de água, causam poluição e perda de habitats selvagens e de biodiversidade. Aqui reside a encruzilhada na proteção das 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Evidences about their quality of life (QoL) are, nevertheless, still limited. Different conceptualizations of QoL, the overvaluation of the negative aspects of advanced age and the heterogeneity of the oldest old are some issues that could explain the dif􏰀culties in this assessment. Objectives: This study aims to analyze the perceived QoL in a sample of centenarians and analyze if there are significant life context (community vs institutional) and health (objective and subjective perception) differences.\nMethods: A subsample of 59 Portuguese centenarians who participated in the PT100_Oporto Centenarian Study, conducted in 2013 was considered. Descriptive and chi-square analysis were conducted.\nResults: Most centenarians perceived their QoL in a very positive manner (50.8% rated it as “good”, 6.8% as “very good” and 3.4% as “excellent”); 28.8% perceived it as “acceptable” and 10.2% as “bad”. No significant statistical differences were found for the considered variables.\nConclusions: Centenarians seem to present high levels of perceived QoL, which can be associated with a great ability to adapt to adverse situations that occur through their lives. Neither contextual and health aspects seem to in􏰂uence the perception of QoL in this particular sample study. Nonetheless, more research is \nneeded to understand the speci􏰀cities of the QoL in the centenarian population, namely the role of psychological and social variables.\ninfo:eu-repo/semantics/publishedVersion","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2014-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":null,"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":null,"context":[{"id":"http://zenodo.org/communities/edenis"},{"id":"http://zenodo.org/communities/aginfra"}, {"id":"http://zenodo.org/communities/primefish"}],"externalReference":[],"instance":[{"license":null,"accessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"instancetype":{"classid":"0020","classname":"Other ORP type","schemeid":"dnet:publication_resource","schemename":"dnet:publication_resource"},"hostedby":{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null},"url":["http://hdl.handle.net/10400.19/5415"],"distributionlocation":"","collectedfrom":{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null},"dateofacceptance":{"value":"2014-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"processingchargeamount":null,"processingchargecurrency":null,"refereed":null}],"contactperson":[],"contactgroup":[],"tool":[]} +{"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1585055423836,"id":"50|od______2017::1e400f1747487fd15998735c41a55c72","originalId":["od______2017::1e400f1747487fd15998735c41a55c72"],"collectedfrom":[{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null}],"pid":[],"dateofcollection":"2019-02-25T04:30:56.996Z","dateoftransformation":"2019-11-30T04:19:59.556Z","extraInfo":[],"oaiprovenance":{"originDescription":{"harvestDate":"2019-02-25T04:30:56.996Z","altered":true,"baseURL":"http://repositorio.ipv.pt/oai/openaire","identifier":"oai:repositorio.ipv.pt:10400.19/5422","datestamp":"2019-02-23T03:01:29Z","metadataNamespace":"http://www.openarchives.org/OAI/2.0/oai_dc/"}},"author":[{"fullname":"Brandão, Daniela","name":"Daniela","surname":"Brandão","rank":1,"pid":null,"affiliation":null},{"fullname":"Ribeiro, Oscar","name":"Oscar","surname":"Ribeiro","rank":2,"pid":null,"affiliation":null},{"fullname":"Araújo, Lia","name":"Lia","surname":"Araújo","rank":3,"pid":null,"affiliation":null},{"fullname":"Paul, Constança","name":"Constança","surname":"Paul","rank":4,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"TWITTER","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Census","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"What about the Portuguese oldest old? A global overview using census data","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[],"description":[{"value":"Background\nThe older population is itself aging, and achieving an advanced age is becoming more common worldwide. In Portugal, individuals aged 80+ represent 5.6 % of the total population and 26.5 % of the popu- lation were aged 65 and over in 2011. Having a national profile on this population will give important information to develop interven- tion programs and identify the areas requiring most attention. Ob- jective: This study aims to provide a profile of the Portuguese oldest old, as given by the last national census data.\nMethods\nThe characteristics of all residents aged 80+ (N = 532,219) were ana- lysed considering socio-demographic information (gender, marital status, education, type of residence, place of birth, income) and the existence of difficulties in functional, sensorial and cognitive activities due to health problems or ageing.