From 5130eac24747237213a80ce552c891128adf6366 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 24 Jun 2022 17:16:42 +0200 Subject: [PATCH 01/33] mapping by participant project contribution --- .../dhp/schema/oaf/utils/OafMapperUtils.java | 58 +++++++ .../raw/AbstractMdRecordToOafMapper.java | 52 ++---- .../raw/MigrateDbEntitiesApplication.java | 155 +++++------------- .../oa/graph/sql/queryProjectOrganization.sql | 1 + 4 files changed, 114 insertions(+), 152 deletions(-) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java index ac9cfe330..6f452e846 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java @@ -419,4 +419,62 @@ public class OafMapperUtils { m.setUnit(Arrays.asList(newKeyValueInstance(key, value, dataInfo))); return m; } + + public static Relation getRelation(final String source, + final String target, + final String relType, + final String subRelType, + final String relClass, + final OafEntity entity) { + return getRelation(source, target, relType, subRelType, relClass, entity, null); + } + + public static Relation getRelation(final String source, + final String target, + final String relType, + final String subRelType, + final String relClass, + final OafEntity entity, + final String validationDate) { + return getRelation( + source, target, relType, subRelType, relClass, entity.getCollectedfrom(), entity.getDataInfo(), + entity.getLastupdatetimestamp(), validationDate, null); + } + + public static Relation getRelation(final String source, + final String target, + final String relType, + final String subRelType, + final String relClass, + final List collectedfrom, + final DataInfo dataInfo, + final Long lastupdatetimestamp) { + return getRelation( + source, target, relType, subRelType, relClass, collectedfrom, dataInfo, lastupdatetimestamp, null, null); + } + + public static Relation getRelation(final String source, + final String target, + final String relType, + final String subRelType, + final String relClass, + final List collectedfrom, + final DataInfo dataInfo, + final Long lastupdatetimestamp, + final String validationDate, + final List properties) { + final Relation rel = new Relation(); + rel.setRelType(relType); + rel.setSubRelType(subRelType); + rel.setRelClass(relClass); + rel.setSource(source); + rel.setTarget(target); + rel.setCollectedfrom(collectedfrom); + rel.setDataInfo(dataInfo); + rel.setLastupdatetimestamp(lastupdatetimestamp); + rel.setValidated(StringUtils.isNotBlank(validationDate)); + rel.setValidationDate(StringUtils.isNotBlank(validationDate) ? validationDate : null); + rel.setProperties(properties); + return rel; + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index 739be3df4..846440a69 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -267,10 +267,13 @@ public abstract class AbstractMdRecordToOafMapper { res .add( - getRelation( - docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, entity, validationdDate)); + OafMapperUtils + .getRelation( + docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, entity, validationdDate)); res - .add(getRelation(projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, entity, validationdDate)); + .add( + OafMapperUtils + .getRelation(projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, entity, validationdDate)); } } @@ -303,13 +306,16 @@ public abstract class AbstractMdRecordToOafMapper { final String targetId = createOpenaireId(targetType, target, true); rels .add( - getRelation( - entity.getId(), targetId, relType, subRelType, relClass, entity, validationdDate)); + OafMapperUtils + .getRelation( + entity.getId(), targetId, relType, subRelType, relClass, entity, + validationdDate)); rels .add( - getRelation( - targetId, entity.getId(), relType, subRelType, relClassInverse, entity, - validationdDate)); + OafMapperUtils + .getRelation( + targetId, entity.getId(), relType, subRelType, relClassInverse, entity, + validationdDate)); } } } @@ -317,36 +323,6 @@ public abstract class AbstractMdRecordToOafMapper { return rels; } - protected Relation getRelation(final String source, - final String target, - final String relType, - final String subRelType, - final String relClass, - final OafEntity entity) { - return getRelation(source, target, relType, subRelType, relClass, entity, null); - } - - protected Relation getRelation(final String source, - final String target, - final String relType, - final String subRelType, - final String relClass, - final OafEntity entity, - final String validationDate) { - final Relation rel = new Relation(); - rel.setRelType(relType); - rel.setSubRelType(subRelType); - rel.setRelClass(relClass); - rel.setSource(source); - rel.setTarget(target); - rel.setCollectedfrom(entity.getCollectedfrom()); - rel.setDataInfo(entity.getDataInfo()); - rel.setLastupdatetimestamp(entity.getLastupdatetimestamp()); - rel.setValidated(StringUtils.isNotBlank(validationDate)); - rel.setValidationDate(StringUtils.isNotBlank(validationDate) ? validationDate : null); - return rel; - } - protected abstract List addOtherResultRels( final Document doc, final OafEntity entity); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java index 63fa8b7e0..8296e99cd 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java @@ -1,32 +1,7 @@ package eu.dnetlib.dhp.oa.graph.raw; -import static eu.dnetlib.dhp.schema.common.ModelConstants.DATASET_DEFAULT_RESULTTYPE; -import static eu.dnetlib.dhp.schema.common.ModelConstants.DATASOURCE_ORGANIZATION; -import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PROVENANCE_ACTIONS; -import static eu.dnetlib.dhp.schema.common.ModelConstants.ENTITYREGISTRY_PROVENANCE_ACTION; -import static eu.dnetlib.dhp.schema.common.ModelConstants.HAS_PARTICIPANT; -import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_MERGED_IN; -import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_PARTICIPANT; -import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_PRODUCED_BY; -import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_PROVIDED_BY; -import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_RELATED_TO; -import static eu.dnetlib.dhp.schema.common.ModelConstants.MERGES; -import static eu.dnetlib.dhp.schema.common.ModelConstants.ORG_ORG_RELTYPE; -import static eu.dnetlib.dhp.schema.common.ModelConstants.ORP_DEFAULT_RESULTTYPE; -import static eu.dnetlib.dhp.schema.common.ModelConstants.OUTCOME; -import static eu.dnetlib.dhp.schema.common.ModelConstants.PARTICIPATION; -import static eu.dnetlib.dhp.schema.common.ModelConstants.PRODUCES; -import static eu.dnetlib.dhp.schema.common.ModelConstants.PROJECT_ORGANIZATION; -import static eu.dnetlib.dhp.schema.common.ModelConstants.PROVIDES; -import static eu.dnetlib.dhp.schema.common.ModelConstants.PROVISION; -import static eu.dnetlib.dhp.schema.common.ModelConstants.PUBLICATION_DATASET; -import static eu.dnetlib.dhp.schema.common.ModelConstants.PUBLICATION_DEFAULT_RESULTTYPE; -import static eu.dnetlib.dhp.schema.common.ModelConstants.RELATIONSHIP; -import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_PROJECT; -import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_RESULT; -import static eu.dnetlib.dhp.schema.common.ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE; -import static eu.dnetlib.dhp.schema.common.ModelConstants.USER_CLAIM; +import static eu.dnetlib.dhp.schema.common.ModelConstants.*; import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.*; import java.io.Closeable; @@ -45,6 +20,8 @@ import org.apache.commons.lang3.StringUtils; import org.slf4j.Logger; import org.slf4j.LoggerFactory; +import com.google.common.collect.Lists; + import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.DbClient; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; @@ -68,6 +45,7 @@ import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.Software; import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; import eu.dnetlib.dhp.utils.ISLookupClientFactory; public class MigrateDbEntitiesApplication extends AbstractMigrationApplication implements Closeable { @@ -437,25 +415,14 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i final List collectedFrom = listKeyValues( createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname")); - final Relation r1 = new Relation(); - r1.setRelType(DATASOURCE_ORGANIZATION); - r1.setSubRelType(PROVISION); - r1.setRelClass(IS_PROVIDED_BY); - r1.setSource(dsId); - r1.setTarget(orgId); - r1.setCollectedfrom(collectedFrom); - r1.setDataInfo(info); - r1.setLastupdatetimestamp(lastUpdateTimestamp); + final Relation r1 = OafMapperUtils + .getRelation( + dsId, orgId, DATASOURCE_ORGANIZATION, PRODUCES, IS_PROVIDED_BY, collectedFrom, info, + lastUpdateTimestamp); - final Relation r2 = new Relation(); - r2.setRelType(DATASOURCE_ORGANIZATION); - r2.setSubRelType(PROVISION); - r2.setRelClass(PROVIDES); - r2.setSource(orgId); - r2.setTarget(dsId); - r2.setCollectedfrom(collectedFrom); - r2.setDataInfo(info); - r2.setLastupdatetimestamp(lastUpdateTimestamp); + final Relation r2 = OafMapperUtils + .getRelation( + orgId, dsId, DATASOURCE_ORGANIZATION, PRODUCES, PROVIDES, collectedFrom, info, lastUpdateTimestamp); return Arrays.asList(r1, r2); } catch (final Exception e) { @@ -471,25 +438,20 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i final List collectedFrom = listKeyValues( createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname")); - final Relation r1 = new Relation(); - r1.setRelType(PROJECT_ORGANIZATION); - r1.setSubRelType(PARTICIPATION); - r1.setRelClass(HAS_PARTICIPANT); - r1.setSource(projectId); - r1.setTarget(orgId); - r1.setCollectedfrom(collectedFrom); - r1.setDataInfo(info); - r1.setLastupdatetimestamp(lastUpdateTimestamp); + final List properties = Lists + .newArrayList( + keyValue("contribution", String.valueOf(rs.getDouble("totalcost"))), + keyValue("currency", rs.getString("currency"))); - final Relation r2 = new Relation(); - r2.setRelType(PROJECT_ORGANIZATION); - r2.setSubRelType(PARTICIPATION); - r2.setRelClass(IS_PARTICIPANT); - r2.setSource(orgId); - r2.setTarget(projectId); - r2.setCollectedfrom(collectedFrom); - r2.setDataInfo(info); - r2.setLastupdatetimestamp(lastUpdateTimestamp); + final Relation r1 = OafMapperUtils + .getRelation( + projectId, orgId, PROJECT_ORGANIZATION, PARTICIPATION, HAS_PARTICIPANT, collectedFrom, info, + lastUpdateTimestamp, null, properties); + + final Relation r2 = OafMapperUtils + .getRelation( + orgId, projectId, PROJECT_ORGANIZATION, PARTICIPATION, IS_PARTICIPANT, collectedFrom, info, + lastUpdateTimestamp, null, properties); return Arrays.asList(r1, r2); } catch (final Exception e) { @@ -703,25 +665,12 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i final List collectedFrom = listKeyValues( createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname")); - final Relation r1 = new Relation(); - r1.setRelType(ORG_ORG_RELTYPE); - r1.setSubRelType(ModelConstants.DEDUP); - r1.setRelClass(MERGES); - r1.setSource(orgId1); - r1.setTarget(orgId2); - r1.setCollectedfrom(collectedFrom); - r1.setDataInfo(info); - r1.setLastupdatetimestamp(lastUpdateTimestamp); + final Relation r1 = OafMapperUtils + .getRelation(orgId1, orgId2, ORG_ORG_RELTYPE, DEDUP, MERGES, collectedFrom, info, lastUpdateTimestamp); - final Relation r2 = new Relation(); - r2.setRelType(ORG_ORG_RELTYPE); - r2.setSubRelType(ModelConstants.DEDUP); - r2.setRelClass(IS_MERGED_IN); - r2.setSource(orgId2); - r2.setTarget(orgId1); - r2.setCollectedfrom(collectedFrom); - r2.setDataInfo(info); - r2.setLastupdatetimestamp(lastUpdateTimestamp); + final Relation r2 = OafMapperUtils + .getRelation( + orgId2, orgId1, ORG_ORG_RELTYPE, DEDUP, IS_MERGED_IN, collectedFrom, info, lastUpdateTimestamp); return Arrays.asList(r1, r2); } catch (final Exception e) { throw new RuntimeException(e); @@ -738,17 +687,12 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i final List collectedFrom = listKeyValues( createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname")); - final Relation r = new Relation(); - r.setRelType(ORG_ORG_RELTYPE); - r.setSubRelType(ModelConstants.RELATIONSHIP); - r.setRelClass(rs.getString("type")); - r.setSource(orgId1); - r.setTarget(orgId2); - r.setCollectedfrom(collectedFrom); - r.setDataInfo(info); - r.setLastupdatetimestamp(lastUpdateTimestamp); - - return Arrays.asList(r); + return Arrays + .asList( + OafMapperUtils + .getRelation( + orgId1, orgId2, ORG_ORG_RELTYPE, RELATIONSHIP, rs.getString("type"), collectedFrom, info, + lastUpdateTimestamp)); } catch (final Exception e) { throw new RuntimeException(e); } @@ -765,29 +709,12 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i final List collectedFrom = listKeyValues( createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname")); - final Relation r1 = new Relation(); - r1.setRelType(ORG_ORG_RELTYPE); - r1.setSubRelType(ModelConstants.DEDUP); - r1.setRelClass(relClass); - r1.setSource(orgId1); - r1.setTarget(orgId2); - r1.setCollectedfrom(collectedFrom); - r1.setDataInfo(info); - r1.setLastupdatetimestamp(lastUpdateTimestamp); - - // removed because there's no difference between two sides //TODO - // final Relation r2 = new Relation(); - // r2.setRelType(ORG_ORG_RELTYPE); - // r2.setSubRelType(ORG_ORG_SUBRELTYPE); - // r2.setRelClass(relClass); - // r2.setSource(orgId2); - // r2.setTarget(orgId1); - // r2.setCollectedfrom(collectedFrom); - // r2.setDataInfo(info); - // r2.setLastupdatetimestamp(lastUpdateTimestamp); - // return Arrays.asList(r1, r2); - - return Arrays.asList(r1); + return Arrays + .asList( + OafMapperUtils + .getRelation( + orgId1, orgId2, ORG_ORG_RELTYPE, DEDUP, relClass, collectedFrom, info, + lastUpdateTimestamp)); } catch (final Exception e) { throw new RuntimeException(e); } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjectOrganization.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjectOrganization.sql index d9a77427d..9a5133e4b 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjectOrganization.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjectOrganization.sql @@ -3,6 +3,7 @@ SELECT po.resporganization AS resporganization, po.participantnumber AS participantnumber, po.contribution AS contribution, + po.currency AS currency, NULL AS startdate, NULL AS enddate, false AS inferred, From 0a4f4d98fa8f73d296ef92f4dbf9f12a760ef735 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Wed, 13 Jul 2022 15:27:17 +0200 Subject: [PATCH 02/33] added PMCId to PmArticle --- .../dnetlib/dhp/sx/bio/pubmed/PMArticle.java | 24 +- .../dnetlib/dhp/sx/bio/pubmed/PMParser.scala | 1 + .../dhp/sx/bio/pubmed/PubMedToOaf.scala | 48 +++- .../eu/dnetlib/dhp/sx/graph/bio/pubmed.xml | 257 ++++++++++++++++-- .../dnetlib/dhp/sx/bio/BioScholixTest.scala | 71 ++++- 5 files changed, 371 insertions(+), 30 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMArticle.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMArticle.java index af0d5169d..9287a8cdd 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMArticle.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMArticle.java @@ -17,6 +17,9 @@ public class PMArticle implements Serializable { * the Pubmed Identifier */ private String pmid; + + private String pmcId; + /** * the DOI */ @@ -122,7 +125,7 @@ public class PMArticle implements Serializable { /** * The full journal title (taken from NLM cataloging data following NLM rules for how to compile a serial name) is exported in this element. - * Some characters that are not part of the NLM MEDLINE/PubMed Character Set reside in a relatively small number of full journal titles. + * Some characters that are not part of the NLM MEDLINE/PubMed Character Set reside in a relatively small number of full journal titles. * The NLM journal title abbreviation is exported in the element. * * @return the pubmed Journal Extracted @@ -140,10 +143,11 @@ public class PMArticle implements Serializable { } /** - * English-language abstracts are taken directly from the published article. - * If the article does not have a published abstract, the National Library of Medicine does not create one, - * thus the record lacks the and elements. However, in the absence of a formally - * labeled abstract in the published article, text from a substantive "summary", "summary and conclusions" or "conclusions and summary" may be used. + * contains the entire title of the journal article. is always in English; + * those titles originally published in a non-English language and translated for are enclosed in square brackets. + * All titles end with a period unless another punctuation mark such as a question mark or bracket is present. + * Explanatory information about the title itself is enclosed in parentheses, e.g.: (author's transl). + * Corporate/collective authors may appear at the end of for citations up to about the year 2000. * * @return the extracted pubmed Title */ @@ -250,4 +254,14 @@ public class PMArticle implements Serializable { public List getGrants() { return grants; } + + + public String getPmcId() { + return pmcId; + } + + public PMArticle setPmcId(String pmcId) { + this.pmcId = pmcId; + return this; + } } diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PMParser.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PMParser.scala index 49a271641..9102c12c4 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PMParser.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PMParser.scala @@ -98,6 +98,7 @@ class PMParser(xml: XMLEventReader) extends Iterator[PMArticle] { case "PMID" => currentArticle.setPmid(text.trim) case "ArticleId" => if ("doi".equalsIgnoreCase(currentArticleType)) currentArticle.setDoi(text.trim) + if ("pmc".equalsIgnoreCase(currentArticleType)) currentArticle.setPmcId(text.trim) case "Language" => currentArticle.setLanguage(text.trim) case "ISSN" => currentJournal.setIssn(text.trim) case "GrantID" => currentGrant.setGrantID(text.trim) diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala index 92ad22c57..24a1fa62b 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala @@ -4,9 +4,12 @@ import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup import eu.dnetlib.dhp.schema.common.ModelConstants import eu.dnetlib.dhp.schema.oaf.utils.