From 1699d41d39a5d70e681589b3cf03b9d61d1a9a06 Mon Sep 17 00:00:00 2001 From: miconis Date: Thu, 5 Nov 2020 15:48:42 +0100 Subject: [PATCH 01/11] relations for openorgs: not it choose only one master --- .../dhp/oa/dedup/SparkPrepareOrgRels.java | 50 ++++++++++--------- 1 file changed, 26 insertions(+), 24 deletions(-) diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPrepareOrgRels.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPrepareOrgRels.java index e9933c4e5..19e6127f6 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPrepareOrgRels.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPrepareOrgRels.java @@ -1,13 +1,9 @@ + package eu.dnetlib.dhp.oa.dedup; -import com.google.common.collect.Lists; -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.dedup.model.OrgSimRel; -import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.dhp.schema.oaf.Organization; -import eu.dnetlib.dhp.schema.oaf.Relation; -import eu.dnetlib.dhp.utils.ISLookupClientFactory; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; +import java.io.IOException; +import java.util.*; + import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; @@ -17,12 +13,19 @@ import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; import org.slf4j.LoggerFactory; + +import com.google.common.collect.Lists; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.oa.dedup.model.OrgSimRel; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.oaf.Organization; +import eu.dnetlib.dhp.schema.oaf.Relation; +import eu.dnetlib.dhp.utils.ISLookupClientFactory; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import scala.Tuple2; import scala.Tuple3; -import java.io.IOException; -import java.util.*; - public class SparkPrepareOrgRels extends AbstractSparkAction { private static final Logger log = LoggerFactory.getLogger(SparkCreateDedupRecord.class); @@ -125,12 +128,11 @@ public class SparkPrepareOrgRels extends AbstractSparkAction { List ids = sortIds(l); List> rels = new ArrayList<>(); - for (String source : ids) { - if (source.contains("openorgs____") || ids.indexOf(source) == 0) - for (String target : ids) { - rels.add(new Tuple3<>(source, target, groupId)); - } + String source = ids.get(0); + for (String target : ids) { + rels.add(new Tuple3<>(source, target, groupId)); } + return rels.iterator(); }) .rdd(), @@ -235,14 +237,14 @@ public class SparkPrepareOrgRels extends AbstractSparkAction { .joinWith(entities, relations.col("_2").equalTo(entities.col("_1")), "inner") .map( (MapFunction, Tuple2>, OrgSimRel>) r -> new OrgSimRel( - r._1()._1(), - r._2()._2().getOriginalId().get(0), - r._2()._2().getLegalname() != null ? r._2()._2().getLegalname().getValue() : "", - r._2()._2().getLegalshortname() != null ? r._2()._2().getLegalshortname().getValue() : "", - r._2()._2().getCountry() != null ? r._2()._2().getCountry().getClassid() : "", - r._2()._2().getWebsiteurl() != null ? r._2()._2().getWebsiteurl().getValue() : "", - r._2()._2().getCollectedfrom().get(0).getValue(), - "group::" + r._1()._1()), + r._1()._1(), + r._2()._2().getOriginalId().get(0), + r._2()._2().getLegalname() != null ? r._2()._2().getLegalname().getValue() : "", + r._2()._2().getLegalshortname() != null ? r._2()._2().getLegalshortname().getValue() : "", + r._2()._2().getCountry() != null ? r._2()._2().getCountry().getClassid() : "", + r._2()._2().getWebsiteurl() != null ? r._2()._2().getWebsiteurl().getValue() : "", + r._2()._2().getCollectedfrom().get(0).getValue(), + "group::" + r._1()._1()), Encoders.bean(OrgSimRel.class)) .map( (MapFunction>) o -> new Tuple2<>(o.getLocal_id(), o), From 1cb79719a7295bd3fb0f145bc9bc9217d8f116bf Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 28 Sep 2022 11:44:55 +0200 Subject: [PATCH 02/11] [BulkTag] fixed issues --- .../dhp/bulktag/community/ResultTagger.java | 11 ++++++----- .../eu/dnetlib/dhp/bulktag/BulkTagJobTest.java | 15 +-------------- .../update_subject_datasource/dataset_10.json | 10 ++++++++++ .../update_subject_datasource/dataset_10.json.gz | Bin 6968 -> 0 bytes 4 files changed, 17 insertions(+), 19 deletions(-) create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject_datasource/dataset_10.json delete mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject_datasource/dataset_10.json.gz diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java index ccb69a97d..9286c7385 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java @@ -152,7 +152,8 @@ public class ResultTagger implements Serializable { } result.getContext().forEach(c -> { - if (communities.contains(c.getId())) { + String cId = c.getId(); + if (communities.contains(cId)) { Optional> opt_dataInfoList = Optional.ofNullable(c.getDataInfo()); List dataInfoList; if (opt_dataInfoList.isPresent()) @@ -161,19 +162,19 @@ public class ResultTagger implements Serializable { dataInfoList = new ArrayList<>(); c.setDataInfo(dataInfoList); } - if (subjects.contains(c)) + if (subjects.contains(cId)) dataInfoList .add(OafMapperUtils.dataInfo(false, BULKTAG_DATA_INFO_TYPE, true, false, OafMapperUtils.qualifier(CLASS_ID_SUBJECT, CLASS_NAME_BULKTAG_SUBJECT, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), TAGGING_TRUST)); - if (datasources.contains(c)) + if (datasources.contains(cId)) dataInfoList .add(OafMapperUtils.dataInfo(false, BULKTAG_DATA_INFO_TYPE, true, false, OafMapperUtils.qualifier(CLASS_ID_DATASOURCE, CLASS_NAME_BULKTAG_DATASOURCE, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), TAGGING_TRUST)); - if (czenodo.contains(c)) + if (czenodo.contains(cId)) dataInfoList .add(OafMapperUtils.dataInfo(false, BULKTAG_DATA_INFO_TYPE, true, false, OafMapperUtils.qualifier(CLASS_ID_CZENODO, CLASS_NAME_BULKTAG_ZENODO, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), TAGGING_TRUST)); - if (aconstraints.contains(c)) + if (aconstraints.contains(cId)) dataInfoList .add( OafMapperUtils.dataInfo(false, BULKTAG_DATA_INFO_TYPE, true, false, diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java index 0212f4a49..30d9a43b2 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java @@ -21,6 +21,7 @@ import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.ForeachFunction; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.Row; import org.apache.spark.sql.SparkSession; @@ -778,18 +779,4 @@ public class BulkTagJobTest { 1, idExplodeCommunity.filter("provenance = 'community:advconstraint'").count()); } -// @Test -// void test1(){ -// ProtoMap params = new Gson().fromJson(pathMap, ProtoMap.class); -// HashMap param = new HashMap<>(); -// for (String key : params.keySet()) { -// try { -// param.put(key, jsonContext.read(params.get(key))); -// } catch (com.jayway.jsonpath.PathNotFoundException e) { -// param.put(key, new ArrayList<>()); -// } -// } -// return param; -// } -// } } diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject_datasource/dataset_10.json b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject_datasource/dataset_10.json new file mode 100644 index 000000000..210719e29 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject_datasource/dataset_10.json @@ -0,0 +1,10 @@ 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se están desarrollando en la Universidad Camilo José Cela (UCJC) sobre la cafeína y sus efectos cuando se realiza deporte. https://www.ucjc.edu/2016/08/la-bbc-s...\n\nJuan Del Coso, director del Laboratorio de Fisiología del Ejercicio de la Universidad Camilo José Cela, nos describe cómo está siendo la investigación que desarrolla con deportistas de alto rendimiento y el consumo de cafeína.\n\n\"Nuestra investigación se enmarca dentro del campo de la fisiología del ejercicio y el objetivo que tenemos es investigar los efectos que tiene la cafeína en los deportistas, principalmente saber si es una ayuda ergogénica en la mayor parte de los deportes, pero también conocer qué perjuicios existen para aquellos deportistas que la utilizan para incrementar el rendimiento deportivo\", explica Del Coso.\n\nY es que los datos son muy llamativos: tres de cada cuatro deportistas de alto rendimiento utilizan la cafeína antes de la competición y muchas veces se utiliza sin saber los perjuicios que puede tener para el deportista. \"Lo que estamos investigando es cómo una sustancia, que te puede hacer rendir mejor, cómo puede afectar negativamente cuando termina una competición\".\n\nPero esta investigación no sólo puede extraer conclusiones interesantes y útiles para los deportistas profesionales, \"investigando el deporte de alto rendimiento podemos conocer los beneficios y perjuicios de la cafeína que también afectarían al deportista amateur y hacer un deporte en general más seguro\".\n\nPara el desarrollo de este proyecto de investigación están colaborando el Laboratorio de Fisiología del Ejercicio de la Universidad Camilo José Cela y la Agencia para la Protección de la Salud en el Deporte.\nPara el desarrollo de este proyecto de investigación están colaborando el Laboratorio de Fisiología del Ejercicio de la Universidad Camilo José Cela y la Agencia para la Protección de la Salud en el 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El formato es al estilo inglés, similar al de la Oxford Union, donde algunos jóvenes se reunían a debatir sobre temas de la más candente actualidad y polemizaban con la intención de formarse en tan valoradas habilidades.\n\nLa Liga de Debate CICAE-UCJC es una ocasión única para los alumnos de ponerse en contacto con herramientas tan útiles como la oratoria y la comunicación efectiva. Pero, sobre todo, una oportunidad de fomentar el pensamiento crítico y la socialización entre alumnos con espíritu emprendedor. La Liga de Debate CICAE - Universidad Camilo José Cela se diferencia del resto de torneos en que potenciamos que sea eminentemente formativa. Alumnos y profesores reciben formación en comunicación, oratoria y debate por parte de alguno de los expertos en debate españoles más reconocidos en la escena internacional.\n\nDatos de la III Liga de Debate CICAE - UCJC http://ligacicae.ucjc.edu/","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2018-10-23","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":null,"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[{"value":"Universidad 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zaPvMp_=Kv6E9vMW_v#LJxzy$RPN$A8((rmXx`?BT{9frI=oRcXUBr#ZjxO@%PyY{f KBST|kQ~?0ZJb}sp From 7fda05e3803bebd087c382411d88914e21c6f2db Mon Sep 17 00:00:00 2001 From: dimitrispie Date: Tue, 1 Nov 2022 13:59:40 +0200 Subject: [PATCH 03/11] Added Autonomous University of Barcelona --- .../graph/stats/oozie_app/scripts/step20-createMonitorDB.sql | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql index 2505c3a34..5dbedfa67 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql @@ -48,7 +48,8 @@ create table TARGET.result stored as parquet as 'openorgs____::3e8d1f8c3f6cd7f418b09f1f58b4873b', -- Aristotle University of Thessaloniki 'openorgs____::3fcef6e1c469c10f2a84b281372c9814', -- World Bank 'openorgs____::1698a2eb1885ef8adb5a4a969e745ad3', -- École des Ponts ParisTech - 'openorgs____::e15adb13c4dadd49de4d35c39b5da93a' -- Nanyang Technological University + 'openorgs____::e15adb13c4dadd49de4d35c39b5da93a', -- Nanyang Technological University + 'openorgs____::4b34103bde246228fcd837f5f1bf4212' -- Autonomous University of Barcelona ) )) foo; compute stats TARGET.result; From 992fc5b628ccad566acf218019cf576408564f73 Mon Sep 17 00:00:00 2001 From: dimitrispie Date: Thu, 3 Nov 2022 11:02:18 +0200 Subject: [PATCH 04/11] Added McMaster University Institution --- .../graph/stats/oozie_app/scripts/step20-createMonitorDB.sql | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql index 5dbedfa67..2bdcbfa3d 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql @@ -49,7 +49,8 @@ create table TARGET.result stored as parquet as 'openorgs____::3fcef6e1c469c10f2a84b281372c9814', -- World Bank 'openorgs____::1698a2eb1885ef8adb5a4a969e745ad3', -- École des Ponts ParisTech 'openorgs____::e15adb13c4dadd49de4d35c39b5da93a', -- Nanyang Technological University - 'openorgs____::4b34103bde246228fcd837f5f1bf4212' -- Autonomous University of Barcelona + 'openorgs____::4b34103bde246228fcd837f5f1bf4212', -- Autonomous University of Barcelona + 'openorgs____::72ec75fcfc4e0df1a76dc4c49007fceb' -- McMaster University ) )) foo; compute stats TARGET.result; From 5af5a8ae42c5c3303bad4f0eeaccee518ef0480f Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 9 Nov 2022 14:20:59 +0100 Subject: [PATCH 05/11] added IdentifierComparator --- .../dhp/oa/dedup/DedupRecordFactory.java | 21 ++++- .../eu/dnetlib/dhp/oa/dedup/IdGenerator.java | 4 + .../dhp/oa/dedup/IdentifierComparator.java | 81 +++++++++++++++++++ .../dhp/oa/dedup/model/Identifier.java | 53 +----------- .../dhp/oa/dedup/SparkOpenorgsDedupTest.java | 4 +- .../dnetlib/dhp/oa/dedup/SparkStatsTest.java | 4 +- .../src/test/resources/log4j.properties | 25 ++++++ 7 files changed, 134 insertions(+), 58 deletions(-) create mode 100644 dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/IdentifierComparator.java create mode 100644 dhp-workflows/dhp-dedup-openaire/src/test/resources/log4j.properties diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java index d345cf98f..c3b6751ba 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java @@ -2,8 +2,10 @@ package eu.dnetlib.dhp.oa.dedup; import java.util.Collection; +import java.util.Comparator; import java.util.Iterator; import java.util.List; +import java.util.stream.Collectors; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.MapGroupsFunction; @@ -13,11 +15,14 @@ import org.apache.spark.sql.SparkSession; import com.fasterxml.jackson.databind.DeserializationFeature; import com.fasterxml.jackson.databind.ObjectMapper; +import com.google.common.collect.Iterators; import com.google.common.collect.Lists; +import eu.dnetlib.dhp.oa.dedup.model.Identifier; import eu.dnetlib.dhp.oa.merge.AuthorMerger; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; import scala.Tuple2; public class DedupRecordFactory { @@ -82,11 +87,19 @@ public class DedupRecordFactory { final Collection dates = Lists.newArrayList(); final List> authors = Lists.newArrayList(); - entities - .forEachRemaining( - t -> { - T duplicate = t._2(); + final Comparator> idComparator = new IdentifierComparator().reversed(); + final List entityList = Lists + .newArrayList(entities) + .stream() + .map(t -> Identifier.newInstance(t._2())) + .sorted(idComparator) + .map(Identifier::getEntity) + .collect(Collectors.toList()); + + entityList + .forEach( + duplicate -> { entity.mergeFrom(duplicate); if (ModelSupport.isSubClass(duplicate, Result.class)) { Result r1 = (Result) duplicate; diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/IdGenerator.