diff --git a/dhp-build/dhp-build-assembly-resources/pom.xml b/dhp-build/dhp-build-assembly-resources/pom.xml index 012ff89a3..44165995d 100644 --- a/dhp-build/dhp-build-assembly-resources/pom.xml +++ b/dhp-build/dhp-build-assembly-resources/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp-build - 1.2.4-SNAPSHOT + 1.2.5-SNAPSHOT dhp-build-assembly-resources diff --git a/dhp-build/dhp-build-properties-maven-plugin/pom.xml b/dhp-build/dhp-build-properties-maven-plugin/pom.xml index 256017e2c..7579bdf45 100644 --- a/dhp-build/dhp-build-properties-maven-plugin/pom.xml +++ b/dhp-build/dhp-build-properties-maven-plugin/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp-build - 1.2.4-SNAPSHOT + 1.2.5-SNAPSHOT dhp-build-properties-maven-plugin diff --git a/dhp-build/dhp-code-style/pom.xml b/dhp-build/dhp-code-style/pom.xml index db0097d64..5a86efe17 100644 --- a/dhp-build/dhp-code-style/pom.xml +++ b/dhp-build/dhp-code-style/pom.xml @@ -5,7 +5,7 @@ eu.dnetlib.dhp dhp-code-style - 1.2.4-SNAPSHOT + 1.2.5-SNAPSHOT jar @@ -47,12 +47,16 @@ org.apache.maven.plugins maven-site-plugin 3.9.1 + + true + + UTF-8 sftp://dnet-hadoop@static-web.d4science.org/dnet-hadoop diff --git a/dhp-build/pom.xml b/dhp-build/pom.xml index 97fbdf45b..9040ea94e 100644 --- a/dhp-build/pom.xml +++ b/dhp-build/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp - 1.2.4-SNAPSHOT + 1.2.5-SNAPSHOT dhp-build pom diff --git a/dhp-common/pom.xml b/dhp-common/pom.xml index 7b18f0105..6df11f4ea 100644 --- a/dhp-common/pom.xml +++ b/dhp-common/pom.xml @@ -5,7 +5,7 @@ eu.dnetlib.dhp dhp - 1.2.4-SNAPSHOT + 1.2.5-SNAPSHOT ../pom.xml diff --git a/dhp-workflows/dhp-actionmanager/pom.xml b/dhp-workflows/dhp-actionmanager/pom.xml index f63f3aa01..29e1fab1f 100644 --- a/dhp-workflows/dhp-actionmanager/pom.xml +++ b/dhp-workflows/dhp-actionmanager/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp-workflows - 1.2.4-SNAPSHOT + 1.2.5-SNAPSHOT dhp-actionmanager diff --git a/dhp-workflows/dhp-aggregation/pom.xml b/dhp-workflows/dhp-aggregation/pom.xml index c89cc9d1d..53d349d2a 100644 --- a/dhp-workflows/dhp-aggregation/pom.xml +++ b/dhp-workflows/dhp-aggregation/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp-workflows - 1.2.4-SNAPSHOT + 1.2.5-SNAPSHOT dhp-aggregation diff --git a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala index 136b0fb93..8e41de83c 100644 --- a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala +++ b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala @@ -72,7 +72,6 @@ class DataciteToOAFTest extends AbstractVocabularyTest { spark.read.load(targetPath).printSchema(); - val result: Dataset[Oaf] = spark.read.load(targetPath).as[Oaf] result diff --git a/dhp-workflows/dhp-blacklist/pom.xml b/dhp-workflows/dhp-blacklist/pom.xml index 047767d33..479a9e8c6 100644 --- a/dhp-workflows/dhp-blacklist/pom.xml +++ b/dhp-workflows/dhp-blacklist/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.5-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-broker-events/pom.xml b/dhp-workflows/dhp-broker-events/pom.xml index afbd93dcb..5a41a0090 100644 --- a/dhp-workflows/dhp-broker-events/pom.xml +++ b/dhp-workflows/dhp-broker-events/pom.xml @@ -1,11 +1,9 @@ - + dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.5-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-dedup-openaire/pom.xml b/dhp-workflows/dhp-dedup-openaire/pom.xml index f47f8ba6e..a14076a78 100644 --- a/dhp-workflows/dhp-dedup-openaire/pom.xml +++ b/dhp-workflows/dhp-dedup-openaire/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.5-SNAPSHOT 4.0.0 dhp-dedup-openaire diff --git a/dhp-workflows/dhp-distcp/pom.xml b/dhp-workflows/dhp-distcp/pom.xml index 8c10538c0..c3d3a7375 100644 --- a/dhp-workflows/dhp-distcp/pom.xml +++ b/dhp-workflows/dhp-distcp/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.5-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-doiboost/pom.xml b/dhp-workflows/dhp-doiboost/pom.xml index f496ea9a2..37accbc4f 100644 --- a/dhp-workflows/dhp-doiboost/pom.xml +++ b/dhp-workflows/dhp-doiboost/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.5-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala index 0cb08ea94..b4d6d67e2 100644 --- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala +++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala @@ -446,16 +446,12 @@ case object Crossref2Oaf { case "10.13039/501100000781" => generateSimpleRelationFromAward(funder, "corda_______", extractECAward) generateSimpleRelationFromAward(funder, "corda__h2020", extractECAward) - case "10.13039/100000001" => - generateSimpleRelationFromAward(funder, "nsf_________", a => a) - case "10.13039/501100001665" => - generateSimpleRelationFromAward(funder, "anr_________", a => a) - case "10.13039/501100002341" => - generateSimpleRelationFromAward(funder, "aka_________", a => a) + case "10.13039/100000001" => generateSimpleRelationFromAward(funder, "nsf_________", a => a) + case "10.13039/501100001665" => generateSimpleRelationFromAward(funder, "anr_________", a => a) + case "10.13039/501100002341" => generateSimpleRelationFromAward(funder, "aka_________", a => a) case "10.13039/501100001602" => - generateSimpleRelationFromAward(funder, "aka_________", a => a.replace("SFI", "")) - case "10.13039/501100000923" => - generateSimpleRelationFromAward(funder, "arc_________", a => a) + generateSimpleRelationFromAward(funder, "sfi_________", a => a.replace("SFI", "")) + case "10.13039/501100000923" => generateSimpleRelationFromAward(funder, "arc_________", a => a) case "10.13039/501100000038" => val targetId = getProjectId("nserc_______", "1e5e62235d094afd01cd56e65112fc63") queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY) @@ -468,14 +464,10 @@ case object Crossref2Oaf { val targetId = getProjectId("cihr________", "1e5e62235d094afd01cd56e65112fc63") queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY) queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES) - case "10.13039/501100002848" => - generateSimpleRelationFromAward(funder, "conicytf____", a => a) - case "10.13039/501100003448" => - generateSimpleRelationFromAward(funder, "gsrt________", extractECAward) - case "10.13039/501100010198" => - generateSimpleRelationFromAward(funder, "sgov________", a => a) - case "10.13039/501100004564" => - generateSimpleRelationFromAward(funder, "mestd_______", extractECAward) + case "10.13039/501100002848" => generateSimpleRelationFromAward(funder, "conicytf____", a => a) + case "10.13039/501100003448" => generateSimpleRelationFromAward(funder, "gsrt________", extractECAward) + case "10.13039/501100010198" => generateSimpleRelationFromAward(funder, "sgov________", a => a) + case "10.13039/501100004564" => generateSimpleRelationFromAward(funder, "mestd_______", extractECAward) case "10.13039/501100003407" => generateSimpleRelationFromAward(funder, "miur________", a => a) val targetId = getProjectId("miur________", "1e5e62235d094afd01cd56e65112fc63") @@ -487,15 +479,11 @@ case object Crossref2Oaf { "irb_hr______", a => a.replaceAll("Project No.", "").replaceAll("HRZZ-", "") ) - case "10.13039/501100006769" => - generateSimpleRelationFromAward(funder, "rsf_________", a => a) - case "10.13039/501100001711" => - generateSimpleRelationFromAward(funder, "snsf________", snsfRule) - case "10.13039/501100004410" => - generateSimpleRelationFromAward(funder, "tubitakf____", a => a) - case "10.10.13039/100004440" => - generateSimpleRelationFromAward(funder, "wt__________", a => a) + case "10.13039/501100006769" => generateSimpleRelationFromAward(funder, "rsf_________", a => a) + case "10.13039/501100001711" => generateSimpleRelationFromAward(funder, "snsf________", snsfRule) + case "10.13039/501100004410" => generateSimpleRelationFromAward(funder, "tubitakf____", a => a) case "10.13039/100004440" => + generateSimpleRelationFromAward(funder, "wt__________", a => a) val targetId = getProjectId("wt__________", "1e5e62235d094afd01cd56e65112fc63") queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY) queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES) @@ -516,6 +504,7 @@ case object Crossref2Oaf { case "CONICYT, Programa de Formación de Capital Humano Avanzado" => generateSimpleRelationFromAward(funder, "conicytf____", extractECAward) case "Wellcome Trust Masters Fellowship" => + generateSimpleRelationFromAward(funder, "wt__________", a => a) val targetId = getProjectId("wt__________", "1e5e62235d094afd01cd56e65112fc63") queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY) queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES) diff --git a/dhp-workflows/dhp-enrichment/pom.xml b/dhp-workflows/dhp-enrichment/pom.xml index 0b4269acd..591cad252 100644 --- a/dhp-workflows/dhp-enrichment/pom.xml +++ b/dhp-workflows/dhp-enrichment/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.5-SNAPSHOT 4.0.0 @@ -51,7 +51,7 @@ eu.dnetlib.dhp dhp-aggregation - 1.2.4-SNAPSHOT + 1.2.5-SNAPSHOT compile diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/oozie_app/workflow.xml index 202c86a6d..271ccbf72 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/oozie_app/workflow.xml @@ -274,7 +274,6 @@ --sourcePath${sourcePath}/publication --preparedInfoPath${workingDir}/publication - --saveGraph${saveGraph} --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication --outputPath${outputPath}/publication @@ -304,7 +303,6 @@ --sourcePath${sourcePath}/dataset --preparedInfoPath${workingDir}/dataset - --saveGraph${saveGraph} --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset --outputPath${outputPath}/dataset @@ -334,7 +332,6 @@ --sourcePath${sourcePath}/otherresearchproduct --preparedInfoPath${workingDir}/otherresearchproduct - --saveGraph${saveGraph} --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct --outputPath${outputPath}/otherresearchproduct @@ -364,7 +361,6 @@ --sourcePath${sourcePath}/software --preparedInfoPath${workingDir}/software - --saveGraph${saveGraph} --resultTableNameeu.dnetlib.dhp.schema.oaf.Software --outputPath${outputPath}/software diff --git a/dhp-workflows/dhp-graph-mapper/pom.xml b/dhp-workflows/dhp-graph-mapper/pom.xml index 17146903a..687f0de66 100644 --- a/dhp-workflows/dhp-graph-mapper/pom.xml +++ b/dhp-workflows/dhp-graph-mapper/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.5-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java new file mode 100644 index 000000000..b20dcb67b --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java @@ -0,0 +1,113 @@ +package eu.dnetlib.dhp.oa.graph.clean; + +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.Context; +import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.schema.oaf.OafEntity; +import eu.dnetlib.dhp.schema.oaf.Result; +import eu.dnetlib.dhp.utils.ISLookupClientFactory; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.Serializable; +import java.util.List; +import java.util.Optional; +import java.util.stream.Collectors; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +public class CleanContextSparkJob implements Serializable { + private static final Logger log = LoggerFactory.getLogger(CleanContextSparkJob.class); + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + public static void main(String[] args) throws Exception { + + String jsonConfiguration = IOUtils + .toString( + CleanContextSparkJob.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/input_clean_context_parameters.json")); + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + String inputPath = parser.get("inputPath"); + log.info("inputPath: {}", inputPath); + + String workingPath = parser.get("workingPath"); + log.info("workingPath: {}", workingPath); + + String contextId = parser.get("contextId"); + log.info("contextId: {}", contextId); + + String verifyParam = parser.get("verifyParam"); + log.info("verifyParam: {}", verifyParam); + + + String graphTableClassName = parser.get("graphTableClassName"); + log.info("graphTableClassName: {}", graphTableClassName); + + Class