{GraphCleaningFunctions, IdentifierFactory, OafMapperUtils, PidType} import eu.dnetlib.dhp.schema.oaf._ -import collection.JavaConverters._ +import eu.dnetlib.dhp.utils.DHPUtils +import org.apache.commons.lang3.StringUtils +import collection.JavaConverters._ import java.util.regex.Pattern +import scala.collection.mutable.ListBuffer /** */ @@ -14,6 +17,9 @@ object PubMedToOaf { val SUBJ_CLASS = "keywords" + val OAI_HEADER = "oai:pubmedcentral.nih.gov:" + val OLD_PMC_PREFIX = "od_______267::" + val urlMap = Map( "pmid" -> "https://pubmed.ncbi.nlm.nih.gov/", "doi" -> "https://dx.doi.org/" @@ -50,6 +56,17 @@ object PubMedToOaf { null } + + def createOriginalOpenaireId(article:PMArticle) :String = { + if (StringUtils.isNotEmpty(article.getPmcId)) { + val md5 = DHPUtils.md5(s"$OAI_HEADER${article.getPmcId.replace("PMC","")}") + s"$OLD_PMC_PREFIX$md5" + } + else + null + + } + /** Create an instance of class extends Result * starting from OAF instanceType value * @@ -122,8 +139,9 @@ object PubMedToOaf { return null // MAP PMID into pid with classid = classname = pmid - val pidList: List[StructuredProperty] = List( - OafMapperUtils.structuredProperty( + val pidList = ListBuffer[StructuredProperty]() + + pidList += OafMapperUtils.structuredProperty( article.getPmid, PidType.pmid.toString, PidType.pmid.toString, @@ -131,7 +149,19 @@ object PubMedToOaf { ModelConstants.DNET_PID_TYPES, dataInfo ) - ) + + + if (StringUtils.isNotBlank(article.getPmcId)) + { + pidList += OafMapperUtils.structuredProperty( + article.getPmcId, + PidType.pmc.toString, + PidType.pmc.toString, + ModelConstants.DNET_PID_TYPES, + ModelConstants.DNET_PID_TYPES, + dataInfo + ) + } if (pidList == null) return null @@ -186,6 +216,7 @@ object PubMedToOaf { val urlLists: List[String] = pidList .map(s => (urlMap.getOrElse(s.getQualifier.getClassid, ""), s.getValue)) .filter(t => t._1.nonEmpty) + .toList .map(t => t._1 + t._2) if (urlLists != null) pubmedInstance.setUrl(urlLists.asJava) @@ -262,7 +293,14 @@ object PubMedToOaf { if (authors != null && authors.nonEmpty) result.setAuthor(authors.asJava) - result.setOriginalId(pidList.map(s => s.getValue).asJava) + + if (StringUtils.isNotEmpty(article.getPmcId)) { + val originalIDS = ListBuffer[String]() + originalIDS += createOriginalOpenaireId(article) + pidList.map(s => s.getValue).foreach(p =>originalIDS += p) + result.setOriginalId(originalIDS.asJava) + } else + result.setOriginalId(pidList.map(s => s.getValue).asJava) result.setId(article.getPmid) diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml index 22da07e29..58a73ae5d 100644 --- a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml @@ -195,7 +195,9 @@ Biochemical and biophysical research communications Biochem Biophys Res Commun - Delineation of the intimate details of the backbone conformation of pyridine nucleotide coenzymes in aqueous solution. + Delineation of the intimate details of the backbone conformation of pyridine nucleotide + coenzymes in aqueous solution. + 1173-9 @@ -473,7 +475,9 @@ Biochemical and biophysical research communications Biochem Biophys Res Commun - Effect of chloroquine on cultured fibroblasts: release of lysosomal hydrolases and inhibition of their uptake. + Effect of chloroquine on cultured fibroblasts: release of lysosomal hydrolases and + inhibition of their uptake. + 1338-43 @@ -657,7 +661,8 @@ Biochemical and biophysical research communications Biochem Biophys Res Commun - Atomic models for the polypeptide backbones of myohemerythrin and hemerythrin. + Atomic models for the polypeptide backbones of myohemerythrin and hemerythrin. + 1349-56 @@ -1627,7 +1632,9 @@ Biochemical pharmacology Biochem Pharmacol - Comparison between procaine and isocarboxazid metabolism in vitro by a liver microsomal amidase-esterase. + Comparison between procaine and isocarboxazid metabolism in vitro by a liver microsomal + amidase-esterase. + 1517-21 @@ -2030,7 +2037,9 @@ Biochemical pharmacology Biochem Pharmacol - Radiochemical assay of glutathione S-epoxide transferase and its enhancement by phenobarbital in rat liver in vivo. + Radiochemical assay of glutathione S-epoxide transferase and its enhancement by + phenobarbital in rat liver in vivo. + 1569-72 @@ -2350,7 +2359,9 @@ Biochemical pharmacology Biochem Pharmacol - Identification of adenylate cyclase-coupled beta-adrenergic receptors with radiolabeled beta-adrenergic antagonists. + Identification of adenylate cyclase-coupled beta-adrenergic receptors with radiolabeled + beta-adrenergic antagonists. + 1651-8 @@ -2598,7 +2609,9 @@ Biochemical pharmacology Biochem Pharmacol - The effect of adrenaline and of alpha- and beta-adrenergic blocking agents on ATP concentration and on incorporation of 32Pi into ATP in rat fat cells. + The effect of adrenaline and of alpha- and beta-adrenergic blocking agents on ATP + concentration and on incorporation of 32Pi into ATP in rat fat cells. + 1659-62 @@ -2851,7 +2864,9 @@ Biochemical pharmacology Biochem Pharmacol - Action of propranolol on mitochondrial functions--effects on energized ion fluxes in the presence of valinomycin. + Action of propranolol on mitochondrial functions--effects on energized ion fluxes in the + presence of valinomycin. + 1701-5 @@ -3265,7 +3280,8 @@ EC 2.6.1.16 - Glutamine-Fructose-6-Phosphate Transaminase (Isomerizing) + Glutamine-Fructose-6-Phosphate Transaminase (Isomerizing) + EC 2.7.- @@ -3324,7 +3340,9 @@ Glucosamine - Glutamine-Fructose-6-Phosphate Transaminase (Isomerizing) + Glutamine-Fructose-6-Phosphate Transaminase + (Isomerizing) + metabolism @@ -3463,7 +3481,8 @@ Biochemical pharmacology Biochem Pharmacol - Inhibition of aldehyde reductase by acidic metabolites of the biogenic amines. + Inhibition of aldehyde reductase by acidic metabolites of the biogenic amines. + 1731-3 @@ -3696,7 +3715,9 @@ Biochemical pharmacology Biochem Pharmacol - Effects of 5,6-dihydroxytryptamine on tyrosine-hydroxylase activity in central catecholaminergic neurons of the rat. + Effects of 5,6-dihydroxytryptamine on tyrosine-hydroxylase activity in central + catecholaminergic neurons of the rat. + 1739-42 @@ -4602,12 +4623,19 @@ Arzneimittel-Forschung Arzneimittelforschung - [Biochemical studies on camomile components/III. In vitro studies about the antipeptic activity of (--)-alpha-bisabolol (author's transl)]. + [Biochemical studies on camomile components/III. In vitro studies about the antipeptic + activity of (--)-alpha-bisabolol (author's transl)]. + 1352-4 - (--)-alpha-Bisabolol has a primary antipeptic action depending on dosage, which is not caused by an alteration of the pH-value. The proteolytic activity of pepsin is reduced by 50 percent through addition of bisabolol in the ratio of 1/0.5. The antipeptic action of bisabolol only occurs in case of direct contact. In case of a previous contact with the substrate, the inhibiting effect is lost. + (--)-alpha-Bisabolol has a primary antipeptic action depending on dosage, which is not + caused by an alteration of the pH-value. The proteolytic activity of pepsin is reduced by 50 + percent through addition of bisabolol in the ratio of 1/0.5. The antipeptic action of bisabolol + only occurs in case of direct contact. In case of a previous contact with the substrate, the + inhibiting effect is lost. + @@ -4626,7 +4654,9 @@ English Abstract Journal Article - Biochemische Untersuchungen von Kamilleninhaltsstoffen. III. In-vitro-Versuche über die antipeptische Wirkung des (-)-alpha-Bisabolols + Biochemische Untersuchungen von Kamilleninhaltsstoffen. III. In-vitro-Versuche über die + antipeptische Wirkung des (-)-alpha-Bisabolols + Germany @@ -4753,12 +4783,37 @@ Arzneimittel-Forschung Arzneimittelforschung - [Demonstration of tumor inhibiting properties of a strongly immunostimulating low-molecular weight substance. Comparative studies with ifosfamide on the immuno-labile DS carcinosarcoma. Stimulation of the autoimmune activity for approx. 20 days by BA 1, a N-(2-cyanoethylene)-urea. Novel prophylactic possibilities]. + [Demonstration of tumor inhibiting properties of a strongly immunostimulating + low-molecular weight substance. Comparative studies with ifosfamide on the immuno-labile DS + carcinosarcoma. Stimulation of the autoimmune activity for approx. 20 days by BA 1, a + N-(2-cyanoethylene)-urea. Novel prophylactic possibilities]. + 1369-79 - A report is given on the recent discovery of outstanding immunological properties in BA 1 [N-(2-cyanoethylene)-urea] having a (low) molecular mass M = 111.104. Experiments in 214 DS carcinosarcoma bearing Wistar rats have shown that BA 1, at a dosage of only about 12 percent LD50 (150 mg kg) and negligible lethality (1.7 percent), results in a recovery rate of 40 percent without hyperglycemia and, in one test, of 80 percent with hyperglycemia. Under otherwise unchanged conditions the reference substance ifosfamide (IF) -- a further development of cyclophosphamide -- applied without hyperglycemia in its most efficient dosage of 47 percent LD50 (150 mg kg) brought about a recovery rate of 25 percent at a lethality of 18 percent. (Contrary to BA 1, 250-min hyperglycemia caused no further improvement of the recovery rate.) However this comparison is characterized by the fact that both substances exhibit two quite different (complementary) mechanisms of action. Leucocyte counts made after application of the said cancerostatics and dosages have shown a pronounced stimulation with BA 1 and with ifosfamide, the known suppression in the post-therapeutic interval usually found with standard cancerostatics. In combination with the cited plaque test for BA 1, blood pictures then allow conclusions on the immunity status. Since IF can be taken as one of the most efficient cancerostatics--there is no other chemotherapeutic known up to now that has a more significant effect on the DS carcinosarcoma in rats -- these findings are of special importance. Finally, the total amount of leucocytes and lymphocytes as well as their time behaviour was determined from the blood picture of tumour-free rats after i.v. application of BA 1. The thus obtained numerical values clearly show that further research work on the prophylactic use of this substance seems to be necessary and very promising. + A report is given on the recent discovery of outstanding immunological properties in + BA 1 [N-(2-cyanoethylene)-urea] having a (low) molecular mass M = 111.104. Experiments in 214 DS + carcinosarcoma bearing Wistar rats have shown that BA 1, at a dosage of only about 12 percent + LD50 (150 mg kg) and negligible lethality (1.7 percent), results in a recovery rate of 40 + percent without hyperglycemia and, in one test, of 80 percent with hyperglycemia. Under + otherwise unchanged conditions the reference substance ifosfamide (IF) -- a further development + of cyclophosphamide -- applied without hyperglycemia in its most efficient dosage of 47 percent + LD50 (150 mg kg) brought about a recovery rate of 25 percent at a lethality of 18 percent. + (Contrary to BA 1, 250-min hyperglycemia caused no further improvement of the recovery rate.) + However this comparison is characterized by the fact that both substances exhibit two quite + different (complementary) mechanisms of action. Leucocyte counts made after application of the + said cancerostatics and dosages have shown a pronounced stimulation with BA 1 and with + ifosfamide, the known suppression in the post-therapeutic interval usually found with standard + cancerostatics. In combination with the cited plaque test for BA 1, blood pictures then allow + conclusions on the immunity status. Since IF can be taken as one of the most efficient + cancerostatics--there is no other chemotherapeutic known up to now that has a more significant + effect on the DS carcinosarcoma in rats -- these findings are of special importance. Finally, + the total amount of leucocytes and lymphocytes as well as their time behaviour was determined + from the blood picture of tumour-free rats after i.v. application of BA 1. The thus obtained + numerical values clearly show that further research work on the prophylactic use of this + substance seems to be necessary and very promising. + @@ -4778,7 +4833,11 @@ English Abstract Journal Article - Nachweis krebshemmender Eigenschaften einer stark immunstimulierenden Verbindung kleiner Molekülmasse. Versuche am immunlabilen DS-Karzinosarkom im Vergleich mit Ifosfamid. Stimulierung der körpereigenen Abwehr über etwa 20 Tage durch BA 1, einen N-(2-Cyanthylen)-harnstoff. Neue prophylaktische Möglichkeiten + Nachweis krebshemmender Eigenschaften einer stark immunstimulierenden Verbindung + kleiner Molekülmasse. Versuche am immunlabilen DS-Karzinosarkom im Vergleich mit Ifosfamid. + Stimulierung der körpereigenen Abwehr über etwa 20 Tage durch BA 1, einen + N-(2-Cyanthylen)-harnstoff. Neue prophylaktische Möglichkeiten + Germany @@ -5016,7 +5075,20 @@ 1400-3 - The distribution of blood flow to the subendocardial, medium and subepicardial layers of the left ventricular free wall was studied in anaesthetized dogs under normoxic (A), hypoxic (B) conditions and under pharmacologically induced (etafenone) coronary vasodilation (C). Regional myocardial blood flow was determined by means of the particle distribution method. In normoxia a transmural gradient of flow was observed, with the subendocardial layers receiving a significantly higher flow rate compared with the subepicardial layers. In hypoxia induced vasodilation this transmural gradient of flow was persistent. In contrast a marked redistribution of regional flow was observed under pharmacologically induced vasodilation. The transmural gradient decreased. In contrast to some findings these experiments demonstrate that a considerable vasodilatory capacity exists in all layers of the myocardium and can be utilized by drugs. The differences observed for the intramural distribution pattern of flow under hypoxia and drug induced vasodilation support the hypothesis that this pattern reflects corresponding gradients of regional myocardial metabolism. + The distribution of blood flow to the subendocardial, medium and subepicardial layers + of the left ventricular free wall was studied in anaesthetized dogs under normoxic (A), hypoxic + (B) conditions and under pharmacologically induced (etafenone) coronary vasodilation (C). + Regional myocardial blood flow was determined by means of the particle distribution method. In + normoxia a transmural gradient of flow was observed, with the subendocardial layers receiving a + significantly higher flow rate compared with the subepicardial layers. In hypoxia induced + vasodilation this transmural gradient of flow was persistent. In contrast a marked + redistribution of regional flow was observed under pharmacologically induced vasodilation. The + transmural gradient decreased. In contrast to some findings these experiments demonstrate that a + considerable vasodilatory capacity exists in all layers of the myocardium and can be utilized by + drugs. The differences observed for the intramural distribution pattern of flow under hypoxia + and drug induced vasodilation support the hypothesis that this pattern reflects corresponding + gradients of regional myocardial metabolism. + @@ -5185,4 +5257,151 @@ + + + 4917185 + + 1970 + 10 + 27 + + + 2018 + 11 + 13 + +
+ + 0003-6919 + + 19 + 6 + + 1970 + Jun + + + Applied microbiology + Appl Microbiol + + Bactericidal activity of a broad-spectrum illumination source. + + 1013-4 + + + + Several hours of exposure to Vita-Lite lamps, which have a unique spectral + distribution, give significant killing of cells of Staphylococcus aureus. + + + + + Himmelfarb + P + P + + + Scott + A + A + + + Thayer + P S + PS + + + eng + + Journal Article + +
+ + United States + Appl Microbiol + 7605802 + 0003-6919 + + IM + + + Bacteriological Techniques + instrumentation + + + Light + + + Radiation Effects + + + Serratia marcescens + growth & development + radiation effects + + + Staphylococcus + growth & development + radiation effects + + + Sterilization + + + + + + + 1970 + 6 + 1 + + + 1970 + 6 + 1 + 0 + 1 + + + 1970 + 6 + 1 + 0 + 0 + + + ppublish + + 4917185 + PMC376844 + + + + Photochem Photobiol. 1969 Jan;9(1):99-102 + + 4889809 + + + + Endocrinology. 1969 Dec;85(6):1218-21 + + 5347623 + + + + Arch Mikrobiol. 1956;24(1):60-79 + + 13327987 + + + + J Bacteriol. 1941 Sep;42(3):353-66 + + 16560457 + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala index ea742a04a..37a5808ec 100644 --- a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala +++ b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala @@ -2,7 +2,8 @@ package eu.dnetlib.dhp.sx.bio import com.fasterxml.jackson.databind.{DeserializationFeature, ObjectMapper, SerializationFeature} import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest -import eu.dnetlib.dhp.schema.oaf.{Oaf, Relation, Result} +import eu.dnetlib.dhp.schema.oaf.utils.PidType +import eu.dnetlib.dhp.schema.oaf.{Oaf, Publication, Relation, Result} import eu.dnetlib.dhp.sx.bio.BioDBToOAF.ScholixResolved import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMParser, PubMedToOaf} import org.json4s.DefaultFormats @@ -16,6 +17,7 @@ import org.mockito.junit.jupiter.MockitoExtension import java.io.{BufferedReader, InputStream, InputStreamReader} import java.util.zip.GZIPInputStream import scala.collection.JavaConverters._ +import scala.collection.mutable.ListBuffer import scala.io.Source import scala.xml.pull.XMLEventReader @@ -72,6 +74,73 @@ class BioScholixTest extends AbstractVocabularyTest { ) println(mapper.writeValueAsString(r.head)) + } + + + private def checkPMArticle(article:PMArticle): Unit = { + assertNotNull(article.getPmid) + assertNotNull(article.getTitle) + assertNotNull(article.getAuthors) + article.getAuthors.asScala.foreach{a => + assertNotNull(a) + assertNotNull(a.getFullName) + } + + } + + @Test + def testParsingPubmedXML():Unit = { + val xml = new XMLEventReader(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml"))) + val parser = new PMParser(xml) + parser.foreach(checkPMArticle) + } + + + private def checkPubmedPublication(o:Oaf): Unit = { + assertTrue(o.isInstanceOf[Publication]) + val p:Publication = o.asInstanceOf[Publication] + assertNotNull(p.getId) + assertNotNull(p.getTitle) + p.getTitle.asScala.foreach(t =>assertNotNull(t.getValue)) + p.getAuthor.asScala.foreach(a =>assertNotNull(a.getFullname)) + assertNotNull(p.getInstance()) + p.getInstance().asScala.foreach { i => + assertNotNull(i.getCollectedfrom) + assertNotNull(i.getPid) + assertNotNull(i.getInstancetype) + } + assertNotNull(p.getOriginalId) + p.getOriginalId.asScala.foreach(oId => assertNotNull(oId)) + + + val hasPMC = p.getInstance().asScala.exists(i => i.getPid.asScala.exists(pid => pid.getQualifier.getClassid.equalsIgnoreCase(PidType.pmc.toString))) + + + + if (hasPMC) { + assertTrue(p.getOriginalId.asScala.exists(oId => oId.startsWith("od_______267::"))) + + + } + + + + } + @Test + def testPubmedMapping() :Unit = { + + val xml = new XMLEventReader(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml"))) + val parser = new PMParser(xml) + val results = ListBuffer[Oaf]() + parser.foreach(x => results += PubMedToOaf.convert(x, vocabularies)) + + + + + results.foreach(checkPubmedPublication) + + + } @Test From 00168303dbb4e14ee453a911d3c072314e686864 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Thu, 14 Jul 2022 10:19:59 +0200 Subject: [PATCH 03/33] Added unit test to verify the generation in the OriginalID the old openaire Identifier generated by OAI --- .../dnetlib/dhp/sx/bio/BioScholixTest.scala | 41 ++++++++++++++++--- 1 file changed, 35 insertions(+), 6 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala index 37a5808ec..b021e5e07 100644 --- a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala +++ b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala @@ -5,7 +5,7 @@ import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest import eu.dnetlib.dhp.schema.oaf.utils.PidType import eu.dnetlib.dhp.schema.oaf.{Oaf, Publication, Relation, Result} import eu.dnetlib.dhp.sx.bio.BioDBToOAF.ScholixResolved -import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMParser, PubMedToOaf} +import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMParser, PMSubject, PubMedToOaf} import org.json4s.DefaultFormats import org.json4s.JsonAST.