From 8e8933d41abb871e49e20d7046f235afc6ed875b Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 14 Apr 2022 09:04:24 +0200 Subject: [PATCH 01/46] [BulkTagging] added fix if result.dataInfo is null --- .../main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java index 1a0afb9811..6664d36ec8 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java @@ -5,6 +5,7 @@ import static eu.dnetlib.dhp.PropagationConstant.removeOutputDir; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.util.ArrayList; +import java.util.Objects; import java.util.Optional; import org.apache.commons.io.IOUtils; @@ -102,6 +103,7 @@ public class SparkBulkTagJob { ResultTagger resultTagger = new ResultTagger(); readPath(spark, inputPath, resultClazz) .map(patchResult(), Encoders.bean(resultClazz)) + .filter(Objects::nonNull) .map( (MapFunction) value -> resultTagger .enrichContextCriteria( @@ -124,6 +126,9 @@ public class SparkBulkTagJob { // TODO remove this hack as soon as the values fixed by this method will be provided as NON null private static MapFunction patchResult() { return r -> { + if(r.getDataInfo() == null){ + return null; + } if (r.getDataInfo().getDeletedbyinference() == null) { r.getDataInfo().setDeletedbyinference(false); } From c5a863132c124e25d1b75ca8d7c8546a7db33043 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 14 Apr 2022 14:14:13 +0200 Subject: [PATCH 02/46] [BulkTagging] revert it --- .../src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java | 3 --- 1 file changed, 3 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java index 6664d36ec8..ad1e8721ac 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java @@ -126,9 +126,6 @@ public class SparkBulkTagJob { // TODO remove this hack as soon as the values fixed by this method will be provided as NON null private static MapFunction patchResult() { return r -> { - if(r.getDataInfo() == null){ - return null; - } if (r.getDataInfo().getDeletedbyinference() == null) { r.getDataInfo().setDeletedbyinference(false); } From d580e154424a8f211cf35ab1cae079f2624b8e44 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Thu, 21 Apr 2022 11:06:08 +0200 Subject: [PATCH 03/46] Modified last intersection since we lost many titles. this is my last resource, after that, I've to change my job --- .../doiboost/SparkGenerateDoiBoost.scala | 37 +++++++++++++++++-- 1 file changed, 34 insertions(+), 3 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala index 79b9e8183a..bc26e44d6b 100644 --- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala +++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala @@ -60,7 +60,7 @@ object SparkGenerateDoiBoost { val openaireOrganizationPath = parser.get("openaireOrganizationPath") val crossrefAggregator = new Aggregator[(String, Publication), Publication, Publication] with Serializable { - override def zero: Publication = new Publication + override def zero: Publication = null override def reduce(b: Publication, a: (String, Publication)): Publication = { @@ -177,12 +177,43 @@ object SparkGenerateDoiBoost { .map(DoiBoostMappingUtil.fixPublication) .map(p => (p.getId, p)) .groupByKey(_._1) - .agg(crossrefAggregator.toColumn) - .map(p => p._2) + .reduceGroups((left, right) => + { + //Check left is not null + if (left != null && left._1 != null) + { + //If right is null then return left + if (right == null || right._2 == null) + left + else { + // Here Left and Right are not null + // So we have to merge + val b1 = left._2 + val b2 = right._2 + b1.mergeFrom(b2) + b1.mergeOAFDataInfo(b2) + val authors = AuthorMerger.mergeAuthor(b1.getAuthor, b2.getAuthor) + b1.setAuthor(authors) + if (b2.getId != null && b2.getId.nonEmpty) + b1.setId(b2.getId) + //Return publication Merged + (b1.getId, b1) + } + } + else { + // Left is Null so we return right + right + } + } + + ) + .filter(s => s!= null && s._2!=null) + .map(s => s._2) .write .mode(SaveMode.Overwrite) .save(s"$workingDirPath/doiBoostPublicationFiltered") + val affiliationPath = parser.get("affiliationPath") val paperAffiliationPath = parser.get("paperAffiliationPath") From d660895b309d185e84c4ea3d55d1c1351820f0b2 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Thu, 21 Apr 2022 20:41:13 +0200 Subject: [PATCH 04/46] fixed wrong mapping type of dataset --- .../main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala index bc26e44d6b..fbe42ef7c2 100644 --- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala +++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala @@ -208,7 +208,7 @@ object SparkGenerateDoiBoost { ) .filter(s => s!= null && s._2!=null) - .map(s => s._2) + .map(s => s._2._2) .write .mode(SaveMode.Overwrite) .save(s"$workingDirPath/doiBoostPublicationFiltered") From 2a8e0fb72f10ca5a1ae4496e24649e9e86d9f1e7 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 9 May 2022 16:06:04 +0200 Subject: [PATCH 05/46] [openorgs] mapping parent/child relations without massaging the semantic labels --- .../dhp/oa/graph/raw/MigrateDbEntitiesApplication.java | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java index b5801ca5c5..3e23e34931 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java @@ -711,10 +711,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i final Relation r = new Relation(); r.setRelType(ORG_ORG_RELTYPE); r.setSubRelType(ModelConstants.RELATIONSHIP); - r - .setRelClass( - rs.getString("type").equalsIgnoreCase("parent") ? ModelConstants.IS_PARENT_OF - : ModelConstants.IS_CHILD_OF); + r.setRelClass(rs.getString("type")); r.setSource(orgId1); r.setTarget(orgId2); r.setCollectedfrom(collectedFrom); From 6031acb2e3a0a268ac2a837183d35a54999c5c91 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 16 May 2022 09:20:30 +0200 Subject: [PATCH 06/46] [openorgs] fixed parent/child query, using the correct semantic labels --- .../dnetlib/dhp/oa/graph/sql/queryParentChildRelsOpenOrgs.sql | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryParentChildRelsOpenOrgs.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryParentChildRelsOpenOrgs.sql index 388fee3f58..0ac8434011 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryParentChildRelsOpenOrgs.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryParentChildRelsOpenOrgs.sql @@ -10,4 +10,4 @@ SELECT 'OpenOrgs Database' AS collectedfromname, 'sysimport:crosswalk:entityregistry@@@dnet:provenance_actions' AS provenanceaction FROM relationships -WHERE reltype = 'Child' OR reltype = 'Parent' \ No newline at end of file +WHERE reltype = 'IsChildOf' OR reltype = 'IsParentOf' \ No newline at end of file From 46c07e0724f655d8cc86e6af1a4ec34fd19d7d21 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Mon, 16 May 2022 09:39:54 +0200 Subject: [PATCH 07/46] deleted hierarchical rels from ror action set --- .../ror/GenerateRorActionSetJob.java | 62 ++++--------------- 1 file changed, 11 insertions(+), 51 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java index e4d4587804..6c76f8a4d5 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java @@ -3,7 +3,6 @@ package eu.dnetlib.dhp.actionmanager.ror; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import static eu.dnetlib.dhp.schema.common.ModelConstants.ENTITYREGISTRY_PROVENANCE_ACTION; -import static eu.dnetlib.dhp.schema.common.ModelConstants.ORG_ORG_RELTYPE; import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.dataInfo; import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.field; import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.listKeyValues; @@ -39,7 +38,6 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.actionmanager.ror.model.ExternalIdType; -import eu.dnetlib.dhp.actionmanager.ror.model.Relationship; import eu.dnetlib.dhp.actionmanager.ror.model.RorOrganization; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; @@ -51,7 +49,6 @@ import eu.dnetlib.dhp.schema.oaf.KeyValue; import eu.dnetlib.dhp.schema.oaf.Oaf; import eu.dnetlib.dhp.schema.oaf.Organization; import eu.dnetlib.dhp.schema.oaf.Qualifier; -import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.StructuredProperty; import eu.dnetlib.dhp.utils.DHPUtils; import scala.Tuple2; @@ -64,21 +61,17 @@ public class GenerateRorActionSetJob { private static final String ROR_NS_PREFIX = "ror_________"; - private static final List ROR_COLLECTED_FROM = listKeyValues( - "10|openaire____::993a7ae7a863813cf95028b50708e222", "ROR"); + private static final List ROR_COLLECTED_FROM = listKeyValues("10|openaire____::993a7ae7a863813cf95028b50708e222", "ROR"); - private static final DataInfo ROR_DATA_INFO = dataInfo( - false, "", false, false, ENTITYREGISTRY_PROVENANCE_ACTION, "0.92"); + private static final DataInfo ROR_DATA_INFO = dataInfo(false, "", false, false, ENTITYREGISTRY_PROVENANCE_ACTION, "0.92"); - private static final Qualifier ROR_PID_TYPE = qualifier( - "ROR", "ROR", ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES); + private static final Qualifier ROR_PID_TYPE = qualifier("ROR", "ROR", ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES); public static void main(final String[] args) throws Exception { final String jsonConfiguration = IOUtils - .toString( - GenerateRorActionSetJob.class - .getResourceAsStream("/eu/dnetlib/dhp/actionmanager/ror/action_set_parameters.json")); + .toString(GenerateRorActionSetJob.class + .getResourceAsStream("/eu/dnetlib/dhp/actionmanager/ror/action_set_parameters.json")); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); @@ -116,9 +109,8 @@ public class GenerateRorActionSetJob { readInputPath(spark, inputPath) .map(GenerateRorActionSetJob::convertRorOrg) .flatMap(List::iterator) - .mapToPair( - aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), - new Text(OBJECT_MAPPER.writeValueAsString(aa)))) + .mapToPair(aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), + new Text(OBJECT_MAPPER.writeValueAsString(aa)))) .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class); } @@ -153,12 +145,9 @@ public class GenerateRorActionSetJob { o.setEcnutscode(null); if (r.getCountry() != null) { o - .setCountry( - qualifier( - r.getCountry().getCountryCode(), r - .getCountry() - .getCountryName(), - ModelConstants.DNET_COUNTRY_TYPE, ModelConstants.DNET_COUNTRY_TYPE)); + .setCountry(qualifier(r.getCountry().getCountryCode(), r + .getCountry() + .getCountryName(), ModelConstants.DNET_COUNTRY_TYPE, ModelConstants.DNET_COUNTRY_TYPE)); } else { o.setCountry(null); } @@ -168,38 +157,10 @@ public class GenerateRorActionSetJob { final List> res = new ArrayList<>(); res.add(new AtomicAction<>(Organization.class, o)); - for (final Relationship rorRel : r.getRelationships()) { - if (rorRel.getType().equalsIgnoreCase("parent")) { - final String orgId1 = calculateOpenaireId(r.getId()); - final String orgId2 = calculateOpenaireId(rorRel.getId()); - res - .add( - new AtomicAction<>(Relation.class, - calculateHierarchyRel(orgId1, orgId2, ModelConstants.IS_PARENT_OF))); - res - .add( - new AtomicAction<>(Relation.class, - calculateHierarchyRel(orgId2, orgId1, ModelConstants.IS_CHILD_OF))); - } - } - return res; } - private static Relation calculateHierarchyRel(final String source, final String target, final String relClass) { - final Relation rel = new Relation(); - rel.setSource(source); - rel.setTarget(target); - rel.setRelType(ORG_ORG_RELTYPE); - rel.setSubRelType(ModelConstants.RELATIONSHIP); - rel.setRelClass(relClass); - rel.setCollectedfrom(ROR_COLLECTED_FROM); - rel.setDataInfo(ROR_DATA_INFO); - rel.setLastupdatetimestamp(System.currentTimeMillis()); - return rel; - } - private static String calculateOpenaireId(final String rorId) { return String.format("20|%s::%s", ROR_NS_PREFIX, DHPUtils.md5(rorId)); } @@ -212,8 +173,7 @@ public class GenerateRorActionSetJob { final String type = e.getKey(); final List all = e.getValue().getAll(); if (all != null) { - final Qualifier qualifier = qualifier( - type, type, ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES); + final Qualifier qualifier = qualifier(type, type, ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES); for (final String pid : all) { pids .add(structuredProperty(pid, qualifier, ROR_DATA_INFO)); From 52cb086506161dfdbd98a331b4ff004e5fb8f2bd Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 16 May 2022 12:07:40 +0200 Subject: [PATCH 08/46] [graph grouping] drop relation target path before copying from source --- .../dnetlib/dhp/oa/graph/group/oozie_app/workflow.xml | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/group/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/group/oozie_app/workflow.xml index f77b46105a..888a873c53 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/group/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/group/oozie_app/workflow.xml @@ -283,7 +283,15 @@ - + + + + + + + + + From 8dd5517548d1224e5067c4f48c68bda5817431ca Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 16 May 2022 14:35:24 +0200 Subject: [PATCH 09/46] code formatting --- .../ror/GenerateRorActionSetJob.java | 31 +++++++---- .../doiboost/SparkGenerateDoiBoost.scala | 52 ++++++++----------- 2 files changed, 43 insertions(+), 40 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java index 6c76f8a4d5..6b5bed5b8b 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java @@ -61,17 +61,21 @@ public class GenerateRorActionSetJob { private static final String ROR_NS_PREFIX = "ror_________"; - private static final List ROR_COLLECTED_FROM = listKeyValues("10|openaire____::993a7ae7a863813cf95028b50708e222", "ROR"); + private static final List ROR_COLLECTED_FROM = listKeyValues( + "10|openaire____::993a7ae7a863813cf95028b50708e222", "ROR"); - private static final DataInfo ROR_DATA_INFO = dataInfo(false, "", false, false, ENTITYREGISTRY_PROVENANCE_ACTION, "0.92"); + private static final DataInfo ROR_DATA_INFO = dataInfo( + false, "", false, false, ENTITYREGISTRY_PROVENANCE_ACTION, "0.92"); - private static final Qualifier ROR_PID_TYPE = qualifier("ROR", "ROR", ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES); + private static final Qualifier ROR_PID_TYPE = qualifier( + "ROR", "ROR", ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES); public static void main(final String[] args) throws Exception { final String jsonConfiguration = IOUtils - .toString(GenerateRorActionSetJob.class - .getResourceAsStream("/eu/dnetlib/dhp/actionmanager/ror/action_set_parameters.json")); + .toString( + GenerateRorActionSetJob.class + .getResourceAsStream("/eu/dnetlib/dhp/actionmanager/ror/action_set_parameters.json")); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); @@ -109,8 +113,9 @@ public class GenerateRorActionSetJob { readInputPath(spark, inputPath) .map(GenerateRorActionSetJob::convertRorOrg) .flatMap(List::iterator) - .mapToPair(aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), - new Text(OBJECT_MAPPER.writeValueAsString(aa)))) + .mapToPair( + aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), + new Text(OBJECT_MAPPER.writeValueAsString(aa)))) .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class); } @@ -145,9 +150,12 @@ public class GenerateRorActionSetJob { o.setEcnutscode(null); if (r.getCountry() != null) { o - .setCountry(qualifier(r.getCountry().getCountryCode(), r - .getCountry() - .getCountryName(), ModelConstants.DNET_COUNTRY_TYPE, ModelConstants.DNET_COUNTRY_TYPE)); + .setCountry( + qualifier( + r.getCountry().getCountryCode(), r + .getCountry() + .getCountryName(), + ModelConstants.DNET_COUNTRY_TYPE, ModelConstants.DNET_COUNTRY_TYPE)); } else { o.setCountry(null); } @@ -173,7 +181,8 @@ public class GenerateRorActionSetJob { final String type = e.getKey(); final List all = e.getValue().getAll(); if (all != null) { - final Qualifier qualifier = qualifier(type, type, ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES); + final Qualifier qualifier = qualifier( + type, type, ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES); for (final String pid : all) { pids .add(structuredProperty(pid, qualifier, ROR_DATA_INFO)); diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala index fbe42ef7c2..72b93749ba 100644 --- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala +++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala @@ -177,43 +177,37 @@ object SparkGenerateDoiBoost { .map(DoiBoostMappingUtil.fixPublication) .map(p => (p.getId, p)) .groupByKey(_._1) - .reduceGroups((left, right) => - { - //Check left is not null - if (left != null && left._1 != null) - { - //If right is null then return left - if (right == null || right._2 == null) - left - else { - // Here Left and Right are not null - // So we have to merge - val b1 = left._2 - val b2 = right._2 - b1.mergeFrom(b2) - b1.mergeOAFDataInfo(b2) - val authors = AuthorMerger.mergeAuthor(b1.getAuthor, b2.getAuthor) - b1.setAuthor(authors) - if (b2.getId != null && b2.getId.nonEmpty) - b1.setId(b2.getId) - //Return publication Merged - (b1.getId, b1) - } - } + .reduceGroups((left, right) => { + //Check left is not null + if (left != null && left._1 != null) { + //If right is null then return left + if (right == null || right._2 == null) + left else { - // Left is Null so we return right - right + // Here Left and Right are not null + // So we have to merge + val b1 = left._2 + val b2 = right._2 + b1.mergeFrom(b2) + b1.mergeOAFDataInfo(b2) + val authors = AuthorMerger.mergeAuthor(b1.getAuthor, b2.getAuthor) + b1.setAuthor(authors) + if (b2.getId != null && b2.getId.nonEmpty) + b1.setId(b2.getId) + //Return publication Merged + (b1.getId, b1) } + } else { + // Left is Null so we return right + right } - - ) - .filter(s => s!= null && s._2!=null) + }) + .filter(s => s != null && s._2 != null) .map(s => s._2._2) .write .mode(SaveMode.Overwrite) .save(s"$workingDirPath/doiBoostPublicationFiltered") - val affiliationPath = parser.get("affiliationPath") val paperAffiliationPath = parser.get("paperAffiliationPath") From 1dda11e0319eebe5ec3a772b1fafd6c75912ff56 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 16 May 2022 15:53:27 +0200 Subject: [PATCH 10/46] [hb patch] updated map --- .../eu/dnetlib/dhp/datacite/hostedBy_map.json | 15 ++++++++++----- 1 file changed, 10 insertions(+), 5 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/hostedBy_map.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/hostedBy_map.json index 947a9a255a..ecae6811a1 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/hostedBy_map.json +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/hostedBy_map.json @@ -15,7 +15,7 @@ "official_name": "Aperta TÜBİTAK Open Archive" }, "BL.CAM": { - "openaire_id": "re3data_____::r3d100010620", + "openaire_id": "opendoar____::109", "datacite_name": "Apollo", "official_name": "Apollo" }, @@ -196,7 +196,7 @@ }, "CSIC.DIGITAL": { "openaire_id": "re3data_____::r3d100011076", - "datacite_name": "DIGITAL.CSIC", + "datacite_name": "Digital CSIC", "official_name": "DIGITAL.CSIC" }, "BL.DRI": { @@ -644,6 +644,11 @@ "datacite_name": "PANGAEA", "official_name": "PANGAEA" }, + "TIB.PANGAEA": { + "openaire_id": "re3data_____::r3d100010134", + "datacite_name": "PANGAEA", + "official_name": "PANGAEA" + }, "NASAPDS.NASAPDS": { "openaire_id": "re3data_____::r3d100010121", "datacite_name": "PDS", @@ -896,7 +901,7 @@ }, "FIGSHARE.UCT": { "openaire_id": "re3data_____::r3d100012633", - "datacite_name": "ZivaHub", + "datacite_name": "University of Cape Town (UCT)", "official_name": "ZivaHub" }, "BL.UCLAN": { @@ -1030,9 +1035,9 @@ "official_name": "ZBW Journal Data Archive" }, "CERN.ZENODO": { - "openaire_id": "re3data_____::r3d100010468", + "openaire_id": "opendoar____::2659", "datacite_name": "Zenodo", - "official_name": "Zenodo" + "official_name": "ZENODO" }, "ZBW.ZEW": { "openaire_id": "re3data_____::r3d100010399", From 4b6913787bb48b92c9ae8b6f4cab0b59392798f9 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 8 Jun 2022 14:55:19 +0200 Subject: [PATCH 11/46] [DOI-BOOST] added one method in test of crossref mapping to aof and one resource. Related to ticket 7807 --- .../doiboost/crossref/article_nojournal.json | 368 ++++++++++++++++++ .../crossref/CrossrefMappingTest.scala | 28 ++ 2 files changed, 396 insertions(+) create mode 100644 dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/article_nojournal.json diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/article_nojournal.json b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/article_nojournal.json new file mode 100644 index 0000000000..48a3777b79 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/article_nojournal.json @@ -0,0 +1,368 @@ + +{ + + "indexed": { + "date-parts": [ + [ + 2022, + 4, + 22 + ] + ], + "date-time": "2022-04-22T15:30:54Z", + "timestamp": 1650641454218 + }, + "reference-count": 31, + "publisher": "Cambridge University Press (CUP)", + "issue": "2", + "license": [ + { + "start": { + "date-parts": [ + [ + 2017, + 8, + 22 + ] + ], + "date-time": "2017-08-22T00:00:00Z", + "timestamp": 1503360000000 + }, + "content-version": "unspecified", + "delay-in-days": 21, + "URL": "https://www.cambridge.org/core/terms" + } + ], + "content-domain": { + "domain": [ + + ], + "crossmark-restriction": false + }, + "short-container-title": [ + "Dance Res. J." + ], + "published-print": { + "date-parts": [ + [ + 2017, + 8 + ] + ] + }, + "abstract": "Gaga, a practice developed by Israeli choreographer Ohad Naharin, is one of the most popular training methods on the global dance market. Structured as a metatechnique, or a system for negotiating techniques within one's body, Gaga teaches students to both draw on and reject multiple movement techniques to create their own movement. I consider how the paradigms of choreography, technique, and improvisation are blurred together in the pedagogical model of a metatechnique and how training dancers to shift between choreographer, dancer, and improviser has significant ramifications for understanding their agency. The metatechnique model of Gaga falls in line with neoliberal values of efficiency and a wide range of skills and knowledge; this analysis provides an understanding of recent trends in dance training in relation to contemporary political and socioeconomic structures.", + "DOI": "10.1017/s0149767717000183", + "type": "journal-article", + "created": { + "date-parts": [ + [ + 2017, + 8, + 22 + ] + ], + "date-time": "2017-08-22T13:32:38Z", + "timestamp": 1503408758000 + }, + "page": "26-43", + "source": "Crossref", + "is-referenced-by-count": 10, + "title": [ + "Gaga as Metatechnique: Negotiating Choreography, Improvisation, and Technique in a Neoliberal Dance Market" + ], + "prefix": "10.1017", + "volume": "49", + "author": [ + { + "given": "Meghan", + "family": "Quinlan", + "sequence": "first", + "affiliation": [ + + ] + } + ], + "member": "56", + "published-online": { + "date-parts": [ + [ + 2017, + 8, + 22 + ] + ] + }, + "reference": [ + { + "key": "S0149767717000183_ref22", + "first-page": "38", + "article-title": "‘I Don't Want to do African … What About My Technique?’: Transforming Dancing Places into Spaces in the Academy", + "volume": "4", + "author": "Monroe", + "year": "2011", + "journal-title": "The Journal of Pan African Studies" + }, + { + "key": "S0149767717000183_ref8", + "volume-title": "Discipline and Punish: The Birth of the Prison", + "author": "Foucault", + "year": "1995" + }, + { + "key": "S0149767717000183_ref24", + "volume-title": "Sharing the Dance: Contact Improvisation and American Culture", + "author": "Novack", + "year": "1990" + }, + { + "key": "S0149767717000183_ref26", + "doi-asserted-by": "publisher", + "DOI": "10.1215/9780822387879" + }, + { + "key": "S0149767717000183_ref10", + "doi-asserted-by": "publisher", + "DOI": "10.1080/01472526.2015.1085759" + }, + { + "key": "S0149767717000183_ref4", + "doi-asserted-by": "crossref", + "first-page": "235", + "volume-title": "Meaning in Motion", + "author": "Foster", + "year": "1997", + "DOI": "10.1215/9780822397281-013" + }, + { + "key": "S0149767717000183_ref17", + "doi-asserted-by": "publisher", + "DOI": "10.1093/acprof:oso/9780199360369.001.0001" + }, + { + "key": "S0149767717000183_ref30", + "volume-title": "The Precariat: The New Dangerous Class", + "author": "Standing", + "year": "2011" + }, + { + "key": "S0149767717000183_ref7", + "volume-title": "Choreographing Empathy: Kinesthesia in Performance", + "author": "Foster", + "year": "2011" + }, + { + "key": "S0149767717000183_ref14", + "volume-title": "A Brief History of Neoliberalism", + "author": "Harvey", + "year": "2007" + }, + { + "key": "S0149767717000183_ref27", + "unstructured": "Quinlan Meghan . 2016. “Gaga as Politics: A Case Study of Contemporary Dance Training.” PhD diss., University of California, Riverside." + }, + { + "key": "S0149767717000183_ref11", + "first-page": "xiii", + "volume-title": "Taken by Surprise: A Dance Improvisation Reader", + "author": "Gere", + "year": "2003" + }, + { + "key": "S0149767717000183_ref13", + "volume-title": "Declaration", + "author": "Hardt", + "year": "2012" + }, + { + "key": "S0149767717000183_ref29", + "doi-asserted-by": "publisher", + "DOI": "10.1057/9780230236844_9" + }, + { + "key": "S0149767717000183_ref5", + "doi-asserted-by": "publisher", + "DOI": "10.1057/9780230236844_6" + }, + { + "key": "S0149767717000183_ref28", + "doi-asserted-by": "publisher", + "DOI": "10.1017/S0149767700000528" + }, + { + "key": "S0149767717000183_ref12", + "doi-asserted-by": "publisher", + "DOI": "10.3998/mpub.287881" + }, + { + "key": "S0149767717000183_ref18", + "first-page": "135", + "volume-title": "Taken by Surprise: A Dance Improvisation Reader", + "author": "Marks", + "year": "2003" + }, + { + "key": "S0149767717000183_ref3", + "doi-asserted-by": "crossref", + "volume-title": "Bodies That Matter: On the Discursive Limits of Sex", + "author": "Butler", + "year": "2011", + "DOI": "10.4324/9780203828274" + }, + { + "key": "S0149767717000183_ref32", + "volume-title": "Choreographing Difference: The Body and Identity in Contemporary Dance", + "author": "Albright", + "year": "1997" + }, + { + "key": "S0149767717000183_ref16", + "doi-asserted-by": "publisher", + "DOI": "10.1017/S0149767714000163" + }, + { + "key": "S0149767717000183_ref15", + "doi-asserted-by": "publisher", + "DOI": "10.2307/1477803" + }, + { + "key": "S0149767717000183_ref21", + "first-page": "455", + "volume-title": "Incorporations", + "author": "Mauss", + "year": "1992" + }, + { + "key": "S0149767717000183_ref1", + "volume-title": "The Body Eclectic: Evolving Practices in Dance Training", + "author": "Bales", + "year": "2008" + }, + { + "key": "S0149767717000183_ref9", + "unstructured": "Gaga Movement Ltd. 2016. Gaga People. Dancers. Accessed June 28, 2016. http://gagapeople.com/english/." + }, + { + "key": "S0149767717000183_ref19", + "volume-title": "Critical Moves: Dance Studies in Theory and Politics", + "author": "Martin", + "year": "1998" + }, + { + "key": "S0149767717000183_ref2", + "volume-title": "Undoing the Demos: Neoliberalism's Stealth Revolution", + "author": "Brown", + "year": "2015" + }, + { + "key": "S0149767717000183_ref20", + "doi-asserted-by": "publisher", + "DOI": "10.1162/DRAM_a_00214" + }, + { + "key": "S0149767717000183_ref6", + "doi-asserted-by": "publisher", + "DOI": "10.1215/01610775-2009-016" + }, + { + "key": "S0149767717000183_ref23", + "doi-asserted-by": "publisher", + "DOI": "10.1093/acprof:oso/9780190201661.001.0001" + }, + { + "key": "S0149767717000183_ref25", + "volume-title": "Flexible Citizenship: The Cultural Logics of Transnationality", + "author": "Ong", + "year": "1999" + } + ], + "container-title": [ + "Dance Research Journal" + ], + "original-title": [ + + ], + "language": "en", + "link": [ + { + "URL": "https://www.cambridge.org/core/services/aop-cambridge-core/content/view/S0149767717000183", + "content-type": "unspecified", + "content-version": "vor", + "intended-application": "similarity-checking" + } + ], + "deposited": { + "date-parts": [ + [ + 2020, + 10, + 16 + ] + ], + "date-time": "2020-10-16T01:00:32Z", + "timestamp": 1602810032000 + }, + "score": 1, + "resource": { + "primary": { + "URL": "https://www.cambridge.org/core/product/identifier/S0149767717000183/type/journal_article" + } + }, + "subtitle": [ + + ], + "short-title": [ + + ], + "issued": { + "date-parts": [ + [ + 2017, + 8 + ] + ] + }, + "references-count": 31, + "journal-issue": { + "issue": "2", + "published-print": { + "date-parts": [ + [ + 2017, + 8 + ] + ] + } + }, + "alternative-id": [ + "S0149767717000183" + ], + "URL": "http://dx.doi.org/10.1017/s0149767717000183", + "relation": { + + }, + "ISSN": [ + "0149-7677", + "1940-509X" + ], + "issn-type": [ + { + "value": "0149-7677", + "type": "print" + }, + { + "value": "1940-509X", + "type": "electronic" + } + ], + "subject": [ + "Visual Arts and Performing Arts" + ], + "published": { + "date-parts": [ + [ + 2017, + 8 + ] + ] + } + } diff --git a/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala b/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala index 78ed375c67..30928fdd0c 100644 --- a/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala +++ b/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala @@ -473,6 +473,34 @@ class CrossrefMappingTest { }) + } + + @Test + def testConvertFromCrossRef2OafIssue(): Unit = { + val json = Source + .fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/article_nojournal.json")) + .mkString + assertNotNull(json) + + assertFalse(json.isEmpty); + + val resultList: List[Oaf] = Crossref2Oaf.convert(json) + + assertTrue(resultList.nonEmpty) + + val items = resultList.filter(p => p.isInstanceOf[Publication]) + + assert(items.nonEmpty) + assert(items.size == 1) + val pub: Publication = items.head.asInstanceOf[Publication] + + assertNotNull(pub.getJournal.getIssnPrinted) + assertNotNull(pub.getJournal.getIssnOnline) + assertNotNull(pub.getJournal.getName) + + + + } @Test From ab8868bd3a5b170efc1d2fdc62812a6b308c589f Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 8 Jun 2022 17:03:15 +0200 Subject: [PATCH 12/46] [ZENODO-API] changed to iterate in all the deposited products and not just the last ten --- .../dhp/common/api/ZenodoAPIClient.java | 29 ++++++++++++------- 1 file changed, 18 insertions(+), 11 deletions(-) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/ZenodoAPIClient.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/ZenodoAPIClient.java index 3f5c6ad4a5..56366bc725 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/ZenodoAPIClient.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/ZenodoAPIClient.java @@ -191,7 +191,7 @@ public class ZenodoAPIClient implements Serializable { * @throws MissingConceptDoiException */ public int newVersion(String concept_rec_id) throws IOException, MissingConceptDoiException { - setDepositionId(concept_rec_id); + setDepositionId(concept_rec_id, 1); String json = "{}"; OkHttpClient httpClient = new OkHttpClient.Builder().connectTimeout(600, TimeUnit.SECONDS).build(); @@ -253,9 +253,9 @@ public class ZenodoAPIClient implements Serializable { } - private void setDepositionId(String concept_rec_id) throws IOException, MissingConceptDoiException { + private void setDepositionId(String concept_rec_id, Integer page) throws IOException, MissingConceptDoiException { - ZenodoModelList zenodoModelList = new Gson().fromJson(getPrevDepositions(), ZenodoModelList.class); + ZenodoModelList zenodoModelList = new Gson().fromJson(getPrevDepositions(String.valueOf(page)), ZenodoModelList.class); for (ZenodoModel zm : zenodoModelList) { if (zm.getConceptrecid().equals(concept_rec_id)) { @@ -263,20 +263,26 @@ public class ZenodoAPIClient implements Serializable { return; } } - - throw new MissingConceptDoiException("The concept record id specified was missing in the list of depositions"); + if(zenodoModelList.size() == 0) + throw new MissingConceptDoiException("The concept record id specified was missing in the list of depositions"); + setDepositionId(concept_rec_id, page + 1); } - private String getPrevDepositions() throws IOException { + private String getPrevDepositions(String page) throws IOException { + OkHttpClient httpClient = new OkHttpClient.Builder().connectTimeout(600, TimeUnit.SECONDS).build(); + HttpUrl.Builder urlBuilder = HttpUrl.parse(urlString).newBuilder(); + urlBuilder.addQueryParameter("page", page); + String url = urlBuilder.build().toString(); + Request request = new Request.Builder() - .url(urlString) - .addHeader(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString()) // add request headers - .addHeader(HttpHeaders.AUTHORIZATION, "Bearer " + access_token) - .get() - .build(); + .url(url) + .addHeader(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString()) // add request headers + .addHeader(HttpHeaders.AUTHORIZATION, "Bearer " + access_token) + .get() + .build(); try (Response response = httpClient.newCall(request).execute()) { @@ -289,6 +295,7 @@ public class ZenodoAPIClient implements Serializable { } + private String getBucket(String url) throws IOException { OkHttpClient httpClient = new OkHttpClient.Builder() .connectTimeout(600, TimeUnit.SECONDS) From b94a791bc5fe023aaeb43453c1fe4042e9441d24 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Thu, 9 Jun 2022 12:25:34 +0200 Subject: [PATCH 13/46] unit tests to transform cnr explora --- .../transformation/TransformationJobTest.java | 49 +++- .../dnetlib/dhp/transform/cnr_explora_tr.xslt | 214 ++++++++++++++ .../dhp/transform/input_cnr_explora.xml | 57 ++++ .../eu/dnetlib/dhp/transform/synonyms.txt | 266 +++++++++++++++++- .../eu/dnetlib/dhp/transform/terms.txt | 135 ++++++++- 5 files changed, 704 insertions(+), 17 deletions(-) create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/cnr_explora_tr.xslt create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/input_cnr_explora.xml diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java index 7bd7baaea9..fea7b53ac5 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java @@ -19,7 +19,9 @@ import org.apache.spark.sql.Encoder; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; import org.apache.spark.util.LongAccumulator; -import org.junit.jupiter.api.*; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.DisplayName; +import org.junit.jupiter.api.Test; import org.junit.jupiter.api.extension.ExtendWith; import org.junit.jupiter.api.io.TempDir; import org.mockito.junit.jupiter.MockitoExtension; @@ -50,7 +52,7 @@ class TransformationJobTest extends AbstractVocabularyTest { @Test @DisplayName("Test Date cleaner") void testDateCleaner() throws Exception { - DateCleaner dc = new DateCleaner(); + final DateCleaner dc = new DateCleaner(); assertEquals("1982-09-20", dc.clean("20/09/1982")); assertEquals("2002-09-20", dc.clean("20-09-2002")); assertEquals("2002-09-20", dc.clean("2002-09-20")); @@ -68,9 +70,9 @@ class TransformationJobTest extends AbstractVocabularyTest { mr.setProvenance(new Provenance("DSID", "DSNAME", "PREFIX")); mr.setBody(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/transform/input_zenodo.xml"))); // We Load the XSLT transformation Rule from the classpath - XSLTTransformationFunction tr = loadTransformationRule("/eu/dnetlib/dhp/transform/zenodo_tr.xslt"); + final XSLTTransformationFunction tr = loadTransformationRule("/eu/dnetlib/dhp/transform/zenodo_tr.xslt"); - MetadataRecord result = tr.call(mr); + final MetadataRecord result = tr.call(mr); // Print the record System.out.println(result.getBody()); @@ -86,9 +88,9 @@ class TransformationJobTest extends AbstractVocabularyTest { mr.setProvenance(new Provenance("DSID", "DSNAME", "PREFIX")); mr.setBody(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/transform/input_itgv4.xml"))); // We Load the XSLT transformation Rule from the classpath - XSLTTransformationFunction tr = loadTransformationRule("/eu/dnetlib/dhp/transform/zenodo_tr.xslt"); + final XSLTTransformationFunction tr = loadTransformationRule("/eu/dnetlib/dhp/transform/zenodo_tr.xslt"); - MetadataRecord result = tr.call(mr); + final MetadataRecord result = tr.call(mr); // Print the record System.out.println(result.getBody()); @@ -108,9 +110,9 @@ class TransformationJobTest extends AbstractVocabularyTest { mr.setProvenance(new Provenance("DSID", "DSNAME", "PREFIX")); mr.setBody(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/transform/input_itgv4.xml"))); // We Load the XSLT transformation Rule from the classpath - XSLTTransformationFunction tr = loadTransformationRule(xslTransformationScript); + final XSLTTransformationFunction tr = loadTransformationRule(xslTransformationScript); - MetadataRecord result = tr.call(mr); + final MetadataRecord result = tr.call(mr); // Print the record System.out.println(result.getBody()); @@ -129,9 +131,9 @@ class TransformationJobTest extends AbstractVocabularyTest { mr.setProvenance(new Provenance("DSID", "DSNAME", "PREFIX")); mr.setBody(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/transform/input_omicsdi.xml"))); // We Load the XSLT transformation Rule from the classpath - XSLTTransformationFunction tr = loadTransformationRule(xslTransformationScript); + final XSLTTransformationFunction tr = loadTransformationRule(xslTransformationScript); - MetadataRecord result = tr.call(mr); + final MetadataRecord result = tr.call(mr); // Print the record System.out.println(result.getBody()); @@ -140,7 +142,7 @@ class TransformationJobTest extends AbstractVocabularyTest { @Test @DisplayName("Test TransformSparkJobNode.main with oaiOpenaire_datacite (v4)") - void transformTestITGv4OAIdatacite(@TempDir Path testDir) throws Exception { + void transformTestITGv4OAIdatacite(@TempDir final Path testDir) throws Exception { try (SparkSession spark = SparkSession.builder().config(sparkConf).getOrCreate()) { @@ -150,9 +152,7 @@ class TransformationJobTest extends AbstractVocabularyTest { .getFile(); final String mdstore_output = testDir.toString() + "/version"; - mockupTrasformationRule( - "simpleTRule", - "/eu/dnetlib/dhp/transform/scripts/xslt_cleaning_oaiOpenaire_datacite_ExchangeLandingpagePid.xsl"); + mockupTrasformationRule("simpleTRule", "/eu/dnetlib/dhp/transform/scripts/xslt_cleaning_oaiOpenaire_datacite_ExchangeLandingpagePid.xsl"); final Map parameters = Stream.of(new String[][] { { @@ -203,7 +203,7 @@ class TransformationJobTest extends AbstractVocabularyTest { @Test @DisplayName("Test TransformSparkJobNode.main") - void transformTest(@TempDir Path testDir) throws Exception { + void transformTest(@TempDir final Path testDir) throws Exception { try (SparkSession spark = SparkSession.builder().config(sparkConf).getOrCreate()) { @@ -256,6 +256,25 @@ class TransformationJobTest extends AbstractVocabularyTest { } } + @Test + @DisplayName("Test Transform Single XML using cnr_explora_tr XSLTTransformator") + void testCnrExploraTransformSaxonHE() throws Exception { + + // We Set the input Record getting the XML from the classpath + final MetadataRecord mr = new MetadataRecord(); + + mr.setProvenance(new Provenance("openaire____::cnr_explora", "CNR ExploRA", "cnr_________")); + mr.setBody(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/transform/input_cnr_explora.xml"))); + // We Load the XSLT transformation Rule from the classpath + final XSLTTransformationFunction tr = loadTransformationRule("/eu/dnetlib/dhp/transform/cnr_explora_tr.xslt"); + + final MetadataRecord result = tr.call(mr); + + // Print the record + System.out.println(result.getBody()); + // TODO Create significant Assert + } + private XSLTTransformationFunction loadTransformationRule(final String path) throws Exception { final String trValue = IOUtils.toString(this.getClass().getResourceAsStream(path)); final LongAccumulator la = new LongAccumulator(); diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/cnr_explora_tr.xslt b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/cnr_explora_tr.xslt new file mode 100644 index 0000000000..78b167fdef --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/cnr_explora_tr.xslt @@ -0,0 +1,214 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/input_cnr_explora.xml b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/input_cnr_explora.xml new file mode 100644 index 0000000000..220c4ddbe8 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/input_cnr_explora.xml @@ -0,0 +1,57 @@ + + +
+ + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/synonyms.txt b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/synonyms.txt index 4fd95554a3..74a75e46a7 100644 --- a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/synonyms.txt +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/synonyms.txt @@ -1232,4 +1232,268 @@ dnet:review_levels @=@ 0001 @=@ 印刷物/電子媒体-学術雑誌論文（査 dnet:review_levels @=@ 0001 @=@ 印刷物/電子媒体-紀要論文（査読有り） dnet:review_levels @=@ 0001 @=@ 印刷物/電子媒体-雑誌記事（査読有り） dnet:review_levels @=@ 0001 @=@ 原著論文（査読有り） -dnet:review_levels @=@ 0001 @=@ 査読論文 \ No newline at end of file +dnet:review_levels @=@ 0001 @=@ 査読論文 +cnr:institutes @=@ https://ror.org/00brf2d87 @=@ CDS001 +cnr:institutes @=@ https://ror.org/00brf2d87 @=@ IDASC - Istituto di Acustica e Sensoristica \"Orso Mario Corbino\" +cnr:institutes @=@ https://ror.org/006qkqr45 @=@ CDS002 +cnr:institutes @=@ https://ror.org/006qkqr45 @=@ IAMC - Istituto per l'ambiente marino costiero +cnr:institutes @=@ https://ror.org/054ye0e45 @=@ CDS003 +cnr:institutes @=@ https://ror.org/054ye0e45 @=@ IASI - Istituto di analisi dei sistemi ed informatica \"Antonio Ruberti\" +cnr:institutes @=@ https://ror.org/00ygy3d85 @=@ CDS004 +cnr:institutes @=@ https://ror.org/00ygy3d85 @=@ IAC - Istituto per le applicazioni del calcolo \"Mauro Picone\" +cnr:institutes @=@ https://ror.org/000sy1f36 @=@ CDS005 +cnr:institutes @=@ https://ror.org/000sy1f36 @=@ IASF - Istituto di astrofisica spaziale e fisica cosmica +cnr:institutes @=@ https://ror.org/00x5wpm25 @=@ CDS006 +cnr:institutes @=@ https://ror.org/00x5wpm25 @=@ IBAM - Istituto per i beni archeologici e monumentali +cnr:institutes @=@ https://ror.org/03eqeqg74 @=@ CDS007 +cnr:institutes @=@ https://ror.org/03eqeqg74 @=@ IBP - Istituto di biochimica delle proteine +cnr:institutes @=@ https://ror.org/041xzk838 @=@ CDS008 +cnr:institutes @=@ https://ror.org/041xzk838 @=@ IBF - Istituto di biofisica +cnr:institutes @=@ https://ror.org/00s2j5046 @=@ CDS009 +cnr:institutes @=@ https://ror.org/00s2j5046 @=@ IBFM - Istituto di bioimmagini e fisiologia molecolare +cnr:institutes @=@ __CDS010__ @=@ CDS010 +cnr:institutes @=@ __CDS010__ @=@ IBAF - Istituto di biologia agro-ambientale e forestale +cnr:institutes @=@ __CDS011__ @=@ CDS011 +cnr:institutes @=@ __CDS011__ @=@ IBC - Istituto di biologia cellulare +cnr:institutes @=@ https://ror.org/02e5sbe24 @=@ CDS012 +cnr:institutes @=@ https://ror.org/02e5sbe24 @=@ IBBA - Istituto di biologia e biotecnologia agraria +cnr:institutes @=@ https://ror.org/01nyatq71 @=@ CDS013 +cnr:institutes @=@ https://ror.org/01nyatq71 @=@ IBPM - Istituto di biologia e patologia molecolari +cnr:institutes @=@ https://ror.org/01dy2q607 @=@ CDS014 +cnr:institutes @=@ https://ror.org/01dy2q607 @=@ IBIM - Istituto di biomedicina e di immunologia molecolare \"Alberto Monroy\" +cnr:institutes @=@ https://ror.org/05nzf7q96 @=@ CDS015 +cnr:institutes @=@ https://ror.org/05nzf7q96 @=@ IBIOM - Istituto di Biomembrane, Bioenergetica e Biotecnologie Molecolari +cnr:institutes @=@ https://ror.org/05m1yqp60 @=@ CDS016 +cnr:institutes @=@ https://ror.org/05m1yqp60 @=@ IBIMET - Istituto di biometeorologia +cnr:institutes @=@ https://ror.org/03rqtqb02 @=@ CDS017 +cnr:institutes @=@ https://ror.org/03rqtqb02 @=@ IBB - Istituto di biostrutture e bioimmagini +cnr:institutes @=@ https://ror.org/04r5fge26 @=@ CDS018 +cnr:institutes @=@ https://ror.org/04r5fge26 @=@ ICAR - Istituto di calcolo e reti ad alte prestazioni +cnr:institutes @=@ https://ror.org/03wyf0g15 @=@ CDS019 +cnr:institutes @=@ https://ror.org/03wyf0g15 @=@ ICB - Istituto di chimica biomolecolare +cnr:institutes @=@ https://ror.org/02fkw1114 @=@ CDS020 +cnr:institutes @=@ https://ror.org/02fkw1114 @=@ ICCOM - Istituto di chimica dei composti organo metallici +cnr:institutes @=@ https://ror.org/0141vn777 @=@ CDS021 +cnr:institutes @=@ https://ror.org/0141vn777 @=@ ICRM - Istituto di chimica del riconoscimento molecolare +cnr:institutes @=@ __CDS022__ @=@ CDS022 +cnr:institutes @=@ __CDS022__ @=@ ICTP - Istituto di chimica e tecnologia dei polimeri +cnr:institutes @=@ __CDS023__ @=@ CDS023 +cnr:institutes @=@ __CDS023__ @=@ ICIS - Istituto di chimica inorganica e delle superfici +cnr:institutes @=@ https://ror.org/00be3zh53 @=@ CDS024 +cnr:institutes @=@ https://ror.org/00be3zh53 @=@ ISASI - Istituto di Scienze Applicate e Sistemi Intelligenti \"Eduardo Caianiello\" +cnr:institutes @=@ __CDS025__ @=@ CDS025 +cnr:institutes @=@ __CDS025__ @=@ ICEVO - Istituto di Studi sulle Civiltà dell'Egeo e del Vicino Oriente +cnr:institutes @=@ https://ror.org/02ynrme92 @=@ CDS026 +cnr:institutes @=@ https://ror.org/02ynrme92 @=@ ICVBC - Istituto per la conservazione e valorizzazione dei beni culturali +cnr:institutes @=@ https://ror.org/05wba8r86 @=@ CDS027 +cnr:institutes @=@ https://ror.org/05wba8r86 @=@ IC - Istituto di cristallografia +cnr:institutes @=@ https://ror.org/03z58xd74 @=@ CDS028 +cnr:institutes @=@ https://ror.org/03z58xd74 @=@ IDPA - Istituto per la dinamica dei processi ambientali +cnr:institutes @=@ https://ror.org/00n4jbh84 @=@ CDS029 +cnr:institutes @=@ https://ror.org/00n4jbh84 @=@ IEIIT - Istituto di elettronica e di ingegneria dell'informazione e delle telecomunicazioni +cnr:institutes @=@ https://ror.org/04sn06036 @=@ CDS030 +cnr:institutes @=@ https://ror.org/04sn06036 @=@ IEOS - Istituto per l'endocrinologia e l'oncologia \"Gaetano Salvatore\" +cnr:institutes @=@ https://ror.org/01rg40y89 @=@ CDS031 +cnr:institutes @=@ https://ror.org/01rg40y89 @=@ ICMATE - Istituto di Chimica della Materia Condensata e di Tecnologie per l'Energia +cnr:institutes @=@ https://ror.org/00dqega85 @=@ CDS032 +cnr:institutes @=@ https://ror.org/00dqega85 @=@ IFAC - Istituto di fisica applicata \"Nello Carrara\" +cnr:institutes @=@ https://ror.org/02n2bgz18 @=@ CDS033 +cnr:institutes @=@ https://ror.org/02n2bgz18 @=@ IFP - Istituto di fisica del plasma \"Piero Caldirola\" +cnr:institutes @=@ __CDS034__ @=@ CDS034 +cnr:institutes @=@ __CDS034__ @=@ IFSI - Istituto di fisica dello spazio interplanetario +cnr:institutes @=@ https://ror.org/01kdj2848 @=@ CDS035 +cnr:institutes @=@ https://ror.org/01kdj2848 @=@ IFC - Istituto di fisiologia clinica +cnr:institutes @=@ https://ror.org/049ebw417 @=@ CDS036 +cnr:institutes @=@ https://ror.org/049ebw417 @=@ IFN - Istituto di fotonica e nanotecnologie +cnr:institutes @=@ https://ror.org/01f5tnx94 @=@ CDS037 +cnr:institutes @=@ https://ror.org/01f5tnx94 @=@ IGI - Istituto gas ionizzati +cnr:institutes @=@ __CDS038__ @=@ CDS038 +cnr:institutes @=@ __CDS038__ @=@ IGP - Istituto di genetica delle popolazioni +cnr:institutes @=@ https://ror.org/04hadk112 @=@ CDS039 +cnr:institutes @=@ https://ror.org/04hadk112 @=@ IGB - Istituto di genetica e biofisica \"Adriano Buzzati Traverso\" +cnr:institutes @=@ https://ror.org/03qpd8w66 @=@ CDS040 +cnr:institutes @=@ https://ror.org/03qpd8w66 @=@ IGM - Istituto di genetica molecolare \"Luigi Luca Cavalli Sforza\" +cnr:institutes @=@ https://ror.org/01gtsa866 @=@ CDS041 +cnr:institutes @=@ https://ror.org/01gtsa866 @=@ IBBR - Istituto di Bioscienze e Biorisorse +cnr:institutes @=@ https://ror.org/00ytw6m58 @=@ CDS042 +cnr:institutes @=@ https://ror.org/00ytw6m58 @=@ IGAG - Istituto di geologia ambientale e geoingegneria +cnr:institutes @=@ https://ror.org/015bmra78 @=@ CDS043 +cnr:institutes @=@ https://ror.org/015bmra78 @=@ IGG - Istituto di geoscienze e georisorse +cnr:institutes @=@ https://ror.org/02gdcn153 @=@ CDS044 +cnr:institutes @=@ https://ror.org/02gdcn153 @=@ IIT - Istituto di informatica e telematica +cnr:institutes @=@ __CDS045__ @=@ CDS045 +cnr:institutes @=@ __CDS045__ @=@ ISIB - Istituto di ingegneria biomedica +cnr:institutes @=@ https://ror.org/05hky6p02 @=@ CDS046 +cnr:institutes @=@ https://ror.org/05hky6p02 @=@ IIA - Istituto sull'inquinamento atmosferico +cnr:institutes @=@ https://ror.org/011n2hw53 @=@ CDS047 +cnr:institutes @=@ https://ror.org/011n2hw53 @=@ ILIESI - Istituto per il lessico intellettuale europeo e storia delle idee +cnr:institutes @=@ https://ror.org/028g3pe33 @=@ CDS048 +cnr:institutes @=@ https://ror.org/028g3pe33 @=@ ILC - Istituto di linguistica computazionale \"Antonio Zampolli\" +cnr:institutes @=@ __CDS049__ @=@ CDS049 +cnr:institutes @=@ __CDS049__ @=@ IMAMOTER - Istituto per le macchine agricole e movimento terra +cnr:institutes @=@ https://ror.org/03m0n3c07 @=@ CDS050 +cnr:institutes @=@ https://ror.org/03m0n3c07 @=@ IMATI - Istituto di matematica applicata e tecnologie informatiche \"Enrico Magenes\" +cnr:institutes @=@ __CDS051__ @=@ CDS051 +cnr:institutes @=@ __CDS051__ @=@ IMCB - Istituto per i materiali compositi e biomedici +cnr:institutes @=@ https://ror.org/00z8ws214 @=@ CDS052 +cnr:institutes @=@ https://ror.org/00z8ws214 @=@ IMEM - Istituto dei materiali per l'elettronica ed il magnetismo +cnr:institutes @=@ __CDS053__ @=@ CDS053 +cnr:institutes @=@ __CDS053__ @=@ ISB - Istituto per i Sistemi Biologici +cnr:institutes @=@ https://ror.org/00bc51d88 @=@ CDS054 +cnr:institutes @=@ https://ror.org/00bc51d88 @=@ NANOTEC - Istituto di Nanotecnologia +cnr:institutes @=@ https://ror.org/024ye7w89 @=@ CDS055 +cnr:institutes @=@ https://ror.org/024ye7w89 @=@ IMAA - Istituto di metodologie per l'analisi ambientale +cnr:institutes @=@ __CDS056__ @=@ CDS056 +cnr:institutes @=@ __CDS056__ @=@ IMGC - Istituto di metrologia \"Gustavo Colonnetti\" +cnr:institutes @=@ https://ror.org/05vk2g845 @=@ CDS057 +cnr:institutes @=@ https://ror.org/05vk2g845 @=@ IMM - Istituto per la microelettronica e microsistemi +cnr:institutes @=@ https://ror.org/02qwy8e97 @=@ CDS058 +cnr:institutes @=@ https://ror.org/02qwy8e97 @=@ IM - Istituto motori +cnr:institutes @=@ __CDS059__ @=@ CDS059 +cnr:institutes @=@ __CDS059__ @=@ INMM - Istituto di neurobiologia e medicina molecolare +cnr:institutes @=@ https://ror.org/02dr63s31 @=@ CDS060 +cnr:institutes @=@ https://ror.org/02dr63s31 @=@ IRGB - Istituto di Ricerca Genetica e Biomedica +cnr:institutes @=@ https://ror.org/0240rwx68 @=@ CDS061 +cnr:institutes @=@ https://ror.org/0240rwx68 @=@ IN - Istituto di neuroscienze +cnr:institutes @=@ https://ror.org/02rzxrg25 @=@ CDS062 +cnr:institutes @=@ https://ror.org/02rzxrg25 @=@ OVI - Istituto opera del vocabolario italiano +cnr:institutes @=@ https://ror.org/05patmk97 @=@ CDS063 +cnr:institutes @=@ https://ror.org/05patmk97 @=@ IPCF - Istituto per i processi chimico-fisici +cnr:institutes @=@ __CDS064__ @=@ CDS064 +cnr:institutes @=@ __CDS064__ @=@ IPP - Istituto per la protezione delle piante +cnr:institutes @=@ https://ror.org/029st3z03 @=@ CDS065 +cnr:institutes @=@ https://ror.org/029st3z03 @=@ IRA - Istituto di radioastronomia +cnr:institutes @=@ https://ror.org/0040zx077 @=@ CDS066 +cnr:institutes @=@ https://ror.org/0040zx077 @=@ IRPI - Istituto di ricerca per la protezione idrogeologica +cnr:institutes @=@ https://ror.org/044bfsy89 @=@ CDS067 +cnr:institutes @=@ https://ror.org/044bfsy89 @=@ IRCRES - Istituto di Ricerca sulla Crescita Economica Sostenibile +cnr:institutes @=@ https://ror.org/01n1ayq61 @=@ CDS068 +cnr:institutes @=@ https://ror.org/01n1ayq61 @=@ IRPPS - Istituto di ricerche sulla popolazione e le politiche sociali +cnr:institutes @=@ https://ror.org/02db0kh50 @=@ CDS069 +cnr:institutes @=@ https://ror.org/02db0kh50 @=@ IRSA - Istituto di ricerca sulle acque +cnr:institutes @=@ https://ror.org/05813wx75 @=@ CDS070 +cnr:institutes @=@ https://ror.org/05813wx75 @=@ IRC - Istituto di ricerche sulla combustione +cnr:institutes @=@ https://ror.org/04vnwke91 @=@ CDS071 +cnr:institutes @=@ https://ror.org/04vnwke91 @=@ IRISS - Istituto di Ricerca su Innovazione e Servizi per lo Sviluppo +cnr:institutes @=@ https://ror.org/02wxw4x45 @=@ CDS072 +cnr:institutes @=@ https://ror.org/02wxw4x45 @=@ IREA - Istituto per il rilevamento elettromagnetico dell'ambiente +cnr:institutes @=@ https://ror.org/01j6drw72 @=@ CDS073 +cnr:institutes @=@ https://ror.org/01j6drw72 @=@ ISTEC - Istituto di scienza e tecnologia dei materiali ceramici +cnr:institutes @=@ https://ror.org/05kacka20 @=@ CDS074 +cnr:institutes @=@ https://ror.org/05kacka20 @=@ ISTI - Istituto di scienza e tecnologie dell'informazione \"Alessandro Faedo\" +cnr:institutes @=@ https://ror.org/00n8ttd98 @=@ CDS075 +cnr:institutes @=@ https://ror.org/00n8ttd98 @=@ ISAC - Istituto di scienze dell'atmosfera e del clima +cnr:institutes @=@ https://ror.org/0013zhk30 @=@ CDS076 +cnr:institutes @=@ https://ror.org/0013zhk30 @=@ ISA - Istituto di Scienze dell'Alimentazione +cnr:institutes @=@ https://ror.org/03x7xkr71 @=@ CDS077 +cnr:institutes @=@ https://ror.org/03x7xkr71 @=@ ISPA - Istituto di scienze delle produzioni alimentari +cnr:institutes @=@ https://ror.org/05w9g2j85 @=@ CDS078 +cnr:institutes @=@ https://ror.org/05w9g2j85 @=@ ISTC - Istituto di scienze e tecnologie della cognizione +cnr:institutes @=@ https://ror.org/032tyv240 @=@ CDS079 +cnr:institutes @=@ https://ror.org/032tyv240 @=@ ISTM - Istituto di scienze e tecnologie molecolari +cnr:institutes @=@ https://ror.org/02hdf6119 @=@ CDS080 +cnr:institutes @=@ https://ror.org/02hdf6119 @=@ ISMAR - Istituto di scienze marine +cnr:institutes @=@ https://ror.org/01yg57d71 @=@ CDS081 +cnr:institutes @=@ https://ror.org/01yg57d71 @=@ ISN - Istituto di scienze neurologiche +cnr:institutes @=@ https://ror.org/021z1mz76 @=@ CDS082 +cnr:institutes @=@ https://ror.org/021z1mz76 @=@ ISOF - Istituto per la sintesi organica e la fotoreattività +cnr:institutes @=@ https://ror.org/01wqae691 @=@ CDS083 +cnr:institutes @=@ https://ror.org/01wqae691 @=@ ISPAAM - Istituto per il sistema produzione animale in ambiente Mediterraneo +cnr:institutes @=@ __CDS084__ @=@ CDS084 +cnr:institutes @=@ __CDS084__ @=@ ISAFoM - Istituto per i sistemi agricoli e forestali del mediterraneo +cnr:institutes @=@ https://ror.org/00awwz417 @=@ CDS085 +cnr:institutes @=@ https://ror.org/00awwz417 @=@ ISPF - Istituto per la storia del pensiero filosofico e scientifico moderno +cnr:institutes @=@ https://ror.org/03a111314 @=@ CDS086 +cnr:institutes @=@ https://ror.org/03a111314 @=@ ISEM - Istituto di storia dell'Europa mediterranea +cnr:institutes @=@ https://ror.org/01zz9wh30 @=@ CDS087 +cnr:institutes @=@ https://ror.org/01zz9wh30 @=@ ISM - Istituto di struttura della materia +cnr:institutes @=@ https://ror.org/035y5td47 @=@ CDS088 +cnr:institutes @=@ https://ror.org/035y5td47 @=@ ISGI - Istituto di studi giuridici internazionali +cnr:institutes @=@ __CDS089__ @=@ CDS089 +cnr:institutes @=@ __CDS089__ @=@ ISPRI - Istituto sperimentale di studi socio - economici sull'innovazione e le politiche della ricerca +cnr:institutes @=@ https://ror.org/051t1q308 @=@ CDS090 +cnr:institutes @=@ https://ror.org/051t1q308 @=@ ISSIA - Istituto di studi sui sistemi intelligenti per l'automazione +cnr:institutes @=@ https://ror.org/05k3cs357 @=@ CDS091 +cnr:institutes @=@ https://ror.org/05k3cs357 @=@ ISSIRFA - Istituto di studi sui sistemi regionali federali e sulle autonomie \"Massimo Severo Giannini\" +cnr:institutes @=@ https://ror.org/02gcxw165 @=@ CDS092 +cnr:institutes @=@ https://ror.org/02gcxw165 @=@ ISMA - Istituto di Studi sul Mediterraneo Antico +cnr:institutes @=@ https://ror.org/05db0es39 @=@ CDS093 +cnr:institutes @=@ https://ror.org/05db0es39 @=@ ISMed - Istituto di studi sul Mediterraneo +cnr:institutes @=@ https://ror.org/029k6t707 @=@ CDS094 +cnr:institutes @=@ https://ror.org/029k6t707 @=@ ISE - Istituto per lo studio degli ecosistemi +cnr:institutes @=@ https://ror.org/00w6r1881 @=@ CDS095 +cnr:institutes @=@ https://ror.org/00w6r1881 @=@ ISMN - Istituto per lo studio dei materiali nanostrutturati +cnr:institutes @=@ https://ror.org/01mfmr054 @=@ CDS096 +cnr:institutes @=@ https://ror.org/01mfmr054 @=@ ISMAC - Istituto per lo studio delle macromolecole +cnr:institutes @=@ https://ror.org/058nrs650 @=@ CDS097 +cnr:institutes @=@ https://ror.org/058nrs650 @=@ ITM - Istituto per la tecnologia delle membrane +cnr:institutes @=@ https://ror.org/0331xj092 @=@ CDS098 +cnr:institutes @=@ https://ror.org/0331xj092 @=@ ITABC - Istituto per le tecnologie applicate ai beni culturali +cnr:institutes @=@ https://ror.org/052q58629 @=@ CDS099 +cnr:institutes @=@ https://ror.org/052q58629 @=@ ITAE - Istituto di tecnologie avanzate per l'energia \"Nicola Giordano\" +cnr:institutes @=@ https://ror.org/04ehykb85 @=@ CDS100 +cnr:institutes @=@ https://ror.org/04ehykb85 @=@ ITB - Istituto di tecnologie biomediche +cnr:institutes @=@ https://ror.org/0221agg28 @=@ CDS101 +cnr:institutes @=@ https://ror.org/0221agg28 @=@ ITC - Istituto per le tecnologie della costruzione +cnr:institutes @=@ https://ror.org/02xz4xc25 @=@ CDS102 +cnr:institutes @=@ https://ror.org/02xz4xc25 @=@ ITD - Istituto per le tecnologie didattiche +cnr:institutes @=@ __CDS103__ @=@ CDS103 +cnr:institutes @=@ __CDS103__ @=@ STIIMA - Istituto di Sistemi e Tecnologie Industriali Intelligenti per il Manifatturiero Avanzato +cnr:institutes @=@ https://ror.org/01as2bh37 @=@ CDS104 +cnr:institutes @=@ https://ror.org/01as2bh37 @=@ ITTIG - Istituto di teoria e tecniche dell'informazione giuridica +cnr:institutes @=@ https://ror.org/01y5w6t76 @=@ CDS105 +cnr:institutes @=@ https://ror.org/01y5w6t76 @=@ ITOI - Istituto per i trapianti d'organo e immunocitologia +cnr:institutes @=@ https://ror.org/04xy2mq71 @=@ CDS106 +cnr:institutes @=@ https://ror.org/04xy2mq71 @=@ IVALSA - Istituto per la valorizzazione del legno e delle specie arboree +cnr:institutes @=@ __CDS107__ @=@ CDS107 +cnr:institutes @=@ __CDS107__ @=@ IVV - Istituto di virologia vegetale +cnr:institutes @=@ https://ror.org/013nxtf56 @=@ CDS108 +cnr:institutes @=@ https://ror.org/013nxtf56 @=@ IRSIG - Istituto di ricerca sui sistemi giudiziari +cnr:institutes @=@ https://ror.org/05rcgef49 @=@ CDS109 +cnr:institutes @=@ https://ror.org/05rcgef49 @=@ ISC - Istituto dei sistemi complessi +cnr:institutes @=@ __CDS110__ @=@ CDS110 +cnr:institutes @=@ __CDS110__ @=@ INFM - Centro di responsabilità scientifica INFM +cnr:institutes @=@ https://ror.org/02dp3a879 @=@ CDS111 +cnr:institutes @=@ https://ror.org/02dp3a879 @=@ INO - Istituto nazionale di ottica +cnr:institutes @=@ __CDS112__ @=@ CDS112 +cnr:institutes @=@ __CDS112__ @=@ IDAIC - Centro di responsabilità di attività scientifica IDAIC +cnr:institutes @=@ https://ror.org/00p03yg71 @=@ CDS113 +cnr:institutes @=@ https://ror.org/00p03yg71 @=@ SPIN - Istituto superconduttori, materiali innovativi e dispositivi +cnr:institutes @=@ https://ror.org/00yfw2296 @=@ CDS114 +cnr:institutes @=@ https://ror.org/00yfw2296 @=@ IOM - Istituto officina dei materiali +cnr:institutes @=@ https://ror.org/0042e5975 @=@ CDS115 +cnr:institutes @=@ https://ror.org/0042e5975 @=@ NANO - Istituto Nanoscienze +cnr:institutes @=@ https://ror.org/03ta8pf33 @=@ CDS116 +cnr:institutes @=@ https://ror.org/03ta8pf33 @=@ IFT - Istituto di Farmacologia Traslazionale +cnr:institutes @=@ https://ror.org/040xhth73 @=@ CDS117 +cnr:institutes @=@ https://ror.org/040xhth73 @=@ IBCN - Istituto di Biologia Cellulare e Neurobiologia +cnr:institutes @=@ https://ror.org/02qnx8e75 @=@ CDS118 +cnr:institutes @=@ https://ror.org/02qnx8e75 @=@ INM - Istituto di iNgegneria del Mare +cnr:institutes @=@ https://ror.org/05nr7xa08 @=@ CDS119 +cnr:institutes @=@ https://ror.org/05nr7xa08 @=@ IPCB - Istituto per i Polimeri, Compositi e Biomateriali +cnr:institutes @=@ https://ror.org/008fjbg42 @=@ CDS121 +cnr:institutes @=@ https://ror.org/008fjbg42 @=@ IPSP - Istituto per la Protezione Sostenibile delle Piante +cnr:institutes @=@ __CDS122__ @=@ CDS122 +cnr:institutes @=@ __CDS122__ @=@ IRBIM - Istituto per le Risorse Biologiche e le Biotecnologie Marine +cnr:institutes @=@ __CDS123__ @=@ CDS123 +cnr:institutes @=@ __CDS123__ @=@ ISPC - Istituto di Scienze del Patrimonio Culturale +cnr:institutes @=@ __CDS124__ @=@ CDS124 +cnr:institutes @=@ __CDS124__ @=@ IAS - Istituto per lo studio degli impatti Antropici e Sostenibilità in ambiente marino +cnr:institutes @=@ __CDS125__ @=@ CDS125 +cnr:institutes @=@ __CDS125__ @=@ IRET - Istituto di Ricerca sugli Ecosistemi Terrestri +cnr:institutes @=@ https://ror.org/03a0vt050 @=@ CDS126 +cnr:institutes @=@ https://ror.org/03a0vt050 @=@ ISTP - Istituto per la Scienza e Tecnologia dei Plasmi +cnr:institutes @=@ __CDS127__ @=@ CDS127 +cnr:institutes @=@ __CDS127__ @=@ ISP - Istituto di Scienze Polari +cnr:institutes @=@ https://ror.org/03byxpq91 @=@ CDS128 +cnr:institutes @=@ https://ror.org/03byxpq91 @=@ IRIB - Istituto per la Ricerca e l'Innovazione Biomedica +cnr:institutes @=@ __CDS129__ @=@ CDS129 +cnr:institutes @=@ __CDS129__ @=@ IGSG - Istituto di Informatica Giuridica e Sistemi Giudiziari +cnr:institutes @=@ __CDS130__ @=@ CDS130 +cnr:institutes @=@ __CDS130__ @=@ IBBC - Istituto di Biochimica e Biologia Cellulare +cnr:institutes @=@ __CDS131__ @=@ CDS131 +cnr:institutes @=@ __CDS131__ @=@ IBE - Istituto per la BioEconomia +cnr:institutes @=@ https://ror.org/0263zy895 @=@ CDS132 +cnr:institutes @=@ https://ror.org/0263zy895 @=@ SCITEC - Istituto di Scienze e Tecnologie Chimiche \"Giulio Natta\" +cnr:institutes @=@ __CDS133__ @=@ CDS133 +cnr:institutes @=@ __CDS133__ @=@ STEMS - Istituto di Scienze e Tecnologie per l'Energia e la Mobilità Sostenibili \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/terms.txt b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/terms.txt index 93cc00eca4..0f0ebaad42 100644 --- a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/terms.txt +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/terms.txt @@ -1077,4 +1077,137 @@ dnet:topic_types @=@ dnet:topic_types 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@=@ https://ror.org/03ta8pf33 +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/040xhth73 @=@ https://ror.org/040xhth73 +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/02qnx8e75 @=@ https://ror.org/02qnx8e75 +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/05nr7xa08 @=@ https://ror.org/05nr7xa08 +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/008fjbg42 @=@ https://ror.org/008fjbg42 +cnr:institutes @=@ cnr:institutes @=@ __CDS122__ @=@ __CDS122__ +cnr:institutes @=@ cnr:institutes @=@ __CDS123__ @=@ __CDS123__ +cnr:institutes @=@ cnr:institutes @=@ __CDS124__ @=@ __CDS124__ +cnr:institutes @=@ cnr:institutes @=@ __CDS125__ @=@ __CDS125__ +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/03a0vt050 @=@ https://ror.org/03a0vt050 +cnr:institutes @=@ cnr:institutes @=@ __CDS127__ @=@ __CDS127__ +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/03byxpq91 @=@ https://ror.org/03byxpq91 +cnr:institutes @=@ cnr:institutes @=@ __CDS129__ @=@ __CDS129__ +cnr:institutes @=@ cnr:institutes @=@ __CDS130__ @=@ __CDS130__ +cnr:institutes @=@ cnr:institutes @=@ __CDS131__ @=@ __CDS131__ +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/0263zy895 @=@ https://ror.org/0263zy895 +cnr:institutes @=@ cnr:institutes @=@ __CDS133__ @=@ __CDS133__ + From 7423577a082318d6d7648945243e237c9f847029 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 21 Jun 2022 14:51:38 +0200 Subject: [PATCH 14/46] [Graph DUMP] add code to produce the delta of new projects with respect to the previous delta/dump --- .../ProjectsSubsetSparkJob.java | 80 ++++++++ .../graph/dump/project_subset_parameters.json | 27 +++ .../oozie_app/config-default.xml | 30 +++ .../dump/projectsubset/oozie_app/workflow.xml | 171 ++++++++++++++++++ 4 files changed, 308 insertions(+) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/project_subset_parameters.json create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/oozie_app/config-default.xml create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/oozie_app/workflow.xml diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java new file mode 100644 index 0000000000..67da24185b --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java @@ -0,0 +1,80 @@ +package eu.dnetlib.dhp.oa.graph.dump.projectssubset; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; +import java.io.Serializable; +import java.util.List; +import java.util.Objects; +import java.util.Optional; +import java.util.stream.Collectors; +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.FilterFunction; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.jetbrains.annotations.NotNull; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.oa.graph.dump.Utils; +import eu.dnetlib.dhp.schema.dump.oaf.community.Funder; +import eu.dnetlib.dhp.schema.dump.oaf.graph.Project; +import scala.Tuple2; +public class ProjectsSubsetSparkJob implements Serializable { + private static final Logger log = LoggerFactory.getLogger(ProjectsSubsetSparkJob.class); + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + ProjectsSubsetSparkJob.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump/project_subset_parameters.json")); + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + final String inputPath = parser.get("sourcePath"); + log.info("inputPath: {}", inputPath); + final String outputPath = parser.get("outputPath"); + log.info("outputPath: {}", outputPath); + final String projectListPath = parser.get("projectListPath"); + log.info("projectListPath: {}", projectListPath); + SparkConf conf = new SparkConf(); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath); + getNewProjectList(spark, inputPath, outputPath, projectListPath); + }); + } + private static void getNewProjectList(SparkSession spark, String inputPath, String outputPath, + String projectListPath) { + Dataset projectList = spark.read().textFile(projectListPath); + // projectList.show(false); + Dataset projects; + projects = Utils.readPath(spark, inputPath, Project.class); + projects + .joinWith(projectList, projects.col("id").equalTo(projectList.col("value")), "left") + .map((MapFunction, Project>) t2 -> { + if (Optional.ofNullable(t2._2()).isPresent()) + return null; + return t2._1(); + }, Encoders.bean(Project.class)) + .filter(Objects::nonNull) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath); + Utils + .readPath(spark, outputPath, Project.class) + .map((MapFunction) p -> p.getId(), Encoders.STRING()) + .write() + .mode(SaveMode.Append) + .option("compression", "gzip") + .text(projectListPath); + } +} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/project_subset_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/project_subset_parameters.json new file mode 100644 index 0000000000..ed23136806 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/project_subset_parameters.json @@ -0,0 +1,27 @@ +[ + { + "paramName":"s", + "paramLongName":"sourcePath", + "paramDescription": "the path of the sequencial file to read", + "paramRequired": true + }, + { + "paramName": "out", + "paramLongName": "outputPath", + "paramDescription": "the path used to store temporary output files", + "paramRequired": true + }, + { + "paramName": "ssm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "true if the spark session is managed, false otherwise", + "paramRequired": false + }, + { + "paramName": "pl", + "paramLongName": "projectListPath", + "paramDescription": "the path of the association result projectlist", + "paramRequired": true + } +] + diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/oozie_app/config-default.xml new file mode 100644 index 0000000000..d262cb6e05 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/oozie_app/config-default.xml @@ -0,0 +1,30 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + hiveMetastoreUris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + hiveJdbcUrl + jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000 + + + hiveDbName + openaire + + + oozie.launcher.mapreduce.user.classpath.first + true + + diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/oozie_app/workflow.xml new file mode 100644 index 0000000000..619e3aa207 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/oozie_app/workflow.xml @@ -0,0 +1,171 @@ + + + + sourcePath + the source path + + + projectListPath + the path to the project list + + + outputPath + the output path + + + accessToken + the access token used for the deposition in Zenodo + + + connectionUrl + the connection url for Zenodo + + + metadata + the metadata associated to the deposition + + + depositionType + the type of deposition we want to perform. "new" for brand new deposition, "version" for a new version of a published deposition (in this case the concept record id must be provided), "upload" to upload content to an open deposition for which we already have the deposition id (in this case the deposition id should be provided) + + + conceptRecordId + for new version, the id of the record for the old deposition + + + depositionId + the depositionId of a deposition open that has to be added content + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + + + spark2YarnHistoryServerAddress + spark 2.* yarn history server address + + + spark2EventLogDir + spark 2.* event log dir location + + + + ${jobTracker} + ${nameNode} + + + mapreduce.job.queuename + ${queueName} + + + oozie.launcher.mapred.job.queue.name + ${oozieLauncherQueueName} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + yarn + cluster + Dump table project + eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/project + --resultTableNameeu.dnetlib.dhp.schema.oaf.Project + --outputPath${workingDir}/project + --communityMapPathnoneed + + + + + + + yarn + cluster + Dump table project + eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectsSubsetSparkJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/project + --outputPath${workingDir}/tar/project + --projectListPath${projectListPath} + + + + + + + eu.dnetlib.dhp.oa.graph.dump.MakeTar + --hdfsPath${outputPath} + --nameNode${nameNode} + --sourcePath${workingDir}/tar + + + + + + + eu.dnetlib.dhp.oa.graph.dump.SendToZenodoHDFS + --hdfsPath${outputPath} + --nameNode${nameNode} + --accessToken${accessToken} + --connectionUrl${connectionUrl} + --metadata${metadata} + --conceptRecordId${conceptRecordId} + --depositionType${depositionType} + --depositionId${depositionId} + + + + + + \ No newline at end of file From b98f904d48a2923b13225a656510da850c07d533 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 21 Jun 2022 17:52:27 +0200 Subject: [PATCH 15/46] [Funder Products Dump] new way to avoid using hive --- .../community/SparkPrepareResultProject.java | 6 +- .../funderresults/SparkDumpFunderResults.java | 171 ++++----- .../SparkResultLinkedToProject.java | 102 ++--- .../graph/dump/funder_result_parameters.json | 12 +- .../dump/input_parameter_select_relation.json | 20 + .../graph/dump/input_parameters_link_prj.json | 6 + .../oozie_app/config-default.xml | 30 -- .../oozie_app/workflow.xml | 347 ------------------ .../community/oozie_app/import.txt | 2 - .../community/oozie_app/workflow.xml | 273 ++++++++++++-- .../complete/oozie_app/workflow.xml | 1 + .../subworkflows/funder/oozie_app/import.txt | 2 - .../funder/oozie_app/workflow.xml | 71 ++-- .../dump/PrepareResultProjectJobTest.java | 281 +++++++------- .../ResultLinkedToProjectTest.java | 85 +++-- .../dump/funderresult/SplitPerFunderTest.java | 74 ++-- .../communityMapPath/communityMap | 1 + .../{extendeddump/orp => ext/dataset} | 0 .../funderresource/ext/otherresearchproduct | 0 .../oa/graph/dump/funderresource/ext/project | 12 + .../graph/dump/funderresource/ext/publication | 13 + .../oa/graph/dump/funderresource/ext/software | 0 .../extendeddump/otherresearchproduct | 32 ++ .../dump/funderresource/fundersList/list | 8 + .../funderresource/preparedInfo/resultProject | 1 + 25 files changed, 744 insertions(+), 806 deletions(-) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameter_select_relation.json delete mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/config-default.xml delete mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/workflow.xml delete mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/import.txt delete mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/import.txt create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/communityMapPath/communityMap rename dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/{extendeddump/orp => ext/dataset} (100%) create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext/otherresearchproduct create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext/project create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext/publication create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext/software create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/otherresearchproduct create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/fundersList/list create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo/resultProject diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java index 87ac20948a..410feea02b 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java @@ -10,6 +10,7 @@ import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.MapGroupsFunction; import org.apache.spark.sql.Dataset; @@ -81,8 +82,9 @@ public class SparkPrepareResultProject implements Serializable { Dataset relation = Utils .readPath(spark, inputPath + "/relation", Relation.class) .filter( - "dataInfo.deletedbyinference = false and lower(relClass) = '" - + ModelConstants.IS_PRODUCED_BY.toLowerCase() + "'"); + (FilterFunction) r -> !r.getDataInfo().getDeletedbyinference() && + r.getRelClass().equalsIgnoreCase(ModelConstants.IS_PRODUCED_BY)); + Dataset projects = Utils .readPath(spark, inputPath + "/project", eu.dnetlib.dhp.schema.oaf.Project.class); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java index 6aed9d7a8c..cfe47f29f9 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java @@ -1,140 +1,119 @@ - package eu.dnetlib.dhp.oa.graph.dump.funderresults; - import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - import java.io.Serializable; import java.util.List; import java.util.Objects; import java.util.Optional; - +import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.FlatMapFunction; +import org.apache.spark.api.java.function.ForeachFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.*; +import org.jetbrains.annotations.NotNull; import org.slf4j.Logger; import org.slf4j.LoggerFactory; - import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; +import eu.dnetlib.dhp.schema.dump.oaf.community.Funder; import eu.dnetlib.dhp.schema.dump.oaf.community.Project; - /** * Splits the dumped results by funder and stores them in a folder named as the funder nsp (for all the funders, but the EC * for the EC it specifies also the fundingStream (FP7 or H2020) */ public class SparkDumpFunderResults implements Serializable { private static final Logger log = LoggerFactory.getLogger(SparkDumpFunderResults.class); - public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils - .toString( - SparkDumpFunderResults.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json")); - + .toString( + SparkDumpFunderResults.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json")); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); parser.parseArgument(args); - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String inputPath = parser.get("sourcePath"); log.info("inputPath: {}", inputPath); - final String outputPath = parser.get("outputPath"); log.info("outputPath: {}", outputPath); - - final String graphPath = parser.get("graphPath"); - log.info("relationPath: {}", graphPath); - SparkConf conf = new SparkConf(); - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - writeResultProjectList(spark, inputPath, outputPath, graphPath); - }); + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath); + writeResultProjectList(spark, inputPath, outputPath); + }); } - - private static void writeResultProjectList(SparkSession spark, String inputPath, String outputPath, - String graphPath) { - - Dataset project = Utils - .readPath(spark, graphPath + "/project", eu.dnetlib.dhp.schema.oaf.Project.class); - + private static void writeResultProjectList(SparkSession spark, String inputPath, String outputPath) { Dataset result = Utils - .readPath(spark, inputPath + "/publication", CommunityResult.class) - .union(Utils.readPath(spark, inputPath + "/dataset", CommunityResult.class)) - .union(Utils.readPath(spark, inputPath + "/orp", CommunityResult.class)) - .union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class)); - - List funderList = project - .select("id") - .map((MapFunction) value -> value.getString(0).substring(0, 15), Encoders.STRING()) - .distinct() - .collectAsList(); - + .readPath(spark, inputPath + "/publication", CommunityResult.class) + .union(Utils.readPath(spark, inputPath + "/dataset", CommunityResult.class)) + .union(Utils.readPath(spark, inputPath + "/otherresearchproduct", CommunityResult.class)) + .union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class)); + log.info("Number of result {}", result.count()); + Dataset tmp = result + .flatMap((FlatMapFunction) cr -> cr.getProjects().stream().map(p -> { + return getFunderName(p); + }).collect(Collectors.toList()).iterator(), Encoders.STRING()) + .distinct(); + List funderList = tmp.collectAsList(); funderList.forEach(funder -> { - String fundernsp = funder.substring(3); - String funderdump; - if (fundernsp.startsWith("corda")) { - funderdump = "EC_"; - if (fundernsp.endsWith("h2020")) { - funderdump += "H2020"; - } else { - funderdump += "FP7"; - } - } else { - funderdump = fundernsp.substring(0, fundernsp.indexOf("_")).toUpperCase(); - } - writeFunderResult(funder, result, outputPath, funderdump); + dumpResults(funder, result, outputPath); }); - } - - private static void dumpResults(String nsp, Dataset results, String outputPath, - String funderName) { - - results.map((MapFunction) r -> { - if (!Optional.ofNullable(r.getProjects()).isPresent()) { - return null; + @NotNull + private static String getFunderName(Project p) { + Optional ofunder = Optional.ofNullable(p.getFunder()); + if (ofunder.isPresent()) { + String fName = ofunder.get().getShortName(); + if (fName.equalsIgnoreCase("ec")) { + fName += "_" + ofunder.get().getFundingStream(); } - for (Project p : r.getProjects()) { - if (p.getId().startsWith(nsp)) { - if (nsp.startsWith("40|irb")) { - if (p.getFunder().getShortName().equals(funderName)) - return r; - else - return null; - } - return r; + return fName; + } else { + String fName = p.getId().substring(3, p.getId().indexOf("_")).toUpperCase(); + if (fName.equalsIgnoreCase("ec")) { + if (p.getId().contains("h2020")) { + fName += "_H2020"; + } else { + fName += "_FP7"; } + } else if (fName.equalsIgnoreCase("conicytf")) { + fName = "CONICYT"; + } else if (fName.equalsIgnoreCase("dfgf")) { + fName = "DFG"; + } else if (fName.equalsIgnoreCase("tubitakf")) { + fName = "TUBITAK"; + } else if (fName.equalsIgnoreCase("euenvagency")) { + fName = "EEA"; } - return null; - }, Encoders.bean(CommunityResult.class)) - .filter(Objects::nonNull) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath + "/" + funderName); + return fName; + } } - - private static void writeFunderResult(String funder, Dataset results, String outputPath, - String funderDump) { - - if (funder.startsWith("40|irb")) { - dumpResults(funder, results, outputPath, "HRZZ"); - dumpResults(funder, results, outputPath, "MZOS"); - } else - dumpResults(funder, results, outputPath, funderDump); - + private static void dumpResults(String funder, Dataset results, String outputPath) { + results.map((MapFunction) r -> { + if (!Optional.ofNullable(r.getProjects()).isPresent()) { + return null; + } + for (Project p : r.getProjects()) { + String fName = getFunderName(p); + if (fName.equalsIgnoreCase(funder)) { + return r; + } + } + return null; + }, Encoders.bean(CommunityResult.class)) + .filter(Objects::nonNull) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath + "/" + funder); } - -} +} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java index d89b9e86dd..5eed64e892 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java @@ -5,9 +5,12 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.io.Serializable; import java.util.Optional; +import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.FilterFunction; +import org.apache.spark.api.java.function.FlatMapFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.MapGroupsFunction; import org.apache.spark.sql.Dataset; @@ -18,11 +21,18 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.oa.graph.dump.Constants; +import eu.dnetlib.dhp.oa.graph.dump.DumpProducts; +import eu.dnetlib.dhp.oa.graph.dump.ResultMapper; import eu.dnetlib.dhp.oa.graph.dump.Utils; +import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; +import eu.dnetlib.dhp.oa.graph.dump.community.ResultProject; import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; import eu.dnetlib.dhp.schema.oaf.Project; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Result; +import scala.Tuple2; /** * Selects the results linked to projects. Only for these results the dump will be performed. @@ -35,18 +45,18 @@ public class SparkResultLinkedToProject implements Serializable { public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils - .toString( - SparkResultLinkedToProject.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json")); + .toString( + SparkResultLinkedToProject.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json")); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); parser.parseArgument(args); Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); final String inputPath = parser.get("sourcePath"); @@ -58,59 +68,51 @@ public class SparkResultLinkedToProject implements Serializable { final String resultClassName = parser.get("resultTableName"); log.info("resultTableName: {}", resultClassName); - final String graphPath = parser.get("graphPath"); - log.info("graphPath: {}", graphPath); + final String resultProjectsPath = parser.get("graphPath"); + log.info("graphPath: {}", resultProjectsPath); + + String communityMapPath = parser.get("communityMapPath"); @SuppressWarnings("unchecked") Class inputClazz = (Class) Class.forName(resultClassName); SparkConf conf = new SparkConf(); runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - writeResultsLinkedToProjects(spark, inputClazz, inputPath, outputPath, graphPath); - }); + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath); + writeResultsLinkedToProjects( + communityMapPath, spark, inputClazz, inputPath, outputPath, resultProjectsPath); + }); } - private static void writeResultsLinkedToProjects(SparkSession spark, Class inputClazz, - String inputPath, String outputPath, String graphPath) { + private static void writeResultsLinkedToProjects(String communityMapPath, SparkSession spark, + Class inputClazz, + String inputPath, String outputPath, String resultProjectsPath) { Dataset results = Utils - .readPath(spark, inputPath, inputClazz) - .filter("dataInfo.deletedbyinference = false and datainfo.invisible = false"); - Dataset relations = Utils - .readPath(spark, graphPath + "/relation", Relation.class) - .filter( - "dataInfo.deletedbyinference = false and lower(relClass) = '" - + ModelConstants.IS_PRODUCED_BY.toLowerCase() + "'"); - Dataset project = Utils.readPath(spark, graphPath + "/project", Project.class); - - results.createOrReplaceTempView("result"); - relations.createOrReplaceTempView("relation"); - project.createOrReplaceTempView("project"); - - Dataset tmp = spark - .sql( - "Select res.* " + - "from relation rel " + - "join result res " + - "on rel.source = res.id " + - "join project p " + - "on rel.target = p.id " + - "") - .as(Encoders.bean(inputClazz)); - tmp - .groupByKey( - (MapFunction) value -> value - .getId(), - Encoders.STRING()) - .mapGroups((MapGroupsFunction) (k, it) -> it.next(), Encoders.bean(inputClazz)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); + .readPath(spark, inputPath, inputClazz) + .filter( + (FilterFunction) r -> !r.getDataInfo().getDeletedbyinference() && + !r.getDataInfo().getInvisible()); + Dataset resultProjectDataset = Utils + .readPath(spark, resultProjectsPath, ResultProject.class); + CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath); + results + .joinWith(resultProjectDataset, results.col("id").equalTo(resultProjectDataset.col("resultId"))) + .map((MapFunction, CommunityResult>) t2 -> { + CommunityResult cr = (CommunityResult) ResultMapper + .map( + t2._1(), + communityMap, Constants.DUMPTYPE.FUNDER.getType()); + cr.setProjects(t2._2().getProjectsList()); + return cr; + }, Encoders.bean(CommunityResult.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json index 5dc8e8910e..5669dca375 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json @@ -17,10 +17,10 @@ "paramDescription": "true if the spark session is managed, false otherwise", "paramRequired": false }, -{ - "paramName": "gp", - "paramLongName": "graphPath", - "paramDescription": "the relationPath", - "paramRequired": true -} + { + "paramName": "gp", + "paramLongName": "graphPath", + "paramDescription": "the relationPath", + "paramRequired": false + } ] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameter_select_relation.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameter_select_relation.json new file mode 100644 index 0000000000..1a67134a6b --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameter_select_relation.json @@ -0,0 +1,20 @@ +[ + { + "paramName":"s", + "paramLongName":"sourcePath", + "paramDescription": "the path of the sequencial file to read", + "paramRequired": true + }, + { + "paramName": "out", + "paramLongName": "outputPath", + "paramDescription": "the path used to store temporary output files", + "paramRequired": true + }, + { + "paramName": "ssm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "true if the spark session is managed, false otherwise", + "paramRequired": false + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json index f5641bc456..6c45538cfe 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json @@ -28,6 +28,12 @@ "paramLongName":"graphPath", "paramDescription": "the path to the relations", "paramRequired": true + }, + { + "paramName":"cmp", + "paramLongName":"communityMapPath", + "paramDescription": "the path to the relations", + "paramRequired": true } ] diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/config-default.xml deleted file mode 100644 index e5ec3d0aee..0000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/config-default.xml +++ /dev/null @@ -1,30 +0,0 @@ - - - jobTracker - yarnRM - - - nameNode - hdfs://nameservice1 - - - oozie.use.system.libpath - true - - - hiveMetastoreUris - thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 - - - hiveJdbcUrl - jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000 - - - hiveDbName - openaire - - - oozie.launcher.mapreduce.user.classpath.first - true - - \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/workflow.xml deleted file mode 100644 index 5f954ff38a..0000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/workflow.xml +++ /dev/null @@ -1,347 +0,0 @@ - - - - - sourcePath - the source path - - - outputPath - the output path - - - communityMapPath - the path to the community map - - - selectedResults - the path the the possible subset ot results to be dumped - - - hiveDbName - the target hive database name - - - hiveJdbcUrl - hive server jdbc url - - - hiveMetastoreUris - hive server metastore URIs - - - sparkDriverMemory - memory for driver process - - - sparkExecutorMemory - memory for individual executor - - - sparkExecutorCores - number of cores used by single executor - - - oozieActionShareLibForSpark2 - oozie action sharelib for spark 2.* - - - spark2ExtraListeners - com.cloudera.spark.lineage.NavigatorAppListener - spark 2.* extra listeners classname - - - spark2SqlQueryExecutionListeners - com.cloudera.spark.lineage.NavigatorQueryListener - spark 2.* sql query execution listeners classname - - - spark2YarnHistoryServerAddress - spark 2.* yarn history server address - - - spark2EventLogDir - spark 2.