entityClazz = (Class) Class.forName(graphTableClassName); + + + SparkConf conf = new SparkConf(); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + + cleanContext(spark, contextId, verifyParam, inputPath, entityClazz, workingPath); + }); + } + + private static void cleanContext(SparkSession spark, String contextId, String verifyParam, String inputPath, Class entityClazz, String workingPath) { + Dataset res = spark + .read() + .textFile(inputPath) + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, entityClazz), + Encoders.bean(entityClazz)); + + res.map((MapFunction) r -> { + if(!r.getTitle() + .stream() + .filter(t -> t.getQualifier().getClassid() + .equalsIgnoreCase(ModelConstants.MAIN_TITLE_QUALIFIER.getClassid())) + .anyMatch(t -> t.getValue().toLowerCase().startsWith(verifyParam.toLowerCase()))){ + return r; + } + r.setContext(r.getContext().stream().filter(c -> !c.getId().split("::")[0] + .equalsIgnoreCase(contextId)).collect(Collectors.toList())); + return r; + } ,Encoders.bean(entityClazz)) + .write() + .mode(SaveMode.Overwrite) + .option("compression","gzip") + .json(workingPath); + + spark.read().textFile(workingPath).map((MapFunction) value -> OBJECT_MAPPER.readValue(value, entityClazz), + Encoders.bean(entityClazz)) + .write() + .mode(SaveMode.Overwrite) + .option("compression","gzip") + .json(inputPath); + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/BibJson.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/BibJson.java index f7c0d501f..4de687ec7 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/BibJson.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/BibJson.java @@ -4,8 +4,6 @@ package eu.dnetlib.dhp.oa.graph.hostedbymap.model.doaj; import java.io.Serializable; import java.util.List; -import com.fasterxml.jackson.annotation.JsonIgnore; - public class BibJson implements Serializable { private Editorial editorial; private PidScheme pid_scheme; diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_context_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_context_parameters.json new file mode 100644 index 000000000..e3d31d69f --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_context_parameters.json @@ -0,0 +1,37 @@ +[ + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "when true will stop SparkSession after job execution", + "paramRequired": false + }, + { + "paramName": "in", + "paramLongName": "inputPath", + "paramDescription": "the path to the graph data dump to read", + "paramRequired": true + }, + { + "paramName": "wp", + "paramLongName": "workingPath", + "paramDescription": "the path to store the output graph", + "paramRequired": true + }, + { + "paramName": "ci", + "paramLongName": "contextId", + "paramDescription": "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 context", + "paramRequired": true +} +] diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java new file mode 100644 index 000000000..bba814346 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java @@ -0,0 +1,159 @@ +package eu.dnetlib.dhp.oa.graph.clean; + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.oa.graph.dump.Constants; +import eu.dnetlib.dhp.oa.graph.dump.DumpJobTest; +import eu.dnetlib.dhp.oa.graph.dump.DumpProducts; +import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.dump.oaf.Instance; +import eu.dnetlib.dhp.schema.dump.oaf.OpenAccessRoute; +import eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Software; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import org.apache.commons.io.FileUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.List; +import java.util.Locale; + +public class CleanContextTest { + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path workingDir; + + private static final Logger log = LoggerFactory.getLogger(CleanContextTest.class); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files.createTempDirectory(DumpJobTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(DumpJobTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(DumpJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + public void testResultClean() throws Exception { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/clean/publication_clean_context.json") + .getPath(); + final String prefix = "gcube "; + + + spark.read().textFile(sourcePath).map((MapFunction) r -> OBJECT_MAPPER.readValue(r, Publication.class), Encoders.bean(Publication.class)) + .write().json(workingDir.toString() + "/publication"); + + + CleanContextSparkJob.main(new String[] { + "--isSparkSessionManaged", Boolean.FALSE.toString(), + "--inputPath", workingDir.toString() + "/publication", + "-graphTableClassName", Publication.class.getCanonicalName(), + "-workingPath", workingDir.toString() + "/working", + "-contextId","sobigdata", + "-verifyParam","gCube " + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/publication") + .map(item -> OBJECT_MAPPER.readValue(item, Publication.class)); + + Assertions.assertEquals(7, tmp.count()); + + //original result with sobigdata context and gcube as starting string in the main title for the publication + Assertions.assertEquals(0, + tmp.filter(p->p.getId().equals("50|DansKnawCris::0224aae28af558f21768dbc6439c7a95")).collect().get(0).getContext().size()); + + //original result with sobigdata context without gcube as starting string in the main title for the publication + Assertions.assertEquals(1, + tmp.filter(p->p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")).collect().get(0).getContext().size()); + Assertions.assertEquals("sobigdata::projects::2",tmp.filter(p->p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")).collect().get(0).getContext().get(0).getId() ); + + //original result with sobigdata context with gcube as starting string in the subtitle + Assertions.assertEquals(1, + tmp.filter(p->p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")).collect().get(0).getContext().size()); + Assertions.assertEquals("sobigdata::projects::2",tmp.filter(p->p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")).collect().get(0).getContext().get(0).getId() ); + List titles = tmp.filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")).collect().get(0).getTitle(); + Assertions.assertEquals(1, titles.size()); + Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix) ); + Assertions.assertEquals("subtitle", titles.get(0).getQualifier().getClassid()); + + //original result with sobigdata context with gcube not as starting string in the main title + Assertions.assertEquals(1, + tmp.filter(p->p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")).collect().get(0).getContext().size()); + Assertions.assertEquals("sobigdata::projects::1",tmp.filter(p->p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")).collect().get(0).getContext().get(0).getId() ); + titles = tmp.filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")).collect().get(0).getTitle(); + Assertions.assertEquals(1, titles.size()); + Assertions.assertFalse(titles.get(0).getValue().toLowerCase().startsWith(prefix) ); + Assertions.assertTrue(titles.get(0).getValue().toLowerCase().contains(prefix.trim()) ); + Assertions.assertEquals("main title", titles.get(0).getQualifier().getClassid()); + + //original result with sobigdata in context and also other contexts with gcube as starting string for the main title + Assertions.assertEquals(1, + tmp.filter(p->p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")).collect().get(0).getContext().size()); + Assertions.assertEquals("dh-ch",tmp.filter(p->p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")).collect().get(0).getContext().get(0).getId() ); + titles = tmp.filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")).collect().get(0).getTitle(); + Assertions.assertEquals(1, titles.size()); + Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix) ); + Assertions.assertEquals("main title", titles.get(0).getQualifier().getClassid()); + + //original result with multiple main title one