{JField, JObject, JString} import org.json4s.jackson.JsonMethods.parse @@ -119,13 +119,42 @@ class BioScholixTest extends AbstractVocabularyTest { if (hasPMC) { assertTrue(p.getOriginalId.asScala.exists(oId => oId.startsWith("od_______267::"))) - - } - - - } + + + @Test + def testPubmedOriginalID():Unit = { + val article:PMArticle = new PMArticle + + + article.setPmid("1234") + + article.setTitle("a Title") + + // VERIFY PUBLICATION IS NOT NULL + article.getPublicationTypes.add( new PMSubject("article",null, null)) + var publication = PubMedToOaf.convert(article, vocabularies).asInstanceOf[Publication] + assertNotNull(publication) + assertEquals("50|pmid________::81dc9bdb52d04dc20036dbd8313ed055", publication.getId) + + // VERIFY PUBLICATION ID DOES NOT CHANGE ALSO IF SETTING PMC IDENTIFIER + article.setPmcId("PMC1517292") + publication = PubMedToOaf.convert(article, vocabularies).asInstanceOf[Publication] + assertNotNull(publication) + assertEquals("50|pmid________::81dc9bdb52d04dc20036dbd8313ed055", publication.getId) + + // VERIFY ORIGINAL ID GENERATE IN OLD WAY USING PMC IDENTIFIER EXISTS + + + val oldOpenaireID ="od_______267::0000072375bc0e68fa09d4e6b7658248" + + val hasOldOpenAIREID = publication.getOriginalId.asScala.exists(o => o.equalsIgnoreCase(oldOpenaireID)) + + assertTrue(hasOldOpenAIREID) + } + + @Test def testPubmedMapping() :Unit = { From 438abdf96fcdc340dfdbe18fa51c56c8a3ce5657 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 20 Jul 2022 18:07:54 +0200 Subject: [PATCH 04/33] [EOSC TAG] adding eosc interoperability guidelines in the specific element in the result. Removed from subjects. Removed also the deletion of EOSC Jupyter Notebook from subject since now the criteria are searchd for in a different place --- .../eu/dnetlib/dhp/bulktag/SparkEoscTag.java | 82 ++++++------------- pom.xml | 2 +- 2 files changed, 27 insertions(+), 57 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java index b9de5dd11..d31934081 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java @@ -28,28 +28,7 @@ import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; public class SparkEoscTag { private static final Logger log = LoggerFactory.getLogger(SparkEoscTag.class); public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - public static final Qualifier EOSC_QUALIFIER = OafMapperUtils - .qualifier( - "EOSC", - "European Open Science Cloud", - ModelConstants.DNET_SUBJECT_TYPOLOGIES, ModelConstants.DNET_SUBJECT_TYPOLOGIES); - public static final DataInfo EOSC_DATAINFO = OafMapperUtils - .dataInfo( - false, "propagation", true, false, - OafMapperUtils - .qualifier( - "propagation:subject", "Inferred by OpenAIRE", - ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS), - "0.9"); - public final static StructuredProperty EOSC_NOTEBOOK = OafMapperUtils - .structuredProperty( - "EOSC::Jupyter Notebook", EOSC_QUALIFIER, EOSC_DATAINFO); - public final static StructuredProperty EOSC_GALAXY = OafMapperUtils - .structuredProperty( - "EOSC::Galaxy Workflow", EOSC_QUALIFIER, EOSC_DATAINFO); - public final static StructuredProperty EOSC_TWITTER = OafMapperUtils - .structuredProperty( - "EOSC::Twitter Data", EOSC_QUALIFIER, EOSC_DATAINFO); + public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils @@ -84,29 +63,30 @@ public class SparkEoscTag { }); } + public static EoscIfGuidelines newInstance(String code, String label, String url, String semantics){ + EoscIfGuidelines eig = new EoscIfGuidelines(); + eig.setCode( code); + eig.setLabel(label); + eig.setUrl(url); + eig.setSemanticRelation(semantics); + return eig; + + } private static void execEoscTag(SparkSession spark, String inputPath, String workingPath) { readPath(spark, inputPath + "/software", Software.class) .map((MapFunction) s -> { - List sbject; - if (!Optional.ofNullable(s.getSubject()).isPresent()) - s.setSubject(new ArrayList<>()); - sbject = s.getSubject(); if (containsCriteriaNotebook(s)) { - sbject.add(EOSC_NOTEBOOK); - if (sbject.stream().anyMatch(sb -> sb.getValue().equals("EOSC Jupyter Notebook"))) { - sbject = sbject.stream().map(sb -> { - if (sb.getValue().equals("EOSC Jupyter Notebook")) { - return null; - } - return sb; - }).filter(Objects::nonNull).collect(Collectors.toList()); - s.setSubject(sbject); - } + if (!Optional.ofNullable(s.getEoscifguidelines()).isPresent()) + s.setEoscifguidelines(new ArrayList<>()); + s.getEoscifguidelines().add(newInstance("EOSC::Jupyter Notebook", "EOSC::Jupyter Notebook", "", "compliesWith")); } if (containsCriteriaGalaxy(s)) { - sbject.add(EOSC_GALAXY); + if (!Optional.ofNullable(s.getEoscifguidelines()).isPresent()) + s.setEoscifguidelines(new ArrayList<>()); + + s.getEoscifguidelines().add(newInstance("EOSC::Galaxy Workflow", "EOSC::Galaxy Workflow", "", "compliesWith")); } return s; }, Encoders.bean(Software.class)) @@ -124,14 +104,14 @@ public class SparkEoscTag { readPath(spark, inputPath + "/otherresearchproduct", OtherResearchProduct.class) .map((MapFunction) orp -> { List sbject; - if (!Optional.ofNullable(orp.getSubject()).isPresent()) - orp.setSubject(new ArrayList<>()); - sbject = orp.getSubject(); + if (!Optional.ofNullable(orp.getEoscifguidelines()).isPresent()) + orp.setEoscifguidelines(new ArrayList<>()); + if (containsCriteriaGalaxy(orp)) { - sbject.add(EOSC_GALAXY); + orp.getEoscifguidelines().add(newInstance("EOSC::Galaxy Workflow", "EOSC::Galaxy Workflow", "", "compliesWith")); } if (containscriteriaTwitter(orp)) { - sbject.add(EOSC_TWITTER); + orp.getEoscifguidelines().add(newInstance("EOSC::Twitter Data", "EOSC::Twitter Data", "", "compliesWith")); } return orp; }, Encoders.bean(OtherResearchProduct.class)) @@ -149,11 +129,10 @@ public class SparkEoscTag { readPath(spark, inputPath + "/dataset", Dataset.class) .map((MapFunction) d -> { List sbject; - if (!Optional.ofNullable(d.getSubject()).isPresent()) - d.setSubject(new ArrayList<>()); - sbject = d.getSubject(); + if (!Optional.ofNullable(d.getEoscifguidelines()).isPresent()) + d.setEoscifguidelines(new ArrayList<>()); if (containscriteriaTwitter(d)) { - sbject.add(EOSC_TWITTER); + d.getEoscifguidelines().add(newInstance("EOSC::Twitter Data", "EOSC::Twitter Data", "", "compliesWith")); } return d; }, Encoders.bean(Dataset.class)) @@ -212,13 +191,6 @@ public class SparkEoscTag { return false; } - private static Set getSubjects(List s) { - Set subjects = new HashSet<>(); - s.stream().forEach(sbj -> subjects.addAll(Arrays.asList(sbj.getValue().toLowerCase().split(" ")))); - s.stream().forEach(sbj -> subjects.add(sbj.getValue().toLowerCase())); - return subjects; - } - private static Set getWordsSP(List elem) { Set words = new HashSet<>(); Optional @@ -242,9 +214,7 @@ public class SparkEoscTag { t -> words .addAll( Arrays.asList(t.getValue().toLowerCase().replaceAll("[^a-zA-Z ]", "").split(" "))))); -// elem -// .forEach( -// t -> words.addAll(Arrays.asList(t.getValue().toLowerCase().replaceAll("[^a-zA-Z ]", "").split(" ")))); + return words; } diff --git a/pom.xml b/pom.xml index 54070f654..973bc3773 100644 --- a/pom.xml +++ b/pom.xml @@ -801,7 +801,7 @@ 3.3.3 3.4.2 [2.12,3.0) - [2.12.0] + [2.12.2-SNAPSHOT] [4.0.3] [6.0.5] [3.1.6] From 5143a802320b3a64a16b09f298f005d4fbce78e9 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 21 Jul 2022 11:56:51 +0200 Subject: [PATCH 05/33] [EOSC TAG] modification of test class to align with new element --- .../dnetlib/dhp/bulktag/EOSCTagJobTest.java | 174 ++++++++++++++++-- 1 file changed, 155 insertions(+), 19 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java index 1ea254157..b1c0cbb84 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java @@ -126,8 +126,9 @@ public class EOSCTagJobTest { .assertEquals( 4, tmp + .filter(s -> s.getEoscifguidelines()!= null) .filter( - s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook"))) + s -> s.getEoscifguidelines().stream().anyMatch(eig -> eig.getCode().equals("EOSC::Jupyter Notebook"))) .count()); Assertions @@ -136,17 +137,36 @@ public class EOSCTagJobTest { .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) .collect() .get(0) - .getSubject() + .getEoscifguidelines() .size()); + + Assertions + .assertEquals( + 1, tmp + .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) + .collect() + .get(0) + .getSubject() + .size()); Assertions .assertTrue( tmp .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) .collect() .get(0) - .getSubject() + .getEoscifguidelines() .stream() - .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); + .anyMatch(s -> s.getCode().equals("EOSC::Jupyter Notebook"))); + + Assertions + .assertFalse( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) + .collect() + .get(0) + .getSubject() + .stream() + .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); Assertions .assertEquals( @@ -166,16 +186,23 @@ public class EOSCTagJobTest { .stream() .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); + Assertions.assertTrue(tmp + .filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11")) + .collect() + .get(0) + .getEoscifguidelines() == null + ); + Assertions .assertEquals( - 9, tmp + 8, tmp .filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")) .collect() .get(0) .getSubject() .size()); Assertions - .assertTrue( + .assertFalse( tmp .filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")) .collect() @@ -183,6 +210,23 @@ public class EOSCTagJobTest { .getSubject() .stream() .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); + Assertions + .assertEquals( + 1, tmp + .filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")) + .collect() + .get(0) + .getEoscifguidelines() + .size()); + Assertions + .assertTrue( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")) + .collect() + .get(0) + .getEoscifguidelines() + .stream() + .anyMatch(s -> s.getCode().equals("EOSC::Jupyter Notebook"))); Assertions .assertEquals( @@ -201,17 +245,24 @@ public class EOSCTagJobTest { .getSubject() .stream() .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); + Assertions.assertTrue( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::5aec1186054301b66c0c5dc35972a589")) + .collect() + .get(0) + .getEoscifguidelines() == null + ); Assertions .assertEquals( - 9, tmp + 8, tmp .filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0")) .collect() .get(0) .getSubject() .size()); Assertions - .assertTrue( + .assertFalse( tmp .filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0")) .collect() @@ -219,14 +270,27 @@ public class EOSCTagJobTest { .getSubject() .stream() .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); + Assertions.assertEquals(1, + tmp + .filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0")) + .collect() + .get(0) + .getEoscifguidelines() + .size()); + Assertions.assertTrue(tmp + .filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0")) + .collect() + .get(0) + .getEoscifguidelines() + .stream() + .anyMatch(s -> s.getCode().equals("EOSC::Jupyter Notebook"))); List subjects = tmp .filter(sw -> sw.getId().equals("50|od______1582::6e7a9b21a2feef45673890432af34244")) .collect() .get(0) .getSubject(); - Assertions.assertEquals(8, subjects.size()); - Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); + Assertions.assertEquals(7, subjects.size()); Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("jupyter"))); Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("Modeling and Simulation"))); Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("structure granulaire"))); @@ -250,6 +314,14 @@ public class EOSCTagJobTest { .filter( ds -> ds.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook"))) .count()); + Assertions + .assertEquals( + 0, sc + .textFile(workingDir.toString() + "/input/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)) + .filter( + ds -> ds.getEoscifguidelines().stream().anyMatch(eig -> eig.getCode().equals("EOSC::Jupyter Notebook"))) + .count()); Assertions .assertEquals( @@ -264,9 +336,18 @@ public class EOSCTagJobTest { .textFile(workingDir.toString() + "/input/otherresearchproduct") .map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)) .filter( - ds -> ds.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook"))) + orp -> orp.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook"))) .count()); + Assertions + .assertEquals( + 0, sc + .textFile(workingDir.toString() + "/input/otherresearchproduct") + .map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)) + .filter( + orp -> orp.getSubject().stream().anyMatch(eig -> eig.getValue().equals("EOSC::Jupyter Notebook"))) + .count()); + // spark.stop(); } @@ -326,22 +407,37 @@ public class EOSCTagJobTest { Assertions .assertEquals( - 1, + 0, tmp .filter( s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Galaxy Workflow"))) .count()); + Assertions + .assertEquals( + 1, + tmp + .filter( + s -> s.getEoscifguidelines()!=null) + .count()); + Assertions + .assertEquals( + 1, + tmp + .filter( + s -> s.getEoscifguidelines()!=null) + .filter(s -> s.getEoscifguidelines().stream().anyMatch(eig -> eig.getCode().equals("EOSC::Galaxy Workflow"))) + .count()); Assertions .assertEquals( - 2, tmp + 1, tmp .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) .collect() .get(0) .getSubject() .size()); Assertions - .assertTrue( + .assertFalse( tmp .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) .collect() @@ -350,6 +446,19 @@ public class EOSCTagJobTest { .stream() .anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); + Assertions.assertEquals(1, tmp + .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) + .collect() + .get(0) + .getEoscifguidelines() + .size() ); + Assertions.assertTrue(tmp + .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) + .collect() + .get(0) + .getEoscifguidelines() + .stream().anyMatch(eig -> eig.getCode().equals("EOSC::Galaxy Workflow"))); + Assertions .assertEquals( 5, tmp @@ -385,22 +494,26 @@ public class EOSCTagJobTest { Assertions .assertEquals( - 1, + 0, orp .filter( s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Galaxy Workflow"))) .count()); + orp.foreach(o-> System.out.println(OBJECT_MAPPER.writeValueAsString(o))); + + Assertions.assertEquals(1, orp.filter(o -> o.getEoscifguidelines() != null) + .filter(o -> o.getEoscifguidelines().stream().anyMatch(eig -> eig.getCode().equals("EOSC::Galaxy Workflow"))).count()); Assertions .assertEquals( - 3, orp + 2, orp .filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07")) .collect() .get(0) .getSubject() .size()); Assertions - .assertTrue( + .assertFalse( orp .filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07")) .collect() @@ -408,6 +521,23 @@ public class EOSCTagJobTest { .getSubject() .stream() .anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); + Assertions + .assertEquals( + 1, orp + .filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07")) + .collect() + .get(0) + .getEoscifguidelines() + .size()); + Assertions + .assertTrue( + orp + .filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07")) + .collect() + .get(0) + .getEoscifguidelines() + .stream() + .anyMatch(s -> s.getCode().equals("EOSC::Galaxy Workflow"))); Assertions .assertEquals( @@ -516,10 +646,16 @@ public class EOSCTagJobTest { Assertions .assertEquals( - 3, + 0, orp .filter(s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Twitter Data"))) .count()); + Assertions + .assertEquals( + 3, + orp + .filter(s -> s.getEoscifguidelines().stream().anyMatch(eig -> eig.getCode().equals("EOSC::Twitter Data"))) + .count()); JavaRDD dats = sc .textFile(workingDir.toString() + "/input/dataset") @@ -531,7 +667,7 @@ public class EOSCTagJobTest { .assertEquals( 3, dats - .filter(s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Twitter Data"))) + .filter(s -> s.getEoscifguidelines().stream().anyMatch(eig -> eig.getCode().equals("EOSC::Twitter Data"))) .count()); } From 56d09e6348d63d531250ea6f075c1d306c07ed66 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 21 Jul 2022 14:36:48 +0200 Subject: [PATCH 06/33] [EOSC TAG] before adding the tag added a step to verify the same tag is not already present --- .../eu/dnetlib/dhp/bulktag/SparkEoscTag.java | 21 ++++++++++++------- 1 file changed, 14 insertions(+), 7 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java index d31934081..c5ed0b45c 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java @@ -80,13 +80,14 @@ public class SparkEoscTag { if (containsCriteriaNotebook(s)) { if (!Optional.ofNullable(s.getEoscifguidelines()).isPresent()) s.setEoscifguidelines(new ArrayList<>()); - s.getEoscifguidelines().add(newInstance("EOSC::Jupyter Notebook", "EOSC::Jupyter Notebook", "", "compliesWith")); + addEIG(s.getEoscifguidelines(), "EOSC::Jupyter Notebook", "EOSC::Jupyter Notebook", "", "compliesWith"); + } if (containsCriteriaGalaxy(s)) { if (!Optional.ofNullable(s.getEoscifguidelines()).isPresent()) s.setEoscifguidelines(new ArrayList<>()); - s.getEoscifguidelines().add(newInstance("EOSC::Galaxy Workflow", "EOSC::Galaxy Workflow", "", "compliesWith")); + addEIG(s.getEoscifguidelines(),"EOSC::Galaxy Workflow", "EOSC::Galaxy Workflow", "", "compliesWith"); } return s; }, Encoders.bean(Software.class)) @@ -103,15 +104,15 @@ public class SparkEoscTag { readPath(spark, inputPath + "/otherresearchproduct", OtherResearchProduct.class) .map((MapFunction) orp -> { - List sbject; + if (!Optional.ofNullable(orp.getEoscifguidelines()).isPresent()) orp.setEoscifguidelines(new ArrayList<>()); if (containsCriteriaGalaxy(orp)) { - orp.getEoscifguidelines().add(newInstance("EOSC::Galaxy Workflow", "EOSC::Galaxy Workflow", "", "compliesWith")); + addEIG(orp.getEoscifguidelines(),"EOSC::Galaxy Workflow", "EOSC::Galaxy Workflow", "", "compliesWith"); } if (containscriteriaTwitter(orp)) { - orp.getEoscifguidelines().add(newInstance("EOSC::Twitter Data", "EOSC::Twitter Data", "", "compliesWith")); + addEIG(orp.getEoscifguidelines(),"EOSC::Twitter Data", "EOSC::Twitter Data", "", "compliesWith"); } return orp; }, Encoders.bean(OtherResearchProduct.class)) @@ -128,11 +129,11 @@ public class SparkEoscTag { readPath(spark, inputPath + "/dataset", Dataset.class) .map((MapFunction) d -> { - List sbject; + if (!Optional.ofNullable(d.getEoscifguidelines()).isPresent()) d.setEoscifguidelines(new ArrayList<>()); if (containscriteriaTwitter(d)) { - d.getEoscifguidelines().add(newInstance("EOSC::Twitter Data", "EOSC::Twitter Data", "", "compliesWith")); + addEIG(d.getEoscifguidelines(),"EOSC::Twitter Data", "EOSC::Twitter Data", "", "compliesWith"); } return d; }, Encoders.bean(Dataset.class)) @@ -148,6 +149,12 @@ public class SparkEoscTag { .json(inputPath + "/dataset"); } + private static void addEIG(List eoscifguidelines, String code, String label, String url, String sem) { + if (!eoscifguidelines.stream().anyMatch(eig -> eig.getCode().equals(code))) + eoscifguidelines.add(newInstance(code, label, url, sem)); + } + + private static boolean containscriteriaTwitter(Result r) { Set words = getWordsSP(r.getTitle()); words.addAll(getWordsF(r.getDescription())); From 3be036f290f3cb569465cf9566557e51c4660288 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 21 Jul 2022 14:45:43 +0200 Subject: [PATCH 07/33] [EOSC TAG] refactoring after compilation --- .../eu/dnetlib/dhp/bulktag/SparkEoscTag.java | 25 +- .../dnetlib/dhp/bulktag/EOSCTagJobTest.java | 284 ++++++++++-------- 2 files changed, 178 insertions(+), 131 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java index c5ed0b45c..730e8a3fe 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java @@ -29,7 +29,6 @@ public class SparkEoscTag { private static final Logger log = LoggerFactory.getLogger(SparkEoscTag.class); public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils .toString( @@ -63,15 +62,16 @@ public class SparkEoscTag { }); } - public static EoscIfGuidelines newInstance(String code, String label, String url, String semantics){ + public static EoscIfGuidelines newInstance(String code, String label, String url, String semantics) { EoscIfGuidelines eig = new EoscIfGuidelines(); - eig.setCode( code); + eig.setCode(code); eig.setLabel(label); eig.setUrl(url); eig.setSemanticRelation(semantics); return eig; } + private static void execEoscTag(SparkSession spark, String inputPath, String workingPath) { readPath(spark, inputPath + "/software", Software.class) @@ -80,14 +80,17 @@ public class SparkEoscTag { if (containsCriteriaNotebook(s)) { if (!Optional.ofNullable(s.getEoscifguidelines()).isPresent()) s.setEoscifguidelines(new ArrayList<>()); - addEIG(s.getEoscifguidelines(), "EOSC::Jupyter Notebook", "EOSC::Jupyter Notebook", "", "compliesWith"); + addEIG( + s.getEoscifguidelines(), "EOSC::Jupyter Notebook", "EOSC::Jupyter Notebook", "", + "compliesWith"); } if (containsCriteriaGalaxy(s)) { if (!Optional.ofNullable(s.getEoscifguidelines()).isPresent()) s.setEoscifguidelines(new ArrayList<>()); - addEIG(s.getEoscifguidelines(),"EOSC::Galaxy Workflow", "EOSC::Galaxy Workflow", "", "compliesWith"); + addEIG( + s.getEoscifguidelines(), "EOSC::Galaxy Workflow", "EOSC::Galaxy Workflow", "", "compliesWith"); } return s; }, Encoders.bean(Software.class)) @@ -109,10 +112,12 @@ public class SparkEoscTag { orp.setEoscifguidelines(new ArrayList<>()); if (containsCriteriaGalaxy(orp)) { - addEIG(orp.getEoscifguidelines(),"EOSC::Galaxy Workflow", "EOSC::Galaxy Workflow", "", "compliesWith"); + addEIG( + orp.getEoscifguidelines(), "EOSC::Galaxy Workflow", "EOSC::Galaxy Workflow", "", + "compliesWith"); } if (containscriteriaTwitter(orp)) { - addEIG(orp.getEoscifguidelines(),"EOSC::Twitter Data", "EOSC::Twitter Data", "", "compliesWith"); + addEIG(orp.getEoscifguidelines(), "EOSC::Twitter Data", "EOSC::Twitter Data", "", "compliesWith"); } return orp; }, Encoders.bean(OtherResearchProduct.class)) @@ -133,7 +138,7 @@ public class SparkEoscTag { if (!Optional.ofNullable(d.getEoscifguidelines()).isPresent()) d.setEoscifguidelines(new ArrayList<>()); if (containscriteriaTwitter(d)) { - addEIG(d.getEoscifguidelines(),"EOSC::Twitter Data", "EOSC::Twitter Data", "", "compliesWith"); + addEIG(d.getEoscifguidelines(), "EOSC::Twitter Data", "EOSC::Twitter Data", "", "compliesWith"); } return d; }, Encoders.bean(Dataset.class)) @@ -149,12 +154,12 @@ public class SparkEoscTag { .json(inputPath + "/dataset"); } - private static void addEIG(List eoscifguidelines, String code, String label, String url, String sem) { + private static void addEIG(List eoscifguidelines, String code, String label, String url, + String sem) { if (!eoscifguidelines.stream().anyMatch(eig -> eig.getCode().equals(code))) eoscifguidelines.add(newInstance(code, label, url, sem)); } - private static boolean containscriteriaTwitter(Result r) { Set words = getWordsSP(r.getTitle()); words.addAll(getWordsF(r.getDescription())); diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java index b1c0cbb84..5f47da10e 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java @@ -126,9 +126,12 @@ public class EOSCTagJobTest { .assertEquals( 4, tmp - .filter(s -> s.getEoscifguidelines()!