* event log dir location - - - - - ${jobTracker} - ${nameNode} - - - mapreduce.job.queuename - ${queueName} - - - oozie.launcher.mapred.job.queue.name - ${oozieLauncherQueueName} - - - oozie.action.sharelib.for.spark - ${oozieActionShareLibForSpark2} - - - - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - - - - - - - - - - - yarn - cluster - Dump table publication for community/funder related products - eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${selectedResults}/publication - --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication - --outputPath${workingDir}/dump/publication - --communityMapPath${communityMapPath} - --dumpType${dumpType} - - - - - - - - yarn - cluster - Dump table dataset for community/funder related products - eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${selectedResults}/dataset - --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset - --outputPath${workingDir}/dump/dataset - --communityMapPath${communityMapPath} - - - - - - - - yarn - cluster - Dump table ORP for community related products - eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${selectedResults}/otherresearchproduct - --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct - --outputPath${workingDir}/dump/otherresearchproduct - --communityMapPath${communityMapPath} - - - - - - - - yarn - cluster - Dump table software for community related products - eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${selectedResults}/software - --resultTableNameeu.dnetlib.dhp.schema.oaf.Software - --outputPath${workingDir}/dump/software - --communityMapPath${communityMapPath} - - - - - - - - - - yarn - cluster - Prepare association result subset of project info - eu.dnetlib.dhp.oa.graph.dump.community.SparkPrepareResultProject - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath} - --outputPath${workingDir}/preparedInfo - - - - - - - - - - - - - - - yarn - cluster - Extend dumped publications with information about project - eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${workingDir}/dump/publication - --outputPath${outputPath}/ext/publication - --preparedInfoPath${workingDir}/preparedInfo - - - - - - - - yarn - cluster - Extend dumped dataset with information about project - eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${workingDir}/dump/dataset - --outputPath${outputPath}/ext/dataset - --preparedInfoPath${workingDir}/preparedInfo - - - - - - - - yarn - cluster - Extend dumped ORP with information about project - eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${workingDir}/dump/otherresearchproduct - --outputPath${outputPath}/ext/orp - --preparedInfoPath${workingDir}/preparedInfo - - - - - - - - yarn - cluster - Extend dumped software with information about project - eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${workingDir}/dump/software - --outputPath${outputPath}/ext/software - --preparedInfoPath${workingDir}/preparedInfo - - - - - - - - - - - diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/import.txt b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/import.txt deleted file mode 100644 index 15387e988d..0000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/import.txt +++ /dev/null @@ -1,2 +0,0 @@ -## This is a classpath-based import file (this header is required) -dump_common classpath eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml index 319517026a..b559a25dc6 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml @@ -77,42 +77,259 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - ${wf:appPath()}/dump_common - - - - - sourcePath - ${sourcePath} - - - selectedResults - ${sourcePath} - - - communityMapPath - ${workingDir}/communityMap - - - outputPath - ${workingDir} - - - - - + + + + + + + + + + yarn + cluster + Dump table publication for community/funder related products + eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${selectedResults}/publication + --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication + --outputPath${workingDir}/dump/publication + --communityMapPath${communityMapPath} + --dumpType${dumpType} + + + + + + + + yarn + cluster + Dump table dataset for community/funder related products + eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${selectedResults}/dataset + --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset + --outputPath${workingDir}/dump/dataset + --communityMapPath${communityMapPath} + + + + + + + + yarn + cluster + Dump table ORP for community related products + eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${selectedResults}/otherresearchproduct + --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct + --outputPath${workingDir}/dump/otherresearchproduct + --communityMapPath${communityMapPath} + + + + + + + + yarn + cluster + Dump table software for community related products + eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${selectedResults}/software + --resultTableNameeu.dnetlib.dhp.schema.oaf.Software + --outputPath${workingDir}/dump/software + --communityMapPath${communityMapPath} + + + + + + + + + + yarn + cluster + Prepare association result subset of project info + eu.dnetlib.dhp.oa.graph.dump.community.SparkPrepareResultProject + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath} + --outputPath${workingDir}/preparedInfo + + + + + + + + + + + + + + + yarn + cluster + Extend dumped publications with information about project + eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/dump/publication + --outputPath${outputPath}/ext/publication + --preparedInfoPath${workingDir}/preparedInfo + + + + + + + + yarn + cluster + Extend dumped dataset with information about project + eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/dump/dataset + --outputPath${outputPath}/ext/dataset + --preparedInfoPath${workingDir}/preparedInfo + + + + + + + + yarn + cluster + Extend dumped ORP with information about project + eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/dump/otherresearchproduct + --outputPath${outputPath}/ext/orp + --preparedInfoPath${workingDir}/preparedInfo + + + + + + + + yarn + cluster + Extend dumped software with information about project + eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/dump/software + --outputPath${outputPath}/ext/software + --preparedInfoPath${workingDir}/preparedInfo + + + - + yarn diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/workflow.xml index 8eab569928..7cc1333233 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/workflow.xml @@ -298,6 +298,7 @@ --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + --conf spark.sql.shuffle.partitions=3840 --sourcePath${sourcePath} --outputPath${workingDir}/validrelation diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/import.txt b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/import.txt deleted file mode 100644 index 15387e988d..0000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/import.txt +++ /dev/null @@ -1,2 +0,0 @@ -## This is a classpath-based import file (this header is required) -dump_common classpath eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/workflow.xml index b990f4e49b..2c05256cf4 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/workflow.xml @@ -77,12 +77,36 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + yarn + cluster + Prepare association result subset of project info + eu.dnetlib.dhp.oa.graph.dump.community.SparkPrepareResultProject + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath} + --outputPath${workingDir}/preparedInfo + + + + + @@ -111,7 +135,8 @@ --sourcePath${sourcePath}/publication --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication --outputPath${workingDir}/result/publication - --graphPath${sourcePath} + --graphPath${workingDir}/preparedInfo + --communityMapPath${communityMapPath} @@ -137,7 +162,8 @@ --sourcePath${sourcePath}/dataset --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset --outputPath${workingDir}/result/dataset - --graphPath${sourcePath} + --graphPath${workingDir}/preparedInfo + --communityMapPath${communityMapPath} @@ -163,7 +189,8 @@ --sourcePath${sourcePath}/otherresearchproduct --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct --outputPath${workingDir}/result/otherresearchproduct - --graphPath${sourcePath} + --graphPath${workingDir}/preparedInfo + --communityMapPath${communityMapPath} @@ -189,41 +216,14 @@ --sourcePath${sourcePath}/software --resultTableNameeu.dnetlib.dhp.schema.oaf.Software --outputPath${workingDir}/result/software - --graphPath${sourcePath} + --graphPath${workingDir}/preparedInfo + --communityMapPath${communityMapPath} - - - - - ${wf:appPath()}/dump_common - - - - - sourcePath - ${sourcePath} - - - selectedResults - ${workingDir}/result - - - communityMapPath - ${workingDir}/communityMap - - - outputPath - ${workingDir} - - - - - - + @@ -242,9 +242,8 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - --sourcePath${workingDir}/ext + --sourcePath${workingDir}/result --outputPath${outputPath} - --graphPath${sourcePath} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java index 86d2f93c9c..c6798ac581 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java @@ -35,12 +35,12 @@ public class PrepareResultProjectJobTest { private static Path workingDir; private static final Logger log = LoggerFactory - .getLogger(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class); + .getLogger(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class); @BeforeAll public static void beforeAll() throws IOException { workingDir = Files - .createTempDirectory(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class.getSimpleName()); + .createTempDirectory(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class.getSimpleName()); log.info("using work dir {}", workingDir); SparkConf conf = new SparkConf(); @@ -54,10 +54,10 @@ public class PrepareResultProjectJobTest { conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); spark = SparkSession - .builder() - .appName(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); + .builder() + .appName(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); } @AfterAll @@ -70,23 +70,23 @@ public class PrepareResultProjectJobTest { void testNoMatch() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/no_match") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/no_match") + .getPath(); SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); + .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); assertEquals(0, verificationDataset.count()); @@ -96,37 +96,37 @@ public class PrepareResultProjectJobTest { void testMatchOne() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_one") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_one") + .getPath(); SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); + .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); assertEquals(1, verificationDataset.count()); assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); verificationDataset.createOrReplaceTempView("table"); Dataset check = spark - .sql( - "Select projList.provenance.provenance " + - "from table " + - "lateral view explode (projectsList) pl as projList"); + .sql( + "Select projList.provenance.provenance " + + "from table " + + "lateral view explode (projectsList) pl as projList"); assertEquals(1, check.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); @@ -138,88 +138,88 @@ public class PrepareResultProjectJobTest { void testMatch() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match") + .getPath(); SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); + .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); assertEquals(2, verificationDataset.count()); assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); verificationDataset.createOrReplaceTempView("dataset"); String query = "select resultId, MyT.id project , MyT.title title, MyT.acronym acronym , MyT.provenance.provenance provenance " - + "from dataset " - + "lateral view explode(projectsList) p as MyT "; + + "from dataset " + + "lateral view explode(projectsList) p as MyT "; org.apache.spark.sql.Dataset resultExplodedProvenance = spark.sql(query); assertEquals(3, resultExplodedProvenance.count()); assertEquals( - 2, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") - .count()); + 2, + resultExplodedProvenance + .filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") - .count()); + 1, + resultExplodedProvenance + .filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") + .count()); assertEquals( - 2, - resultExplodedProvenance - .filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'") - .count()); + 2, + resultExplodedProvenance + .filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'") - .count()); + 1, + resultExplodedProvenance + .filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::03376222b28a3aebf2730ac514818d04' and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::03376222b28a3aebf2730ac514818d04' and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") + .count()); assertEquals( - 3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); + 3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); } @@ -227,98 +227,121 @@ public class PrepareResultProjectJobTest { public void testMatchValidated() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_validatedRels") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_validatedRels") + .getPath(); SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); + .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); assertEquals(2, verificationDataset.count()); assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); verificationDataset.createOrReplaceTempView("dataset"); String query = "select resultId, MyT.id project , MyT.title title, MyT.acronym acronym , MyT.provenance.provenance provenance, " - + - "MyT.validated.validatedByFunder, MyT.validated.validationDate " - + "from dataset " - + "lateral view explode(projectsList) p as MyT "; + + + "MyT.validated.validatedByFunder, MyT.validated.validationDate " + + "from dataset " + + "lateral view explode(projectsList) p as MyT "; org.apache.spark.sql.Dataset resultExplodedProvenance = spark.sql(query); assertEquals(3, resultExplodedProvenance.count()); assertEquals(3, resultExplodedProvenance.filter("validatedByFunder = true").count()); assertEquals( - 2, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") - .count()); + 2, + resultExplodedProvenance + .filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") - .count()); + 1, + resultExplodedProvenance + .filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") + .count()); assertEquals( - 2, - resultExplodedProvenance - .filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'") - .count()); + 2, + resultExplodedProvenance + .filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + - "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + - "and validatedByFunder = true " + - "and validationDate = '2021-08-06'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + + "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + + "and validatedByFunder = true " + + "and validationDate = '2021-08-06'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + - "and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80' " + - "and validatedByFunder = true and validationDate = '2021-08-04'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + + "and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80' " + + "and validatedByFunder = true and validationDate = '2021-08-04'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'") - .count()); + 1, + resultExplodedProvenance + .filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::03376222b28a3aebf2730ac514818d04' " + - "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + - "and validatedByFunder = true and validationDate = '2021-08-05'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::03376222b28a3aebf2730ac514818d04' " + + "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + + "and validatedByFunder = true and validationDate = '2021-08-05'") + .count()); assertEquals( - 3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); + 3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); } + + @Test + void testMatchx() throws Exception { + + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match") + .getPath(); + + SparkPrepareResultProject.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); + + tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r))); + } + } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java index 4967ae5a53..579958a624 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java @@ -22,6 +22,7 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject; +import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; import eu.dnetlib.dhp.schema.oaf.Publication; import eu.dnetlib.dhp.schema.oaf.Result; @@ -34,15 +35,15 @@ public class ResultLinkedToProjectTest { private static Path workingDir; private static final Logger log = LoggerFactory - .getLogger(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class); + .getLogger(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class); private static final HashMap map = new HashMap<>(); @BeforeAll public static void beforeAll() throws IOException { workingDir = Files - .createTempDirectory( - eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()); + .createTempDirectory( + eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()); log.info("using work dir {}", workingDir); SparkConf conf = new SparkConf(); @@ -56,10 +57,10 @@ public class ResultLinkedToProjectTest { conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); spark = SparkSession - .builder() - .appName(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); + .builder() + .appName(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); } @AfterAll @@ -72,32 +73,34 @@ public class ResultLinkedToProjectTest { void testNoMatch() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json") + .getPath(); final String graphPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo") + .getPath(); + + final String communityMapPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/communityMapPath") + .getPath(); SparkResultLinkedToProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-graphPath", graphPath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath, + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", + "-graphPath", graphPath, + "-communityMapPath", communityMapPath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, Result.class)); + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Result.class)); - - Assertions.assertEquals(0, verificationDataset.count()); + Assertions.assertEquals(0, tmp.count()); } @@ -105,32 +108,34 @@ public class ResultLinkedToProjectTest { void testMatchOne() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/papers.json") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/papers.json") + .getPath(); - final String relationPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match") - .getPath(); + final String graphPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo") + .getPath(); + + final String communityMapPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/communityMapPath") + .getPath(); SparkResultLinkedToProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-graphPath", relationPath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath, + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", + "-graphPath", graphPath, + "-communityMapPath", communityMapPath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, Publication.class)); + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Publication.class)); - - Assertions.assertEquals(1, verificationDataset.count()); + Assertions.assertEquals(1, tmp.count()); } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java index 477481c080..5bb5a11789 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java @@ -5,10 +5,14 @@ import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; +// import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkDumpFunderResults2; +// import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkGetFunderList; import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.ForeachFunction; +import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; import org.junit.jupiter.api.AfterAll; @@ -52,10 +56,10 @@ public class SplitPerFunderTest { conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); spark = SparkSession - .builder() - .appName(SplitPerFunderTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); + .builder() + .appName(SplitPerFunderTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); } @AfterAll @@ -68,86 +72,80 @@ public class SplitPerFunderTest { void test1() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext") + .getPath(); SparkDumpFunderResults.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/split", - "-sourcePath", sourcePath, - "-graphPath", sourcePath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/split", + "-sourcePath", sourcePath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - // FP7 3 + // FP7 3 and H2020 3 JavaRDD tmp = sc - .textFile(workingDir.toString() + "/split/EC_FP7") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/EC_FP7") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); + .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); Assertions.assertEquals(3, verificationDataset.count()); Assertions - .assertEquals( - 1, verificationDataset.filter("id = '50|dedup_wf_001::0d16b1714ab3077df73893a8ea57d776'").count()); + .assertEquals( + 1, verificationDataset.filter("id = '50|dedup_wf_001::0d16b1714ab3077df73893a8ea57d776'").count()); // CIHR 2 tmp = sc - .textFile(workingDir.toString() + "/split/CIHR") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/CIHR") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(2, tmp.count()); // NWO 1 tmp = sc - .textFile(workingDir.toString() + "/split/NWO") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/NWO") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(1, tmp.count()); // NIH 3 tmp = sc - .textFile(workingDir.toString() + "/split/NIH") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/NIH") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(2, tmp.count()); // NSF 1 tmp = sc - .textFile(workingDir.toString() + "/split/NSF") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/NSF") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(1, tmp.count()); // SNSF 1 tmp = sc - .textFile(workingDir.toString() + "/split/SNSF") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/SNSF") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(1, tmp.count()); // NHMRC 1 tmp = sc - .textFile(workingDir.toString() + "/split/NHMRC") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/NHMRC") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(1, tmp.count()); // H2020 3 tmp = sc - .textFile(workingDir.toString() + "/split/EC_H2020") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/EC_H2020") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(3, tmp.count()); // MZOS 1 tmp = sc - .textFile(workingDir.toString() + "/split/MZOS") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/MZOS") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(1, tmp.count()); - // CONICYT 0 - tmp = sc - .textFile(workingDir.toString() + "/split/CONICYTF") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - Assertions.assertEquals(0, tmp.count()); - } + } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/communityMapPath/communityMap b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/communityMapPath/communityMap new file mode 100644 index 0000000000..905cdabe92 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/communityMapPath/communityMap @@ -0,0 +1 @@ +{"ee":"SDSN - Greece","epos":"EPOS","enrmaps":"Energy Research","fet-h2020":"FET H2020","instruct":"Instruct-Eric","egi":"EGI Federation","euromarine":"Euromarine","covid-19":"COVID-19","dariah":"DARIAH EU","rda":"Research Data Alliance","clarin":"CLARIN","aginfra":"Agricultural and Food Sciences","risis":"RISI","fam":"Fisheries and Aquaculture Management","beopen":"Transport Research","elixir-gr":"ELIXIR GR","fet-fp7":"FET FP7","ifremer":"Ifremer","science-innovation-policy":"Science and Innovation Policy Studies","mes":"European Marine Scinece","oa-pg":"EC Post-Grant Open Access Pilot","ni":"Neuroinformatics","dh-ch":"Digital Humanities and Cultural Heritage"} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/orp b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext/dataset similarity index 100% rename from dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/orp rename to dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext/dataset diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext/otherresearchproduct b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext/otherresearchproduct new file mode 100644 index 0000000000..e69de29bb2 diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext/project b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext/project new file mode 100644 index 0000000000..f68cead77a --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext/project @@ -0,0 +1,12 @@ 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Departamento de Ciencias Ambientales y Recursos Naturales","Universidad de Alicante. Centro Iberoamericano de la Biodiversidad","Biodiversidad y Biotecnología aplicadas a la Biología de la Conservación","Terrestrial Ecology (TE)"],"country":[{"code":"NL","label":"Netherlands","provenance":{"provenance":"Propagation of country to result collected from datasources of type institutional repositories","trust":"0.85"}},{"code":"ES","label":"Spain","provenance":{"provenance":"Propagation of country to result collected from datasources of type institutional repositories","trust":"0.85"}}],"coverage":[],"dateofcollection":"2018-10-03T06:57:46.116Z","description":["Herbivory affects subsequent herbivores, mainly regulated by the phytohormones jasmonic (JA) and salicylic acid (SA). Additionally, organisms such as soil microbes belowground or parasitoids that develop inside their herbivorous hosts aboveground, can change plant responses to herbivory. However, it is not yet well known how organisms of trophic levels other than herbivores, below- and above-ground, alter the interactions between insect species sharing a host plant. Here, we investigated whether the parasitoid Aphidius colemani and different soil microbial communities (created through plant-soil feedbacks) affect the JA and SA signalling pathways in response to the aphid Myzus persicae and the thrips Frankliniella occidentalis, as well as subsequent thrips performance. Our results show that the expression of the JA-responsive gene CaPINII in sweet pepper was more suppressed by aphids than by parasitised aphids. However, parasitism did not affect the expression of CaPAL1, a biosynthetic gene of SA. Furthermore, aphid feeding enhanced thrips performance compared with uninfested plants, but this was not observed when aphids were parasitised. Soils where different plant species were previously grown, did not affect plant responses or the interaction between herbivores. Our study shows that members of the third trophic level can modify herbivore interactions by altering plant physiology.\nThis work and T.V.’s activities were supported by Spanish Ministry of Science and Innovation, (CGL2016-79054), the Open Technology Program of NWO (TTW-13848), and the STSM Cost Action FA1405 funded by the European Union. A.P. research activities were supported by the Netherlands Organisation for Scientific Research (NWO, project no. 870.15.080)."],"format":["application/pdf","application/octet-stream"],"id":"50|dedup_wf_001::01644aebfe64e809f593492e515bc070","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::e820a45f1dfc7b95282d10b6087e11c0","value":"Repositorio Institucional de la Universidad de Alicante"},"hostedby":{"key":"10|opendoar____::e820a45f1dfc7b95282d10b6087e11c0","value":"Repositorio Institucional de la Universidad de Alicante"},"license":"Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.","publicationdate":"2018-09-26","refereed":"UNKNOWN","type":"Article","url":["http://hdl.handle.net/10045/80968"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"},"hostedby":{"key":"10|doajarticles::70703810b20723fe33cba6ffd7128212","value":"Scientific 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interactions"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Herbivores"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Feeding guilds"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Parasitism"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Belowground interactions"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Zoología"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Medicine"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"R"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Science"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Q"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"international"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Laboratorium voor Entomologie"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"PE&RC"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Laboratory of Entomology"}},{"subject":{"scheme":"keywords","value":"Multidisciplinary"}}],"type":"publication"} +{"author":[{"fullname":"Bonnie Berger","name":"Bonnie","pid":{"id":{"scheme":"orcid","value":"0000-0002-2724-7228"}},"rank":1,"surname":"Berger"}],"bestaccessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":[{"key":"10|opendoar____::958adb57686c2fdec5796398de5f317a","value":"MPG.PuRe"},{"key":"10|share_______::bbd802baad85d1fd440f32a7a3a2c2b1","value":"bioRxiv"},{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"},{"key":"10|openaire____::8ac8380272269217cb09a928c8caa993","value":"UnpayWall"},{"key":"10|openaire____::806360c771262b4d6770e7cdf04b5c5a","value":"ORCID"},{"key":"10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a","value":"Microsoft Academic Graph"},{"key":"10|opendoar____::89f0fd5c927d466d6ec9a21b9ac34ffa","value":"eScholarship - University of 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Computer Science and Artificial Intelligence Laboratory","Massachusetts Institute of Technology. Department of Mathematics","Lipson, Mark","Loh, Po-Ru","Berger, Bonnie"],"country":[{"code":"DZ","label":"Algeria","provenance":{"provenance":"Propagation of country to result collected from datasources of type institutional repositories","trust":"0.85"}},{"code":"US","label":"United States","provenance":{"provenance":"Propagation of country to result collected from datasources of type institutional repositories","trust":"0.85"}}],"coverage":[],"dateofcollection":"2020-09-12T07:56:34.334Z","description":["Austronesian languages are spread across half the globe, from Easter Island to Madagascar. Evidence from linguistics and archaeology indicates that the ‘Austronesian expansion,’ which began 4,000–5,000 years ago, likely had roots in Taiwan, but the ancestry of present-day Austronesian-speaking populations remains controversial. Here, we analyse genome-wide data from 56 populations using new methods for tracing ancestral gene flow, focusing primarily on Island Southeast Asia. We show that all sampled Austronesian groups harbour ancestry that is more closely related to aboriginal Taiwanese than to any present-day mainland population. Surprisingly, western Island Southeast Asian populations have also inherited ancestry from a source nested within the variation of present-day populations speaking Austro-Asiatic languages, which have historically been nearly exclusive to the mainland. Thus, either there was once a substantial Austro-Asiatic presence in Island Southeast Asia, or Austronesian speakers migrated to and through the mainland, admixing there before continuing to western Indonesia.","National Science Foundation (U.S.). Graduate Research Fellowship Program","Simons Foundation","National Institutes of Health (U.S.) (Grant R01GM108348)","National Institutes of Health (U.S.) (Training Grant 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In terms of stimuli, passively heard normatively associated word pairs produced the highest detection rate of N400 effects (50% of the participants), compared with semantically-similar word pairs (0%) and high-cloze sentences (17%). This result is consistent with a prediction error account of N400 magnitude, with highly predictable targets leading to smaller N400 waves, and therefore larger N400 effects. Overall, our data indicate that non-repeating normatively associated word pairs provide the highest probability of detecting single-subject N400s during passive listening, and may thereby provide a clinically viable means of assessing residual linguistic function. 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New polyethers, such as iubol (2), 22-hydroxy-15(28)- dehydrovenustatriol (3), 1,2-dehydropseudodehydrothyrsiferol (4), and secodehydrothyrsiferol (5) have been isolated and characterized from this alga. The structures were determined through the interpretation of NMR spectroscopic data and the relative configuration was proposed on the basis of NOESY spectrum and biogenetic considerations. All new compounds exhibited significant cytotoxic activity against a panel of cancer cell lines. © 2011 by the authors.","Financial support was provided by the grants MAREX (FP 7; KBBE-3-245137) (EU), CTQ2008-06754-C04-01 and SAF2008-02251 (MICINN); C2008000145 and EXMAR (ACISII); RD06/0020/1037 from Red Temática de Investigación Cooperativa en Cáncer, Instituto de Salud Carlos III, co-funded by the Fondo Europeo de Desarrollo Regional of the European Union, and Junta de Castilla y León (CSI052A11-2, and GR15-Experimental Therapeutics and Translational Oncology Program). 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Participants were privately interviewed at age 18 concerning several psychiatric problems including depression, anxiety, self-injury, alcohol/cannabis dependence, and conduct disorder. There was only slight to fair agreement between prospective and retrospective reports of childhood maltreatment (all Kappa's ≤ 0.31). Both prospective and retrospective reports of maltreatment were associated with age-18 psychiatric problems, though the strongest associations were found when maltreatment was retrospectively self-reported. These findings indicate that prospective and retrospective reports of childhood maltreatment capture largely non-overlapping groups of individuals. 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Vertical velocities can be estimated indirectly from in situ observations by theoretical frameworks like the-equation. Direct measures of vertical exchanges are challenging due to their typically ephemeral spatiotemporal scales. In this study we address this problem with an adaptive sampling strategy coupling various biophysical instruments. We analyze the 3-D organization of a cyclonic mesoscale structure finely sampled during the Observing Submesoscale Coupling At High Resolution cruise in the Ligurian Sea during fall 2015. The observations, acquired with a moving vessel profiler, highlight a subsurface low-salinity layer (≃50 m), as well as rising isopycnals, generated by geostrophic cyclonic circulation, in the structure's center. Reconstructed 3-D fields of density and horizontal velocities are used to estimate the vertical velocity field down to 250 m by applying the adiabatic QG-equation, for the first time in this region. The vertical motions are characterized by multipolar patterns of downward and upward velocities on the edges of the structure and significantly smaller vertical velocities in its center. Both the 3-D distribution of particles (size ≥100 μm), measured with a laser optical plankton counter, and the Synechococcus and Prochlorococcus abundances (cell per cubic meter) measured by flow cytometry are consistent with the 3-D velocity field. In particular, a secondary vertical recirculation is identified that upwells particles (from 250 to 100 m) along isohalines to the structure's center. 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Personality traits, affective status and stress are some of the relevant factors contributing to lower quality of life and symptom exacerbation in IBS patients. In order to examine the role of stress in IBS symptom exacerbation, the aims of this study were to explore the relationship of daily stressful events and symptom severity in a prospective manner and to explore the roles of neuroticism, anxiety, depression and stress in the vicious circle of symptom perpetuation. A total of 49 patients with IBS reported their symptom severity and daily stressful events intensity each day for 14 consecutive days. They also completed the Big five personality inventory, the Beck Depression Inventory and the State-trait anxiety inventory. Cross-correlation analyses were performed on the time series data for daily stress and symptom severity for each participant separately. Four different patterns of relationships were found in different subgroups of participants: positive cross-correlations of symptom severity and stress intensity on the same day; higher symptom severity on days following stressful days; lower symptom severity on days following stressful days; and lower stress intensity on days following severe symptoms. Using average scores for daily stress and symptom severity, as well as scores for neuroticism, anxiety and depression, we performed a path analysis to test a model of symptom exacerbation. It showed that, on the group level, average stress intensity predicts average symptom severity. Neuroticism and anxiety were not significant predictors of symptom severity, while depression showed a marginally significant relationship with symptom severity, mediated by stress intensity. In conclusion, depression and daily stress seem to be important contributors to the vicious circle of IBS symptom perpetuation.","Síndrome del intestino irritable se considera un trastorno biopsicosocial, el resultado de la combinación compleja de factores predisponentes, precipitantes y perpetuos. Rasgos de personalidad, estado afectivo y estrés son algunos de los factores relevantes que contribuyen a la calidad de vida más baja y la exacerbación sintomática de los pacientes con SII. Para examinar el papel del estrés en la exacerbación sintomática de SII, el objetivo de este estudio era explorar la relación entre los acontecimientos cotidianos estresantes y la intensidad de los síntomas de forma prospectiva, tanto como explorar los papeles del neuroticismo, ansiedad, depresión y estrés en el círculo vicioso de perpetuación de los síntomas. Todos los 49 pacientes con SII informaron sobre la intensidad de los síntomas y la intensidad de los acontecimientos cotidianos estresantes cada día durante 14 días consecutivos. Además, completaron el Test de personalidad de los cinco grandes, Inventario de depresión de Beck e Inventario de ansiedad estado-rasgo. En los datos de series temporales se hizo el análisis de correlación cruzada para la intensidad del estrés diario y de los síntomas para cada participante por separado. Se encontraron cuatro patrones de relación diferentes en diferentes subgrupos de participantes: correlación cruzada positiva de la intensidad de los síntomas y del estrés el mismo día; intensidad de los síntomas más alta en los días después de los días estresantes; intensidad de los síntomas más baja en los días después de los días estresantes e intensidad del estrés más baja en los días después de los síntomas graves. Usando resultados promedios para el estrés diario y la intensidad de los síntomas, tanto como resultados para el neuroticismo, ansiedad y depresión, realizamos un análisis del camino para examinar el modelo de la exacerbación de los síntomas. Mostró que, al nivel de grupo, la intensidad del estrés promedia predice la intensidad de los síntomas promedia. Neuroticismo y ansiedad no eran predictores significativos de la intensidad de los síntomas, mientras que la depresión demostró una relación marginalmente significante con la intensidad de los síntomas, mediada por la intensidad del estrés. En conclusión, la depresión y el estrés diario parecen ser contribuidores importantes al círculo vicioso de la perpetuación de los síntomas SII."],"format":["application/pdf"],"id":"50|dedup_wf_001::054ea3bc3ccc386d150d900776e1070d","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::2e3d2c4f33a7a1f58bc6c81cacd21e9c","value":"Repository of the University of Rijeka, Faculty of Humanities and Social Sciences"},"hostedby":{"key":"10|opendoar____::2e3d2c4f33a7a1f58bc6c81cacd21e9c","value":"Repository of the University of Rijeka, Faculty of Humanities and Social Sciences"},"license":"http://creativecommons.org/licenses/by/4.0/","publicationdate":"2016-04-01","refereed":"UNKNOWN","type":"Article","url":["https://repository.ffri.uniri.hr/islandora/object/ffri:1182","https://urn.nsk.hr/urn:nbn:hr:186:701987","https://repository.ffri.uniri.hr/islandora/object/ffri:1182/datastream/FILE0"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::1c1d4df596d01da60385f0bb17a4a9e0","value":"HRČAK - Portal of scientific journals of Croatia"},"hostedby":{"key":"10|opendoar____::1c1d4df596d01da60385f0bb17a4a9e0","value":"HRČAK - Portal of scientific journals of Croatia"},"publicationdate":"2016-01-01","refereed":"UNKNOWN","type":"Other literature type","url":["https://hrcak.srce.hr/156331","https://hrcak.srce.hr/file/230444"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"},"hostedby":{"key":"10|doajarticles::23738aeeb586d9f9b652c75aaff54dd4","value":"Psychological Topics"},"publicationdate":"2016-04-01","refereed":"UNKNOWN","type":"Article","url":["http://pt.ffri.hr/index.php/pt/article/view/317","https://doaj.org/toc/1332-0742"]}],"language":{"code":"eng","label":"English"},"lastupdatetimestamp":1603727328518,"maintitle":"The role of stress in IBS symptom severity","originalId":["oai:repository.ffri.uniri.hr:ffri_1182","oai:hrcak.srce.hr:156331","oai:doaj.org/article:4394c5a4f62849ffac7ea485a91540a3"],"pid":[],"projects":[{"code":"009-0092660-2655","funder":{"jurisdiction":"HR","name":"Ministry of Science, Education and Sports of the Republic of Croatia (MSES)","shortName":"MZOS"},"id":"40|irb_hr______::ad496254144c27606e4058841e060fa0","provenance":{"provenance":"Harvested","trust":"0.900000000000000022"},"title":"Psychosomatic aspects of chronic functional and inflammatory bowel diseases"}],"publicationdate":"2016-04-01","subjects":[{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"irritable bowel syndrome"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"symptom severity"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"daily stress"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"depression"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"DRUŠTVENE ZNANOSTI. 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dependence of the recovery of the transition temperature shift after annealing (475 °C, 100 h) on copper and phosphorus contents has been studied on irradiated reactor pressure vessel (RPV) materials. A set of model alloys with low nickel content, lower than 0.2 mass%, was used for the study. Copper and phosphorus contents were varied in a wide range: 0.005–0.99 and 0.002–0.039 mass%, respectively. Recovery efficiency has been estimated by the value of residual embrittlement after annealing, measured in terms of a shift in transition temperature (ΔTKres). A comparison of the results obtained on model alloys with data for VVER-440 RPV materials has also been carried out. Comparative analysis has confirmed the conclusion that ΔTKres is independent of phosphorus content while the effect of copper on ΔTKres is not significant for typical VVER-440 RPV materials with a typical range of Cu contents between 0.10 and 0.24 mass%. 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The bi-functionality of the protein also allowed the binding of hydrophobic solid drug nanoparticles to cellulose nanofibrils and thereby improving their long-term stability under physiological conditions."}],"externalReference":[],"extraInfo":[],"format":[],"fulltext":[],"id":"50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb","instance":[{"accessright":{"classid":"CLOSED","classname":"Closed Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"collectedfrom":{"key":"10|openaire____::4692342f0992d91f9e705c26959f09e0","value":"VTT Research Information 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Ce qui nous frappe en premier lieu dans le roman de Melchior Mbonimpa, Le Totem des Baranda, c'est l'efficacité de sa fonction didactique. Le livre est porteur d'un message, d'une vision sur l'histoire de l'Afrique des Grands Lacs qu'on rencontre rarement dans l'actualité ou l'histoire immédiate que nous livrent les médias.