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/IdGenerator.java index 81cd30f88..7e0d66062 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/IdGenerator.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/IdGenerator.java @@ -18,6 +18,10 @@ public class IdGenerator implements Serializable { if (pids == null || pids.isEmpty()) return defaultID; + return generateId(pids); + } + + private static String generateId(List> pids) { Identifier bp = pids .stream() .min(Identifier::compareTo) diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/IdentifierComparator.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/IdentifierComparator.java new file mode 100644 index 000000000..ba4e31128 --- /dev/null +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/IdentifierComparator.java @@ -0,0 +1,81 @@ + +package eu.dnetlib.dhp.oa.dedup; + +import java.util.Comparator; +import java.util.List; +import java.util.Optional; +import java.util.Set; +import java.util.stream.Collectors; + +import com.google.common.collect.Sets; + +import eu.dnetlib.dhp.oa.dedup.model.Identifier; +import eu.dnetlib.dhp.schema.common.EntityType; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.DataInfo; +import eu.dnetlib.dhp.schema.oaf.KeyValue; +import eu.dnetlib.dhp.schema.oaf.OafEntity; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; +import eu.dnetlib.dhp.schema.oaf.utils.PidComparator; +import eu.dnetlib.dhp.schema.oaf.utils.PidType; + +public class IdentifierComparator implements Comparator> { + + public static int compareIdentifiers(Identifier left, Identifier right) { + return new IdentifierComparator<>().compare(left, right); + } + + @Override + public int compare(Identifier left, Identifier i) { + // priority in comparisons: 1) pidtype, 2) collectedfrom (depending on the entity type) , 3) date 4) + // alphabetical order of the originalID + + Set lKeys = Optional + .ofNullable(left.getCollectedFrom()) + .map(c -> c.stream().map(KeyValue::getKey).collect(Collectors.toSet())) + .orElse(Sets.newHashSet()); + + final Optional> cf = Optional.ofNullable(i.getCollectedFrom()); + Set rKeys = cf + .map(c -> c.stream().map(KeyValue::getKey).collect(Collectors.toSet())) + .orElse(Sets.newHashSet()); + + if (left.getPidType().compareTo(i.getPidType()) == 0) { // same type + if (left.getEntityType() == EntityType.publication) { + if (isFromDatasourceID(lKeys, ModelConstants.CROSSREF_ID) + && !isFromDatasourceID(rKeys, ModelConstants.CROSSREF_ID)) + return -1; + if (isFromDatasourceID(rKeys, ModelConstants.CROSSREF_ID) + && !isFromDatasourceID(lKeys, ModelConstants.CROSSREF_ID)) + return 1; + } + if (left.getEntityType() == EntityType.dataset) { + if (isFromDatasourceID(lKeys, ModelConstants.DATACITE_ID) + && !isFromDatasourceID(rKeys, ModelConstants.DATACITE_ID)) + return -1; + if (isFromDatasourceID(rKeys, ModelConstants.DATACITE_ID) + && !isFromDatasourceID(lKeys, ModelConstants.DATACITE_ID)) + return 1; + } + + if (left.getDate().compareTo(i.getDate()) == 0) {// same date + // we need to take the alphabetically lower id + return left.getOriginalID().compareTo(i.getOriginalID()); + } else + // we need to take the elder date + return left.getDate().compareTo(i.getDate()); + } else { + return new PidComparator<>(left.getEntity()).compare(toSP(left.getPidType()), toSP(i.getPidType())); + } + } + + public boolean isFromDatasourceID(Set collectedFrom, String dsId) { + return collectedFrom.contains(dsId); + } + + private StructuredProperty toSP(PidType pidType) { + return OafMapperUtils.structuredProperty("", pidType.toString(), pidType.toString(), "", "", new DataInfo()); + } + +} diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/model/Identifier.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/model/Identifier.java index a25a853ef..0cba4fc3b 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/model/Identifier.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/model/Identifier.java @@ -11,6 +11,7 @@ import org.apache.commons.lang3.StringUtils; import com.google.common.collect.Sets; import eu.dnetlib.dhp.oa.dedup.DatePicker; +import eu.dnetlib.dhp.oa.dedup.IdentifierComparator; import eu.dnetlib.dhp.schema.common.EntityType; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelSupport; @@ -83,60 +84,12 @@ public class Identifier implements Serializable, Comparable return entity.getId(); } - private PidType getPidType() { + public PidType getPidType() { return PidType.tryValueOf(StringUtils.substringBefore(StringUtils.substringAfter(entity.getId(), "|"), "_")); } @Override public int compareTo(Identifier i) { - // priority in comparisons: 1) pidtype, 2) collectedfrom (depending on the entity type) , 3) date 4) - // alphabetical order of the originalID - - Set lKeys = Optional - .ofNullable(getCollectedFrom()) - .map(c -> c.stream().map(KeyValue::getKey).collect(Collectors.toSet())) - .orElse(Sets.newHashSet()); - - final Optional> cf = Optional.ofNullable(i.getCollectedFrom()); - Set rKeys = cf - .map(c -> c.stream().map(KeyValue::getKey).collect(Collectors.toSet())) - .orElse(Sets.newHashSet()); - - if (this.getPidType().compareTo(i.getPidType()) == 0) { // same type - if (getEntityType() == EntityType.publication) { - if (isFromDatasourceID(lKeys, ModelConstants.CROSSREF_ID) - && !isFromDatasourceID(rKeys, ModelConstants.CROSSREF_ID)) - return -1; - if (isFromDatasourceID(rKeys, ModelConstants.CROSSREF_ID) - && !isFromDatasourceID(lKeys, ModelConstants.CROSSREF_ID)) - return 1; - } - if (getEntityType() == EntityType.dataset) { - if (isFromDatasourceID(lKeys, ModelConstants.DATACITE_ID) - && !isFromDatasourceID(rKeys, ModelConstants.DATACITE_ID)) - return -1; - if (isFromDatasourceID(rKeys, ModelConstants.DATACITE_ID) - && !isFromDatasourceID(lKeys, ModelConstants.DATACITE_ID)) - return 1; - } - - if (this.getDate().compareTo(i.getDate()) == 0) {// same date - // we need to take the alphabetically lower id - return this.getOriginalID().compareTo(i.getOriginalID()); - } else - // we need to take the elder date - return this.getDate().compareTo(i.getDate()); - } else { - return new PidComparator<>(getEntity()).compare(toSP(getPidType()), toSP(i.getPidType())); - } - - } - - private StructuredProperty toSP(PidType pidType) { - return OafMapperUtils.structuredProperty("", pidType.toString(), pidType.toString(), "", "", new DataInfo()); - } - - public boolean isFromDatasourceID(Set collectedFrom, String dsId) { - return collectedFrom.contains(dsId); + return IdentifierComparator.compareIdentifiers(this, i); } } diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkOpenorgsDedupTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkOpenorgsDedupTest.java index 9312d83b1..88c28ab2f 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkOpenorgsDedupTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkOpenorgsDedupTest.java @@ -143,7 +143,7 @@ public class SparkOpenorgsDedupTest implements Serializable { .load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "organization")) .count(); - assertEquals(288, orgs_simrel); + assertEquals(290, orgs_simrel); } @Test @@ -172,7 +172,7 @@ public class SparkOpenorgsDedupTest implements Serializable { .load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "organization")) .count(); - assertEquals(324, orgs_simrel); + assertEquals(326, orgs_simrel); } @Test diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkStatsTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkStatsTest.java index 1ba2c717c..b33b627e7 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkStatsTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkStatsTest.java @@ -168,11 +168,11 @@ public class SparkStatsTest implements Serializable { .textFile(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_blockstats") .count(); - assertEquals(477, orgs_blocks); + assertEquals(480, orgs_blocks); assertEquals(295, pubs_blocks); assertEquals(122, sw_blocks); assertEquals(191, ds_blocks); - assertEquals(171, orp_blocks); + assertEquals(178, orp_blocks); } @AfterAll diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/log4j.properties b/dhp-workflows/dhp-dedup-openaire/src/test/resources/log4j.properties new file mode 100644 index 000000000..ce37270c6 --- /dev/null +++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/log4j.properties @@ -0,0 +1,25 @@ +# Root logger option +log4j.rootLogger=DEBUG, stdout + +# Direct log messages to stdout +log4j.appender.stdout=org.apache.log4j.ConsoleAppender +log4j.appender.stdout.Target=System.out +log4j.appender.stdout.layout=org.apache.log4j.PatternLayout +log4j.appender.stdout.layout.ConversionPattern=%d{yyyy-MM-dd HH:mm:ss} %-5p %c{1}:%L - %m%n + +# Change this to set Spark log level +log4j.logger.org.apache.spark=ERROR +log4j.rootCategory=WARN + +# Silence akka remoting +log4j.logger.Remoting=WARN + +# Ignore messages below warning level from Jetty, because it's a bit verbose +log4j.logger.org.eclipse.jetty=WARN + +log4j.logger.org.apache.hadoop.mapreduce.lib.output.FileOutputCommitterFactory=WARN +log4j.logger.org.apache.hadoop.mapreduce.lib.output.FileOutputCommitter=WARN +log4j.logger.org.apache.parquet.hadoop.ParquetOutputFormat=WARN +log4j.logger.org.apache.parquet.hadoop.InternalParquetRecordWriter=WARN +log4j.logger.org.apache.hadoop.io.compress.CodecPool=WARN +log4j.logger.org.apache.parquet.hadoop.codec.CodecConfig=WARN \ No newline at end of file From ddff0e8999b392bdec7b9d6263e5c53e16a6bf59 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 11 Nov 2022 16:10:25 +0100 Subject: [PATCH 06/11] merging duplicates using IdentifierComparator --- .../dhp/oa/dedup/DedupRecordFactory.java | 35 +- .../dhp/oa/dedup/EntityMergerTest.java | 15 +- .../oa/dedup/SparkDedupPublicationTest.java | 389 ++++++++++++++++++ .../dnetlib/dhp/oa/dedup/SparkDedupTest.java | 210 ++++++---- .../dedup/entities/publication/publication.gz | Bin 578793 -> 581926 bytes .../entities2/publication/publication.gz | Bin 0 -> 9056 bytes .../mock_orchestrator_publication.xml | 24 ++ .../src/test/resources/log4j.properties | 28 +- 8 files changed, 590 insertions(+), 111 deletions(-) create mode 100644 dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupPublicationTest.java create mode 100644 dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities2/publication/publication.gz create mode 100644 dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator_publication.xml diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java index c3b6751ba..f9fc8a21a 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java @@ -1,12 +1,12 @@ package eu.dnetlib.dhp.oa.dedup; -import java.util.Collection; -import java.util.Comparator; -import java.util.Iterator; -import java.util.List; +import java.lang.reflect.InvocationTargetException; +import java.util.*; import java.util.stream.Collectors; +import org.apache.commons.beanutils.BeanUtils; +import org.apache.commons.lang3.StringUtils; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.MapGroupsFunction; import org.apache.spark.sql.Dataset; @@ -15,14 +15,12 @@ import org.apache.spark.sql.SparkSession; import com.fasterxml.jackson.databind.DeserializationFeature; import com.fasterxml.jackson.databind.ObjectMapper; -import com.google.common.collect.Iterators; import com.google.common.collect.Lists; import eu.dnetlib.dhp.oa.dedup.model.Identifier; import eu.dnetlib.dhp.oa.merge.AuthorMerger; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.