= null) + .filter(s -> s.getEoscifguidelines() != null) .filter( - s -> s.getEoscifguidelines().stream().anyMatch(eig -> eig.getCode().equals("EOSC::Jupyter Notebook"))) + s -> s + .getEoscifguidelines() + .stream() + .anyMatch(eig -> eig.getCode().equals("EOSC::Jupyter Notebook"))) .count()); Assertions @@ -141,13 +144,13 @@ public class EOSCTagJobTest { .size()); Assertions - .assertEquals( - 1, tmp - .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) - .collect() - .get(0) - .getSubject() - .size()); + .assertEquals( + 1, tmp + .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) + .collect() + .get(0) + .getSubject() + .size()); Assertions .assertTrue( tmp @@ -159,14 +162,14 @@ public class EOSCTagJobTest { .anyMatch(s -> s.getCode().equals("EOSC::Jupyter Notebook"))); Assertions - .assertFalse( - tmp - .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) - .collect() - .get(0) - .getSubject() - .stream() - .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); + .assertFalse( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) + .collect() + .get(0) + .getSubject() + .stream() + .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); Assertions .assertEquals( @@ -186,12 +189,13 @@ public class EOSCTagJobTest { .stream() .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); - Assertions.assertTrue(tmp - .filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11")) - .collect() - .get(0) - .getEoscifguidelines() == null - ); + Assertions + .assertTrue( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11")) + .collect() + .get(0) + .getEoscifguidelines() == null); Assertions .assertEquals( @@ -211,22 +215,22 @@ public class EOSCTagJobTest { .stream() .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); Assertions - .assertEquals( - 1, tmp - .filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")) - .collect() - .get(0) - .getEoscifguidelines() - .size()); + .assertEquals( + 1, tmp + .filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")) + .collect() + .get(0) + .getEoscifguidelines() + .size()); Assertions - .assertTrue( - tmp - .filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")) - .collect() - .get(0) - .getEoscifguidelines() - .stream() - .anyMatch(s -> s.getCode().equals("EOSC::Jupyter Notebook"))); + .assertTrue( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")) + .collect() + .get(0) + .getEoscifguidelines() + .stream() + .anyMatch(s -> s.getCode().equals("EOSC::Jupyter Notebook"))); Assertions .assertEquals( @@ -245,13 +249,13 @@ public class EOSCTagJobTest { .getSubject() .stream() .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); - Assertions.assertTrue( + Assertions + .assertTrue( tmp - .filter(sw -> sw.getId().equals("50|od______1582::5aec1186054301b66c0c5dc35972a589")) - .collect() - .get(0) - .getEoscifguidelines() == null - ); + .filter(sw -> sw.getId().equals("50|od______1582::5aec1186054301b66c0c5dc35972a589")) + .collect() + .get(0) + .getEoscifguidelines() == null); Assertions .assertEquals( @@ -270,20 +274,24 @@ public class EOSCTagJobTest { .getSubject() .stream() .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); - Assertions.assertEquals(1, + Assertions + .assertEquals( + 1, tmp - .filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0")) - .collect() - .get(0) - .getEoscifguidelines() - .size()); - Assertions.assertTrue(tmp - .filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0")) - .collect() - .get(0) - .getEoscifguidelines() - .stream() - .anyMatch(s -> s.getCode().equals("EOSC::Jupyter Notebook"))); + .filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0")) + .collect() + .get(0) + .getEoscifguidelines() + .size()); + Assertions + .assertTrue( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0")) + .collect() + .get(0) + .getEoscifguidelines() + .stream() + .anyMatch(s -> s.getCode().equals("EOSC::Jupyter Notebook"))); List subjects = tmp .filter(sw -> sw.getId().equals("50|od______1582::6e7a9b21a2feef45673890432af34244")) @@ -315,13 +323,16 @@ public class EOSCTagJobTest { ds -> ds.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook"))) .count()); Assertions - .assertEquals( - 0, sc - .textFile(workingDir.toString() + "/input/dataset") - .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)) - .filter( - ds -> ds.getEoscifguidelines().stream().anyMatch(eig -> eig.getCode().equals("EOSC::Jupyter Notebook"))) - .count()); + .assertEquals( + 0, sc + .textFile(workingDir.toString() + "/input/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)) + .filter( + ds -> ds + .getEoscifguidelines() + .stream() + .anyMatch(eig -> eig.getCode().equals("EOSC::Jupyter Notebook"))) + .count()); Assertions .assertEquals( @@ -336,17 +347,23 @@ public class EOSCTagJobTest { .textFile(workingDir.toString() + "/input/otherresearchproduct") .map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)) .filter( - orp -> orp.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook"))) + orp -> orp + .getSubject() + .stream() + .anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook"))) .count()); Assertions - .assertEquals( - 0, sc - .textFile(workingDir.toString() + "/input/otherresearchproduct") - .map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)) - .filter( - orp -> orp.getSubject().stream().anyMatch(eig -> eig.getValue().equals("EOSC::Jupyter Notebook"))) - .count()); + .assertEquals( + 0, sc + .textFile(workingDir.toString() + "/input/otherresearchproduct") + .map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)) + .filter( + orp -> orp + .getSubject() + .stream() + .anyMatch(eig -> eig.getValue().equals("EOSC::Jupyter Notebook"))) + .count()); // spark.stop(); } @@ -413,20 +430,24 @@ public class EOSCTagJobTest { s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Galaxy Workflow"))) .count()); Assertions - .assertEquals( - 1, - tmp - .filter( - s -> s.getEoscifguidelines()!=null) - .count()); + .assertEquals( + 1, + tmp + .filter( + s -> s.getEoscifguidelines() != null) + .count()); Assertions - .assertEquals( - 1, - tmp - .filter( - s -> s.getEoscifguidelines()!=null) - .filter(s -> s.getEoscifguidelines().stream().anyMatch(eig -> eig.getCode().equals("EOSC::Galaxy Workflow"))) - .count()); + .assertEquals( + 1, + tmp + .filter( + s -> s.getEoscifguidelines() != null) + .filter( + s -> s + .getEoscifguidelines() + .stream() + .anyMatch(eig -> eig.getCode().equals("EOSC::Galaxy Workflow"))) + .count()); Assertions .assertEquals( @@ -446,18 +467,23 @@ public class EOSCTagJobTest { .stream() .anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); - Assertions.assertEquals(1, tmp - .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) - .collect() - .get(0) - .getEoscifguidelines() - .size() ); - Assertions.assertTrue(tmp - .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) - .collect() - .get(0) - .getEoscifguidelines() - .stream().anyMatch(eig -> eig.getCode().equals("EOSC::Galaxy Workflow"))); + Assertions + .assertEquals( + 1, tmp + .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) + .collect() + .get(0) + .getEoscifguidelines() + .size()); + Assertions + .assertTrue( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) + .collect() + .get(0) + .getEoscifguidelines() + .stream() + .anyMatch(eig -> eig.getCode().equals("EOSC::Galaxy Workflow"))); Assertions .assertEquals( @@ -499,10 +525,18 @@ public class EOSCTagJobTest { .filter( s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Galaxy Workflow"))) .count()); - orp.foreach(o-> System.out.println(OBJECT_MAPPER.writeValueAsString(o))); + orp.foreach(o -> System.out.println(OBJECT_MAPPER.writeValueAsString(o))); - Assertions.assertEquals(1, orp.filter(o -> o.getEoscifguidelines() != null) - .filter(o -> o.getEoscifguidelines().stream().anyMatch(eig -> eig.getCode().equals("EOSC::Galaxy Workflow"))).count()); + Assertions + .assertEquals( + 1, orp + .filter(o -> o.getEoscifguidelines() != null) + .filter( + o -> o + .getEoscifguidelines() + .stream() + .anyMatch(eig -> eig.getCode().equals("EOSC::Galaxy Workflow"))) + .count()); Assertions .assertEquals( @@ -522,22 +556,22 @@ public class EOSCTagJobTest { .stream() .anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); Assertions - .assertEquals( - 1, orp - .filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07")) - .collect() - .get(0) - .getEoscifguidelines() - .size()); + .assertEquals( + 1, orp + .filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07")) + .collect() + .get(0) + .getEoscifguidelines() + .size()); Assertions - .assertTrue( - orp - .filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07")) - .collect() - .get(0) - .getEoscifguidelines() - .stream() - .anyMatch(s -> s.getCode().equals("EOSC::Galaxy Workflow"))); + .assertTrue( + orp + .filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07")) + .collect() + .get(0) + .getEoscifguidelines() + .stream() + .anyMatch(s -> s.getCode().equals("EOSC::Galaxy Workflow"))); Assertions .assertEquals( @@ -651,11 +685,15 @@ public class EOSCTagJobTest { .filter(s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Twitter Data"))) .count()); Assertions - .assertEquals( - 3, - orp - .filter(s -> s.getEoscifguidelines().stream().anyMatch(eig -> eig.getCode().equals("EOSC::Twitter Data"))) - .count()); + .assertEquals( + 3, + orp + .filter( + s -> s + .getEoscifguidelines() + .stream() + .anyMatch(eig -> eig.getCode().equals("EOSC::Twitter Data"))) + .count()); JavaRDD dats = sc .textFile(workingDir.toString() + "/input/dataset") @@ -667,7 +705,11 @@ public class EOSCTagJobTest { .assertEquals( 3, dats - .filter(s -> s.getEoscifguidelines().stream().anyMatch(eig -> eig.getCode().equals("EOSC::Twitter Data"))) + .filter( + s -> s + .getEoscifguidelines() + .stream() + .anyMatch(eig -> eig.getCode().equals("EOSC::Twitter Data"))) .count()); } From 317a4a56ef9019bd4cc3280673ec34cc8c5b58d0 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 21 Jul 2022 17:37:48 +0200 Subject: [PATCH 08/33] [EOSC context TAG] first implementation of the logic to tag results imported from datasources registered in the EOSC --- .../dhp/bulktag/eosc/DatasourceMaster.java | 28 ++++ .../eosc/ReadMasterDatasourceFromDB.java | 134 ++++++++++++++++ .../dhp/bulktag/eosc/SparkEoscBulkTag.java | 145 ++++++++++++++++++ pom.xml | 2 +- 4 files changed, 308 insertions(+), 1 deletion(-) create mode 100644 dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/DatasourceMaster.java create mode 100644 dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java create mode 100644 dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/DatasourceMaster.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/DatasourceMaster.java new file mode 100644 index 000000000..537356586 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/DatasourceMaster.java @@ -0,0 +1,28 @@ +package eu.dnetlib.dhp.bulktag.eosc; + +import java.io.Serializable; + +/** + * @author miriam.baglioni + * @Date 21/07/22 + */ +public class DatasourceMaster implements Serializable { + private String datasource; + private String master; + + public String getDatasource() { + return datasource; + } + + public void setDatasource(String datasource) { + this.datasource = datasource; + } + + public String getMaster() { + return master; + } + + public void setMaster(String master) { + this.master = master; + } +} diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java new file mode 100644 index 000000000..7d6964707 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java @@ -0,0 +1,134 @@ + +package eu.dnetlib.dhp.bulktag.eosc; + +/** + * @author miriam.baglioni + * @Date 21/07/22 + */ + +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.DbClient; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.common.RelationInverse; +import eu.dnetlib.dhp.schema.oaf.Relation; +import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FSDataOutputStream; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; + +import java.io.BufferedWriter; +import java.io.Closeable; +import java.io.IOException; +import java.io.OutputStreamWriter; +import java.nio.charset.StandardCharsets; +import java.sql.ResultSet; +import java.sql.SQLException; +import java.util.Arrays; +import java.util.List; +import java.util.function.Consumer; +import java.util.function.Function; + +public class ReadMasterDatasourceFromDB implements Closeable { + + private final DbClient dbClient; + private static final Log log = LogFactory.getLog(ReadMasterDatasourceFromDB.class); + + private final BufferedWriter writer; + private final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static final String QUERY = "SELECT dso.id datasource, d.id master FROM " + + "(SELECT id FROM dsm_services WHERE id like 'eosc%') dso " + + "FULL JOIN " + + "(SELECT id, duplicate FROM dsm_dedup_services WHERE duplicate like 'eosc%')d " + + "ON dso.id = d.duplicate"; + + public static void main(final String[] args) throws Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + ReadMasterDatasourceFromDB.class + .getResourceAsStream( + "/eu/dnetlib/dhp/blacklist/blacklist_parameters.json"))); + + parser.parseArgument(args); + + final String dbUrl = parser.get("postgresUrl"); + final String dbUser = parser.get("postgresUser"); + final String dbPassword = parser.get("postgresPassword"); + final String hdfsPath = parser.get("hdfsPath") + "/datasourceMasters"; + final String hdfsNameNode = parser.get("hdfsNameNode"); + + try (final ReadMasterDatasourceFromDB rmd = new ReadMasterDatasourceFromDB(hdfsPath, hdfsNameNode, dbUrl, dbUser, + dbPassword)) { + + log.info("Processing datasources..."); + rmd.execute(QUERY, rmd::datasourceMasterMap); + + } + } + + public void execute(final String sql, final Function producer) { + + dbClient.processResults(sql, rs -> writeMap(producer.apply(rs))); + } + + public DatasourceMaster datasourceMasterMap(ResultSet rs) { + try { + DatasourceMaster dm = new DatasourceMaster(); + String datasource = rs.getString("datasource"); + dm.setDatasource(datasource); + String master = rs.getString("master"); + if (StringUtils.isNotBlank(master)) + dm.setMaster(OafMapperUtils.createOpenaireId(10, master, true)); + else + dm.setMaster(OafMapperUtils.createOpenaireId(10, datasource, true)); + return dm; + + } catch (final SQLException e) { + throw new RuntimeException(e); + } + } + + @Override + public void close() throws IOException { + dbClient.close(); + writer.close(); + } + + public ReadMasterDatasourceFromDB( + final String hdfsPath, String hdfsNameNode, final String dbUrl, final String dbUser, final String dbPassword) + throws IOException { + + this.dbClient = new DbClient(dbUrl, dbUser, dbPassword); + + Configuration conf = new Configuration(); + conf.set("fs.defaultFS", hdfsNameNode); + + FileSystem fileSystem = FileSystem.get(conf); + Path hdfsWritePath = new Path(hdfsPath); + FSDataOutputStream fsDataOutputStream = null; + if (fileSystem.exists(hdfsWritePath)) { + fsDataOutputStream = fileSystem.append(hdfsWritePath); + } else { + fsDataOutputStream = fileSystem.create(hdfsWritePath); + } + + this.writer = new BufferedWriter(new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8)); + } + + protected void writeMap(final DatasourceMaster dm) { + try { + writer.write(OBJECT_MAPPER.writeValueAsString(dm)); + writer.newLine(); + } catch (final IOException e) { + throw new RuntimeException(e); + } + } + +} diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java new file mode 100644 index 000000000..aa709cb29 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java @@ -0,0 +1,145 @@ +package eu.dnetlib.dhp.bulktag.eosc; + +import com.fasterxml.jackson.databind.ObjectMapper; +import com.google.gson.Gson; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.bulktag.SparkBulkTagJob; +import eu.dnetlib.dhp.bulktag.community.*; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.oaf.Context; +import eu.dnetlib.dhp.schema.oaf.DataInfo; +import eu.dnetlib.dhp.schema.oaf.Qualifier; +import eu.dnetlib.dhp.schema.oaf.Result; +import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import javax.print.attribute.DocAttributeSet; +import java.io.Serializable; +import java.util.*; +import java.util.stream.Collectors; + +import static eu.dnetlib.dhp.PropagationConstant.removeOutputDir; +import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.*; +import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.TAGGING_TRUST; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; +import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PROVENANCE_ACTIONS; + +/** + * @author miriam.baglioni + * @Date 21/07/22 + */ +public class SparkEoscBulkTag implements Serializable { + + private static final Logger log = LoggerFactory.getLogger(SparkEoscBulkTag.class); + public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + SparkEoscBulkTag.class + .getResourceAsStream( + "/eu/dnetlib/dhp/bulktag/input_bulkTag_parameters.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String inputPath = parser.get("sourcePath"); + log.info("inputPath: {}", inputPath); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath: {}", outputPath); + + String datasourceMapPath = parser.get("datasourceMapPath"); + log.info("datasourceMapPath: {}", datasourceMapPath); + + final String resultClassName = parser.get("resultTableName"); + log.info("resultTableName: {}", resultClassName); + + Class resultClazz = (Class) Class.forName(resultClassName); + + SparkConf conf = new SparkConf(); + CommunityConfiguration cc; + + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + removeOutputDir(spark, outputPath); + execBulkTag(spark, inputPath, outputPath, datasourceMapPath, resultClazz); + }); + } + + private static void execBulkTag( + SparkSession spark, + String inputPath, + String outputPath, + String datasourceMapPath, + Class resultClazz) { + + final List hostedByList = Arrays.asList(readPath(spark, datasourceMapPath, DatasourceMaster.class) + .map((MapFunction) dm -> dm.getMaster(), Encoders.STRING()) + .collect()); + + readPath(spark, inputPath, resultClazz) + .map(patchResult(), Encoders.bean(resultClazz)) + .filter(Objects::nonNull) + .map( + (MapFunction) value -> enrich(value, hostedByList), + Encoders.bean(resultClazz)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath); + } + + private static R enrich(R value, List hostedByList) { + if(value.getInstance().stream().anyMatch(i -> hostedByList.contains(i.getHostedby().getKey())) || + (value.getEoscifguidelines() != null && value.getEoscifguidelines().size() > 0)){ + Context context = new Context(); + context.setId("eosc"); + OafMapperUtils.dataInfo(false, BULKTAG_DATA_INFO_TYPE,true,false, + OafMapperUtils.qualifier(CLASS_ID_DATASOURCE, CLASS_NAME_BULKTAG_DATASOURCE, + DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), TAGGING_TRUST); + value.getContext().add(context); + + } + return value; + + } + + public static Dataset readPath( + SparkSession spark, String inputPath, Class clazz) { + return spark + .read() + .textFile(inputPath) + .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz)); + } + + // TODO remove this hack as soon as the values fixed by this method will be provided as NON null + private static MapFunction patchResult() { + return r -> { + if (r.getDataInfo().getDeletedbyinference() == null) { + r.getDataInfo().setDeletedbyinference(false); + } + if (r.getContext() == null) { + r.setContext(new ArrayList<>()); + } + return r; + }; + } + +} diff --git a/pom.xml b/pom.xml index 54070f654..821ce3124 100644 --- a/pom.xml +++ b/pom.xml @@ -801,7 +801,7 @@ 3.3.3 3.4.2 [2.12,3.0) - [2.12.0] + [2.12.1] [4.0.3] [6.0.5] [3.1.6] From 7a1c1b6f53b8c7ca51633b440338fffc997e81bb Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 22 Jul 2022 14:36:02 +0200 Subject: [PATCH 09/33] [EOSC context TAG] Add test class and resourcesK --- .../dhp/bulktag/eosc/DatasourceMaster.java | 29 +- .../eosc/ReadMasterDatasourceFromDB.java | 62 ++-- .../dhp/bulktag/eosc/SparkEoscBulkTag.java | 229 +++++++------ .../bulktag/datasourcemaster_parameters.json | 32 ++ .../input_eosc_bulkTag_parameters.json | 34 ++ .../dhp/bulktag/oozie_app/workflow.xml | 139 +++++++- .../dhp/bulktag/EOSCContextTaggingTest.java | 152 +++++++++ .../dhp/bulktag/eosc/dataset/dataset_10.json | 10 + .../datasourceMaster | 318 ++++++++++++++++++ 9 files changed, 855 insertions(+), 150 deletions(-) create mode 100644 dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/datasourcemaster_parameters.json create mode 100644 dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/input_eosc_bulkTag_parameters.json create mode 100644 dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCContextTaggingTest.java create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/eosc/dataset/dataset_10.json create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/eosc/datasourceMasterAssociation/datasourceMaster diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/DatasourceMaster.