From 8e8933d41abb871e49e20d7046f235afc6ed875b Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 14 Apr 2022 09:04:24 +0200 Subject: [PATCH 01/23] [BulkTagging] added fix if result.dataInfo is null --- .../main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java index 1a0afb981..6664d36ec 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java @@ -5,6 +5,7 @@ import static eu.dnetlib.dhp.PropagationConstant.removeOutputDir; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.util.ArrayList; +import java.util.Objects; import java.util.Optional; import org.apache.commons.io.IOUtils; @@ -102,6 +103,7 @@ public class SparkBulkTagJob { ResultTagger resultTagger = new ResultTagger(); readPath(spark, inputPath, resultClazz) .map(patchResult(), Encoders.bean(resultClazz)) + .filter(Objects::nonNull) .map( (MapFunction) value -> resultTagger .enrichContextCriteria( @@ -124,6 +126,9 @@ public class SparkBulkTagJob { // TODO remove this hack as soon as the values fixed by this method will be provided as NON null private static MapFunction patchResult() { return r -> { + if(r.getDataInfo() == null){ + return null; + } if (r.getDataInfo().getDeletedbyinference() == null) { r.getDataInfo().setDeletedbyinference(false); } From c5a863132c124e25d1b75ca8d7c8546a7db33043 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 14 Apr 2022 14:14:13 +0200 Subject: [PATCH 02/23] [BulkTagging] revert it --- .../src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java | 3 --- 1 file changed, 3 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java index 6664d36ec..ad1e8721a 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java @@ -126,9 +126,6 @@ public class SparkBulkTagJob { // TODO remove this hack as soon as the values fixed by this method will be provided as NON null private static MapFunction patchResult() { return r -> { - if(r.getDataInfo() == null){ - return null; - } if (r.getDataInfo().getDeletedbyinference() == null) { r.getDataInfo().setDeletedbyinference(false); } From d580e154424a8f211cf35ab1cae079f2624b8e44 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Thu, 21 Apr 2022 11:06:08 +0200 Subject: [PATCH 03/23] Modified last intersection since we lost many titles. this is my last resource, after that, I've to change my job --- .../doiboost/SparkGenerateDoiBoost.scala | 37 +++++++++++++++++-- 1 file changed, 34 insertions(+), 3 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala index 79b9e8183..bc26e44d6 100644 --- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala +++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala @@ -60,7 +60,7 @@ object SparkGenerateDoiBoost { val openaireOrganizationPath = parser.get("openaireOrganizationPath") val crossrefAggregator = new Aggregator[(String, Publication), Publication, Publication] with Serializable { - override def zero: Publication = new Publication + override def zero: Publication = null override def reduce(b: Publication, a: (String, Publication)): Publication = { @@ -177,12 +177,43 @@ object SparkGenerateDoiBoost { .map(DoiBoostMappingUtil.fixPublication) .map(p => (p.getId, p)) .groupByKey(_._1) - .agg(crossrefAggregator.toColumn) - .map(p => p._2) + .reduceGroups((left, right) => + { + //Check left is not null + if (left != null && left._1 != null) + { + //If right is null then return left + if (right == null || right._2 == null) + left + else { + // Here Left and Right are not null + // So we have to merge + val b1 = left._2 + val b2 = right._2 + b1.mergeFrom(b2) + b1.mergeOAFDataInfo(b2) + val authors = AuthorMerger.mergeAuthor(b1.getAuthor, b2.getAuthor) + b1.setAuthor(authors) + if (b2.getId != null && b2.getId.nonEmpty) + b1.setId(b2.getId) + //Return publication Merged + (b1.getId, b1) + } + } + else { + // Left is Null so we return right + right + } + } + + ) + .filter(s => s!= null && s._2!=null) + .map(s => s._2) .write .mode(SaveMode.Overwrite) .save(s"$workingDirPath/doiBoostPublicationFiltered") + val affiliationPath = parser.get("affiliationPath") val paperAffiliationPath = parser.get("paperAffiliationPath") From d660895b309d185e84c4ea3d55d1c1351820f0b2 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Thu, 21 Apr 2022 20:41:13 +0200 Subject: [PATCH 04/23] fixed wrong mapping type of dataset --- .../main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala index bc26e44d6..fbe42ef7c 100644 --- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala +++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala @@ -208,7 +208,7 @@ object SparkGenerateDoiBoost { ) .filter(s => s!= null && s._2!=null) - .map(s => s._2) + .map(s => s._2._2) .write .mode(SaveMode.Overwrite) .save(s"$workingDirPath/doiBoostPublicationFiltered") From 2a8e0fb72f10ca5a1ae4496e24649e9e86d9f1e7 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 9 May 2022 16:06:04 +0200 Subject: [PATCH 05/23] [openorgs] mapping parent/child relations without massaging the semantic labels --- .../dhp/oa/graph/raw/MigrateDbEntitiesApplication.java | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java index b5801ca5c..3e23e3493 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java @@ -711,10 +711,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i final Relation r = new Relation(); r.setRelType(ORG_ORG_RELTYPE); r.setSubRelType(ModelConstants.RELATIONSHIP); - r - .setRelClass( - rs.getString("type").equalsIgnoreCase("parent") ? ModelConstants.IS_PARENT_OF - : ModelConstants.IS_CHILD_OF); + r.setRelClass(rs.getString("type")); r.setSource(orgId1); r.setTarget(orgId2); r.setCollectedfrom(collectedFrom); From 6031acb2e3a0a268ac2a837183d35a54999c5c91 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 16 May 2022 09:20:30 +0200 Subject: [PATCH 06/23] [openorgs] fixed parent/child query, using the correct semantic labels --- .../dnetlib/dhp/oa/graph/sql/queryParentChildRelsOpenOrgs.sql | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryParentChildRelsOpenOrgs.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryParentChildRelsOpenOrgs.sql index 388fee3f5..0ac843401 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryParentChildRelsOpenOrgs.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryParentChildRelsOpenOrgs.sql @@ -10,4 +10,4 @@ SELECT 'OpenOrgs Database' AS collectedfromname, 'sysimport:crosswalk:entityregistry@@@dnet:provenance_actions' AS provenanceaction FROM relationships -WHERE reltype = 'Child' OR reltype = 'Parent' \ No newline at end of file +WHERE reltype = 'IsChildOf' OR reltype = 'IsParentOf' \ No newline at end of file From 46c07e0724f655d8cc86e6af1a4ec34fd19d7d21 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Mon, 16 May 2022 09:39:54 +0200 Subject: [PATCH 07/23] deleted hierarchical rels from ror action set --- .../ror/GenerateRorActionSetJob.java | 62 ++++--------------- 1 file changed, 11 insertions(+), 51 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java index e4d458780..6c76f8a4d 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java @@ -3,7 +3,6 @@ package eu.dnetlib.dhp.actionmanager.ror; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import static eu.dnetlib.dhp.schema.common.ModelConstants.ENTITYREGISTRY_PROVENANCE_ACTION; -import static eu.dnetlib.dhp.schema.common.ModelConstants.ORG_ORG_RELTYPE; import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.dataInfo; import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.field; import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.listKeyValues; @@ -39,7 +38,6 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.actionmanager.ror.model.ExternalIdType; -import eu.dnetlib.dhp.actionmanager.ror.model.Relationship; import eu.dnetlib.dhp.actionmanager.ror.model.RorOrganization; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; @@ -51,7 +49,6 @@ import eu.dnetlib.dhp.schema.oaf.KeyValue; import eu.dnetlib.dhp.schema.oaf.Oaf; import eu.dnetlib.dhp.schema.oaf.Organization; import eu.dnetlib.dhp.schema.oaf.Qualifier; -import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.StructuredProperty; import eu.dnetlib.dhp.utils.DHPUtils; import scala.Tuple2; @@ -64,21 +61,17 @@ public class GenerateRorActionSetJob { private static final String ROR_NS_PREFIX = "ror_________"; - private static final List ROR_COLLECTED_FROM = listKeyValues( - "10|openaire____::993a7ae7a863813cf95028b50708e222", "ROR"); + private static final List ROR_COLLECTED_FROM = listKeyValues("10|openaire____::993a7ae7a863813cf95028b50708e222", "ROR"); - private static final DataInfo ROR_DATA_INFO = dataInfo( - false, "", false, false, ENTITYREGISTRY_PROVENANCE_ACTION, "0.92"); + private static final DataInfo ROR_DATA_INFO = dataInfo(false, "", false, false, ENTITYREGISTRY_PROVENANCE_ACTION, "0.92"); - private static final Qualifier ROR_PID_TYPE = qualifier( - "ROR", "ROR", ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES); + private static final Qualifier ROR_PID_TYPE = qualifier("ROR", "ROR", ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES); public static void main(final String[] args) throws Exception { final String jsonConfiguration = IOUtils - .toString( - GenerateRorActionSetJob.class - .getResourceAsStream("/eu/dnetlib/dhp/actionmanager/ror/action_set_parameters.json")); + .toString(GenerateRorActionSetJob.class + .getResourceAsStream("/eu/dnetlib/dhp/actionmanager/ror/action_set_parameters.json")); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); @@ -116,9 +109,8 @@ public class GenerateRorActionSetJob { readInputPath(spark, inputPath) .map(GenerateRorActionSetJob::convertRorOrg) .flatMap(List::iterator) - .mapToPair( - aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), - new Text(OBJECT_MAPPER.writeValueAsString(aa)))) + .mapToPair(aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), + new Text(OBJECT_MAPPER.writeValueAsString(aa)))) .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class); } @@ -153,12 +145,9 @@ public class GenerateRorActionSetJob { o.setEcnutscode(null); if (r.getCountry() != null) { o - .setCountry( - qualifier( - r.getCountry().getCountryCode(), r - .getCountry() - .getCountryName(), - ModelConstants.DNET_COUNTRY_TYPE, ModelConstants.DNET_COUNTRY_TYPE)); + .setCountry(qualifier(r.getCountry().getCountryCode(), r + .getCountry() + .getCountryName(), ModelConstants.DNET_COUNTRY_TYPE, ModelConstants.DNET_COUNTRY_TYPE)); } else { o.setCountry(null); } @@ -168,38 +157,10 @@ public class GenerateRorActionSetJob { final List> res = new ArrayList<>(); res.add(new AtomicAction<>(Organization.class, o)); - for (final Relationship rorRel : r.getRelationships()) { - if (rorRel.getType().equalsIgnoreCase("parent")) { - final String orgId1 = calculateOpenaireId(r.getId()); - final String orgId2 = calculateOpenaireId(rorRel.getId()); - res - .add( - new AtomicAction<>(Relation.class, - calculateHierarchyRel(orgId1, orgId2, ModelConstants.IS_PARENT_OF))); - res - .add( - new AtomicAction<>(Relation.class, - calculateHierarchyRel(orgId2, orgId1, ModelConstants.IS_CHILD_OF))); - } - } - return res; } - private static Relation calculateHierarchyRel(final String source, final String target, final String relClass) { - final Relation rel = new Relation(); - rel.setSource(source); - rel.setTarget(target); - rel.setRelType(ORG_ORG_RELTYPE); - rel.setSubRelType(ModelConstants.RELATIONSHIP); - rel.setRelClass(relClass); - rel.setCollectedfrom(ROR_COLLECTED_FROM); - rel.setDataInfo(ROR_DATA_INFO); - rel.setLastupdatetimestamp(System.currentTimeMillis()); - return rel; - } - private static String calculateOpenaireId(final String rorId) { return String.format("20|%s::%s", ROR_NS_PREFIX, DHPUtils.md5(rorId)); } @@ -212,8 +173,7 @@ public class GenerateRorActionSetJob { final String type = e.getKey(); final List all = e.getValue().getAll(); if (all != null) { - final Qualifier qualifier = qualifier( - type, type, ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES); + final Qualifier qualifier = qualifier(type, type, ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES); for (final String pid : all) { pids .add(structuredProperty(pid, qualifier, ROR_DATA_INFO)); From 52cb086506161dfdbd98a331b4ff004e5fb8f2bd Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 16 May 2022 12:07:40 +0200 Subject: [PATCH 08/23] [graph grouping] drop relation target path before copying from source --- .../dnetlib/dhp/oa/graph/group/oozie_app/workflow.xml | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/group/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/group/oozie_app/workflow.xml index f77b46105..888a873c5 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/group/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/group/oozie_app/workflow.xml @@ -283,7 +283,15 @@ - + + + + + + + + + From 8dd5517548d1224e5067c4f48c68bda5817431ca Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 16 May 2022 14:35:24 +0200 Subject: [PATCH 09/23] code formatting --- .../ror/GenerateRorActionSetJob.java | 31 +++++++---- .../doiboost/SparkGenerateDoiBoost.scala | 52 ++++++++----------- 2 files changed, 43 insertions(+), 40 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java index 6c76f8a4d..6b5bed5b8 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java @@ -61,17 +61,21 @@ public class GenerateRorActionSetJob { private static final String ROR_NS_PREFIX = "ror_________"; - private static final List ROR_COLLECTED_FROM = listKeyValues("10|openaire____::993a7ae7a863813cf95028b50708e222", "ROR"); + private static final List ROR_COLLECTED_FROM = listKeyValues( + "10|openaire____::993a7ae7a863813cf95028b50708e222", "ROR"); - private static final DataInfo ROR_DATA_INFO = dataInfo(false, "", false, false, ENTITYREGISTRY_PROVENANCE_ACTION, "0.92"); + private static final DataInfo ROR_DATA_INFO = dataInfo( + false, "", false, false, ENTITYREGISTRY_PROVENANCE_ACTION, "0.92"); - private static final Qualifier ROR_PID_TYPE = qualifier("ROR", "ROR", ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES); + private static final Qualifier ROR_PID_TYPE = qualifier( + "ROR", "ROR", ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES); public static void main(final String[] args) throws Exception { final String jsonConfiguration = IOUtils - .toString(GenerateRorActionSetJob.class - .getResourceAsStream("/eu/dnetlib/dhp/actionmanager/ror/action_set_parameters.json")); + .toString( + GenerateRorActionSetJob.class + .getResourceAsStream("/eu/dnetlib/dhp/actionmanager/ror/action_set_parameters.json")); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); @@ -109,8 +113,9 @@ public class GenerateRorActionSetJob { readInputPath(spark, inputPath) .map(GenerateRorActionSetJob::convertRorOrg) .flatMap(List::iterator) - .mapToPair(aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), - new Text(OBJECT_MAPPER.writeValueAsString(aa)))) + .mapToPair( + aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), + new Text(OBJECT_MAPPER.writeValueAsString(aa)))) .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class); } @@ -145,9 +150,12 @@ public class GenerateRorActionSetJob { o.setEcnutscode(null); if (r.getCountry() != null) { o - .setCountry(qualifier(r.getCountry().getCountryCode(), r - .getCountry() - .getCountryName(), ModelConstants.DNET_COUNTRY_TYPE, ModelConstants.DNET_COUNTRY_TYPE)); + .setCountry( + qualifier( + r.getCountry().getCountryCode(), r + .getCountry() + .getCountryName(), + ModelConstants.DNET_COUNTRY_TYPE, ModelConstants.DNET_COUNTRY_TYPE)); } else { o.setCountry(null); } @@ -173,7 +181,8 @@ public class GenerateRorActionSetJob { final String type = e.getKey(); final List all = e.getValue().getAll(); if (all != null) { - final Qualifier qualifier = qualifier(type, type, ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES); + final Qualifier qualifier = qualifier( + type, type, ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES); for (final String pid : all) { pids .add(structuredProperty(pid, qualifier, ROR_DATA_INFO)); diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala index fbe42ef7c..72b93749b 100644 --- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala +++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala @@ -177,43 +177,37 @@ object SparkGenerateDoiBoost { .map(DoiBoostMappingUtil.fixPublication) .map(p => (p.getId, p)) .groupByKey(_._1) - .reduceGroups((left, right) => - { - //Check left is not null - if (left != null && left._1 != null) - { - //If right is null then return left - if (right == null || right._2 == null) - left - else { - // Here Left and Right are not null - // So we have to merge - val b1 = left._2 - val b2 = right._2 - b1.mergeFrom(b2) - b1.mergeOAFDataInfo(b2) - val authors = AuthorMerger.mergeAuthor(b1.getAuthor, b2.getAuthor) - b1.setAuthor(authors) - if (b2.getId != null && b2.getId.nonEmpty) - b1.setId(b2.getId) - //Return publication Merged - (b1.getId, b1) - } - } + .reduceGroups((left, right) => { + //Check left is not null + if (left != null && left._1 != null) { + //If right is null then return left + if (right == null || right._2 == null) + left else { - // Left is Null so we return right - right + // Here Left and Right are not null + // So we have to merge + val b1 = left._2 + val b2 = right._2 + b1.mergeFrom(b2) + b1.mergeOAFDataInfo(b2) + val authors = AuthorMerger.mergeAuthor(b1.getAuthor, b2.getAuthor) + b1.setAuthor(authors) + if (b2.getId != null && b2.getId.nonEmpty) + b1.setId(b2.getId) + //Return publication Merged + (b1.getId, b1) } + } else { + // Left is Null so we return right + right } - - ) - .filter(s => s!= null && s._2!=null) + }) + .filter(s => s != null && s._2 != null) .map(s => s._2._2) .write .mode(SaveMode.Overwrite) .save(s"$workingDirPath/doiBoostPublicationFiltered") - val affiliationPath = parser.get("affiliationPath") val paperAffiliationPath = parser.get("paperAffiliationPath") From 1dda11e0319eebe5ec3a772b1fafd6c75912ff56 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 16 May 2022 15:53:27 +0200 Subject: [PATCH 10/23] [hb patch] updated map --- .../eu/dnetlib/dhp/datacite/hostedBy_map.json | 15 ++++++++++----- 1 file changed, 10 insertions(+), 5 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/hostedBy_map.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/hostedBy_map.json index 947a9a255..ecae6811a 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/hostedBy_map.json +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/hostedBy_map.json @@ -15,7 +15,7 @@ "official_name": "Aperta TÜBİTAK Open Archive" }, "BL.CAM": { - "openaire_id": "re3data_____::r3d100010620", + "openaire_id": "opendoar____::109", "datacite_name": "Apollo", "official_name": "Apollo" }, @@ -196,7 +196,7 @@ }, "CSIC.DIGITAL": { "openaire_id": "re3data_____::r3d100011076", - "datacite_name": "DIGITAL.CSIC", + "datacite_name": "Digital CSIC", "official_name": "DIGITAL.CSIC" }, "BL.DRI": { @@ -644,6 +644,11 @@ "datacite_name": "PANGAEA", "official_name": "PANGAEA" }, + "TIB.PANGAEA": { + "openaire_id": "re3data_____::r3d100010134", + "datacite_name": "PANGAEA", + "official_name": "PANGAEA" + }, "NASAPDS.NASAPDS": { "openaire_id": "re3data_____::r3d100010121", "datacite_name": "PDS", @@ -896,7 +901,7 @@ }, "FIGSHARE.UCT": { "openaire_id": "re3data_____::r3d100012633", - "datacite_name": "ZivaHub", + "datacite_name": "University of Cape Town (UCT)", "official_name": "ZivaHub" }, "BL.UCLAN": { @@ -1030,9 +1035,9 @@ "official_name": "ZBW Journal Data Archive" }, "CERN.ZENODO": { - "openaire_id": "re3data_____::r3d100010468", + "openaire_id": "opendoar____::2659", "datacite_name": "Zenodo", - "official_name": "Zenodo" + "official_name": "ZENODO" }, "ZBW.ZEW": { "openaire_id": "re3data_____::r3d100010399", From ab8868bd3a5b170efc1d2fdc62812a6b308c589f Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 8 Jun 2022 17:03:15 +0200 Subject: [PATCH 11/23] [ZENODO-API] changed to iterate in all the deposited products and not just the last ten --- .../dhp/common/api/ZenodoAPIClient.java | 29 ++++++++++++------- 1 file changed, 18 insertions(+), 11 deletions(-) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/ZenodoAPIClient.