of which whith gcube as starting string and with 2 contextes + Assertions.assertEquals(1, + tmp.filter(p->p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")).collect().get(0).getContext().size()); + Assertions.assertEquals("dh-ch",tmp.filter(p->p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")).collect().get(0).getContext().get(0).getId() ); + titles = tmp.filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")).collect().get(0).getTitle(); + Assertions.assertEquals(2, titles.size()); + Assertions.assertTrue(titles.stream().anyMatch(t -> t.getQualifier().getClassid().equals("main title") && t.getValue().toLowerCase().startsWith(prefix)) ); + + + //original result without sobigdata in context with gcube as starting string for the main title + Assertions.assertEquals(1, + tmp.filter(p->p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")).collect().get(0).getContext().size()); + Assertions.assertEquals("dh-ch",tmp.filter(p->p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")).collect().get(0).getContext().get(0).getId() ); + titles = tmp.filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")).collect().get(0).getTitle(); + Assertions.assertEquals(2, titles.size()); + + Assertions.assertTrue(titles.stream().anyMatch(t -> t.getQualifier().getClassid().equals("main title") && t.getValue().toLowerCase().startsWith(prefix))); + + + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/publication_clean_context.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/publication_clean_context.json new file mode 100644 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+compute stats indi_pub_green_oa; + create table indi_pub_grey_lit stored as parquet as select distinct p.id, coalesce(grey_lit, 0) as grey_lit from publication p @@ -22,6 +24,8 @@ join result_classifications rt on rt.id = p.id where rt.type not in ('Article','Part of book or chapter of book','Book','Doctoral thesis','Master thesis','Data Paper', 'Thesis', 'Bachelor thesis', 'Conference object') and not exists (select 1 from result_classifications rc where type ='Other literature type' and rc.id=p.id)) tmp on p.id=tmp.id; +compute stats indi_pub_grey_lit; + create table indi_pub_doi_from_crossref stored as parquet as select distinct p.id, coalesce(doi_from_crossref, 0) as doi_from_crossref from publication p @@ -31,6 +35,7 @@ join datasource d on d.id = ri.collectedfrom where pidtype='Digital Object Identifier' and d.name ='Crossref') tmp on tmp.id=p.id; +compute stats indi_pub_doi_from_crossref; ---- Sprint 2 ---- create table indi_result_has_cc_licence stored as parquet as select distinct r.id, (case when lic='' or lic is null then 0 else 1 end) as has_cc_license @@ -40,6 +45,8 @@ join result_licenses as license on license.id = r.id where lower(license.type) LIKE '%creativecommons.org%' OR lower(license.type) LIKE '%cc-%') tmp on r.id= tmp.id; +compute stats indi_result_has_cc_licence; + create table indi_result_has_cc_licence_url stored as parquet as select distinct r.id, case when lic_host='' or lic_host is null then 0 else 1 end as has_cc_license_url from result r @@ -49,16 +56,21 @@ join result_licenses as license on license.id = r.id WHERE lower(parse_url(license.type, "HOST")) = "creativecommons.org") tmp on r.id= tmp.id; +compute stats indi_result_has_cc_licence_url; + create table indi_pub_has_abstract stored as parquet as select distinct publication.id, coalesce(abstract, 1) has_abstract from publication; +compute stats indi_pub_has_abstract; + create table indi_result_with_orcid stored as parquet as select distinct r.id, coalesce(has_orcid, 0) as has_orcid from result r left outer join (select id, 1 as has_orcid from result_orcid) tmp on r.id= tmp.id; +compute stats indi_result_with_orcid; ---- Sprint 3 ---- create table indi_funded_result_with_fundref stored as parquet as @@ -68,6 +80,8 @@ left outer join (select distinct id, 1 as fundref from project_results where provenance='Harvested') tmp on r.id= tmp.id; +compute