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/DatasourceMaster.java index 537356586..ee01597e7 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/DatasourceMaster.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/DatasourceMaster.java @@ -1,3 +1,4 @@ + package eu.dnetlib.dhp.bulktag.eosc; import java.io.Serializable; @@ -7,22 +8,22 @@ import java.io.Serializable; * @Date 21/07/22 */ public class DatasourceMaster implements Serializable { - private String datasource; - private String master; + private String datasource; + private String master; - public String getDatasource() { - return datasource; - } + public String getDatasource() { + return datasource; + } - public void setDatasource(String datasource) { - this.datasource = datasource; - } + public void setDatasource(String datasource) { + this.datasource = datasource; + } - public String getMaster() { - return master; - } + public String getMaster() { + return master; + } - public void setMaster(String master) { - this.master = master; - } + public void setMaster(String master) { + this.master = master; + } } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java index 7d6964707..9ad108749 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java @@ -1,27 +1,6 @@ package eu.dnetlib.dhp.bulktag.eosc; -/** - * @author miriam.baglioni - * @Date 21/07/22 - */ - -import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.common.DbClient; -import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.dhp.schema.common.RelationInverse; -import eu.dnetlib.dhp.schema.oaf.Relation; -import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; -import org.apache.commons.io.IOUtils; -import org.apache.commons.lang3.StringUtils; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; -import org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.FSDataOutputStream; -import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.fs.Path; - import java.io.BufferedWriter; import java.io.Closeable; import java.io.IOException; @@ -34,6 +13,28 @@ import java.util.List; import java.util.function.Consumer; import java.util.function.Function; +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FSDataOutputStream; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; + +/** + * @author miriam.baglioni + * @Date 21/07/22 + */ +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.DbClient; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.common.RelationInverse; +import eu.dnetlib.dhp.schema.oaf.Relation; +import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; + public class ReadMasterDatasourceFromDB implements Closeable { private final DbClient dbClient; @@ -43,18 +44,18 @@ public class ReadMasterDatasourceFromDB implements Closeable { private final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); private static final String QUERY = "SELECT dso.id datasource, d.id master FROM " + - "(SELECT id FROM dsm_services WHERE id like 'eosc%') dso " + - "FULL JOIN " + - "(SELECT id, duplicate FROM dsm_dedup_services WHERE duplicate like 'eosc%')d " + - "ON dso.id = d.duplicate"; + "(SELECT id FROM dsm_services WHERE id like 'eosc%') dso " + + "FULL JOIN " + + "(SELECT id, duplicate FROM dsm_dedup_services WHERE duplicate like 'eosc%')d " + + "ON dso.id = d.duplicate"; public static void main(final String[] args) throws Exception { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils .toString( - ReadMasterDatasourceFromDB.class + ReadMasterDatasourceFromDB.class .getResourceAsStream( - "/eu/dnetlib/dhp/blacklist/blacklist_parameters.json"))); + "/eu/dnetlib/dhp/bulktag/datasourcemaster_parameters.json"))); parser.parseArgument(args); @@ -64,8 +65,9 @@ public class ReadMasterDatasourceFromDB implements Closeable { final String hdfsPath = parser.get("hdfsPath") + "/datasourceMasters"; final String hdfsNameNode = parser.get("hdfsNameNode"); - try (final ReadMasterDatasourceFromDB rmd = new ReadMasterDatasourceFromDB(hdfsPath, hdfsNameNode, dbUrl, dbUser, - dbPassword)) { + try ( + final ReadMasterDatasourceFromDB rmd = new ReadMasterDatasourceFromDB(hdfsPath, hdfsNameNode, dbUrl, dbUser, + dbPassword)) { log.info("Processing datasources..."); rmd.execute(QUERY, rmd::datasourceMasterMap); @@ -75,7 +77,7 @@ public class ReadMasterDatasourceFromDB implements Closeable { public void execute(final String sql, final Function producer) { - dbClient.processResults(sql, rs -> writeMap(producer.apply(rs))); + dbClient.processResults(sql, rs -> writeMap(producer.apply(rs))); } public DatasourceMaster datasourceMasterMap(ResultSet rs) { diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java index aa709cb29..600a5cec8 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java @@ -1,18 +1,22 @@ + package eu.dnetlib.dhp.bulktag.eosc; -import com.fasterxml.jackson.databind.ObjectMapper; -import com.google.gson.Gson; -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.bulktag.SparkBulkTagJob; -import eu.dnetlib.dhp.bulktag.community.*; -import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.dhp.schema.oaf.Context; -import eu.dnetlib.dhp.schema.oaf.DataInfo; -import eu.dnetlib.dhp.schema.oaf.Qualifier; -import eu.dnetlib.dhp.schema.oaf.Result; -import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; +import static eu.dnetlib.dhp.PropagationConstant.readPath; +import static eu.dnetlib.dhp.PropagationConstant.removeOutputDir; +import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.*; +import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.TAGGING_TRUST; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; +import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PROVENANCE_ACTIONS; + +import java.io.Serializable; +import java.util.*; +import java.util.stream.Collectors; + +import javax.print.attribute.DocAttributeSet; + import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.ForeachFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; @@ -21,16 +25,15 @@ import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import javax.print.attribute.DocAttributeSet; -import java.io.Serializable; -import java.util.*; -import java.util.stream.Collectors; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.google.gson.Gson; -import static eu.dnetlib.dhp.PropagationConstant.removeOutputDir; -import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.*; -import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.TAGGING_TRUST; -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; -import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PROVENANCE_ACTIONS; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.bulktag.SparkBulkTagJob; +import eu.dnetlib.dhp.bulktag.community.*; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; /** * @author miriam.baglioni @@ -38,108 +41,124 @@ import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PROVENANCE_ACTION */ public class SparkEoscBulkTag implements Serializable { - private static final Logger log = LoggerFactory.getLogger(SparkEoscBulkTag.class); - public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static final Logger log = LoggerFactory.getLogger(SparkEoscBulkTag.class); + public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkEoscBulkTag.class - .getResourceAsStream( - "/eu/dnetlib/dhp/bulktag/input_bulkTag_parameters.json")); + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + SparkEoscBulkTag.class + .getResourceAsStream( + "/eu/dnetlib/dhp/bulktag/input_eosc_bulkTag_parameters.json")); - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); + final String inputPath = parser.get("sourcePath"); + log.info("inputPath: {}", inputPath); - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); + final String workingPath = parser.get("workingPath"); + log.info("workingPath: {}", workingPath); - String datasourceMapPath = parser.get("datasourceMapPath"); - log.info("datasourceMapPath: {}", datasourceMapPath); + String datasourceMapPath = parser.get("datasourceMapPath"); + log.info("datasourceMapPath: {}", datasourceMapPath); - final String resultClassName = parser.get("resultTableName"); - log.info("resultTableName: {}", resultClassName); + final String resultClassName = parser.get("resultTableName"); + log.info("resultTableName: {}", resultClassName); - Class resultClazz = (Class) Class.forName(resultClassName); + Class resultClazz = (Class) Class.forName(resultClassName); - SparkConf conf = new SparkConf(); - CommunityConfiguration cc; + SparkConf conf = new SparkConf(); + CommunityConfiguration cc; - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - removeOutputDir(spark, outputPath); - execBulkTag(spark, inputPath, outputPath, datasourceMapPath, resultClazz); - }); - } + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + removeOutputDir(spark, workingPath); + execBulkTag(spark, inputPath, workingPath, datasourceMapPath, resultClazz); + }); + } - private static void execBulkTag( - SparkSession spark, - String inputPath, - String outputPath, - String datasourceMapPath, - Class resultClazz) { + private static void execBulkTag( + SparkSession spark, + String inputPath, + String workingPath, + String datasourceMapPath, + Class resultClazz) { - final List hostedByList = Arrays.asList(readPath(spark, datasourceMapPath, DatasourceMaster.class) - .map((MapFunction) dm -> dm.getMaster(), Encoders.STRING()) - .collect()); - readPath(spark, inputPath, resultClazz) - .map(patchResult(), Encoders.bean(resultClazz)) - .filter(Objects::nonNull) - .map( - (MapFunction) value -> enrich(value, hostedByList), - Encoders.bean(resultClazz)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); - } + List hostedByList = readPath(spark, datasourceMapPath, DatasourceMaster.class) + .map((MapFunction) dm -> dm.getMaster(), Encoders.STRING()) + .collectAsList(); - private static R enrich(R value, List hostedByList) { - if(value.getInstance().stream().anyMatch(i -> hostedByList.contains(i.getHostedby().getKey())) || - (value.getEoscifguidelines() != null && value.getEoscifguidelines().size() > 0)){ - Context context = new Context(); - context.setId("eosc"); - OafMapperUtils.dataInfo(false, BULKTAG_DATA_INFO_TYPE,true,false, - OafMapperUtils.qualifier(CLASS_ID_DATASOURCE, CLASS_NAME_BULKTAG_DATASOURCE, - DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), TAGGING_TRUST); - value.getContext().add(context); - } - return value; - } - public static Dataset readPath( - SparkSession spark, String inputPath, Class clazz) { - return spark - .read() - .textFile(inputPath) - .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz)); - } + readPath(spark, inputPath, resultClazz) + .map(patchResult(), Encoders.bean(resultClazz)) + .filter(Objects::nonNull) + .map( + (MapFunction) value -> enrich(value, hostedByList), + Encoders.bean(resultClazz)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingPath); - // TODO remove this hack as soon as the values fixed by this method will be provided as NON null - private static MapFunction patchResult() { - return r -> { - if (r.getDataInfo().getDeletedbyinference() == null) { - r.getDataInfo().setDeletedbyinference(false); - } - if (r.getContext() == null) { - r.setContext(new ArrayList<>()); - } - return r; - }; - } + readPath(spark, workingPath, resultClazz) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(inputPath); + + } + + private static R enrich(R value, List hostedByList) { + if (value.getInstance().stream().anyMatch(i -> hostedByList.contains(i.getHostedby().getKey())) || + (value.getEoscifguidelines() != null && value.getEoscifguidelines().size() > 0)) { + Context context = new Context(); + context.setId("eosc"); + OafMapperUtils + .dataInfo( + false, BULKTAG_DATA_INFO_TYPE, true, false, + OafMapperUtils + .qualifier( + CLASS_ID_DATASOURCE, CLASS_NAME_BULKTAG_DATASOURCE, + DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), + TAGGING_TRUST); + value.getContext().add(context); + + } + return value; + + } + + public static Dataset readPath( + SparkSession spark, String inputPath, Class clazz) { + return spark + .read() + .textFile(inputPath) + .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz)); + } + + // TODO remove this hack as soon as the values fixed by this method will be provided as NON null + private static MapFunction patchResult() { + return r -> { + if (r.getDataInfo().getDeletedbyinference() == null) { + r.getDataInfo().setDeletedbyinference(false); + } + if (r.getContext() == null) { + r.setContext(new ArrayList<>()); + } + return r; + }; + } } diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/datasourcemaster_parameters.json b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/datasourcemaster_parameters.json new file mode 100644 index 000000000..9a2eadaa7 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/datasourcemaster_parameters.json @@ -0,0 +1,32 @@ +[ + { + "paramName": "p", + "paramLongName": "hdfsPath", + "paramDescription": "the path where storing the sequential file", + "paramRequired": true + }, + { + "paramName": "nn", + "paramLongName": "hdfsNameNode", + "paramDescription": "the name node on hdfs", + "paramRequired": true + }, + { + "paramName": "pgurl", + "paramLongName": "postgresUrl", + "paramDescription": "postgres url, example: jdbc:postgresql://localhost:5432/testdb", + "paramRequired": true + }, + { + "paramName": "pguser", + "paramLongName": "postgresUser", + "paramDescription": "postgres user", + "paramRequired": false + }, + { + "paramName": "pgpasswd", + "paramLongName": "postgresPassword", + "paramDescription": "postgres password", + "paramRequired": false + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/input_eosc_bulkTag_parameters.json b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/input_eosc_bulkTag_parameters.json new file mode 100644 index 000000000..ebbbd408b --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/input_eosc_bulkTag_parameters.json @@ -0,0 +1,34 @@ +[ + + { + "paramName":"s", + "paramLongName":"sourcePath", + "paramDescription": "the path of the sequencial file to read", + "paramRequired": true + }, + { + "paramName": "dmp", + "paramLongName":"datasourceMapPath", + "paramDescription": "the path where the association datasource master has been stored", + "paramRequired": true + }, + { + "paramName":"tn", + "paramLongName":"resultTableName", + "paramDescription": "the name of the result table we are currently working on", + "paramRequired": true + }, + { + "paramName": "wp", + "paramLongName": "workingPath", + "paramDescription": "the path used to store temporary output files", + "paramRequired": true + }, + { + "paramName": "ssm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "true if the spark session is managed, false otherwise", + "paramRequired": false + } + +] \ No newline at end of file diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml index f34c5110f..6016e0179 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml @@ -16,6 +16,21 @@ outputPath the output path + + + + postgresURL + the url of the postgress server to query + + + postgresUser + the username to access the postgres db + + + postgresPassword + the postgres password + + @@ -29,7 +44,7 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] @@ -226,10 +241,132 @@ --sourcePath${outputPath} --workingPath${workingDir}/eoscTag + + + + + + + eu.dnetlib.dhp.bulktag.eosc.ReadMasterDatasourceFromDB + --hdfsPath${workingDir}/datasourcemaster + --hdfsNameNode${nameNode} + --postgresUrl${postgresURL} + --postgresUser${postgresUser} + --postgresPassword${postgresPassword} + + + + + + + + + + + yarn-cluster + cluster + EOSC_tagging + eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag + dhp-enrichment-${projectVersion}.jar + + --num-executors=${sparkExecutorNumber} + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --sourcePath${outputPath}/publication + --workingPath${workingDir}/eoscContextTag/publication + --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication + --datasourceMapPath${workingDir}/datasourcemaster + + + + + + + + yarn-cluster + cluster + EOSC_tagging + eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag + dhp-enrichment-${projectVersion}.jar + + --num-executors=${sparkExecutorNumber} + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --sourcePath${outputPath}/dataset + --workingPath${workingDir}/eoscContextTag/dataset + --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset + --datasourceMapPath${workingDir}/datasourcemaster + + + + + + + yarn-cluster + cluster + EOSC_tagging + eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag + dhp-enrichment-${projectVersion}.jar + + --num-executors=${sparkExecutorNumber} + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --sourcePath${outputPath}/software + --workingPath${workingDir}/eoscContextTag/software + --resultTableNameeu.dnetlib.dhp.schema.oaf.Software + --datasourceMapPath${workingDir}/datasourcemaster + + + + + + + yarn-cluster + cluster + EOSC_tagging + eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag + dhp-enrichment-${projectVersion}.jar + + --num-executors=${sparkExecutorNumber} + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --sourcePath${outputPath}/otherresearchproduct + --workingPath${workingDir}/eoscContextTag/otherresearchproduct + --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct + --datasourceMapPath${workingDir}/datasourcemaster + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCContextTaggingTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCContextTaggingTest.java new file mode 100644 index 000000000..d6785acc7 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCContextTaggingTest.java @@ -0,0 +1,152 @@ + +package eu.dnetlib.dhp.bulktag; +/** + * @author miriam.baglioni + * @Date 22/07/22 + */ + +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag; +import eu.dnetlib.dhp.schema.oaf.Dataset; +import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct; +import eu.dnetlib.dhp.schema.oaf.Software; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import org.apache.commons.io.FileUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.List; + +//"50|475c1990cbb2::0fecfb874d9395aa69d2f4d7cd1acbea" has instance hostedby eosc +//"50|475c1990cbb2::3185cd5d8a2b0a06bb9b23ef11748eb1" has instance hostedby eosc +//"50|475c1990cbb2::449f28eefccf9f70c04ad70d61e041c7" has two instance one hostedby eosc +//"50|475c1990cbb2::3894c94123e96df8a21249957cf160cb" has EoscTag + +public class EOSCContextTaggingTest { + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path workingDir; + + private static final Logger log = LoggerFactory.getLogger(EOSCContextTaggingTest.class); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files.createTempDirectory(EOSCContextTaggingTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(EOSCContextTaggingTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(EOSCTagJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + void EoscContextTagTest() throws Exception { + + spark + .read() + .textFile(getClass().getResource("/eu/dnetlib/dhp/bulktag/eosc/dataset/dataset_10.json").getPath()) + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, Dataset.class), + Encoders.bean(Dataset.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingDir.toString() + "/input/dataset"); + + + SparkEoscBulkTag + .main( + new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", + workingDir.toString() + "/input/dataset", + "-workingPath", workingDir.toString() + "/working/dataset", + "-datasourceMapPath", getClass().getResource("/eu/dnetlib/dhp/bulktag/eosc/datasourceMasterAssociation/datasourceMaster").getPath(), + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset" + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/input/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); + + Assertions.assertEquals(10, tmp.count()); + + Assertions + .assertEquals( + 4, + tmp + .filter( + s -> s.