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/ZenodoAPIClient.java index 3f5c6ad4a..56366bc72 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/ZenodoAPIClient.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/ZenodoAPIClient.java @@ -191,7 +191,7 @@ public class ZenodoAPIClient implements Serializable { * @throws MissingConceptDoiException */ public int newVersion(String concept_rec_id) throws IOException, MissingConceptDoiException { - setDepositionId(concept_rec_id); + setDepositionId(concept_rec_id, 1); String json = "{}"; OkHttpClient httpClient = new OkHttpClient.Builder().connectTimeout(600, TimeUnit.SECONDS).build(); @@ -253,9 +253,9 @@ public class ZenodoAPIClient implements Serializable { } - private void setDepositionId(String concept_rec_id) throws IOException, MissingConceptDoiException { + private void setDepositionId(String concept_rec_id, Integer page) throws IOException, MissingConceptDoiException { - ZenodoModelList zenodoModelList = new Gson().fromJson(getPrevDepositions(), ZenodoModelList.class); + ZenodoModelList zenodoModelList = new Gson().fromJson(getPrevDepositions(String.valueOf(page)), ZenodoModelList.class); for (ZenodoModel zm : zenodoModelList) { if (zm.getConceptrecid().equals(concept_rec_id)) { @@ -263,20 +263,26 @@ public class ZenodoAPIClient implements Serializable { return; } } - - throw new MissingConceptDoiException("The concept record id specified was missing in the list of depositions"); + if(zenodoModelList.size() == 0) + throw new MissingConceptDoiException("The concept record id specified was missing in the list of depositions"); + setDepositionId(concept_rec_id, page + 1); } - private String getPrevDepositions() throws IOException { + private String getPrevDepositions(String page) throws IOException { + OkHttpClient httpClient = new OkHttpClient.Builder().connectTimeout(600, TimeUnit.SECONDS).build(); + HttpUrl.Builder urlBuilder = HttpUrl.parse(urlString).newBuilder(); + urlBuilder.addQueryParameter("page", page); + String url = urlBuilder.build().toString(); + Request request = new Request.Builder() - .url(urlString) - .addHeader(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString()) // add request headers - .addHeader(HttpHeaders.AUTHORIZATION, "Bearer " + access_token) - .get() - .build(); + .url(url) + .addHeader(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString()) // add request headers + .addHeader(HttpHeaders.AUTHORIZATION, "Bearer " + access_token) + .get() + .build(); try (Response response = httpClient.newCall(request).execute()) { @@ -289,6 +295,7 @@ public class ZenodoAPIClient implements Serializable { } + private String getBucket(String url) throws IOException { OkHttpClient httpClient = new OkHttpClient.Builder() .connectTimeout(600, TimeUnit.SECONDS) From b94a791bc5fe023aaeb43453c1fe4042e9441d24 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Thu, 9 Jun 2022 12:25:34 +0200 Subject: [PATCH 12/23] unit tests to transform cnr explora --- .../transformation/TransformationJobTest.java | 49 +++- .../dnetlib/dhp/transform/cnr_explora_tr.xslt | 214 ++++++++++++++ .../dhp/transform/input_cnr_explora.xml | 57 ++++ .../eu/dnetlib/dhp/transform/synonyms.txt | 266 +++++++++++++++++- .../eu/dnetlib/dhp/transform/terms.txt | 135 ++++++++- 5 files changed, 704 insertions(+), 17 deletions(-) create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/cnr_explora_tr.xslt create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/input_cnr_explora.xml diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java index 7bd7baaea..fea7b53ac 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java @@ -19,7 +19,9 @@ import org.apache.spark.sql.Encoder; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; import org.apache.spark.util.LongAccumulator; -import org.junit.jupiter.api.*; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.DisplayName; +import org.junit.jupiter.api.Test; import org.junit.jupiter.api.extension.ExtendWith; import org.junit.jupiter.api.io.TempDir; import org.mockito.junit.jupiter.MockitoExtension; @@ -50,7 +52,7 @@ class TransformationJobTest extends AbstractVocabularyTest { @Test @DisplayName("Test Date cleaner") void testDateCleaner() throws Exception { - DateCleaner dc = new DateCleaner(); + final DateCleaner dc = new DateCleaner(); assertEquals("1982-09-20", dc.clean("20/09/1982")); assertEquals("2002-09-20", dc.clean("20-09-2002")); assertEquals("2002-09-20", dc.clean("2002-09-20")); @@ -68,9 +70,9 @@ class TransformationJobTest extends AbstractVocabularyTest { mr.setProvenance(new Provenance("DSID", "DSNAME", "PREFIX")); mr.setBody(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/transform/input_zenodo.xml"))); // We Load the XSLT transformation Rule from the classpath - XSLTTransformationFunction tr = loadTransformationRule("/eu/dnetlib/dhp/transform/zenodo_tr.xslt"); + final XSLTTransformationFunction tr = loadTransformationRule("/eu/dnetlib/dhp/transform/zenodo_tr.xslt"); - MetadataRecord result = tr.call(mr); + final MetadataRecord result = tr.call(mr); // Print the record System.out.println(result.getBody()); @@ -86,9 +88,9 @@ class TransformationJobTest extends AbstractVocabularyTest { mr.setProvenance(new Provenance("DSID", "DSNAME", "PREFIX")); mr.setBody(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/transform/input_itgv4.xml"))); // We Load the XSLT transformation Rule from the classpath - XSLTTransformationFunction tr = loadTransformationRule("/eu/dnetlib/dhp/transform/zenodo_tr.xslt"); + final XSLTTransformationFunction tr = loadTransformationRule("/eu/dnetlib/dhp/transform/zenodo_tr.xslt"); - MetadataRecord result = tr.call(mr); + final MetadataRecord result = tr.call(mr); // Print the record System.out.println(result.getBody()); @@ -108,9 +110,9 @@ class TransformationJobTest extends AbstractVocabularyTest { mr.setProvenance(new Provenance("DSID", "DSNAME", "PREFIX")); mr.setBody(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/transform/input_itgv4.xml"))); // We Load the XSLT transformation Rule from the classpath - XSLTTransformationFunction tr = loadTransformationRule(xslTransformationScript); + final XSLTTransformationFunction tr = loadTransformationRule(xslTransformationScript); - MetadataRecord result = tr.call(mr); + final MetadataRecord result = tr.call(mr); // Print the record System.out.println(result.getBody()); @@ -129,9 +131,9 @@ class TransformationJobTest extends AbstractVocabularyTest { mr.setProvenance(new Provenance("DSID", "DSNAME", "PREFIX")); mr.setBody(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/transform/input_omicsdi.xml"))); // We Load the XSLT transformation Rule from the classpath - XSLTTransformationFunction tr = loadTransformationRule(xslTransformationScript); + final XSLTTransformationFunction tr = loadTransformationRule(xslTransformationScript); - MetadataRecord result = tr.call(mr); + final MetadataRecord result = tr.call(mr); // Print the record System.out.println(result.getBody()); @@ -140,7 +142,7 @@ class TransformationJobTest extends AbstractVocabularyTest { @Test @DisplayName("Test TransformSparkJobNode.main with oaiOpenaire_datacite (v4)") - void transformTestITGv4OAIdatacite(@TempDir Path testDir) throws Exception { + void transformTestITGv4OAIdatacite(@TempDir final Path testDir) throws Exception { try (SparkSession spark = SparkSession.builder().config(sparkConf).getOrCreate()) { @@ -150,9 +152,7 @@ class TransformationJobTest extends AbstractVocabularyTest { .getFile(); final String mdstore_output = testDir.toString() + "/version"; - mockupTrasformationRule( - "simpleTRule", - "/eu/dnetlib/dhp/transform/scripts/xslt_cleaning_oaiOpenaire_datacite_ExchangeLandingpagePid.xsl"); + mockupTrasformationRule("simpleTRule", "/eu/dnetlib/dhp/transform/scripts/xslt_cleaning_oaiOpenaire_datacite_ExchangeLandingpagePid.xsl"); final Map parameters = Stream.of(new String[][] { { @@ -203,7 +203,7 @@ class TransformationJobTest extends AbstractVocabularyTest { @Test @DisplayName("Test TransformSparkJobNode.main") - void transformTest(@TempDir Path testDir) throws Exception { + void transformTest(@TempDir final Path testDir) throws Exception { try (SparkSession spark = SparkSession.builder().config(sparkConf).getOrCreate()) { @@ -256,6 +256,25 @@ class TransformationJobTest extends AbstractVocabularyTest { } } + @Test + @DisplayName("Test Transform Single XML using cnr_explora_tr XSLTTransformator") + void testCnrExploraTransformSaxonHE() throws Exception { + + // We Set the input Record getting the XML from the classpath + final MetadataRecord mr = new MetadataRecord(); + + mr.setProvenance(new Provenance("openaire____::cnr_explora", "CNR ExploRA", "cnr_________")); + mr.setBody(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/transform/input_cnr_explora.xml"))); + // We Load the XSLT transformation Rule from the classpath + final XSLTTransformationFunction tr = loadTransformationRule("/eu/dnetlib/dhp/transform/cnr_explora_tr.xslt"); + + final MetadataRecord result = tr.call(mr); + + // Print the record + System.out.println(result.getBody()); + // TODO Create significant Assert + } + private XSLTTransformationFunction loadTransformationRule(final String path) throws Exception { final String trValue = IOUtils.toString(this.getClass().getResourceAsStream(path)); final LongAccumulator la = new LongAccumulator(); diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/cnr_explora_tr.xslt b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/cnr_explora_tr.xslt new file mode 100644 index 000000000..78b167fde --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/cnr_explora_tr.xslt @@ -0,0 +1,214 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/input_cnr_explora.xml b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/input_cnr_explora.xml new file mode 100644 index 000000000..220c4ddbe --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/input_cnr_explora.xml @@ -0,0 +1,57 @@ + + +
+ + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/synonyms.txt b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/synonyms.txt index 4fd95554a..74a75e46a 100644 --- a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/synonyms.txt +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/synonyms.txt @@ -1232,4 +1232,268 @@ dnet:review_levels @=@ 0001 @=@ 印刷物/電子媒体-学術雑誌論文(査 dnet:review_levels @=@ 0001 @=@ 印刷物/電子媒体-紀要論文(査読有り) dnet:review_levels @=@ 0001 @=@ 印刷物/電子媒体-雑誌記事(査読有り) dnet:review_levels @=@ 0001 @=@ 原著論文(査読有り) -dnet:review_levels @=@ 0001 @=@ 査読論文 \ No newline at end of file +dnet:review_levels @=@ 0001 @=@ 査読論文 +cnr:institutes @=@ https://ror.org/00brf2d87 @=@ CDS001 +cnr:institutes @=@ https://ror.org/00brf2d87 @=@ IDASC - Istituto di Acustica e Sensoristica \"Orso Mario Corbino\" +cnr:institutes @=@ https://ror.org/006qkqr45 @=@ CDS002 +cnr:institutes @=@ https://ror.org/006qkqr45 @=@ IAMC - Istituto per l'ambiente marino costiero +cnr:institutes @=@ https://ror.org/054ye0e45 @=@ CDS003 +cnr:institutes @=@ https://ror.org/054ye0e45 @=@ IASI - Istituto di analisi dei sistemi ed informatica \"Antonio Ruberti\" +cnr:institutes @=@ https://ror.org/00ygy3d85 @=@ CDS004 +cnr:institutes @=@ https://ror.org/00ygy3d85 @=@ IAC - Istituto per le applicazioni del calcolo \"Mauro Picone\" +cnr:institutes @=@ https://ror.org/000sy1f36 @=@ CDS005 +cnr:institutes @=@ https://ror.org/000sy1f36 @=@ IASF - Istituto di astrofisica spaziale e fisica cosmica +cnr:institutes @=@ https://ror.org/00x5wpm25 @=@ CDS006 +cnr:institutes @=@ https://ror.org/00x5wpm25 @=@ IBAM - Istituto per i beni archeologici e monumentali +cnr:institutes @=@ https://ror.org/03eqeqg74 @=@ CDS007 +cnr:institutes @=@ https://ror.org/03eqeqg74 @=@ IBP - Istituto di biochimica delle proteine +cnr:institutes @=@ https://ror.org/041xzk838 @=@ CDS008 +cnr:institutes @=@ 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- Istituto di cristallografia +cnr:institutes @=@ https://ror.org/03z58xd74 @=@ CDS028 +cnr:institutes @=@ https://ror.org/03z58xd74 @=@ IDPA - Istituto per la dinamica dei processi ambientali +cnr:institutes @=@ https://ror.org/00n4jbh84 @=@ CDS029 +cnr:institutes @=@ https://ror.org/00n4jbh84 @=@ IEIIT - Istituto di elettronica e di ingegneria dell'informazione e delle telecomunicazioni +cnr:institutes @=@ https://ror.org/04sn06036 @=@ CDS030 +cnr:institutes @=@ https://ror.org/04sn06036 @=@ IEOS - Istituto per l'endocrinologia e l'oncologia \"Gaetano Salvatore\" +cnr:institutes @=@ https://ror.org/01rg40y89 @=@ CDS031 +cnr:institutes @=@ https://ror.org/01rg40y89 @=@ ICMATE - Istituto di Chimica della Materia Condensata e di Tecnologie per l'Energia +cnr:institutes @=@ https://ror.org/00dqega85 @=@ CDS032 +cnr:institutes @=@ https://ror.org/00dqega85 @=@ IFAC - Istituto di fisica applicata \"Nello Carrara\" +cnr:institutes @=@ https://ror.org/02n2bgz18 @=@ CDS033 +cnr:institutes @=@ https://ror.org/02n2bgz18 @=@ IFP - Istituto di fisica del plasma \"Piero Caldirola\" +cnr:institutes @=@ __CDS034__ @=@ CDS034 +cnr:institutes @=@ __CDS034__ @=@ IFSI - Istituto di fisica dello spazio interplanetario +cnr:institutes @=@ https://ror.org/01kdj2848 @=@ CDS035 +cnr:institutes @=@ https://ror.org/01kdj2848 @=@ IFC - Istituto di fisiologia clinica +cnr:institutes @=@ https://ror.org/049ebw417 @=@ CDS036 +cnr:institutes @=@ https://ror.org/049ebw417 @=@ IFN - Istituto di fotonica e nanotecnologie +cnr:institutes @=@ https://ror.org/01f5tnx94 @=@ CDS037 +cnr:institutes @=@ https://ror.org/01f5tnx94 @=@ IGI - Istituto gas ionizzati +cnr:institutes @=@ __CDS038__ @=@ CDS038 +cnr:institutes @=@ __CDS038__ @=@ IGP - Istituto di genetica delle popolazioni +cnr:institutes @=@ https://ror.org/04hadk112 @=@ CDS039 +cnr:institutes @=@ https://ror.org/04hadk112 @=@ IGB - Istituto di genetica e biofisica \"Adriano Buzzati Traverso\" +cnr:institutes @=@ https://ror.org/03qpd8w66 @=@ CDS040 +cnr:institutes @=@ https://ror.org/03qpd8w66 @=@ IGM - Istituto di genetica molecolare \"Luigi Luca Cavalli Sforza\" +cnr:institutes @=@ https://ror.org/01gtsa866 @=@ CDS041 +cnr:institutes @=@ https://ror.org/01gtsa866 @=@ IBBR - Istituto di Bioscienze e Biorisorse +cnr:institutes @=@ https://ror.org/00ytw6m58 @=@ CDS042 +cnr:institutes @=@ https://ror.org/00ytw6m58 @=@ IGAG - Istituto di geologia ambientale e geoingegneria +cnr:institutes @=@ https://ror.org/015bmra78 @=@ CDS043 +cnr:institutes @=@ https://ror.org/015bmra78 @=@ IGG - Istituto di geoscienze e georisorse +cnr:institutes @=@ https://ror.org/02gdcn153 @=@ CDS044 +cnr:institutes @=@ https://ror.org/02gdcn153 @=@ IIT - Istituto di informatica e telematica +cnr:institutes @=@ __CDS045__ @=@ CDS045 +cnr:institutes @=@ __CDS045__ @=@ ISIB - Istituto di ingegneria biomedica +cnr:institutes @=@ https://ror.org/05hky6p02 @=@ CDS046 +cnr:institutes @=@ https://ror.org/05hky6p02 @=@ IIA - Istituto sull'inquinamento atmosferico +cnr:institutes @=@ https://ror.org/011n2hw53 @=@ CDS047 +cnr:institutes @=@ https://ror.org/011n2hw53 @=@ ILIESI - Istituto per il lessico intellettuale europeo e storia delle idee +cnr:institutes @=@ https://ror.org/028g3pe33 @=@ CDS048 +cnr:institutes @=@ https://ror.org/028g3pe33 @=@ ILC - Istituto di linguistica computazionale \"Antonio Zampolli\" +cnr:institutes @=@ __CDS049__ @=@ CDS049 +cnr:institutes @=@ __CDS049__ @=@ IMAMOTER - Istituto per le macchine agricole e movimento terra +cnr:institutes @=@ https://ror.org/03m0n3c07 @=@ CDS050 +cnr:institutes @=@ https://ror.org/03m0n3c07 @=@ IMATI - Istituto di matematica applicata e tecnologie informatiche \"Enrico Magenes\" +cnr:institutes @=@ __CDS051__ @=@ CDS051 +cnr:institutes @=@ __CDS051__ @=@ IMCB - Istituto per i materiali compositi e biomedici +cnr:institutes @=@ https://ror.org/00z8ws214 @=@ CDS052 +cnr:institutes @=@ https://ror.org/00z8ws214 @=@ IMEM - Istituto dei materiali per l'elettronica ed il magnetismo +cnr:institutes @=@ __CDS053__ @=@ CDS053 +cnr:institutes @=@ __CDS053__ @=@ ISB - Istituto per i Sistemi Biologici +cnr:institutes @=@ https://ror.org/00bc51d88 @=@ CDS054 +cnr:institutes @=@ https://ror.org/00bc51d88 @=@ NANOTEC - Istituto di Nanotecnologia +cnr:institutes @=@ https://ror.org/024ye7w89 @=@ CDS055 +cnr:institutes @=@ https://ror.org/024ye7w89 @=@ IMAA - Istituto di metodologie per l'analisi ambientale +cnr:institutes @=@ __CDS056__ @=@ CDS056 +cnr:institutes @=@ __CDS056__ @=@ IMGC - Istituto di metrologia \"Gustavo Colonnetti\" +cnr:institutes @=@ https://ror.org/05vk2g845 @=@ CDS057 +cnr:institutes @=@ https://ror.org/05vk2g845 @=@ IMM - Istituto per la microelettronica e microsistemi +cnr:institutes @=@ https://ror.org/02qwy8e97 @=@ CDS058 +cnr:institutes @=@ https://ror.org/02qwy8e97 @=@ IM - Istituto motori +cnr:institutes @=@ __CDS059__ @=@ CDS059 +cnr:institutes @=@ __CDS059__ @=@ INMM - Istituto di neurobiologia e medicina molecolare +cnr:institutes @=@ https://ror.org/02dr63s31 @=@ CDS060 +cnr:institutes @=@ https://ror.org/02dr63s31 @=@ IRGB - Istituto di Ricerca Genetica e Biomedica +cnr:institutes @=@ https://ror.org/0240rwx68 @=@ CDS061 +cnr:institutes @=@ https://ror.org/0240rwx68 @=@ IN - Istituto di neuroscienze +cnr:institutes @=@ https://ror.org/02rzxrg25 @=@ CDS062 +cnr:institutes @=@ https://ror.org/02rzxrg25 @=@ OVI - Istituto opera del vocabolario italiano +cnr:institutes @=@ https://ror.org/05patmk97 @=@ CDS063 +cnr:institutes @=@ https://ror.org/05patmk97 @=@ IPCF - Istituto per i processi chimico-fisici +cnr:institutes @=@ __CDS064__ @=@ CDS064 +cnr:institutes @=@ __CDS064__ @=@ IPP - Istituto per la protezione delle piante +cnr:institutes @=@ https://ror.org/029st3z03 @=@ CDS065 +cnr:institutes @=@ https://ror.org/029st3z03 @=@ IRA - Istituto di radioastronomia +cnr:institutes @=@ https://ror.org/0040zx077 @=@ CDS066 +cnr:institutes @=@ https://ror.org/0040zx077 @=@ IRPI - Istituto di ricerca per la protezione idrogeologica +cnr:institutes @=@ https://ror.org/044bfsy89 @=@ CDS067 +cnr:institutes @=@ https://ror.org/044bfsy89 @=@ IRCRES - Istituto di Ricerca sulla Crescita Economica Sostenibile +cnr:institutes @=@ https://ror.org/01n1ayq61 @=@ CDS068 +cnr:institutes @=@ https://ror.org/01n1ayq61 @=@ IRPPS - Istituto di ricerche sulla popolazione e le politiche sociali +cnr:institutes @=@ https://ror.org/02db0kh50 @=@ CDS069 +cnr:institutes @=@ https://ror.org/02db0kh50 @=@ IRSA - Istituto di ricerca sulle acque +cnr:institutes @=@ https://ror.org/05813wx75 @=@ CDS070 +cnr:institutes @=@ https://ror.org/05813wx75 @=@ IRC - Istituto di ricerche sulla combustione +cnr:institutes @=@ https://ror.org/04vnwke91 @=@ CDS071 +cnr:institutes @=@ https://ror.org/04vnwke91 @=@ IRISS - Istituto di Ricerca su Innovazione e Servizi per lo Sviluppo +cnr:institutes @=@ https://ror.org/02wxw4x45 @=@ CDS072 +cnr:institutes @=@ https://ror.org/02wxw4x45 @=@ IREA - Istituto per il rilevamento elettromagnetico dell'ambiente +cnr:institutes @=@ https://ror.org/01j6drw72 @=@ CDS073 +cnr:institutes @=@ https://ror.org/01j6drw72 @=@ ISTEC - Istituto di scienza e tecnologia dei materiali ceramici +cnr:institutes @=@ https://ror.org/05kacka20 @=@ CDS074 +cnr:institutes @=@ https://ror.org/05kacka20 @=@ ISTI - Istituto di scienza e tecnologie dell'informazione \"Alessandro Faedo\" +cnr:institutes @=@ https://ror.org/00n8ttd98 @=@ CDS075 +cnr:institutes @=@ https://ror.org/00n8ttd98 @=@ ISAC - Istituto di scienze dell'atmosfera e del clima +cnr:institutes @=@ https://ror.org/0013zhk30 @=@ CDS076 +cnr:institutes @=@ https://ror.org/0013zhk30 @=@ ISA - Istituto di Scienze dell'Alimentazione +cnr:institutes @=@ https://ror.org/03x7xkr71 @=@ CDS077 +cnr:institutes @=@ https://ror.org/03x7xkr71 @=@ ISPA - Istituto di scienze delle produzioni alimentari +cnr:institutes @=@ https://ror.org/05w9g2j85 @=@ CDS078 +cnr:institutes @=@ https://ror.org/05w9g2j85 @=@ ISTC - Istituto di scienze e tecnologie della cognizione +cnr:institutes @=@ https://ror.org/032tyv240 @=@ CDS079 +cnr:institutes @=@ https://ror.org/032tyv240 @=@ ISTM - Istituto di scienze e tecnologie molecolari +cnr:institutes @=@ https://ror.org/02hdf6119 @=@ CDS080 +cnr:institutes @=@ https://ror.org/02hdf6119 @=@ ISMAR - Istituto di scienze marine +cnr:institutes @=@ https://ror.org/01yg57d71 @=@ CDS081 +cnr:institutes @=@ https://ror.org/01yg57d71 @=@ ISN - Istituto di scienze neurologiche +cnr:institutes @=@ https://ror.org/021z1mz76 @=@ CDS082 +cnr:institutes @=@ https://ror.org/021z1mz76 @=@ ISOF - Istituto per la sintesi organica e la fotoreattività +cnr:institutes @=@ https://ror.org/01wqae691 @=@ CDS083 +cnr:institutes @=@ https://ror.org/01wqae691 @=@ ISPAAM - Istituto per il sistema produzione animale in ambiente Mediterraneo +cnr:institutes @=@ __CDS084__ @=@ CDS084 +cnr:institutes @=@ __CDS084__ @=@ ISAFoM - Istituto per i sistemi agricoli e forestali del mediterraneo +cnr:institutes @=@ https://ror.org/00awwz417 @=@ CDS085 +cnr:institutes @=@ https://ror.org/00awwz417 @=@ ISPF - Istituto per la storia del pensiero filosofico e scientifico moderno +cnr:institutes @=@ https://ror.org/03a111314 @=@ CDS086 +cnr:institutes @=@ https://ror.org/03a111314 @=@ ISEM - Istituto di storia dell'Europa mediterranea +cnr:institutes @=@ https://ror.org/01zz9wh30 @=@ CDS087 +cnr:institutes @=@ https://ror.org/01zz9wh30 @=@ ISM - Istituto di struttura della materia +cnr:institutes @=@ https://ror.org/035y5td47 @=@ CDS088 +cnr:institutes @=@ https://ror.org/035y5td47 @=@ ISGI - Istituto di studi giuridici internazionali +cnr:institutes @=@ __CDS089__ @=@ CDS089 +cnr:institutes @=@ __CDS089__ @=@ ISPRI - Istituto sperimentale di studi socio - economici sull'innovazione e le politiche della ricerca +cnr:institutes @=@ https://ror.org/051t1q308 @=@ CDS090 +cnr:institutes @=@ https://ror.org/051t1q308 @=@ ISSIA - Istituto di studi sui sistemi intelligenti per l'automazione +cnr:institutes @=@ https://ror.org/05k3cs357 @=@ CDS091 +cnr:institutes @=@ https://ror.org/05k3cs357 @=@ ISSIRFA - Istituto di studi sui sistemi regionali federali e sulle autonomie \"Massimo Severo Giannini\" +cnr:institutes @=@ https://ror.org/02gcxw165 @=@ CDS092 +cnr:institutes @=@ https://ror.org/02gcxw165 @=@ ISMA - Istituto di Studi sul Mediterraneo Antico +cnr:institutes @=@ https://ror.org/05db0es39 @=@ CDS093 +cnr:institutes @=@ https://ror.org/05db0es39 @=@ ISMed - Istituto di studi sul Mediterraneo +cnr:institutes @=@ https://ror.org/029k6t707 @=@ CDS094 +cnr:institutes @=@ https://ror.org/029k6t707 @=@ ISE - Istituto per lo studio degli ecosistemi +cnr:institutes @=@ https://ror.org/00w6r1881 @=@ CDS095 +cnr:institutes @=@ https://ror.org/00w6r1881 @=@ ISMN - Istituto per lo studio dei materiali nanostrutturati +cnr:institutes @=@ https://ror.org/01mfmr054 @=@ CDS096 +cnr:institutes @=@ https://ror.org/01mfmr054 @=@ ISMAC - Istituto per lo studio delle macromolecole +cnr:institutes @=@ https://ror.org/058nrs650 @=@ CDS097 +cnr:institutes @=@ https://ror.org/058nrs650 @=@ ITM - Istituto per la tecnologia delle membrane +cnr:institutes @=@ https://ror.org/0331xj092 @=@ CDS098 +cnr:institutes @=@ https://ror.org/0331xj092 @=@ ITABC - Istituto per le tecnologie applicate ai beni culturali +cnr:institutes @=@ https://ror.org/052q58629 @=@ CDS099 +cnr:institutes @=@ https://ror.org/052q58629 @=@ ITAE - Istituto di tecnologie avanzate per l'energia \"Nicola Giordano\" +cnr:institutes @=@ https://ror.org/04ehykb85 @=@ CDS100 +cnr:institutes @=@ https://ror.org/04ehykb85 @=@ ITB - Istituto di tecnologie biomediche +cnr:institutes @=@ https://ror.org/0221agg28 @=@ CDS101 +cnr:institutes @=@ https://ror.org/0221agg28 @=@ ITC - Istituto per le tecnologie della costruzione +cnr:institutes @=@ https://ror.org/02xz4xc25 @=@ CDS102 +cnr:institutes @=@ https://ror.org/02xz4xc25 @=@ ITD - Istituto per le tecnologie didattiche +cnr:institutes @=@ __CDS103__ @=@ CDS103 +cnr:institutes @=@ __CDS103__ @=@ STIIMA - Istituto di Sistemi e Tecnologie Industriali Intelligenti per il Manifatturiero Avanzato +cnr:institutes @=@ https://ror.org/01as2bh37 @=@ CDS104 +cnr:institutes @=@ https://ror.org/01as2bh37 @=@ ITTIG - Istituto di teoria e tecniche dell'informazione giuridica +cnr:institutes @=@ https://ror.org/01y5w6t76 @=@ CDS105 +cnr:institutes @=@ https://ror.org/01y5w6t76 @=@ ITOI - Istituto per i trapianti d'organo e immunocitologia +cnr:institutes @=@ https://ror.org/04xy2mq71 @=@ CDS106 +cnr:institutes @=@ https://ror.org/04xy2mq71 @=@ IVALSA - Istituto per la valorizzazione del legno e delle specie arboree +cnr:institutes @=@ __CDS107__ @=@ CDS107 +cnr:institutes @=@ __CDS107__ @=@ IVV - Istituto di virologia vegetale +cnr:institutes @=@ https://ror.org/013nxtf56 @=@ CDS108 +cnr:institutes @=@ https://ror.org/013nxtf56 @=@ IRSIG - Istituto di ricerca sui sistemi giudiziari +cnr:institutes @=@ https://ror.org/05rcgef49 @=@ CDS109 +cnr:institutes @=@ https://ror.org/05rcgef49 @=@ ISC - Istituto dei sistemi complessi +cnr:institutes @=@ __CDS110__ @=@ CDS110 +cnr:institutes @=@ __CDS110__ @=@ INFM - Centro di responsabilità scientifica INFM +cnr:institutes @=@ https://ror.org/02dp3a879 @=@ CDS111 +cnr:institutes @=@ https://ror.org/02dp3a879 @=@ INO - Istituto nazionale di ottica +cnr:institutes @=@ __CDS112__ @=@ CDS112 +cnr:institutes @=@ __CDS112__ @=@ IDAIC - Centro di responsabilità di attività scientifica IDAIC +cnr:institutes @=@ https://ror.org/00p03yg71 @=@ CDS113 +cnr:institutes @=@ https://ror.org/00p03yg71 @=@ SPIN - Istituto superconduttori, materiali innovativi e dispositivi +cnr:institutes @=@ https://ror.org/00yfw2296 @=@ CDS114 +cnr:institutes @=@ https://ror.org/00yfw2296 @=@ IOM - Istituto officina dei materiali +cnr:institutes @=@ https://ror.org/0042e5975 @=@ CDS115 +cnr:institutes @=@ https://ror.org/0042e5975 @=@ NANO - Istituto Nanoscienze +cnr:institutes @=@ https://ror.org/03ta8pf33 @=@ CDS116 +cnr:institutes @=@ https://ror.org/03ta8pf33 @=@ IFT - Istituto di Farmacologia Traslazionale +cnr:institutes @=@ https://ror.org/040xhth73 @=@ CDS117 +cnr:institutes @=@ https://ror.org/040xhth73 @=@ IBCN - Istituto di Biologia Cellulare e Neurobiologia +cnr:institutes @=@ https://ror.org/02qnx8e75 @=@ CDS118 +cnr:institutes @=@ https://ror.org/02qnx8e75 @=@ INM - Istituto di iNgegneria del Mare +cnr:institutes @=@ https://ror.org/05nr7xa08 @=@ CDS119 +cnr:institutes @=@ https://ror.org/05nr7xa08 @=@ IPCB - Istituto per i Polimeri, Compositi e Biomateriali +cnr:institutes @=@ https://ror.org/008fjbg42 @=@ CDS121 +cnr:institutes @=@ https://ror.org/008fjbg42 @=@ IPSP - Istituto per la Protezione Sostenibile delle Piante +cnr:institutes @=@ __CDS122__ @=@ CDS122 +cnr:institutes @=@ __CDS122__ @=@ IRBIM - Istituto per le Risorse Biologiche e le Biotecnologie Marine +cnr:institutes @=@ __CDS123__ @=@ CDS123 +cnr:institutes @=@ __CDS123__ @=@ ISPC - Istituto di Scienze del Patrimonio Culturale +cnr:institutes @=@ __CDS124__ @=@ CDS124 +cnr:institutes @=@ __CDS124__ @=@ IAS - Istituto per lo studio degli impatti Antropici e Sostenibilità in ambiente marino +cnr:institutes @=@ __CDS125__ @=@ CDS125 +cnr:institutes @=@ __CDS125__ @=@ IRET - Istituto di Ricerca sugli Ecosistemi Terrestri +cnr:institutes @=@ https://ror.org/03a0vt050 @=@ CDS126 +cnr:institutes @=@ https://ror.org/03a0vt050 @=@ ISTP - Istituto per la Scienza e Tecnologia dei Plasmi +cnr:institutes @=@ __CDS127__ @=@ CDS127 +cnr:institutes @=@ __CDS127__ @=@ ISP - Istituto di Scienze Polari +cnr:institutes @=@ https://ror.org/03byxpq91 @=@ CDS128 +cnr:institutes @=@ https://ror.org/03byxpq91 @=@ IRIB - Istituto per la Ricerca e l'Innovazione Biomedica +cnr:institutes @=@ __CDS129__ @=@ CDS129 +cnr:institutes @=@ __CDS129__ @=@ IGSG - Istituto di Informatica Giuridica e Sistemi Giudiziari +cnr:institutes @=@ __CDS130__ @=@ CDS130 +cnr:institutes @=@ __CDS130__ @=@ IBBC - Istituto di Biochimica e Biologia Cellulare +cnr:institutes @=@ __CDS131__ @=@ CDS131 +cnr:institutes @=@ __CDS131__ @=@ IBE - Istituto per la BioEconomia +cnr:institutes @=@ https://ror.org/0263zy895 @=@ CDS132 +cnr:institutes @=@ https://ror.org/0263zy895 @=@ SCITEC - Istituto di Scienze e Tecnologie Chimiche \"Giulio Natta\" +cnr:institutes @=@ __CDS133__ @=@ CDS133 +cnr:institutes @=@ __CDS133__ @=@ STEMS - Istituto di Scienze e Tecnologie per l'Energia e la Mobilità Sostenibili \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/terms.txt b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/terms.txt index 93cc00eca..0f0ebaad4 100644 --- a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/terms.txt +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/terms.txt @@ -1077,4 +1077,137 @@ dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/DATASET/IS_SUPPLEMENTED dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/AUTHOR/ORCID @=@ An Open Researcher and Contributor ID (ORCID) that can be associated to an author of your publications dnet:review_levels @=@ dnet:review_levels @=@ 0000 @=@ Unknown dnet:review_levels @=@ dnet:review_levels @=@ 0002 @=@ nonPeerReviewed -dnet:review_levels @=@ dnet:review_levels @=@ 0001 @=@ peerReviewed \ No newline at end of file +dnet:review_levels @=@ dnet:review_levels @=@ 0001 @=@ peerReviewed +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/00brf2d87 @=@ https://ror.org/00brf2d87 +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/006qkqr45 @=@ https://ror.org/006qkqr45 +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/054ye0e45 @=@ https://ror.org/054ye0e45 +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/00ygy3d85 @=@ https://ror.org/00ygy3d85 +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/000sy1f36 @=@ https://ror.org/000sy1f36 +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/00x5wpm25 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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 13/23] [Graph DUMP] add code to produce the delta of new projects with respect to the previous delta/dump --- .../ProjectsSubsetSparkJob.java | 80 ++++++++ .../graph/dump/project_subset_parameters.json | 27 +++ .../oozie_app/config-default.xml | 30 +++ .../dump/projectsubset/oozie_app/workflow.xml | 171 ++++++++++++++++++ 4 files changed, 308 insertions(+) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/project_subset_parameters.json create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/oozie_app/config-default.xml create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/oozie_app/workflow.xml diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java new file mode 100644 index 000000000..67da24185 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java @@ -0,0 +1,80 @@ +package eu.dnetlib.dhp.oa.graph.dump.projectssubset; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; +import java.io.Serializable; +import java.util.List; +import java.util.Objects; +import java.util.Optional; +import java.util.stream.Collectors; +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.FilterFunction; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.jetbrains.annotations.NotNull; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.oa.graph.dump.Utils; +import eu.dnetlib.dhp.schema.dump.oaf.community.Funder; +import eu.dnetlib.dhp.schema.dump.oaf.graph.Project; +import scala.Tuple2; +public class ProjectsSubsetSparkJob implements Serializable { + private static final Logger log = LoggerFactory.getLogger(ProjectsSubsetSparkJob.class); + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + ProjectsSubsetSparkJob.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump/project_subset_parameters.json")); + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + final String inputPath = parser.get("sourcePath"); + log.info("inputPath: {}", inputPath); + final String outputPath = parser.get("outputPath"); + log.info("outputPath: {}", outputPath); + final String projectListPath = parser.get("projectListPath"); + log.info("projectListPath: {}", projectListPath); + SparkConf conf = new SparkConf(); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath); + getNewProjectList(spark, inputPath, outputPath, projectListPath); + }); + } + private static void getNewProjectList(SparkSession spark, String inputPath, String outputPath, + String projectListPath) { + Dataset projectList = spark.read().textFile(projectListPath); + // projectList.show(false); + Dataset projects; + projects = Utils.readPath(spark, inputPath, Project.class); + projects + .joinWith(projectList, projects.col("id").equalTo(projectList.col("value")), "left") + .map((MapFunction, Project>) t2 -> { + if (Optional.ofNullable(t2._2()).isPresent()) + return null; + return t2._1(); + }, Encoders.bean(Project.class)) + .filter(Objects::nonNull) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath); + Utils + .readPath(spark, outputPath, Project.class) + .map((MapFunction) p -> p.getId(), Encoders.STRING()) + .write() + .mode(SaveMode.Append) + .option("compression", "gzip") + .text(projectListPath); + } +} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/project_subset_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/project_subset_parameters.json new file mode 100644 index 000000000..ed2313680 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/project_subset_parameters.json @@ -0,0 +1,27 @@ +[ + { + "paramName":"s", + "paramLongName":"sourcePath", + "paramDescription": "the path of the sequencial file to read", + "paramRequired": true + }, + { + "paramName": "out", + "paramLongName": "outputPath", + "paramDescription": "the path used to store temporary output files", + "paramRequired": true + }, + { + "paramName": "ssm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "true if the spark session is managed, false otherwise", + "paramRequired": false + }, + { + "paramName": "pl", + "paramLongName": "projectListPath", + "paramDescription": "the path of the association result projectlist", + "paramRequired": true + } +] + diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/oozie_app/config-default.xml new file mode 100644 index 000000000..d262cb6e0 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/oozie_app/config-default.xml @@ -0,0 +1,30 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + hiveMetastoreUris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + hiveJdbcUrl + jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000 + + + hiveDbName + openaire + + + oozie.launcher.mapreduce.user.classpath.first + true + + diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/oozie_app/workflow.xml new file mode 100644 index 000000000..619e3aa20 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/oozie_app/workflow.xml @@ -0,0 +1,171 @@ + + + + sourcePath + the source path + + + projectListPath + the path to the project list + + + outputPath + the output path + + + accessToken + the access token used for the deposition in Zenodo + + + connectionUrl + the connection url for Zenodo + + + metadata + the metadata associated to the deposition + + + depositionType + the type of deposition we want to perform. "new" for brand new deposition, "version" for a new version of a published deposition (in this case the concept record id must be provided), "upload" to upload content to an open deposition for which we already have the deposition id (in this case the deposition id should be provided) + + + conceptRecordId + for new version, the id of the record for the old deposition + + + depositionId + the depositionId of a deposition open that has to be added content + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + + + spark2YarnHistoryServerAddress + spark 2.* yarn history server address + + + spark2EventLogDir + spark 2.* event log dir location + + + + ${jobTracker} + ${nameNode} + + + mapreduce.job.queuename + ${queueName} + + + oozie.launcher.mapred.job.queue.name + ${oozieLauncherQueueName} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + yarn + cluster + Dump table project + eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/project + --resultTableNameeu.dnetlib.dhp.schema.oaf.Project + --outputPath${workingDir}/project + --communityMapPathnoneed + + + + + + + yarn + cluster + Dump table project + eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectsSubsetSparkJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/project + --outputPath${workingDir}/tar/project + --projectListPath${projectListPath} + + + + + + + eu.dnetlib.dhp.oa.graph.dump.MakeTar + --hdfsPath${outputPath} + --nameNode${nameNode} + --sourcePath${workingDir}/tar + + + + + + + eu.dnetlib.dhp.oa.graph.dump.SendToZenodoHDFS + --hdfsPath${outputPath} + --nameNode${nameNode} + --accessToken${accessToken} + --connectionUrl${connectionUrl} + --metadata${metadata} + --conceptRecordId${conceptRecordId} + --depositionType${depositionType} + --depositionId${depositionId} + + + + + + \ No newline at end of file From b98f904d48a2923b13225a656510da850c07d533 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 21 Jun 2022 17:52:27 +0200 Subject: [PATCH 14/23] [Funder Products Dump] new way to avoid using hive --- .../community/SparkPrepareResultProject.java | 6 +- .../funderresults/SparkDumpFunderResults.java | 171 ++++----- .../SparkResultLinkedToProject.java | 102 ++--- .../graph/dump/funder_result_parameters.json | 12 +- .../dump/input_parameter_select_relation.json | 20 + .../graph/dump/input_parameters_link_prj.json | 6 + .../oozie_app/config-default.xml | 30 -- .../oozie_app/workflow.xml | 347 ------------------ .../community/oozie_app/import.txt | 2 - .../community/oozie_app/workflow.xml | 273 ++++++++++++-- .../complete/oozie_app/workflow.xml | 1 + .../subworkflows/funder/oozie_app/import.txt | 2 - .../funder/oozie_app/workflow.xml | 71 ++-- .../dump/PrepareResultProjectJobTest.java | 281 +++++++------- .../ResultLinkedToProjectTest.java | 85 +++-- .../dump/funderresult/SplitPerFunderTest.java | 74 ++-- .../communityMapPath/communityMap | 1 + .../{extendeddump/orp => ext/dataset} | 0 .../funderresource/ext/otherresearchproduct | 0 .../oa/graph/dump/funderresource/ext/project | 12 + .../graph/dump/funderresource/ext/publication | 13 + .../oa/graph/dump/funderresource/ext/software | 0 .../extendeddump/otherresearchproduct | 32 ++ .../dump/funderresource/fundersList/list | 8 + .../funderresource/preparedInfo/resultProject | 1 + 25 files changed, 744 insertions(+), 806 deletions(-) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameter_select_relation.json delete mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/config-default.xml delete mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/workflow.xml delete mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/import.txt delete mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/import.txt create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/communityMapPath/communityMap rename dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/{extendeddump/orp => ext/dataset} (100%) create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext/otherresearchproduct create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext/project create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext/publication create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext/software create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/otherresearchproduct create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/fundersList/list create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo/resultProject diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java index 87ac20948..410feea02 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java @@ -10,6 +10,7 @@ import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.MapGroupsFunction; import org.apache.spark.sql.Dataset; @@ -81,8 +82,9 @@ public class SparkPrepareResultProject implements Serializable { Dataset relation = Utils .readPath(spark, inputPath + "/relation", Relation.class) .filter( - "dataInfo.deletedbyinference = false and lower(relClass) = '" - + ModelConstants.IS_PRODUCED_BY.toLowerCase() + "'"); + (FilterFunction) r -> !r.getDataInfo().getDeletedbyinference() && + r.getRelClass().equalsIgnoreCase(ModelConstants.IS_PRODUCED_BY)); + Dataset projects = Utils .readPath(spark, inputPath + "/project", eu.dnetlib.dhp.schema.oaf.Project.class); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java index 6aed9d7a8..cfe47f29f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java @@ -1,140 +1,119 @@ - package eu.dnetlib.dhp.oa.graph.dump.funderresults; - import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - import java.io.Serializable; import java.util.List; import java.util.Objects; import java.util.Optional; - +import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.FlatMapFunction; +import org.apache.spark.api.java.function.ForeachFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.