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

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

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

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

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La NDI a été étudiée dans le cas de diverses applications, y compris en aéronautique et en aérospatiale. Elle permet de calculer des lois de contrôle capables de linéariser et de découpler un modèle non-linéaire à tout point de fonctionnement de son enveloppe d'état. Cependant cette méthode est intrinsèquement non-robuste aux erreurs de modélisation et aux saturations en entrée. En outre, dans un contexte non-linéaire, l'obtention d'une garantie quantifiable du domaine de stabilité atteint reste à l'heure actuelle complexe. Contrairement aux approches classiques de la NDI, notre méthodologie peut être considérée comme un cadre de compensation non-linéaire généralisé qui permet d'intégrer les incertitudes et les saturations en entrée dans le processus de conception. En utilisant des stratégies de contrôle antiwindup, la loi de pilotage peut être calculée grâce à un simple processus en deux phases. Dans ce cadre de travail généralisé des transformations linéaires fractionnaires (LFT - Linear Fractional Transformations) de la boucle fermée non-linéaire peuvent être facilement déduites pour l'analyse de la stabilité robuste en utilisant des outils standards pour de systèmes linéaires. La méthode proposée est testée pour le pilotage d'un véhicule de rentrée atmosphérique de type aile delta lors de ses phases hypersonique, transsonique et subsonique. Pour cette thèse, un simulateur du vol incluant divers facteurs externes ainsi que des erreurs de modélisation a été développé dans Simulink.\n\nThis thesis work is devoted to extending Nonlinear Dynamic Inversion (NDI) for a large scale of\nnonlinear systems while guaranteeing sufficient stability conditions. NDI has been studied in a wide range of applications, including aeronautics and aerospace. It allows to compute nonlinear control laws able to decouple and linearize a model at any operating point of its state envelope. 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00:00:00 2001 From: "miriam.baglioni" Date: Tue, 21 Jun 2022 18:02:51 +0200 Subject: [PATCH 16/46] [DUMP NEW FUNDED PRODUCTS] change in resources --- .../dhp/oa/graph/dump/funderresource/nomatch/papers.json | 2 +- .../dhp/oa/graph/dump/funderresource/preparedInfo/resultProject | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json index fda631c2f2..dd60269809 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json @@ -12,7 +12,7 @@ {"author":[{"fullname":"Sharp, 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This study examines Leonard Cohen's novel Beautiful Losers through the lenses of allegorical and authorial theories to appreciate how the novel uses allegorical techniques to code into symbolic terms an exploration of the polysemous nature of the word ''translation.'' The first chapter studies the stylistic and conceptual dimensions of allegory as a literary genre - as critics like Northrop Frye, Angus Fletchet, and Maureen Quilligan help to define it - while arguing that Cohen's novel is consciously allegorical, challenging readers to interpret what it \"means,\" or may mean. The second chapter performs an intensive re-reading of Beautiful Losers, examining how the novel uses complex systems of verbal play (particularly puns) to coordinate a reunification of various dichotomies historical \"reality\"/imaginative myth, secularity/spirituality, enslavement/sanctification, among others - employed throughout the text. The thesis concludes that the novel is perpetually playing with various types of translation (spiritual, linguistic, physical, and so forth), affirming the need for emotionally-charged, devotional forms of expression (like song and prayer) over more clinical attempts to reorder or recreate the world and its inhabitants. Ultimately, this discussion argues that an understanding of the allegorical dimensions of Beautiful Losers may illuminate how Cohen's other works (particularly his songs) may be studied as attempts to associate word with voice, to emphasize the process of expression (translation) rather than just the finished product.

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ry."},"relevantdate":[],"resourcetype":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:dataCite_resource","schemename":"dnet:dataCite_resource"},"resulttype":{"classid":"publication","classname":"publication","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"source":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"Studia Celtica Fennica"}],"subject":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:subject_classification_typologies","schemename":"dnet:subject_classification_typologies"},"value":"Editorial"}],"title":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"value":"Editorial"}]} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo/resultProject b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo/resultProject index 515d1c9a68..5749f731dc 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo/resultProject +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo/resultProject @@ -1 +1 @@ -{"resultId":"50|a89337edbe55::43e8b61e5e8d682545cb867be8118585","projectsList":[{"id":"40|aka_________::01bb7b48e29d732a1c7bc5150b9195c4","code":"135027","acronym":null,"title":"Dynamic 3D resolution-enhanced low-coherence interferometric imaging / Consortium: Hi-Lo","funder":{"shortName":"AKA","name":"Academy of Finland","jurisdiction":"FI","fundingStream":null},"provenance":{"provenance":"Harvested","trust":"0.900000000000000022"},"validated":null},{"id":"40|aka_________::9d1af21dbd0f5bc719f71553d19a6b3a","code":"316061","acronym":null,"title":"Finnish Imaging of Degenerative Shoulder Study (FIMAGE): A study on the prevalence of degenerative imaging changes of the shoulder and their relevance to clinical symptoms in the general population.","funder":{"shortName":"AKA","name":"Academy of Finland","jurisdiction":"FI","fundingStream":null},"provenance":{"provenance":"Harvested","trust":"0.900000000000000022"},"validated":null}]} +{"resultId":"50|a89337edbe55::43e8b61e5e8d682545cb867be8118585","projectsList":[{"id":"40|aka_________::01bb7b48e29d732a1c7bc5150b9195c4","code":"135027","acronym":null,"title":"Dynamic 3D resolution-enhanced low-coherence interferometric imaging / Consortium: Hi-Lo","funder":{"shortName":"AKA","name":"Academy of Finland","jurisdiction":"FI","fundingStream":null},"provenance":{"provenance":"Harvested","trust":"0.900000000000000022"},"validated":null},{"id":"40|aka_________::9d1af21dbd0f5bc719f71553d19a6b3a","code":"316061","acronym":null,"title":"Finnish Imaging of Degenerative Shoulder Study (FIMAGE): A study on the prevalence of degenerative imaging changes of the shoulder and their relevance to clinical symptoms in the general population.","funder":{"shortName":"AKA","name":"Academy of Finland","jurisdiction":"FI","fundingStream":null},"provenance":{"provenance":"Harvested","trust":"0.900000000000000022"},"validated":null}]} \ No newline at end of file From f561f13dd9d9796613198c1cdb54f8f74b166d5a Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 21 Jun 2022 18:18:17 +0200 Subject: [PATCH 17/46] [Funder Products Dump] fixed names of parameters in workflow --- .../community/oozie_app/workflow.xml | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml index b559a25dc6..dfbe93b672 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml @@ -107,7 +107,7 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - --sourcePath${selectedResults}/publication + --sourcePath${sourcePath}/publication --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication --outputPath${workingDir}/dump/publication --communityMapPath${communityMapPath} @@ -134,7 +134,7 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - --sourcePath${selectedResults}/dataset + --sourcePath${sourcePath}/dataset --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset --outputPath${workingDir}/dump/dataset --communityMapPath${communityMapPath} @@ -160,7 +160,7 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - --sourcePath${selectedResults}/otherresearchproduct + --sourcePath${sourcePath}/otherresearchproduct --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct --outputPath${workingDir}/dump/otherresearchproduct --communityMapPath${communityMapPath} @@ -186,7 +186,7 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - --sourcePath${selectedResults}/software + --sourcePath${sourcePath}/software --resultTableNameeu.dnetlib.dhp.schema.oaf.Software --outputPath${workingDir}/dump/software --communityMapPath${communityMapPath} @@ -246,7 +246,7 @@ --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} --sourcePath${workingDir}/dump/publication - --outputPath${outputPath}/ext/publication + --outputPath${workingDir}/ext/publication --preparedInfoPath${workingDir}/preparedInfo @@ -271,7 +271,7 @@ --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} --sourcePath${workingDir}/dump/dataset - --outputPath${outputPath}/ext/dataset + --outputPath${workingDir}/ext/dataset --preparedInfoPath${workingDir}/preparedInfo @@ -296,7 +296,7 @@ --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} --sourcePath${workingDir}/dump/otherresearchproduct - --outputPath${outputPath}/ext/orp + --outputPath${workingDir}/ext/orp --preparedInfoPath${workingDir}/preparedInfo @@ -321,7 +321,7 @@ --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} --sourcePath${workingDir}/dump/software - --outputPath${outputPath}/ext/software + --outputPath${workingDir}/ext/software --preparedInfoPath${workingDir}/preparedInfo From edddfc6c637d601823681c190305aa1105ee5834 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 21 Jun 2022 18:28:53 +0200 Subject: [PATCH 18/46] [DUMP DELTA PROJECTS] adding test and resource --- .../projectssubset/ProjectSubsetTest.java | 118 ++++++++++++++++++ .../graph/dump/projectsubset/allnew/projects | 12 ++ .../dump/projectsubset/matchOne/projects | 12 ++ .../dhp/oa/graph/dump/projectsubset/projectId | 28 +++++ 4 files changed, 170 insertions(+) create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/allnew/projects create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/matchOne/projects create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/projectId diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java new file mode 100644 index 0000000000..d5b1ce776f --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java @@ -0,0 +1,118 @@ +package eu.dnetlib.dhp.oa.graph.dump.projectssubset; +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.HashMap; +import org.apache.commons.io.FileUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject; +import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; +import eu.dnetlib.dhp.schema.dump.oaf.graph.Project; +public class ProjectSubsetTest { + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static SparkSession spark; + private static Path workingDir; + private static final Logger log = LoggerFactory + .getLogger(eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class); + private static final HashMap map = new HashMap<>(); + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files + .createTempDirectory( + eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + SparkConf conf = new SparkConf(); + conf.setAppName(eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class.getSimpleName()); + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + spark = SparkSession + .builder() + .appName(eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + @Test + void testAllNew() throws Exception { + final String projectListPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/projectId") + .getPath(); + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/allnew/projects") + .getPath(); + spark + .read() + .textFile(projectListPath) + .write() + .mode(SaveMode.Overwrite) + .text(workingDir.toString() + "/projectIds"); + ProjectsSubsetSparkJob.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/projects", + "-sourcePath", sourcePath, + "-projectListPath", workingDir.toString() + "/projectIds" + }); + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/projects") + .map(item -> OBJECT_MAPPER.readValue(item, Project.class)); + Assertions.assertEquals(12, tmp.count()); + Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("aka_________")).count()); + Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("anr_________")).count()); + Assertions.assertEquals(4, tmp.filter(p -> p.getId().substring(3, 15).equals("arc_________")).count()); + Assertions.assertEquals(3, tmp.filter(p -> p.getId().substring(3, 15).equals("conicytf____")).count()); + Assertions.assertEquals(1, tmp.filter(p -> p.getId().substring(3, 15).equals("corda_______")).count()); + Assertions.assertEquals(40, sc.textFile(workingDir.toString() + "/projectIds").count()); + } + @Test + void testMatchOne() throws Exception { + final String projectListPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/projectId") + .getPath(); + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/matchOne/projects") + .getPath(); + spark + .read() + .textFile(projectListPath) + .write() + .mode(SaveMode.Overwrite) + .text(workingDir.toString() + "/projectIds"); + ProjectsSubsetSparkJob.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/projects", + "-sourcePath", sourcePath, + "-projectListPath", workingDir.toString() + "/projectIds" + }); + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/projects") + .map(item -> OBJECT_MAPPER.readValue(item, Project.class)); + Assertions.assertEquals(11, tmp.count()); + Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("aka_________")).count()); + Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("anr_________")).count()); + Assertions.assertEquals(4, tmp.filter(p -> p.getId().substring(3, 15).equals("arc_________")).count()); + Assertions.assertEquals(3, tmp.filter(p -> p.getId().substring(3, 15).equals("conicytf____")).count()); + Assertions.assertEquals(0, tmp.filter(p -> p.getId().substring(3, 15).equals("corda__h2020")).count()); + Assertions.assertEquals(39, sc.textFile(workingDir.toString() + "/projectIds").count()); + } +} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/allnew/projects b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/allnew/projects new file mode 100644 index 0000000000..82d9bef76d --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/allnew/projects @@ -0,0 +1,12 @@ +{"id":"40|aka_________::01bb7b48e29d732a1c7bc5150b9195c4","websiteurl":null,"code":"135027","acronym":null,"title":"Dynamic 3D resolution-enhanced low-coherence interferometric imaging / Consortium: Hi-Lo","startdate":null,"enddate":null,"callidentifier":"Fotoniikka ja modernit kuvantamismenetelmät LT","keywords":null,"openaccessmandateforpublications":false,"openaccessmandatefordataset":false,"subject":[],"funding":[{"shortName":"AKA","name":"Academy of Finland","jurisdiction":"FI","funding_stream":null}],"summary":null,"granted":null,"h2020programme":[]} +{"id":"40|aka_________::9d1af21dbd0f5bc719f71553d19a6b3a","websiteurl":null,"code":"316061","acronym":null,"title":"Finnish Imaging of Degenerative Shoulder Study (FIMAGE): A study on the prevalence of degenerative imaging changes of the shoulder and their relevance to clinical symptoms in the general population.","startdate":null,"enddate":null,"callidentifier":"Academy Project Funding TT","keywords":null,"openaccessmandateforpublications":false,"openaccessmandatefordataset":false,"subject":[],"funding":[{"shortName":"AKA","name":"Academy of Finland","jurisdiction":"FI","funding_stream":null}],"summary":null,"granted":null,"h2020programme":[]} +{"id":"40|anr_________::1f21edc5c902be305ee47148955c6e50","websiteurl":null,"code":"ANR-17-CE05-0033","acronym":"MOISE","title":"METAL OXIDES AS LOW LOADED NANO-IRIDIUM SUPPORT FOR COMPETITIVE WATER ELECTROLYSIS","startdate":null,"enddate":null,"callidentifier":null,"keywords":null,"openaccessmandateforpublications":false,"openaccessmandatefordataset":false,"subject":[],"funding":[{"shortName":"ANR","name":"French National Research Agency (ANR)","jurisdiction":"FR","funding_stream":null}],"summary":null,"granted":null,"h2020programme":[]} +{"id":"40|anr_________::547e78ffdcb7d72a1ef31058dede3a33","websiteurl":null,"code":"ANR-09-SEGI-0005","acronym":"GALAXY","title":"DEVELOPPEMENT COLLABORATIF DE SYSTEMES COMPLEXES SELON UNE APPROCHE GUIDEE PAR LES MODELES","startdate":null,"enddate":null,"callidentifier":null,"keywords":null,"openaccessmandateforpublications":false,"openaccessmandatefordataset":false,"subject":[],"funding":[{"shortName":"ANR","name":"French National Research Agency (ANR)","jurisdiction":"FR","funding_stream":null}],"summary":null,"granted":null,"h2020programme":[]} +{"id":"40|arc_________::838e781a8d479e27a11101421fd8b296","websiteurl":"http://purl.org/au-research/grants/arc/LE0347462","code":"LE0347462","acronym":null,"title":"Femtosecond laser micromachining facility","startdate":"2003-01-01","enddate":"2003-12-31","callidentifier":null,"keywords":"biomedical nanostructures,femtosecond laser machining,laser manufacturing,laser micromachining,microphotonics,photonic bandgap structures","openaccessmandateforpublications":false,"openaccessmandatefordataset":false,"subject":[],"funding":[{"shortName":"ARC","name":"Australian Research Council (ARC)","jurisdiction":"AU","funding_stream":{"id":"ARC::Linkage Infrastructure, Equipment and Facilities","description":"Linkage Infrastructure, Equipment and Facilities"}}],"summary":null,"granted":null,"h2020programme":[]} +{"id":"40|arc_________::a461f180f7b6700c0499d4d3d53e58c7","websiteurl":"http://purl.org/au-research/grants/arc/LP140100567","code":"LP140100567","acronym":null,"title":"Linkage Projects - Grant ID: LP140100567","startdate":"2014-01-01","enddate":"2017-12-31","callidentifier":null,"keywords":"EDUCATIONAL MEASUREMENT; EDUCATIONAL MEASUREMENT; HIGH-STAKES TESTING; HIGH-STAKES TESTING; PERFORMANCE ASSESSMENT; PERFORMANCE ASSESSMENT; PERFORMANCE ASSESSMENT","openaccessmandateforpublications":false,"openaccessmandatefordataset":false,"subject":[],"funding":[{"shortName":"ARC","name":"Australian Research Council (ARC)","jurisdiction":"AU","funding_stream":{"id":"ARC::Linkage Projects","description":"Linkage Projects"}}],"summary":null,"granted":null,"h2020programme":[]} +{"id":"40|arc_________::b46b9e07d4cea67ccf497520a75ad0c8","websiteurl":"http://purl.org/au-research/grants/arc/DP180101235","code":"DP180101235","acronym":null,"title":"Discovery Projects - Grant ID: 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+{"id":"40|arc_________::b46b9e07d4cea67ccf497520a75ad0c8","websiteurl":"http://purl.org/au-research/grants/arc/DP180101235","code":"DP180101235","acronym":null,"title":"Discovery Projects - Grant ID: DP180101235","startdate":"2018-01-01","enddate":"2023-12-31","callidentifier":null,"keywords":null,"openaccessmandateforpublications":false,"openaccessmandatefordataset":false,"subject":[],"funding":[{"shortName":"ARC","name":"Australian Research Council (ARC)","jurisdiction":"AU","funding_stream":{"id":"ARC::Discovery Projects","description":"Discovery Projects"}}],"summary":null,"granted":null,"h2020programme":[]} +{"id":"40|arc_________::c5f86314ce288f91a7f31c219b128fab","websiteurl":"http://purl.org/au-research/grants/arc/LE0989831","code":"LE0989831","acronym":null,"title":"The Australian Music Navigator: research infrastructure for discovering, accessing and analysing Australia's musical 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+40|nih_________::4bb8c14729a0082378bb04db8321ce14 +40|nih_________::08a8eed6c17c6d8e427afcfd29f87c7b +40|nsf_________::c314f3d35af1990121bf5b803937e112 +40|nih_________::3ad6a2e6ebd561206f0da69468337f50 +40|nih_________::d02c60c65a59629e69a30abcf2ceaed1 +40|nih_________::d5a241cc94253feb72181cde15f51e96 +40|nih_________::b5df718bbca69af50d4b7213e26af3f0 +40|nih_________::bc90893c1be80503578e48f6ef6b7061 +40|rcuk________::2c39b38c26c260b14a9816b88c91c132 +40|nih_________::ab103ad117cd0579df66f7592a7d4adf +40|nih_________::147aa6ad8bd201e2a02c7b6cc3f68348 +40|corda__h2020::bf5d35ec8d24ae4abfb4a1c6a0af3856 +40|nih_________::b8083208156f2764d07c736ba9b49dd2 +40|nih_________::f4d1e0aece0e6a9eff8d054c28e082db +40|nsf_________::56297da8b472a4be8ac3f09af813c9f6 +40|nsf_________::6b6dc3398eeebb3de1ab66e6eb8c5cb3 +40|nih_________::93289a36ebffb0bee3d6b01c6fc0a3d6 +40|nih_________::6c3b00dd4ae9d43d6630ff18f189ebae +40|nih_________::1d983a87768f13bc8377b1b7d17290a2 +40|nih_________::c3b56e91859b114644c1403e892eb80f +40|rcuk________::c1e15330fc7956063652f9c06e584548 \ No newline at end of file From 1d1fe3b151646e52a60d4c5f9fd70d313c506b2a Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 27 Jun 2022 18:04:59 +0200 Subject: [PATCH 19/46] [DUMP DELTA PROJECTS] refactoring --- .../projectssubset/ProjectSubsetTest.java | 204 +++++++++--------- 1 file changed, 106 insertions(+), 98 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java index d5b1ce776f..4ff1e1b968 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java @@ -1,8 +1,11 @@ + package eu.dnetlib.dhp.oa.graph.dump.projectssubset; + import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; import java.util.HashMap; + import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; @@ -15,104 +18,109 @@ import org.junit.jupiter.api.BeforeAll; import org.junit.jupiter.api.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; + import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject; -import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; + import eu.dnetlib.dhp.schema.dump.oaf.graph.Project; + public class ProjectSubsetTest { - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - private static SparkSession spark; - private static Path workingDir; - private static final Logger log = LoggerFactory - .getLogger(eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class); - private static final HashMap map = new HashMap<>(); - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory( - eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - SparkConf conf = new SparkConf(); - conf.setAppName(eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class.getSimpleName()); - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - spark = SparkSession - .builder() - .appName(eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - @Test - void testAllNew() throws Exception { - final String projectListPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/projectId") - .getPath(); - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/allnew/projects") - .getPath(); - spark - .read() - .textFile(projectListPath) - .write() - .mode(SaveMode.Overwrite) - .text(workingDir.toString() + "/projectIds"); - ProjectsSubsetSparkJob.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/projects", - "-sourcePath", sourcePath, - "-projectListPath", workingDir.toString() + "/projectIds" - }); - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/projects") - .map(item -> OBJECT_MAPPER.readValue(item, Project.class)); - Assertions.assertEquals(12, tmp.count()); - Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("aka_________")).count()); - Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("anr_________")).count()); - Assertions.assertEquals(4, tmp.filter(p -> p.getId().substring(3, 15).equals("arc_________")).count()); - Assertions.assertEquals(3, tmp.filter(p -> p.getId().substring(3, 15).equals("conicytf____")).count()); - Assertions.assertEquals(1, tmp.filter(p -> p.getId().substring(3, 15).equals("corda_______")).count()); - Assertions.assertEquals(40, sc.textFile(workingDir.toString() + "/projectIds").count()); - } - @Test - void testMatchOne() throws Exception { - final String projectListPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/projectId") - .getPath(); - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/matchOne/projects") - .getPath(); - spark - .read() - .textFile(projectListPath) - .write() - .mode(SaveMode.Overwrite) - .text(workingDir.toString() + "/projectIds"); - ProjectsSubsetSparkJob.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/projects", - "-sourcePath", sourcePath, - "-projectListPath", workingDir.toString() + "/projectIds" - }); - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/projects") - .map(item -> OBJECT_MAPPER.readValue(item, Project.class)); - Assertions.assertEquals(11, tmp.count()); - Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("aka_________")).count()); - Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("anr_________")).count()); - Assertions.assertEquals(4, tmp.filter(p -> p.getId().substring(3, 15).equals("arc_________")).count()); - Assertions.assertEquals(3, tmp.filter(p -> p.getId().substring(3, 15).equals("conicytf____")).count()); - Assertions.assertEquals(0, tmp.filter(p -> p.getId().substring(3, 15).equals("corda__h2020")).count()); - Assertions.assertEquals(39, sc.textFile(workingDir.toString() + "/projectIds").count()); - } -} \ No newline at end of file + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static SparkSession spark; + private static Path workingDir; + private static final Logger log = LoggerFactory + .getLogger(eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class); + + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files + .createTempDirectory( + eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + SparkConf conf = new SparkConf(); + conf.setAppName(eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class.getSimpleName()); + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + spark = SparkSession + .builder() + .appName(eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + void testAllNew() throws Exception { + final String projectListPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/projectId") + .getPath(); + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/allnew/projects") + .getPath(); + spark + .read() + .textFile(projectListPath) + .write() + .mode(SaveMode.Overwrite) + .text(workingDir.toString() + "/projectIds"); + ProjectsSubsetSparkJob.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/projects", + "-sourcePath", sourcePath, + "-projectListPath", workingDir.toString() + "/projectIds" + }); + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/projects") + .map(item -> OBJECT_MAPPER.readValue(item, Project.class)); + Assertions.assertEquals(12, tmp.count()); + Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("aka_________")).count()); + Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("anr_________")).count()); + Assertions.assertEquals(4, tmp.filter(p -> p.getId().substring(3, 15).equals("arc_________")).count()); + Assertions.assertEquals(3, tmp.filter(p -> p.getId().substring(3, 15).equals("conicytf____")).count()); + Assertions.assertEquals(1, tmp.filter(p -> p.getId().substring(3, 15).equals("corda_______")).count()); + Assertions.assertEquals(40, sc.textFile(workingDir.toString() + "/projectIds").count()); + } + + @Test + void testMatchOne() throws Exception { + final String projectListPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/projectId") + .getPath(); + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/matchOne/projects") + .getPath(); + spark + .read() + .textFile(projectListPath) + .write() + .mode(SaveMode.Overwrite) + .text(workingDir.toString() + "/projectIds"); + ProjectsSubsetSparkJob.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/projects", + "-sourcePath", sourcePath, + "-projectListPath", workingDir.toString() + "/projectIds" + }); + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/projects") + .map(item -> OBJECT_MAPPER.readValue(item, Project.class)); + Assertions.assertEquals(11, tmp.count()); + Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("aka_________")).count()); + Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("anr_________")).count()); + Assertions.assertEquals(4, tmp.filter(p -> p.getId().substring(3, 15).equals("arc_________")).count()); + Assertions.assertEquals(3, tmp.filter(p -> p.getId().substring(3, 15).equals("conicytf____")).count()); + Assertions.assertEquals(0, tmp.filter(p -> p.getId().substring(3, 15).equals("corda__h2020")).count()); + Assertions.assertEquals(39, sc.textFile(workingDir.toString() + "/projectIds").count()); + } +} From 71744a1f5274957a48e761a95c14370ec8f488a1 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 27 Jun 2022 18:07:58 +0200 Subject: [PATCH 20/46] [DUMP DELTA PROJECTS] refactoring --- .../ProjectsSubsetSparkJob.java | 121 +++++++++--------- 1 file changed, 60 insertions(+), 61 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java index 67da24185b..83a9f34645 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java @@ -1,80 +1,79 @@ + package eu.dnetlib.dhp.oa.graph.dump.projectssubset; + import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.io.Serializable; -import java.util.List; import java.util.Objects; import java.util.Optional; -import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; -import org.jetbrains.annotations.NotNull; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.schema.dump.oaf.community.Funder; import eu.dnetlib.dhp.schema.dump.oaf.graph.Project; import scala.Tuple2; + public class ProjectsSubsetSparkJob implements Serializable { - private static final Logger log = LoggerFactory.getLogger(ProjectsSubsetSparkJob.class); - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - ProjectsSubsetSparkJob.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/project_subset_parameters.json")); - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - final String projectListPath = parser.get("projectListPath"); - log.info("projectListPath: {}", projectListPath); - SparkConf conf = new SparkConf(); - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - getNewProjectList(spark, inputPath, outputPath, projectListPath); - }); - } - private static void getNewProjectList(SparkSession spark, String inputPath, String outputPath, - String projectListPath) { - Dataset projectList = spark.read().textFile(projectListPath); - // projectList.show(false); - Dataset projects; - projects = Utils.readPath(spark, inputPath, Project.class); - projects - .joinWith(projectList, projects.col("id").equalTo(projectList.col("value")), "left") - .map((MapFunction, Project>) t2 -> { - if (Optional.ofNullable(t2._2()).isPresent()) - return null; - return t2._1(); - }, Encoders.bean(Project.class)) - .filter(Objects::nonNull) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); - Utils - .readPath(spark, outputPath, Project.class) - .map((MapFunction) p -> p.getId(), Encoders.STRING()) - .write() - .mode(SaveMode.Append) - .option("compression", "gzip") - .text(projectListPath); - } -} \ No newline at end of file + private static final Logger log = LoggerFactory.getLogger(ProjectsSubsetSparkJob.class); + + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + ProjectsSubsetSparkJob.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump/project_subset_parameters.json")); + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + final String inputPath = parser.get("sourcePath"); + log.info("inputPath: {}", inputPath); + final String outputPath = parser.get("outputPath"); + log.info("outputPath: {}", outputPath); + final String projectListPath = parser.get("projectListPath"); + log.info("projectListPath: {}", projectListPath); + SparkConf conf = new SparkConf(); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath); + getNewProjectList(spark, inputPath, outputPath, projectListPath); + }); + } + + private static void getNewProjectList(SparkSession spark, String inputPath, String outputPath, + String projectListPath) { + Dataset projectList = spark.read().textFile(projectListPath); + Dataset projects; + projects = Utils.readPath(spark, inputPath, Project.class); + projects + .joinWith(projectList, projects.col("id").equalTo(projectList.col("value")), "left") + .map((MapFunction, Project>) t2 -> { + if (Optional.ofNullable(t2._2()).isPresent()) + return null; + return t2._1(); + }, Encoders.bean(Project.class)) + .filter(Objects::nonNull) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath); + Utils + .readPath(spark, outputPath, Project.class) + .map((MapFunction) p -> p.getId(), Encoders.STRING()) + .write() + .mode(SaveMode.Append) + .option("compression", "gzip") + .text(projectListPath); + } +} From 7da24c1dec2e942b85aa821f2140094fd8886dcf Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 28 Jun 2022 13:47:49 +0200 Subject: [PATCH 21/46] added more logging --- .../src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java | 5 +++++ .../oa/graph/raw/MigrateHdfsMdstoresApplication.java | 10 ++++++++++ 2 files changed, 15 insertions(+) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java index 5a59bc0dfe..e10d0c500c 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java @@ -75,9 +75,14 @@ public class DHPUtils { final HttpGet req = new HttpGet(url); + log.info("MDStoreManager request: {}", req); + try (final CloseableHttpClient client = HttpClients.createDefault()) { try (final CloseableHttpResponse response = client.execute(req)) { final String json = IOUtils.toString(response.getEntity().getContent()); + + log.info("MDStoreManager response: {}", json); + final MDStoreWithInfo[] mdstores = objectMapper.readValue(json, MDStoreWithInfo[].class); return Arrays .stream(mdstores) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateHdfsMdstoresApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateHdfsMdstoresApplication.java index 6c72e4dfc4..ab6f54b92a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateHdfsMdstoresApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateHdfsMdstoresApplication.java @@ -65,11 +65,19 @@ public class MigrateHdfsMdstoresApplication extends AbstractMigrationApplication log.info("isSparkSessionManaged: {}", isSparkSessionManaged); final String mdstoreManagerUrl = parser.get("mdstoreManagerUrl"); + log.info("mdstoreManagerUrl: {}", mdstoreManagerUrl); + final String mdFormat = parser.get("mdFormat"); + log.info("mdFormat: {}", mdFormat); + final String mdLayout = parser.get("mdLayout"); + log.info("mdLayout: {}", mdLayout); + final String mdInterpretation = parser.get("mdInterpretation"); + log.info("mdInterpretation: {}", mdInterpretation); final String hdfsPath = parser.get("hdfsPath"); + log.info("hdfsPath: {}", hdfsPath); final Set paths = mdstorePaths(mdstoreManagerUrl, mdFormat, mdLayout, mdInterpretation); @@ -95,6 +103,8 @@ public class MigrateHdfsMdstoresApplication extends AbstractMigrationApplication .filter(p -> HdfsSupport.exists(p, sc.hadoopConfiguration())) .toArray(size -> new String[size]); + log.info("Processing existing paths {}", Arrays.asList(validPaths)); + if (validPaths.length > 0) { spark .read() From a88103bcf940b323d6950ebbc80dea04fd115f44 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 1 Jul 2022 09:06:59 +0200 Subject: [PATCH 22/46] [action manager] added more testing --- ...moteActionPayloadForGraphTableJobTest.java | 55 +++++++++++++++++++ .../publication_table/result.json | 3 +- 2 files changed, 57 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJobTest.java b/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJobTest.java index 99ce961aa8..df9202ed88 100644 --- a/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJobTest.java +++ b/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJobTest.java @@ -172,6 +172,61 @@ public class PromoteActionPayloadForGraphTableJobTest { } } + @Test + void shouldPromoteActionPayload_custom() throws Exception { + + Class rowClazz = Publication.class; + Class actionPayloadClazz = Result.class; + MergeAndGet.Strategy strategy = MergeAndGet.Strategy.MERGE_FROM_AND_GET; + + // given + Path inputGraphTableDir = createGraphTable(inputGraphRootDir, rowClazz); + Path inputActionPayloadDir = createActionPayload(inputActionPayloadRootDir, rowClazz, actionPayloadClazz); + Path outputGraphTableDir = outputDir.resolve("graph").resolve(rowClazz.getSimpleName().toLowerCase()); + + // when + PromoteActionPayloadForGraphTableJob + .main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-inputGraphTablePath", + inputGraphTableDir.toString(), + "-graphTableClassName", + rowClazz.getCanonicalName(), + "-inputActionPayloadPath", + inputActionPayloadDir.toString(), + "-actionPayloadClassName", + actionPayloadClazz.getCanonicalName(), + "-outputGraphTablePath", + outputGraphTableDir.toString(), + "-mergeAndGetStrategy", + strategy.name(), + "--shouldGroupById", + "true" + }); + + // then + assertTrue(Files.exists(outputGraphTableDir)); + + List actualOutputRows = readGraphTableFromJobOutput(outputGraphTableDir.toString(), rowClazz) + .collectAsList() + .stream() + .sorted(Comparator.comparingInt(Object::hashCode)) + .collect(Collectors.toList()); + + Publication p = actualOutputRows + .stream() + .map(o -> (Publication) o) + .filter(o -> "50|4ScienceCRIS::6a67ed3daba1c380bf9de3c13ed9c879".equals(o.getId())) + .findFirst() + .get(); + + assertNotNull(p.getMeasures()); + assertTrue(p.getMeasures().size() > 0); + + } + public static Stream promoteJobTestParams() { return Stream .of( diff --git a/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/input/action_payload/publication_table/result.json b/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/input/action_payload/publication_table/result.json index f98ee4b78c..d98bfe98f1 100644 --- a/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/input/action_payload/publication_table/result.json +++ b/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/input/action_payload/publication_table/result.json @@ -17,4 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available","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"context":[],"externalReference":null,"instance":[]} \ No newline at end of file +{"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"","inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}},"lastupdatetimestamp":1572018240982,"id":"50|CSC_________::0001d663c95c4132355e1765375a5275","originalId":[],"collectedfrom":[],"pid":[],"dateofcollection":"","dateoftransformation":"","extraInfo":[],"oaiprovenance":null,"author":[],"resulttype":{"classid":"","classname":"","schemeid":"","schemename":""},"language":{"classid":"","classname":"","schemeid":"","schemename":""},"country":[],"subject":[{"value":"animal 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available","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"context":[],"externalReference":null,"instance":[]} +{"collectedfrom":null,"dataInfo":null,"lastupdatetimestamp":null,"id":"50|4ScienceCRIS::6a67ed3daba1c380bf9de3c13ed9c879","originalId":null,"pid":null,"dateofcollection":null,"dateoftransformation":null,"extraInfo":null,"oaiprovenance":null,"processingchargeamount":null,"processingchargecurrency":null,"measures":[{"id":"influence","unit":[{"key":"score","value":"1.64385446761e-08","dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"","inferenceprovenance":"update","provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}]},{"id":"popularity_alt","unit":[{"key":"score","value":"18.9590813696","dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"","inferenceprovenance":"update","provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}]},{"id":"popularity","unit":[{"key":"score","value":"6.00577981643e-08","dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"","inferenceprovenance":"update","provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}]}],"author":null,"resulttype":null,"language":null,"country":null,"subject":null,"title":null,"relevantdate":null,"description":null,"dateofacceptance":null,"publisher":null,"embargoenddate":null,"source":null,"fulltext":null,"format":null,"contributor":null,"resourcetype":null,"coverage":null,"bestaccessright":null,"context":null,"externalReference":null,"instance":null} \ No newline at end of file From 072f19285387fa3df2a8fcd0dfd2acbf448bdcb5 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 1 Jul 2022 09:54:56 +0200 Subject: [PATCH 23/46] include the class information in the measure XML serialization --- .../oa/provision/utils/XmlRecordFactory.java | 16 +- .../oa/provision/XmlRecordFactoryTest.java | 15 +- .../dnetlib/dhp/oa/provision/publication.json | 174 +++++++++++++++++- 3 files changed, 188 insertions(+), 17 deletions(-) diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java index 27128138cd..b34ec96934 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java @@ -999,17 +999,11 @@ public class XmlRecordFactory implements Serializable { private List measuresAsXml(List measures) { return measures .stream() - .flatMap( - m -> m - .getUnit() - .stream() - .map( - u -> Lists - .newArrayList( - new Tuple2<>("id", m.getId()), - new Tuple2<>("key", u.getKey()), - new Tuple2<>("value", u.getValue()))) - .map(l -> XmlSerializationUtils.asXmlElement("measure", l))) + .map(m -> { + List> l = Lists.newArrayList(new Tuple2<>("id", m.getId())); + m.getUnit().forEach(kv -> l.add(new Tuple2<>(kv.getKey(), kv.getValue()))); + return XmlSerializationUtils.asXmlElement("measure", l); + }) .collect(Collectors.toList()); } diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java index f4763618b5..92d9f497fb 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java @@ -73,11 +73,20 @@ public class XmlRecordFactoryTest { assertEquals("EUR", doc.valueOf("//processingchargecurrency/text()")); assertEquals( - "1.00889953098e-08", doc.valueOf("//*[local-name() = 'result']/measure[./@id = 'influence']/@value")); + "5.06690394631e-09", doc.valueOf("//*[local-name() = 'result']/measure[./@id = 'influence']/@score")); assertEquals( - "30.6576853333", doc.valueOf("//*[local-name() = 'result']/measure[./@id = 'popularity_alt']/@value")); + "C", doc.valueOf("//*[local-name() = 'result']/measure[./@id = 'influence']/@class")); + assertEquals( - "4.62970429725e-08", doc.valueOf("//*[local-name() = 'result']/measure[./@id = 'popularity']/@value")); + "0.0", doc.valueOf("//*[local-name() = 'result']/measure[./@id = 'popularity_alt']/@score")); + assertEquals( + "C", doc.valueOf("//*[local-name() = 'result']/measure[./@id = 'popularity_alt']/@class")); + + assertEquals( + "3.11855618382e-09", doc.valueOf("//*[local-name() = 'result']/measure[./@id = 'popularity']/@score")); + assertEquals( + "C", doc.valueOf("//*[local-name() = 'result']/measure[./@id = 'popularity']/@class")); + } @Test diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json index 2c52ce269f..41ced45ae4 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json @@ -5,7 +5,37 @@ "unit": [ { "key": "score", - "value": "1.00889953098e-08" + "value": "5.06690394631e-09", + "dataInfo": { + "invisible": false, + "inferred": true, + "deletedbyinference": false, + "trust": "", + "inferenceprovenance": "update", + "provenanceaction": { + "classid": "measure:bip", + "classname": "Inferred by OpenAIRE", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + { + "key": "class", + "value": "C", + "dataInfo": { + "invisible": false, + "inferred": true, + "deletedbyinference": false, + "trust": "", + "inferenceprovenance": "update", + "provenanceaction": { + "classid": "measure:bip", + "classname": "Inferred by OpenAIRE", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } } ] }, @@ -14,7 +44,37 @@ "unit": [ { "key": "score", - "value": "30.6576853333" + "value": "0.0", + "dataInfo": { + "invisible": false, + "inferred": true, + "deletedbyinference": false, + "trust": "", + "inferenceprovenance": "update", + "provenanceaction": { + "classid": "measure:bip", + "classname": "Inferred by OpenAIRE", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + { + "key": "class", + "value": "C", + "dataInfo": { + "invisible": false, + "inferred": true, + "deletedbyinference": false, + "trust": "", + "inferenceprovenance": "update", + "provenanceaction": { + "classid": "measure:bip", + "classname": "Inferred by OpenAIRE", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } } ] }, @@ -23,7 +83,115 @@ "unit": [ { "key": "score", - "value": "4.62970429725e-08" + "value": "3.11855618382e-09", + "dataInfo": { + "invisible": false, + "inferred": true, + "deletedbyinference": false, + "trust": "", + "inferenceprovenance": "update", + "provenanceaction": { + "classid": "measure:bip", + "classname": "Inferred by OpenAIRE", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + { + "key": "class", + "value": "C", + "dataInfo": { + "invisible": false, + "inferred": true, + "deletedbyinference": false, + "trust": "", + "inferenceprovenance": "update", + "provenanceaction": { + "classid": "measure:bip", + "classname": "Inferred by OpenAIRE", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + } + ] + }, + { + "id": "influence_alt", + "unit": [ + { + "key": "score", + "value": "0.0", + "dataInfo": { + "invisible": false, + "inferred": true, + "deletedbyinference": false, + "trust": "", + "inferenceprovenance": "update", + "provenanceaction": { + "classid": "measure:bip", + "classname": "Inferred by OpenAIRE", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + { + "key": "class", + "value": "C", + "dataInfo": { + "invisible": false, + "inferred": true, + "deletedbyinference": false, + "trust": "", + "inferenceprovenance": "update", + "provenanceaction": { + "classid": "measure:bip", + "classname": "Inferred by OpenAIRE", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + } + ] + }, + { + "id": "impulse", + "unit": [ + { + "key": "score", + "value": "0.0", + "dataInfo": { + "invisible": false, + "inferred": true, + "deletedbyinference": false, + "trust": "", + "inferenceprovenance": "update", + "provenanceaction": { + "classid": "measure:bip", + "classname": "Inferred by OpenAIRE", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + { + "key": "class", + "value": "C", + "dataInfo": { + "invisible": false, + "inferred": true, + "deletedbyinference": false, + "trust": "", + "inferenceprovenance": "update", + "provenanceaction": { + "classid": "measure:bip", + "classname": "Inferred by OpenAIRE", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } } ] } From 0cb1c7078826ceca91a652ab8e23931728621a97 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 1 Jul 2022 10:44:08 +0200 Subject: [PATCH 24/46] code formatting --- .../dhp/common/api/ZenodoAPIClient.java | 19 +- .../transformation/TransformationJobTest.java | 10 +- .../dnetlib/dhp/bulktag/SparkBulkTagJob.java | 2 +- .../funderresults/SparkDumpFunderResults.java | 86 +++--- .../SparkResultLinkedToProject.java | 68 ++--- .../ProjectsSubsetSparkJob.java | 3 + .../dump/PrepareResultProjectJobTest.java | 272 +++++++++--------- .../ResultLinkedToProjectTest.java | 70 ++--- .../dump/funderresult/SplitPerFunderTest.java | 60 ++-- .../projectssubset/ProjectSubsetTest.java | 1 - 10 files changed, 304 insertions(+), 287 deletions(-) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/ZenodoAPIClient.