*; -import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; import scala.Tuple2; public class DedupRecordFactory { @@ -79,23 +77,25 @@ public class DedupRecordFactory { public static T entityMerger( String id, Iterator> entities, long ts, DataInfo dataInfo, Class clazz) - throws IllegalAccessException, InstantiationException { + throws IllegalAccessException, InstantiationException, InvocationTargetException { - T entity = clazz.newInstance(); - entity.setDataInfo(dataInfo); + final Comparator> idComparator = new IdentifierComparator<>(); - final Collection dates = Lists.newArrayList(); - final List> authors = Lists.newArrayList(); - - final Comparator> idComparator = new IdentifierComparator().reversed(); - - final List entityList = Lists + final LinkedList entityList = Lists .newArrayList(entities) .stream() .map(t -> Identifier.newInstance(t._2())) .sorted(idComparator) .map(Identifier::getEntity) - .collect(Collectors.toList()); + .collect(Collectors.toCollection(LinkedList::new)); + + final T entity = clazz.newInstance(); + final T first = entityList.removeFirst(); + + BeanUtils.copyProperties(entity, first); + + final Collection dates = Lists.newArrayList(); + final List> authors = Lists.newArrayList(); entityList .forEach( @@ -103,12 +103,11 @@ public class DedupRecordFactory { entity.mergeFrom(duplicate); if (ModelSupport.isSubClass(duplicate, Result.class)) { Result r1 = (Result) duplicate; - if (r1.getAuthor() != null && !r1.getAuthor().isEmpty()) + if (r1.getAuthor() != null && StringUtils.isNotBlank(r1.getDateofacceptance().getValue())) authors.add(r1.getAuthor()); if (r1.getDateofacceptance() != null) dates.add(r1.getDateofacceptance().getValue()); } - }); // set authors and date diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java index aa3722ce5..c9cfb8cb2 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java @@ -7,6 +7,7 @@ import java.io.BufferedReader; import java.io.FileReader; import java.io.IOException; import java.io.Serializable; +import java.lang.reflect.InvocationTargetException; import java.nio.file.Paths; import java.util.*; import java.util.stream.Collectors; @@ -54,7 +55,7 @@ class EntityMergerTest implements Serializable { } @Test - void softwareMergerTest() throws InstantiationException, IllegalAccessException { + void softwareMergerTest() throws InstantiationException, IllegalAccessException, InvocationTargetException { List> softwares = readSample( testEntityBasePath + "/software_merge.json", Software.class); @@ -69,7 +70,7 @@ class EntityMergerTest implements Serializable { } @Test - void publicationMergerTest() throws InstantiationException, IllegalAccessException { + void publicationMergerTest() throws InstantiationException, IllegalAccessException, InvocationTargetException { Publication pub_merged = DedupRecordFactory .entityMerger(dedupId, publications.iterator(), 0, dataInfo, Publication.class); @@ -134,7 +135,7 @@ class EntityMergerTest implements Serializable { } @Test - void publicationMergerTest2() throws InstantiationException, IllegalAccessException { + void publicationMergerTest2() throws InstantiationException, IllegalAccessException, InvocationTargetException { Publication pub_merged = DedupRecordFactory .entityMerger(dedupId, publications2.iterator(), 0, dataInfo, Publication.class); @@ -146,7 +147,7 @@ class EntityMergerTest implements Serializable { } @Test - void publicationMergerTest3() throws InstantiationException, IllegalAccessException { + void publicationMergerTest3() throws InstantiationException, IllegalAccessException, InvocationTargetException { Publication pub_merged = DedupRecordFactory .entityMerger(dedupId, publications3.iterator(), 0, dataInfo, Publication.class); @@ -156,7 +157,8 @@ class EntityMergerTest implements Serializable { } @Test - void publicationMergerTest4() throws InstantiationException, IllegalStateException, IllegalAccessException { + void publicationMergerTest4() + throws InstantiationException, IllegalStateException, IllegalAccessException, InvocationTargetException { Publication pub_merged = DedupRecordFactory .entityMerger(dedupId, publications4.iterator(), 0, dataInfo, Publication.class); @@ -166,7 +168,8 @@ class EntityMergerTest implements Serializable { } @Test - void publicationMergerTest5() throws InstantiationException, IllegalStateException, IllegalAccessException { + void publicationMergerTest5() + throws InstantiationException, IllegalStateException, IllegalAccessException, InvocationTargetException { System.out .println( diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupPublicationTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupPublicationTest.java new file mode 100644 index 000000000..c657d1865 --- /dev/null +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupPublicationTest.java @@ -0,0 +1,389 @@ + +package eu.dnetlib.dhp.oa.dedup; + +import static java.nio.file.Files.createTempDirectory; + +import static org.apache.spark.sql.functions.count; +import static org.junit.jupiter.api.Assertions.*; +import static org.mockito.Mockito.lenient; + +import java.io.File; +import java.io.IOException; +import java.io.Serializable; +import java.net.URISyntaxException; +import java.nio.file.Paths; +import java.util.*; +import java.util.stream.Collectors; + +import com.fasterxml.jackson.core.JsonProcessingException; +import org.apache.commons.io.FileUtils; +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaSparkContext; +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.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.*; +import org.junit.jupiter.api.extension.ExtendWith; +import org.mockito.Mock; +import org.mockito.Mockito; +import org.mockito.junit.jupiter.MockitoExtension; + +import com.fasterxml.jackson.databind.DeserializationFeature; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.google.common.collect.Sets; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; + +@ExtendWith(MockitoExtension.class) +@TestMethodOrder(MethodOrderer.OrderAnnotation.class) +public class SparkDedupPublicationTest implements Serializable { + + @Mock(serializable = true) + ISLookUpService isLookUpService; + + private static SparkSession spark; + private static JavaSparkContext jsc; + + private static String testGraphBasePath; + private static String testOutputBasePath; + private static String testDedupGraphBasePath; + private static final String testActionSetId = "test-orchestrator"; + + @BeforeAll + public static void cleanUp() throws IOException, URISyntaxException { + + testGraphBasePath = Paths + .get(SparkDedupPublicationTest.class.getResource("/eu/dnetlib/dhp/dedup/entities2").toURI()) + .toFile() + .getAbsolutePath(); + testOutputBasePath = createTempDirectory(SparkDedupPublicationTest.class.getSimpleName() + "-") + .toAbsolutePath() + .toString(); + + testDedupGraphBasePath = createTempDirectory(SparkDedupPublicationTest.class.getSimpleName() + "-") + .toAbsolutePath() + .toString(); + + FileUtils.deleteDirectory(new File(testOutputBasePath)); + FileUtils.deleteDirectory(new File(testDedupGraphBasePath)); + + final SparkConf conf = new SparkConf(); + conf.set("spark.sql.shuffle.partitions", "10"); + spark = SparkSession + .builder() + .appName(SparkDedupPublicationTest.class.getSimpleName()) + .master("local[*]") + .config(conf) + .getOrCreate(); + + jsc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + } + + @BeforeEach + public void setUp() throws IOException, ISLookUpException { + + lenient() + .when(isLookUpService.getResourceProfileByQuery(Mockito.contains(testActionSetId))) + .thenReturn(classPathResourceAsString("/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator_publication.xml")); + + lenient() + .when(isLookUpService.getResourceProfileByQuery(Mockito.contains("publication"))) + .thenReturn(classPathResourceAsString("/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json")); + } + + @Test + @Order(1) + void createSimRelsTest() throws Exception { + + ArgumentApplicationParser parser = new ArgumentApplicationParser( + classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json")); + + parser + .parseArgument( + new String[] { + "--graphBasePath", testGraphBasePath, + "--actionSetId", testActionSetId, + "--isLookUpUrl", "lookupurl", + "--workingPath", testOutputBasePath, + "--numPartitions", "5" + }); + + new SparkCreateSimRels(parser, spark).run(isLookUpService); + + long pubs_simrel = spark + .read() + .load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "publication")) + .count(); + + assertEquals(62, pubs_simrel); + } + + @Test + @Order(2) + void cutMergeRelsTest() throws Exception { + + ArgumentApplicationParser parser = new ArgumentApplicationParser( + classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json")); + + parser + .parseArgument( + new String[] { + "--graphBasePath", testGraphBasePath, + "--actionSetId", testActionSetId, + "--isLookUpUrl", "lookupurl", + "--workingPath", testOutputBasePath, + "--cutConnectedComponent", "3" + }); + + new SparkCreateMergeRels(parser, spark).run(isLookUpService); + + long pubs_mergerel = spark + .read() + .load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel") + .as(Encoders.bean(Relation.class)) + .filter((FilterFunction) r -> r.getRelClass().equalsIgnoreCase("merges")) + .groupBy("source") + .agg(count("target").alias("cnt")) + .select("source", "cnt") + .where("cnt > 3") + .count(); + + assertEquals(0, pubs_mergerel); + + FileUtils.deleteDirectory(new File(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel")); + } + + @Test + @Order(3) + void createMergeRelsTest() throws Exception { + + ArgumentApplicationParser parser = new ArgumentApplicationParser( + classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json")); + + parser + .parseArgument( + new String[] { + "--graphBasePath", testGraphBasePath, + "--actionSetId", testActionSetId, + "--isLookUpUrl", "lookupurl", + "--workingPath", testOutputBasePath + }); + + new SparkCreateMergeRels(parser, spark).run(isLookUpService); + + final Dataset pubs = spark + .read() + .load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel") + .as(Encoders.bean(Relation.class)); + + final List merges = pubs + .filter("source == '50|doi_dedup___::d5021b53204e4fdeab6ff5d5bc468032'") + .collectAsList(); + assertEquals(3, merges.size()); + Set dups = Sets + .newHashSet( + "50|doi_________::3b1d0d8e8f930826665df9d6b82fbb73", + "50|doi_________::d5021b53204e4fdeab6ff5d5bc468032", + "50|arXiv_______::c93aeb433eb90ed7a86e29be00791b7c"); + merges.forEach(r -> { + assertEquals(ModelConstants.RESULT_RESULT, r.getRelType()); + assertEquals(ModelConstants.DEDUP, r.getSubRelType()); + assertEquals(ModelConstants.MERGES, r.getRelClass()); + assertTrue(dups.contains(r.getTarget())); + }); + + final List mergedIn = pubs + .filter("target == '50|doi_dedup___::d5021b53204e4fdeab6ff5d5bc468032'") + .collectAsList(); + assertEquals(3, mergedIn.size()); + mergedIn.forEach(r -> { + assertEquals(ModelConstants.RESULT_RESULT, r.getRelType()); + assertEquals(ModelConstants.DEDUP, r.getSubRelType()); + assertEquals(ModelConstants.IS_MERGED_IN, r.getRelClass()); + assertTrue(dups.contains(r.getSource())); + }); + + assertEquals(24, pubs.count()); + } + + @Test + @Order(4) + void createDedupRecordTest() throws Exception { + + ArgumentApplicationParser parser = new ArgumentApplicationParser( + classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json")); + parser + .parseArgument( + new String[] { + "--graphBasePath", testGraphBasePath, + "--actionSetId", testActionSetId, + "--isLookUpUrl", "lookupurl", + "--workingPath", testOutputBasePath + }); + + new SparkCreateDedupRecord(parser, spark).run(isLookUpService); + + final ObjectMapper mapper = new ObjectMapper() + .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); + + final Dataset roots = spark + .read() + .textFile(testOutputBasePath + "/" + testActionSetId + "/publication_deduprecord") + .map( + (MapFunction) value -> mapper.readValue(value, Publication.class), + Encoders.bean(Publication.class)); + + assertEquals(2, roots.count()); + + final Dataset pubs = spark + .read() + .textFile(DedupUtility.createEntityPath(testGraphBasePath, "publication")) + .map( + (MapFunction) value -> mapper.readValue(value, Publication.class), + Encoders.bean(Publication.class)); + + verifyRoot_case_1(roots, pubs); + verifyRoot_case_2(roots, pubs); + } + + private static void verifyRoot_case_1(Dataset roots, Dataset pubs) { + Publication root = roots + .filter("id = '50|doi_dedup___::d5021b53204e4fdeab6ff5d5bc468032'") + .first(); + assertNotNull(root); + + Publication crossref_duplicate = pubs + .filter("id = '50|doi_________::d5021b53204e4fdeab6ff5d5bc468032'") + .collectAsList() + .get(0); + + assertEquals(crossref_duplicate.getJournal().getName(), root.getJournal().getName()); + assertEquals(crossref_duplicate.getJournal().getIssnPrinted(), root.getJournal().getIssnPrinted()); + assertEquals(crossref_duplicate.getPublisher().getValue(), root.getPublisher().getValue()); + + Set rootPids = root + .getPid() + .stream() + .map(StructuredProperty::getValue) + .collect(Collectors.toCollection(HashSet::new)); + Set dupPids = crossref_duplicate + .getPid() + .stream() + .map(StructuredProperty::getValue) + .collect(Collectors.toCollection(HashSet::new)); + + assertFalse(Sets.intersection(rootPids, dupPids).isEmpty()); + assertTrue(rootPids.contains("10.1109/jstqe.2022.3205716")); + + Optional instance_cr = root + .getInstance() + .stream() + .filter(i -> i.getCollectedfrom().getValue().equals("Crossref")) + .findFirst(); + assertTrue(instance_cr.isPresent()); + assertEquals("OPEN", instance_cr.get().getAccessright().getClassid()); + assertEquals("Open Access", instance_cr.get().getAccessright().getClassname()); + assertEquals(OpenAccessRoute.hybrid, instance_cr.get().getAccessright().getOpenAccessRoute()); + assertEquals( + "IEEE Journal of Selected Topics in Quantum Electronics", instance_cr.get().getHostedby().getValue()); + assertEquals("0001", instance_cr.get().getInstancetype().getClassid()); + assertEquals("Article", instance_cr.get().getInstancetype().getClassname()); + } + + private void verifyRoot_case_2(Dataset roots, Dataset pubs) throws JsonProcessingException { + Publication root = roots + .filter("id = '50|doi_dedup___::18aff3b55fb6876466a5d4bd82434885'") + .first(); + assertNotNull(root); + + Publication crossref_duplicate = pubs + .filter("id = '50|doi_________::18aff3b55fb6876466a5d4bd82434885'") + .first(); + + //System.err.println(new