stats indi_funded_result_with_fundref; + create table indi_result_org_country_collab stored as parquet as with tmp as (select o.id as id, o.country , ro.id as result,r.type from organization o @@ -79,6 +93,8 @@ join tmp as o2 on o1.result=o2.result where o1.id<>o2.id and o1.country<>o2.country group by o1.id, o1.type,o2.country; +compute stats indi_result_org_country_collab; + create table indi_result_org_collab stored as parquet as with tmp as (select o.id, ro.id as result,r.type from organization o @@ -90,6 +106,8 @@ join tmp as o2 on o1.result=o2.result where o1.id<>o2.id group by o1.id, o2.id, o1.type; +compute stats indi_result_org_collab; + create table indi_funder_country_collab stored as parquet as with tmp as (select funder, project, country from organization_projects op join organization o on o.id=op.id @@ -101,6 +119,8 @@ join tmp as f2 on f1.project=f2.project where f1.country<>f2.country group by f1.funder, f2.country, f1.country; +compute stats indi_funder_country_collab; + create table indi_result_country_collab stored as parquet as with tmp as (select country, ro.id as result,r.type from organization o @@ -112,6 +132,8 @@ join tmp as o2 on o1.result=o2.result where o1.country<>o2.country group by o1.country, o2.country, o1.type; +compute stats indi_result_country_collab; + ---- Sprint 4 ---- create table indi_pub_diamond stored as parquet as select distinct pd.id, coalesce(in_diamond_journal, 0) as in_diamond_journal @@ -123,6 +145,8 @@ join stats_ext.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_onli and (ps.journal_is_in_doaj=true or ps.journal_is_oa=true) and ps.has_apc=false) tmp on pd.id=tmp.id; +compute stats indi_pub_diamond; + create table indi_pub_hybrid stored as parquet as select distinct pd.id, coalesce(is_hybrid, 0) as is_hybrid from publication_datasources pd @@ -133,6 +157,8 @@ join stats_ext.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_onli and (ps.journal_is_in_doaj=false and ps.journal_is_oa=false)) tmp on pd.id=tmp.id; +compute stats indi_pub_hybrid; + create table indi_pub_in_transformative stored as parquet as select distinct pd.id, coalesce(is_transformative, 0) as is_transformative from publication pd @@ -143,6 +169,8 @@ join stats_ext.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_onli and ps.is_transformative_journal=true) tmp on pd.id=tmp.id; +compute stats indi_pub_in_transformative; + create table indi_pub_closed_other_open stored as parquet as select distinct ri.id, coalesce(pub_closed_other_open, 0) as pub_closed_other_open from result_instance ri left outer join @@ -153,11 +181,12 @@ where d.type like '%Journal%' and ri.accessright='Closed Access' and (p.bestlicence='Open Access' or p.bestlicence='Open Source')) tmp on tmp.id=ri.id; - +compute stats indi_pub_closed_other_open; ---- Sprint 5 ---- create table indi_result_no_of_copies stored as parquet as select id, count(id) as number_of_copies from result_instance group by id; +compute stats indi_result_no_of_copies; ---- Sprint 6 ---- create table indi_pub_gold_oa stored as parquet as WITH gold_oa AS ( @@ -183,6 +212,8 @@ LEFT OUTER JOIN ( JOIN issn on issn.id=pd.datasource JOIN gold_oa on issn.issn = gold_oa.issn) tmp ON pd.id=tmp.id; +compute stats indi_pub_gold_oa; + create table indi_datasets_gold_oa stored as parquet as WITH gold_oa AS ( SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_1 as issn @@ -210,6 +241,8 @@ LEFT OUTER JOIN ( JOIN issn on issn.id=pd.datasource JOIN gold_oa on issn.issn = gold_oa.issn) tmp ON pd.id=tmp.id; +compute stats indi_datasets_gold_oa; + create table indi_software_gold_oa stored as parquet as WITH gold_oa AS ( SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_1 as issn @@ -237,6 +270,8 @@ LEFT OUTER JOIN ( JOIN issn on issn.id=pd.datasource JOIN gold_oa on issn.issn = gold_oa.issn) tmp ON pd.id=tmp.id; +compute stats indi_software_gold_oa; + create table indi_org_findable stored as parquet as with result_with_pid as ( select