\nResults\nThe majority of the most aged are females (64.5 %), widowed (53.9 %), and present low educational levels (46.1 % never attended school and 31.6 % do not know how to read/write). Own pensions constitute the main source of income (96.3 %) and the majority live in private households (88.8 %), with 43.2 % currently living in the place where they were born. The majority (73.0 %) reported major difficulties in at least one functional activity – bathing/dressing, walk- ing/climbing stairs, seeing, hearing, memory/concentration, under- standing others/being understood.\nConclusions\nThe high percentage of oldest old living in private households and the presence of functional limitations point to the importance of in- formal care and community care services to support this population. Further studies paying attention to their needs and utilisation of ser- vices are 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Constança","name":"Constança","surname":"Paul","rank":5,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Twitter data","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Centenarians","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"Centenarians in Europe","qualifier":{"classid":"main title","classname":"main 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Following this tendency, the number of centenarian studies has also exponentially augmented. Given the complexity to conduct research with centenarians, elementary information on this specific age group remains unknown at a European level. This paper compares basic characteristics of centenarians from 32 European coun- tries based on Census 2011. Results revealed that France is the country with higher ratio of centenarians, followed by Italy and Greece; on the other hand Croatia, Romania and Bulgaria present the lower ratio. The distribution accord- ing to gender is similar for all countries, with higher ratio of women reaching 100 years old. Different patterns of education level were found on countries where this infor- mation was reliable: Portugal and Greece are the countries with lower levels of education, with more than half without formal education; Finland, UK and Iceland are the countries with higher levels of education, with all centenarians having at least lower secondary education. Analysing the residence situation (living in the community or living in the institu- tion), Romania, Bulgaria, Lithuania, Greece and Latvia are the countries that present higher percentages of centenarians living in the community; Iceland is the country with lower percentage of centenarians living in the community. A posi- tive correlation between the number of centenarians and the percentage of Total Health Expenditure of GDP is observed. This study provides important information about the current profile of European centenarians, which is compared to gen- eral information on the centenarian population from EUA and Asia.\ninfo:eu-repo/semantics/publishedVersion","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2017-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":null,"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":null,"context":[],"externalReference":[],"instance":[{"license":null,"accessright":{"classid":"OPEN","classname":"Open 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Oscar","name":"Oscar","surname":"Ribeiro","rank":4,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Survival","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"100 years 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individuals aged 80 and over is growing faster than other segment of the population, and within this group the number of centenarians has risen exponentially worldwide. This phenomena lead to an increasing number of centenarian studies, improving the knowledge about this population, validating the idea of heterogeneity that char- acterizes this group. However, the factors influencing their aging survival remains understudied. The present study aims to identify factors associated with survival after 100 years old in a sample of Portuguese centenarians. After being included in a population-based study on centenarians (PT100–Oporto Centenarian Study), each participant was assessed by a tel- ephone interview every 6 months in order to assess his/her health condition. Follow-up was considered as the time (in months) between 100th birthday and death or the last tel- ephone contact. Survival analysis was performed to iden- tify factors associated with survival after 100 years old. Sociological and medical factors were considered. 