ObjectMapper().writeValueAsString(root)); + + assertEquals(crossref_duplicate.getJournal().getName(), root.getJournal().getName()); + assertEquals(crossref_duplicate.getJournal().getIssnOnline(), root.getJournal().getIssnOnline()); + assertEquals(crossref_duplicate.getJournal().getVol(), root.getJournal().getVol()); + + assertEquals(crossref_duplicate.getPublisher().getValue(), root.getPublisher().getValue()); + + Set dups_cf = pubs + .collectAsList() + .stream() + .flatMap(p -> p.getCollectedfrom().stream()) + .map(KeyValue::getValue) + .collect(Collectors.toCollection(HashSet::new)); + + Set root_cf = root + .getCollectedfrom() + .stream() + .map(KeyValue::getValue) + .collect(Collectors.toCollection(HashSet::new)); + + assertTrue(Sets.difference(root_cf, dups_cf).isEmpty()); + } + + @Test + @Order(6) + void updateEntityTest() throws Exception { + + ArgumentApplicationParser parser = new ArgumentApplicationParser( + classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json")); + parser + .parseArgument( + new String[] { + "-i", testGraphBasePath, "-w", testOutputBasePath, "-o", testDedupGraphBasePath + }); + + new SparkUpdateEntity(parser, spark).run(isLookUpService); + + long publications = jsc.textFile(testDedupGraphBasePath + "/publication").count(); + + long mergedPubs = spark + .read() + .load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel") + .as(Encoders.bean(Relation.class)) + .where("relClass=='merges'") + .javaRDD() + .map(Relation::getTarget) + .distinct() + .count(); + + assertEquals(14, publications); + + long deletedPubs = jsc + .textFile(testDedupGraphBasePath + "/publication") + .filter(this::isDeletedByInference) + .count(); + + assertEquals(mergedPubs, deletedPubs); + } + + @AfterAll + public static void finalCleanUp() throws IOException { + FileUtils.deleteDirectory(new File(testOutputBasePath)); + FileUtils.deleteDirectory(new File(testDedupGraphBasePath)); + } + + public boolean isDeletedByInference(String s) { + return s.contains("\"deletedbyinference\":true"); + } + + private static String classPathResourceAsString(String path) throws IOException { + return IOUtils + .toString( + SparkDedupPublicationTest.class + .getResourceAsStream(path)); + } + +} diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java index 9c9ec43d5..3de14f577 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java @@ -4,8 +4,7 @@ package eu.dnetlib.dhp.oa.dedup; import static java.nio.file.Files.createTempDirectory; import static org.apache.spark.sql.functions.count; -import static org.junit.jupiter.api.Assertions.assertEquals; -import static org.junit.jupiter.api.Assertions.assertTrue; +import static org.junit.jupiter.api.Assertions.*; import static org.mockito.Mockito.lenient; import java.io.File; @@ -14,7 +13,11 @@ import java.io.IOException; import java.io.Serializable; import java.net.URISyntaxException; import java.nio.file.Paths; +import java.util.HashSet; import java.util.List; +import java.util.Optional; +import java.util.Set; +import java.util.stream.Collectors; import org.apache.commons.io.FileUtils; import org.apache.commons.io.IOUtils; @@ -35,10 +38,13 @@ import org.mockito.Mock; import org.mockito.Mockito; import org.mockito.junit.jupiter.MockitoExtension; +import com.fasterxml.jackson.databind.DeserializationFeature; import com.fasterxml.jackson.databind.ObjectMapper; +import com.google.common.collect.Sets; import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.schema.oaf.Relation; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import eu.dnetlib.pace.util.MapDocumentUtil; @@ -105,57 +111,27 @@ public class SparkDedupTest implements Serializable { lenient() .when(isLookUpService.getResourceProfileByQuery(Mockito.contains(testActionSetId))) - .thenReturn( - IOUtils - .toString( - SparkDedupTest.class - .getResourceAsStream( - "/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml"))); + .thenReturn(classPathResourceAsString("/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml")); lenient() .when(isLookUpService.getResourceProfileByQuery(Mockito.contains("organization"))) - .thenReturn( - IOUtils - .toString( - SparkDedupTest.class - .getResourceAsStream( - "/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json"))); + .thenReturn(classPathResourceAsString("/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json")); lenient() .when(isLookUpService.getResourceProfileByQuery(Mockito.contains("publication"))) - .thenReturn( - IOUtils - .toString( - SparkDedupTest.class - .getResourceAsStream( - "/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json"))); + .thenReturn(classPathResourceAsString("/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json")); lenient() .when(isLookUpService.getResourceProfileByQuery(Mockito.contains("software"))) - .thenReturn( - IOUtils - .toString( - SparkDedupTest.class - .getResourceAsStream( - "/eu/dnetlib/dhp/dedup/conf/sw.curr.conf.json"))); + .thenReturn(classPathResourceAsString("/eu/dnetlib/dhp/dedup/conf/sw.curr.conf.json")); lenient() .when(isLookUpService.getResourceProfileByQuery(Mockito.contains("dataset"))) - .thenReturn( - IOUtils - .toString( - SparkDedupTest.class - .getResourceAsStream( - "/eu/dnetlib/dhp/dedup/conf/ds.curr.conf.json"))); + .thenReturn(classPathResourceAsString("/eu/dnetlib/dhp/dedup/conf/ds.curr.conf.json")); lenient() .when(isLookUpService.getResourceProfileByQuery(Mockito.contains("otherresearchproduct"))) - .thenReturn( - IOUtils - .toString( - SparkDedupTest.class - .getResourceAsStream( - "/eu/dnetlib/dhp/dedup/conf/orp.curr.conf.json"))); + .thenReturn(classPathResourceAsString("/eu/dnetlib/dhp/dedup/conf/orp.curr.conf.json")); } @Test @@ -163,11 +139,7 @@ public class SparkDedupTest implements Serializable { void createSimRelsTest() throws Exception { ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils - .toString( - SparkCreateSimRels.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json"))); + classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json")); parser .parseArgument( @@ -207,7 +179,7 @@ public class SparkDedupTest implements Serializable { .count(); assertEquals(3076, orgs_simrel); - assertEquals(7040, pubs_simrel); + assertEquals(7046, pubs_simrel); assertEquals(336, sw_simrel); assertEquals(442, ds_simrel); assertEquals(6784, orp_simrel); @@ -223,11 +195,7 @@ public class SparkDedupTest implements Serializable { void whitelistSimRelsTest() throws Exception { ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils - .toString( - SparkWhitelistSimRels.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/dedup/whitelistSimRels_parameters.json"))); + classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/whitelistSimRels_parameters.json")); parser .parseArgument( @@ -264,7 +232,7 @@ public class SparkDedupTest implements Serializable { // entities simrels supposed to be equal to the number of previous step (no rels in whitelist) assertEquals(3076, orgs_simrel); - assertEquals(7040, pubs_simrel); + assertEquals(7046, pubs_simrel); assertEquals(442, ds_simrel); assertEquals(6784, orp_simrel); // System.out.println("orgs_simrel = " + orgs_simrel); @@ -306,11 +274,7 @@ public class SparkDedupTest implements Serializable { void cutMergeRelsTest() throws Exception { ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils - .toString( - SparkCreateMergeRels.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json"))); + classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json")); parser .parseArgument( @@ -402,11 +366,7 @@ public class SparkDedupTest implements Serializable { void createMergeRelsTest() throws Exception { ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils - .toString( - SparkCreateMergeRels.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json"))); + classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json")); parser .parseArgument( @@ -427,10 +387,10 @@ public class SparkDedupTest implements Serializable { .read() .load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel") .count(); - long pubs_mergerel = spark + final Dataset pubs = spark .read() .load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel") - .count(); + .as(Encoders.bean(Relation.class)); long sw_mergerel = spark .read() .load(testOutputBasePath + "/" + testActionSetId + "/software_mergerel") @@ -445,8 +405,35 @@ public class SparkDedupTest implements Serializable { .load(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_mergerel") .count(); + final List merges = pubs + .filter("source == '50|doi_dedup___::d5021b53204e4fdeab6ff5d5bc468032'") + .collectAsList(); + assertEquals(3, merges.size()); + Set dups = Sets + .newHashSet( + "50|doi_________::3b1d0d8e8f930826665df9d6b82fbb73", + "50|doi_________::d5021b53204e4fdeab6ff5d5bc468032", + "50|arXiv_______::c93aeb433eb90ed7a86e29be00791b7c"); + merges.forEach(r -> { + assertEquals(ModelConstants.RESULT_RESULT, r.getRelType()); + assertEquals(ModelConstants.DEDUP, r.getSubRelType()); + assertEquals(ModelConstants.MERGES, r.getRelClass()); + assertTrue(dups.contains(r.getTarget())); + }); + + final List mergedIn = pubs + .filter("target == '50|doi_dedup___::d5021b53204e4fdeab6ff5d5bc468032'") + .collectAsList(); + assertEquals(3, mergedIn.size()); + mergedIn.forEach(r -> { + assertEquals(ModelConstants.RESULT_RESULT, r.getRelType()); + assertEquals(ModelConstants.DEDUP, r.getSubRelType()); + assertEquals(ModelConstants.IS_MERGED_IN, r.getRelClass()); + assertTrue(dups.contains(r.getSource())); + }); + assertEquals(1268, orgs_mergerel); - assertEquals(1444, pubs_mergerel); + assertEquals(1450, pubs.count()); assertEquals(286, sw_mergerel); assertEquals(472, ds_mergerel); assertEquals(738, orp_mergerel); @@ -463,11 +450,7 @@ public class SparkDedupTest implements Serializable { void createDedupRecordTest() throws Exception { ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils - .toString( - SparkCreateDedupRecord.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json"))); + classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json")); parser .parseArgument( new String[] { @@ -483,12 +466,18 @@ public class SparkDedupTest implements Serializable { new SparkCreateDedupRecord(parser, spark).run(isLookUpService); + final ObjectMapper mapper = new ObjectMapper() + .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); + + final Dataset pubs = spark + .read() + .textFile(testOutputBasePath + "/" + testActionSetId + "/publication_deduprecord") + .map( + (MapFunction) value -> mapper.readValue(value, Publication.class), + Encoders.bean(Publication.class)); long orgs_deduprecord = jsc .textFile(testOutputBasePath + "/" + testActionSetId + "/organization_deduprecord") .count(); - long pubs_deduprecord = jsc - .textFile(testOutputBasePath + "/" + testActionSetId + "/publication_deduprecord") - .count(); long sw_deduprecord = jsc .textFile(testOutputBasePath + "/" + testActionSetId + "/software_deduprecord") .count(); @@ -499,11 +488,13 @@ public class SparkDedupTest implements Serializable { .count(); assertEquals(86, orgs_deduprecord); - assertEquals(67, pubs_deduprecord); + assertEquals(68, pubs.count()); assertEquals(49, sw_deduprecord); assertEquals(97, ds_deduprecord); assertEquals(92, orp_deduprecord); + verifyRoot_1(mapper, pubs); + // System.out.println("orgs_deduprecord = " + orgs_deduprecord); // System.out.println("pubs_deduprecord = " + pubs_deduprecord); // System.out.println("sw_deduprecord = " + sw_deduprecord); @@ -511,16 +502,63 @@ public class SparkDedupTest implements Serializable { // System.out.println("orp_deduprecord = " + orp_deduprecord); } + private static void verifyRoot_1(ObjectMapper mapper, Dataset pubs) { + Publication root = pubs + .filter("id = '50|doi_dedup___::d5021b53204e4fdeab6ff5d5bc468032'") + .first(); + assertNotNull(root); + + final Dataset publication = spark + .read() + .textFile(DedupUtility.createEntityPath(testGraphBasePath, "publication")); + + Publication crossref_duplicate = publication + .map( + (MapFunction) value -> mapper.readValue(value, Publication.class), + Encoders.bean(Publication.class)) + .filter("id = '50|doi_________::d5021b53204e4fdeab6ff5d5bc468032'") + .collectAsList() + .get(0); + + assertEquals(crossref_duplicate.getJournal().getName(), root.getJournal().getName()); + assertEquals(crossref_duplicate.getJournal().getIssnPrinted(), root.getJournal().getIssnPrinted()); + assertEquals(crossref_duplicate.getPublisher().getValue(), root.getPublisher().getValue()); + + Set rootPids = root + .getPid() + .stream() + .map(StructuredProperty::getValue) + .collect(Collectors.toCollection(HashSet::new)); + Set dupPids = crossref_duplicate + .getPid() + .stream() + .map(StructuredProperty::getValue) + .collect(Collectors.toCollection(HashSet::new)); + + assertFalse(Sets.intersection(rootPids, dupPids).isEmpty()); + assertTrue(rootPids.contains("10.1109/jstqe.2022.3205716")); + + Optional instance_cr = root + .getInstance() + .stream() + .filter(i -> i.getCollectedfrom().getValue().equals("Crossref")) + .findFirst(); + assertTrue(instance_cr.isPresent()); + assertEquals("OPEN", instance_cr.get().getAccessright().getClassid()); + assertEquals("Open Access", instance_cr.get().getAccessright().getClassname()); + assertEquals(OpenAccessRoute.hybrid, instance_cr.get().getAccessright().getOpenAccessRoute()); + assertEquals( + "IEEE Journal of Selected Topics in Quantum Electronics", instance_cr.get().getHostedby().getValue()); + assertEquals("0001", instance_cr.get().getInstancetype().getClassid()); + assertEquals("Article", instance_cr.get().getInstancetype().getClassname()); + } + @Test @Order(6) void updateEntityTest() throws Exception { ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils - .toString( - SparkUpdateEntity.