*; +import org.jetbrains.annotations.NotNull; import org.slf4j.Logger; import org.slf4j.LoggerFactory; - import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; +import eu.dnetlib.dhp.schema.dump.oaf.community.Funder; import eu.dnetlib.dhp.schema.dump.oaf.community.Project; - /** * Splits the dumped results by funder and stores them in a folder named as the funder nsp (for all the funders, but the EC * for the EC it specifies also the fundingStream (FP7 or H2020) */ public class SparkDumpFunderResults implements Serializable { private static final Logger log = LoggerFactory.getLogger(SparkDumpFunderResults.class); - public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils - .toString( - SparkDumpFunderResults.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json")); - + .toString( + SparkDumpFunderResults.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json")); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); parser.parseArgument(args); - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String inputPath = parser.get("sourcePath"); log.info("inputPath: {}", inputPath); - final String outputPath = parser.get("outputPath"); log.info("outputPath: {}", outputPath); - - final String graphPath = parser.get("graphPath"); - log.info("relationPath: {}", graphPath); - SparkConf conf = new SparkConf(); - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - writeResultProjectList(spark, inputPath, outputPath, graphPath); - }); + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath); + writeResultProjectList(spark, inputPath, outputPath); + }); } - - private static void writeResultProjectList(SparkSession spark, String inputPath, String outputPath, - String graphPath) { - - Dataset project = Utils - .readPath(spark, graphPath + "/project", eu.dnetlib.dhp.schema.oaf.Project.class); - + private static void writeResultProjectList(SparkSession spark, String inputPath, String outputPath) { Dataset result = Utils - .readPath(spark, inputPath + "/publication", CommunityResult.class) - .union(Utils.readPath(spark, inputPath + "/dataset", CommunityResult.class)) - .union(Utils.readPath(spark, inputPath + "/orp", CommunityResult.class)) - .union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class)); - - List funderList = project - .select("id") - .map((MapFunction) value -> value.getString(0).substring(0, 15), Encoders.STRING()) - .distinct() - .collectAsList(); - + .readPath(spark, inputPath + "/publication", CommunityResult.class) + .union(Utils.readPath(spark, inputPath + "/dataset", CommunityResult.class)) + .union(Utils.readPath(spark, inputPath + "/otherresearchproduct", CommunityResult.class)) + .union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class)); + log.info("Number of result {}", result.count()); + Dataset tmp = result + .flatMap((FlatMapFunction) cr -> cr.getProjects().stream().map(p -> { + return getFunderName(p); + }).collect(Collectors.toList()).iterator(), Encoders.STRING()) + .distinct(); + List funderList = tmp.collectAsList(); funderList.forEach(funder -> { - String fundernsp = funder.substring(3); - String funderdump; - if (fundernsp.startsWith("corda")) { - funderdump = "EC_"; - if (fundernsp.endsWith("h2020")) { - funderdump += "H2020"; - } else { - funderdump += "FP7"; - } - } else { - funderdump = fundernsp.substring(0, fundernsp.indexOf("_")).toUpperCase(); - } - writeFunderResult(funder, result, outputPath, funderdump); + dumpResults(funder, result, outputPath); }); - } - - private static void dumpResults(String nsp, Dataset results, String outputPath, - String funderName) { - - results.map((MapFunction) r -> { - if (!Optional.ofNullable(r.getProjects()).isPresent()) { - return null; + @NotNull + private static String getFunderName(Project p) { + Optional ofunder = Optional.ofNullable(p.getFunder()); + if (ofunder.isPresent()) { + String fName = ofunder.get().getShortName(); + if (fName.equalsIgnoreCase("ec")) { + fName += "_" + ofunder.get().getFundingStream(); } - for (Project p : r.getProjects()) { - if (p.getId().startsWith(nsp)) { - if (nsp.startsWith("40|irb")) { - if (p.getFunder().getShortName().equals(funderName)) - return r; - else - return null; - } - return r; + return fName; + } else { + String fName = p.getId().substring(3, p.getId().indexOf("_")).toUpperCase(); + if (fName.equalsIgnoreCase("ec")) { + if (p.getId().contains("h2020")) { + fName += "_H2020"; + } else { + fName += "_FP7"; } + } else if (fName.equalsIgnoreCase("conicytf")) { + fName = "CONICYT"; + } else if (fName.equalsIgnoreCase("dfgf")) { + fName = "DFG"; + } else if (fName.equalsIgnoreCase("tubitakf")) { + fName = "TUBITAK"; + } else if (fName.equalsIgnoreCase("euenvagency")) { + fName = "EEA"; } - return null; - }, Encoders.bean(CommunityResult.class)) - .filter(Objects::nonNull) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath + "/" + funderName); + return fName; + } } - - private static void writeFunderResult(String funder, Dataset results, String outputPath, - String funderDump) { - - if (funder.startsWith("40|irb")) { - dumpResults(funder, results, outputPath, "HRZZ"); - dumpResults(funder, results, outputPath, "MZOS"); - } else - dumpResults(funder, results, outputPath, funderDump); - + private static void dumpResults(String funder, Dataset results, String outputPath) { + results.map((MapFunction) r -> { + if (!Optional.ofNullable(r.getProjects()).isPresent()) { + return null; + } + for (Project p : r.getProjects()) { + String fName = getFunderName(p); + if (fName.equalsIgnoreCase(funder)) { + return r; + } + } + return null; + }, Encoders.bean(CommunityResult.class)) + .filter(Objects::nonNull) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath + "/" + funder); } - -} +} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java index d89b9e86d..5eed64e89 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java @@ -5,9 +5,12 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.io.Serializable; import java.util.Optional; +import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.FilterFunction; +import org.apache.spark.api.java.function.FlatMapFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.MapGroupsFunction; import org.apache.spark.sql.Dataset; @@ -18,11 +21,18 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.oa.graph.dump.Constants; +import eu.dnetlib.dhp.oa.graph.dump.DumpProducts; +import eu.dnetlib.dhp.oa.graph.dump.ResultMapper; import eu.dnetlib.dhp.oa.graph.dump.Utils; +import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; +import eu.dnetlib.dhp.oa.graph.dump.community.ResultProject; import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; import eu.dnetlib.dhp.schema.oaf.Project; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Result; +import scala.Tuple2; /** * Selects the results linked to projects. Only for these results the dump will be performed. @@ -35,18 +45,18 @@ public class SparkResultLinkedToProject implements Serializable { public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils - .toString( - SparkResultLinkedToProject.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json")); + .toString( + SparkResultLinkedToProject.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json")); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); parser.parseArgument(args); Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); final String inputPath = parser.get("sourcePath"); @@ -58,59 +68,51 @@ public class SparkResultLinkedToProject implements Serializable { final String resultClassName = parser.get("resultTableName"); log.info("resultTableName: {}", resultClassName); - final String graphPath = parser.get("graphPath"); - log.info("graphPath: {}", graphPath); + final String resultProjectsPath = parser.get("graphPath"); + log.info("graphPath: {}", resultProjectsPath); + + String communityMapPath = parser.get("communityMapPath"); @SuppressWarnings("unchecked") Class inputClazz = (Class) Class.forName(resultClassName); SparkConf conf = new SparkConf(); runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - writeResultsLinkedToProjects(spark, inputClazz, inputPath, outputPath, graphPath); - }); + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath); + writeResultsLinkedToProjects( + communityMapPath, spark, inputClazz, inputPath, outputPath, resultProjectsPath); + }); } - private static void writeResultsLinkedToProjects(SparkSession spark, Class inputClazz, - String inputPath, String outputPath, String graphPath) { + private static void writeResultsLinkedToProjects(String communityMapPath, SparkSession spark, + Class inputClazz, + String inputPath, String outputPath, String resultProjectsPath) { Dataset results = Utils - .readPath(spark, inputPath, inputClazz) - .filter("dataInfo.deletedbyinference = false and datainfo.invisible = false"); - Dataset relations = Utils - .readPath(spark, graphPath + "/relation", Relation.class) - .filter( - "dataInfo.deletedbyinference = false and lower(relClass) = '" - + ModelConstants.IS_PRODUCED_BY.toLowerCase() + "'"); - Dataset project = Utils.readPath(spark, graphPath + "/project", Project.class); - - results.createOrReplaceTempView("result"); - relations.createOrReplaceTempView("relation"); - project.createOrReplaceTempView("project"); - - Dataset tmp = spark - .sql( - "Select res.* " + - "from relation rel " + - "join result res " + - "on rel.source = res.id " + - "join project p " + - "on rel.target = p.id " + - "") - .as(Encoders.bean(inputClazz)); - tmp - .groupByKey( - (MapFunction) value -> value - .getId(), - Encoders.STRING()) - .mapGroups((MapGroupsFunction) (k, it) -> it.next(), Encoders.bean(inputClazz)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); + .readPath(spark, inputPath, inputClazz) + .filter( + (FilterFunction) r -> !r.getDataInfo().getDeletedbyinference() && + !r.getDataInfo().getInvisible()); + Dataset resultProjectDataset = Utils + .readPath(spark, resultProjectsPath, ResultProject.class); + CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath); + results + .joinWith(resultProjectDataset, results.col("id").equalTo(resultProjectDataset.col("resultId"))) + .map((MapFunction, CommunityResult>) t2 -> { + CommunityResult cr = (CommunityResult) ResultMapper + .map( + t2._1(), + communityMap, Constants.DUMPTYPE.FUNDER.getType()); + cr.setProjects(t2._2().getProjectsList()); + return cr; + }, Encoders.bean(CommunityResult.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json index 5dc8e8910..5669dca37 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json @@ -17,10 +17,10 @@ "paramDescription": "true if the spark session is managed, false otherwise", "paramRequired": false }, -{ - "paramName": "gp", - "paramLongName": "graphPath", - "paramDescription": "the relationPath", - "paramRequired": true -} + { + "paramName": "gp", + "paramLongName": "graphPath", + "paramDescription": "the relationPath", + "paramRequired": false + } ] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameter_select_relation.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameter_select_relation.json new file mode 100644 index 000000000..1a67134a6 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameter_select_relation.json @@ -0,0 +1,20 @@ +[ + { + "paramName":"s", + "paramLongName":"sourcePath", + "paramDescription": "the path of the sequencial file to read", + "paramRequired": true + }, + { + "paramName": "out", + "paramLongName": "outputPath", + "paramDescription": "the path used to store temporary output files", + "paramRequired": true + }, + { + "paramName": "ssm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "true if the spark session is managed, false otherwise", + "paramRequired": false + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json index f5641bc45..6c45538cf 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json @@ -28,6 +28,12 @@ "paramLongName":"graphPath", "paramDescription": "the path to the relations", "paramRequired": true + }, + { + "paramName":"cmp", + "paramLongName":"communityMapPath", + "paramDescription": "the path to the relations", + "paramRequired": true } ] diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/config-default.xml deleted file mode 100644 index e5ec3d0ae..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/config-default.xml +++ /dev/null @@ -1,30 +0,0 @@ - - - jobTracker - yarnRM - - - nameNode - hdfs://nameservice1 - - - oozie.use.system.libpath - true - - - hiveMetastoreUris - thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 - - - hiveJdbcUrl - jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000 - - - hiveDbName - openaire - - - oozie.launcher.mapreduce.user.classpath.first - true - - \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/workflow.xml deleted file mode 100644 index 5f954ff38..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/workflow.xml +++ /dev/null @@ -1,347 +0,0 @@ - - - - - sourcePath - the source path - - - outputPath - the output path - - - communityMapPath - the path to the community map - - - selectedResults - the path the the possible subset ot results to be dumped - - - hiveDbName - the target hive database name - - - hiveJdbcUrl - hive server jdbc url - - - hiveMetastoreUris - hive server metastore URIs - - - sparkDriverMemory - memory for driver process - - - sparkExecutorMemory - memory for individual executor - - - sparkExecutorCores - number of cores used by single executor - - - oozieActionShareLibForSpark2 - oozie action sharelib for spark 2.* - - - spark2ExtraListeners - com.cloudera.spark.lineage.NavigatorAppListener - spark 2.* extra listeners classname - - - spark2SqlQueryExecutionListeners - com.cloudera.spark.lineage.NavigatorQueryListener - spark 2.* sql query execution listeners classname - - - spark2YarnHistoryServerAddress - spark 2.* yarn history server address - - - spark2EventLogDir - spark 2.* event log dir location - - - - - ${jobTracker} - ${nameNode} - - - mapreduce.job.queuename - ${queueName} - - - oozie.launcher.mapred.job.queue.name - ${oozieLauncherQueueName} - - - oozie.action.sharelib.for.spark - ${oozieActionShareLibForSpark2} - - - - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - - - - - - - - - - - yarn - cluster - Dump table publication for community/funder related products - eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${selectedResults}/publication - --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication - --outputPath${workingDir}/dump/publication - --communityMapPath${communityMapPath} - --dumpType${dumpType} - - - - - - - - yarn - cluster - Dump table dataset for community/funder related products - eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${selectedResults}/dataset - --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset - --outputPath${workingDir}/dump/dataset - --communityMapPath${communityMapPath} - - - - - - - - yarn - cluster - Dump table ORP for community related products - eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${selectedResults}/otherresearchproduct - --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct - --outputPath${workingDir}/dump/otherresearchproduct - --communityMapPath${communityMapPath} - - - - - - - - yarn - cluster - Dump table software for community related products - eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${selectedResults}/software - --resultTableNameeu.dnetlib.dhp.schema.oaf.Software - --outputPath${workingDir}/dump/software - --communityMapPath${communityMapPath} - - - - - - - - - - yarn - cluster - Prepare association result subset of project info - eu.dnetlib.dhp.oa.graph.dump.community.SparkPrepareResultProject - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath} - --outputPath${workingDir}/preparedInfo - - - - - - - - - - - - - - - yarn - cluster - Extend dumped publications with information about project - eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${workingDir}/dump/publication - --outputPath${outputPath}/ext/publication - --preparedInfoPath${workingDir}/preparedInfo - - - - - - - - yarn - cluster - Extend dumped dataset with information about project - eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${workingDir}/dump/dataset - --outputPath${outputPath}/ext/dataset - --preparedInfoPath${workingDir}/preparedInfo - - - - - - - - yarn - cluster - Extend dumped ORP with information about project - eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${workingDir}/dump/otherresearchproduct - --outputPath${outputPath}/ext/orp - --preparedInfoPath${workingDir}/preparedInfo - - - - - - - - yarn - cluster - Extend dumped software with information about project - eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${workingDir}/dump/software - --outputPath${outputPath}/ext/software - --preparedInfoPath${workingDir}/preparedInfo - - - - - - - - - - - diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/import.txt b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/import.txt deleted file mode 100644 index 15387e988..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/import.txt +++ /dev/null @@ -1,2 +0,0 @@ -## This is a classpath-based import file (this header is required) -dump_common classpath eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml index 319517026..b559a25dc 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml @@ -77,42 +77,259 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - ${wf:appPath()}/dump_common - - - - - sourcePath - ${sourcePath} - - - selectedResults - ${sourcePath} - - - communityMapPath - ${workingDir}/communityMap - - - outputPath - ${workingDir} - - - - - + + + + + + + + + + yarn + cluster + Dump table publication for community/funder related products + eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${selectedResults}/publication + --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication + --outputPath${workingDir}/dump/publication + --communityMapPath${communityMapPath} + --dumpType${dumpType} + + + + + + + + yarn + cluster + Dump table dataset for community/funder related products + eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${selectedResults}/dataset + --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset + --outputPath${workingDir}/dump/dataset + --communityMapPath${communityMapPath} + + + + + + + + yarn + cluster + Dump table ORP for community related products + eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${selectedResults}/otherresearchproduct + --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct + --outputPath${workingDir}/dump/otherresearchproduct + --communityMapPath${communityMapPath} + + + + + + + + yarn + cluster + Dump table software for community related products + eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${selectedResults}/software + --resultTableNameeu.dnetlib.dhp.schema.oaf.Software + --outputPath${workingDir}/dump/software + --communityMapPath${communityMapPath} + + + + + + + + + + yarn + cluster + Prepare association result subset of project info + eu.dnetlib.dhp.oa.graph.dump.community.SparkPrepareResultProject + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath} + --outputPath${workingDir}/preparedInfo + + + + + + + + + + + + + + + yarn + cluster + Extend dumped publications with information about project + eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/dump/publication + --outputPath${outputPath}/ext/publication + --preparedInfoPath${workingDir}/preparedInfo + + + + + + + + yarn + cluster + Extend dumped dataset with information about project + eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/dump/dataset + --outputPath${outputPath}/ext/dataset + --preparedInfoPath${workingDir}/preparedInfo + + + + + + + + yarn + cluster + Extend dumped ORP with information about project + eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/dump/otherresearchproduct + --outputPath${outputPath}/ext/orp + --preparedInfoPath${workingDir}/preparedInfo + + + + + + + + yarn + cluster + Extend dumped software with information about project + eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/dump/software + --outputPath${outputPath}/ext/software + --preparedInfoPath${workingDir}/preparedInfo + + + - + yarn diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/workflow.xml index 8eab56992..7cc133323 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/workflow.xml @@ -298,6 +298,7 @@ --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + --conf spark.sql.shuffle.partitions=3840 --sourcePath${sourcePath} --outputPath${workingDir}/validrelation diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/import.txt b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/import.txt deleted file mode 100644 index 15387e988..