140 cen- tenarians were assessed and 115 (82.1%) died. The median survival time after 100 years old was 38 months. Survival after age 100 was associated with acute disease (last month), self-perception of physical condition and drinking status. This study intends do identify factors that predict longevity in long-lived individuals. Findings recognize the importance of factors related with health status, self-perception of physi- cal condition and life style (no alcohol consume) for survival. Further studies should explore the predictive value of these factors, as well as psychosocial aspects, considering living longer but also the quality of time beyond one hundred.\ninfo:eu-repo/semantics/publishedVersion","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2018-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":null,"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":null,"context":[],"externalReference":[],"instance":[{"license":null,"accessright":{"classid":"OPEN","classname":"Open 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João","surname":"Azevedo","rank":5,"pid":null,"affiliation":null},{"fullname":"Ribeiro, Oscar","name":"Oscar","surname":"Ribeiro","rank":6,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Cognition","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Survival","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Functional capacity","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"Cognition and functionality: how do they related to time lived after 100 years of age?","qualifier":{"classid":"main title","classname":"main 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Therefore, the analysis of survival time after becoming a centenarian and related factors constitute an import- ant issue for the quality of care provision. The objective of this study is to identify health related factors associated with the time lived after being 100 years of age. Methods: Data come from the population-based study PT100 (Oporto Centenarian Study) and considers information gathered through face-to-face interviews with centenarians and their proxies during 2013. Study eligibility criteria included being 100 and more years old and living in the Oporto Metropolitan Area. Survival analyses were performed in order to identify factors associated with survival after the 100. Functional status (e.g., walking, being bedrid- den) and specific health conditions (e.g. presence/absence of cognitive impairment) were considered as potential factors. Results: The sam- ple comprises 140 centenarians with approximately 14.5 months as median survival time after their 100th anniversary. Centenarians who were bedridden presented a higher probability to live after 100 years when compared with functionally independent centenarians. Presence of cognitive impairment was not associated with the time lived after 100 years old. Conclusions: Given the increasing number of centenarians in Portugal, different studies based on this population need to be consid- ered. The present study, focused on the life after 100 years old, provides new information about this topic contributing to the formulation of new scientific questions for this population.\ninfo:eu-repo/semantics/publishedVersion","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2014-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":null,"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":null,"context":[],"externalReference":[],"instance":[{"license":null,"accessright":{"classid":"OPEN","classname":"Open 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{"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1585055427049,"id":"50|od______2017::4a1bcdd965b879fbac86a7d3b947a6cc","originalId":["od______2017::4a1bcdd965b879fbac86a7d3b947a6cc"],"collectedfrom":[{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de 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Porto","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":null,"context":[],"externalReference":[],"instance":[{"license":null,"accessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"instancetype":{"classid":"0010","classname":"Lecture","schemeid":"dnet:publication_resource","schemename":"dnet:publication_resource"},"hostedby":{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de 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into account the distances between haplotypes (ie, that consider all haplotypes equally divergent).[br/] The source file should be an ASCII file (its name should have 8 characters maximum: 12345678.txt) and should include the following information:[br/] First line :[br/] Number of cytotypes Number of populations Number of characters distinguishing the variants (for instance number of polymorphic fragments, or of polymorphic nucleotide sites). The program asks for the number of permutations to be made.[br/] see the example (\\ExamplePermut\\input.txt and \\ExamplePermut\\output.out).