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json"))); + classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json")); parser .parseArgument( new String[] { @@ -587,7 +625,7 @@ public class SparkDedupTest implements Serializable { .distinct() .count(); - assertEquals(898, publications); + assertEquals(902, publications); assertEquals(839, organizations); assertEquals(100, projects); assertEquals(100, datasource); @@ -640,11 +678,7 @@ public class SparkDedupTest implements Serializable { void propagateRelationTest() throws Exception { ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils - .toString( - SparkPropagateRelation.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/dedup/propagateRelation_parameters.json"))); + classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/propagateRelation_parameters.json")); parser .parseArgument( new String[] { @@ -714,4 +748,12 @@ public class SparkDedupTest implements Serializable { public boolean isDeletedByInference(String s) { return s.contains("\"deletedbyinference\":true"); } + + private static String classPathResourceAsString(String path) throws IOException { + return IOUtils + .toString( + SparkDedupTest.class + .getResourceAsStream(path)); + } + } diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/publication/publication.gz b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/publication/publication.gz index cf513d7302bda81e6bdae0dbb430f5852a91307f..a7457063bcbe59481e11c944d4dff7a3244e4831 100644 GIT binary patch delta 24067 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z$qTL0yZP6%Cvm{iLOALdV4>VW8(%Sjf-3kcIjb)eegCF!^py6Tku2tISGc$5fhIpH zcU%>c5nlc>jqg*-z3SKV744#3%H6)0ezT&w&9Z` z;U1(jrC4r6Z%V=3kh&a#U>4HIl#22x`&&>vJ-gft8`{;`J9o?4C&0+ z3Cc=mhID4^G;yVk{s=l#iluaB?2uqeXNFXiPcM(p+?lbyf8xG5CmrdaxSNAw=3{E9 z`lZ-iO+Qx*Pc{YnP!(%t^x{zUYDg{7r8~#FY86Ce S(Trx%jQ<63B6;BU&H(_01)C@U literal 0 HcmV?d00001 diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator_publication.xml b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator_publication.xml new file mode 100644 index 000000000..b47d99b92 --- /dev/null +++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator_publication.xml @@ -0,0 +1,24 @@ + +
+ + + + + +
+ + + + + + + + + + + + + + SECURITY_PARAMETERS + + \ No newline at end of file diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/log4j.properties b/dhp-workflows/dhp-dedup-openaire/src/test/resources/log4j.properties index ce37270c6..d3e717dfa 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/resources/log4j.properties +++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/log4j.properties @@ -19,7 +19,29 @@ log4j.logger.org.eclipse.jetty=WARN log4j.logger.org.apache.hadoop.mapreduce.lib.output.FileOutputCommitterFactory=WARN log4j.logger.org.apache.hadoop.mapreduce.lib.output.FileOutputCommitter=WARN -log4j.logger.org.apache.parquet.hadoop.ParquetOutputFormat=WARN -log4j.logger.org.apache.parquet.hadoop.InternalParquetRecordWriter=WARN +#log4j.logger.org.apache.parquet.hadoop.ParquetOutputFormat=WARN +#log4j.logger.org.apache.parquet.hadoop.InternalParquetRecordWriter=WARN log4j.logger.org.apache.hadoop.io.compress.CodecPool=WARN -log4j.logger.org.apache.parquet.hadoop.codec.CodecConfig=WARN \ No newline at end of file +#log4j.logger.org.apache.hadoop.io.compress=WARN +#log4j.logger.org.apache.parquet.hadoop.codec.CodecConfig=WARN +log4j.logger.parquet.hadoop.ColumnChunkPageWriteStore=ERROR +log4j.logger.com.jayway.jsonpath.internal.path.CompiledPath=WARN +log4j.logger.org.apache.parquet.hadoop.ParquetRecordReader=ERROR +log4j.logger.parquet.hadoop=WARN +log4j.logger.org.eclipse.jetty.server.handler.ContextHandlerCollection=WARN +log4j.logger.org.spark_project.jetty.util.component.ContainerLifeCycle=WARN +log4j.logger.org.apache.hadoop.mapred.FileInputFormat=WARN +log4j.logger.org.spark_project.jetty.servlet.ServletHandler=WARN +log4j.logger.org.apache.commons.beanutils.converters.BooleanConverter=WARN +log4j.logger.org.apache.commons.beanutils.converters.StringConverter=WARN +log4j.logger.org.apache.commons.beanutils.converters.LongConverter=WARN +log4j.logger.org.apache.commons.beanutils.converters.ArrayConverter=WARN +log4j.logger.org.apache.commons.beanutils.converters.FloatConverter=WARN +log4j.logger.org.apache.commons.beanutils.converters.IntegerConverter=WARN +log4j.logger.org.apache.commons.beanutils.converters.DoubleConverter=WARN +log4j.logger.org.apache.commons.beanutils.converters.CharacterConverter=WARN +log4j.logger.org.apache.commons.beanutils.converters.ByteConverter=WARN +log4j.logger.org.apache.commons.beanutils.converters.BigIntegerConverter=WARN +log4j.logger.org.apache.commons.beanutils.converters.BigDecimalConverter=WARN +log4j.logger.org.apache.commons.beanutils.converters.ShortConverter=WARN +log4j.logger.org.apache.commons.beanutils.BeanUtils=WARN From 3dbc637d3e8e8a5a8c775821998b1991e10690bc Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 17 Nov 2022 09:55:41 +0100 Subject: [PATCH 07/11] code formatting --- .../oa/dedup/SparkDedupPublicationTest.java | 19 ++++++++++--------- 1 file changed, 10 insertions(+), 9 deletions(-) diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupPublicationTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupPublicationTest.java index c657d1865..773de65fa 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupPublicationTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupPublicationTest.java @@ -15,7 +15,6 @@ import java.nio.file.Paths; import java.util.*; import java.util.stream.Collectors; -import com.fasterxml.jackson.core.JsonProcessingException; import org.apache.commons.io.FileUtils; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; @@ -32,6 +31,7 @@ import org.mockito.Mock; import org.mockito.Mockito; import org.mockito.junit.jupiter.MockitoExtension; +import com.fasterxml.jackson.core.JsonProcessingException; import com.fasterxml.jackson.databind.DeserializationFeature; import com.fasterxml.jackson.databind.ObjectMapper; import com.google.common.collect.Sets; @@ -299,17 +299,18 @@ public class SparkDedupPublicationTest implements Serializable { assertEquals("Article", instance_cr.get().getInstancetype().getClassname()); } - private void verifyRoot_case_2(Dataset roots, Dataset pubs) throws JsonProcessingException { + private void verifyRoot_case_2(Dataset roots, Dataset pubs) + throws JsonProcessingException { Publication root = roots .filter("id = '50|doi_dedup___::18aff3b55fb6876466a5d4bd82434885'") .first(); assertNotNull(root); Publication crossref_duplicate = pubs - .filter("id = '50|doi_________::18aff3b55fb6876466a5d4bd82434885'") - .first(); + .filter("id = '50|doi_________::18aff3b55fb6876466a5d4bd82434885'") + .first(); - //System.err.println(new ObjectMapper().writeValueAsString(root)); + // System.err.println(new ObjectMapper().writeValueAsString(root)); assertEquals(crossref_duplicate.getJournal().getName(), root.getJournal().getName()); assertEquals(crossref_duplicate.getJournal().getIssnOnline(), root.getJournal().getIssnOnline()); @@ -325,10 +326,10 @@ public class SparkDedupPublicationTest implements Serializable { .collect(Collectors.toCollection(HashSet::new)); Set root_cf = root - .getCollectedfrom() - .stream() - .map(KeyValue::getValue) - .collect(Collectors.toCollection(HashSet::new)); + .getCollectedfrom() + .stream() + .map(KeyValue::getValue) + .collect(Collectors.toCollection(HashSet::new)); assertTrue(Sets.difference(root_cf, dups_cf).isEmpty()); } From 0aa725083f66875b4eef7ad6513b24bf557eb5ec Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 17 Nov 2022 16:13:43 +0100 Subject: [PATCH 08/11] extended dedup testing --- .../dhp/oa/dedup/DedupRecordFactory.java | 2 +- ...st.java => SparkPublicationRootsTest.java} | 283 +++++++++--------- .../oa/dedup/SparkPublicationRootsTest2.java | 251 ++++++++++++++++ .../entities2/publication/publication.gz | Bin 9056 -> 0 bytes .../alterations/publication/publication_1.gz | Bin 0 -> 1488 bytes .../entities/publication/publication_0.gz | Bin 0 -> 10874 bytes 6 files changed, 400 insertions(+), 136 deletions(-) rename dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/{SparkDedupPublicationTest.java => SparkPublicationRootsTest.java} (57%) create mode 100644 dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkPublicationRootsTest2.java delete mode 100644 dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities2/publication/publication.gz create mode 100644 dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/root/alterations/publication/publication_1.gz create mode 100644 dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/root/entities/publication/publication_0.gz diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java index f9fc8a21a..82bf87cca 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java @@ -112,7 +112,7 @@ public class DedupRecordFactory { // set authors and date if (ModelSupport.isSubClass(entity, Result.class)) { - ((Result) entity).setDateofacceptance(DatePicker.pick(dates)); + // ((Result) entity).setDateofacceptance(DatePicker.pick(dates)); ((Result) entity).setAuthor(AuthorMerger.merge(authors)); } diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupPublicationTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkPublicationRootsTest.java similarity index 57% rename from dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupPublicationTest.java rename to dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkPublicationRootsTest.java index 773de65fa..3cff836eb 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupPublicationTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkPublicationRootsTest.java @@ -11,16 +11,17 @@ import java.io.File; import java.io.IOException; import java.io.Serializable; import java.net.URISyntaxException; +import java.nio.file.Path; import java.nio.file.Paths; import java.util.*; import java.util.stream.Collectors; +import org.apache.commons.cli.ParseException; import org.apache.commons.io.FileUtils; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaSparkContext; 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.sql.Dataset; import org.apache.spark.sql.Encoders; @@ -31,7 +32,6 @@ import org.mockito.Mock; import org.mockito.Mockito; import org.mockito.junit.jupiter.MockitoExtension; -import com.fasterxml.jackson.core.JsonProcessingException; import com.fasterxml.jackson.databind.DeserializationFeature; import com.fasterxml.jackson.databind.ObjectMapper; import com.google.common.collect.Sets; @@ -44,48 +44,52 @@ import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; @ExtendWith(MockitoExtension.class) @TestMethodOrder(MethodOrderer.OrderAnnotation.class) -public class SparkDedupPublicationTest implements Serializable { +public class SparkPublicationRootsTest implements Serializable { @Mock(serializable = true) ISLookUpService isLookUpService; private static SparkSession spark; - private static JavaSparkContext jsc; + private static String workingPath; - private static String testGraphBasePath; - private static String testOutputBasePath; - private static String testDedupGraphBasePath; + private static String graphInputPath; + private static String graphOutputPath; private static final String testActionSetId = "test-orchestrator"; + private static Path testBaseTmpPath; + + private static final ObjectMapper MAPPER = new ObjectMapper() + .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); + @BeforeAll - public static void cleanUp() throws IOException, URISyntaxException { + public static void init() throws IOException, URISyntaxException { - testGraphBasePath = Paths - .get(SparkDedupPublicationTest.class.getResource("/eu/dnetlib/dhp/dedup/entities2").toURI()) - .toFile() - .getAbsolutePath(); - testOutputBasePath = createTempDirectory(SparkDedupPublicationTest.class.getSimpleName() + "-") - .toAbsolutePath() - .toString(); + testBaseTmpPath = createTempDirectory(SparkPublicationRootsTest.class.getSimpleName() + "-"); - testDedupGraphBasePath = createTempDirectory(SparkDedupPublicationTest.class.getSimpleName() + "-") - .toAbsolutePath() - .toString(); + final File entitiesSources = Paths + .get(SparkPublicationRootsTest.class.getResource("/eu/dnetlib/dhp/dedup/root").toURI()) + .toFile(); - FileUtils.deleteDirectory(new File(testOutputBasePath)); - FileUtils.deleteDirectory(new File(testDedupGraphBasePath)); + FileUtils + .copyDirectory( + entitiesSources, + testBaseTmpPath.resolve("input").toFile()); + + workingPath = testBaseTmpPath.resolve("workingPath").toString(); + graphInputPath = testBaseTmpPath.resolve("input").resolve("entities").toString(); + graphOutputPath = testBaseTmpPath.resolve("output").toString(); + + FileUtils.deleteDirectory(new File(workingPath)); + FileUtils.deleteDirectory(new File(graphOutputPath)); final SparkConf conf = new SparkConf(); conf.set("spark.sql.shuffle.partitions", "10"); spark = SparkSession .builder() - .appName(SparkDedupPublicationTest.class.getSimpleName()) + .appName(SparkPublicationRootsTest.class.getSimpleName()) .master("local[*]") .config(conf) .getOrCreate(); - - jsc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - } @BeforeEach @@ -100,55 +104,51 @@ public class SparkDedupPublicationTest implements Serializable { .thenReturn(classPathResourceAsString("/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json")); } + @AfterAll + public static void tearDown() throws IOException { + FileUtils.deleteDirectory(testBaseTmpPath.toFile()); + spark.close(); + } + @Test @Order(1) void createSimRelsTest() throws Exception { - - ArgumentApplicationParser parser = new ArgumentApplicationParser( - classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json")); - - parser - .parseArgument( - new String[] { - "--graphBasePath", testGraphBasePath, - "--actionSetId", testActionSetId, - "--isLookUpUrl", "lookupurl", - "--workingPath", testOutputBasePath, - "--numPartitions", "5" - }); - - new SparkCreateSimRels(parser, spark).run(isLookUpService); + new SparkCreateSimRels(args( + "/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json", + new String[] { + "--graphBasePath", graphInputPath, + "--actionSetId", testActionSetId, + "--isLookUpUrl", "lookupurl", + "--workingPath", workingPath, + "--numPartitions", "5" + }), spark) + .run(isLookUpService); long pubs_simrel = spark .read() - .load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "publication")) + .load(DedupUtility.createSimRelPath(workingPath, testActionSetId, "publication")) .count(); - assertEquals(62, pubs_simrel); + assertEquals(74, pubs_simrel); } @Test @Order(2) void cutMergeRelsTest() throws Exception { - - ArgumentApplicationParser parser = new ArgumentApplicationParser( - classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json")); - - parser - .parseArgument( - new String[] { - "--graphBasePath", testGraphBasePath, - "--actionSetId", testActionSetId, - "--isLookUpUrl", "lookupurl", - "--workingPath", testOutputBasePath, - "--cutConnectedComponent", "3" - }); - - new SparkCreateMergeRels(parser, spark).run(isLookUpService); + new SparkCreateMergeRels(args( + "/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json", + new String[] { + "--graphBasePath", graphInputPath, + "--actionSetId", testActionSetId, + "--isLookUpUrl", "lookupurl", + "--workingPath", workingPath, + "--cutConnectedComponent", "3" + }), spark) + .run(isLookUpService); long pubs_mergerel = spark .read() - .load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel") + .load(workingPath + "/" + testActionSetId + "/publication_mergerel") .as(Encoders.bean(Relation.class)) .filter((FilterFunction) r -> r.getRelClass().equalsIgnoreCase("merges")) .groupBy("source") @@ -159,49 +159,44 @@ public class SparkDedupPublicationTest implements Serializable { assertEquals(0, pubs_mergerel); - FileUtils.deleteDirectory(new File(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel")); + FileUtils.deleteDirectory(new File(workingPath + "/" + testActionSetId + "/publication_mergerel")); } @Test @Order(3) void createMergeRelsTest() throws Exception { + new SparkCreateMergeRels(args( + "/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json", + new String[] { + "--graphBasePath", graphInputPath, + "--actionSetId", testActionSetId, + "--isLookUpUrl", "lookupurl", + "--workingPath", workingPath + }), spark) + .run(isLookUpService); - ArgumentApplicationParser parser = new ArgumentApplicationParser( - classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json")); - - parser - .parseArgument( - new String[] { - "--graphBasePath", testGraphBasePath, - "--actionSetId", testActionSetId, - "--isLookUpUrl", "lookupurl", - "--workingPath", testOutputBasePath - }); - - new SparkCreateMergeRels(parser, spark).run(isLookUpService); - - final Dataset pubs = spark + final Dataset merges = spark .read() - .load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel") + .load(workingPath + "/" + testActionSetId + "/publication_mergerel") .as(Encoders.bean(Relation.class)); - final List merges = pubs + final List mergeList = merges .filter("source == '50|doi_dedup___::d5021b53204e4fdeab6ff5d5bc468032'") .collectAsList(); - assertEquals(3, merges.size()); + assertEquals(3, mergeList.size()); Set dups = Sets .newHashSet( "50|doi_________::3b1d0d8e8f930826665df9d6b82fbb73", "50|doi_________::d5021b53204e4fdeab6ff5d5bc468032", "50|arXiv_______::c93aeb433eb90ed7a86e29be00791b7c"); - merges.forEach(r -> { + mergeList.forEach(r -> { assertEquals(ModelConstants.RESULT_RESULT, r.getRelType()); assertEquals(ModelConstants.DEDUP, r.getSubRelType()); assertEquals(ModelConstants.MERGES, r.getRelClass()); assertTrue(dups.contains(r.getTarget())); }); - final List mergedIn = pubs + final List mergedIn = merges .filter("target == '50|doi_dedup___::d5021b53204e4fdeab6ff5d5bc468032'") .collectAsList(); assertEquals(3, mergedIn.size()); @@ -212,47 +207,37 @@ public class SparkDedupPublicationTest implements Serializable { assertTrue(dups.contains(r.getSource())); }); - assertEquals(24, pubs.count()); + assertEquals(32, merges.count()); } @Test @Order(4) void createDedupRecordTest() throws Exception { - - ArgumentApplicationParser parser = new ArgumentApplicationParser( - classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json")); - parser - .parseArgument( - new String[] { - "--graphBasePath", testGraphBasePath, - "--actionSetId", testActionSetId, - "--isLookUpUrl", "lookupurl", - "--workingPath", testOutputBasePath - }); - - new SparkCreateDedupRecord(parser, spark).run(isLookUpService); - - final ObjectMapper mapper = new ObjectMapper() - .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); + new SparkCreateDedupRecord(args( + "/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json", + new String[] { + "--graphBasePath", graphInputPath, + "--actionSetId", testActionSetId, + "--isLookUpUrl", "lookupurl", + "--workingPath", workingPath + }), spark) + .run(isLookUpService); final Dataset roots = spark .read() - .textFile(testOutputBasePath + "/" + testActionSetId + "/publication_deduprecord") - .map( - (MapFunction) value -> mapper.readValue(value, Publication.class), - Encoders.bean(Publication.class)); + .textFile(workingPath + "/" + testActionSetId + "/publication_deduprecord") + .map(asEntity(Publication.class), Encoders.bean(Publication.class)); - assertEquals(2, roots.count()); + assertEquals(3, roots.count()); final Dataset pubs = spark .read() - .textFile(DedupUtility.createEntityPath(testGraphBasePath, "publication")) - .map( - (MapFunction) value -> mapper.readValue(value, Publication.class), - Encoders.bean(Publication.class)); + .textFile(DedupUtility.createEntityPath(graphInputPath, "publication")) + .map(asEntity(Publication.class), Encoders.bean(Publication.class)); verifyRoot_case_1(roots, pubs); verifyRoot_case_2(roots, pubs); + verifyRoot_case_3(roots, pubs); } private static void verifyRoot_case_1(Dataset roots, Dataset pubs) { @@ -299,8 +284,7 @@ public class SparkDedupPublicationTest implements Serializable { assertEquals("Article", instance_cr.get().getInstancetype().getClassname()); } - private void verifyRoot_case_2(Dataset roots, Dataset pubs) - throws JsonProcessingException { + private void verifyRoot_case_2(Dataset roots, Dataset pubs) { Publication root = roots .filter("id = '50|doi_dedup___::18aff3b55fb6876466a5d4bd82434885'") .first(); @@ -334,57 +318,86 @@ public class SparkDedupPublicationTest implements Serializable { assertTrue(Sets.difference(root_cf, dups_cf).isEmpty()); } + private void verifyRoot_case_3(Dataset roots, Dataset pubs) { + Publication root = roots + .filter("id = '50|dedup_wf_001::31ca734cc22181b704c4aa8fd050062a'") + .first(); + assertNotNull(root); + + Publication pivot_duplicate = pubs + .filter("id = '50|od_______166::31ca734cc22181b704c4aa8fd050062a'") + .first(); + + assertEquals(pivot_duplicate.getPublisher().getValue(), root.getPublisher().getValue()); + + Set dups_cf = pubs + .collectAsList() + .stream() + .flatMap(p -> p.getCollectedfrom().stream()) + .map(KeyValue::getValue) + .collect(Collectors.toCollection(HashSet::new)); + + Set root_cf = root + .getCollectedfrom() + .stream() + .map(KeyValue::getValue) + .collect(Collectors.toCollection(HashSet::new)); + + assertTrue(Sets.difference(root_cf, dups_cf).isEmpty()); + } + @Test @Order(6) void updateEntityTest() throws Exception { + new SparkUpdateEntity(args( + "/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json", + new String[] { + "--graphBasePath", graphInputPath, + "--workingPath", workingPath, + "--dedupGraphPath", graphOutputPath + }), spark) + .run(isLookUpService); - ArgumentApplicationParser parser = new ArgumentApplicationParser( - classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json")); - parser - .parseArgument( - new String[] { - "-i", testGraphBasePath, "-w", testOutputBasePath, "-o", testDedupGraphBasePath - }); - - new SparkUpdateEntity(parser, spark).run(isLookUpService); - - long publications = jsc.textFile(testDedupGraphBasePath + "/publication").count(); + long publications = spark.read().textFile(graphOutputPath + "/publication").count(); long mergedPubs = spark .read() - .load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel") + .load(workingPath + "/" + testActionSetId + "/publication_mergerel") .as(Encoders.bean(Relation.class)) .where("relClass=='merges'") - .javaRDD() - .map(Relation::getTarget) + .map((MapFunction) Relation::getTarget, Encoders.STRING()) .distinct() .count(); - assertEquals(14, publications); + assertEquals(19, publications); // 16 originals + 3 roots - long deletedPubs = jsc - .textFile(testDedupGraphBasePath + "/publication") - .filter(this::isDeletedByInference) + long deletedPubs = spark + .read() + .textFile(graphOutputPath + "/publication") + .map(asEntity(Publication.class), Encoders.bean(Publication.class)) + .filter("datainfo.deletedbyinference == true") + .map((MapFunction) OafEntity::getId, Encoders.STRING()) + .distinct() .count(); assertEquals(mergedPubs, deletedPubs); } - @AfterAll - public static void finalCleanUp() throws IOException { - FileUtils.deleteDirectory(new File(testOutputBasePath)); - FileUtils.deleteDirectory(new File(testDedupGraphBasePath)); - } - - public boolean isDeletedByInference(String s) { - return s.contains("\"deletedbyinference\":true"); - } - private static String classPathResourceAsString(String path) throws IOException { return IOUtils .toString( - SparkDedupPublicationTest.class + SparkPublicationRootsTest.class .getResourceAsStream(path)); } + private static MapFunction asEntity(Class clazz) { + return value -> MAPPER.readValue(value, clazz); + } + + private ArgumentApplicationParser args(String paramSpecs, String[] args) throws IOException, ParseException { + ArgumentApplicationParser parser = new ArgumentApplicationParser(classPathResourceAsString(paramSpecs)); + parser.parseArgument(args); + return parser; + } + } diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkPublicationRootsTest2.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkPublicationRootsTest2.java new file mode 100644 index 000000000..9afe1e34b --- /dev/null +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkPublicationRootsTest2.java @@ -0,0 +1,251 @@ + +package eu.dnetlib.dhp.oa.dedup; + +import static java.nio.file.Files.createTempDirectory; + +import static org.apache.spark.sql.functions.count; +import static org.junit.jupiter.api.Assertions.*; +import static org.mockito.Mockito.lenient; + +import java.io.File; +import java.io.IOException; +import java.io.Serializable; +import java.net.URISyntaxException; +import java.nio.file.Path; +import java.nio.file.Paths; +import java.util.HashSet; +import java.util.List; +import java.util.Optional; +import java.util.Set; +import java.util.stream.Collectors; + +import org.apache.commons.cli.ParseException; +import org.apache.commons.io.FileUtils; +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.FilterFunction; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.*; +import org.junit.jupiter.api.extension.ExtendWith; +import org.mockito.Mock; +import org.mockito.Mockito; +import org.mockito.junit.jupiter.MockitoExtension; + +import com.fasterxml.jackson.databind.DeserializationFeature; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.google.common.collect.Sets; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; + +@ExtendWith(MockitoExtension.class) +@TestMethodOrder(MethodOrderer.OrderAnnotation.class) +public class SparkPublicationRootsTest2 implements Serializable { + + @Mock(serializable = true) + ISLookUpService isLookUpService; + private static SparkSession spark; + + private static String workingPath; + + private static String graphInputPath; + + private static String graphOutputPath; + + private static final String testActionSetId = "test-orchestrator"; + + private static Path testBaseTmpPath; + + private static final ObjectMapper MAPPER = new ObjectMapper() + .