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/import.txt +++ /dev/null @@ -1,2 +0,0 @@ -## This is a classpath-based import file (this header is required) -dump_common classpath eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/workflow.xml index b990f4e49..2c05256cf 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/workflow.xml @@ -77,12 +77,36 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + yarn + cluster + Prepare association result subset of project info + eu.dnetlib.dhp.oa.graph.dump.community.SparkPrepareResultProject + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath} + --outputPath${workingDir}/preparedInfo + + + + + @@ -111,7 +135,8 @@ --sourcePath${sourcePath}/publication --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication --outputPath${workingDir}/result/publication - --graphPath${sourcePath} + --graphPath${workingDir}/preparedInfo + --communityMapPath${communityMapPath} @@ -137,7 +162,8 @@ --sourcePath${sourcePath}/dataset --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset --outputPath${workingDir}/result/dataset - --graphPath${sourcePath} + --graphPath${workingDir}/preparedInfo + --communityMapPath${communityMapPath} @@ -163,7 +189,8 @@ --sourcePath${sourcePath}/otherresearchproduct --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct --outputPath${workingDir}/result/otherresearchproduct - --graphPath${sourcePath} + --graphPath${workingDir}/preparedInfo + --communityMapPath${communityMapPath} @@ -189,41 +216,14 @@ --sourcePath${sourcePath}/software --resultTableNameeu.dnetlib.dhp.schema.oaf.Software --outputPath${workingDir}/result/software - --graphPath${sourcePath} + --graphPath${workingDir}/preparedInfo + --communityMapPath${communityMapPath} - - - - - ${wf:appPath()}/dump_common - - - - - sourcePath - ${sourcePath} - - - selectedResults - ${workingDir}/result - - - communityMapPath - ${workingDir}/communityMap - - - outputPath - ${workingDir} - - - - - - + @@ -242,9 +242,8 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - --sourcePath${workingDir}/ext + --sourcePath${workingDir}/result --outputPath${outputPath} - --graphPath${sourcePath} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java index 86d2f93c9..c6798ac58 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java @@ -35,12 +35,12 @@ public class PrepareResultProjectJobTest { private static Path workingDir; private static final Logger log = LoggerFactory - .getLogger(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class); + .getLogger(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class); @BeforeAll public static void beforeAll() throws IOException { workingDir = Files - .createTempDirectory(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class.getSimpleName()); + .createTempDirectory(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class.getSimpleName()); log.info("using work dir {}", workingDir); SparkConf conf = new SparkConf(); @@ -54,10 +54,10 @@ public class PrepareResultProjectJobTest { conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); spark = SparkSession - .builder() - .appName(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); + .builder() + .appName(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); } @AfterAll @@ -70,23 +70,23 @@ public class PrepareResultProjectJobTest { void testNoMatch() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/no_match") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/no_match") + .getPath(); SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); + .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); assertEquals(0, verificationDataset.count()); @@ -96,37 +96,37 @@ public class PrepareResultProjectJobTest { void testMatchOne() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_one") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_one") + .getPath(); SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); + .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); assertEquals(1, verificationDataset.count()); assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); verificationDataset.createOrReplaceTempView("table"); Dataset check = spark - .sql( - "Select projList.provenance.provenance " + - "from table " + - "lateral view explode (projectsList) pl as projList"); + .sql( + "Select projList.provenance.provenance " + + "from table " + + "lateral view explode (projectsList) pl as projList"); assertEquals(1, check.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); @@ -138,88 +138,88 @@ public class PrepareResultProjectJobTest { void testMatch() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match") + .getPath(); SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); + .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); assertEquals(2, verificationDataset.count()); assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); verificationDataset.createOrReplaceTempView("dataset"); String query = "select resultId, MyT.id project , MyT.title title, MyT.acronym acronym , MyT.provenance.provenance provenance " - + "from dataset " - + "lateral view explode(projectsList) p as MyT "; + + "from dataset " + + "lateral view explode(projectsList) p as MyT "; org.apache.spark.sql.Dataset resultExplodedProvenance = spark.sql(query); assertEquals(3, resultExplodedProvenance.count()); assertEquals( - 2, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") - .count()); + 2, + resultExplodedProvenance + .filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") - .count()); + 1, + resultExplodedProvenance + .filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") + .count()); assertEquals( - 2, - resultExplodedProvenance - .filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'") - .count()); + 2, + resultExplodedProvenance + .filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'") - .count()); + 1, + resultExplodedProvenance + .filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::03376222b28a3aebf2730ac514818d04' and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::03376222b28a3aebf2730ac514818d04' and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") + .count()); assertEquals( - 3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); + 3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); } @@ -227,98 +227,121 @@ public class PrepareResultProjectJobTest { public void testMatchValidated() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_validatedRels") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_validatedRels") + .getPath(); SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); + .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); assertEquals(2, verificationDataset.count()); assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); verificationDataset.createOrReplaceTempView("dataset"); String query = "select resultId, MyT.id project , MyT.title title, MyT.acronym acronym , MyT.provenance.provenance provenance, " - + - "MyT.validated.validatedByFunder, MyT.validated.validationDate " - + "from dataset " - + "lateral view explode(projectsList) p as MyT "; + + + "MyT.validated.validatedByFunder, MyT.validated.validationDate " + + "from dataset " + + "lateral view explode(projectsList) p as MyT "; org.apache.spark.sql.Dataset resultExplodedProvenance = spark.sql(query); assertEquals(3, resultExplodedProvenance.count()); assertEquals(3, resultExplodedProvenance.filter("validatedByFunder = true").count()); assertEquals( - 2, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") - .count()); + 2, + resultExplodedProvenance + .filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") - .count()); + 1, + resultExplodedProvenance + .filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") + .count()); assertEquals( - 2, - resultExplodedProvenance - .filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'") - .count()); + 2, + resultExplodedProvenance + .filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + - "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + - "and validatedByFunder = true " + - "and validationDate = '2021-08-06'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + + "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + + "and validatedByFunder = true " + + "and validationDate = '2021-08-06'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + - "and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80' " + - "and validatedByFunder = true and validationDate = '2021-08-04'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + + "and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80' " + + "and validatedByFunder = true and validationDate = '2021-08-04'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'") - .count()); + 1, + resultExplodedProvenance + .filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::03376222b28a3aebf2730ac514818d04' " + - "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + - "and validatedByFunder = true and validationDate = '2021-08-05'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::03376222b28a3aebf2730ac514818d04' " + + "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + + "and validatedByFunder = true and validationDate = '2021-08-05'") + .count()); assertEquals( - 3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); + 3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); } + + @Test + void testMatchx() throws Exception { + + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match") + .getPath(); + + SparkPrepareResultProject.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); + + tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r))); + } + } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java index 4967ae5a5..579958a62 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java @@ -22,6 +22,7 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject; +import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; import eu.dnetlib.dhp.schema.oaf.Publication; import eu.dnetlib.dhp.schema.oaf.Result; @@ -34,15 +35,15 @@ public class ResultLinkedToProjectTest { private static Path workingDir; private static final Logger log = LoggerFactory - .getLogger(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class); + .getLogger(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class); private static final HashMap map = new HashMap<>(); @BeforeAll public static void beforeAll() throws IOException { workingDir = Files - .createTempDirectory( - eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()); + .createTempDirectory( + eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()); log.info("using work dir {}", workingDir); SparkConf conf = new SparkConf(); @@ -56,10 +57,10 @@ public class ResultLinkedToProjectTest { conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); spark = SparkSession - .builder() - .appName(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); + .builder() + .appName(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); } @AfterAll @@ -72,32 +73,34 @@ public class ResultLinkedToProjectTest { void testNoMatch() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json") + .getPath(); final String graphPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo") + .getPath(); + + final String communityMapPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/communityMapPath") + .getPath(); SparkResultLinkedToProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-graphPath", graphPath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath, + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", + "-graphPath", graphPath, + "-communityMapPath", communityMapPath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, Result.class)); + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Result.class)); - - Assertions.assertEquals(0, verificationDataset.count()); + Assertions.assertEquals(0, tmp.count()); } @@ -105,32 +108,34 @@ public class ResultLinkedToProjectTest { void testMatchOne() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/papers.json") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/papers.json") + .getPath(); - final String relationPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match") - .getPath(); + final String graphPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo") + .getPath(); + + final String communityMapPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/communityMapPath") + .getPath(); SparkResultLinkedToProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-graphPath", relationPath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath, + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", + "-graphPath", graphPath, + "-communityMapPath", communityMapPath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, Publication.class)); + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Publication.class)); - - Assertions.assertEquals(1, verificationDataset.count()); + Assertions.assertEquals(1, tmp.count()); } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java index 477481c08..5bb5a1178 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java @@ -5,10 +5,14 @@ import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; +// import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkDumpFunderResults2; +// import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkGetFunderList; import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.ForeachFunction; +import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; import org.junit.jupiter.api.AfterAll; @@ -52,10 +56,10 @@ public class SplitPerFunderTest { conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); spark = SparkSession - .builder() - .appName(SplitPerFunderTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); + .builder() + .appName(SplitPerFunderTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); } @AfterAll @@ -68,86 +72,80 @@ public class SplitPerFunderTest { void test1() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext") + .getPath(); SparkDumpFunderResults.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/split", - "-sourcePath", sourcePath, - "-graphPath", sourcePath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/split", + "-sourcePath", sourcePath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - // FP7 3 + // FP7 3 and H2020 3 JavaRDD tmp = sc - .textFile(workingDir.toString() + "/split/EC_FP7") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/EC_FP7") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); + .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); Assertions.assertEquals(3, verificationDataset.count()); Assertions - .assertEquals( - 1, verificationDataset.filter("id = '50|dedup_wf_001::0d16b1714ab3077df73893a8ea57d776'").count()); + .assertEquals( + 1, verificationDataset.filter("id = '50|dedup_wf_001::0d16b1714ab3077df73893a8ea57d776'").count()); // CIHR 2 tmp = sc - .textFile(workingDir.toString() + "/split/CIHR") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/CIHR") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(2, tmp.count()); // NWO 1 tmp = sc - .textFile(workingDir.toString() + "/split/NWO") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/NWO") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(1, tmp.count()); // NIH 3 tmp = sc - .textFile(workingDir.toString() + "/split/NIH") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/NIH") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(2, tmp.count()); // NSF 1 tmp = sc - .textFile(workingDir.toString() + "/split/NSF") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/NSF") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(1, tmp.count()); // SNSF 1 tmp = sc - .textFile(workingDir.toString() + "/split/SNSF") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/SNSF") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(1, tmp.count()); // NHMRC 1 tmp = sc - .textFile(workingDir.toString() + "/split/NHMRC") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/NHMRC") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(1, tmp.count()); // H2020 3 tmp = sc - .textFile(workingDir.toString() + "/split/EC_H2020") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/EC_H2020") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(3, tmp.count()); // MZOS 1 tmp = sc - .textFile(workingDir.toString() + "/split/MZOS") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/MZOS") + .map(item -> 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 000000000..905cdabe9 --- /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 000000000..e69de29bb 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 000000000..f68cead77 --- /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":"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 15/23] [DUMP NEW FUNDED PRODUCTS] change in resources --- .../dhp/oa/graph/dump/funderresource/nomatch/papers.json | 2 +- .../dhp/oa/graph/dump/funderresource/preparedInfo/resultProject | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json index fda631c2f..dd6026980 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json @@ -12,7 +12,7 @@ {"author":[{"fullname":"Sharp, 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This study examines Leonard Cohen's novel Beautiful Losers through the lenses of allegorical and authorial theories to appreciate how the novel uses allegorical techniques to code into symbolic terms an exploration of the polysemous nature of the word ''translation.'' The first chapter studies the stylistic and conceptual dimensions of allegory as a literary genre - as critics like Northrop Frye, Angus Fletchet, and Maureen Quilligan help to define it - while arguing that Cohen's novel is consciously allegorical, challenging readers to interpret what it \"means,\" or may mean. The second chapter performs an intensive re-reading of Beautiful Losers, examining how the novel uses complex systems of verbal play (particularly puns) to coordinate a reunification of various dichotomies historical \"reality\"/imaginative myth, secularity/spirituality, enslavement/sanctification, among others - employed throughout the text. The thesis concludes that the novel is perpetually playing with various types of translation (spiritual, linguistic, physical, and so forth), affirming the need for emotionally-charged, devotional forms of expression (like song and prayer) over more clinical attempts to reorder or recreate the world and its inhabitants. Ultimately, this discussion argues that an understanding of the allegorical dimensions of Beautiful Losers may illuminate how Cohen's other works (particularly his songs) may be studied as attempts to associate word with voice, to emphasize the process of expression (translation) rather than just the finished product.