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/ZenodoAPIClient.java index 56366bc725..63f890a102 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/ZenodoAPIClient.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/ZenodoAPIClient.java @@ -255,7 +255,8 @@ public class ZenodoAPIClient implements Serializable { private void setDepositionId(String concept_rec_id, Integer page) throws IOException, MissingConceptDoiException { - ZenodoModelList zenodoModelList = new Gson().fromJson(getPrevDepositions(String.valueOf(page)), ZenodoModelList.class); + ZenodoModelList zenodoModelList = new Gson() + .fromJson(getPrevDepositions(String.valueOf(page)), ZenodoModelList.class); for (ZenodoModel zm : zenodoModelList) { if (zm.getConceptrecid().equals(concept_rec_id)) { @@ -263,8 +264,9 @@ public class ZenodoAPIClient implements Serializable { return; } } - if(zenodoModelList.size() == 0) - throw new MissingConceptDoiException("The concept record id specified was missing in the list of depositions"); + if (zenodoModelList.size() == 0) + throw new MissingConceptDoiException( + "The concept record id specified was missing in the list of depositions"); setDepositionId(concept_rec_id, page + 1); } @@ -278,11 +280,11 @@ public class ZenodoAPIClient implements Serializable { String url = urlBuilder.build().toString(); Request request = new Request.Builder() - .url(url) - .addHeader(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString()) // add request headers - .addHeader(HttpHeaders.AUTHORIZATION, "Bearer " + access_token) - .get() - .build(); + .url(url) + .addHeader(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString()) // add request headers + .addHeader(HttpHeaders.AUTHORIZATION, "Bearer " + access_token) + .get() + .build(); try (Response response = httpClient.newCall(request).execute()) { @@ -295,7 +297,6 @@ public class ZenodoAPIClient implements Serializable { } - private String getBucket(String url) throws IOException { OkHttpClient httpClient = new OkHttpClient.Builder() .connectTimeout(600, TimeUnit.SECONDS) diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java index fea7b53ac5..7fc80d1681 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java @@ -142,7 +142,8 @@ class TransformationJobTest extends AbstractVocabularyTest { @Test @DisplayName("Test TransformSparkJobNode.main with oaiOpenaire_datacite (v4)") - void transformTestITGv4OAIdatacite(@TempDir final Path testDir) throws Exception { + void transformTestITGv4OAIdatacite(@TempDir + final Path testDir) throws Exception { try (SparkSession spark = SparkSession.builder().config(sparkConf).getOrCreate()) { @@ -152,7 +153,9 @@ class TransformationJobTest extends AbstractVocabularyTest { .getFile(); final String mdstore_output = testDir.toString() + "/version"; - mockupTrasformationRule("simpleTRule", "/eu/dnetlib/dhp/transform/scripts/xslt_cleaning_oaiOpenaire_datacite_ExchangeLandingpagePid.xsl"); + mockupTrasformationRule( + "simpleTRule", + "/eu/dnetlib/dhp/transform/scripts/xslt_cleaning_oaiOpenaire_datacite_ExchangeLandingpagePid.xsl"); final Map parameters = Stream.of(new String[][] { { @@ -203,7 +206,8 @@ class TransformationJobTest extends AbstractVocabularyTest { @Test @DisplayName("Test TransformSparkJobNode.main") - void transformTest(@TempDir final Path testDir) throws Exception { + void transformTest(@TempDir + final Path testDir) throws Exception { try (SparkSession spark = SparkSession.builder().config(sparkConf).getOrCreate()) { diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java index ad1e8721ac..982e8ea750 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java @@ -103,7 +103,7 @@ public class SparkBulkTagJob { ResultTagger resultTagger = new ResultTagger(); readPath(spark, inputPath, resultClazz) .map(patchResult(), Encoders.bean(resultClazz)) - .filter(Objects::nonNull) + .filter(Objects::nonNull) .map( (MapFunction) value -> resultTagger .enrichContextCriteria( diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java index cfe47f29f9..34ca6697c4 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java @@ -1,10 +1,14 @@ + package eu.dnetlib.dhp.oa.graph.dump.funderresults; + import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + import java.io.Serializable; import java.util.List; import java.util.Objects; import java.util.Optional; import java.util.stream.Collectors; + import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.FlatMapFunction; @@ -14,29 +18,32 @@ import org.apache.spark.sql.*; import org.jetbrains.annotations.NotNull; import org.slf4j.Logger; import org.slf4j.LoggerFactory; + import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; import eu.dnetlib.dhp.schema.dump.oaf.community.Funder; import eu.dnetlib.dhp.schema.dump.oaf.community.Project; + /** * Splits the dumped results by funder and stores them in a folder named as the funder nsp (for all the funders, but the EC * for the EC it specifies also the fundingStream (FP7 or H2020) */ public class SparkDumpFunderResults implements Serializable { private static final Logger log = LoggerFactory.getLogger(SparkDumpFunderResults.class); + public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils - .toString( - SparkDumpFunderResults.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json")); + .toString( + SparkDumpFunderResults.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json")); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); parser.parseArgument(args); Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); final String inputPath = parser.get("sourcePath"); log.info("inputPath: {}", inputPath); @@ -44,30 +51,32 @@ public class SparkDumpFunderResults implements Serializable { log.info("outputPath: {}", outputPath); SparkConf conf = new SparkConf(); runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - writeResultProjectList(spark, inputPath, outputPath); - }); + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath); + writeResultProjectList(spark, inputPath, outputPath); + }); } + private static void writeResultProjectList(SparkSession spark, String inputPath, String outputPath) { Dataset result = Utils - .readPath(spark, inputPath + "/publication", CommunityResult.class) - .union(Utils.readPath(spark, inputPath + "/dataset", CommunityResult.class)) - .union(Utils.readPath(spark, inputPath + "/otherresearchproduct", CommunityResult.class)) - .union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class)); + .readPath(spark, inputPath + "/publication", CommunityResult.class) + .union(Utils.readPath(spark, inputPath + "/dataset", CommunityResult.class)) + .union(Utils.readPath(spark, inputPath + "/otherresearchproduct", CommunityResult.class)) + .union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class)); log.info("Number of result {}", result.count()); Dataset tmp = result - .flatMap((FlatMapFunction) cr -> cr.getProjects().stream().map(p -> { - return getFunderName(p); - }).collect(Collectors.toList()).iterator(), Encoders.STRING()) - .distinct(); + .flatMap((FlatMapFunction) cr -> cr.getProjects().stream().map(p -> { + return getFunderName(p); + }).collect(Collectors.toList()).iterator(), Encoders.STRING()) + .distinct(); List funderList = tmp.collectAsList(); funderList.forEach(funder -> { dumpResults(funder, result, outputPath); }); } + @NotNull private static String getFunderName(Project p) { Optional ofunder = Optional.ofNullable(p.getFunder()); @@ -97,23 +106,24 @@ public class SparkDumpFunderResults implements Serializable { return fName; } } + private static void dumpResults(String funder, Dataset results, String outputPath) { results.map((MapFunction) r -> { - if (!Optional.ofNullable(r.getProjects()).isPresent()) { - return null; - } - for (Project p : r.getProjects()) { - String fName = getFunderName(p); - if (fName.equalsIgnoreCase(funder)) { - return r; - } - } - return null; - }, Encoders.bean(CommunityResult.class)) - .filter(Objects::nonNull) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath + "/" + funder); + if (!Optional.ofNullable(r.getProjects()).isPresent()) { + return null; + } + for (Project p : r.getProjects()) { + String fName = getFunderName(p); + if (fName.equalsIgnoreCase(funder)) { + return r; + } + } + return null; + }, Encoders.bean(CommunityResult.class)) + .filter(Objects::nonNull) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath + "/" + funder); } -} \ No newline at end of file +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java index 5eed64e892..4b00729448 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java @@ -45,18 +45,18 @@ public class SparkResultLinkedToProject implements Serializable { public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils - .toString( - SparkResultLinkedToProject.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json")); + .toString( + SparkResultLinkedToProject.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json")); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); parser.parseArgument(args); Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); final String inputPath = parser.get("sourcePath"); @@ -78,41 +78,41 @@ public class SparkResultLinkedToProject implements Serializable { SparkConf conf = new SparkConf(); runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - writeResultsLinkedToProjects( - communityMapPath, spark, inputClazz, inputPath, outputPath, resultProjectsPath); - }); + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath); + writeResultsLinkedToProjects( + communityMapPath, spark, inputClazz, inputPath, outputPath, resultProjectsPath); + }); } private static void writeResultsLinkedToProjects(String communityMapPath, SparkSession spark, - Class inputClazz, - String inputPath, String outputPath, String resultProjectsPath) { + Class inputClazz, + String inputPath, String outputPath, String resultProjectsPath) { Dataset results = Utils - .readPath(spark, inputPath, inputClazz) - .filter( - (FilterFunction) r -> !r.getDataInfo().getDeletedbyinference() && - !r.getDataInfo().getInvisible()); + .readPath(spark, inputPath, inputClazz) + .filter( + (FilterFunction) r -> !r.getDataInfo().getDeletedbyinference() && + !r.getDataInfo().getInvisible()); Dataset resultProjectDataset = Utils - .readPath(spark, resultProjectsPath, ResultProject.class); + .readPath(spark, resultProjectsPath, ResultProject.class); CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath); results - .joinWith(resultProjectDataset, results.col("id").equalTo(resultProjectDataset.col("resultId"))) - .map((MapFunction, CommunityResult>) t2 -> { - CommunityResult cr = (CommunityResult) ResultMapper - .map( - t2._1(), - communityMap, Constants.DUMPTYPE.FUNDER.getType()); - cr.setProjects(t2._2().getProjectsList()); - return cr; - }, Encoders.bean(CommunityResult.class)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); + .joinWith(resultProjectDataset, results.col("id").equalTo(resultProjectDataset.col("resultId"))) + .map((MapFunction, CommunityResult>) t2 -> { + CommunityResult cr = (CommunityResult) ResultMapper + .map( + t2._1(), + communityMap, Constants.DUMPTYPE.FUNDER.getType()); + cr.setProjects(t2._2().getProjectsList()); + return cr; + }, Encoders.bean(CommunityResult.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java index 83a9f34645..38eb3cb370 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java @@ -2,9 +2,11 @@ package eu.dnetlib.dhp.oa.graph.dump.projectssubset; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + import java.io.Serializable; import java.util.Objects; import java.util.Optional; + import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; @@ -14,6 +16,7 @@ import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; import org.slf4j.LoggerFactory; + import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.schema.dump.oaf.graph.Project; diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java index c6798ac581..f3b7246b1a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java @@ -35,12 +35,12 @@ public class PrepareResultProjectJobTest { private static Path workingDir; private static final Logger log = LoggerFactory - .getLogger(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class); + .getLogger(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class); @BeforeAll public static void beforeAll() throws IOException { workingDir = Files - .createTempDirectory(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class.getSimpleName()); + .createTempDirectory(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class.getSimpleName()); log.info("using work dir {}", workingDir); SparkConf conf = new SparkConf(); @@ -54,10 +54,10 @@ public class PrepareResultProjectJobTest { conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); spark = SparkSession - .builder() - .appName(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); + .builder() + .appName(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); } @AfterAll @@ -70,23 +70,23 @@ public class PrepareResultProjectJobTest { void testNoMatch() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/no_match") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/no_match") + .getPath(); SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); + .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); assertEquals(0, verificationDataset.count()); @@ -96,37 +96,37 @@ public class PrepareResultProjectJobTest { void testMatchOne() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_one") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_one") + .getPath(); SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); + .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); assertEquals(1, verificationDataset.count()); assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); verificationDataset.createOrReplaceTempView("table"); Dataset check = spark - .sql( - "Select projList.provenance.provenance " + - "from table " + - "lateral view explode (projectsList) pl as projList"); + .sql( + "Select projList.provenance.provenance " + + "from table " + + "lateral view explode (projectsList) pl as projList"); assertEquals(1, check.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); @@ -138,88 +138,88 @@ public class PrepareResultProjectJobTest { void testMatch() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match") + .getPath(); SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); + .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); assertEquals(2, verificationDataset.count()); assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); verificationDataset.createOrReplaceTempView("dataset"); String query = "select resultId, MyT.id project , MyT.title title, MyT.acronym acronym , MyT.provenance.provenance provenance " - + "from dataset " - + "lateral view explode(projectsList) p as MyT "; + + "from dataset " + + "lateral view explode(projectsList) p as MyT "; org.apache.spark.sql.Dataset resultExplodedProvenance = spark.sql(query); assertEquals(3, resultExplodedProvenance.count()); assertEquals( - 2, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") - .count()); + 2, + resultExplodedProvenance + .filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") - .count()); + 1, + resultExplodedProvenance + .filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") + .count()); assertEquals( - 2, - resultExplodedProvenance - .filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'") - .count()); + 2, + resultExplodedProvenance + .filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'") - .count()); + 1, + resultExplodedProvenance + .filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::03376222b28a3aebf2730ac514818d04' and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::03376222b28a3aebf2730ac514818d04' and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") + .count()); assertEquals( - 3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); + 3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); } @@ -227,98 +227,98 @@ public class PrepareResultProjectJobTest { public void testMatchValidated() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_validatedRels") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_validatedRels") + .getPath(); SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); + .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); assertEquals(2, verificationDataset.count()); assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); verificationDataset.createOrReplaceTempView("dataset"); String query = "select resultId, MyT.id project , MyT.title title, MyT.acronym acronym , MyT.provenance.provenance provenance, " - + - "MyT.validated.validatedByFunder, MyT.validated.validationDate " - + "from dataset " - + "lateral view explode(projectsList) p as MyT "; + + + "MyT.validated.validatedByFunder, MyT.validated.validationDate " + + "from dataset " + + "lateral view explode(projectsList) p as MyT "; org.apache.spark.sql.Dataset resultExplodedProvenance = spark.sql(query); assertEquals(3, resultExplodedProvenance.count()); assertEquals(3, resultExplodedProvenance.filter("validatedByFunder = true").count()); assertEquals( - 2, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") - .count()); + 2, + resultExplodedProvenance + .filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") - .count()); + 1, + resultExplodedProvenance + .filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") + .count()); assertEquals( - 2, - resultExplodedProvenance - .filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'") - .count()); + 2, + resultExplodedProvenance + .filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + - "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + - "and validatedByFunder = true " + - "and validationDate = '2021-08-06'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + + "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + + "and validatedByFunder = true " + + "and validationDate = '2021-08-06'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + - "and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80' " + - "and validatedByFunder = true and validationDate = '2021-08-04'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + + "and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80' " + + "and validatedByFunder = true and validationDate = '2021-08-04'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'") - .count()); + 1, + resultExplodedProvenance + .filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::03376222b28a3aebf2730ac514818d04' " + - "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + - "and validatedByFunder = true and validationDate = '2021-08-05'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::03376222b28a3aebf2730ac514818d04' " + + "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + + "and validatedByFunder = true and validationDate = '2021-08-05'") + .count()); assertEquals( - 3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); + 3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); } @@ -326,20 +326,20 @@ public class PrepareResultProjectJobTest { void testMatchx() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match") + .getPath(); SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r))); } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java index 579958a624..7046b02c22 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java @@ -35,15 +35,15 @@ public class ResultLinkedToProjectTest { private static Path workingDir; private static final Logger log = LoggerFactory - .getLogger(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class); + .getLogger(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class); private static final HashMap map = new HashMap<>(); @BeforeAll public static void beforeAll() throws IOException { workingDir = Files - .createTempDirectory( - eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()); + .createTempDirectory( + eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()); log.info("using work dir {}", workingDir); SparkConf conf = new SparkConf(); @@ -57,10 +57,10 @@ public class ResultLinkedToProjectTest { conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); spark = SparkSession - .builder() - .appName(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); + .builder() + .appName(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); } @AfterAll @@ -73,32 +73,32 @@ public class ResultLinkedToProjectTest { void testNoMatch() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json") + .getPath(); final String graphPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo") + .getPath(); final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/communityMapPath") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/communityMapPath") + .getPath(); SparkResultLinkedToProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-graphPath", graphPath, - "-communityMapPath", communityMapPath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath, + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", + "-graphPath", graphPath, + "-communityMapPath", communityMapPath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(0, tmp.count()); @@ -108,32 +108,32 @@ public class ResultLinkedToProjectTest { void testMatchOne() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/papers.json") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/papers.json") + .getPath(); final String graphPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo") + .getPath(); final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/communityMapPath") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/communityMapPath") + .getPath(); SparkResultLinkedToProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-graphPath", graphPath, - "-communityMapPath", communityMapPath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath, + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", + "-graphPath", graphPath, + "-communityMapPath", communityMapPath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(1, tmp.count()); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java index 5bb5a11789..e9d739db28 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java @@ -56,10 +56,10 @@ public class SplitPerFunderTest { conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); spark = SparkSession - .builder() - .appName(SplitPerFunderTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); + .builder() + .appName(SplitPerFunderTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); } @AfterAll @@ -72,13 +72,13 @@ public class SplitPerFunderTest { void test1() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext") + .getPath(); SparkDumpFunderResults.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/split", - "-sourcePath", sourcePath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/split", + "-sourcePath", sourcePath }); @@ -86,64 +86,64 @@ public class SplitPerFunderTest { // FP7 3 and H2020 3 JavaRDD tmp = sc - .textFile(workingDir.toString() + "/split/EC_FP7") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/EC_FP7") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); + .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); Assertions.assertEquals(3, verificationDataset.count()); Assertions - .assertEquals( - 1, verificationDataset.filter("id = '50|dedup_wf_001::0d16b1714ab3077df73893a8ea57d776'").count()); + .assertEquals( + 1, verificationDataset.filter("id = '50|dedup_wf_001::0d16b1714ab3077df73893a8ea57d776'").count()); // CIHR 2 tmp = sc - .textFile(workingDir.toString() + "/split/CIHR") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/CIHR") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(2, tmp.count()); // NWO 1 tmp = sc - .textFile(workingDir.toString() + "/split/NWO") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/NWO") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(1, tmp.count()); // NIH 3 tmp = sc - .textFile(workingDir.toString() + "/split/NIH") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/NIH") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(2, tmp.count()); // NSF 1 tmp = sc - .textFile(workingDir.toString() + "/split/NSF") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/NSF") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(1, tmp.count()); // SNSF 1 tmp = sc - .textFile(workingDir.toString() + "/split/SNSF") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/SNSF") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(1, tmp.count()); // NHMRC 1 tmp = sc - .textFile(workingDir.toString() + "/split/NHMRC") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/NHMRC") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(1, tmp.count()); // H2020 3 tmp = sc - .textFile(workingDir.toString() + "/split/EC_H2020") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/EC_H2020") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(3, tmp.count()); // MZOS 1 tmp = sc - .textFile(workingDir.toString() + "/split/MZOS") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/MZOS") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(1, tmp.count()); } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java index 4ff1e1b968..8cdb285e4b 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java @@ -30,7 +30,6 @@ public class ProjectSubsetTest { private static final Logger log = LoggerFactory .getLogger(eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class); - @BeforeAll public static void beforeAll() throws IOException { workingDir = Files From fae681fea1812513f900ad6457455dad9c1f80bc Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Sun, 3 Jul 2022 17:39:58 +0200 Subject: [PATCH 25/46] [Country Propagation] add check to avoid NPE on datasource.getDatasourceType().getClassis() --- .../PrepareDatasourceCountryAssociation.java | 3 +++ 1 file changed, 3 insertions(+) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java index 42b7804ea4..b9f3bff523 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java @@ -6,6 +6,7 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.util.Arrays; import java.util.List; +import java.util.Optional; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; @@ -87,6 +88,8 @@ public class PrepareDatasourceCountryAssociation { Dataset datasource = readPath(spark, inputPath + "/datasource", Datasource.class) .filter( (FilterFunction) ds -> !ds.getDataInfo().getDeletedbyinference() && + Optional.ofNullable(ds.getDatasourcetype()).isPresent() && + Optional.ofNullable(ds.getDatasourcetype().getClassid()).isPresent() && (allowedtypes.contains(ds.getDatasourcetype().getClassid()) || whitelist.contains(ds.getId()))); From 0c1cfee39684be0afba50a80e401690cbc5c75d5 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 11 Jul 2022 17:34:59 +0200 Subject: [PATCH 26/46] mapping oaf:fulltext elements in the result.fulltext field --- .../dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java | 2 +- .../test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java | 4 ++++ 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index 739be3df42..a05faab805 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -379,7 +379,7 @@ public abstract class AbstractMdRecordToOafMapper { r.setPublisher(preparePublisher(doc, info)); r.setEmbargoenddate(prepareField(doc, "//oaf:embargoenddate", info)); r.setSource(prepareSources(doc, info)); - r.setFulltext(new ArrayList<>()); // NOT PRESENT IN MDSTORES + r.setFulltext(prepareListFields(doc, "//oaf:fulltext", info)); r.setFormat(prepareFormats(doc, info)); r.setContributor(prepareContributors(doc, info)); r.setResourcetype(prepareResourceType(doc, info)); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index f5cb86bfda..b75f626d61 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -122,6 +122,10 @@ class MappersTest { assertNotNull(p.getBestaccessright()); assertEquals("OPEN", p.getBestaccessright().getClassid()); + assertNotNull(p.getFulltext()); + assertEquals(1, p.getFulltext().size()); + assertEquals("https://oneecosystem.pensoft.net/article/13718/", p.getFulltext().get(0).getValue()); + // RESULT PROJECT List resultProject = list .stream() From 0a4f4d98fa8f73d296ef92f4dbf9f12a760ef735 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Wed, 13 Jul 2022 15:27:17 +0200 Subject: [PATCH 27/46] added PMCId to PmArticle --- .../dnetlib/dhp/sx/bio/pubmed/PMArticle.java | 24 +- .../dnetlib/dhp/sx/bio/pubmed/PMParser.scala | 1 + .../dhp/sx/bio/pubmed/PubMedToOaf.scala | 48 +++- .../eu/dnetlib/dhp/sx/graph/bio/pubmed.xml | 257 ++++++++++++++++-- .../dnetlib/dhp/sx/bio/BioScholixTest.scala | 71 ++++- 5 files changed, 371 insertions(+), 30 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMArticle.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMArticle.java index af0d5169d3..9287a8cdd6 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMArticle.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMArticle.java @@ -17,6 +17,9 @@ public class PMArticle implements Serializable { * the Pubmed Identifier */ private String pmid; + + private String pmcId; + /** * the DOI */ @@ -122,7 +125,7 @@ public class PMArticle implements Serializable { /** * The full journal title (taken from NLM cataloging data following NLM rules for how to compile a serial name) is exported in this element. - * Some characters that are not part of the NLM MEDLINE/PubMed Character Set reside in a relatively small number of full journal titles. + * Some characters that are not part of the NLM MEDLINE/PubMed Character Set reside in a relatively small number of full journal titles. * The NLM journal title abbreviation is exported in the element. * * @return the pubmed Journal Extracted @@ -140,10 +143,11 @@ public class PMArticle implements Serializable { } /** - * English-language abstracts are taken directly from the published article. - * If the article does not have a published abstract, the National Library of Medicine does not create one, - * thus the record lacks the and elements. However, in the absence of a formally - * labeled abstract in the published article, text from a substantive "summary", "summary and conclusions" or "conclusions and summary" may be used. + * contains the entire title of the journal article. is always in English; + * those titles originally published in a non-English language and translated for are enclosed in square brackets. + * All titles end with a period unless another punctuation mark such as a question mark or bracket is present. + * Explanatory information about the title itself is enclosed in parentheses, e.g.: (author's transl). + * Corporate/collective authors may appear at the end of for citations up to about the year 2000. * * @return the extracted pubmed Title */ @@ -250,4 +254,14 @@ public class PMArticle implements Serializable { public List getGrants() { return grants; } + + + public String getPmcId() { + return pmcId; + } + + public PMArticle setPmcId(String pmcId) { + this.pmcId = pmcId; + return this; + } } diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PMParser.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PMParser.scala index 49a2716415..9102c12c43 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PMParser.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PMParser.scala @@ -98,6 +98,7 @@ class PMParser(xml: XMLEventReader) extends Iterator[PMArticle] { case "PMID" => currentArticle.setPmid(text.trim) case "ArticleId" => if ("doi".equalsIgnoreCase(currentArticleType)) currentArticle.setDoi(text.trim) + if ("pmc".equalsIgnoreCase(currentArticleType)) currentArticle.setPmcId(text.trim) case "Language" => currentArticle.setLanguage(text.trim) case "ISSN" => currentJournal.setIssn(text.trim) case "GrantID" => currentGrant.setGrantID(text.trim) diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala index 92ad22c573..24a1fa62b9 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala @@ -4,9 +4,12 @@ import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup import eu.dnetlib.dhp.schema.common.ModelConstants import eu.dnetlib.dhp.schema.oaf.utils.{GraphCleaningFunctions, IdentifierFactory, OafMapperUtils, PidType} import eu.dnetlib.dhp.schema.oaf._ -import collection.JavaConverters._ +import eu.dnetlib.dhp.utils.DHPUtils +import org.apache.commons.lang3.StringUtils +import collection.JavaConverters._ import java.util.regex.Pattern +import scala.collection.mutable.ListBuffer /** */ @@ -14,6 +17,9 @@ object PubMedToOaf { val SUBJ_CLASS = "keywords" + val OAI_HEADER = "oai:pubmedcentral.nih.gov:" + val OLD_PMC_PREFIX = "od_______267::" + val urlMap = Map( "pmid" -> "https://pubmed.ncbi.nlm.nih.gov/", "doi" -> "https://dx.doi.org/" @@ -50,6 +56,17 @@ object PubMedToOaf { null } + + def createOriginalOpenaireId(article:PMArticle) :String = { + if (StringUtils.isNotEmpty(article.getPmcId)) { + val md5 = DHPUtils.md5(s"$OAI_HEADER${article.getPmcId.replace("PMC","")}") + s"$OLD_PMC_PREFIX$md5" + } + else + null + + } + /** Create an instance of class extends Result * starting from OAF instanceType value * @@ -122,8 +139,9 @@ object PubMedToOaf { return null // MAP PMID into pid with classid = classname = pmid - val pidList: List[StructuredProperty] = List( - OafMapperUtils.structuredProperty( + val pidList = ListBuffer[StructuredProperty]() + + pidList += OafMapperUtils.structuredProperty( article.getPmid, PidType.pmid.toString, PidType.pmid.toString, @@ -131,7 +149,19 @@ object PubMedToOaf { ModelConstants.DNET_PID_TYPES, dataInfo ) - ) + + + if (StringUtils.isNotBlank(article.getPmcId)) + { + pidList += OafMapperUtils.structuredProperty( + article.getPmcId, + PidType.pmc.toString, + PidType.pmc.toString, + ModelConstants.DNET_PID_TYPES, + ModelConstants.DNET_PID_TYPES, + dataInfo + ) + } if (pidList == null) return null @@ -186,6 +216,7 @@ object PubMedToOaf { val urlLists: List[String] = pidList .map(s => (urlMap.getOrElse(s.getQualifier.getClassid, ""), s.getValue)) .filter(t => t._1.nonEmpty) + .toList .map(t => t._1 + t._2) if (urlLists != null) pubmedInstance.setUrl(urlLists.asJava) @@ -262,7 +293,14 @@ object PubMedToOaf { if (authors != null && authors.nonEmpty) result.setAuthor(authors.asJava) - result.setOriginalId(pidList.map(s => s.getValue).asJava) + + if (StringUtils.isNotEmpty(article.getPmcId)) { + val originalIDS = ListBuffer[String]() + originalIDS += createOriginalOpenaireId(article) + pidList.map(s => s.getValue).foreach(p =>originalIDS += p) + result.setOriginalId(originalIDS.asJava) + } else + result.setOriginalId(pidList.map(s => s.getValue).asJava) result.setId(article.getPmid) diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml index 22da07e299..58a73ae5d3 100644 --- a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml @@ -195,7 +195,9 @@ Biochemical and biophysical research communications Biochem Biophys Res Commun - Delineation of the intimate details of the backbone conformation of pyridine nucleotide coenzymes in aqueous solution. + Delineation of the intimate details of the backbone conformation of pyridine nucleotide + coenzymes in aqueous solution. + 1173-9 @@ -473,7 +475,9 @@ Biochemical and biophysical research communications Biochem Biophys Res Commun - Effect of chloroquine on cultured fibroblasts: release of lysosomal hydrolases and inhibition of their uptake. + Effect of chloroquine on cultured fibroblasts: release of lysosomal hydrolases and + inhibition of their uptake. + 1338-43 @@ -657,7 +661,8 @@ Biochemical and biophysical research communications Biochem Biophys Res Commun - Atomic models for the polypeptide backbones of myohemerythrin and hemerythrin. + Atomic models for the polypeptide backbones of myohemerythrin and hemerythrin. + 1349-56 @@ -1627,7 +1632,9 @@ Biochemical pharmacology Biochem Pharmacol - Comparison between procaine and isocarboxazid metabolism in vitro by a liver microsomal amidase-esterase. + Comparison between procaine and isocarboxazid metabolism in vitro by a liver microsomal + amidase-esterase. + 1517-21 @@ -2030,7 +2037,9 @@ Biochemical pharmacology Biochem Pharmacol - Radiochemical assay of glutathione S-epoxide transferase and its enhancement by phenobarbital in rat liver in vivo. + Radiochemical assay of glutathione S-epoxide transferase and its enhancement by + phenobarbital in rat liver in vivo. + 1569-72 @@ -2350,7 +2359,9 @@ Biochemical pharmacology Biochem Pharmacol - Identification of adenylate cyclase-coupled beta-adrenergic receptors with radiolabeled beta-adrenergic antagonists. + Identification of adenylate cyclase-coupled beta-adrenergic receptors with radiolabeled + beta-adrenergic antagonists. + 1651-8 @@ -2598,7 +2609,9 @@ Biochemical pharmacology Biochem Pharmacol - The effect of adrenaline and of alpha- and beta-adrenergic blocking agents on ATP concentration and on incorporation of 32Pi into ATP in rat fat cells. + The effect of adrenaline and of alpha- and beta-adrenergic blocking agents on ATP + concentration and on incorporation of 32Pi into ATP in rat fat cells. + 1659-62 @@ -2851,7 +2864,9 @@ Biochemical pharmacology Biochem Pharmacol - Action of propranolol on mitochondrial functions--effects on energized ion fluxes in the presence of valinomycin. + Action of propranolol on mitochondrial functions--effects on energized ion fluxes in the + presence of valinomycin. + 1701-5 @@ -3265,7 +3280,8 @@ EC 2.6.1.16 - Glutamine-Fructose-6-Phosphate Transaminase (Isomerizing) + Glutamine-Fructose-6-Phosphate Transaminase (Isomerizing) + EC 2.7.