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); + + @BeforeAll + public static void init() throws IOException, URISyntaxException { + + testBaseTmpPath = createTempDirectory(SparkPublicationRootsTest2.class.getSimpleName() + "-"); + + final File entitiesSources = Paths + .get(SparkPublicationRootsTest2.class.getResource("/eu/dnetlib/dhp/dedup/root").toURI()) + .toFile(); + + FileUtils + .copyDirectory( + entitiesSources, + testBaseTmpPath.resolve("input").toFile()); + + FileUtils + .copyFileToDirectory( + Paths + .get( + SparkPublicationRootsTest2.class + .getResource( + "/eu/dnetlib/dhp/dedup/root/alterations/publication/publication_1.gz") + .toURI()) + .toFile(), + testBaseTmpPath.resolve("input").resolve("entities").resolve("publication").toFile()); + + workingPath = testBaseTmpPath.resolve("workingPath").toString(); + graphInputPath = testBaseTmpPath.resolve("input").resolve("entities").toString(); + graphOutputPath = testBaseTmpPath.resolve("output").toString(); + + final SparkConf conf = new SparkConf(); + conf.set("spark.sql.shuffle.partitions", "10"); + spark = SparkSession + .builder() + .appName(SparkPublicationRootsTest2.class.getSimpleName()) + .master("local[*]") + .config(conf) + .getOrCreate(); + } + + @BeforeEach + public void setUp() throws IOException, ISLookUpException { + + lenient() + .when(isLookUpService.getResourceProfileByQuery(Mockito.contains(testActionSetId))) + .thenReturn(classPathResourceAsString("/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator_publication.xml")); + + lenient() + .when(isLookUpService.getResourceProfileByQuery(Mockito.contains("publication"))) + .thenReturn(classPathResourceAsString("/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json")); + } + + @AfterAll + public static void tearDown() throws IOException { + FileUtils.deleteDirectory(testBaseTmpPath.toFile()); + } + + @Test + @Order(7) + void dedupAlteredDatasetTest() throws Exception { + + new SparkCreateSimRels(args( + "/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json", + new String[] { + "--graphBasePath", graphInputPath, + "--actionSetId", testActionSetId, + "--isLookUpUrl", "lookupurl", + "--workingPath", workingPath, + "--numPartitions", "5" + }), spark) + .run(isLookUpService); + + new SparkCreateMergeRels(args( + "/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json", + new String[] { + "--graphBasePath", graphInputPath, + "--actionSetId", testActionSetId, + "--isLookUpUrl", "lookupurl", + "--workingPath", workingPath + }), spark) + .run(isLookUpService); + + final Dataset merges = spark + .read() + .load(workingPath + "/" + testActionSetId + "/publication_mergerel") + .as(Encoders.bean(Relation.class)); + + assertEquals( + 3, merges + .filter("relclass == 'isMergedIn'") + .map((MapFunction) Relation::getTarget, Encoders.STRING()) + .distinct() + .count()); + assertEquals( + 4, merges + .filter("source == '50|doi_dedup___::b3aec7985136e36827176aaa1dd5082d'") + .count()); + + new SparkCreateDedupRecord(args( + "/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json", + new String[] { + "--graphBasePath", graphInputPath, + "--actionSetId", testActionSetId, + "--isLookUpUrl", "lookupurl", + "--workingPath", workingPath + }), spark) + .run(isLookUpService); + + final Dataset roots = spark + .read() + .textFile(workingPath + "/" + testActionSetId + "/publication_deduprecord") + .map(asEntity(Publication.class), Encoders.bean(Publication.class)); + + assertEquals(3, roots.count()); + + final Dataset pubs = spark + .read() + .textFile(DedupUtility.createEntityPath(graphInputPath, "publication")) + .map(asEntity(Publication.class), Encoders.bean(Publication.class)); + + Publication root = roots + .filter("id = '50|doi_dedup___::b3aec7985136e36827176aaa1dd5082d'") + .first(); + assertNotNull(root); + + Publication crossref_duplicate = pubs + .filter("id = '50|doi_________::b3aec7985136e36827176aaa1dd5082d'") + .collectAsList() + .get(0); + + assertEquals(crossref_duplicate.getDateofacceptance().getValue(), root.getDateofacceptance().getValue()); + assertEquals(crossref_duplicate.getJournal().getName(), root.getJournal().getName()); + assertEquals(crossref_duplicate.getJournal().getIssnPrinted(), root.getJournal().getIssnPrinted()); + assertEquals(crossref_duplicate.getPublisher().getValue(), root.getPublisher().getValue()); + + Set rootPids = root + .getPid() + .stream() + .map(StructuredProperty::getValue) + .collect(Collectors.toCollection(HashSet::new)); + Set dupPids = crossref_duplicate + .getPid() + .stream() + .map(StructuredProperty::getValue) + .collect(Collectors.toCollection(HashSet::new)); + + assertFalse(Sets.intersection(rootPids, dupPids).isEmpty()); + assertTrue(rootPids.contains("10.1109/jstqe.2022.3205716")); + assertTrue(rootPids.contains("10.1109/jstqe.2023.9999999")); + + Optional instance_cr = root + .getInstance() + .stream() + .filter(i -> i.getCollectedfrom().getValue().equals("Crossref")) + .findFirst(); + assertTrue(instance_cr.isPresent()); + assertEquals("OPEN", instance_cr.get().getAccessright().getClassid()); + assertEquals("Open Access", instance_cr.get().getAccessright().getClassname()); + assertEquals(OpenAccessRoute.hybrid, instance_cr.get().getAccessright().getOpenAccessRoute()); + assertEquals( + "IEEE Journal of Selected Topics in Quantum Electronics", instance_cr.get().getHostedby().getValue()); + assertEquals("0001", instance_cr.get().getInstancetype().getClassid()); + assertEquals("Article", instance_cr.get().getInstancetype().getClassname()); + + } + + private static String classPathResourceAsString(String path) throws IOException { + return IOUtils + .toString( + SparkPublicationRootsTest2.class + .getResourceAsStream(path)); + } + + private static MapFunction asEntity(Class clazz) { + return value -> MAPPER.readValue(value, clazz); + } + + private ArgumentApplicationParser args(String paramSpecs, String[] args) throws IOException, ParseException { + ArgumentApplicationParser parser = new ArgumentApplicationParser(classPathResourceAsString(paramSpecs)); + parser.parseArgument(args); + return parser; + } + +} 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"miriam.baglioni" Date: Mon, 28 Nov 2022 14:51:20 +0100 Subject: [PATCH 09/11] [Bulk Tag horizontal] added new path in definition of constraint (to recognize fos subjects) - changed test and resource class to test this new aspect --- .../community/QueryInformationSystem.java | 3 + .../dnetlib/dhp/bulktag/BulkTagJobTest.java | 8 +- .../communityconfiguration/tagging_conf.xml | 85 +++++++++++++++++++ .../dataset_10.json | 4 +- 4 files changed, 95 insertions(+), 5 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/QueryInformationSystem.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/QueryInformationSystem.java index f06c0d47a..ec89edc63 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/QueryInformationSystem.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/QueryInformationSystem.java @@ -26,6 +26,9 @@ public class QueryInformationSystem { + " return " + " " + " { $x//CONFIGURATION/context/@id} " + + " " + + "{$x//CONFIGURATION/context/param[./@name='advancedConstraints']/text() }" + + "" + " " + " {for $y in tokenize($subj,',') " + " return " diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java index eaf34c824..364e53376 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java @@ -46,7 +46,9 @@ public class BulkTagJobTest { + " \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\"," + " \"contributor\" : \"$['contributor'][*]['value']\"," + " \"description\" : \"$['description'][*]['value']\", " - + " \"subject\" :\"$['subject'][*]['value']\" }"; + + " \"subject\" :\"$['subject'][*]['value']\" , " + + + "\"fos\" : \"$['subject'][?(@['qualifier']['classid']=='subject:fos')].value\"} "; private static SparkSession spark; @@ -770,14 +772,14 @@ public class BulkTagJobTest { org.apache.spark.sql.Dataset idExplodeCommunity = spark.sql(query); idExplodeCommunity.show(false); - Assertions.assertEquals(4, idExplodeCommunity.count()); + Assertions.assertEquals(5, idExplodeCommunity.count()); Assertions .assertEquals( 3, idExplodeCommunity.filter("provenance = 'community:datasource'").count()); Assertions .assertEquals( - 1, idExplodeCommunity.filter("provenance = 'community:advconstraint'").count()); + 2, idExplodeCommunity.filter("provenance = 'community:advconstraint'").count()); } } diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf.xml b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf.xml index 4e580edf5..b2e33df12 100644 --- a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf.xml +++ b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf.xml @@ -844,6 +844,89 @@ + + { + "criteria": [ + { + "constraint": [ + { + "verb": "equals_caseinsensitive", + "field": "subject", + "value": "North America" + }, + { + "verb": "contains", + "field": "fos", + "value": "05" + } + ] + }, + { + "constraint": [ + { + "verb": "equals_caseinsensitive", + "field": "subject", + "value": "North America" + }, + { + "verb": "contains", + "field": "fos", + "value": "06" + } + ] + }, + { + "constraint": [ + { + "verb": "equals_caseinsensitive", + "field": "subject", + "value": "Mexico" + }, + { + "verb": "equals_caseinsensitive", + "field": "subject", + "value": "United States" + }, + { + "verb": "equals_caseinsensitive", + "field": "subject", + "value": "Canada" + }, + { + "verb": "contains", + "field": "fos", + "value": "05" + } + ] + }, + { + "constraint": [ + { + "verb": "equals_caseinsensitive", + "field": "subject", + "value": "Mexico" + }, + { + "verb": "equals_caseinsensitive", + "field": "subject", + "value": "United States" + }, + { + "verb": "equals_caseinsensitive", + "field": "subject", + "value": "Canada" + }, + { + "verb": "contains", + "field": "fos", + "value": "06" + } + ] + } + ] + } + + @@ -1174,7 +1257,9 @@ + + diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/update_datasourcewithconstraints/dataset_10.json b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/update_datasourcewithconstraints/dataset_10.json index 168343401..17553eb83 100644 --- a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/update_datasourcewithconstraints/dataset_10.json +++ b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/update_datasourcewithconstraints/dataset_10.json @@ -6,5 +6,5 @@ {"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1585055869498,"id":"50|od______3989::2f4f3c820c450bd08dac08d07cc82dcf","originalId":["od______3989::2f4f3c820c450bd08dac08d07cc82dcf"],"collectedfrom":[{"key":"opendoar____::3989","value":"Depósito Digital 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El formato es al estilo inglés, similar al de la Oxford Union, donde algunos jóvenes se reunían a debatir sobre temas de la más candente actualidad y polemizaban con la intención de formarse en tan valoradas habilidades.\n\nLa Liga de Debate CICAE-UCJC es una ocasión única para los alumnos de ponerse en contacto con herramientas tan útiles como la oratoria y la comunicación efectiva. Pero, sobre todo, una oportunidad de fomentar el pensamiento crítico y la socialización entre alumnos con espíritu emprendedor. La Liga de Debate CICAE - Universidad Camilo José Cela se diferencia del resto de torneos en que potenciamos que sea eminentemente formativa. Alumnos y profesores reciben formación en comunicación, oratoria y debate por parte de alguno de los expertos en debate españoles más reconocidos en la escena internacional.\n\nDatos de la III Liga de Debate CICAE - UCJC http://ligacicae.ucjc.edu/","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2018-10-23","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":null,"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[{"value":"Universidad 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+ +import java.io.Serializable; + +@VerbClass("starts_with") +public class StartsWithVerb implements Selection, Serializable { + + private String param; + + public StartsWithVerb() { + } + + public StartsWithVerb(final String param) { + this.param = param; + } + + @Override + public boolean apply(String value) { + return value.startsWith(param); + } + + public String getParam() { + return param; + } + + public void setParam(String param) { + this.param = param; + } +} From ce020f2c837207bc7e2f6b9062d56d07196f0cd5 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 30 Nov 2022 09:57:30 +0100 Subject: [PATCH 11/11] [EOSC FUTURE] added resources and test for review --- .../provision/IndexRecordTransformerTest.java | 20 ++++ .../provision/eosc-future/zenodo7351221.xml | 99 +++++++++++++++++ .../provision/eosc-future/zenodo7351393.xml | 100 ++++++++++++++++++ .../provision/eosc-future/zenodo7353841.xml | 85 +++++++++++++++ 4 files changed, 304 insertions(+) create mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/eosc-future/zenodo7351221.xml create mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/eosc-future/zenodo7351393.xml create mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/eosc-future/zenodo7353841.xml diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java index 17c3cdb30..d9dc609d8 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java @@ -142,6 +142,26 @@ public class IndexRecordTransformerTest { testRecordTransformation(record); } + @Test + public void testForEOSCFutureZenodo7353841() throws IOException, TransformerException { + final String record = IOUtils + .toString(getClass().getResourceAsStream("eosc-future/zenodo7353841.xml")); + testRecordTransformation(record); + } + + @Test + public void testForEOSCFutureZenodo7351393() throws IOException, TransformerException { + final String record = IOUtils + .toString(getClass().getResourceAsStream("eosc-future/zenodo7351393.xml")); + testRecordTransformation(record); + } + + @Test + public void testForEOSCFutureZenodo7351221() throws IOException, TransformerException { + final String record = IOUtils + .toString(getClass().getResourceAsStream("eosc-future/zenodo7351221.xml")); + testRecordTransformation(record); + } @Test void testDoiUrlNormalization() throws MalformedURLException { diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/eosc-future/zenodo7351221.xml b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/eosc-future/zenodo7351221.xml new file mode 100644 index 000000000..7f1e66dac --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/eosc-future/zenodo7351221.xml @@ -0,0 +1,99 @@ + + +
+ doi_________::9cb0664d4c891c4baaf73f007c0c9de0 + 2022-11-25T12:55:13Z + under curation + +
+ + + + + COVID-19 Knowledge Graph: A semantic resource embedding biological and chemical entities + Karki, Reagon + + + +