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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 515d1c9a6..5749f731d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo/resultProject +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo/resultProject @@ -1 +1 @@ -{"resultId":"50|a89337edbe55::43e8b61e5e8d682545cb867be8118585","projectsList":[{"id":"40|aka_________::01bb7b48e29d732a1c7bc5150b9195c4","code":"135027","acronym":null,"title":"Dynamic 3D resolution-enhanced low-coherence interferometric imaging / Consortium: Hi-Lo","funder":{"shortName":"AKA","name":"Academy of 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 16/23] [Funder Products Dump] fixed names of parameters in workflow --- .../community/oozie_app/workflow.xml | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml index b559a25dc..dfbe93b67 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml @@ -107,7 +107,7 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - --sourcePath${selectedResults}/publication + --sourcePath${sourcePath}/publication --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication --outputPath${workingDir}/dump/publication --communityMapPath${communityMapPath} @@ -134,7 +134,7 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - --sourcePath${selectedResults}/dataset + --sourcePath${sourcePath}/dataset --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset --outputPath${workingDir}/dump/dataset --communityMapPath${communityMapPath} @@ -160,7 +160,7 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - --sourcePath${selectedResults}/otherresearchproduct + --sourcePath${sourcePath}/otherresearchproduct --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct --outputPath${workingDir}/dump/otherresearchproduct --communityMapPath${communityMapPath} @@ -186,7 +186,7 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - --sourcePath${selectedResults}/software + --sourcePath${sourcePath}/software --resultTableNameeu.dnetlib.dhp.schema.oaf.Software --outputPath${workingDir}/dump/software --communityMapPath${communityMapPath} @@ -246,7 +246,7 @@ --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} --sourcePath${workingDir}/dump/publication - --outputPath${outputPath}/ext/publication + --outputPath${workingDir}/ext/publication --preparedInfoPath${workingDir}/preparedInfo @@ -271,7 +271,7 @@ --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} --sourcePath${workingDir}/dump/dataset - --outputPath${outputPath}/ext/dataset + --outputPath${workingDir}/ext/dataset --preparedInfoPath${workingDir}/preparedInfo @@ -296,7 +296,7 @@ --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} --sourcePath${workingDir}/dump/otherresearchproduct - --outputPath${outputPath}/ext/orp + --outputPath${workingDir}/ext/orp --preparedInfoPath${workingDir}/preparedInfo @@ -321,7 +321,7 @@ --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} --sourcePath${workingDir}/dump/software - --outputPath${outputPath}/ext/software + --outputPath${workingDir}/ext/software --preparedInfoPath${workingDir}/preparedInfo From edddfc6c637d601823681c190305aa1105ee5834 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 21 Jun 2022 18:28:53 +0200 Subject: [PATCH 17/23] [DUMP DELTA PROJECTS] adding test and resource --- .../projectssubset/ProjectSubsetTest.java | 118 ++++++++++++++++++ .../graph/dump/projectsubset/allnew/projects | 12 ++ .../dump/projectsubset/matchOne/projects | 12 ++ .../dhp/oa/graph/dump/projectsubset/projectId | 28 +++++ 4 files changed, 170 insertions(+) create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/allnew/projects create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/matchOne/projects create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/projectId diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java new file mode 100644 index 000000000..d5b1ce776 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java @@ -0,0 +1,118 @@ +package eu.dnetlib.dhp.oa.graph.dump.projectssubset; +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.HashMap; +import org.apache.commons.io.FileUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject; +import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; +import eu.dnetlib.dhp.schema.dump.oaf.graph.Project; +public class ProjectSubsetTest { + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static SparkSession spark; + private static Path workingDir; + private static final Logger log = LoggerFactory + .getLogger(eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class); + private static final HashMap map = new HashMap<>(); + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files + .createTempDirectory( + eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + SparkConf conf = new SparkConf(); + conf.setAppName(eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class.getSimpleName()); + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + spark = SparkSession + .builder() + .appName(eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + @Test + void testAllNew() throws Exception { + final String projectListPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/projectId") + .getPath(); + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/allnew/projects") + .getPath(); + spark + .read() + .textFile(projectListPath) + .write() + .mode(SaveMode.Overwrite) + .text(workingDir.toString() + "/projectIds"); + ProjectsSubsetSparkJob.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/projects", + "-sourcePath", sourcePath, + "-projectListPath", workingDir.toString() + "/projectIds" + }); + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/projects") + .map(item -> OBJECT_MAPPER.readValue(item, Project.class)); + Assertions.assertEquals(12, tmp.count()); + Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("aka_________")).count()); + Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("anr_________")).count()); + Assertions.assertEquals(4, tmp.filter(p -> p.getId().substring(3, 15).equals("arc_________")).count()); + Assertions.assertEquals(3, tmp.filter(p -> p.getId().substring(3, 15).equals("conicytf____")).count()); + Assertions.assertEquals(1, tmp.filter(p -> p.getId().substring(3, 15).equals("corda_______")).count()); + Assertions.assertEquals(40, sc.textFile(workingDir.toString() + "/projectIds").count()); + } + @Test + void testMatchOne() throws Exception { + final String projectListPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/projectId") + .getPath(); + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/matchOne/projects") + .getPath(); + spark + .read() + .textFile(projectListPath) + .write() + .mode(SaveMode.Overwrite) + .text(workingDir.toString() + "/projectIds"); + ProjectsSubsetSparkJob.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/projects", + "-sourcePath", sourcePath, + "-projectListPath", workingDir.toString() + "/projectIds" + }); + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/projects") + .map(item -> OBJECT_MAPPER.readValue(item, Project.class)); + Assertions.assertEquals(11, tmp.count()); + Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("aka_________")).count()); + Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("anr_________")).count()); + Assertions.assertEquals(4, tmp.filter(p -> p.getId().substring(3, 15).equals("arc_________")).count()); + Assertions.assertEquals(3, tmp.filter(p -> p.getId().substring(3, 15).equals("conicytf____")).count()); + Assertions.assertEquals(0, tmp.filter(p -> p.getId().substring(3, 15).equals("corda__h2020")).count()); + Assertions.assertEquals(39, sc.textFile(workingDir.toString() + "/projectIds").count()); + } +} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/allnew/projects b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/allnew/projects new file mode 100644 index 000000000..82d9bef76 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/allnew/projects @@ -0,0 +1,12 @@ +{"id":"40|aka_________::01bb7b48e29d732a1c7bc5150b9195c4","websiteurl":null,"code":"135027","acronym":null,"title":"Dynamic 3D resolution-enhanced low-coherence interferometric imaging / Consortium: Hi-Lo","startdate":null,"enddate":null,"callidentifier":"Fotoniikka ja modernit kuvantamismenetelmät LT","keywords":null,"openaccessmandateforpublications":false,"openaccessmandatefordataset":false,"subject":[],"funding":[{"shortName":"AKA","name":"Academy of Finland","jurisdiction":"FI","funding_stream":null}],"summary":null,"granted":null,"h2020programme":[]} +{"id":"40|aka_________::9d1af21dbd0f5bc719f71553d19a6b3a","websiteurl":null,"code":"316061","acronym":null,"title":"Finnish Imaging of Degenerative Shoulder Study (FIMAGE): A study on the prevalence of degenerative imaging changes of the shoulder and their relevance to clinical symptoms in the general population.","startdate":null,"enddate":null,"callidentifier":"Academy Project Funding TT","keywords":null,"openaccessmandateforpublications":false,"openaccessmandatefordataset":false,"subject":[],"funding":[{"shortName":"AKA","name":"Academy of Finland","jurisdiction":"FI","funding_stream":null}],"summary":null,"granted":null,"h2020programme":[]} +{"id":"40|anr_________::1f21edc5c902be305ee47148955c6e50","websiteurl":null,"code":"ANR-17-CE05-0033","acronym":"MOISE","title":"METAL OXIDES AS LOW LOADED NANO-IRIDIUM SUPPORT FOR COMPETITIVE WATER 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|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 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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 18/23] [DUMP DELTA PROJECTS] refactoring --- .../projectssubset/ProjectSubsetTest.java | 204 +++++++++--------- 1 file changed, 106 insertions(+), 98 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java index d5b1ce776..4ff1e1b96 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java @@ -1,8 +1,11 @@ + package eu.dnetlib.dhp.oa.graph.dump.projectssubset; + import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; import java.util.HashMap; + import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; @@ -15,104 +18,109 @@ import org.junit.jupiter.api.BeforeAll; import org.junit.jupiter.api.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; + import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject; -import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; + import eu.dnetlib.dhp.schema.dump.oaf.graph.Project; + public class ProjectSubsetTest { - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - private static SparkSession spark; - private static Path workingDir; - private static final Logger log = LoggerFactory - .getLogger(eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class); - private static final HashMap map = new HashMap<>(); - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory( - eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - SparkConf conf = new SparkConf(); - conf.setAppName(eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class.getSimpleName()); - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - spark = SparkSession - .builder() - .appName(eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - @Test - void testAllNew() throws Exception { - final String projectListPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/projectId") - .getPath(); - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/allnew/projects") - .getPath(); - spark - .read() - .textFile(projectListPath) - .write() - .mode(SaveMode.Overwrite) - .text(workingDir.toString() + "/projectIds"); - ProjectsSubsetSparkJob.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/projects", - "-sourcePath", sourcePath, - "-projectListPath", workingDir.toString() + "/projectIds" - }); - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/projects") - .map(item -> OBJECT_MAPPER.readValue(item, Project.class)); - Assertions.assertEquals(12, tmp.count()); - Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("aka_________")).count()); - Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("anr_________")).count()); - Assertions.assertEquals(4, tmp.filter(p -> p.getId().substring(3, 15).equals("arc_________")).count()); - Assertions.assertEquals(3, tmp.filter(p -> p.getId().substring(3, 15).equals("conicytf____")).count()); - Assertions.assertEquals(1, tmp.filter(p -> p.getId().substring(3, 15).equals("corda_______")).count()); - Assertions.assertEquals(40, sc.textFile(workingDir.toString() + "/projectIds").count()); - } - @Test - void testMatchOne() throws Exception { - final String projectListPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/projectId") - .getPath(); - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/matchOne/projects") - .getPath(); - spark - .read() - .textFile(projectListPath) - .write() - .mode(SaveMode.Overwrite) - .text(workingDir.toString() + "/projectIds"); - ProjectsSubsetSparkJob.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/projects", - "-sourcePath", sourcePath, - "-projectListPath", workingDir.toString() + "/projectIds" - }); - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/projects") - .map(item -> OBJECT_MAPPER.readValue(item, Project.class)); - Assertions.assertEquals(11, tmp.count()); - Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("aka_________")).count()); - Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("anr_________")).count()); - Assertions.assertEquals(4, tmp.filter(p -> p.getId().substring(3, 15).equals("arc_________")).count()); - Assertions.assertEquals(3, tmp.filter(p -> p.getId().substring(3, 15).equals("conicytf____")).count()); - Assertions.assertEquals(0, tmp.filter(p -> p.getId().substring(3, 15).equals("corda__h2020")).count()); - Assertions.assertEquals(39, sc.textFile(workingDir.toString() + "/projectIds").count()); - } -} \ No newline at end of file + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static SparkSession spark; + private static Path workingDir; + private static final Logger log = LoggerFactory + .getLogger(eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class); + + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files + .createTempDirectory( + eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + SparkConf conf = new SparkConf(); + conf.setAppName(eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class.getSimpleName()); + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + spark = SparkSession + .builder() + .appName(eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + void testAllNew() throws Exception { + final String projectListPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/projectId") + .getPath(); + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/allnew/projects") + .getPath(); + spark + .read() + .textFile(projectListPath) + .write() + .mode(SaveMode.Overwrite) + .text(workingDir.toString() + "/projectIds"); + ProjectsSubsetSparkJob.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/projects", + "-sourcePath", sourcePath, + "-projectListPath", workingDir.toString() + "/projectIds" + }); + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/projects") + .map(item -> OBJECT_MAPPER.readValue(item, Project.class)); + Assertions.assertEquals(12, tmp.count()); + Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("aka_________")).count()); + Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("anr_________")).count()); + Assertions.assertEquals(4, tmp.filter(p -> p.getId().substring(3, 15).equals("arc_________")).count()); + Assertions.assertEquals(3, tmp.filter(p -> p.getId().substring(3, 15).equals("conicytf____")).count()); + Assertions.assertEquals(1, tmp.filter(p -> p.getId().substring(3, 15).equals("corda_______")).count()); + Assertions.assertEquals(40, sc.textFile(workingDir.toString() + "/projectIds").count()); + } + + @Test + void testMatchOne() throws Exception { + final String projectListPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/projectId") + .getPath(); + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/matchOne/projects") + .getPath(); + spark + .read() + .textFile(projectListPath) + .write() + .mode(SaveMode.Overwrite) + .text(workingDir.toString() + "/projectIds"); + ProjectsSubsetSparkJob.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/projects", + "-sourcePath", sourcePath, + "-projectListPath", workingDir.toString() + "/projectIds" + }); + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/projects") + .map(item -> OBJECT_MAPPER.readValue(item, Project.class)); + Assertions.assertEquals(11, tmp.count()); + Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("aka_________")).count()); + Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("anr_________")).count()); + Assertions.assertEquals(4, tmp.filter(p -> p.getId().substring(3, 15).equals("arc_________")).count()); + Assertions.assertEquals(3, tmp.filter(p -> p.getId().substring(3, 15).equals("conicytf____")).count()); + Assertions.assertEquals(0, tmp.filter(p -> p.getId().substring(3, 15).equals("corda__h2020")).count()); + Assertions.assertEquals(39, sc.textFile(workingDir.toString() + "/projectIds").count()); + } +} From 71744a1f5274957a48e761a95c14370ec8f488a1 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 27 Jun 2022 18:07:58 +0200 Subject: [PATCH 19/23] [DUMP DELTA PROJECTS] refactoring --- .../ProjectsSubsetSparkJob.java | 121 +++++++++--------- 1 file changed, 60 insertions(+), 61 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java index 67da24185..83a9f3464 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java @@ -1,80 +1,79 @@ + package eu.dnetlib.dhp.oa.graph.dump.projectssubset; + import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.io.Serializable; -import java.util.List; import java.util.Objects; import java.util.Optional; -import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; -import org.jetbrains.annotations.NotNull; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.schema.dump.oaf.community.Funder; import eu.dnetlib.dhp.schema.dump.oaf.graph.Project; import scala.Tuple2; + public class ProjectsSubsetSparkJob implements Serializable { - private static final Logger log = LoggerFactory.getLogger(ProjectsSubsetSparkJob.class); - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - ProjectsSubsetSparkJob.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/project_subset_parameters.json")); - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - final String projectListPath = parser.get("projectListPath"); - log.info("projectListPath: {}", projectListPath); - SparkConf conf = new SparkConf(); - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - getNewProjectList(spark, inputPath, outputPath, projectListPath); - }); - } - private static void getNewProjectList(SparkSession spark, String inputPath, String outputPath, - String projectListPath) { - Dataset projectList = spark.read().textFile(projectListPath); - // projectList.show(false); - Dataset projects; - projects = Utils.readPath(spark, inputPath, Project.class); - projects - .joinWith(projectList, projects.col("id").equalTo(projectList.col("value")), "left") - .map((MapFunction, Project>) t2 -> { - if (Optional.ofNullable(t2._2()).isPresent()) - return null; - return t2._1(); - }, Encoders.bean(Project.class)) - .filter(Objects::nonNull) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); - Utils - .readPath(spark, outputPath, Project.class) - .map((MapFunction) p -> p.getId(), Encoders.STRING()) - .write() - .mode(SaveMode.Append) - .option("compression", "gzip") - .text(projectListPath); - } -} \ No newline at end of file + private static final Logger log = LoggerFactory.getLogger(ProjectsSubsetSparkJob.class); + + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + ProjectsSubsetSparkJob.