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))) + .count()); + + Assertions + .assertEquals(1, + tmp + .filter(d -> d.getId().equals("50|475c1990cbb2::0fecfb874d9395aa69d2f4d7cd1acbea") + && + d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))).count() + ); + Assertions + .assertEquals(1, + tmp + .filter(d -> d.getId().equals("50|475c1990cbb2::3185cd5d8a2b0a06bb9b23ef11748eb1") + && + d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))).count() + ); + + + Assertions + .assertEquals(1, + tmp + .filter(d -> d.getId().equals("50|475c1990cbb2::3894c94123e96df8a21249957cf160cb") + && + d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))).count() + ); + + Assertions + .assertEquals(1, + tmp + .filter(d -> d.getId().equals("50|475c1990cbb2::3894c94123e96df8a21249957cf160cb") + && + d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))).count() + ); + } + + +} diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/eosc/dataset/dataset_10.json 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+{"datasource":"eosc________::wenmr::wenmr.disvis_web_portal","master":"10|eosc________::2539ec693b683284c4e243b969ae3fc0"} +{"datasource":"eosc________::wenmr::wenmr.fanten_finding_anisotropy_tensor","master":"10|eosc________::99c793e3f3b856c48eaaa36682038b28"} +{"datasource":"eosc________::wenmr::wenmr.haddock24_web_portal","master":"10|eosc________::0f198f6a0885105809f420be23614be3"} +{"datasource":"eosc________::wenmr::wenmr.metalpdb","master":"10|eosc________::84676bc3d2ce17de70309dc58f428296"} +{"datasource":"eosc________::wenmr::wenmr.pdb-tools_web","master":"10|eosc________::b37eed45624ac30f3476f71640e59a61"} +{"datasource":"eosc________::wenmr::wenmr.powerfit_web_portal","master":"10|eosc________::93d4d621ed1da378c0e7dc891cefc007"} +{"datasource":"eosc________::wenmr::wenmr.spoton","master":"10|eosc________::76e7e0552f9c6b89db94b31ddc366b9f"} \ No newline at end of file From 627332526b4a82b09190d3f3aefd106e274e38dd Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 22 Jul 2022 14:55:11 +0200 Subject: [PATCH 10/33] [EOSC context TAG] workflow start from reset_outputpath action --- .../resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml index 6016e0179..17fc76aad 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml @@ -44,7 +44,7 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] @@ -254,7 +254,7 @@ --postgresUser${postgresUser} --postgresPassword${postgresPassword} - + From 06a95daf60c49d9b0781d0e1f37965fc804a6491 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 22 Jul 2022 14:57:06 +0200 Subject: [PATCH 11/33] [EOSC context TAG] refactoring after compilation --- .../dhp/bulktag/eosc/SparkEoscBulkTag.java | 6 +- .../dhp/bulktag/EOSCContextTaggingTest.java | 224 +++++++++--------- 2 files changed, 118 insertions(+), 112 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java index 600a5cec8..3ed910184 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java @@ -93,13 +93,9 @@ public class SparkEoscBulkTag implements Serializable { String datasourceMapPath, Class resultClazz) { - List hostedByList = readPath(spark, datasourceMapPath, DatasourceMaster.class) .map((MapFunction) dm -> dm.getMaster(), Encoders.STRING()) - .collectAsList(); - - - + .collectAsList(); readPath(spark, inputPath, resultClazz) .map(patchResult(), Encoders.bean(resultClazz)) diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCContextTaggingTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCContextTaggingTest.java index d6785acc7..cbdab7628 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCContextTaggingTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCContextTaggingTest.java @@ -1,16 +1,11 @@ package eu.dnetlib.dhp.bulktag; -/** - * @author miriam.baglioni - * @Date 22/07/22 - */ -import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag; -import eu.dnetlib.dhp.schema.oaf.Dataset; -import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct; -import eu.dnetlib.dhp.schema.oaf.Software; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.List; + import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; @@ -26,10 +21,17 @@ import org.junit.jupiter.api.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.List; +/** + * @author miriam.baglioni + * @Date 22/07/22 + */ +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag; +import eu.dnetlib.dhp.schema.oaf.Dataset; +import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct; +import eu.dnetlib.dhp.schema.oaf.Software; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; //"50|475c1990cbb2::0fecfb874d9395aa69d2f4d7cd1acbea" has instance hostedby eosc //"50|475c1990cbb2::3185cd5d8a2b0a06bb9b23ef11748eb1" has instance hostedby eosc @@ -37,116 +39,124 @@ import java.util.List; //"50|475c1990cbb2::3894c94123e96df8a21249957cf160cb" has EoscTag public class EOSCContextTaggingTest { - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - private static SparkSession spark; + private static SparkSession spark; - private static Path workingDir; + private static Path workingDir; - private static final Logger log = LoggerFactory.getLogger(EOSCContextTaggingTest.class); + private static final Logger log = LoggerFactory.getLogger(EOSCContextTaggingTest.class); - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files.createTempDirectory(EOSCContextTaggingTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files.createTempDirectory(EOSCContextTaggingTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); - SparkConf conf = new SparkConf(); - conf.setAppName(EOSCContextTaggingTest.class.getSimpleName()); + SparkConf conf = new SparkConf(); + conf.setAppName(EOSCContextTaggingTest.class.getSimpleName()); - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - spark = SparkSession - .builder() - .appName(EOSCTagJobTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } + spark = SparkSession + .builder() + .appName(EOSCTagJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } - @Test - void EoscContextTagTest() throws Exception { + @Test + void EoscContextTagTest() throws Exception { - spark - .read() - .textFile(getClass().getResource("/eu/dnetlib/dhp/bulktag/eosc/dataset/dataset_10.json").getPath()) - .map( - (MapFunction) value -> OBJECT_MAPPER.readValue(value, Dataset.class), - Encoders.bean(Dataset.class)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(workingDir.toString() + "/input/dataset"); + spark + .read() + .textFile(getClass().getResource("/eu/dnetlib/dhp/bulktag/eosc/dataset/dataset_10.json").getPath()) + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, Dataset.class), + Encoders.bean(Dataset.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingDir.toString() + "/input/dataset"); + SparkEoscBulkTag + .main( + new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", + workingDir.toString() + "/input/dataset", + "-workingPath", workingDir.toString() + "/working/dataset", + "-datasourceMapPath", + getClass() + .getResource("/eu/dnetlib/dhp/bulktag/eosc/datasourceMasterAssociation/datasourceMaster") + .getPath(), + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset" + }); - SparkEoscBulkTag - .main( - new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", - workingDir.toString() + "/input/dataset", - "-workingPath", workingDir.toString() + "/working/dataset", - "-datasourceMapPath", getClass().getResource("/eu/dnetlib/dhp/bulktag/eosc/datasourceMasterAssociation/datasourceMaster").getPath(), - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset" - }); + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/input/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/input/dataset") - .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); + Assertions.assertEquals(10, tmp.count()); - Assertions.assertEquals(10, tmp.count()); + Assertions + .assertEquals( + 4, + tmp + .filter( + s -> s.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))) + .count()); - Assertions - .assertEquals( - 4, - tmp - .filter( - s -> s.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))) - .count()); + Assertions + .assertEquals( + 1, + tmp + .filter( + d -> d.getId().equals("50|475c1990cbb2::0fecfb874d9395aa69d2f4d7cd1acbea") + && + d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))) + .count()); + Assertions + .assertEquals( + 1, + tmp + .filter( + d -> d.getId().equals("50|475c1990cbb2::3185cd5d8a2b0a06bb9b23ef11748eb1") + && + d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))) + .count()); - Assertions - .assertEquals(1, - tmp - .filter(d -> d.getId().equals("50|475c1990cbb2::0fecfb874d9395aa69d2f4d7cd1acbea") - && - d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))).count() - ); - Assertions - .assertEquals(1, - tmp - .filter(d -> d.getId().equals("50|475c1990cbb2::3185cd5d8a2b0a06bb9b23ef11748eb1") - && - d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))).count() - ); - - - Assertions - .assertEquals(1, - tmp - .filter(d -> d.getId().equals("50|475c1990cbb2::3894c94123e96df8a21249957cf160cb") - && - d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))).count() - ); - - Assertions - .assertEquals(1, - tmp - .filter(d -> d.getId().equals("50|475c1990cbb2::3894c94123e96df8a21249957cf160cb") - && - d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))).count() - ); - } + Assertions + .assertEquals( + 1, + tmp + .filter( + d -> d.getId().equals("50|475c1990cbb2::3894c94123e96df8a21249957cf160cb") + && + d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))) + .count()); + Assertions + .assertEquals( + 1, + tmp + .filter( + d -> d.getId().equals("50|475c1990cbb2::3894c94123e96df8a21249957cf160cb") + && + d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))) + .count()); + } } From d091866e48ce0f814256c2f40ee5eddeb60511a3 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 25 Jul 2022 11:12:22 +0200 Subject: [PATCH 12/33] [EOSC Context Tagging] refactoring --- .../dhp/bulktag/eosc/SparkEoscBulkTag.java | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java index 3ed910184..99ff92223 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java @@ -121,14 +121,14 @@ public class SparkEoscBulkTag implements Serializable { (value.getEoscifguidelines() != null && value.getEoscifguidelines().size() > 0)) { Context context = new Context(); context.setId("eosc"); - OafMapperUtils - .dataInfo( - false, BULKTAG_DATA_INFO_TYPE, true, false, - OafMapperUtils - .qualifier( - CLASS_ID_DATASOURCE, CLASS_NAME_BULKTAG_DATASOURCE, - DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), - TAGGING_TRUST); + context.setDataInfo(Arrays.asList(OafMapperUtils + .dataInfo( + false, BULKTAG_DATA_INFO_TYPE, true, false, + OafMapperUtils + .qualifier( + CLASS_ID_DATASOURCE, CLASS_NAME_BULKTAG_DATASOURCE, + DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), + TAGGING_TRUST))); value.getContext().add(context); } From 144c103b672c3165f8af4bc27f5515f620b3c7d2 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 25 Jul 2022 13:52:45 +0200 Subject: [PATCH 13/33] [EOSC Context Tagging] add check to avoid the insertion of the context if already present --- .../java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java index 99ff92223..24520ff26 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java @@ -117,8 +117,9 @@ public class SparkEoscBulkTag implements Serializable { } private static R enrich(R value, List hostedByList) { - if (value.getInstance().stream().anyMatch(i -> hostedByList.contains(i.getHostedby().getKey())) || - (value.getEoscifguidelines() != null && value.getEoscifguidelines().size() > 0)) { + if (value.getInstance().stream().anyMatch(i -> (hostedByList.contains(i.getHostedby().getKey())) || + (value.getEoscifguidelines() != null && value.getEoscifguidelines().size() > 0)) && + !value.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))) { Context context = new Context(); context.setId("eosc"); context.setDataInfo(Arrays.asList(OafMapperUtils From 0172bab25136b1a3f974c2d66ddee434a712e26f Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 25 Jul 2022 14:16:45 +0200 Subject: [PATCH 14/33] [EOSC Context Tagging] refactoring --- .../dhp/bulktag/eosc/SparkEoscBulkTag.java | 25 +++++++++++++------ 1 file changed, 17 insertions(+), 8 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java index 24520ff26..66e0c8af4 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java @@ -117,19 +117,28 @@ public class SparkEoscBulkTag implements Serializable { } private static R enrich(R value, List hostedByList) { - if (value.getInstance().stream().anyMatch(i -> (hostedByList.contains(i.getHostedby().getKey())) || - (value.getEoscifguidelines() != null && value.getEoscifguidelines().size() > 0)) && - !value.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))) { + if (value + .getInstance() + .stream() + .anyMatch( + i -> (hostedByList.contains(i.getHostedby().getKey())) || + (value.getEoscifguidelines() != null && value.getEoscifguidelines().size() > 0)) + && + !value.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))) { Context context = new Context(); context.setId("eosc"); - context.setDataInfo(Arrays.asList(OafMapperUtils - .dataInfo( - false, BULKTAG_DATA_INFO_TYPE, true, false, + context + .setDataInfo( + Arrays + .asList( OafMapperUtils - .qualifier( + .dataInfo( + false, BULKTAG_DATA_INFO_TYPE, true, false, + OafMapperUtils + .qualifier( CLASS_ID_DATASOURCE, CLASS_NAME_BULKTAG_DATASOURCE, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), - TAGGING_TRUST))); + TAGGING_TRUST))); value.getContext().add(context); } From 1c82acb16835ea7ce3f70f8c847204f0ac487708 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 25 Jul 2022 14:26:39 +0200 Subject: [PATCH 15/33] [EOSC Context Tagging] refactoring: moved EOSC IF tagging in package eosc under bulkTag --- .../eu/dnetlib/dhp/bulktag/{ => eosc}/SparkEoscTag.java | 7 +------ .../eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml | 2 +- .../test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java | 5 +---- 3 files changed, 3 insertions(+), 11 deletions(-) rename dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/{ => eosc}/SparkEoscTag.java (96%) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscTag.java similarity index 96% rename from dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java rename to dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscTag.java index 730e8a3fe..736496641 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscTag.java @@ -1,13 +1,10 @@ -package eu.dnetlib.dhp.bulktag; +package eu.dnetlib.dhp.bulktag.eosc; import static eu.dnetlib.dhp.PropagationConstant.readPath; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.util.*; -import java.util.function.Function; -import java.util.stream.Collectors; -import java.util.stream.Stream; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; @@ -21,9 +18,7 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.*; -import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; public class SparkEoscTag { private static final Logger log = LoggerFactory.getLogger(SparkEoscTag.class); diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml index 17fc76aad..9c1bbdf72 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml @@ -226,7 +226,7 @@ yarn-cluster cluster EOSC_tagging - eu.dnetlib.dhp.bulktag.SparkEoscTag + eu.dnetlib.dhp.bulktag.eosc.SparkEoscTag dhp-enrichment-${projectVersion}.jar --num-executors=${sparkExecutorNumber} diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java index 5f47da10e..17e570fdf 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java @@ -1,21 +1,18 @@ package eu.dnetlib.dhp.bulktag; -import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.ZENODO_COMMUNITY_INDICATOR; - import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; import java.util.List; +import eu.dnetlib.dhp.bulktag.eosc.SparkEoscTag; import org.apache.commons.io.FileUtils; -import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.Row; import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; import org.junit.jupiter.api.AfterAll; From 35bcd9422d60be622a0dd6f71a4a5be03513e07b Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 25 Jul 2022 15:45:22 +0200 Subject: [PATCH 16/33] [EOSC Context Tagging] removed not needed specification in path --- .../eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java index 9ad108749..e9b1d3cfd 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java @@ -62,7 +62,7 @@ public class ReadMasterDatasourceFromDB implements Closeable { final String dbUrl = parser.get("postgresUrl"); final String dbUser = parser.get("postgresUser"); final String dbPassword = parser.get("postgresPassword"); - final String hdfsPath = parser.get("hdfsPath") + "/datasourceMasters"; + final String hdfsPath = parser.get("hdfsPath"); final String hdfsNameNode = parser.get("hdfsNameNode"); try ( From d43663d30f6a3039a28ad8a6ac9723dd3fce4e9c Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 25 Jul 2022 17:54:10 +0200 Subject: [PATCH 17/33] adapted RorActionSet test, it should not create parent/child rels --- .../ror/GenerateRorActionSetJobTest.java | 22 ++++++++----------- 1 file changed, 9 insertions(+), 13 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJobTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJobTest.java index d50c1d5f3..5736bd95e 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJobTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJobTest.java @@ -2,6 +2,7 @@ package eu.dnetlib.dhp.actionmanager.ror; import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertNotNull; import java.io.FileInputStream; import java.util.List; @@ -38,25 +39,20 @@ class GenerateRorActionSetJobTest { .readValue(IOUtils.toString(getClass().getResourceAsStream("ror_org.json")), RorOrganization.class); final List> aas = GenerateRorActionSetJob.convertRorOrg(r); - Assertions.assertEquals(3, aas.size()); + Assertions.assertEquals(1, aas.size()); assertEquals(Organization.class, aas.get(0).getClazz()); - assertEquals(Relation.class, aas.get(1).getClazz()); - assertEquals(Relation.class, aas.get(2).getClazz()); final Organization o = (Organization) aas.get(0).getPayload(); - final Relation r1 = (Relation) aas.get(1).getPayload(); - final Relation r2 = (Relation) aas.get(2).getPayload(); - assertEquals(o.getId(), r1.getSource()); - assertEquals(r1.getSource(), r2.getTarget()); - assertEquals(r2.getSource(), r1.getTarget()); - assertEquals(ModelConstants.IS_PARENT_OF, r1.getRelClass()); - assertEquals(ModelConstants.IS_CHILD_OF, r2.getRelClass()); + assertNotNull(o); + + assertNotNull(o.getCountry()); + assertEquals("AU", o.getCountry().getClassid()); + + assertNotNull(o.getLegalname()); + assertEquals("Mount Stromlo Observatory", o.getLegalname().getValue()); System.out.println(mapper.writeValueAsString(o)); - System.out.println(mapper.writeValueAsString(r1)); - System.out.println(mapper.writeValueAsString(r2)); - } @Test From 67525076ec9ec4ff7b190a0bc1a15b5a31333388 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Tue, 26 Jul 2022 15:35:17 +0200 Subject: [PATCH 18/33] fixed test, now it compiles after commit a6977197b3925c520f76961cfff7b05c37a51d6f --- .../dhp/datacite/DataciteToOAFTest.scala | 17 +++++++--- .../dhp/datacite/DataciteUtilityTest.scala | 31 +++++++++++++++++++ 2 files changed, 43 insertions(+), 5 deletions(-) create mode 100644 dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteUtilityTest.scala diff --git a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala index 31784c7e9..68230b477 100644 --- a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala +++ b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala @@ -2,11 +2,14 @@ package eu.dnetlib.dhp.datacite import com.fasterxml.jackson.databind.{ObjectMapper, SerializationFeature} import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest -import eu.dnetlib.dhp.schema.oaf.Oaf +import eu.dnetlib.dhp.schema.oaf.{Dataset => OafDataset, _} import org.apache.commons.io.FileUtils import org.apache.spark.SparkConf import org.apache.spark.sql.functions.{col, count} import org.apache.spark.sql.{Dataset, Encoder, Encoders, SparkSession} +import org.json4s.DefaultFormats +import org.json4s.JsonAST.{JField, JObject, JString} +import org.json4s.jackson.JsonMethods.parse import org.junit.jupiter.api.Assertions._ import org.junit.jupiter.api.extension.ExtendWith import org.junit.jupiter.api.{AfterEach, BeforeEach, Test} @@ -45,6 +48,9 @@ class DataciteToOAFTest extends AbstractVocabularyTest { } + + + @Test def testConvert(): Unit = { @@ -70,17 +76,18 @@ class DataciteToOAFTest extends AbstractVocabularyTest { assertEquals(100, nativeSize) - spark.read.load(targetPath).printSchema(); + val result: Dataset[String] = spark.read.text(targetPath).as[String].map(DataciteUtilityTest.convertToOAF)(Encoders.STRING) + + + - val result: Dataset[Oaf] = spark.read.load(targetPath).as[Oaf] result - .map(s => s.getClass.getSimpleName) .groupBy(col("value").alias("class")) .agg(count("value").alias("Total")) .show(false) - val t = spark.read.load(targetPath).count() + val t = spark.read.text(targetPath).as[String].count() assertTrue(t > 0) diff --git a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteUtilityTest.scala b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteUtilityTest.scala new file mode 100644 index 000000000..04d3c4a58 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteUtilityTest.scala @@ -0,0 +1,31 @@ +package eu.dnetlib.dhp.datacite + +import org.json4s.DefaultFormats +import org.json4s.JsonAST.