From 65cc736e2fb2848bef81f47715370b0f6a9064a4 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 20 Jul 2022 17:05:56 +0200 Subject: [PATCH 01/13] [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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Die wörter άγαλμα, είχών, ξόανον, ανδρuις und verwandte, in ihren verschiedenen beziehungen. 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 a12d28c6444616ac914d79b43e5360c4e92d714b Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 22 Jul 2022 16:23:12 +0200 Subject: [PATCH 02/13] [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 03/13] [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 62d2138806a9740085174e819b361ee19640366f Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 8 Aug 2022 14:10:47 +0200 Subject: [PATCH 04/13] [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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"miriam.baglioni" Date: Wed, 10 Aug 2022 15:13:10 +0200 Subject: [PATCH 05/13] [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 5240ac3d7bdfeba3ce7f5bb2bbacab7fa8c84641 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 19 Sep 2022 11:02:18 +0200 Subject: [PATCH 06/13] [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 dcd85f8cd79ab8342e03eca6ef9530f35dd242ab Mon Sep 17 00:00:00 2001 From: dimitrispie Date: Thu, 22 Sep 2022 13:33:07 +0300 Subject: [PATCH 07/13] - 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 960cb861a0ace5556213016942ca0b05039632ca Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 23 Sep 2022 11:14:04 +0200 Subject: [PATCH 08/13] 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 c86cc53520216a7890cdfa0574187ce488ac27f6 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 23 Sep 2022 15:19:50 +0200 Subject: [PATCH 09/13] 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 55da4d871509f5f1e71c5939298d49eac9d9d92b Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 23 Sep 2022 16:02:19 +0200 Subject: [PATCH 10/13] [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 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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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"miriam.baglioni" Date: Fri, 23 Sep 2022 16:47:19 +0200 Subject: [PATCH 11/13] [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 12/13] [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 57dbeb08d2e07bacd2ba7c559e2f8fc9dace0ee1 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 27 Sep 2022 14:55:10 +0200 Subject: [PATCH 13/13] 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) {