[br/] Then follows the number of individuals having a given cytotype (column) in a given population (row). Finally, and without interruption, provide the table of character states for all haplotypes, where each line corresponds to one haplotype, and each column to a character. No column should be empty (no missing haplotype) and each population (row) should be composed of AT LEAST 3 individuals![br/] The output file provides permutated values of Nst in a single row, and the value of the last 5% and last 1%. The mean of the permutated values is also given and should be close to the Gst value (by construction). To test if the observed Nst value is larger than the Gst, we count how many permutated values are larger than the observed Nst. If you have 5% of the permutated values greater than the observed value of Nst, then your test is not significant, otherwise it is and you know the P-value. This is akin to testing if Gst = Nst.[br/] [br/] README CpSSR :[br/] It computes measures of diversity and differenciation from haploid population genetic data, when the difference in number of repeats between alleles is available, and tests whether the differentiation and diversity measures differ from the equivalent measures when the distances between haplotypes is not considered (ie, when all haplotypes are considered equally divergent). The source file should be an ASCII file (its name should have 8 characters maximum: 12345678.txt) and should include the following information:[br/] First line :[br/] Number of cytotypes Number of populations Number of cpSSR loci. The program asks for the number of permutations to be made. See the example (\\ExampleCpSSR\\input.txt and \\ExamplePermut\\CpSSR.out).[br/] Then follows the number of individuals having a given haplotype (column) in a given population (row). Finally, and without interruption, provide the table of length variant states for all haplotypes, where each line corresponds to one haplotype, and each column to a character. No column should be empty (no missing haplotype) and each population (row) should be composed of AT LEAST 3 individuals![br/] The output file provides permutated values of Rst in a single row, and the value of the last 5% and last 1%. The mean of the permutated values is also given and should be close to the Gst value (by construction). To test if the observed Rst value is larger than the Gst, you count how many permutated values are larger than the observed Rst. If you have 5% of the permutated values greater than the observed value of Rst, then your test is not significant, otherwise it is and you know the P-value. This is akin to testing if Gst = Rst. I usually go for a one-sided test (i.e. I test if Rst>Gst, and not 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17 00:00:00 2001 From: Claudio Atzori Date: Tue, 3 May 2022 11:55:45 +0200 Subject: [PATCH 047/214] EOSC Services - removed field knowledgegraph; depending on the released schema module --- .../eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java | 5 ----- pom.xml | 2 +- 2 files changed, 1 insertion(+), 6 deletions(-) diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java index b811a7a0f..27128138c 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java @@ -774,11 +774,6 @@ public class XmlRecordFactory implements Serializable { metadata.add(XmlSerializationUtils.asXmlElement("thematic", ds.getThematic().toString())); } - if (ds.getKnowledgegraph() != null) { - metadata - .add(XmlSerializationUtils.asXmlElement("knowledgegraph", ds.getKnowledgegraph().toString())); - } - if (ds.getContentpolicies() != null) { metadata .addAll( diff --git a/pom.xml b/pom.xml index 03a4496d7..54070f654 100644 --- a/pom.xml +++ b/pom.xml @@ -801,7 +801,7 @@ 3.3.3 3.4.2 [2.12,3.0) - [2.11.34-eosc-SNAPSHOT] + [2.12.0] [4.0.3] [6.0.5] [3.1.6] From 3aeedd931a055dca66d0ef4aabed23a0608770f2 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 4 May 2022 10:06:38 +0200 Subject: [PATCH 048/214] [EOSCTag] fixed issue in case description is null. Modified test resources and classes --- .../eu/dnetlib/dhp/bulktag/SparkEoscTag.java | 30 +++++++++++++------ .../dhp/bulktag/oozie_app/workflow.xml | 4 +-- .../dnetlib/dhp/bulktag/EOSCTagJobTest.java | 6 ++-- .../eosctag/galaxy/dataset/dataset_10.json | 2 +- .../eosctag/galaxy/software/software_10.json | 3 +- .../eosctag/twitter/dataset/dataset_10.json | 1 + 6 files changed, 30 insertions(+), 16 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java index 1d0aaa631..561e1d57e 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java @@ -179,12 +179,11 @@ public class SparkEoscTag { Set words = getWordsSP(r.getTitle()); words.addAll(getWordsF(r.getDescription())); if (words.contains("galaxy") && - (words.contains("workflow") || words.contains("software"))) + words.contains("workflow")) return true; if (r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("galaxy")) && - (r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("workflow"))) || - r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("software"))) + r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("workflow"))) return true; return false; } @@ -214,17 +213,30 @@ public class SparkEoscTag { private static Set getWordsSP(List elem) { Set words = new HashSet<>(); - elem - .forEach( - t -> words.addAll(Arrays.asList(t.getValue().toLowerCase().replaceAll("[^a-zA-Z ]", "").split(" ")))); + Optional + .ofNullable(elem) + .ifPresent( + e -> e + .forEach( + t -> words + .addAll( + Arrays.asList(t.getValue().toLowerCase().replaceAll("[^a-zA-Z ]", "").split(" "))))); return words; } private static Set getWordsF(List> elem) { Set words = new HashSet<>(); - elem - .forEach( - t -> words.addAll(Arrays.asList(t.getValue().toLowerCase().replaceAll("[^a-zA-Z ]", "").split(" ")))); + Optional + .ofNullable(elem) + .ifPresent( + e -> e + .forEach( + t -> words + .addAll( + Arrays.asList(t.getValue().toLowerCase().replaceAll("[^a-zA-Z ]", "").split(" "))))); +// elem +// .forEach( +// t -> words.addAll(Arrays.asList(t.getValue().toLowerCase().replaceAll("[^a-zA-Z ]", "").split(" ")))); return words; } diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml index 91fca7d61..4c34886e6 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml @@ -29,7 +29,7 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] @@ -226,7 +226,7 @@ --sourcePath${outputPath} --workingPath${workingDir}/eoscTag - + diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java index d96dc7f6c..55d3939e1 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java @@ -322,7 +322,7 @@ public class EOSCTagJobTest { .textFile(workingDir.toString() + "/input/software") .map(item -> OBJECT_MAPPER.readValue(item, Software.class)); - Assertions.assertEquals(10, tmp.count()); + Assertions.assertEquals(11, tmp.count()); Assertions .assertEquals( @@ -534,11 +534,11 @@ public class EOSCTagJobTest { .textFile(workingDir.toString() + "/input/dataset") .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); - Assertions.assertEquals(10, dats.count()); + Assertions.assertEquals(11, dats.count()); Assertions .assertEquals( - 2, + 3, dats .filter(s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Twitter Data"))) .count()); diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/galaxy/dataset/dataset_10.json b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/galaxy/dataset/dataset_10.json index 0243a4e3d..645a7522f 100644 --- a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/galaxy/dataset/dataset_10.json +++ b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/galaxy/dataset/dataset_10.json @@ -7,4 +7,4 @@ {"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1585055870582,"id":"50|od______3989::752fd0b2bbac1ea1cc50e52fd46eb663","originalId":["od______3989::752fd0b2bbac1ea1cc50e52fd46eb663"],"collectedfrom":[{"key":"opendoar____::3989","value":"Depósito Digital e-UCJC","dataInfo":null}],"pid":[],"dateofcollection":"2020-03-03T13:05:34.561Z","dateoftransformation":"2020-03-03T13:06:55.716Z","extraInfo":[],"oaiprovenance":{"originDescription":{"harvestDate":"2020-03-03T13:05:34.561Z","altered":true,"baseURL":"http%3A%2F%2Frepositorio.ucjc.edu%2Foai%2Frequest","identifier":"oai:repositorio.ucjc.edu:20.500.12020/798","datestamp":"2018-11-14T12:57:26Z","metadataNamespace":"http://www.openarchives.org/OAI/2.0/oai_dc/"}},"author":[{"fullname":"Universidad Camilo José Cela, Vicerrectorado de Innovación","name":"Vicerrectorado Innovación","surname":"Universidad Camilo José Cela","rank":1,"pid":null,"affiliation":null}],"resulttype":{"classid":"dataset","classname":"dataset","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"esl/spa","classname":"Spanish","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Psicología","qualifier":{"classid":"","classname":"","schemeid":"","schemename":""},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Alcohol","qualifier":{"classid":"","classname":"","schemeid":"","schemename":""},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Dependencia","qualifier":{"classid":"","classname":"","schemeid":"","schemename":""},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Proyectos de investigación","qualifier":{"classid":"","classname":"","schemeid":"","schemename":""},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Alcoholismo","qualifier":{"classid":"","classname":"","schemeid":"","schemename":""},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Realidad virtual","qualifier":{"classid":"","classname":"","schemeid":"","schemename":""},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Psicología conductual","qualifier":{"classid":"","classname":"","schemeid":"","schemename":""},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"Investigación - 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La fase final del tratamiento se enfoca en que el paciente \"sea capaz de reconstruir su vida\" a través de programas de entrenamiento de habilidades sociales, asertividad, familias... \"Juntando todas las áreas de intervención, la abstinencia se mantiene mucho más tiempo y las recaídas 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