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump/project_subset_parameters.json")); + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + final String inputPath = parser.get("sourcePath"); + log.info("inputPath: {}", inputPath); + final String outputPath = parser.get("outputPath"); + log.info("outputPath: {}", outputPath); + final String projectListPath = parser.get("projectListPath"); + log.info("projectListPath: {}", projectListPath); + SparkConf conf = new SparkConf(); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath); + getNewProjectList(spark, inputPath, outputPath, projectListPath); + }); + } + + private static void getNewProjectList(SparkSession spark, String inputPath, String outputPath, + String projectListPath) { + Dataset projectList = spark.read().textFile(projectListPath); + Dataset projects; + projects = Utils.readPath(spark, inputPath, Project.class); + projects + .joinWith(projectList, projects.col("id").equalTo(projectList.col("value")), "left") + .map((MapFunction, Project>) t2 -> { + if (Optional.ofNullable(t2._2()).isPresent()) + return null; + return t2._1(); + }, Encoders.bean(Project.class)) + .filter(Objects::nonNull) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath); + Utils + .readPath(spark, outputPath, Project.class) + .map((MapFunction) p -> p.getId(), Encoders.STRING()) + .write() + .mode(SaveMode.Append) + .option("compression", "gzip") + .text(projectListPath); + } +} From 0cb1c7078826ceca91a652ab8e23931728621a97 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 1 Jul 2022 10:44:08 +0200 Subject: [PATCH 20/23] code formatting --- .../dhp/common/api/ZenodoAPIClient.java | 19 +- .../transformation/TransformationJobTest.java | 10 +- .../dnetlib/dhp/bulktag/SparkBulkTagJob.java | 2 +- .../funderresults/SparkDumpFunderResults.java | 86 +++--- .../SparkResultLinkedToProject.java | 68 ++--- .../ProjectsSubsetSparkJob.java | 3 + .../dump/PrepareResultProjectJobTest.java | 272 +++++++++--------- .../ResultLinkedToProjectTest.java | 70 ++--- .../dump/funderresult/SplitPerFunderTest.java | 60 ++-- .../projectssubset/ProjectSubsetTest.java | 1 - 10 files changed, 304 insertions(+), 287 deletions(-) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/ZenodoAPIClient.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/ZenodoAPIClient.java index 56366bc72..63f890a10 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/ZenodoAPIClient.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/ZenodoAPIClient.java @@ -255,7 +255,8 @@ public class ZenodoAPIClient implements Serializable { private void setDepositionId(String concept_rec_id, Integer page) throws IOException, MissingConceptDoiException { - ZenodoModelList zenodoModelList = new Gson().fromJson(getPrevDepositions(String.valueOf(page)), ZenodoModelList.class); + ZenodoModelList zenodoModelList = new Gson() + .fromJson(getPrevDepositions(String.valueOf(page)), ZenodoModelList.class); for (ZenodoModel zm : zenodoModelList) { if (zm.getConceptrecid().equals(concept_rec_id)) { @@ -263,8 +264,9 @@ public class ZenodoAPIClient implements Serializable { return; } } - if(zenodoModelList.size() == 0) - throw new MissingConceptDoiException("The concept record id specified was missing in the list of depositions"); + if (zenodoModelList.size() == 0) + throw new MissingConceptDoiException( + "The concept record id specified was missing in the list of depositions"); setDepositionId(concept_rec_id, page + 1); } @@ -278,11 +280,11 @@ public class ZenodoAPIClient implements Serializable { String url = urlBuilder.build().toString(); Request request = new Request.Builder() - .url(url) - .addHeader(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString()) // add request headers - .addHeader(HttpHeaders.AUTHORIZATION, "Bearer " + access_token) - .get() - .build(); + .url(url) + .addHeader(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString()) // add request headers + .addHeader(HttpHeaders.AUTHORIZATION, "Bearer " + access_token) + .get() + .build(); try (Response response = httpClient.newCall(request).execute()) { @@ -295,7 +297,6 @@ public class ZenodoAPIClient implements Serializable { } - private String getBucket(String url) throws IOException { OkHttpClient httpClient = new OkHttpClient.Builder() .connectTimeout(600, TimeUnit.SECONDS) diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java index fea7b53ac..7fc80d168 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java @@ -142,7 +142,8 @@ class TransformationJobTest extends AbstractVocabularyTest { @Test @DisplayName("Test TransformSparkJobNode.main with oaiOpenaire_datacite (v4)") - void transformTestITGv4OAIdatacite(@TempDir final Path testDir) throws Exception { + void transformTestITGv4OAIdatacite(@TempDir + final Path testDir) throws Exception { try (SparkSession spark = SparkSession.builder().config(sparkConf).getOrCreate()) { @@ -152,7 +153,9 @@ class TransformationJobTest extends AbstractVocabularyTest { .getFile(); final String mdstore_output = testDir.toString() + "/version"; - mockupTrasformationRule("simpleTRule", "/eu/dnetlib/dhp/transform/scripts/xslt_cleaning_oaiOpenaire_datacite_ExchangeLandingpagePid.xsl"); + mockupTrasformationRule( + "simpleTRule", + "/eu/dnetlib/dhp/transform/scripts/xslt_cleaning_oaiOpenaire_datacite_ExchangeLandingpagePid.xsl"); final Map parameters = Stream.of(new String[][] { { @@ -203,7 +206,8 @@ class TransformationJobTest extends AbstractVocabularyTest { @Test @DisplayName("Test TransformSparkJobNode.main") - void transformTest(@TempDir final Path testDir) throws Exception { + void transformTest(@TempDir + final Path testDir) throws Exception { try (SparkSession spark = SparkSession.builder().config(sparkConf).getOrCreate()) { diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java index ad1e8721a..982e8ea75 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java @@ -103,7 +103,7 @@ public class SparkBulkTagJob { ResultTagger resultTagger = new ResultTagger(); readPath(spark, inputPath, resultClazz) .map(patchResult(), Encoders.bean(resultClazz)) - .filter(Objects::nonNull) + .filter(Objects::nonNull) .map( (MapFunction) value -> resultTagger .enrichContextCriteria( diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java index cfe47f29f..34ca6697c 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java @@ -1,10 +1,14 @@ + package eu.dnetlib.dhp.oa.graph.dump.funderresults; + import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + import java.io.Serializable; import java.util.List; import java.util.Objects; import java.util.Optional; import java.util.stream.Collectors; + import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.FlatMapFunction; @@ -14,29 +18,32 @@ import org.apache.spark.sql.*; import org.jetbrains.annotations.NotNull; import org.slf4j.Logger; import org.slf4j.LoggerFactory; + import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; import eu.dnetlib.dhp.schema.dump.oaf.community.Funder; import eu.dnetlib.dhp.schema.dump.oaf.community.Project; + /** * Splits the dumped results by funder and stores them in a folder named as the funder nsp (for all the funders, but the EC * for the EC it specifies also the fundingStream (FP7 or H2020) */ public class SparkDumpFunderResults implements Serializable { private static final Logger log = LoggerFactory.getLogger(SparkDumpFunderResults.class); + public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils - .toString( - SparkDumpFunderResults.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json")); + .toString( + SparkDumpFunderResults.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json")); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); parser.parseArgument(args); Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); final String inputPath = parser.get("sourcePath"); log.info("inputPath: {}", inputPath); @@ -44,30 +51,32 @@ public class SparkDumpFunderResults implements Serializable { log.info("outputPath: {}", outputPath); SparkConf conf = new SparkConf(); runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - writeResultProjectList(spark, inputPath, outputPath); - }); + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath); + writeResultProjectList(spark, inputPath, outputPath); + }); } + private static void writeResultProjectList(SparkSession spark, String inputPath, String outputPath) { Dataset result = Utils - .readPath(spark, inputPath + "/publication", CommunityResult.class) - .union(Utils.readPath(spark, inputPath + "/dataset", CommunityResult.class)) - .union(Utils.readPath(spark, inputPath + "/otherresearchproduct", CommunityResult.class)) - .union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class)); + .readPath(spark, inputPath + "/publication", CommunityResult.class) + .union(Utils.readPath(spark, inputPath + "/dataset", CommunityResult.class)) + .union(Utils.readPath(spark, inputPath + "/otherresearchproduct", CommunityResult.class)) + .union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class)); log.info("Number of result {}", result.count()); Dataset tmp = result - .flatMap((FlatMapFunction) cr -> cr.getProjects().stream().map(p -> { - return getFunderName(p); - }).collect(Collectors.toList()).iterator(), Encoders.STRING()) - .distinct(); + .flatMap((FlatMapFunction) cr -> cr.getProjects().stream().map(p -> { + return getFunderName(p); + }).collect(Collectors.toList()).iterator(), Encoders.STRING()) + .distinct(); List funderList = tmp.collectAsList(); funderList.forEach(funder -> { dumpResults(funder, result, outputPath); }); } + @NotNull private static String getFunderName(Project p) { Optional ofunder = Optional.ofNullable(p.getFunder()); @@ -97,23 +106,24 @@ public class SparkDumpFunderResults implements Serializable { return fName; } } + private static void dumpResults(String funder, Dataset results, String outputPath) { results.map((MapFunction) r -> { - if (!Optional.ofNullable(r.getProjects()).isPresent()) { - return null; - } - for (Project p : r.getProjects()) { - String fName = getFunderName(p); - if (fName.equalsIgnoreCase(funder)) { - return r; - } - } - return null; - }, Encoders.bean(CommunityResult.class)) - .filter(Objects::nonNull) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath + "/" + funder); + if (!Optional.ofNullable(r.getProjects()).isPresent()) { + return null; + } + for (Project p : r.getProjects()) { + String fName = getFunderName(p); + if (fName.equalsIgnoreCase(funder)) { + return r; + } + } + return null; + }, Encoders.bean(CommunityResult.class)) + .filter(Objects::nonNull) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath + "/" + funder); } -} \ No newline at end of file +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java index 5eed64e89..4b0072944 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java @@ -45,18 +45,18 @@ public class SparkResultLinkedToProject implements Serializable { public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils - .toString( - SparkResultLinkedToProject.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json")); + .toString( + SparkResultLinkedToProject.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json")); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); parser.parseArgument(args); Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); final String inputPath = parser.get("sourcePath"); @@ -78,41 +78,41 @@ public class SparkResultLinkedToProject implements Serializable { SparkConf conf = new SparkConf(); runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - writeResultsLinkedToProjects( - communityMapPath, spark, inputClazz, inputPath, outputPath, resultProjectsPath); - }); + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath); + writeResultsLinkedToProjects( + communityMapPath, spark, inputClazz, inputPath, outputPath, resultProjectsPath); + }); } private static void writeResultsLinkedToProjects(String communityMapPath, SparkSession spark, - Class inputClazz, - String inputPath, String outputPath, String resultProjectsPath) { + Class inputClazz, + String inputPath, String outputPath, String resultProjectsPath) { Dataset results = Utils - .readPath(spark, inputPath, inputClazz) - .filter( - (FilterFunction) r -> !r.getDataInfo().getDeletedbyinference() && - !r.getDataInfo().getInvisible()); + .readPath(spark, inputPath, inputClazz) + .filter( + (FilterFunction) r -> !r.getDataInfo().getDeletedbyinference() && + !r.getDataInfo().getInvisible()); Dataset resultProjectDataset = Utils - .readPath(spark, resultProjectsPath, ResultProject.class); + .readPath(spark, resultProjectsPath, ResultProject.class); CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath); results - .joinWith(resultProjectDataset, results.col("id").equalTo(resultProjectDataset.col("resultId"))) - .map((MapFunction, CommunityResult>) t2 -> { - CommunityResult cr = (CommunityResult) ResultMapper - .map( - t2._1(), - communityMap, Constants.DUMPTYPE.FUNDER.getType()); - cr.setProjects(t2._2().getProjectsList()); - return cr; - }, Encoders.bean(CommunityResult.class)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); + .joinWith(resultProjectDataset, results.col("id").equalTo(resultProjectDataset.col("resultId"))) + .map((MapFunction, CommunityResult>) t2 -> { + CommunityResult cr = (CommunityResult) ResultMapper + .map( + t2._1(), + communityMap, Constants.DUMPTYPE.FUNDER.getType()); + cr.setProjects(t2._2().getProjectsList()); + return cr; + }, Encoders.bean(CommunityResult.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java index 83a9f3464..38eb3cb37 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java @@ -2,9 +2,11 @@ package eu.dnetlib.dhp.oa.graph.dump.projectssubset; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + import java.io.Serializable; import java.util.Objects; import java.util.Optional; + import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; @@ -14,6 +16,7 @@ import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; import org.slf4j.LoggerFactory; + import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.schema.dump.oaf.graph.Project; diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java index c6798ac58..f3b7246b1 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java @@ -35,12 +35,12 @@ public class PrepareResultProjectJobTest { private static Path workingDir; private static final Logger log = LoggerFactory - .getLogger(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class); + .getLogger(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class); @BeforeAll public static void beforeAll() throws IOException { workingDir = Files - .createTempDirectory(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class.getSimpleName()); + .createTempDirectory(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class.getSimpleName()); log.info("using work dir {}", workingDir); SparkConf conf = new SparkConf(); @@ -54,10 +54,10 @@ public class PrepareResultProjectJobTest { conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); spark = SparkSession - .builder() - .appName(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); + .builder() + .appName(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); } @AfterAll @@ -70,23 +70,23 @@ public class PrepareResultProjectJobTest { void testNoMatch() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/no_match") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/no_match") + .getPath(); SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); + .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); assertEquals(0, verificationDataset.count()); @@ -96,37 +96,37 @@ public class PrepareResultProjectJobTest { void testMatchOne() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_one") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_one") + .getPath(); SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); + .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); assertEquals(1, verificationDataset.count()); assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); verificationDataset.createOrReplaceTempView("table"); Dataset check = spark - .sql( - "Select projList.provenance.provenance " + - "from table " + - "lateral view explode (projectsList) pl as projList"); + .sql( + "Select projList.provenance.provenance " + + "from table " + + "lateral view explode (projectsList) pl as projList"); assertEquals(1, check.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); @@ -138,88 +138,88 @@ public class PrepareResultProjectJobTest { void testMatch() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match") + .getPath(); SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); + .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); assertEquals(2, verificationDataset.count()); assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); verificationDataset.createOrReplaceTempView("dataset"); String query = "select resultId, MyT.id project , MyT.title title, MyT.acronym acronym , MyT.provenance.provenance provenance " - + "from dataset " - + "lateral view explode(projectsList) p as MyT "; + + "from dataset " + + "lateral view explode(projectsList) p as MyT "; org.apache.spark.sql.Dataset resultExplodedProvenance = spark.sql(query); assertEquals(3, resultExplodedProvenance.count()); assertEquals( - 2, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") - .count()); + 2, + resultExplodedProvenance + .filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") - .count()); + 1, + resultExplodedProvenance + .filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") + .count()); assertEquals( - 2, - resultExplodedProvenance - .filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'") - .count()); + 2, + resultExplodedProvenance + .filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'") - .count()); + 1, + resultExplodedProvenance + .filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::03376222b28a3aebf2730ac514818d04' and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::03376222b28a3aebf2730ac514818d04' and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") + .count()); assertEquals( - 3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); + 3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); } @@ -227,98 +227,98 @@ public class PrepareResultProjectJobTest { public void testMatchValidated() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_validatedRels") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_validatedRels") + .getPath(); SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); + .