ro.organization organization, count(distinct rp.id) no_result_with_pid from result_organization ro @@ -263,6 +298,8 @@ join result_with_pid_share on result_with_pid_share.organization=allresults.orga left outer join ( select organization, abstract_share from result_with_abstract_share) tmp on tmp.organization=allresults.organization; +compute stats indi_org_findable; + create table indi_org_openess stored as parquet as WITH datasets_oa as ( SELECT ro.organization, count(dg.id) no_oadatasets FROM indi_datasets_gold_oa dg @@ -313,6 +350,8 @@ left outer join ( left outer join ( select organization,s from allsoftwaresshare) tmp1 on tmp1.organization=allpubsshare.organization; +compute stats indi_org_openess; + create table indi_pub_hybrid_oa_with_cc stored as parquet as WITH hybrid_oa AS ( SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_print as issn @@ -343,6 +382,8 @@ LEFT OUTER JOIN ( JOIN indi_result_has_cc_licence cc on pd.id=cc.id where cc.has_cc_license=1) tmp on pd.id=tmp.id; +compute stats indi_pub_hybrid_oa_with_cc; + create table indi_pub_downloads stored as parquet as SELECT result_id, sum(downloads) no_dowloads from openaire_prod_usage_stats.usage_stats join publication on result_id=id @@ -350,6 +391,8 @@ where downloads>0 GROUP BY result_id order by no_dowloads desc; +compute stats indi_pub_downloads; + create table indi_pub_downloads_datasource stored as parquet as SELECT result_id, repository_id, sum(downloads) no_dowloads from openaire_prod_usage_stats.usage_stats join publication on result_id=id @@ -357,15 +400,21 @@ where downloads>0 GROUP BY result_id, repository_id order by result_id; +compute stats indi_pub_downloads_datasource; + create table indi_pub_downloads_year stored as parquet as SELECT result_id, substring(us.`date`, 1,4) as `year`, sum(downloads) no_dowloads from openaire_prod_usage_stats.usage_stats us join publication on result_id=id where downloads>0 GROUP BY result_id, `year` order by `year` asc; +compute stats indi_pub_downloads_year; + create table indi_pub_downloads_datasource_year stored as parquet as SELECT result_id, substring(us.`date`, 1,4) as `year`, repository_id, sum(downloads) no_dowloads from openaire_prod_usage_stats.usage_stats us join publication on result_id=id where downloads>0 GROUP BY result_id, repository_id, `year` order by `year` asc, result_id; + +compute stats indi_pub_downloads_datasource_year; \ No newline at end of file diff --git a/dhp-workflows/dhp-usage-raw-data-update/pom.xml b/dhp-workflows/dhp-usage-raw-data-update/pom.xml index a78f92d41..954c8bd39 100644 --- a/dhp-workflows/dhp-usage-raw-data-update/pom.xml +++ b/dhp-workflows/dhp-usage-raw-data-update/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.5-SNAPSHOT 4.0.0 dhp-usage-raw-data-update diff --git a/dhp-workflows/dhp-usage-stats-build/pom.xml b/dhp-workflows/dhp-usage-stats-build/pom.xml index 20d2f5b76..54e18580b 100644 --- a/dhp-workflows/dhp-usage-stats-build/pom.xml +++ b/dhp-workflows/dhp-usage-stats-build/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.5-SNAPSHOT 4.0.0 dhp-usage-stats-build diff --git a/dhp-workflows/dhp-workflow-profiles/pom.xml b/dhp-workflows/dhp-workflow-profiles/pom.xml index b1c51c497..8c71a5ca1 100644 --- a/dhp-workflows/dhp-workflow-profiles/pom.xml +++ b/dhp-workflows/dhp-workflow-profiles/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.5-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/pom.xml b/dhp-workflows/pom.xml index 143178560..541d59007 100644 --- a/dhp-workflows/pom.xml +++ b/dhp-workflows/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp - 1.2.4-SNAPSHOT + 1.2.5-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 6a14954e5..136b9b867 100644 --- a/pom.xml +++ b/pom.xml @@ -3,7 +3,7 @@ 4.0.0 eu.dnetlib.dhp dhp - 1.2.4-SNAPSHOT + 1.2.5-SNAPSHOT pom @@ -551,6 +551,9 @@ org.apache.maven.plugins maven-site-plugin 3.9.1 + + ${dhp.site.skip} + @@ -791,6 +794,7 @@ 2.4.0.cloudera2 2.9.6 3.5 + true 11.0.2 2.11.12 5.6.1