- @@ -3324,7 +3340,9 @@ Glucosamine - Glutamine-Fructose-6-Phosphate Transaminase (Isomerizing) + Glutamine-Fructose-6-Phosphate Transaminase + (Isomerizing) + metabolism @@ -3463,7 +3481,8 @@ Biochemical pharmacology Biochem Pharmacol - Inhibition of aldehyde reductase by acidic metabolites of the biogenic amines. + Inhibition of aldehyde reductase by acidic metabolites of the biogenic amines. + 1731-3 @@ -3696,7 +3715,9 @@ Biochemical pharmacology Biochem Pharmacol - Effects of 5,6-dihydroxytryptamine on tyrosine-hydroxylase activity in central catecholaminergic neurons of the rat. + Effects of 5,6-dihydroxytryptamine on tyrosine-hydroxylase activity in central + catecholaminergic neurons of the rat. + 1739-42 @@ -4602,12 +4623,19 @@ Arzneimittel-Forschung Arzneimittelforschung - [Biochemical studies on camomile components/III. In vitro studies about the antipeptic activity of (--)-alpha-bisabolol (author's transl)]. + [Biochemical studies on camomile components/III. In vitro studies about the antipeptic + activity of (--)-alpha-bisabolol (author's transl)]. + 1352-4 - (--)-alpha-Bisabolol has a primary antipeptic action depending on dosage, which is not caused by an alteration of the pH-value. The proteolytic activity of pepsin is reduced by 50 percent through addition of bisabolol in the ratio of 1/0.5. The antipeptic action of bisabolol only occurs in case of direct contact. In case of a previous contact with the substrate, the inhibiting effect is lost. + (--)-alpha-Bisabolol has a primary antipeptic action depending on dosage, which is not + caused by an alteration of the pH-value. The proteolytic activity of pepsin is reduced by 50 + percent through addition of bisabolol in the ratio of 1/0.5. The antipeptic action of bisabolol + only occurs in case of direct contact. In case of a previous contact with the substrate, the + inhibiting effect is lost. + @@ -4626,7 +4654,9 @@ English Abstract Journal Article - Biochemische Untersuchungen von Kamilleninhaltsstoffen. III. In-vitro-Versuche über die antipeptische Wirkung des (-)-alpha-Bisabolols + Biochemische Untersuchungen von Kamilleninhaltsstoffen. III. In-vitro-Versuche über die + antipeptische Wirkung des (-)-alpha-Bisabolols + Germany @@ -4753,12 +4783,37 @@ Arzneimittel-Forschung Arzneimittelforschung - [Demonstration of tumor inhibiting properties of a strongly immunostimulating low-molecular weight substance. Comparative studies with ifosfamide on the immuno-labile DS carcinosarcoma. Stimulation of the autoimmune activity for approx. 20 days by BA 1, a N-(2-cyanoethylene)-urea. Novel prophylactic possibilities]. + [Demonstration of tumor inhibiting properties of a strongly immunostimulating + low-molecular weight substance. Comparative studies with ifosfamide on the immuno-labile DS + carcinosarcoma. Stimulation of the autoimmune activity for approx. 20 days by BA 1, a + N-(2-cyanoethylene)-urea. Novel prophylactic possibilities]. + 1369-79 - A report is given on the recent discovery of outstanding immunological properties in BA 1 [N-(2-cyanoethylene)-urea] having a (low) molecular mass M = 111.104. Experiments in 214 DS carcinosarcoma bearing Wistar rats have shown that BA 1, at a dosage of only about 12 percent LD50 (150 mg kg) and negligible lethality (1.7 percent), results in a recovery rate of 40 percent without hyperglycemia and, in one test, of 80 percent with hyperglycemia. Under otherwise unchanged conditions the reference substance ifosfamide (IF) -- a further development of cyclophosphamide -- applied without hyperglycemia in its most efficient dosage of 47 percent LD50 (150 mg kg) brought about a recovery rate of 25 percent at a lethality of 18 percent. (Contrary to BA 1, 250-min hyperglycemia caused no further improvement of the recovery rate.) However this comparison is characterized by the fact that both substances exhibit two quite different (complementary) mechanisms of action. Leucocyte counts made after application of the said cancerostatics and dosages have shown a pronounced stimulation with BA 1 and with ifosfamide, the known suppression in the post-therapeutic interval usually found with standard cancerostatics. In combination with the cited plaque test for BA 1, blood pictures then allow conclusions on the immunity status. Since IF can be taken as one of the most efficient cancerostatics--there is no other chemotherapeutic known up to now that has a more significant effect on the DS carcinosarcoma in rats -- these findings are of special importance. Finally, the total amount of leucocytes and lymphocytes as well as their time behaviour was determined from the blood picture of tumour-free rats after i.v. application of BA 1. The thus obtained numerical values clearly show that further research work on the prophylactic use of this substance seems to be necessary and very promising. + A report is given on the recent discovery of outstanding immunological properties in + BA 1 [N-(2-cyanoethylene)-urea] having a (low) molecular mass M = 111.104. Experiments in 214 DS + carcinosarcoma bearing Wistar rats have shown that BA 1, at a dosage of only about 12 percent + LD50 (150 mg kg) and negligible lethality (1.7 percent), results in a recovery rate of 40 + percent without hyperglycemia and, in one test, of 80 percent with hyperglycemia. Under + otherwise unchanged conditions the reference substance ifosfamide (IF) -- a further development + of cyclophosphamide -- applied without hyperglycemia in its most efficient dosage of 47 percent + LD50 (150 mg kg) brought about a recovery rate of 25 percent at a lethality of 18 percent. + (Contrary to BA 1, 250-min hyperglycemia caused no further improvement of the recovery rate.) + However this comparison is characterized by the fact that both substances exhibit two quite + different (complementary) mechanisms of action. Leucocyte counts made after application of the + said cancerostatics and dosages have shown a pronounced stimulation with BA 1 and with + ifosfamide, the known suppression in the post-therapeutic interval usually found with standard + cancerostatics. In combination with the cited plaque test for BA 1, blood pictures then allow + conclusions on the immunity status. Since IF can be taken as one of the most efficient + cancerostatics--there is no other chemotherapeutic known up to now that has a more significant + effect on the DS carcinosarcoma in rats -- these findings are of special importance. Finally, + the total amount of leucocytes and lymphocytes as well as their time behaviour was determined + from the blood picture of tumour-free rats after i.v. application of BA 1. The thus obtained + numerical values clearly show that further research work on the prophylactic use of this + substance seems to be necessary and very promising. + @@ -4778,7 +4833,11 @@ English Abstract Journal Article - Nachweis krebshemmender Eigenschaften einer stark immunstimulierenden Verbindung kleiner Molekülmasse. Versuche am immunlabilen DS-Karzinosarkom im Vergleich mit Ifosfamid. Stimulierung der körpereigenen Abwehr über etwa 20 Tage durch BA 1, einen N-(2-Cyanthylen)-harnstoff. Neue prophylaktische Möglichkeiten + Nachweis krebshemmender Eigenschaften einer stark immunstimulierenden Verbindung + kleiner Molekülmasse. Versuche am immunlabilen DS-Karzinosarkom im Vergleich mit Ifosfamid. + Stimulierung der körpereigenen Abwehr über etwa 20 Tage durch BA 1, einen + N-(2-Cyanthylen)-harnstoff. Neue prophylaktische Möglichkeiten + Germany @@ -5016,7 +5075,20 @@ 1400-3 - The distribution of blood flow to the subendocardial, medium and subepicardial layers of the left ventricular free wall was studied in anaesthetized dogs under normoxic (A), hypoxic (B) conditions and under pharmacologically induced (etafenone) coronary vasodilation (C). Regional myocardial blood flow was determined by means of the particle distribution method. In normoxia a transmural gradient of flow was observed, with the subendocardial layers receiving a significantly higher flow rate compared with the subepicardial layers. In hypoxia induced vasodilation this transmural gradient of flow was persistent. In contrast a marked redistribution of regional flow was observed under pharmacologically induced vasodilation. The transmural gradient decreased. In contrast to some findings these experiments demonstrate that a considerable vasodilatory capacity exists in all layers of the myocardium and can be utilized by drugs. The differences observed for the intramural distribution pattern of flow under hypoxia and drug induced vasodilation support the hypothesis that this pattern reflects corresponding gradients of regional myocardial metabolism. + The distribution of blood flow to the subendocardial, medium and subepicardial layers + of the left ventricular free wall was studied in anaesthetized dogs under normoxic (A), hypoxic + (B) conditions and under pharmacologically induced (etafenone) coronary vasodilation (C). + Regional myocardial blood flow was determined by means of the particle distribution method. In + normoxia a transmural gradient of flow was observed, with the subendocardial layers receiving a + significantly higher flow rate compared with the subepicardial layers. In hypoxia induced + vasodilation this transmural gradient of flow was persistent. In contrast a marked + redistribution of regional flow was observed under pharmacologically induced vasodilation. The + transmural gradient decreased. In contrast to some findings these experiments demonstrate that a + considerable vasodilatory capacity exists in all layers of the myocardium and can be utilized by + drugs. The differences observed for the intramural distribution pattern of flow under hypoxia + and drug induced vasodilation support the hypothesis that this pattern reflects corresponding + gradients of regional myocardial metabolism. + @@ -5185,4 +5257,151 @@ + + + 4917185 + + 1970 + 10 + 27 + + + 2018 + 11 + 13 + +
+ + 0003-6919 + + 19 + 6 + + 1970 + Jun + + + Applied microbiology + Appl Microbiol + + Bactericidal activity of a broad-spectrum illumination source. + + 1013-4 + + + + Several hours of exposure to Vita-Lite lamps, which have a unique spectral + distribution, give significant killing of cells of Staphylococcus aureus. + + + + + Himmelfarb + P + P + + + Scott + A + A + + + Thayer + P S + PS + + + eng + + Journal Article + +
+ + United States + Appl Microbiol + 7605802 + 0003-6919 + + IM + + + Bacteriological Techniques + instrumentation + + + Light + + + Radiation Effects + + + Serratia marcescens + growth & development + radiation effects + + + Staphylococcus + growth & development + radiation effects + + + Sterilization + + + + + + + 1970 + 6 + 1 + + + 1970 + 6 + 1 + 0 + 1 + + + 1970 + 6 + 1 + 0 + 0 + + + ppublish + + 4917185 + PMC376844 + + + + Photochem Photobiol. 1969 Jan;9(1):99-102 + + 4889809 + + + + Endocrinology. 1969 Dec;85(6):1218-21 + + 5347623 + + + + Arch Mikrobiol. 1956;24(1):60-79 + + 13327987 + + + + J Bacteriol. 1941 Sep;42(3):353-66 + + 16560457 + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala index ea742a04aa..37a5808ec9 100644 --- a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala +++ b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala @@ -2,7 +2,8 @@ package eu.dnetlib.dhp.sx.bio import com.fasterxml.jackson.databind.{DeserializationFeature, ObjectMapper, SerializationFeature} import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest -import eu.dnetlib.dhp.schema.oaf.{Oaf, Relation, Result} +import eu.dnetlib.dhp.schema.oaf.utils.PidType +import eu.dnetlib.dhp.schema.oaf.{Oaf, Publication, Relation, Result} import eu.dnetlib.dhp.sx.bio.BioDBToOAF.ScholixResolved import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMParser, PubMedToOaf} import org.json4s.DefaultFormats @@ -16,6 +17,7 @@ import org.mockito.junit.jupiter.MockitoExtension import java.io.{BufferedReader, InputStream, InputStreamReader} import java.util.zip.GZIPInputStream import scala.collection.JavaConverters._ +import scala.collection.mutable.ListBuffer import scala.io.Source import scala.xml.pull.XMLEventReader @@ -72,6 +74,73 @@ class BioScholixTest extends AbstractVocabularyTest { ) println(mapper.writeValueAsString(r.head)) + } + + + private def checkPMArticle(article:PMArticle): Unit = { + assertNotNull(article.getPmid) + assertNotNull(article.getTitle) + assertNotNull(article.getAuthors) + article.getAuthors.asScala.foreach{a => + assertNotNull(a) + assertNotNull(a.getFullName) + } + + } + + @Test + def testParsingPubmedXML():Unit = { + val xml = new XMLEventReader(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml"))) + val parser = new PMParser(xml) + parser.foreach(checkPMArticle) + } + + + private def checkPubmedPublication(o:Oaf): Unit = { + assertTrue(o.isInstanceOf[Publication]) + val p:Publication = o.asInstanceOf[Publication] + assertNotNull(p.getId) + assertNotNull(p.getTitle) + p.getTitle.asScala.foreach(t =>assertNotNull(t.getValue)) + p.getAuthor.asScala.foreach(a =>assertNotNull(a.getFullname)) + assertNotNull(p.getInstance()) + p.getInstance().asScala.foreach { i => + assertNotNull(i.getCollectedfrom) + assertNotNull(i.getPid) + assertNotNull(i.getInstancetype) + } + assertNotNull(p.getOriginalId) + p.getOriginalId.asScala.foreach(oId => assertNotNull(oId)) + + + val hasPMC = p.getInstance().asScala.exists(i => i.getPid.asScala.exists(pid => pid.getQualifier.getClassid.equalsIgnoreCase(PidType.pmc.toString))) + + + + if (hasPMC) { + assertTrue(p.getOriginalId.asScala.exists(oId => oId.startsWith("od_______267::"))) + + + } + + + + } + @Test + def testPubmedMapping() :Unit = { + + val xml = new XMLEventReader(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml"))) + val parser = new PMParser(xml) + val results = ListBuffer[Oaf]() + parser.foreach(x => results += PubMedToOaf.convert(x, vocabularies)) + + + + + results.foreach(checkPubmedPublication) + + + } @Test From 00168303dbb4e14ee453a911d3c072314e686864 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Thu, 14 Jul 2022 10:19:59 +0200 Subject: [PATCH 28/46] Added unit test to verify the generation in the OriginalID the old openaire Identifier generated by OAI --- .../dnetlib/dhp/sx/bio/BioScholixTest.scala | 41 ++++++++++++++++--- 1 file changed, 35 insertions(+), 6 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala index 37a5808ec9..b021e5e078 100644 --- a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala +++ b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala @@ -5,7 +5,7 @@ import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest import eu.dnetlib.dhp.schema.oaf.utils.PidType import eu.dnetlib.dhp.schema.oaf.{Oaf, Publication, Relation, Result} import eu.dnetlib.dhp.sx.bio.BioDBToOAF.ScholixResolved -import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMParser, PubMedToOaf} +import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMParser, PMSubject, PubMedToOaf} import org.json4s.DefaultFormats import org.json4s.JsonAST.{JField, JObject, JString} import org.json4s.jackson.JsonMethods.parse @@ -119,13 +119,42 @@ class BioScholixTest extends AbstractVocabularyTest { if (hasPMC) { assertTrue(p.getOriginalId.asScala.exists(oId => oId.startsWith("od_______267::"))) - - } - - - } + + + @Test + def testPubmedOriginalID():Unit = { + val article:PMArticle = new PMArticle + + + article.setPmid("1234") + + article.setTitle("a Title") + + // VERIFY PUBLICATION IS NOT NULL + article.getPublicationTypes.add( new PMSubject("article",null, null)) + var publication = PubMedToOaf.convert(article, vocabularies).asInstanceOf[Publication] + assertNotNull(publication) + assertEquals("50|pmid________::81dc9bdb52d04dc20036dbd8313ed055", publication.getId) + + // VERIFY PUBLICATION ID DOES NOT CHANGE ALSO IF SETTING PMC IDENTIFIER + article.setPmcId("PMC1517292") + publication = PubMedToOaf.convert(article, vocabularies).asInstanceOf[Publication] + assertNotNull(publication) + assertEquals("50|pmid________::81dc9bdb52d04dc20036dbd8313ed055", publication.getId) + + // VERIFY ORIGINAL ID GENERATE IN OLD WAY USING PMC IDENTIFIER EXISTS + + + val oldOpenaireID ="od_______267::0000072375bc0e68fa09d4e6b7658248" + + val hasOldOpenAIREID = publication.getOriginalId.asScala.exists(o => o.equalsIgnoreCase(oldOpenaireID)) + + assertTrue(hasOldOpenAIREID) + } + + @Test def testPubmedMapping() :Unit = { From 5b76321d9cb58f68a52ee01d14ea77f38e81d749 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Wed, 20 Jul 2022 16:34:32 +0200 Subject: [PATCH 29/46] implemented oozie workflow to generate scholix dump filtering relclass semantic --- .../sx/graph/convert_dataset_json_params.json | 1 + .../sx/graph/convert_object_json_params.json | 4 +- .../dumpScholix/oozie_app/config-default.xml | 10 ++ .../graph/dumpScholix/oozie_app/workflow.xml | 145 ++++++++++++++++++ .../sx/graph/SparkConvertObjectToJson.scala | 33 +++- .../sx/graph/SparkConvertRDDtoDataset.scala | 61 +++++--- 6 files changed, 228 insertions(+), 26 deletions(-) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/dumpScholix/oozie_app/config-default.xml create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/dumpScholix/oozie_app/workflow.xml diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/convert_dataset_json_params.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/convert_dataset_json_params.json index 8bfdde5b0d..f3e8cdbade 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/convert_dataset_json_params.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/convert_dataset_json_params.json @@ -2,4 +2,5 @@ {"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true}, {"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the source Path", "paramRequired": true}, {"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the path of the raw graph", "paramRequired": true} + {"paramName":"r", "paramLongName":"filterRelation", "paramDescription": "the relation to filter", "paramRequired": false} ] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/convert_object_json_params.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/convert_object_json_params.json index 890570a0bd..cbb20bfe77 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/convert_object_json_params.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/convert_object_json_params.json @@ -3,5 +3,7 @@ {"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the source Path", "paramRequired": true}, {"paramName":"su", "paramLongName":"scholixUpdatePath", "paramDescription": "the scholix updated Path", "paramRequired": false}, {"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the path of the raw graph", "paramRequired": true}, - {"paramName":"o", "paramLongName":"objectType", "paramDescription": "should be scholix or Summary", "paramRequired": true} + {"paramName":"o", "paramLongName":"objectType", "paramDescription": "should be scholix or Summary", "paramRequired": true}, + {"paramName":"mp", "paramLongName":"maxPidNumberFilter", "paramDescription": "filter max number of pids in source/target", "paramRequired": false} + ] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/dumpScholix/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/dumpScholix/oozie_app/config-default.xml new file mode 100644 index 0000000000..6fb2a1253c --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/dumpScholix/oozie_app/config-default.xml @@ -0,0 +1,10 @@ + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/dumpScholix/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/dumpScholix/oozie_app/workflow.xml new file mode 100644 index 0000000000..a37d85ad41 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/dumpScholix/oozie_app/workflow.xml @@ -0,0 +1,145 @@ + + + + sourcePath + the working dir base path + + + targetPath + the final graph path + + + relationFilter + Filter relation semantic + + + maxNumberOfPid + filter relation with at least #maxNumberOfPid + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + yarn + cluster + Import JSONRDD to Dataset kryo + eu.dnetlib.dhp.sx.graph.SparkConvertRDDtoDataset + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.shuffle.partitions=3000 + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --masteryarn + --sourcePath${sourcePath} + --targetPath${targetPath} + --filterRelation${relationFilter} + + + + + + + + + yarn + cluster + Convert Entities to summaries + eu.dnetlib.dhp.sx.graph.SparkCreateSummaryObject + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.shuffle.partitions=20000 + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --masteryarn + --sourcePath${targetPath}/entities + --targetPath${targetPath}/provision/summaries + + + + + + + + yarn + cluster + Generate Scholix Dataset + eu.dnetlib.dhp.sx.graph.SparkCreateScholix + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.shuffle.partitions=30000 + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --masteryarn + --summaryPath${targetPath}/provision/summaries + --targetPath${targetPath}/provision/scholix + --relationPath${targetPath}/relation + + + + + + + + + + + + + + + + + yarn + cluster + Serialize scholix to JSON + eu.dnetlib.dhp.sx.graph.SparkConvertObjectToJson + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.shuffle.partitions=6000 + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --masteryarn + --sourcePath${targetPath}/provision/scholix/scholix + --targetPath${targetPath}/json/scholix_json + --objectTypescholix + --maxPidNumberFiltermaxNumberOfPid + + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertObjectToJson.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertObjectToJson.scala index bfa07eb69e..6695ebd3c8 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertObjectToJson.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertObjectToJson.scala @@ -4,6 +4,7 @@ import com.fasterxml.jackson.databind.ObjectMapper import eu.dnetlib.dhp.application.ArgumentApplicationParser import eu.dnetlib.dhp.schema.sx.scholix.Scholix import eu.dnetlib.dhp.schema.sx.summary.ScholixSummary +import eu.dnetlib.dhp.sx.graph.SparkConvertObjectToJson.toInt import org.apache.commons.io.IOUtils import org.apache.hadoop.io.compress.GzipCodec import org.apache.spark.SparkConf @@ -12,6 +13,14 @@ import org.slf4j.{Logger, LoggerFactory} object SparkConvertObjectToJson { + def toInt(s: String): Option[Int] = { + try { + Some(s.toInt) + } catch { + case e: Exception => None + } + } + def main(args: Array[String]): Unit = { val log: Logger = LoggerFactory.getLogger(getClass) val conf: SparkConf = new SparkConf() @@ -37,6 +46,8 @@ object SparkConvertObjectToJson { log.info(s"objectType -> $objectType") val scholixUpdatePath = parser.get("scholixUpdatePath") log.info(s"scholixUpdatePath -> $scholixUpdatePath") + val maxPidNumberFilter = parser.get("maxPidNumberFilter") + log.info(s"maxPidNumberFilter -> $maxPidNumberFilter") implicit val scholixEncoder: Encoder[Scholix] = Encoders.kryo[Scholix] implicit val summaryEncoder: Encoder[ScholixSummary] = Encoders.kryo[ScholixSummary] @@ -47,12 +58,22 @@ object SparkConvertObjectToJson { case "scholix" => log.info("Serialize Scholix") val d: Dataset[Scholix] = spark.read.load(sourcePath).as[Scholix] - val u: Dataset[Scholix] = spark.read.load(s"$scholixUpdatePath/scholix").as[Scholix] - d.union(u) - .repartition(8000) - .map(s => mapper.writeValueAsString(s))(Encoders.STRING) - .rdd - .saveAsTextFile(targetPath, classOf[GzipCodec]) +// val u: Dataset[Scholix] = spark.read.load(s"$scholixUpdatePath/scholix").as[Scholix] + if (maxPidNumberFilter != null && toInt(maxPidNumberFilter).isDefined) { + val mp = toInt(maxPidNumberFilter).get + d + .filter(s => (s.getSource.getIdentifier.size() <= mp) && (s.getTarget.getIdentifier.size() <= mp)) + .map(s => mapper.writeValueAsString(s))(Encoders.STRING) + .rdd + .saveAsTextFile(targetPath, classOf[GzipCodec]) + } else { + d + .repartition(8000) + .map(s => mapper.writeValueAsString(s))(Encoders.STRING) + .rdd + .saveAsTextFile(targetPath, classOf[GzipCodec]) + } + case "summary" => log.info("Serialize Summary") val d: Dataset[ScholixSummary] = spark.read.load(sourcePath).as[ScholixSummary] diff --git a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala index bd970a5cf4..f72f8dd160 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala @@ -4,9 +4,11 @@ import com.fasterxml.jackson.databind.ObjectMapper import eu.dnetlib.dhp.application.ArgumentApplicationParser import eu.dnetlib.dhp.schema.oaf.{OtherResearchProduct, Publication, Relation, Result, Software, Dataset => OafDataset} import org.apache.commons.io.IOUtils +import org.apache.commons.lang3.StringUtils import org.apache.spark.SparkConf import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession} import org.slf4j.{Logger, LoggerFactory} + import scala.collection.JavaConverters._ object SparkConvertRDDtoDataset { @@ -34,6 +36,9 @@ object SparkConvertRDDtoDataset { val t = parser.get("targetPath") log.info(s"targetPath -> $t") + val filterRelation = parser.get("filterRelation") + log.info(s"filterRelation -> $filterRelation") + val entityPath = s"$t/entities" val relPath = s"$t/relation" val mapper = new ObjectMapper() @@ -94,28 +99,46 @@ object SparkConvertRDDtoDataset { log.info("Converting Relation") - val relationSemanticFilter = List( -// "cites", -// "iscitedby", - "merges", - "ismergedin", - "HasAmongTopNSimilarDocuments", - "IsAmongTopNSimilarDocuments" - ) + if (filterRelation != null && StringUtils.isNoneBlank(filterRelation)) { - val rddRelation = spark.sparkContext - .textFile(s"$sourcePath/relation") - .map(s => mapper.readValue(s, classOf[Relation])) - .filter(r => r.getDataInfo != null && r.getDataInfo.getDeletedbyinference == false) - .filter(r => r.getSource.startsWith("50") && r.getTarget.startsWith("50")) - //filter OpenCitations relations - .filter(r => - r.getCollectedfrom != null && r.getCollectedfrom.size() > 0 && !r.getCollectedfrom.asScala.exists(k => - "opencitations".equalsIgnoreCase(k.getValue) + val rddRelation = spark.sparkContext + .textFile(s"$sourcePath/relation") + .map(s => mapper.readValue(s, classOf[Relation])) + .filter(r => r.getDataInfo != null && r.getDataInfo.getDeletedbyinference == false) + .filter(r => r.getSource.startsWith("50") && r.getTarget.startsWith("50")) + //filter OpenCitations relations + .filter(r => + r.getCollectedfrom != null && r.getCollectedfrom.size() > 0 && !r.getCollectedfrom.asScala.exists(k => + "opencitations".equalsIgnoreCase(k.getValue) + ) ) + .filter(r => r.getRelClass != null && r.getRelClass.equalsIgnoreCase(filterRelation)) + spark.createDataset(rddRelation).as[Relation].write.mode(SaveMode.Overwrite).save(s"$relPath") + } else { + + val relationSemanticFilter = List( + // "cites", + // "iscitedby", + "merges", + "ismergedin", + "HasAmongTopNSimilarDocuments", + "IsAmongTopNSimilarDocuments" ) - .filter(r => !relationSemanticFilter.exists(k => k.equalsIgnoreCase(r.getRelClass))) - spark.createDataset(rddRelation).as[Relation].write.mode(SaveMode.Overwrite).save(s"$relPath") + + val rddRelation = spark.sparkContext + .textFile(s"$sourcePath/relation") + .map(s => mapper.readValue(s, classOf[Relation])) + .filter(r => r.getDataInfo != null && r.getDataInfo.getDeletedbyinference == false) + .filter(r => r.getSource.startsWith("50") && r.getTarget.startsWith("50")) + //filter OpenCitations relations + .filter(r => + r.getCollectedfrom != null && r.getCollectedfrom.size() > 0 && !r.getCollectedfrom.asScala.exists(k => + "opencitations".equalsIgnoreCase(k.getValue) + ) + ) + .filter(r => !relationSemanticFilter.exists(k => k.equalsIgnoreCase(r.getRelClass))) + spark.createDataset(rddRelation).as[Relation].write.mode(SaveMode.Overwrite).save(s"$relPath") + } } } From 438abdf96fcdc340dfdbe18fa51c56c8a3ce5657 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 20 Jul 2022 18:07:54 +0200 Subject: [PATCH 30/46] [EOSC TAG] adding eosc interoperability guidelines in the specific element in the result. Removed from subjects. Removed also the deletion of EOSC Jupyter Notebook from subject since now the criteria are searchd for in a different place --- .../eu/dnetlib/dhp/bulktag/SparkEoscTag.java | 82 ++++++------------- pom.xml | 2 +- 2 files changed, 27 insertions(+), 57 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java index b9de5dd111..d319340812 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java @@ -28,28 +28,7 @@ import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; public class SparkEoscTag { private static final Logger log = LoggerFactory.getLogger(SparkEoscTag.class); public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - public static final Qualifier EOSC_QUALIFIER = OafMapperUtils - .qualifier( - "EOSC", - "European Open Science Cloud", - ModelConstants.DNET_SUBJECT_TYPOLOGIES, ModelConstants.DNET_SUBJECT_TYPOLOGIES); - public static final DataInfo EOSC_DATAINFO = OafMapperUtils - .dataInfo( - false, "propagation", true, false, - OafMapperUtils - .qualifier( - "propagation:subject", "Inferred by OpenAIRE", - ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS), - "0.9"); - public final static StructuredProperty EOSC_NOTEBOOK = OafMapperUtils - .structuredProperty( - "EOSC::Jupyter Notebook", EOSC_QUALIFIER, EOSC_DATAINFO); - public final static StructuredProperty EOSC_GALAXY = OafMapperUtils - .structuredProperty( - "EOSC::Galaxy Workflow", EOSC_QUALIFIER, EOSC_DATAINFO); - public final static StructuredProperty EOSC_TWITTER = OafMapperUtils - .structuredProperty( - "EOSC::Twitter Data", EOSC_QUALIFIER, EOSC_DATAINFO); + public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils @@ -84,29 +63,30 @@ public class SparkEoscTag { }); } + public static EoscIfGuidelines newInstance(String code, String label, String url, String semantics){ + EoscIfGuidelines eig = new EoscIfGuidelines(); + eig.setCode( code); + eig.setLabel(label); + eig.setUrl(url); + eig.setSemanticRelation(semantics); + return eig; + + } private static void execEoscTag(SparkSession spark, String inputPath, String workingPath) { readPath(spark, inputPath + "/software", Software.class) .map((MapFunction) s -> { - List sbject; - if (!Optional.ofNullable(s.getSubject()).isPresent()) - s.setSubject(new ArrayList<>()); - sbject = s.getSubject(); if (containsCriteriaNotebook(s)) { - sbject.add(EOSC_NOTEBOOK); - if (sbject.stream().anyMatch(sb -> sb.getValue().equals("EOSC Jupyter Notebook"))) { - sbject = sbject.stream().map(sb -> { - if (sb.getValue().equals("EOSC Jupyter Notebook")) { - return null; - } - return sb; - }).filter(Objects::nonNull).collect(Collectors.toList()); - s.setSubject(sbject); - } + if (!Optional.ofNullable(s.getEoscifguidelines()).isPresent()) + s.setEoscifguidelines(new ArrayList<>()); + s.getEoscifguidelines().add(newInstance("EOSC::Jupyter Notebook", "EOSC::Jupyter Notebook", "", "compliesWith")); } if (containsCriteriaGalaxy(s)) { - sbject.add(EOSC_GALAXY); + if (!Optional.ofNullable(s.getEoscifguidelines()).isPresent()) + s.setEoscifguidelines(new ArrayList<>()); + + s.getEoscifguidelines().add(newInstance("EOSC::Galaxy Workflow", "EOSC::Galaxy Workflow", "", "compliesWith")); } return s; }, Encoders.bean(Software.class)) @@ -124,14 +104,14 @@ public class SparkEoscTag { readPath(spark, inputPath + "/otherresearchproduct", OtherResearchProduct.class) .map((MapFunction) orp -> { List sbject; - if (!Optional.ofNullable(orp.getSubject()).isPresent()) - orp.setSubject(new ArrayList<>()); - sbject = orp.getSubject(); + if (!Optional.ofNullable(orp.getEoscifguidelines()).isPresent()) + orp.setEoscifguidelines(new ArrayList<>()); + if (containsCriteriaGalaxy(orp)) { - sbject.add(EOSC_GALAXY); + orp.getEoscifguidelines().add(newInstance("EOSC::Galaxy Workflow", "EOSC::Galaxy Workflow", "", "compliesWith")); } if (containscriteriaTwitter(orp)) { - sbject.add(EOSC_TWITTER); + orp.getEoscifguidelines().add(newInstance("EOSC::Twitter Data", "EOSC::Twitter Data", "", "compliesWith")); } return orp; }, Encoders.bean(OtherResearchProduct.class)) @@ -149,11 +129,10 @@ public class SparkEoscTag { readPath(spark, inputPath + "/dataset", Dataset.class) .map((MapFunction) d -> { List sbject; - if (!Optional.ofNullable(d.getSubject()).isPresent()) - d.setSubject(new ArrayList<>()); - sbject = d.getSubject(); + if (!Optional.ofNullable(d.getEoscifguidelines()).isPresent()) + d.setEoscifguidelines(new ArrayList<>()); if (containscriteriaTwitter(d)) { - sbject.add(EOSC_TWITTER); + d.getEoscifguidelines().add(newInstance("EOSC::Twitter Data", "EOSC::Twitter Data", "", "compliesWith")); } return d; }, Encoders.bean(Dataset.class)) @@ -212,13 +191,6 @@ public class SparkEoscTag { return false; } - private static Set getSubjects(List s) { - Set subjects = new HashSet<>(); - s.stream().forEach(sbj -> subjects.addAll(Arrays.asList(sbj.getValue().toLowerCase().split(" ")))); - s.stream().forEach(sbj -> subjects.add(sbj.getValue().toLowerCase())); - return subjects; - } - private static Set getWordsSP(List elem) { Set words = new HashSet<>(); Optional @@ -242,9 +214,7 @@ public class SparkEoscTag { t -> words .addAll( Arrays.asList(t.getValue().toLowerCase().replaceAll("[^a-zA-Z ]", "").split(" "))))); -// elem -// .forEach( -// t -> words.addAll(Arrays.asList(t.getValue().toLowerCase().replaceAll("[^a-zA-Z ]", "").split(" ")))); + return words; } diff --git a/pom.xml b/pom.xml index 54070f654c..973bc37732 100644 --- a/pom.xml +++ b/pom.xml @@ -801,7 +801,7 @@ 3.3.3 3.4.2 [2.12,3.0) - [2.12.0] + [2.12.2-SNAPSHOT] [4.0.3] [6.0.5] [3.1.6] From 5f651f231650d0e2547bfdf9f7969611e5d43d85 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Thu, 21 Jul 2022 10:11:48 +0200 Subject: [PATCH 31/46] changed filter relation on SubRelType --- .../eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala index f72f8dd160..0073afff5e 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala @@ -112,13 +112,11 @@ object SparkConvertRDDtoDataset { "opencitations".equalsIgnoreCase(k.getValue) ) ) - .filter(r => r.getRelClass != null && r.getRelClass.equalsIgnoreCase(filterRelation)) + .filter(r => r.getSubRelType != null && r.getSubRelType.equalsIgnoreCase(filterRelation)) spark.createDataset(rddRelation).as[Relation].write.mode(SaveMode.Overwrite).save(s"$relPath") } else { val relationSemanticFilter = List( - // "cites", - // "iscitedby", "merges", "ismergedin", "HasAmongTopNSimilarDocuments", From 5143a802320b3a64a16b09f298f005d4fbce78e9 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 21 Jul 2022 11:56:51 +0200 Subject: [PATCH 32/46] [EOSC TAG] modification of test class to align with new element --- .../dnetlib/dhp/bulktag/EOSCTagJobTest.java | 174 ++++++++++++++++-- 1 file changed, 155 insertions(+), 19 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java index 1ea2541576..b1c0cbb84a 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java @@ -126,8 +126,9 @@ public class EOSCTagJobTest { .assertEquals( 4, tmp + .filter(s -> s.getEoscifguidelines()!= null) .filter( - s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook"))) + s -> s.getEoscifguidelines().stream().anyMatch(eig -> eig.getCode().equals("EOSC::Jupyter Notebook"))) .count()); Assertions @@ -136,17 +137,36 @@ public class EOSCTagJobTest { .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) .collect() .get(0) - .getSubject() + .getEoscifguidelines() .size()); + + Assertions + .assertEquals( + 1, tmp + .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) + .collect() + .get(0) + .getSubject() + .size()); Assertions .assertTrue( tmp .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) .collect() .get(0) - .getSubject() + .getEoscifguidelines() .stream() - .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); + .anyMatch(s -> s.getCode().equals("EOSC::Jupyter Notebook"))); + + Assertions + .assertFalse( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) + .collect() + .get(0) + .getSubject() + .stream() + .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); Assertions .assertEquals( @@ -166,16 +186,23 @@ public class EOSCTagJobTest { .stream() .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); + Assertions.assertTrue(tmp + .filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11")) + .collect() + .get(0) + .getEoscifguidelines() == null + ); + Assertions .assertEquals( - 9, tmp + 8, tmp .filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")) .collect() .get(0) .getSubject() .size()); Assertions - .assertTrue( + .assertFalse( tmp .filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")) .collect() @@ -183,6 +210,23 @@ public class EOSCTagJobTest { .getSubject() .stream() .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); + Assertions + .assertEquals( + 1, tmp + .filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")) + .collect() + .get(0) + .getEoscifguidelines() + .size()); + Assertions + .assertTrue( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")) + .collect() + .get(0) + .getEoscifguidelines() + .stream() + .anyMatch(s -> s.getCode().equals("EOSC::Jupyter Notebook"))); Assertions .assertEquals( @@ -201,17 +245,24 @@ public class EOSCTagJobTest { .getSubject() .stream() .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); + Assertions.assertTrue( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::5aec1186054301b66c0c5dc35972a589")) + .collect() + .get(0) + .getEoscifguidelines() == null + ); Assertions .assertEquals( - 9, tmp + 8, tmp .filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0")) .collect() .get(0) .getSubject() .size()); Assertions - .assertTrue( + .assertFalse( tmp .filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0")) .collect() @@ -219,14 +270,27 @@ public class EOSCTagJobTest { .getSubject() .stream() .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); + Assertions.assertEquals(1, + tmp + .filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0")) + .collect() + .get(0) + .getEoscifguidelines() + .size()); + Assertions.assertTrue(tmp + .filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0")) + .collect() + .get(0) + .getEoscifguidelines() + .stream() + .anyMatch(s -> s.getCode().equals("EOSC::Jupyter Notebook"))); List subjects = tmp .filter(sw -> sw.getId().equals("50|od______1582::6e7a9b21a2feef45673890432af34244")) .collect() .get(0) .getSubject(); - Assertions.assertEquals(8, subjects.size()); - Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); + Assertions.assertEquals(7, subjects.size()); Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("jupyter"))); Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("Modeling and Simulation"))); Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("structure granulaire"))); @@ -250,6 +314,14 @@ public class EOSCTagJobTest { .filter( ds -> ds.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook"))) .count()); + Assertions + .assertEquals( + 0, sc + .textFile(workingDir.toString() + "/input/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)) + .filter( + ds -> ds.getEoscifguidelines().stream().anyMatch(eig -> eig.getCode().equals("EOSC::Jupyter Notebook"))) + .count()); Assertions .assertEquals( @@ -264,9 +336,18 @@ public class EOSCTagJobTest { .textFile(workingDir.toString() + "/input/otherresearchproduct") .map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)) .filter( - ds -> ds.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook"))) + orp -> orp.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook"))) .count()); + Assertions + .assertEquals( + 0, sc + .textFile(workingDir.toString() + "/input/otherresearchproduct") + .map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)) + .filter( + orp -> orp.getSubject().stream().anyMatch(eig -> eig.getValue().equals("EOSC::Jupyter Notebook"))) + .count()); + // spark.stop(); } @@ -326,22 +407,37 @@ public class EOSCTagJobTest { Assertions .assertEquals( - 1, + 0, tmp .filter( s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Galaxy Workflow"))) .count()); + Assertions + .assertEquals( + 1, + tmp + .filter( + s -> s.getEoscifguidelines()!=null) + .count()); + Assertions + .assertEquals( + 1, + tmp + .filter( + s -> s.getEoscifguidelines()!=null) + .filter(s -> s.getEoscifguidelines().stream().anyMatch(eig -> eig.getCode().equals("EOSC::Galaxy Workflow"))) + .count()); Assertions .assertEquals( - 2, tmp + 1, tmp .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) .collect() .get(0) .getSubject() .size()); Assertions - .assertTrue( + .assertFalse( tmp .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) .collect() @@ -350,6 +446,19 @@ public class EOSCTagJobTest { .stream() .anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); + Assertions.assertEquals(1, tmp + .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) + .collect() + .get(0) + .getEoscifguidelines() + .size() ); + Assertions.assertTrue(tmp + .