A Knowledge graph representation of compounds and associated biological entities in the BY-COVID and EOSC Future project.

Current status

  • Number of Nodes: 35952
  • Number of Edges: 279462
  • Human Proteins: 1347
  • Assay: 15835
  • Chemical/Compound: 4096
  • Mechanism of Action: 739
  • Pathway: 1513
  • Disease: 1585
  • SideEffect: 7420
  • Biological Process: 2085
  • Molecular Function: 1332

Please check the BY_COVID_update_August.ipynb for understanding step wise process of KG generation and KG statistics. The KG has been exported to formats such as graphml, sif and so on for visualizations in other platforms. For example, the graphml file can be imported to Cytoscape directly. These files are located in 'data\export' folder.

 + + + + Zenodo + + + + + + + + + + + + + + + + + + + oai:zenodo.org:7351221 + + oai:zenodo.org:7351221 + 10.5281/zenodo.7351221 + + + + false + false + 0.9 + + + + + + corda__h2020::256485716fdb9f5ca69007b7ca5a072b + 101017536 + EOSC Future + EOSC Future + + + + ec__________::EC::H2020 + + + + + corda__h2020::4a3254eac2997eee0a9dcb7a7daedb81 + 101046203 + BY-COVID + Beyond COVID + + + + ec__________::EC::Horizon Europe Framework Programme - HORIZON-RIA\HORIZON Action Grant Budget-Based + + + + + + + + + + + + + https://zenodo.org/record/7351221 + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/eosc-future/zenodo7351393.xml b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/eosc-future/zenodo7351393.xml new file mode 100644 index 000000000..21b656d2c --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/eosc-future/zenodo7351393.xml @@ -0,0 +1,100 @@ + + +
+ doi_________::07fdccabd77830e3caccf0b33c083f1b + 2022-11-25T01:08:31Z + under curation + +
+ + + + Monkeypox Knowledge Graph: A semantic resource embedding biological and chemical entities + Karki, Reagon + Andrea, Zaliani + Gadiya, Yojana + Gribbon, Philip + + + +

The Monkeypox KG is built using viral and human proteins reported in different resources. Additionally, the KG represents chemicals tested against Monkeypox and their targets, associated biological processes, molecular functions, diseases and side effects.

KG status

Version 1 stats:

  • Number of Nodes: 8235
  • Number of Edges: 40422

Version 2 stats (2nd September) :

  • Number of Nodes: 9129
  • Number of Edges: 44568

Please check the graph.ipynb for understanding step wise process of KG generation and KG statistics. The KG has been exported to formats such as graphml, sif and so on for visualizations in other platforms. For example, the graphml file can be imported to Cytoscape directly. These files are located in 'data\export' folder.

 + + + + Zenodo + + + + + + + + + + + + + + + + + + + oai:zenodo.org:7351393 + + oai:zenodo.org:7351393 + 10.5281/zenodo.7351393 + + + false + false + 0.9 + + + + + + corda__h2020::256485716fdb9f5ca69007b7ca5a072b + 101017536 + EOSC Future + EOSC Future + + + + ec__________::EC::H2020 + + + + + corda__h2020::4a3254eac2997eee0a9dcb7a7daedb81 + 101046203 + BY-COVID + Beyond COVID + + + + ec__________::EC::Horizon Europe Framework Programme - HORIZON-RIA\HORIZON Action Grant Budget-Based + + + + + + + + + + + + + https://zenodo.org/record/7351393 + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/eosc-future/zenodo7353841.xml b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/eosc-future/zenodo7353841.xml new file mode 100644 index 000000000..4bd287e50 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/eosc-future/zenodo7353841.xml @@ -0,0 +1,85 @@ + + +
+ doi_________::93d39dd7edef016928788c3500e149f1 + 2022-11-24T08:41:37Z + under curation + +
+ + + + ENVRI SP - Dashboard State of the Environment - Ocean Indicators + Tjerk Krijger + + + +

The attached .yaml file is used as input to the Dashboard State of the Environment, which is a science project of the ENVRI-FAIR science cluster within EOSC-FUTURE. The contents of the file enable the visualization of Ocean indicators on the dashboard. It is possible to download the attached file and change the contents to include indicators from different domains such as atmosphere or biodiversity.

 + + + + Zenodo + + + + + + + + + + + + + + + + + + + oai:zenodo.org:7353841 + + oai:zenodo.org:7353841 + 10.5281/zenodo.7353841 + + + false + false + 0.9 + + + + + + corda__h2020::256485716fdb9f5ca69007b7ca5a072b + 101017536 + EOSC Future + EOSC Future + + + + ec__________::EC::H2020 + + + + + + + + + + + + + https://zenodo.org/record/7353841 + + + + + + + +