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); assertEquals(2, verificationDataset.count()); assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); verificationDataset.createOrReplaceTempView("dataset"); String query = "select resultId, MyT.id project , MyT.title title, MyT.acronym acronym , MyT.provenance.provenance provenance, " - + - "MyT.validated.validatedByFunder, MyT.validated.validationDate " - + "from dataset " - + "lateral view explode(projectsList) p as MyT "; + + + "MyT.validated.validatedByFunder, MyT.validated.validationDate " + + "from dataset " + + "lateral view explode(projectsList) p as MyT "; org.apache.spark.sql.Dataset resultExplodedProvenance = spark.sql(query); assertEquals(3, resultExplodedProvenance.count()); assertEquals(3, resultExplodedProvenance.filter("validatedByFunder = true").count()); assertEquals( - 2, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") - .count()); + 2, + resultExplodedProvenance + .filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") - .count()); + 1, + resultExplodedProvenance + .filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") + .count()); assertEquals( - 2, - resultExplodedProvenance - .filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'") - .count()); + 2, + resultExplodedProvenance + .filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + - "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + - "and validatedByFunder = true " + - "and validationDate = '2021-08-06'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + + "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + + "and validatedByFunder = true " + + "and validationDate = '2021-08-06'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + - "and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80' " + - "and validatedByFunder = true and validationDate = '2021-08-04'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + + "and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80' " + + "and validatedByFunder = true and validationDate = '2021-08-04'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'") - .count()); + 1, + resultExplodedProvenance + .filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::03376222b28a3aebf2730ac514818d04' " + - "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + - "and validatedByFunder = true and validationDate = '2021-08-05'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::03376222b28a3aebf2730ac514818d04' " + + "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + + "and validatedByFunder = true and validationDate = '2021-08-05'") + .count()); assertEquals( - 3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); + 3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); } @@ -326,20 +326,20 @@ public class PrepareResultProjectJobTest { void testMatchx() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match") + .getPath(); SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r))); } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java index 579958a62..7046b02c2 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java @@ -35,15 +35,15 @@ public class ResultLinkedToProjectTest { private static Path workingDir; private static final Logger log = LoggerFactory - .getLogger(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class); + .getLogger(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class); private static final HashMap map = new HashMap<>(); @BeforeAll public static void beforeAll() throws IOException { workingDir = Files - .createTempDirectory( - eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()); + .createTempDirectory( + eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()); log.info("using work dir {}", workingDir); SparkConf conf = new SparkConf(); @@ -57,10 +57,10 @@ public class ResultLinkedToProjectTest { conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); spark = SparkSession - .builder() - .appName(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); + .builder() + .appName(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); } @AfterAll @@ -73,32 +73,32 @@ public class ResultLinkedToProjectTest { void testNoMatch() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json") + .getPath(); final String graphPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo") + .getPath(); final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/communityMapPath") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/communityMapPath") + .getPath(); SparkResultLinkedToProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-graphPath", graphPath, - "-communityMapPath", communityMapPath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath, + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", + "-graphPath", graphPath, + "-communityMapPath", communityMapPath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(0, tmp.count()); @@ -108,32 +108,32 @@ public class ResultLinkedToProjectTest { void testMatchOne() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/papers.json") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/papers.json") + .getPath(); final String graphPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo") + .getPath(); final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/communityMapPath") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/communityMapPath") + .getPath(); SparkResultLinkedToProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-graphPath", graphPath, - "-communityMapPath", communityMapPath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath, + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", + "-graphPath", graphPath, + "-communityMapPath", communityMapPath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(1, tmp.count()); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java index 5bb5a1178..e9d739db2 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java @@ -56,10 +56,10 @@ public class SplitPerFunderTest { conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); spark = SparkSession - .builder() - .appName(SplitPerFunderTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); + .builder() + .appName(SplitPerFunderTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); } @AfterAll @@ -72,13 +72,13 @@ public class SplitPerFunderTest { void test1() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext") + .getPath(); SparkDumpFunderResults.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/split", - "-sourcePath", sourcePath + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/split", + "-sourcePath", sourcePath }); @@ -86,64 +86,64 @@ public class SplitPerFunderTest { // FP7 3 and H2020 3 JavaRDD tmp = sc - .textFile(workingDir.toString() + "/split/EC_FP7") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/EC_FP7") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); + .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); Assertions.assertEquals(3, verificationDataset.count()); Assertions - .assertEquals( - 1, verificationDataset.filter("id = '50|dedup_wf_001::0d16b1714ab3077df73893a8ea57d776'").count()); + .assertEquals( + 1, verificationDataset.filter("id = '50|dedup_wf_001::0d16b1714ab3077df73893a8ea57d776'").count()); // CIHR 2 tmp = sc - .textFile(workingDir.toString() + "/split/CIHR") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/CIHR") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(2, tmp.count()); // NWO 1 tmp = sc - .textFile(workingDir.toString() + "/split/NWO") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/NWO") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(1, tmp.count()); // NIH 3 tmp = sc - .textFile(workingDir.toString() + "/split/NIH") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/NIH") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(2, tmp.count()); // NSF 1 tmp = sc - .textFile(workingDir.toString() + "/split/NSF") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/NSF") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(1, tmp.count()); // SNSF 1 tmp = sc - .textFile(workingDir.toString() + "/split/SNSF") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/SNSF") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(1, tmp.count()); // NHMRC 1 tmp = sc - .textFile(workingDir.toString() + "/split/NHMRC") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/NHMRC") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(1, tmp.count()); // H2020 3 tmp = sc - .textFile(workingDir.toString() + "/split/EC_H2020") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/EC_H2020") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(3, tmp.count()); // MZOS 1 tmp = sc - .textFile(workingDir.toString() + "/split/MZOS") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + .textFile(workingDir.toString() + "/split/MZOS") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(1, tmp.count()); } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java index 4ff1e1b96..8cdb285e4 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java @@ -30,7 +30,6 @@ public class ProjectSubsetTest { private static final Logger log = LoggerFactory .getLogger(eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class); - @BeforeAll public static void beforeAll() throws IOException { workingDir = Files From 5b76321d9cb58f68a52ee01d14ea77f38e81d749 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Wed, 20 Jul 2022 16:34:32 +0200 Subject: [PATCH 21/23] implemented oozie workflow to generate scholix dump filtering relclass semantic --- .../sx/graph/convert_dataset_json_params.json | 1 + .../sx/graph/convert_object_json_params.json | 4 +- .../dumpScholix/oozie_app/config-default.xml | 10 ++ .../graph/dumpScholix/oozie_app/workflow.xml | 145 ++++++++++++++++++ .../sx/graph/SparkConvertObjectToJson.scala | 33 +++- .../sx/graph/SparkConvertRDDtoDataset.scala | 61 +++++--- 6 files changed, 228 insertions(+), 26 deletions(-) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/dumpScholix/oozie_app/config-default.xml create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/dumpScholix/oozie_app/workflow.xml diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/convert_dataset_json_params.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/convert_dataset_json_params.json index 8bfdde5b0..f3e8cdbad 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/convert_dataset_json_params.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/convert_dataset_json_params.json @@ -2,4 +2,5 @@ {"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true}, {"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the source Path", "paramRequired": true}, {"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the path of the raw graph", "paramRequired": true} + {"paramName":"r", "paramLongName":"filterRelation", "paramDescription": "the relation to filter", "paramRequired": false} ] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/convert_object_json_params.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/convert_object_json_params.json index 890570a0b..cbb20bfe7 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/convert_object_json_params.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/convert_object_json_params.json @@ -3,5 +3,7 @@ {"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the source Path", "paramRequired": true}, {"paramName":"su", "paramLongName":"scholixUpdatePath", "paramDescription": "the scholix updated Path", "paramRequired": false}, {"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the path of the raw graph", "paramRequired": true}, - {"paramName":"o", "paramLongName":"objectType", "paramDescription": "should be scholix or Summary", "paramRequired": true} + {"paramName":"o", "paramLongName":"objectType", "paramDescription": "should be scholix or Summary", "paramRequired": true}, + {"paramName":"mp", "paramLongName":"maxPidNumberFilter", "paramDescription": "filter max number of pids in source/target", "paramRequired": false} + ] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/dumpScholix/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/dumpScholix/oozie_app/config-default.xml new file mode 100644 index 000000000..6fb2a1253 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/dumpScholix/oozie_app/config-default.xml @@ -0,0 +1,10 @@ + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/dumpScholix/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/dumpScholix/oozie_app/workflow.xml new file mode 100644 index 000000000..a37d85ad4 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/dumpScholix/oozie_app/workflow.xml @@ -0,0 +1,145 @@ + + + + sourcePath + the working dir base path + + + targetPath + the final graph path + + + relationFilter + Filter relation semantic + + + maxNumberOfPid + filter relation with at least #maxNumberOfPid + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + yarn + cluster + Import JSONRDD to Dataset kryo + eu.dnetlib.dhp.sx.graph.SparkConvertRDDtoDataset + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.shuffle.partitions=3000 + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --masteryarn + --sourcePath${sourcePath} + --targetPath${targetPath} + --filterRelation${relationFilter} + + + + + + + + + yarn + cluster + Convert Entities to summaries + eu.dnetlib.dhp.sx.graph.SparkCreateSummaryObject + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.shuffle.partitions=20000 + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --masteryarn + --sourcePath${targetPath}/entities + --targetPath${targetPath}/provision/summaries + + + + + + + + yarn + cluster + Generate Scholix Dataset + eu.dnetlib.dhp.sx.graph.SparkCreateScholix + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.shuffle.partitions=30000 + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --masteryarn + --summaryPath${targetPath}/provision/summaries + --targetPath${targetPath}/provision/scholix + --relationPath${targetPath}/relation + + + + + + + + + + + + + + + + + yarn + cluster + Serialize scholix to JSON + eu.dnetlib.dhp.sx.graph.SparkConvertObjectToJson + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.shuffle.partitions=6000 + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --masteryarn + --sourcePath${targetPath}/provision/scholix/scholix + --targetPath${targetPath}/json/scholix_json + --objectTypescholix + --maxPidNumberFiltermaxNumberOfPid + + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertObjectToJson.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertObjectToJson.scala index bfa07eb69..6695ebd3c 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertObjectToJson.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertObjectToJson.scala @@ -4,6 +4,7 @@ import com.fasterxml.jackson.databind.ObjectMapper import eu.dnetlib.dhp.application.ArgumentApplicationParser import eu.dnetlib.dhp.schema.sx.scholix.Scholix import eu.dnetlib.dhp.schema.sx.summary.ScholixSummary +import eu.dnetlib.dhp.sx.graph.SparkConvertObjectToJson.toInt import org.apache.commons.io.IOUtils import org.apache.hadoop.io.compress.GzipCodec import org.apache.spark.SparkConf @@ -12,6 +13,14 @@ import org.slf4j.{Logger, LoggerFactory} object SparkConvertObjectToJson { + def toInt(s: String): Option[Int] = { + try { + Some(s.toInt) + } catch { + case e: Exception => None + } + } + def main(args: Array[String]): Unit = { val log: Logger = LoggerFactory.getLogger(getClass) val conf: SparkConf = new SparkConf() @@ -37,6 +46,8 @@ object SparkConvertObjectToJson { log.info(s"objectType -> $objectType") val scholixUpdatePath = parser.get("scholixUpdatePath") log.info(s"scholixUpdatePath -> $scholixUpdatePath") + val maxPidNumberFilter = parser.get("maxPidNumberFilter") + log.info(s"maxPidNumberFilter -> $maxPidNumberFilter") implicit val scholixEncoder: Encoder[Scholix] = Encoders.kryo[Scholix] implicit val summaryEncoder: Encoder[ScholixSummary] = Encoders.kryo[ScholixSummary] @@ -47,12 +58,22 @@ object SparkConvertObjectToJson { case "scholix" => log.info("Serialize Scholix") val d: Dataset[Scholix] = spark.read.load(sourcePath).as[Scholix] - val u: Dataset[Scholix] = spark.read.load(s"$scholixUpdatePath/scholix").as[Scholix] - d.union(u) - .repartition(8000) - .map(s => mapper.writeValueAsString(s))(Encoders.STRING) - .rdd - .saveAsTextFile(targetPath, classOf[GzipCodec]) +// val u: Dataset[Scholix] = spark.read.load(s"$scholixUpdatePath/scholix").as[Scholix] + if (maxPidNumberFilter != null && toInt(maxPidNumberFilter).isDefined) { + val mp = toInt(maxPidNumberFilter).get + d + .filter(s => (s.getSource.getIdentifier.size() <= mp) && (s.getTarget.getIdentifier.size() <= mp)) + .map(s => mapper.writeValueAsString(s))(Encoders.STRING) + .rdd + .saveAsTextFile(targetPath, classOf[GzipCodec]) + } else { + d + .repartition(8000) + .map(s => mapper.writeValueAsString(s))(Encoders.STRING) + .rdd + .saveAsTextFile(targetPath, classOf[GzipCodec]) + } + case "summary" => log.info("Serialize Summary") val d: Dataset[ScholixSummary] = spark.read.load(sourcePath).as[ScholixSummary] diff --git a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala index bd970a5cf..f72f8dd16 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala @@ -4,9 +4,11 @@ import com.fasterxml.jackson.databind.ObjectMapper import eu.dnetlib.dhp.application.ArgumentApplicationParser import eu.dnetlib.dhp.schema.oaf.{OtherResearchProduct, Publication, Relation, Result, Software, Dataset => OafDataset} import org.apache.commons.io.IOUtils +import org.apache.commons.lang3.StringUtils import org.apache.spark.SparkConf import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession} import org.slf4j.{Logger, LoggerFactory} + import scala.collection.JavaConverters._ object SparkConvertRDDtoDataset { @@ -34,6 +36,9 @@ object SparkConvertRDDtoDataset { val t = parser.get("targetPath") log.info(s"targetPath -> $t") + val filterRelation = parser.get("filterRelation") + log.info(s"filterRelation -> $filterRelation") + val entityPath = s"$t/entities" val relPath = s"$t/relation" val mapper = new ObjectMapper() @@ -94,28 +99,46 @@ object SparkConvertRDDtoDataset { log.info("Converting Relation") - val relationSemanticFilter = List( -// "cites", -// "iscitedby", - "merges", - "ismergedin", - "HasAmongTopNSimilarDocuments", - "IsAmongTopNSimilarDocuments" - ) + if (filterRelation != null && StringUtils.isNoneBlank(filterRelation)) { - val rddRelation = spark.sparkContext - .textFile(s"$sourcePath/relation") - .map(s => mapper.readValue(s, classOf[Relation])) - .filter(r => r.getDataInfo != null && r.getDataInfo.getDeletedbyinference == false) - .filter(r => r.getSource.startsWith("50") && r.getTarget.startsWith("50")) - //filter OpenCitations relations - .filter(r => - r.getCollectedfrom != null && r.getCollectedfrom.size() > 0 && !r.getCollectedfrom.asScala.exists(k => - "opencitations".equalsIgnoreCase(k.getValue) + val rddRelation = spark.sparkContext + .textFile(s"$sourcePath/relation") + .map(s => mapper.readValue(s, classOf[Relation])) + .filter(r => r.getDataInfo != null && r.getDataInfo.getDeletedbyinference == false) + .filter(r => r.getSource.startsWith("50") && r.getTarget.startsWith("50")) + //filter OpenCitations relations + .filter(r => + r.getCollectedfrom != null && r.getCollectedfrom.size() > 0 && !r.getCollectedfrom.asScala.exists(k => + "opencitations".equalsIgnoreCase(k.getValue) + ) ) + .filter(r => r.getRelClass != null && r.getRelClass.equalsIgnoreCase(filterRelation)) + spark.createDataset(rddRelation).as[Relation].write.mode(SaveMode.Overwrite).save(s"$relPath") + } else { + + val relationSemanticFilter = List( + // "cites", + // "iscitedby", + "merges", + "ismergedin", + "HasAmongTopNSimilarDocuments", + "IsAmongTopNSimilarDocuments" ) - .filter(r => !relationSemanticFilter.exists(k => k.equalsIgnoreCase(r.getRelClass))) - spark.createDataset(rddRelation).as[Relation].write.mode(SaveMode.Overwrite).save(s"$relPath") + + val rddRelation = spark.sparkContext + .textFile(s"$sourcePath/relation") + .map(s => mapper.readValue(s, classOf[Relation])) + .filter(r => r.getDataInfo != null && r.getDataInfo.getDeletedbyinference == false) + .filter(r => r.getSource.startsWith("50") && r.getTarget.startsWith("50")) + //filter OpenCitations relations + .filter(r => + r.getCollectedfrom != null && r.getCollectedfrom.size() > 0 && !r.getCollectedfrom.asScala.exists(k => + "opencitations".equalsIgnoreCase(k.getValue) + ) + ) + .filter(r => !relationSemanticFilter.exists(k => k.equalsIgnoreCase(r.getRelClass))) + spark.createDataset(rddRelation).as[Relation].write.mode(SaveMode.Overwrite).save(s"$relPath") + } } } From 5f651f231650d0e2547bfdf9f7969611e5d43d85 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Thu, 21 Jul 2022 10:11:48 +0200 Subject: [PATCH 22/23] changed filter relation on SubRelType --- .../eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala index f72f8dd16..0073afff5 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala @@ -112,13 +112,11 @@ object SparkConvertRDDtoDataset { "opencitations".equalsIgnoreCase(k.getValue) ) ) - .filter(r => r.getRelClass != null && r.getRelClass.equalsIgnoreCase(filterRelation)) + .filter(r => r.getSubRelType != null && r.getSubRelType.equalsIgnoreCase(filterRelation)) spark.createDataset(rddRelation).as[Relation].write.mode(SaveMode.Overwrite).save(s"$relPath") } else { val relationSemanticFilter = List( - // "cites", - // "iscitedby", "merges", "ismergedin", "HasAmongTopNSimilarDocuments", From ddc414b2586075f2ab32b59480115c826e9a863c Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Fri, 22 Jul 2022 09:43:15 +0200 Subject: [PATCH 23/23] fixed wrong json param --- .../eu/dnetlib/dhp/sx/graph/convert_dataset_json_params.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/convert_dataset_json_params.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/convert_dataset_json_params.json index f3e8cdbad..3a2f90708 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/convert_dataset_json_params.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/convert_dataset_json_params.json @@ -1,6 +1,6 @@ [ {"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true}, {"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the source Path", "paramRequired": true}, - {"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the path of the raw graph", "paramRequired": true} + {"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the path of the raw graph", "paramRequired": true}, {"paramName":"r", "paramLongName":"filterRelation", "paramDescription": "the relation to filter", "paramRequired": false} ] \ No newline at end of file