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) + .collect() + .get(0) + .getEoscifguidelines() + .stream().anyMatch(eig -> eig.getCode().equals("EOSC::Galaxy Workflow"))); + Assertions .assertEquals( 5, tmp @@ -385,22 +494,26 @@ public class EOSCTagJobTest { Assertions .assertEquals( - 1, + 0, orp .filter( s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Galaxy Workflow"))) .count()); + orp.foreach(o-> System.out.println(OBJECT_MAPPER.writeValueAsString(o))); + + Assertions.assertEquals(1, orp.filter(o -> o.getEoscifguidelines() != null) + .filter(o -> o.getEoscifguidelines().stream().anyMatch(eig -> eig.getCode().equals("EOSC::Galaxy Workflow"))).count()); Assertions .assertEquals( - 3, orp + 2, orp .filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07")) .collect() .get(0) .getSubject() .size()); Assertions - .assertTrue( + .assertFalse( orp .filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07")) .collect() @@ -408,6 +521,23 @@ public class EOSCTagJobTest { .getSubject() .stream() .anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); + Assertions + .assertEquals( + 1, orp + .filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07")) + .collect() + .get(0) + .getEoscifguidelines() + .size()); + Assertions + .assertTrue( + orp + .filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07")) + .collect() + .get(0) + .getEoscifguidelines() + .stream() + .anyMatch(s -> s.getCode().equals("EOSC::Galaxy Workflow"))); Assertions .assertEquals( @@ -516,10 +646,16 @@ public class EOSCTagJobTest { Assertions .assertEquals( - 3, + 0, orp .filter(s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Twitter Data"))) .count()); + Assertions + .assertEquals( + 3, + orp + .filter(s -> s.getEoscifguidelines().stream().anyMatch(eig -> eig.getCode().equals("EOSC::Twitter Data"))) + .count()); JavaRDD dats = sc .textFile(workingDir.toString() + "/input/dataset") @@ -531,7 +667,7 @@ public class EOSCTagJobTest { .assertEquals( 3, dats - .filter(s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Twitter Data"))) + .filter(s -> s.getEoscifguidelines().stream().anyMatch(eig -> eig.getCode().equals("EOSC::Twitter Data"))) .count()); } From 56d09e6348d63d531250ea6f075c1d306c07ed66 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 21 Jul 2022 14:36:48 +0200 Subject: [PATCH 33/46] [EOSC TAG] before adding the tag added a step to verify the same tag is not already present --- .../eu/dnetlib/dhp/bulktag/SparkEoscTag.java | 21 ++++++++++++------- 1 file changed, 14 insertions(+), 7 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java index d319340812..c5ed0b45ce 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java @@ -80,13 +80,14 @@ public class SparkEoscTag { if (containsCriteriaNotebook(s)) { if (!Optional.ofNullable(s.getEoscifguidelines()).isPresent()) s.setEoscifguidelines(new ArrayList<>()); - s.getEoscifguidelines().add(newInstance("EOSC::Jupyter Notebook", "EOSC::Jupyter Notebook", "", "compliesWith")); + addEIG(s.getEoscifguidelines(), "EOSC::Jupyter Notebook", "EOSC::Jupyter Notebook", "", "compliesWith"); + } if (containsCriteriaGalaxy(s)) { if (!Optional.ofNullable(s.getEoscifguidelines()).isPresent()) s.setEoscifguidelines(new ArrayList<>()); - s.getEoscifguidelines().add(newInstance("EOSC::Galaxy Workflow", "EOSC::Galaxy Workflow", "", "compliesWith")); + addEIG(s.getEoscifguidelines(),"EOSC::Galaxy Workflow", "EOSC::Galaxy Workflow", "", "compliesWith"); } return s; }, Encoders.bean(Software.class)) @@ -103,15 +104,15 @@ public class SparkEoscTag { readPath(spark, inputPath + "/otherresearchproduct", OtherResearchProduct.class) .map((MapFunction) orp -> { - List sbject; + if (!Optional.ofNullable(orp.getEoscifguidelines()).isPresent()) orp.setEoscifguidelines(new ArrayList<>()); if (containsCriteriaGalaxy(orp)) { - orp.getEoscifguidelines().add(newInstance("EOSC::Galaxy Workflow", "EOSC::Galaxy Workflow", "", "compliesWith")); + addEIG(orp.getEoscifguidelines(),"EOSC::Galaxy Workflow", "EOSC::Galaxy Workflow", "", "compliesWith"); } if (containscriteriaTwitter(orp)) { - orp.getEoscifguidelines().add(newInstance("EOSC::Twitter Data", "EOSC::Twitter Data", "", "compliesWith")); + addEIG(orp.getEoscifguidelines(),"EOSC::Twitter Data", "EOSC::Twitter Data", "", "compliesWith"); } return orp; }, Encoders.bean(OtherResearchProduct.class)) @@ -128,11 +129,11 @@ public class SparkEoscTag { readPath(spark, inputPath + "/dataset", Dataset.class) .map((MapFunction) d -> { - List sbject; + if (!Optional.ofNullable(d.getEoscifguidelines()).isPresent()) d.setEoscifguidelines(new ArrayList<>()); if (containscriteriaTwitter(d)) { - d.getEoscifguidelines().add(newInstance("EOSC::Twitter Data", "EOSC::Twitter Data", "", "compliesWith")); + addEIG(d.getEoscifguidelines(),"EOSC::Twitter Data", "EOSC::Twitter Data", "", "compliesWith"); } return d; }, Encoders.bean(Dataset.class)) @@ -148,6 +149,12 @@ public class SparkEoscTag { .json(inputPath + "/dataset"); } + private static void addEIG(List eoscifguidelines, String code, String label, String url, String sem) { + if (!eoscifguidelines.stream().anyMatch(eig -> eig.getCode().equals(code))) + eoscifguidelines.add(newInstance(code, label, url, sem)); + } + + private static boolean containscriteriaTwitter(Result r) { Set words = getWordsSP(r.getTitle()); words.addAll(getWordsF(r.getDescription())); From 3be036f290f3cb569465cf9566557e51c4660288 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 21 Jul 2022 14:45:43 +0200 Subject: [PATCH 34/46] [EOSC TAG] refactoring after compilation --- .../eu/dnetlib/dhp/bulktag/SparkEoscTag.java | 25 +- .../dnetlib/dhp/bulktag/EOSCTagJobTest.java | 284 ++++++++++-------- 2 files changed, 178 insertions(+), 131 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java index c5ed0b45ce..730e8a3fe7 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java @@ -29,7 +29,6 @@ public class SparkEoscTag { private static final Logger log = LoggerFactory.getLogger(SparkEoscTag.class); public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils .toString( @@ -63,15 +62,16 @@ public class SparkEoscTag { }); } - public static EoscIfGuidelines newInstance(String code, String label, String url, String semantics){ + public static EoscIfGuidelines newInstance(String code, String label, String url, String semantics) { EoscIfGuidelines eig = new EoscIfGuidelines(); - eig.setCode( code); + eig.setCode(code); eig.setLabel(label); eig.setUrl(url); eig.setSemanticRelation(semantics); return eig; } + private static void execEoscTag(SparkSession spark, String inputPath, String workingPath) { readPath(spark, inputPath + "/software", Software.class) @@ -80,14 +80,17 @@ public class SparkEoscTag { if (containsCriteriaNotebook(s)) { if (!Optional.ofNullable(s.getEoscifguidelines()).isPresent()) s.setEoscifguidelines(new ArrayList<>()); - addEIG(s.getEoscifguidelines(), "EOSC::Jupyter Notebook", "EOSC::Jupyter Notebook", "", "compliesWith"); + addEIG( + s.getEoscifguidelines(), "EOSC::Jupyter Notebook", "EOSC::Jupyter Notebook", "", + "compliesWith"); } if (containsCriteriaGalaxy(s)) { if (!Optional.ofNullable(s.getEoscifguidelines()).isPresent()) s.setEoscifguidelines(new ArrayList<>()); - addEIG(s.getEoscifguidelines(),"EOSC::Galaxy Workflow", "EOSC::Galaxy Workflow", "", "compliesWith"); + addEIG( + s.getEoscifguidelines(), "EOSC::Galaxy Workflow", "EOSC::Galaxy Workflow", "", "compliesWith"); } return s; }, Encoders.bean(Software.class)) @@ -109,10 +112,12 @@ public class SparkEoscTag { orp.setEoscifguidelines(new ArrayList<>()); if (containsCriteriaGalaxy(orp)) { - addEIG(orp.getEoscifguidelines(),"EOSC::Galaxy Workflow", "EOSC::Galaxy Workflow", "", "compliesWith"); + addEIG( + orp.getEoscifguidelines(), "EOSC::Galaxy Workflow", "EOSC::Galaxy Workflow", "", + "compliesWith"); } if (containscriteriaTwitter(orp)) { - addEIG(orp.getEoscifguidelines(),"EOSC::Twitter Data", "EOSC::Twitter Data", "", "compliesWith"); + addEIG(orp.getEoscifguidelines(), "EOSC::Twitter Data", "EOSC::Twitter Data", "", "compliesWith"); } return orp; }, Encoders.bean(OtherResearchProduct.class)) @@ -133,7 +138,7 @@ public class SparkEoscTag { if (!Optional.ofNullable(d.getEoscifguidelines()).isPresent()) d.setEoscifguidelines(new ArrayList<>()); if (containscriteriaTwitter(d)) { - addEIG(d.getEoscifguidelines(),"EOSC::Twitter Data", "EOSC::Twitter Data", "", "compliesWith"); + addEIG(d.getEoscifguidelines(), "EOSC::Twitter Data", "EOSC::Twitter Data", "", "compliesWith"); } return d; }, Encoders.bean(Dataset.class)) @@ -149,12 +154,12 @@ public class SparkEoscTag { .json(inputPath + "/dataset"); } - private static void addEIG(List eoscifguidelines, String code, String label, String url, String sem) { + private static void addEIG(List eoscifguidelines, String code, String label, String url, + String sem) { if (!eoscifguidelines.stream().anyMatch(eig -> eig.getCode().equals(code))) eoscifguidelines.add(newInstance(code, label, url, sem)); } - private static boolean containscriteriaTwitter(Result r) { Set words = getWordsSP(r.getTitle()); words.addAll(getWordsF(r.getDescription())); diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java index b1c0cbb84a..5f47da10e5 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java @@ -126,9 +126,12 @@ public class EOSCTagJobTest { .assertEquals( 4, tmp - .filter(s -> s.getEoscifguidelines()!= null) + .filter(s -> s.getEoscifguidelines() != null) .filter( - s -> s.getEoscifguidelines().stream().anyMatch(eig -> eig.getCode().equals("EOSC::Jupyter Notebook"))) + s -> s + .getEoscifguidelines() + .stream() + .anyMatch(eig -> eig.getCode().equals("EOSC::Jupyter Notebook"))) .count()); Assertions @@ -141,13 +144,13 @@ public class EOSCTagJobTest { .size()); Assertions - .assertEquals( - 1, tmp - .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) - .collect() - .get(0) - .getSubject() - .size()); + .assertEquals( + 1, tmp + .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) + .collect() + .get(0) + .getSubject() + .size()); Assertions .assertTrue( tmp @@ -159,14 +162,14 @@ public class EOSCTagJobTest { .anyMatch(s -> s.getCode().equals("EOSC::Jupyter Notebook"))); Assertions - .assertFalse( - tmp - .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) - .collect() - .get(0) - .getSubject() - .stream() - .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); + .assertFalse( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) + .collect() + .get(0) + .getSubject() + .stream() + .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); Assertions .assertEquals( @@ -186,12 +189,13 @@ public class EOSCTagJobTest { .stream() .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); - Assertions.assertTrue(tmp - .filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11")) - .collect() - .get(0) - .getEoscifguidelines() == null - ); + Assertions + .assertTrue( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11")) + .collect() + .get(0) + .getEoscifguidelines() == null); Assertions .assertEquals( @@ -211,22 +215,22 @@ public class EOSCTagJobTest { .stream() .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); Assertions - .assertEquals( - 1, tmp - .filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")) - .collect() - .get(0) - .getEoscifguidelines() - .size()); + .assertEquals( + 1, tmp + .filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")) + .collect() + .get(0) + .getEoscifguidelines() + .size()); Assertions - .assertTrue( - tmp - .filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")) - .collect() - .get(0) - .getEoscifguidelines() - .stream() - .anyMatch(s -> s.getCode().equals("EOSC::Jupyter Notebook"))); + .assertTrue( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")) + .collect() + .get(0) + .getEoscifguidelines() + .stream() + .anyMatch(s -> s.getCode().equals("EOSC::Jupyter Notebook"))); Assertions .assertEquals( @@ -245,13 +249,13 @@ public class EOSCTagJobTest { .getSubject() .stream() .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); - Assertions.assertTrue( + Assertions + .assertTrue( tmp - .filter(sw -> sw.getId().equals("50|od______1582::5aec1186054301b66c0c5dc35972a589")) - .collect() - .get(0) - .getEoscifguidelines() == null - ); + .filter(sw -> sw.getId().equals("50|od______1582::5aec1186054301b66c0c5dc35972a589")) + .collect() + .get(0) + .getEoscifguidelines() == null); Assertions .assertEquals( @@ -270,20 +274,24 @@ public class EOSCTagJobTest { .getSubject() .stream() .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); - Assertions.assertEquals(1, + Assertions + .assertEquals( + 1, tmp - .filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0")) - .collect() - .get(0) - .getEoscifguidelines() - .size()); - Assertions.assertTrue(tmp - .filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0")) - .collect() - .get(0) - .getEoscifguidelines() - .stream() - .anyMatch(s -> s.getCode().equals("EOSC::Jupyter Notebook"))); + .filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0")) + .collect() + .get(0) + .getEoscifguidelines() + .size()); + Assertions + .assertTrue( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0")) + .collect() + .get(0) + .getEoscifguidelines() + .stream() + .anyMatch(s -> s.getCode().equals("EOSC::Jupyter Notebook"))); List subjects = tmp .filter(sw -> sw.getId().equals("50|od______1582::6e7a9b21a2feef45673890432af34244")) @@ -315,13 +323,16 @@ public class EOSCTagJobTest { ds -> ds.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook"))) .count()); Assertions - .assertEquals( - 0, sc - .textFile(workingDir.toString() + "/input/dataset") - .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)) - .filter( - ds -> ds.getEoscifguidelines().stream().anyMatch(eig -> eig.getCode().equals("EOSC::Jupyter Notebook"))) - .count()); + .assertEquals( + 0, sc + .textFile(workingDir.toString() + "/input/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)) + .filter( + ds -> ds + .getEoscifguidelines() + .stream() + .anyMatch(eig -> eig.getCode().equals("EOSC::Jupyter Notebook"))) + .count()); Assertions .assertEquals( @@ -336,17 +347,23 @@ public class EOSCTagJobTest { .textFile(workingDir.toString() + "/input/otherresearchproduct") .map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)) .filter( - orp -> orp.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook"))) + orp -> orp + .getSubject() + .stream() + .anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook"))) .count()); Assertions - .assertEquals( - 0, sc - .textFile(workingDir.toString() + "/input/otherresearchproduct") - .map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)) - .filter( - orp -> orp.getSubject().stream().anyMatch(eig -> eig.getValue().equals("EOSC::Jupyter Notebook"))) - .count()); + .assertEquals( + 0, sc + .textFile(workingDir.toString() + "/input/otherresearchproduct") + .map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)) + .filter( + orp -> orp + .getSubject() + .stream() + .anyMatch(eig -> eig.getValue().equals("EOSC::Jupyter Notebook"))) + .count()); // spark.stop(); } @@ -413,20 +430,24 @@ public class EOSCTagJobTest { s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Galaxy Workflow"))) .count()); Assertions - .assertEquals( - 1, - tmp - .filter( - s -> s.getEoscifguidelines()!=null) - .count()); + .assertEquals( + 1, + tmp + .filter( + s -> s.getEoscifguidelines() != null) + .count()); Assertions - .assertEquals( - 1, - tmp - .filter( - s -> s.getEoscifguidelines()!=null) - .filter(s -> s.getEoscifguidelines().stream().anyMatch(eig -> eig.getCode().equals("EOSC::Galaxy Workflow"))) - .count()); + .assertEquals( + 1, + tmp + .filter( + s -> s.getEoscifguidelines() != null) + .filter( + s -> s + .getEoscifguidelines() + .stream() + .anyMatch(eig -> eig.getCode().equals("EOSC::Galaxy Workflow"))) + .count()); Assertions .assertEquals( @@ -446,18 +467,23 @@ public class EOSCTagJobTest { .stream() .anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); - Assertions.assertEquals(1, tmp - .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) - .collect() - .get(0) - .getEoscifguidelines() - .size() ); - Assertions.assertTrue(tmp - .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) - .collect() - .get(0) - .getEoscifguidelines() - .stream().anyMatch(eig -> eig.getCode().equals("EOSC::Galaxy Workflow"))); + Assertions + .assertEquals( + 1, tmp + .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) + .collect() + .get(0) + .getEoscifguidelines() + .size()); + Assertions + .assertTrue( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) + .collect() + .get(0) + .getEoscifguidelines() + .stream() + .anyMatch(eig -> eig.getCode().equals("EOSC::Galaxy Workflow"))); Assertions .assertEquals( @@ -499,10 +525,18 @@ public class EOSCTagJobTest { .filter( s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Galaxy Workflow"))) .count()); - orp.foreach(o-> System.out.println(OBJECT_MAPPER.writeValueAsString(o))); + orp.foreach(o -> System.out.println(OBJECT_MAPPER.writeValueAsString(o))); - Assertions.assertEquals(1, orp.filter(o -> o.getEoscifguidelines() != null) - .filter(o -> o.getEoscifguidelines().stream().anyMatch(eig -> eig.getCode().equals("EOSC::Galaxy Workflow"))).count()); + Assertions + .assertEquals( + 1, orp + .filter(o -> o.getEoscifguidelines() != null) + .filter( + o -> o + .getEoscifguidelines() + .stream() + .anyMatch(eig -> eig.getCode().equals("EOSC::Galaxy Workflow"))) + .count()); Assertions .assertEquals( @@ -522,22 +556,22 @@ public class EOSCTagJobTest { .stream() .anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); Assertions - .assertEquals( - 1, orp - .filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07")) - .collect() - .get(0) - .getEoscifguidelines() - .size()); + .assertEquals( + 1, orp + .filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07")) + .collect() + .get(0) + .getEoscifguidelines() + .size()); Assertions - .assertTrue( - orp - .filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07")) - .collect() - .get(0) - .getEoscifguidelines() - .stream() - .anyMatch(s -> s.getCode().equals("EOSC::Galaxy Workflow"))); + .assertTrue( + orp + .filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07")) + .collect() + .get(0) + .getEoscifguidelines() + .stream() + .anyMatch(s -> s.getCode().equals("EOSC::Galaxy Workflow"))); Assertions .assertEquals( @@ -651,11 +685,15 @@ public class EOSCTagJobTest { .filter(s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Twitter Data"))) .count()); Assertions - .assertEquals( - 3, - orp - .filter(s -> s.getEoscifguidelines().stream().anyMatch(eig -> eig.getCode().equals("EOSC::Twitter Data"))) - .count()); + .assertEquals( + 3, + orp + .filter( + s -> s + .getEoscifguidelines() + .stream() + .anyMatch(eig -> eig.getCode().equals("EOSC::Twitter Data"))) + .count()); JavaRDD dats = sc .textFile(workingDir.toString() + "/input/dataset") @@ -667,7 +705,11 @@ public class EOSCTagJobTest { .assertEquals( 3, dats - .filter(s -> s.getEoscifguidelines().stream().anyMatch(eig -> eig.getCode().equals("EOSC::Twitter Data"))) + .filter( + s -> s + .getEoscifguidelines() + .stream() + .anyMatch(eig -> eig.getCode().equals("EOSC::Twitter Data"))) .count()); } From 317a4a56ef9019bd4cc3280673ec34cc8c5b58d0 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 21 Jul 2022 17:37:48 +0200 Subject: [PATCH 35/46] [EOSC context TAG] first implementation of the logic to tag results imported from datasources registered in the EOSC --- .../dhp/bulktag/eosc/DatasourceMaster.java | 28 ++++ .../eosc/ReadMasterDatasourceFromDB.java | 134 ++++++++++++++++ .../dhp/bulktag/eosc/SparkEoscBulkTag.java | 145 ++++++++++++++++++ pom.xml | 2 +- 4 files changed, 308 insertions(+), 1 deletion(-) create mode 100644 dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/DatasourceMaster.java create mode 100644 dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java create mode 100644 dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/DatasourceMaster.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/DatasourceMaster.java new file mode 100644 index 0000000000..537356586d --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/DatasourceMaster.java @@ -0,0 +1,28 @@ +package eu.dnetlib.dhp.bulktag.eosc; + +import java.io.Serializable; + +/** + * @author miriam.baglioni + * @Date 21/07/22 + */ +public class DatasourceMaster implements Serializable { + private String datasource; + private String master; + + public String getDatasource() { + return datasource; + } + + public void setDatasource(String datasource) { + this.datasource = datasource; + } + + public String getMaster() { + return master; + } + + public void setMaster(String master) { + this.master = master; + } +} diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java new file mode 100644 index 0000000000..7d6964707d --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java @@ -0,0 +1,134 @@ + +package eu.dnetlib.dhp.bulktag.eosc; + +/** + * @author miriam.baglioni + * @Date 21/07/22 + */ + +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.DbClient; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.common.RelationInverse; +import eu.dnetlib.dhp.schema.oaf.Relation; +import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FSDataOutputStream; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; + +import java.io.BufferedWriter; +import java.io.Closeable; +import java.io.IOException; +import java.io.OutputStreamWriter; +import java.nio.charset.StandardCharsets; +import java.sql.ResultSet; +import java.sql.SQLException; +import java.util.Arrays; +import java.util.List; +import java.util.function.Consumer; +import java.util.function.Function; + +public class ReadMasterDatasourceFromDB implements Closeable { + + private final DbClient dbClient; + private static final Log log = LogFactory.getLog(ReadMasterDatasourceFromDB.class); + + private final BufferedWriter writer; + private final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static final String QUERY = "SELECT dso.id datasource, d.id master FROM " + + "(SELECT id FROM dsm_services WHERE id like 'eosc%') dso " + + "FULL JOIN " + + "(SELECT id, duplicate FROM dsm_dedup_services WHERE duplicate like 'eosc%')d " + + "ON dso.id = d.duplicate"; + + public static void main(final String[] args) throws Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + ReadMasterDatasourceFromDB.class + .getResourceAsStream( + "/eu/dnetlib/dhp/blacklist/blacklist_parameters.json"))); + + parser.parseArgument(args); + + final String dbUrl = parser.get("postgresUrl"); + final String dbUser = parser.get("postgresUser"); + final String dbPassword = parser.get("postgresPassword"); + final String hdfsPath = parser.get("hdfsPath") + "/datasourceMasters"; + final String hdfsNameNode = parser.get("hdfsNameNode"); + + try (final ReadMasterDatasourceFromDB rmd = new ReadMasterDatasourceFromDB(hdfsPath, hdfsNameNode, dbUrl, dbUser, + dbPassword)) { + + log.info("Processing datasources..."); + rmd.execute(QUERY, rmd::datasourceMasterMap); + + } + } + + public void execute(final String sql, final Function producer) { + + dbClient.processResults(sql, rs -> writeMap(producer.apply(rs))); + } + + public DatasourceMaster datasourceMasterMap(ResultSet rs) { + try { + DatasourceMaster dm = new DatasourceMaster(); + String datasource = rs.getString("datasource"); + dm.setDatasource(datasource); + String master = rs.getString("master"); + if (StringUtils.isNotBlank(master)) + dm.setMaster(OafMapperUtils.createOpenaireId(10, master, true)); + else + dm.setMaster(OafMapperUtils.createOpenaireId(10, datasource, true)); + return dm; + + } catch (final SQLException e) { + throw new RuntimeException(e); + } + } + + @Override + public void close() throws IOException { + dbClient.close(); + writer.close(); + } + + public ReadMasterDatasourceFromDB( + final String hdfsPath, String hdfsNameNode, final String dbUrl, final String dbUser, final String dbPassword) + throws IOException { + + this.dbClient = new DbClient(dbUrl, dbUser, dbPassword); + + Configuration conf = new Configuration(); + conf.set("fs.defaultFS", hdfsNameNode); + + FileSystem fileSystem = FileSystem.get(conf); + Path hdfsWritePath = new Path(hdfsPath); + FSDataOutputStream fsDataOutputStream = null; + if (fileSystem.exists(hdfsWritePath)) { + fsDataOutputStream = fileSystem.append(hdfsWritePath); + } else { + fsDataOutputStream = fileSystem.create(hdfsWritePath); + } + + this.writer = new BufferedWriter(new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8)); + } + + protected void writeMap(final DatasourceMaster dm) { + try { + writer.write(OBJECT_MAPPER.writeValueAsString(dm)); + writer.newLine(); + } catch (final IOException e) { + throw new RuntimeException(e); + } + } + +} diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java new file mode 100644 index 0000000000..aa709cb293 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java @@ -0,0 +1,145 @@ +package eu.dnetlib.dhp.bulktag.eosc; + +import com.fasterxml.jackson.databind.ObjectMapper; +import com.google.gson.Gson; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.bulktag.SparkBulkTagJob; +import eu.dnetlib.dhp.bulktag.community.*; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.oaf.Context; +import eu.dnetlib.dhp.schema.oaf.DataInfo; +import eu.dnetlib.dhp.schema.oaf.Qualifier; +import eu.dnetlib.dhp.schema.oaf.Result; +import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import javax.print.attribute.DocAttributeSet; +import java.io.Serializable; +import java.util.*; +import java.util.stream.Collectors; + +import static eu.dnetlib.dhp.PropagationConstant.removeOutputDir; +import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.*; +import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.TAGGING_TRUST; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; +import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PROVENANCE_ACTIONS; + +/** + * @author miriam.baglioni + * @Date 21/07/22 + */ +public class SparkEoscBulkTag implements Serializable { + + private static final Logger log = LoggerFactory.getLogger(SparkEoscBulkTag.class); + public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + SparkEoscBulkTag.class + .getResourceAsStream( + "/eu/dnetlib/dhp/bulktag/input_bulkTag_parameters.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String inputPath = parser.get("sourcePath"); + log.info("inputPath: {}", inputPath); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath: {}", outputPath); + + String datasourceMapPath = parser.get("datasourceMapPath"); + log.info("datasourceMapPath: {}", datasourceMapPath); + + final String resultClassName = parser.get("resultTableName"); + log.info("resultTableName: {}", resultClassName); + + Class resultClazz = (Class) Class.forName(resultClassName); + + SparkConf conf = new SparkConf(); + CommunityConfiguration cc; + + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + removeOutputDir(spark, outputPath); + execBulkTag(spark, inputPath, outputPath, datasourceMapPath, resultClazz); + }); + } + + private static void execBulkTag( + SparkSession spark, + String inputPath, + String outputPath, + String datasourceMapPath, + Class resultClazz) { + + final List hostedByList = Arrays.asList(readPath(spark, datasourceMapPath, DatasourceMaster.class) + .map((MapFunction) dm -> dm.getMaster(), Encoders.STRING()) + .collect()); + + readPath(spark, inputPath, resultClazz) + .map(patchResult(), Encoders.bean(resultClazz)) + .filter(Objects::nonNull) + .map( + (MapFunction) value -> enrich(value, hostedByList), + Encoders.bean(resultClazz)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath); + } + + private static R enrich(R value, List hostedByList) { + if(value.getInstance().stream().anyMatch(i -> hostedByList.contains(i.getHostedby().getKey())) || + (value.getEoscifguidelines() != null && value.getEoscifguidelines().size() > 0)){ + Context context = new Context(); + context.setId("eosc"); + OafMapperUtils.dataInfo(false, BULKTAG_DATA_INFO_TYPE,true,false, + OafMapperUtils.qualifier(CLASS_ID_DATASOURCE, CLASS_NAME_BULKTAG_DATASOURCE, + DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), TAGGING_TRUST); + value.getContext().add(context); + + } + return value; + + } + + public static Dataset readPath( + SparkSession spark, String inputPath, Class clazz) { + return spark + .read() + .textFile(inputPath) + .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz)); + } + + // TODO remove this hack as soon as the values fixed by this method will be provided as NON null + private static MapFunction patchResult() { + return r -> { + if (r.getDataInfo().getDeletedbyinference() == null) { + r.getDataInfo().setDeletedbyinference(false); + } + if (r.getContext() == null) { + r.setContext(new ArrayList<>()); + } + return r; + }; + } + +} diff --git a/pom.xml b/pom.xml index 54070f654c..821ce3124a 100644 --- a/pom.xml +++ b/pom.xml @@ -801,7 +801,7 @@ 3.3.3 3.4.2 [2.12,3.0) - [2.12.0] + [2.12.1] [4.0.3] [6.0.5] [3.1.6] From ddc414b2586075f2ab32b59480115c826e9a863c Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Fri, 22 Jul 2022 09:43:15 +0200 Subject: [PATCH 36/46] fixed wrong json param --- .../eu/dnetlib/dhp/sx/graph/convert_dataset_json_params.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/convert_dataset_json_params.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/convert_dataset_json_params.json index f3e8cdbade..3a2f907089 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/convert_dataset_json_params.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/convert_dataset_json_params.json @@ -1,6 +1,6 @@ [ {"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true}, {"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the source Path", "paramRequired": true}, - {"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the path of the raw graph", "paramRequired": true} + {"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the path of the raw graph", "paramRequired": true}, {"paramName":"r", "paramLongName":"filterRelation", "paramDescription": "the relation to filter", "paramRequired": false} ] \ No newline at end of file From 7a1c1b6f53b8c7ca51633b440338fffc997e81bb Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 22 Jul 2022 14:36:02 +0200 Subject: [PATCH 37/46] [EOSC context TAG] Add test class and resourcesK --- .../dhp/bulktag/eosc/DatasourceMaster.java | 29 +- .../eosc/ReadMasterDatasourceFromDB.java | 62 ++-- .../dhp/bulktag/eosc/SparkEoscBulkTag.java | 229 +++++++------ .../bulktag/datasourcemaster_parameters.json | 32 ++ .../input_eosc_bulkTag_parameters.json | 34 ++ .../dhp/bulktag/oozie_app/workflow.xml | 139 +++++++- .../dhp/bulktag/EOSCContextTaggingTest.java | 152 +++++++++ .../dhp/bulktag/eosc/dataset/dataset_10.json | 10 + .../datasourceMaster | 318 ++++++++++++++++++ 9 files changed, 855 insertions(+), 150 deletions(-) create mode 100644 dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/datasourcemaster_parameters.json create mode 100644 dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/input_eosc_bulkTag_parameters.json create mode 100644 dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCContextTaggingTest.java create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/eosc/dataset/dataset_10.json create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/eosc/datasourceMasterAssociation/datasourceMaster diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/DatasourceMaster.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/DatasourceMaster.java index 537356586d..ee01597e75 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/DatasourceMaster.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/DatasourceMaster.java @@ -1,3 +1,4 @@ + package eu.dnetlib.dhp.bulktag.eosc; import java.io.Serializable; @@ -7,22 +8,22 @@ import java.io.Serializable; * @Date 21/07/22 */ public class DatasourceMaster implements Serializable { - private String datasource; - private String master; + private String datasource; + private String master; - public String getDatasource() { - return datasource; - } + public String getDatasource() { + return datasource; + } - public void setDatasource(String datasource) { - this.datasource = datasource; - } + public void setDatasource(String datasource) { + this.datasource = datasource; + } - public String getMaster() { - return master; - } + public String getMaster() { + return master; + } - public void setMaster(String master) { - this.master = master; - } + public void setMaster(String master) { + this.master = master; + } } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java index 7d6964707d..9ad108749f 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java @@ -1,27 +1,6 @@ package eu.dnetlib.dhp.bulktag.eosc; -/** - * @author miriam.baglioni - * @Date 21/07/22 - */ - -import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.common.DbClient; -import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.dhp.schema.common.RelationInverse; -import eu.dnetlib.dhp.schema.oaf.Relation; -import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; -import org.apache.commons.io.IOUtils; -import org.apache.commons.lang3.StringUtils; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; -import org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.FSDataOutputStream; -import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.fs.Path; - import java.io.BufferedWriter; import java.io.Closeable; import java.io.IOException; @@ -34,6 +13,28 @@ import java.util.List; import java.util.function.Consumer; import java.util.function.Function; +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FSDataOutputStream; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; + +/** + * @author miriam.baglioni + * @Date 21/07/22 + */ +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.DbClient; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.common.RelationInverse; +import eu.dnetlib.dhp.schema.oaf.Relation; +import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; + public class ReadMasterDatasourceFromDB implements Closeable { private final DbClient dbClient; @@ -43,18 +44,18 @@ public class ReadMasterDatasourceFromDB implements Closeable { private final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); private static final String QUERY = "SELECT dso.id datasource, d.id master FROM " + - "(SELECT id FROM dsm_services WHERE id like 'eosc%') dso " + - "FULL JOIN " + - "(SELECT id, duplicate FROM dsm_dedup_services WHERE duplicate like 'eosc%')d " + - "ON dso.id = d.duplicate"; + "(SELECT id FROM dsm_services WHERE id like 'eosc%') dso " + + "FULL JOIN " + + "(SELECT id, duplicate FROM dsm_dedup_services WHERE duplicate like 'eosc%')d " + + "ON dso.id = d.duplicate"; public static void main(final String[] args) throws Exception { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils .toString( - ReadMasterDatasourceFromDB.class + ReadMasterDatasourceFromDB.class .getResourceAsStream( - "/eu/dnetlib/dhp/blacklist/blacklist_parameters.json"))); + "/eu/dnetlib/dhp/bulktag/datasourcemaster_parameters.json"))); parser.parseArgument(args); @@ -64,8 +65,9 @@ public class ReadMasterDatasourceFromDB implements Closeable { final String hdfsPath = parser.get("hdfsPath") + "/datasourceMasters"; final String hdfsNameNode = parser.get("hdfsNameNode"); - try (final ReadMasterDatasourceFromDB rmd = new ReadMasterDatasourceFromDB(hdfsPath, hdfsNameNode, dbUrl, dbUser, - dbPassword)) { + try ( + final ReadMasterDatasourceFromDB rmd = new ReadMasterDatasourceFromDB(hdfsPath, hdfsNameNode, dbUrl, dbUser, + dbPassword)) { log.info("Processing datasources..."); rmd.execute(QUERY, rmd::datasourceMasterMap); @@ -75,7 +77,7 @@ public class ReadMasterDatasourceFromDB implements Closeable { public void execute(final String sql, final Function producer) { - dbClient.processResults(sql, rs -> writeMap(producer.apply(rs))); + dbClient.processResults(sql, rs -> writeMap(producer.apply(rs))); } public DatasourceMaster datasourceMasterMap(ResultSet rs) { diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java index aa709cb293..600a5cec8e 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java @@ -1,18 +1,22 @@ + package eu.dnetlib.dhp.bulktag.eosc; -import com.fasterxml.jackson.databind.ObjectMapper; -import com.google.gson.Gson; -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.bulktag.SparkBulkTagJob; -import eu.dnetlib.dhp.bulktag.community.*; -import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.dhp.schema.oaf.Context; -import eu.dnetlib.dhp.schema.oaf.DataInfo; -import eu.dnetlib.dhp.schema.oaf.Qualifier; -import eu.dnetlib.dhp.schema.oaf.Result; -import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; +import static eu.dnetlib.dhp.PropagationConstant.readPath; +import static eu.dnetlib.dhp.PropagationConstant.removeOutputDir; +import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.*; +import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.TAGGING_TRUST; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; +import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PROVENANCE_ACTIONS; + +import java.io.Serializable; +import java.util.*; +import java.util.stream.Collectors; + +import javax.print.attribute.DocAttributeSet; + import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.ForeachFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; @@ -21,16 +25,15 @@ import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import javax.print.attribute.DocAttributeSet; -import java.io.Serializable; -import java.util.*; -import java.util.stream.Collectors; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.google.gson.Gson; -import static eu.dnetlib.dhp.PropagationConstant.removeOutputDir; -import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.*; -import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.TAGGING_TRUST; -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; -import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PROVENANCE_ACTIONS; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.bulktag.SparkBulkTagJob; +import eu.dnetlib.dhp.bulktag.community.*; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; /** * @author miriam.baglioni @@ -38,108 +41,124 @@ import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PROVENANCE_ACTION */ public class SparkEoscBulkTag implements Serializable { - private static final Logger log = LoggerFactory.getLogger(SparkEoscBulkTag.class); - public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static final Logger log = LoggerFactory.getLogger(SparkEoscBulkTag.class); + public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkEoscBulkTag.class - .getResourceAsStream( - "/eu/dnetlib/dhp/bulktag/input_bulkTag_parameters.json")); + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + SparkEoscBulkTag.class + .getResourceAsStream( + "/eu/dnetlib/dhp/bulktag/input_eosc_bulkTag_parameters.json")); - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); + final String inputPath = parser.get("sourcePath"); + log.info("inputPath: {}", inputPath); - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); + final String workingPath = parser.get("workingPath"); + log.info("workingPath: {}", workingPath); - String datasourceMapPath = parser.get("datasourceMapPath"); - log.info("datasourceMapPath: {}", datasourceMapPath); + String datasourceMapPath = parser.get("datasourceMapPath"); + log.info("datasourceMapPath: {}", datasourceMapPath); - final String resultClassName = parser.get("resultTableName"); - log.info("resultTableName: {}", resultClassName); + final String resultClassName = parser.get("resultTableName"); + log.info("resultTableName: {}", resultClassName); - Class resultClazz = (Class) Class.forName(resultClassName); + Class resultClazz = (Class) Class.forName(resultClassName); - SparkConf conf = new SparkConf(); - CommunityConfiguration cc; + SparkConf conf = new SparkConf(); + CommunityConfiguration cc; - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - removeOutputDir(spark, outputPath); - execBulkTag(spark, inputPath, outputPath, datasourceMapPath, resultClazz); - }); - } + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + removeOutputDir(spark, workingPath); + execBulkTag(spark, inputPath, workingPath, datasourceMapPath, resultClazz); + }); + } - private static void execBulkTag( - SparkSession spark, - String inputPath, - String outputPath, - String datasourceMapPath, - Class resultClazz) { + private static void execBulkTag( + SparkSession spark, + String inputPath, + String workingPath, + String datasourceMapPath, + Class resultClazz) { - final List hostedByList = Arrays.asList(readPath(spark, datasourceMapPath, DatasourceMaster.class) - .map((MapFunction) dm -> dm.getMaster(), Encoders.STRING()) - .collect()); - readPath(spark, inputPath, resultClazz) - .map(patchResult(), Encoders.bean(resultClazz)) - .filter(Objects::nonNull) - .map( - (MapFunction) value -> enrich(value, hostedByList), - Encoders.bean(resultClazz)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); - } + List hostedByList = readPath(spark, datasourceMapPath, DatasourceMaster.class) + .map((MapFunction) dm -> dm.getMaster(), Encoders.STRING()) + .collectAsList(); - private static R enrich(R value, List hostedByList) { - if(value.getInstance().stream().anyMatch(i -> hostedByList.contains(i.getHostedby().getKey())) || - (value.getEoscifguidelines() != null && value.getEoscifguidelines().size() > 0)){ - Context context = new Context(); - context.setId("eosc"); - OafMapperUtils.dataInfo(false, BULKTAG_DATA_INFO_TYPE,true,false, - OafMapperUtils.qualifier(CLASS_ID_DATASOURCE, CLASS_NAME_BULKTAG_DATASOURCE, - DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), TAGGING_TRUST); - value.getContext().add(context); - } - return value; - } - public static Dataset readPath( - SparkSession spark, String inputPath, Class clazz) { - return spark - .read() - .textFile(inputPath) - .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz)); - } + readPath(spark, inputPath, resultClazz) + .map(patchResult(), Encoders.bean(resultClazz)) + .filter(Objects::nonNull) + .map( + (MapFunction) value -> enrich(value, hostedByList), + Encoders.bean(resultClazz)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingPath); - // TODO remove this hack as soon as the values fixed by this method will be provided as NON null - private static MapFunction patchResult() { - return r -> { - if (r.getDataInfo().getDeletedbyinference() == null) { - r.getDataInfo().setDeletedbyinference(false); - } - if (r.getContext() == null) { - r.setContext(new ArrayList<>()); - } - return r; - }; - } + readPath(spark, workingPath, resultClazz) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(inputPath); + + } + + private static R enrich(R value, List hostedByList) { + if (value.getInstance().stream().anyMatch(i -> hostedByList.contains(i.getHostedby().getKey())) || + (value.getEoscifguidelines() != null && value.getEoscifguidelines().size() > 0)) { + Context context = new Context(); + context.setId("eosc"); + OafMapperUtils + .dataInfo( + false, BULKTAG_DATA_INFO_TYPE, true, false, + OafMapperUtils + .qualifier( + CLASS_ID_DATASOURCE, CLASS_NAME_BULKTAG_DATASOURCE, + DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), + TAGGING_TRUST); + value.getContext().add(context); + + } + return value; + + } + + public static Dataset readPath( + SparkSession spark, String inputPath, Class clazz) { + return spark + .read() + .textFile(inputPath) + .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz)); + } + + // TODO remove this hack as soon as the values fixed by this method will be provided as NON null + private static MapFunction patchResult() { + return r -> { + if (r.getDataInfo().getDeletedbyinference() == null) { + r.getDataInfo().setDeletedbyinference(false); + } + if (r.getContext() == null) { + r.setContext(new ArrayList<>()); + } + return r; + }; + } } diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/datasourcemaster_parameters.json b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/datasourcemaster_parameters.json new file mode 100644 index 0000000000..9a2eadaa7d --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/datasourcemaster_parameters.json @@ -0,0 +1,32 @@ +[ + { + "paramName": "p", + "paramLongName": "hdfsPath", + "paramDescription": "the path where storing the sequential file", + "paramRequired": true + }, + { + "paramName": "nn", + "paramLongName": "hdfsNameNode", + "paramDescription": "the name node on hdfs", + "paramRequired": true + }, + { + "paramName": "pgurl", + "paramLongName": "postgresUrl", + "paramDescription": "postgres url, example: jdbc:postgresql://localhost:5432/testdb", + "paramRequired": true + }, + { + "paramName": "pguser", + "paramLongName": "postgresUser", + "paramDescription": "postgres user", + "paramRequired": false + }, + { + "paramName": "pgpasswd", + "paramLongName": "postgresPassword", + "paramDescription": "postgres password", + "paramRequired": false + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/input_eosc_bulkTag_parameters.json b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/input_eosc_bulkTag_parameters.json new file mode 100644 index 0000000000..ebbbd408b5 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/input_eosc_bulkTag_parameters.json @@ -0,0 +1,34 @@ +[ + + { + "paramName":"s", + "paramLongName":"sourcePath", + "paramDescription": "the path of the sequencial file to read", + "paramRequired": true + }, + { + "paramName": "dmp", + "paramLongName":"datasourceMapPath", + "paramDescription": "the path where the association datasource master has been stored", + "paramRequired": true + }, + { + "paramName":"tn", + "paramLongName":"resultTableName", + "paramDescription": "the name of the result table we are currently working on", + "paramRequired": true + }, + { + "paramName": "wp", + "paramLongName": "workingPath", + "paramDescription": "the path used to store temporary output files", + "paramRequired": true + }, + { + "paramName": "ssm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "true if the spark session is managed, false otherwise", + "paramRequired": false + } + +] \ No newline at end of file diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml index f34c5110ff..6016e0179e 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml @@ -16,6 +16,21 @@ outputPath the output path + + + + postgresURL + the url of the postgress server to query + + + postgresUser + the username to access the postgres db + + + postgresPassword + the postgres password + + @@ -29,7 +44,7 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] @@ -226,10 +241,132 @@ --sourcePath${outputPath} --workingPath${workingDir}/eoscTag + + + + + + + eu.dnetlib.dhp.bulktag.eosc.ReadMasterDatasourceFromDB + --hdfsPath${workingDir}/datasourcemaster + --hdfsNameNode${nameNode} + --postgresUrl${postgresURL} + --postgresUser${postgresUser} + --postgresPassword${postgresPassword} + + + + + + + + + + + yarn-cluster + cluster + EOSC_tagging + eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag + dhp-enrichment-${projectVersion}.jar + + --num-executors=${sparkExecutorNumber} + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --sourcePath${outputPath}/publication + --workingPath${workingDir}/eoscContextTag/publication + --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication + --datasourceMapPath${workingDir}/datasourcemaster + + + + + + + + yarn-cluster + cluster + EOSC_tagging + eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag + dhp-enrichment-${projectVersion}.jar + + --num-executors=${sparkExecutorNumber} + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --sourcePath${outputPath}/dataset + --workingPath${workingDir}/eoscContextTag/dataset + --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset + --datasourceMapPath${workingDir}/datasourcemaster + + + + + + + yarn-cluster + cluster + EOSC_tagging + eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag + dhp-enrichment-${projectVersion}.jar + + --num-executors=${sparkExecutorNumber} + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --sourcePath${outputPath}/software + --workingPath${workingDir}/eoscContextTag/software + --resultTableNameeu.dnetlib.dhp.schema.oaf.Software + --datasourceMapPath${workingDir}/datasourcemaster + + + + + + + yarn-cluster + cluster + EOSC_tagging + eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag + dhp-enrichment-${projectVersion}.jar + + --num-executors=${sparkExecutorNumber} + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --sourcePath${outputPath}/otherresearchproduct + --workingPath${workingDir}/eoscContextTag/otherresearchproduct + --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct + --datasourceMapPath${workingDir}/datasourcemaster + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCContextTaggingTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCContextTaggingTest.java new file mode 100644 index 0000000000..d6785acc7d --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCContextTaggingTest.java @@ -0,0 +1,152 @@ + +package eu.dnetlib.dhp.bulktag; +/** + * @author miriam.baglioni + * @Date 22/07/22 + */ + +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag; +import eu.dnetlib.dhp.schema.oaf.Dataset; +import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct; +import eu.dnetlib.dhp.schema.oaf.Software; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import org.apache.commons.io.FileUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.List; + +//"50|475c1990cbb2::0fecfb874d9395aa69d2f4d7cd1acbea" has instance hostedby eosc +//"50|475c1990cbb2::3185cd5d8a2b0a06bb9b23ef11748eb1" has instance hostedby eosc +//"50|475c1990cbb2::449f28eefccf9f70c04ad70d61e041c7" has two instance one hostedby eosc +//"50|475c1990cbb2::3894c94123e96df8a21249957cf160cb" has EoscTag + +public class EOSCContextTaggingTest { + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path workingDir; + + private static final Logger log = LoggerFactory.getLogger(EOSCContextTaggingTest.class); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files.createTempDirectory(EOSCContextTaggingTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(EOSCContextTaggingTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(EOSCTagJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + void EoscContextTagTest() throws Exception { + + spark + .read() + .textFile(getClass().getResource("/eu/dnetlib/dhp/bulktag/eosc/dataset/dataset_10.json").getPath()) + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, Dataset.class), + Encoders.bean(Dataset.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingDir.toString() + "/input/dataset"); + + + SparkEoscBulkTag + .main( + new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", + workingDir.toString() + "/input/dataset", + "-workingPath", workingDir.toString() + "/working/dataset", + "-datasourceMapPath", getClass().getResource("/eu/dnetlib/dhp/bulktag/eosc/datasourceMasterAssociation/datasourceMaster").getPath(), + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset" + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/input/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); + + Assertions.assertEquals(10, tmp.count()); + + Assertions + .assertEquals( + 4, + tmp + .filter( + s -> s.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))) + .count()); + + Assertions + .assertEquals(1, + tmp + .filter(d -> d.getId().equals("50|475c1990cbb2::0fecfb874d9395aa69d2f4d7cd1acbea") + && + d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))).count() + ); + Assertions + .assertEquals(1, + tmp + .filter(d -> d.getId().equals("50|475c1990cbb2::3185cd5d8a2b0a06bb9b23ef11748eb1") + && + d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))).count() + ); + + + Assertions + .assertEquals(1, + tmp + .filter(d -> d.getId().equals("50|475c1990cbb2::3894c94123e96df8a21249957cf160cb") + && + d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))).count() + ); + + Assertions + .assertEquals(1, + tmp + .filter(d -> d.getId().equals("50|475c1990cbb2::3894c94123e96df8a21249957cf160cb") + && + d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))).count() + ); + } + + +} diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/eosc/dataset/dataset_10.json b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/eosc/dataset/dataset_10.json new file mode 100644 index 0000000000..63aa87e936 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/eosc/dataset/dataset_10.json @@ -0,0 +1,10 @@ +{"author":[{"affiliation":[],"fullname":"Government of Alberta | Gouvernement de l'Alberta","name":"Government Of Alberta Gouvernement L.","pid":[],"rank":1,"surname":"Alberta"}],"bestaccessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"collectedfrom":[{"key":"10|openaire____::3795d6478e30e2c9f787d427ff160944","value":"Federated Research Data Repository / Dépôt fédéré de données de 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+{"datasource":"eosc________::operas::operas.gotriple_discovery_platform","master":"10|eosc________::f687e24dc56aaeeb561c95865a5071cc"} +{"datasource":"eosc________::operas::operas.operas_metrics_service","master":"10|eosc________::5960e1289f623625210f720c6173592d"} +{"datasource":"eosc________::oslo_university::oslo_university.services_for_sensitive_data_tsd","master":"10|eosc________::743b01351510f88e24be1c700c581f68"} +{"datasource":"eosc________::osmooc::osmooc.open_science_mooc","master":"10|eosc________::e101101e8653b6607a3ad9fea3b7d1fe"} +{"datasource":"eosc________::oxford_e-research_centre::oxford_e-research_centre.fairsharing","master":"10|openaire____::bf5a61cc330e21ffa90eed3eb1533466"} +{"datasource":"eosc________::phenomenal::phenomenal.phenomenal","master":"10|eosc________::79e19b14aeee0d94e9a79110a6e6ad32"} +{"datasource":"eosc________::plantnet::plantnet.plntnet_identification_service","master":"10|eosc________::5ce89743eafdd8578591d84150f547e4"} +{"datasource":"eosc________::prace::prace.application_enabling_support","master":"10|eosc________::c87fd74ed685337fdbcff504373fc513"} +{"datasource":"eosc________::prace::prace.code_vault","master":"10|eosc________::dbab7889c81b59ec753040a762f6569a"} +{"datasource":"eosc________::prace::prace.deci_access","master":"10|eosc________::c7cedb82b1beea5382601d48807212aa"} +{"datasource":"eosc________::prace::prace.mooc","master":"10|eosc________::d6ff8167d31dccebe33a272513422b53"} +{"datasource":"eosc________::prace::prace.patc","master":"10|eosc________::1ab1b123bd559ee7f7c7ec2ee353f0c0"} +{"datasource":"eosc________::prace::prace.preparatory_access","master":"10|eosc________::39430adf529f1ab9e33da444b3708fcf"} +{"datasource":"eosc________::prace::prace.project_access","master":"10|eosc________::b58e957946983b686c76ee19dfab8d70"} +{"datasource":"eosc________::prace::prace.ptc","master":"10|eosc________::b3ca18e8884bfe2422d3723313fef79c"} +{"datasource":"eosc________::prace::prace.seasonal_schools_and_international_summer_school","master":"10|eosc________::590c71318d9d94c32981e3195567d546"} +{"datasource":"eosc________::prace::prace.shape","master":"10|eosc________::38b5a26f74e4808270a2d4f305d2f3a5"} +{"datasource":"eosc________::prace::prace.training_portal","master":"10|eosc________::25966a269ab2343ac9c4d982c341d87f"} +{"datasource":"eosc________::predictia::predictia.climadjust","master":"10|eosc________::14743eb22da3524893784faf409aac70"} +{"datasource":"eosc________::psi::psi.psi_public_data_repository","master":"10|re3data_____::1e55174ff77ed2d804871281201dbb50"} +{"datasource":"eosc________::psi::psi.remote_desktop_service","master":"10|eosc________::c82e26eb6e65d008de03b349dffc11fc"} +{"datasource":"eosc________::psnc::psnc.rohub","master":"10|eosc________::c87f08707b5235172e85b374e39a82dc"} +{"datasource":"eosc________::psnc::psnc.symbiote","master":"10|eosc________::ef0cd965a0d0a3df80ecfae4b3b08aad"} +{"datasource":"eosc________::rasdaman::rasdaman.datacube","master":"10|eosc________::bb1678f7b15d8c15fde6e240a4f95f93"} +{"datasource":"eosc________::rbi::rbi.dariah_science_gateway","master":"10|eosc________::b51b448421d926293b3781f4ac90f4f4"} +{"datasource":"eosc________::readcoop::readcoop.transkribus","master":"10|eosc________::a80411026809e6eaa896439e1b9764f4"} +{"datasource":"eosc________::rli::rli.open_energy_platform","master":"10|fairsharing_::0cbed40c0d920b94126eaf5e707be1f5"} +{"datasource":"eosc________::ror-org::ror-org.identifier","master":"10|eosc________::6fe92c2346db22322ddf6b677d449b0e"} +{"datasource":"eosc________::sciences_po::sciences_po.ethnic_and_migrant_minority_survey_registry","master":"10|eosc________::0cde986dc2bf015912e407f0f83ee402"} +{"datasource":"eosc________::sciences_po::sciences_po.wpss_for_ess","master":"10|eosc________::9a5bb11c495443aad944b04f5fcb5c07"} +{"datasource":"eosc________::scigne::scigne.cloud_compute","master":"10|eosc________::7c63e3284c36b5977c553192dce506b3"} +{"datasource":"eosc________::scipedia::scipedia.scipedia","master":"10|eosc________::850abcddc76069f2c3c1cf77ad4beec9"} +{"datasource":"eosc________::scipedia::scipedia.topos_for_individuals","master":"10|eosc________::e6214b58f39a25b53eecda340f95ee7b"} +{"datasource":"eosc________::seadatanet::seadatanet.doi_minting_service","master":"10|eosc________::f87f72147a3c82c4f77684e40101e90e"} +{"datasource":"eosc________::seadatanet::seadatanet.european_directory_of_marine_environmental_data_edmed","master":"10|eosc________::d79706389f0b864306feb47aac1f5766"} +{"datasource":"eosc________::seadatanet::seadatanet.european_directory_of_marine_environmental_research_projects","master":"10|eosc________::baa9d2d6cdd8507fcbf76242e4c25d76"} +{"datasource":"eosc________::seadatanet::seadatanet.european_directory_of_marine_organisations_edmo","master":"10|eosc________::5d23c66c26e0df209fc415c1e9ad0316"} +{"datasource":"eosc________::seadatanet::seadatanet.european_directory_of_the_cruise_summary_reports_csr","master":"10|eosc________::fd70912c66037dc11f710587e281eeaf"} +{"datasource":"eosc________::seadatanet::seadatanet.european_directory_of_the_initial_ocean-observing_systems_edios","master":"10|eosc________::846016e987d1feaf2a36083f88dba1f2"} +{"datasource":"eosc________::seadatanet::seadatanet.seadatanet_cdi","master":"10|eosc________::36cd158d6b1bbdbfb443c68b8da00335"} +{"datasource":"eosc________::seadatanet::seadatanet.vocabulary_services_-_underpinned_by_the_nerc_vocabulary_server_nvs","master":"10|eosc________::4416d18ec7a57e553979fbfa4d862483"} +{"datasource":"eosc________::sinergise::sinergise.sentinel_hub","master":"10|eosc________::d36ae944fa207461bcb7b2b3a6c94de8"} +{"datasource":"eosc________::sixsq::sixsq.nuvla_multi-cloud_application_management_platform","master":"10|eosc________::38438cc3190a3815359efb53b9dd98eb"} +{"datasource":"eosc________::sks::sks.digital_production_for_conferences_workshops_roundtables_and_other_academic_and_professional_events","master":"10|eosc________::f6b51bef4a5f1478e980673339f2b2f3"} +{"datasource":"eosc________::smartsmear::smartsmear.smartsmear","master":"10|eosc________::d17a9325ca64ffad59e04659ed5404f7"} +{"datasource":"eosc________::sobigdata::sobigdata.tagme","master":"10|eosc________::0c3b8b80d9d6d38effd28bfa6a140a12"} +{"datasource":"eosc________::suite5::suite5.furniture_enterprise_analytics","master":"10|eosc________::29ed60070bd91bdc19c9f278b104465c"} +{"datasource":"eosc________::switch::switch.switchengines","master":"10|eosc________::d4143918a810115206640cfeb11e0ba6"} +{"datasource":"eosc________::t-systems::t-systems.open_telekom_cloud","master":"10|eosc________::c489ef6564a47922359f7b833919d642"} +{"datasource":"eosc________::terradue::terradue.eo_services_for_earthquake_response_and_landslides_analysis","master":"10|eosc________::ab3140d145deb5fdb02eeefbc5ebc471"} +{"datasource":"eosc________::tib::tib.open_research_knowledge_graph_orkg","master":"10|eosc________::ed6bd695c7a99297f360bc2fc915be90"} +{"datasource":"eosc________::ubora::ubora.ubora","master":"10|eosc________::bacf05aff1c6dcf3133a0352d5eb14c4"} +{"datasource":"eosc________::ubora::ubora.ubora_e-platform","master":"10|eosc________::947fde33605ba61216a07135ee1551f2"} +{"datasource":"eosc________::ugr-es::ugr-es.glacier_lagoons_of_sierra_nevada","master":"10|eosc________::8a966c0efca298ad5ec130d323c29935"} +{"datasource":"eosc________::uit::uit.dataverseno","master":"10|eosc________::92b76aa81a5b8443fcf17d3ae3c34211"} +{"datasource":"eosc________::uit::uit.the_troms_repository_of_language_and_linguistics_trolling","master":"10|fairsharing_::a36b0dcd1e6384abc0e1867860ad3ee3"} +{"datasource":"eosc________::ukaea::ukaea.prominence","master":"10|eosc________::06ce999c7cf77ea5a65f87bb563cd625"} +{"datasource":"eosc________::ukri_-_stfc::ukri_-_stfc.cvmfs_test","master":"10|eosc________::53aaa0a24d0edc47c23e722135c29dde"} +{"datasource":"eosc________::ukri_-_stfc::ukri_-_stfc.rucio","master":"10|eosc________::c19a8251c6bf563365c555572ace903e"} +{"datasource":"eosc________::uni-freiburg::uni-freiburg.european_galaxy_server","master":"10|eosc________::cc00fc2385475b80accec001dfb85efb"} +{"datasource":"eosc________::unibo::unibo.opencitations","master":"10|eosc________::573c29ecaf76ab961743bfc8a7d911ec"} +{"datasource":"eosc________::unifl::unifl.snap4city","master":"10|eosc________::9a55c40c3c082b7a8352ecbc56a87996"} +{"datasource":"eosc________::unige::unige.astronomical_online_data_analysis_astrooda","master":"10|eosc________::63f6119d3170cccf979daada3c5b524e"} +{"datasource":"eosc________::unitartu::unitartu.ut.rocket","master":"10|eosc________::da3450589a9d56212963b20cf729974c"} +{"datasource":"eosc________::upv-es::upv-es.lemonade","master":"10|eosc________::afdd227beada491f77d7944d7a0eafc9"} +{"datasource":"eosc________::vamdc::vamdc.portal","master":"10|eosc________::4dab2bb6e9a9ad223cd63c62c2ea804e"} +{"datasource":"eosc________::vamdc::vamdc.query_store","master":"10|eosc________::33f18bfe544c3c84ac28be6a3292d166"} +{"datasource":"eosc________::vamdc::vamdc.species_database","master":"10|eosc________::ae3587682dec5663a1b3b625036d15d0"} +{"datasource":"eosc________::vilnius-university::vilnius-university.the_national_open_access_research_data_archive_midas","master":"10|eosc________::4987ee0d071f68cf88f6b1a834b6733f"} +{"datasource":"eosc________::wenmr::wenmr.amber-based_portal_server_for_nmr_structures_amps-nmr","master":"10|eosc________::c6cca9747ef3ce296bd626bcbc4e480a"} +{"datasource":"eosc________::wenmr::wenmr.disvis_web_portal","master":"10|eosc________::2539ec693b683284c4e243b969ae3fc0"} +{"datasource":"eosc________::wenmr::wenmr.fanten_finding_anisotropy_tensor","master":"10|eosc________::99c793e3f3b856c48eaaa36682038b28"} +{"datasource":"eosc________::wenmr::wenmr.haddock24_web_portal","master":"10|eosc________::0f198f6a0885105809f420be23614be3"} +{"datasource":"eosc________::wenmr::wenmr.metalpdb","master":"10|eosc________::84676bc3d2ce17de70309dc58f428296"} +{"datasource":"eosc________::wenmr::wenmr.pdb-tools_web","master":"10|eosc________::b37eed45624ac30f3476f71640e59a61"} +{"datasource":"eosc________::wenmr::wenmr.powerfit_web_portal","master":"10|eosc________::93d4d621ed1da378c0e7dc891cefc007"} +{"datasource":"eosc________::wenmr::wenmr.spoton","master":"10|eosc________::76e7e0552f9c6b89db94b31ddc366b9f"} \ No newline at end of file From 627332526b4a82b09190d3f3aefd106e274e38dd Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 22 Jul 2022 14:55:11 +0200 Subject: [PATCH 38/46] [EOSC context TAG] workflow start from reset_outputpath action --- .../resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml index 6016e0179e..17fc76aad4 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml @@ -44,7 +44,7 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] @@ -254,7 +254,7 @@ --postgresUser${postgresUser} --postgresPassword${postgresPassword} - + From 06a95daf60c49d9b0781d0e1f37965fc804a6491 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 22 Jul 2022 14:57:06 +0200 Subject: [PATCH 39/46] [EOSC context TAG] refactoring after compilation --- .../dhp/bulktag/eosc/SparkEoscBulkTag.java | 6 +- .../dhp/bulktag/EOSCContextTaggingTest.java | 224 +++++++++--------- 2 files changed, 118 insertions(+), 112 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java index 600a5cec8e..3ed910184c 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java @@ -93,13 +93,9 @@ public class SparkEoscBulkTag implements Serializable { String datasourceMapPath, Class resultClazz) { - List hostedByList = readPath(spark, datasourceMapPath, DatasourceMaster.class) .map((MapFunction) dm -> dm.getMaster(), Encoders.STRING()) - .collectAsList(); - - - + .collectAsList(); readPath(spark, inputPath, resultClazz) .map(patchResult(), Encoders.bean(resultClazz)) diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCContextTaggingTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCContextTaggingTest.java index d6785acc7d..cbdab7628a 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCContextTaggingTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCContextTaggingTest.java @@ -1,16 +1,11 @@ package eu.dnetlib.dhp.bulktag; -/** - * @author miriam.baglioni - * @Date 22/07/22 - */ -import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag; -import eu.dnetlib.dhp.schema.oaf.Dataset; -import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct; -import eu.dnetlib.dhp.schema.oaf.Software; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.List; + import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; @@ -26,10 +21,17 @@ import org.junit.jupiter.api.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.List; +/** + * @author miriam.baglioni + * @Date 22/07/22 + */ +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag; +import eu.dnetlib.dhp.schema.oaf.Dataset; +import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct; +import eu.dnetlib.dhp.schema.oaf.Software; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; //"50|475c1990cbb2::0fecfb874d9395aa69d2f4d7cd1acbea" has instance hostedby eosc //"50|475c1990cbb2::3185cd5d8a2b0a06bb9b23ef11748eb1" has instance hostedby eosc @@ -37,116 +39,124 @@ import java.util.List; //"50|475c1990cbb2::3894c94123e96df8a21249957cf160cb" has EoscTag public class EOSCContextTaggingTest { - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - private static SparkSession spark; + private static SparkSession spark; - private static Path workingDir; + private static Path workingDir; - private static final Logger log = LoggerFactory.getLogger(EOSCContextTaggingTest.class); + private static final Logger log = LoggerFactory.getLogger(EOSCContextTaggingTest.class); - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files.createTempDirectory(EOSCContextTaggingTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files.createTempDirectory(EOSCContextTaggingTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); - SparkConf conf = new SparkConf(); - conf.setAppName(EOSCContextTaggingTest.class.getSimpleName()); + SparkConf conf = new SparkConf(); + conf.setAppName(EOSCContextTaggingTest.class.getSimpleName()); - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - spark = SparkSession - .builder() - .appName(EOSCTagJobTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } + spark = SparkSession + .builder() + .appName(EOSCTagJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } - @Test - void EoscContextTagTest() throws Exception { + @Test + void EoscContextTagTest() throws Exception { - spark - .read() - .textFile(getClass().getResource("/eu/dnetlib/dhp/bulktag/eosc/dataset/dataset_10.json").getPath()) - .map( - (MapFunction) value -> OBJECT_MAPPER.readValue(value, Dataset.class), - Encoders.bean(Dataset.class)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(workingDir.toString() + "/input/dataset"); + spark + .read() + .textFile(getClass().getResource("/eu/dnetlib/dhp/bulktag/eosc/dataset/dataset_10.json").getPath()) + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, Dataset.class), + Encoders.bean(Dataset.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingDir.toString() + "/input/dataset"); + SparkEoscBulkTag + .main( + new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", + workingDir.toString() + "/input/dataset", + "-workingPath", workingDir.toString() + "/working/dataset", + "-datasourceMapPath", + getClass() + .getResource("/eu/dnetlib/dhp/bulktag/eosc/datasourceMasterAssociation/datasourceMaster") + .getPath(), + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset" + }); - SparkEoscBulkTag - .main( - new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", - workingDir.toString() + "/input/dataset", - "-workingPath", workingDir.toString() + "/working/dataset", - "-datasourceMapPath", getClass().getResource("/eu/dnetlib/dhp/bulktag/eosc/datasourceMasterAssociation/datasourceMaster").getPath(), - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset" - }); + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/input/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/input/dataset") - .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); + Assertions.assertEquals(10, tmp.count()); - Assertions.assertEquals(10, tmp.count()); + Assertions + .assertEquals( + 4, + tmp + .filter( + s -> s.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))) + .count()); - Assertions - .assertEquals( - 4, - tmp - .filter( - s -> s.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))) - .count()); + Assertions + .assertEquals( + 1, + tmp + .filter( + d -> d.getId().equals("50|475c1990cbb2::0fecfb874d9395aa69d2f4d7cd1acbea") + && + d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))) + .count()); + Assertions + .assertEquals( + 1, + tmp + .filter( + d -> d.getId().equals("50|475c1990cbb2::3185cd5d8a2b0a06bb9b23ef11748eb1") + && + d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))) + .count()); - Assertions - .assertEquals(1, - tmp - .filter(d -> d.getId().equals("50|475c1990cbb2::0fecfb874d9395aa69d2f4d7cd1acbea") - && - d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))).count() - ); - Assertions - .assertEquals(1, - tmp - .filter(d -> d.getId().equals("50|475c1990cbb2::3185cd5d8a2b0a06bb9b23ef11748eb1") - && - d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))).count() - ); - - - Assertions - .assertEquals(1, - tmp - .filter(d -> d.getId().equals("50|475c1990cbb2::3894c94123e96df8a21249957cf160cb") - && - d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))).count() - ); - - Assertions - .assertEquals(1, - tmp - .filter(d -> d.getId().equals("50|475c1990cbb2::3894c94123e96df8a21249957cf160cb") - && - d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))).count() - ); - } + Assertions + .assertEquals( + 1, + tmp + .filter( + d -> d.getId().equals("50|475c1990cbb2::3894c94123e96df8a21249957cf160cb") + && + d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))) + .count()); + Assertions + .assertEquals( + 1, + tmp + .filter( + d -> d.getId().equals("50|475c1990cbb2::3894c94123e96df8a21249957cf160cb") + && + d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))) + .count()); + } } From d091866e48ce0f814256c2f40ee5eddeb60511a3 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 25 Jul 2022 11:12:22 +0200 Subject: [PATCH 40/46] [EOSC Context Tagging] refactoring --- .../dhp/bulktag/eosc/SparkEoscBulkTag.java | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java index 3ed910184c..99ff922232 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java @@ -121,14 +121,14 @@ public class SparkEoscBulkTag implements Serializable { (value.getEoscifguidelines() != null && value.getEoscifguidelines().size() > 0)) { Context context = new Context(); context.setId("eosc"); - OafMapperUtils - .dataInfo( - false, BULKTAG_DATA_INFO_TYPE, true, false, - OafMapperUtils - .qualifier( - CLASS_ID_DATASOURCE, CLASS_NAME_BULKTAG_DATASOURCE, - DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), - TAGGING_TRUST); + context.setDataInfo(Arrays.asList(OafMapperUtils + .dataInfo( + false, BULKTAG_DATA_INFO_TYPE, true, false, + OafMapperUtils + .qualifier( + CLASS_ID_DATASOURCE, CLASS_NAME_BULKTAG_DATASOURCE, + DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), + TAGGING_TRUST))); value.getContext().add(context); } From 144c103b672c3165f8af4bc27f5515f620b3c7d2 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 25 Jul 2022 13:52:45 +0200 Subject: [PATCH 41/46] [EOSC Context Tagging] add check to avoid the insertion of the context if already present --- .../java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java index 99ff922232..24520ff26d 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java @@ -117,8 +117,9 @@ public class SparkEoscBulkTag implements Serializable { } private static R enrich(R value, List hostedByList) { - if (value.getInstance().stream().anyMatch(i -> hostedByList.contains(i.getHostedby().getKey())) || - (value.getEoscifguidelines() != null && value.getEoscifguidelines().size() > 0)) { + if (value.getInstance().stream().anyMatch(i -> (hostedByList.contains(i.getHostedby().getKey())) || + (value.getEoscifguidelines() != null && value.getEoscifguidelines().size() > 0)) && + !value.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))) { Context context = new Context(); context.setId("eosc"); context.setDataInfo(Arrays.asList(OafMapperUtils From 0172bab25136b1a3f974c2d66ddee434a712e26f Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 25 Jul 2022 14:16:45 +0200 Subject: [PATCH 42/46] [EOSC Context Tagging] refactoring --- .../dhp/bulktag/eosc/SparkEoscBulkTag.java | 25 +++++++++++++------ 1 file changed, 17 insertions(+), 8 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java index 24520ff26d..66e0c8af4f 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java @@ -117,19 +117,28 @@ public class SparkEoscBulkTag implements Serializable { } private static R enrich(R value, List hostedByList) { - if (value.getInstance().stream().anyMatch(i -> (hostedByList.contains(i.getHostedby().getKey())) || - (value.getEoscifguidelines() != null && value.getEoscifguidelines().size() > 0)) && - !value.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))) { + if (value + .getInstance() + .stream() + .anyMatch( + i -> (hostedByList.contains(i.getHostedby().getKey())) || + (value.getEoscifguidelines() != null && value.getEoscifguidelines().size() > 0)) + && + !value.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))) { Context context = new Context(); context.setId("eosc"); - context.setDataInfo(Arrays.asList(OafMapperUtils - .dataInfo( - false, BULKTAG_DATA_INFO_TYPE, true, false, + context + .setDataInfo( + Arrays + .asList( OafMapperUtils - .qualifier( + .dataInfo( + false, BULKTAG_DATA_INFO_TYPE, true, false, + OafMapperUtils + .qualifier( CLASS_ID_DATASOURCE, CLASS_NAME_BULKTAG_DATASOURCE, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), - TAGGING_TRUST))); + TAGGING_TRUST))); value.getContext().add(context); } From 1c82acb16835ea7ce3f70f8c847204f0ac487708 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 25 Jul 2022 14:26:39 +0200 Subject: [PATCH 43/46] [EOSC Context Tagging] refactoring: moved EOSC IF tagging in package eosc under bulkTag --- .../eu/dnetlib/dhp/bulktag/{ => eosc}/SparkEoscTag.java | 7 +------ .../eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml | 2 +- .../test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java | 5 +---- 3 files changed, 3 insertions(+), 11 deletions(-) rename dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/{ => eosc}/SparkEoscTag.java (96%) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscTag.java similarity index 96% rename from dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java rename to dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscTag.java index 730e8a3fe7..7364966415 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscTag.java @@ -1,13 +1,10 @@ -package eu.dnetlib.dhp.bulktag; +package eu.dnetlib.dhp.bulktag.eosc; import static eu.dnetlib.dhp.PropagationConstant.readPath; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.util.*; -import java.util.function.Function; -import java.util.stream.Collectors; -import java.util.stream.Stream; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; @@ -21,9 +18,7 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.*; -import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; public class SparkEoscTag { private static final Logger log = LoggerFactory.getLogger(SparkEoscTag.class); diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml index 17fc76aad4..9c1bbdf721 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml @@ -226,7 +226,7 @@ yarn-cluster cluster EOSC_tagging - eu.dnetlib.dhp.bulktag.SparkEoscTag + eu.dnetlib.dhp.bulktag.eosc.SparkEoscTag dhp-enrichment-${projectVersion}.jar --num-executors=${sparkExecutorNumber} diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java index 5f47da10e5..17e570fdf4 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java @@ -1,21 +1,18 @@ package eu.dnetlib.dhp.bulktag; -import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.ZENODO_COMMUNITY_INDICATOR; - import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; import java.util.List; +import eu.dnetlib.dhp.bulktag.eosc.SparkEoscTag; import org.apache.commons.io.FileUtils; -import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.Row; import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; import org.junit.jupiter.api.AfterAll; From 35bcd9422d60be622a0dd6f71a4a5be03513e07b Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 25 Jul 2022 15:45:22 +0200 Subject: [PATCH 44/46] [EOSC Context Tagging] removed not needed specification in path --- .../eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java index 9ad108749f..e9b1d3cfd8 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java @@ -62,7 +62,7 @@ public class ReadMasterDatasourceFromDB implements Closeable { final String dbUrl = parser.get("postgresUrl"); final String dbUser = parser.get("postgresUser"); final String dbPassword = parser.get("postgresPassword"); - final String hdfsPath = parser.get("hdfsPath") + "/datasourceMasters"; + final String hdfsPath = parser.get("hdfsPath"); final String hdfsNameNode = parser.get("hdfsNameNode"); try ( From d43663d30f6a3039a28ad8a6ac9723dd3fce4e9c Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 25 Jul 2022 17:54:10 +0200 Subject: [PATCH 45/46] adapted RorActionSet test, it should not create parent/child rels --- .../ror/GenerateRorActionSetJobTest.java | 22 ++++++++----------- 1 file changed, 9 insertions(+), 13 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJobTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJobTest.java index d50c1d5f39..5736bd95ed 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJobTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJobTest.java @@ -2,6 +2,7 @@ package eu.dnetlib.dhp.actionmanager.ror; import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertNotNull; import java.io.FileInputStream; import java.util.List; @@ -38,25 +39,20 @@ class GenerateRorActionSetJobTest { .readValue(IOUtils.toString(getClass().getResourceAsStream("ror_org.json")), RorOrganization.class); final List> aas = GenerateRorActionSetJob.convertRorOrg(r); - Assertions.assertEquals(3, aas.size()); + Assertions.assertEquals(1, aas.size()); assertEquals(Organization.class, aas.get(0).getClazz()); - assertEquals(Relation.class, aas.get(1).getClazz()); - assertEquals(Relation.class, aas.get(2).getClazz()); final Organization o = (Organization) aas.get(0).getPayload(); - final Relation r1 = (Relation) aas.get(1).getPayload(); - final Relation r2 = (Relation) aas.get(2).getPayload(); - assertEquals(o.getId(), r1.getSource()); - assertEquals(r1.getSource(), r2.getTarget()); - assertEquals(r2.getSource(), r1.getTarget()); - assertEquals(ModelConstants.IS_PARENT_OF, r1.getRelClass()); - assertEquals(ModelConstants.IS_CHILD_OF, r2.getRelClass()); + assertNotNull(o); + + assertNotNull(o.getCountry()); + assertEquals("AU", o.getCountry().getClassid()); + + assertNotNull(o.getLegalname()); + assertEquals("Mount Stromlo Observatory", o.getLegalname().getValue()); System.out.println(mapper.writeValueAsString(o)); - System.out.println(mapper.writeValueAsString(r1)); - System.out.println(mapper.writeValueAsString(r2)); - } @Test From 67525076ec9ec4ff7b190a0bc1a15b5a31333388 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Tue, 26 Jul 2022 15:35:17 +0200 Subject: [PATCH 46/46] fixed test, now it compiles after commit a6977197b3925c520f76961cfff7b05c37a51d6f --- .../dhp/datacite/DataciteToOAFTest.scala | 17 +++++++--- .../dhp/datacite/DataciteUtilityTest.scala | 31 +++++++++++++++++++ 2 files changed, 43 insertions(+), 5 deletions(-) create mode 100644 dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteUtilityTest.scala diff --git a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala index 31784c7e92..68230b4778 100644 --- a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala +++ b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala @@ -2,11 +2,14 @@ package eu.dnetlib.dhp.datacite import com.fasterxml.jackson.databind.{ObjectMapper, SerializationFeature} import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest -import eu.dnetlib.dhp.schema.oaf.Oaf +import eu.dnetlib.dhp.schema.oaf.{Dataset => OafDataset, _} import org.apache.commons.io.FileUtils import org.apache.spark.SparkConf import org.apache.spark.sql.functions.{col, count} import org.apache.spark.sql.{Dataset, Encoder, Encoders, SparkSession} +import org.json4s.DefaultFormats +import org.json4s.JsonAST.{JField, JObject, JString} +import org.json4s.jackson.JsonMethods.parse import org.junit.jupiter.api.Assertions._ import org.junit.jupiter.api.extension.ExtendWith import org.junit.jupiter.api.{AfterEach, BeforeEach, Test} @@ -45,6 +48,9 @@ class DataciteToOAFTest extends AbstractVocabularyTest { } + + + @Test def testConvert(): Unit = { @@ -70,17 +76,18 @@ class DataciteToOAFTest extends AbstractVocabularyTest { assertEquals(100, nativeSize) - spark.read.load(targetPath).printSchema(); + val result: Dataset[String] = spark.read.text(targetPath).as[String].map(DataciteUtilityTest.convertToOAF)(Encoders.STRING) + + + - val result: Dataset[Oaf] = spark.read.load(targetPath).as[Oaf] result - .map(s => s.getClass.getSimpleName) .groupBy(col("value").alias("class")) .agg(count("value").alias("Total")) .show(false) - val t = spark.read.load(targetPath).count() + val t = spark.read.text(targetPath).as[String].count() assertTrue(t > 0) diff --git a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteUtilityTest.scala b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteUtilityTest.scala new file mode 100644 index 0000000000..04d3c4a582 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteUtilityTest.scala @@ -0,0 +1,31 @@ +package eu.dnetlib.dhp.datacite + +import org.json4s.DefaultFormats +import org.json4s.JsonAST.{JField, JObject, JString} +import org.json4s.jackson.JsonMethods.parse + +object DataciteUtilityTest { + + def convertToOAF(input:String) : String = { + implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats + lazy val json = parse(input) + + + val isRelation:String = (json \\ "source").extractOrElse("NULL") + + if (isRelation != "NULL") { + return "Relation" + } + + val iType: List[String] = for { + JObject(instance) <- json \\ "instance" + JField("instancetype", JObject(instancetype)) <- instance + JField("classname", JString(classname)) <- instancetype + + } yield classname + + val l:String =iType.head.toLowerCase() + l + } + +}