{JField, JObject, JString} +import org.json4s.jackson.JsonMethods.parse + +object DataciteUtilityTest { + + def convertToOAF(input:String) : String = { + implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats + lazy val json = parse(input) + + + val isRelation:String = (json \\ "source").extractOrElse("NULL") + + if (isRelation != "NULL") { + return "Relation" + } + + val iType: List[String] = for { + JObject(instance) <- json \\ "instance" + JField("instancetype", JObject(instancetype)) <- instance + JField("classname", JString(classname)) <- instancetype + + } yield classname + + val l:String =iType.head.toLowerCase() + l + } + +} From ed98a6d9d04aafd8ed32212e3e77040d1f8338e0 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 28 Jul 2022 10:15:14 +0200 Subject: [PATCH 19/33] [Datacite mapping] include the older datacite prefixed OpenAIRE id among the originalId[] --- .../dnetlib/dhp/datacite/DataciteToOAFTransformation.scala | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala index ff966aaea..a7863d144 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala @@ -584,7 +584,12 @@ object DataciteToOAFTransformation { JField("awardUri", JString(awardUri)) <- fundingReferences } yield awardUri + val oid = result.getId result.setId(IdentifierFactory.createIdentifier(result)) + if (!result.getId.equalsIgnoreCase(oid)) { + result.getOriginalId.add(oid) + } + var relations: List[Relation] = awardUris.flatMap(a => get_projectRelation(a, result.getId)).filter(r => r != null) From 1dd1e4fe3a224935d3c021f09ae4284e2a22b29e Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 28 Jul 2022 11:27:08 +0200 Subject: [PATCH 20/33] extended test for mapping project_organization relations --- .../raw/MigrateDbEntitiesApplication.java | 2 +- .../raw/MigrateDbEntitiesApplicationTest.java | 62 ++++++++++++++----- .../projectorganization_resultset_entry.json | 17 +++-- 3 files changed, 57 insertions(+), 24 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java index 8296e99cd..f40d3d19b 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java @@ -440,7 +440,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i final List properties = Lists .newArrayList( - keyValue("contribution", String.valueOf(rs.getDouble("totalcost"))), + keyValue("contribution", String.valueOf(rs.getDouble("contribution"))), keyValue("currency", rs.getString("currency"))); final Relation r1 = OafMapperUtils diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java index 9048a22ea..06947103a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java @@ -1,9 +1,7 @@ package eu.dnetlib.dhp.oa.graph.raw; -import static org.junit.jupiter.api.Assertions.assertEquals; -import static org.junit.jupiter.api.Assertions.assertNotNull; -import static org.junit.jupiter.api.Assertions.assertTrue; +import static org.junit.jupiter.api.Assertions.*; import static org.mockito.ArgumentMatchers.anyString; import static org.mockito.Mockito.lenient; @@ -31,11 +29,12 @@ import com.fasterxml.jackson.core.type.TypeReference; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; +import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; @ExtendWith(MockitoExtension.class) -public class MigrateDbEntitiesApplicationTest { +class MigrateDbEntitiesApplicationTest { private MigrateDbEntitiesApplication app; @@ -61,7 +60,7 @@ public class MigrateDbEntitiesApplicationTest { } @Test - public void testProcessService() throws Exception { + void testProcessService() throws Exception { final List fields = prepareMocks("services_resultset_entry.json"); final List list = app.processService(rs); @@ -74,7 +73,7 @@ public class MigrateDbEntitiesApplicationTest { .getCollectedfrom() .stream() .map(KeyValue::getKey) - .forEach(dsId -> assertValidId(dsId)); + .forEach(this::assertValidId); assertEquals(1, ds.getPid().size()); assertEquals("r3d100010218", ds.getPid().get(0).getValue()); @@ -163,14 +162,14 @@ public class MigrateDbEntitiesApplicationTest { .stream() .map(Qualifier::getSchemeid) .collect(Collectors.toCollection(HashSet::new)); - assertTrue(cpSchemeId.size() == 1); + assertEquals(1,cpSchemeId.size()); assertTrue(cpSchemeId.contains("eosc:contentpolicies")); HashSet cpSchemeName = ds .getContentpolicies() .stream() .map(Qualifier::getSchemename) .collect(Collectors.toCollection(HashSet::new)); - assertTrue(cpSchemeName.size() == 1); + assertEquals(1, cpSchemeName.size()); assertTrue(cpSchemeName.contains("eosc:contentpolicies")); assertEquals(2, ds.getContentpolicies().size()); assertEquals("Taxonomic classification", ds.getContentpolicies().get(0).getClassid()); @@ -193,7 +192,7 @@ public class MigrateDbEntitiesApplicationTest { } @Test - public void testProcessProject() throws Exception { + void testProcessProject() throws Exception { final List fields = prepareMocks("projects_resultset_entry.json"); final List list = app.processProject(rs); @@ -211,7 +210,7 @@ public class MigrateDbEntitiesApplicationTest { } @Test - public void testProcessOrganization() throws Exception { + void testProcessOrganization() throws Exception { final List fields = prepareMocks("organizations_resultset_entry.json"); final List list = app.processOrganization(rs); @@ -238,7 +237,7 @@ public class MigrateDbEntitiesApplicationTest { } @Test - public void testProcessDatasourceOrganization() throws Exception { + void testProcessDatasourceOrganization() throws Exception { final List fields = prepareMocks("datasourceorganization_resultset_entry.json"); final List list = app.processServiceOrganization(rs); @@ -255,7 +254,7 @@ public class MigrateDbEntitiesApplicationTest { } @Test - public void testProcessProjectOrganization() throws Exception { + void testProcessProjectOrganization() throws Exception { final List fields = prepareMocks("projectorganization_resultset_entry.json"); final List list = app.processProjectOrganization(rs); @@ -271,6 +270,38 @@ public class MigrateDbEntitiesApplicationTest { assertEquals(r2.getSource(), r1.getTarget()); assertValidId(r1.getCollectedfrom().get(0).getKey()); assertValidId(r2.getCollectedfrom().get(0).getKey()); + + assertEquals(ModelConstants.PROJECT_ORGANIZATION, r1.getRelType()); + assertEquals(ModelConstants.PROJECT_ORGANIZATION, r2.getRelType()); + + assertEquals(ModelConstants.PARTICIPATION, r1.getSubRelType()); + assertEquals(ModelConstants.PARTICIPATION, r2.getSubRelType()); + + if (r1.getSource().startsWith("40")) { + assertEquals(ModelConstants.HAS_PARTICIPANT, r1.getRelClass()); + assertEquals(ModelConstants.IS_PARTICIPANT, r2.getRelClass()); + } else if (r1.getSource().startsWith("20")) { + assertEquals(ModelConstants.IS_PARTICIPANT, r1.getRelClass()); + assertEquals(ModelConstants.HAS_PARTICIPANT, r2.getRelClass()); + } + + assertNotNull(r1.getProperties()); + checkProperty(r1, "contribution", "436754.0"); + checkProperty(r2, "contribution", "436754.0"); + + checkProperty(r1, "currency","EUR"); + checkProperty(r2, "currency", "EUR"); + } + + private void checkProperty(Relation r, String property, String value) { + final List p = r + .getProperties() + .stream() + .filter(kv -> kv.getKey().equals(property)) + .collect(Collectors.toList()); + assertFalse(p.isEmpty()); + assertEquals(1, p.size()); + assertEquals(value, p.get(0).getValue()); } @Test @@ -289,7 +320,7 @@ public class MigrateDbEntitiesApplicationTest { } @Test - public void testProcessClaims_rels() throws Exception { + void testProcessClaims_rels() throws Exception { final List fields = prepareMocks("claimsrel_resultset_entry.json"); final List list = app.processClaims(rs); @@ -320,9 +351,6 @@ public class MigrateDbEntitiesApplicationTest { assertValidId(r1.getCollectedfrom().get(0).getKey()); assertValidId(r2.getCollectedfrom().get(0).getKey()); - - // System.out.println(new ObjectMapper().writeValueAsString(r1)); - // System.out.println(new ObjectMapper().writeValueAsString(r2)); } private List prepareMocks(final String jsonFile) throws IOException, SQLException { @@ -385,7 +413,7 @@ public class MigrateDbEntitiesApplicationTest { final String[] values = ((List) tf.getValue()) .stream() .filter(Objects::nonNull) - .map(o -> o.toString()) + .map(Object::toString) .toArray(String[]::new); Mockito.when(arr.getArray()).thenReturn(values); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/projectorganization_resultset_entry.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/projectorganization_resultset_entry.json index a3305926d..02cebae38 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/projectorganization_resultset_entry.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/projectorganization_resultset_entry.json @@ -2,12 +2,12 @@ { "field": "project", "type": "string", - "value": "nsf_________::1700003" + "value": "corda__h2020::824273" }, { "field": "resporganization", "type": "string", - "value": "nsf_________::University_of_Notre_Dame" + "value": "corda__h2020::999945647" }, { "field": "participantnumber", @@ -16,8 +16,13 @@ }, { "field": "contribution", - "type": "not_used", - "value": null + "type": "double", + "value": 436754 + }, + { + "field": "currency", + "type": "string", + "value": "EUR" }, { "field": "startdate", @@ -52,12 +57,12 @@ { "field": "collectedfromid", "type": "string", - "value": "openaire____::nsf" + "value": "openaire____::corda_h2020" }, { "field": "collectedfromname", "type": "string", - "value": "NSF - National Science Foundation" + "value": "CORDA - COmmon Research DAta Warehouse - Horizon 2020" }, { "field": "semantics", From 3329b6ce6bdccdab25c4bb900cc8ad4f78d8c77c Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 29 Jul 2022 10:54:20 +0200 Subject: [PATCH 21/33] [EOSC TAG] added fix for NPE on subjects --- .../src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscTag.java | 2 ++ 1 file changed, 2 insertions(+) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscTag.java index 736496641..a96e6a3bc 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscTag.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscTag.java @@ -183,6 +183,8 @@ public class SparkEoscTag { } private static boolean containsCriteriaNotebook(Software s) { + if(!Optional.ofNullable(s.getSubject()).isPresent()) + return false; if (s.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("jupyter"))) return true; if (s From 0727f0ef481f783dbfcfd670bd4d91ee88a34f7a Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 29 Jul 2022 11:55:34 +0200 Subject: [PATCH 22/33] [EOSC tag] avoid NPEs --- .../dhp/bulktag/eosc/SparkEoscTag.java | 41 +++++++++++-------- .../dnetlib/dhp/bulktag/EOSCTagJobTest.java | 2 +- 2 files changed, 25 insertions(+), 18 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscTag.java index a96e6a3bc..c131399cc 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscTag.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscTag.java @@ -23,6 +23,10 @@ import eu.dnetlib.dhp.schema.oaf.*; public class SparkEoscTag { private static final Logger log = LoggerFactory.getLogger(SparkEoscTag.class); public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + public static final String EOSC_GALAXY_WORKFLOW = "EOSC::Galaxy Workflow"; + public static final String EOSC_TWITTER_DATA = "EOSC::Twitter Data"; + public static final String EOSC_JUPYTER_NOTEBOOK = "EOSC::Jupyter Notebook"; + public static final String COMPLIES_WITH = "compliesWith"; public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils @@ -76,8 +80,8 @@ public class SparkEoscTag { if (!Optional.ofNullable(s.getEoscifguidelines()).isPresent()) s.setEoscifguidelines(new ArrayList<>()); addEIG( - s.getEoscifguidelines(), "EOSC::Jupyter Notebook", "EOSC::Jupyter Notebook", "", - "compliesWith"); + s.getEoscifguidelines(), EOSC_JUPYTER_NOTEBOOK, EOSC_JUPYTER_NOTEBOOK, "", + COMPLIES_WITH); } if (containsCriteriaGalaxy(s)) { @@ -85,7 +89,7 @@ public class SparkEoscTag { s.setEoscifguidelines(new ArrayList<>()); addEIG( - s.getEoscifguidelines(), "EOSC::Galaxy Workflow", "EOSC::Galaxy Workflow", "", "compliesWith"); + s.getEoscifguidelines(), EOSC_GALAXY_WORKFLOW, EOSC_GALAXY_WORKFLOW, "", COMPLIES_WITH); } return s; }, Encoders.bean(Software.class)) @@ -108,11 +112,11 @@ public class SparkEoscTag { if (containsCriteriaGalaxy(orp)) { addEIG( - orp.getEoscifguidelines(), "EOSC::Galaxy Workflow", "EOSC::Galaxy Workflow", "", - "compliesWith"); + orp.getEoscifguidelines(), EOSC_GALAXY_WORKFLOW, EOSC_GALAXY_WORKFLOW, "", + COMPLIES_WITH); } if (containscriteriaTwitter(orp)) { - addEIG(orp.getEoscifguidelines(), "EOSC::Twitter Data", "EOSC::Twitter Data", "", "compliesWith"); + addEIG(orp.getEoscifguidelines(), EOSC_TWITTER_DATA, EOSC_TWITTER_DATA, "", COMPLIES_WITH); } return orp; }, Encoders.bean(OtherResearchProduct.class)) @@ -133,7 +137,7 @@ public class SparkEoscTag { if (!Optional.ofNullable(d.getEoscifguidelines()).isPresent()) d.setEoscifguidelines(new ArrayList<>()); if (containscriteriaTwitter(d)) { - addEIG(d.getEoscifguidelines(), "EOSC::Twitter Data", "EOSC::Twitter Data", "", "compliesWith"); + addEIG(d.getEoscifguidelines(), EOSC_TWITTER_DATA, EOSC_TWITTER_DATA, "", COMPLIES_WITH); } return d; }, Encoders.bean(Dataset.class)) @@ -163,10 +167,12 @@ public class SparkEoscTag { (words.contains("data") || words.contains("dataset"))) return true; - if (r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("twitter")) && - r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("data"))) - return true; - return false; + return Optional + .ofNullable(r.getSubject()) + .map( + s -> s.stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("twitter")) && + s.stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("data"))) + .orElse(false); } private static boolean containsCriteriaGalaxy(Result r) { @@ -176,14 +182,16 @@ public class SparkEoscTag { words.contains("workflow")) return true; - if (r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("galaxy")) && - r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("workflow"))) - return true; - return false; + return Optional + .ofNullable(r.getSubject()) + .map( + s -> s.stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("galaxy")) && + s.stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("workflow"))) + .orElse(false); } private static boolean containsCriteriaNotebook(Software s) { - if(!Optional.ofNullable(s.getSubject()).isPresent()) + if (!Optional.ofNullable(s.getSubject()).isPresent()) return false; if (s.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("jupyter"))) return true; @@ -225,6 +233,5 @@ public class SparkEoscTag { Arrays.asList(t.getValue().toLowerCase().replaceAll("[^a-zA-Z ]", "").split(" "))))); return words; - } } diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java index 17e570fdf..bfe4f6448 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java @@ -6,7 +6,6 @@ import java.nio.file.Files; import java.nio.file.Path; import java.util.List; -import eu.dnetlib.dhp.bulktag.eosc.SparkEoscTag; import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; @@ -24,6 +23,7 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.bulktag.eosc.SparkEoscTag; import eu.dnetlib.dhp.schema.oaf.*; public class EOSCTagJobTest { From f62c4e05cd239830628154dc09fb7d386f135201 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 29 Jul 2022 11:56:01 +0200 Subject: [PATCH 23/33] code formatting --- .../dnetlib/dhp/sx/bio/pubmed/PMArticle.java | 1 - .../dhp/sx/bio/pubmed/PubMedToOaf.scala | 40 +++++++-------- .../dhp/datacite/DataciteToOAFTest.scala | 10 +--- .../dhp/datacite/DataciteUtilityTest.scala | 11 ++-- .../dnetlib/dhp/sx/bio/BioScholixTest.scala | 51 ++++++++----------- .../raw/MigrateDbEntitiesApplicationTest.java | 12 ++--- 6 files changed, 53 insertions(+), 72 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMArticle.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMArticle.java index 9287a8cdd..3fb814606 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMArticle.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMArticle.java @@ -255,7 +255,6 @@ public class PMArticle implements Serializable { return grants; } - public String getPmcId() { return pmcId; } diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala index 24a1fa62b..42bafc93e 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala @@ -56,13 +56,11 @@ object PubMedToOaf { null } - - def createOriginalOpenaireId(article:PMArticle) :String = { + def createOriginalOpenaireId(article: PMArticle): String = { if (StringUtils.isNotEmpty(article.getPmcId)) { - val md5 = DHPUtils.md5(s"$OAI_HEADER${article.getPmcId.replace("PMC","")}") + val md5 = DHPUtils.md5(s"$OAI_HEADER${article.getPmcId.replace("PMC", "")}") s"$OLD_PMC_PREFIX$md5" - } - else + } else null } @@ -142,26 +140,24 @@ object PubMedToOaf { val pidList = ListBuffer[StructuredProperty]() pidList += OafMapperUtils.structuredProperty( - article.getPmid, - PidType.pmid.toString, - PidType.pmid.toString, + article.getPmid, + PidType.pmid.toString, + PidType.pmid.toString, + ModelConstants.DNET_PID_TYPES, + ModelConstants.DNET_PID_TYPES, + dataInfo + ) + + if (StringUtils.isNotBlank(article.getPmcId)) { + pidList += OafMapperUtils.structuredProperty( + article.getPmcId, + PidType.pmc.toString, + PidType.pmc.toString, ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES, dataInfo ) - - - if (StringUtils.isNotBlank(article.getPmcId)) - { - pidList += OafMapperUtils.structuredProperty( - article.getPmcId, - PidType.pmc.toString, - PidType.pmc.toString, - ModelConstants.DNET_PID_TYPES, - ModelConstants.DNET_PID_TYPES, - dataInfo - ) - } + } if (pidList == null) return null @@ -297,7 +293,7 @@ object PubMedToOaf { if (StringUtils.isNotEmpty(article.getPmcId)) { val originalIDS = ListBuffer[String]() originalIDS += createOriginalOpenaireId(article) - pidList.map(s => s.getValue).foreach(p =>originalIDS += p) + pidList.map(s => s.getValue).foreach(p => originalIDS += p) result.setOriginalId(originalIDS.asJava) } else result.setOriginalId(pidList.map(s => s.getValue).asJava) diff --git a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala index 68230b477..48da049da 100644 --- a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala +++ b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala @@ -48,9 +48,6 @@ class DataciteToOAFTest extends AbstractVocabularyTest { } - - - @Test def testConvert(): Unit = { @@ -76,11 +73,8 @@ class DataciteToOAFTest extends AbstractVocabularyTest { assertEquals(100, nativeSize) - val result: Dataset[String] = spark.read.text(targetPath).as[String].map(DataciteUtilityTest.convertToOAF)(Encoders.STRING) - - - - + val result: Dataset[String] = + spark.read.text(targetPath).as[String].map(DataciteUtilityTest.convertToOAF)(Encoders.STRING) result .groupBy(col("value").alias("class")) diff --git a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteUtilityTest.scala b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteUtilityTest.scala index 04d3c4a58..942e0958e 100644 --- a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteUtilityTest.scala +++ b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteUtilityTest.scala @@ -6,25 +6,24 @@ import org.json4s.jackson.JsonMethods.parse object DataciteUtilityTest { - def convertToOAF(input:String) : String = { + def convertToOAF(input: String): String = { implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats lazy val json = parse(input) - - val isRelation:String = (json \\ "source").extractOrElse("NULL") + val isRelation: String = (json \\ "source").extractOrElse("NULL") if (isRelation != "NULL") { return "Relation" } val iType: List[String] = for { - JObject(instance) <- json \\ "instance" + JObject(instance) <- json \\ "instance" JField("instancetype", JObject(instancetype)) <- instance - JField("classname", JString(classname)) <- instancetype + JField("classname", JString(classname)) <- instancetype } yield classname - val l:String =iType.head.toLowerCase() + val l: String = iType.head.toLowerCase() l } diff --git a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala index b021e5e07..827d23e72 100644 --- a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala +++ b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala @@ -76,12 +76,11 @@ class BioScholixTest extends AbstractVocabularyTest { } - - private def checkPMArticle(article:PMArticle): Unit = { + private def checkPMArticle(article: PMArticle): Unit = { assertNotNull(article.getPmid) assertNotNull(article.getTitle) assertNotNull(article.getAuthors) - article.getAuthors.asScala.foreach{a => + article.getAuthors.asScala.foreach { a => assertNotNull(a) assertNotNull(a.getFullName) } @@ -89,20 +88,21 @@ class BioScholixTest extends AbstractVocabularyTest { } @Test - def testParsingPubmedXML():Unit = { - val xml = new XMLEventReader(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml"))) + def testParsingPubmedXML(): Unit = { + val xml = new XMLEventReader( + Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml")) + ) val parser = new PMParser(xml) parser.foreach(checkPMArticle) } - - private def checkPubmedPublication(o:Oaf): Unit = { + private def checkPubmedPublication(o: Oaf): Unit = { assertTrue(o.isInstanceOf[Publication]) - val p:Publication = o.asInstanceOf[Publication] + val p: Publication = o.asInstanceOf[Publication] assertNotNull(p.getId) assertNotNull(p.getTitle) - p.getTitle.asScala.foreach(t =>assertNotNull(t.getValue)) - p.getAuthor.asScala.foreach(a =>assertNotNull(a.getFullname)) + p.getTitle.asScala.foreach(t => assertNotNull(t.getValue)) + p.getAuthor.asScala.foreach(a => assertNotNull(a.getFullname)) assertNotNull(p.getInstance()) p.getInstance().asScala.foreach { i => assertNotNull(i.getCollectedfrom) @@ -112,28 +112,26 @@ class BioScholixTest extends AbstractVocabularyTest { assertNotNull(p.getOriginalId) p.getOriginalId.asScala.foreach(oId => assertNotNull(oId)) - - val hasPMC = p.getInstance().asScala.exists(i => i.getPid.asScala.exists(pid => pid.getQualifier.getClassid.equalsIgnoreCase(PidType.pmc.toString))) - - + val hasPMC = p + .getInstance() + .asScala + .exists(i => i.getPid.asScala.exists(pid => pid.getQualifier.getClassid.equalsIgnoreCase(PidType.pmc.toString))) if (hasPMC) { assertTrue(p.getOriginalId.asScala.exists(oId => oId.startsWith("od_______267::"))) } } - @Test - def testPubmedOriginalID():Unit = { - val article:PMArticle = new PMArticle - + def testPubmedOriginalID(): Unit = { + val article: PMArticle = new PMArticle article.setPmid("1234") article.setTitle("a Title") // VERIFY PUBLICATION IS NOT NULL - article.getPublicationTypes.add( new PMSubject("article",null, null)) + article.getPublicationTypes.add(new PMSubject("article", null, null)) var publication = PubMedToOaf.convert(article, vocabularies).asInstanceOf[Publication] assertNotNull(publication) assertEquals("50|pmid________::81dc9bdb52d04dc20036dbd8313ed055", publication.getId) @@ -146,30 +144,25 @@ class BioScholixTest extends AbstractVocabularyTest { // VERIFY ORIGINAL ID GENERATE IN OLD WAY USING PMC IDENTIFIER EXISTS - - val oldOpenaireID ="od_______267::0000072375bc0e68fa09d4e6b7658248" + val oldOpenaireID = "od_______267::0000072375bc0e68fa09d4e6b7658248" val hasOldOpenAIREID = publication.getOriginalId.asScala.exists(o => o.equalsIgnoreCase(oldOpenaireID)) assertTrue(hasOldOpenAIREID) } - @Test - def testPubmedMapping() :Unit = { + def testPubmedMapping(): Unit = { - val xml = new XMLEventReader(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml"))) + val xml = new XMLEventReader( + Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml")) + ) val parser = new PMParser(xml) val results = ListBuffer[Oaf]() parser.foreach(x => results += PubMedToOaf.convert(x, vocabularies)) - - - results.foreach(checkPubmedPublication) - - } @Test diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java index 06947103a..069edc5a6 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java @@ -162,7 +162,7 @@ class MigrateDbEntitiesApplicationTest { .stream() .map(Qualifier::getSchemeid) .collect(Collectors.toCollection(HashSet::new)); - assertEquals(1,cpSchemeId.size()); + assertEquals(1, cpSchemeId.size()); assertTrue(cpSchemeId.contains("eosc:contentpolicies")); HashSet cpSchemeName = ds .getContentpolicies() @@ -289,16 +289,16 @@ class MigrateDbEntitiesApplicationTest { checkProperty(r1, "contribution", "436754.0"); checkProperty(r2, "contribution", "436754.0"); - checkProperty(r1, "currency","EUR"); + checkProperty(r1, "currency", "EUR"); checkProperty(r2, "currency", "EUR"); } private void checkProperty(Relation r, String property, String value) { final List p = r - .getProperties() - .stream() - .filter(kv -> kv.getKey().equals(property)) - .collect(Collectors.toList()); + .getProperties() + .stream() + .filter(kv -> kv.getKey().equals(property)) + .collect(Collectors.toList()); assertFalse(p.isEmpty()); assertEquals(1, p.size()); assertEquals(value, p.get(0).getValue()); From 92e48f12f70ce7631a78229f1a4ca4da7ace6e48 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 29 Jul 2022 13:54:00 +0200 Subject: [PATCH 24/33] [metadata collection] updated collector plugin name --- .../main/java/eu/dnetlib/dhp/collection/CollectorWorker.java | 2 +- .../java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java index 9d9400068..c35fbb497 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java @@ -118,7 +118,7 @@ public class CollectorWorker extends ReportingJob { return new RestCollectorPlugin(clientParams); case file: return new FileCollectorPlugin(fileSystem); - case fileGZip: + case fileGzip: return new FileGZipCollectorPlugin(fileSystem); case other: final CollectorPlugin.NAME.OTHER_NAME plugin = Optional diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java index 08084e22a..a19ca5c68 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java @@ -10,7 +10,7 @@ import eu.dnetlib.dhp.common.collection.CollectorException; public interface CollectorPlugin { enum NAME { - oai, other, rest_json2xml, file, fileGZip; + oai, other, rest_json2xml, file, fileGzip; public enum OTHER_NAME { mdstore_mongodb_dump, mdstore_mongodb From 9886fe87ecab8d90473a3c62b5cb83c080ec6864 Mon Sep 17 00:00:00 2001 From: Antonis Lempesis Date: Fri, 29 Jul 2022 16:34:50 +0300 Subject: [PATCH 25/33] - Added FOS classification - Added extra orgs in monitor - Fixed result-project and organization-project tables --- .../oozie_app/scripts/step20-createMonitorDB.sql | 12 +++++++++++- .../dhp/oa/graph/stats/oozie_app/scripts/step6.sql | 4 ++-- .../dhp/oa/graph/stats/oozie_app/scripts/step7.sql | 13 ++++++++++++- 3 files changed, 25 insertions(+), 4 deletions(-) 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 7412910a9..cc6b69e34 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 @@ -38,7 +38,14 @@ create table TARGET.result stored as parquet as 'openorgs____::ec3665affa01aeafa28b7852c4176dbd', --Rudjer Boskovic Institute 'openorgs____::5f31346d444a7f06a28c880fb170b0f6', --Ghent University 'openorgs____::2dbe47117fd5409f9c61620813456632', --University of Luxembourg - 'openorgs____::6445d7758d3a40c4d997953b6632a368' --National Institute of Informatics (NII) + 'openorgs____::6445d7758d3a40c4d997953b6632a368', --National Institute of Informatics (NII) + + 'openorgs____::b77c01aa15de3675da34277d48de2ec1', -- Valencia Catholic University Saint Vincent Martyr + 'openorgs____::7fe2f66cdc43983c6b24816bfe9cf6a0', -- Unviersity of Warsaw + 'openorgs____::15e7921fc50d9aa1229a82a84429419e', -- University Of Thessaly + 'openorgs____::11f7919dadc8f8a7251af54bba60c956', -- Technical University of Crete + 'openorgs____::84f0c5f5dbb6daf42748485924efde4b', -- University of Piraeus + 'openorgs____::4ac562f0376fce3539504567649cb373' -- University of Patras ) )) foo; compute stats TARGET.result; @@ -107,6 +114,9 @@ compute stats TARGET.result_sources; create table TARGET.result_topics stored as parquet as select * from SOURCE.result_topics orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.result_topics; +create table TARGET.result_fos stored as parquet as select * from SOURCE.result_fos orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.result_fos; + create view TARGET.foo1 as select * from SOURCE.result_result rr where rr.source in (select id from TARGET.result); create view TARGET.foo2 as select * from SOURCE.result_result rr where rr.target in (select id from TARGET.result); create table TARGET.result_result STORED AS PARQUET as select distinct * from (select * from TARGET.foo1 union all select * from TARGET.foo2) foufou; diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql index dc7c01046..5461afde6 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql @@ -11,13 +11,13 @@ where p.datainfo.deletedbyinference=false and p.datainfo.invisible=false; CREATE TABLE ${stats_db_name}.project_organizations STORED AS PARQUET AS SELECT substr(r.source, 4) AS id, substr(r.target, 4) AS organization from ${openaire_db_name}.relation r -WHERE r.reltype = 'projectOrganization' +WHERE r.reltype = 'projectOrganization' and r.source like '40|%' and r.datainfo.deletedbyinference = false and r.datainfo.invisible=false; CREATE TABLE ${stats_db_name}.project_results STORED AS PARQUET AS SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS result, r.datainfo.provenanceaction.classname as provenance FROM ${openaire_db_name}.relation r -WHERE r.reltype = 'resultProject' +WHERE r.reltype = 'resultProject' and r.target like '40|%' and r.datainfo.deletedbyinference = false and r.datainfo.invisible=false; create table ${stats_db_name}.project_classification STORED AS PARQUET as diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql index b5eba6111..1514ecf52 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql @@ -123,6 +123,16 @@ UNION ALL SELECT * FROM ${stats_db_name}.otherresearchproduct_topics; +create table ${stats_db_name}.result_fos stored as parquet as +with + lvl1 as (select id, topic from ${stats_db_name}.result_topics where topic like '__ %' and type='Fields of Science and Technology classification'), + lvl2 as (select id, topic from ${stats_db_name}.result_topics where topic like '____ %' and type='Fields of Science and Technology classification'), + lvl3 as (select id, topic from ${stats_db_name}.result_topics where topic like '______ %' and type='Fields of Science and Technology classification') +select lvl1.id, lvl1.topic as lvl1, lvl2.topic as lvl2, lvl3.topic as lvl3 +from lvl1 + join lvl2 on lvl1.id=lvl2.id and substr(lvl2.topic, 1, 2)=substr(lvl1.topic, 1, 2) + join lvl3 on lvl3.id=lvl1.id and substr(lvl3.topic, 1, 4)=substr(lvl2.topic, 1, 4); + CREATE TABLE ${stats_db_name}.result_organization STORED AS PARQUET AS SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS organization FROM ${openaire_db_name}.relation r @@ -134,4 +144,5 @@ CREATE TABLE ${stats_db_name}.result_projects STORED AS PARQUET AS select pr.result AS id, pr.id AS project, datediff(p.enddate, p.startdate) AS daysfromend, pr.provenance as provenance FROM ${stats_db_name}.result r JOIN ${stats_db_name}.project_results pr ON r.id = pr.result - JOIN ${stats_db_name}.project_tmp p ON p.id = pr.id; \ No newline at end of file + JOIN ${stats_db_name}.project_tmp p ON p.id = pr.id; + From 209c7e9dab323932dba65bb88addf2c8ab848d92 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 1 Aug 2022 09:05:35 +0200 Subject: [PATCH 26/33] [datacite] avoid UnsupportedOperationException --- .../eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala index a7863d144..0f82ecadf 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala @@ -587,7 +587,7 @@ object DataciteToOAFTransformation { val oid = result.getId result.setId(IdentifierFactory.createIdentifier(result)) if (!result.getId.equalsIgnoreCase(oid)) { - result.getOriginalId.add(oid) + result.setOriginalId((oid::List(doi)).asJava) } var relations: List[Relation] = From 1778d40c40654db9bde707ee2ffdc4e3f922bce9 Mon Sep 17 00:00:00 2001 From: Antonis Lempesis Date: Tue, 2 Aug 2022 13:39:34 +0300 Subject: [PATCH 27/33] latest version of indicators --- .../scripts/step16-createIndicatorsTables.sql | 993 +++++++++++++----- 1 file changed, 709 insertions(+), 284 deletions(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql index db40cf973..25776316b 100755 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql @@ -1,60 +1,62 @@ ----- Sprint 1 ---- +-- Sprint 1 ---- create table indi_pub_green_oa stored as parquet as select distinct p.id, coalesce(green_oa, 0) as green_oa from publication p -left outer join ( -select p.id, 1 as green_oa -from publication p -join result_instance ri on ri.id = p.id -join datasource on datasource.id = ri.hostedby -where datasource.type like '%Repository%' -and (ri.accessright = 'Open Access' -or ri.accessright = 'Embargo' or ri.accessright = 'Open Source')) tmp -on p.id= tmp.id; + left outer join ( + select p.id, 1 as green_oa + from publication p + join result_instance ri on ri.id = p.id + join datasource on datasource.id = ri.hostedby + where datasource.type like '%Repository%' + and (ri.accessright = 'Open Access' + or ri.accessright = 'Embargo' or ri.accessright = 'Open Source')) tmp + on p.id= tmp.id; compute stats indi_pub_green_oa; create table indi_pub_grey_lit stored as parquet as select distinct p.id, coalesce(grey_lit, 0) as grey_lit from publication p -left outer join ( -select p.id, 1 as grey_lit -from publication p -join result_classifications rt on rt.id = p.id -where rt.type not in ('Article','Part of book or chapter of book','Book','Doctoral thesis','Master thesis','Data Paper', 'Thesis', 'Bachelor thesis', 'Conference object') and -not exists (select 1 from result_classifications rc where type ='Other literature type' and rc.id=p.id)) tmp on p.id=tmp.id; + left outer join ( + select p.id, 1 as grey_lit + from publication p + join result_classifications rt on rt.id = p.id + where rt.type not in ('Article','Part of book or chapter of book','Book','Doctoral thesis','Master thesis','Data Paper', 'Thesis', 'Bachelor thesis', 'Conference object') and + not exists (select 1 from result_classifications rc where type ='Other literature type' + and rc.id=p.id)) tmp on p.id=tmp.id; compute stats indi_pub_grey_lit; create table indi_pub_doi_from_crossref stored as parquet as select distinct p.id, coalesce(doi_from_crossref, 0) as doi_from_crossref from publication p -left outer join -(select ri.id, 1 as doi_from_crossref from result_instance ri -join datasource d on d.id = ri.collectedfrom -where pidtype='Digital Object Identifier' and d.name ='Crossref') tmp -on tmp.id=p.id; + left outer join + (select ri.id, 1 as doi_from_crossref from result_instance ri + join datasource d on d.id = ri.collectedfrom + where pidtype='Digital Object Identifier' and d.name ='Crossref') tmp + on tmp.id=p.id; compute stats indi_pub_doi_from_crossref; ----- Sprint 2 ---- + +-- Sprint 2 ---- create table indi_result_has_cc_licence stored as parquet as select distinct r.id, (case when lic='' or lic is null then 0 else 1 end) as has_cc_license from result r -left outer join (select r.id, license.type as lic from result r -join result_licenses as license on license.id = r.id -where lower(license.type) LIKE '%creativecommons.org%' OR lower(license.type) LIKE '%cc-%') tmp -on r.id= tmp.id; + left outer join (select r.id, license.type as lic from result r + join result_licenses as license on license.id = r.id + where lower(license.type) LIKE '%creativecommons.org%' OR lower(license.type) LIKE '%cc-%') tmp + on r.id= tmp.id; compute stats indi_result_has_cc_licence; create table indi_result_has_cc_licence_url stored as parquet as select distinct r.id, case when lic_host='' or lic_host is null then 0 else 1 end as has_cc_license_url from result r -left outer join (select r.id, lower(parse_url(license.type, "HOST")) as lic_host -from result r -join result_licenses as license on license.id = r.id -WHERE lower(parse_url(license.type, "HOST")) = "creativecommons.org") tmp -on r.id= tmp.id; + left outer join (select r.id, lower(parse_url(license.type, "HOST")) as lic_host + from result r + join result_licenses as license on license.id = r.id + WHERE lower(parse_url(license.type, "HOST")) = "creativecommons.org") tmp + on r.id= tmp.id; compute stats indi_result_has_cc_licence_url; @@ -67,8 +69,8 @@ compute stats indi_pub_has_abstract; create table indi_result_with_orcid stored as parquet as select distinct r.id, coalesce(has_orcid, 0) as has_orcid from result r -left outer join (select id, 1 as has_orcid from result_orcid) tmp -on r.id= tmp.id; + left outer join (select id, 1 as has_orcid from result_orcid) tmp + on r.id= tmp.id; compute stats indi_result_with_orcid; @@ -76,59 +78,89 @@ compute stats indi_result_with_orcid; create table indi_funded_result_with_fundref stored as parquet as select distinct r.id, coalesce(fundref, 0) as fundref from project_results r -left outer join (select distinct id, 1 as fundref from project_results -where provenance='Harvested') tmp -on r.id= tmp.id; + left outer join (select distinct id, 1 as fundref from project_results + where provenance='Harvested') tmp + on r.id= tmp.id; compute stats indi_funded_result_with_fundref; --- create table indi_result_org_country_collab stored as parquet as --- with tmp as --- (select o.id as id, o.country , ro.id as result,r.type from organization o --- join result_organization ro on o.id=ro.organization --- join result r on r.id=ro.id where o.country <> 'UNKNOWN') --- select o1.id org1,o2.country country2, o1.type, count(distinct o1.result) as collaborations --- from tmp as o1 --- join tmp as o2 on o1.result=o2.result --- where o1.id<>o2.id and o1.country<>o2.country --- group by o1.id, o1.type,o2.country; --- --- compute stats indi_result_org_country_collab; +create table indi_result_org_collab stored as parquet as +select o1.organization org1, o2.organization org2, count(distinct o1.id) as collaborations +from result_organization as o1 + join result_organization as o2 on o1.id=o2.id and o1.organization!=o2.organization +group by o1.organization, o2.organization; --- create table indi_result_org_collab stored as parquet as --- with tmp as --- (select o.id, ro.id as result,r.type from organization o --- join result_organization ro on o.id=ro.organization --- join result r on r.id=ro.id) --- select o1.id org1,o2.id org2, o1.type, count(distinct o1.result) as collaborations --- from tmp as o1 --- join tmp as o2 on o1.result=o2.result --- where o1.id<>o2.id --- group by o1.id, o2.id, o1.type; --- --- compute stats indi_result_org_collab; +compute stats indi_result_org_collab; + +create table indi_result_org_country_collab stored as parquet as + with tmp as + (select o.id as id, o.country , ro.id as result,r.type from organization o + join result_organization ro on o.id=ro.organization + join result r on r.id=ro.id where o.country <> 'UNKNOWN') +select o1.id org1,o2.country country2, o1.type, count(distinct o1.result) as collaborations +from tmp as o1 + join tmp as o2 on o1.result=o2.result +where o1.id<>o2.id and o1.country<>o2.country +group by o1.id, o1.type,o2.country; + +compute stats indi_result_org_country_collab; + +create table indi_result_org_collab stored as parquet as + with tmp as + (select o.id, ro.id as result,r.type from organization o + join result_organization ro on o.id=ro.organization + join result r on r.id=ro.id) +select o1.id org1,o2.id org2, o1.type, count(distinct o1.result) as collaborations +from tmp as o1 + join tmp as o2 on o1.result=o2.result +where o1.id<>o2.id +group by o1.id, o2.id, o1.type; + +compute stats indi_result_org_collab; + +create table indi_project_collab_org stored as parquet as +select o1.id org1,o2.id org2, count(distinct o1.project) as collaborations +from organization_projects as o1 + join organization_projects as o2 on o1.project=o2.project +where o1.id!=o2.id +group by o1.id, o2.id; + +compute stats indi_project_collab_org; + +create table indi_project_collab_org_country stored as parquet as + with tmp as + (select o.id organization, o.country , ro.project as project from organization o + join organization_projects ro on o.id=ro.id + and o.country <> 'UNKNOWN') +select o1.organization org1,o2.country country2, count(distinct o1.project) as collaborations +from tmp as o1 + join tmp as o2 on o1.project=o2.project +where o1.organization<>o2.organization and o1.country<>o2.country +group by o1.organization, o2.country; + +compute stats indi_project_collab_org_country; create table indi_funder_country_collab stored as parquet as -with tmp as (select funder, project, country from organization_projects op -join organization o on o.id=op.id -join project p on p.id=op.project -where country <> 'UNKNOWN') + with tmp as (select funder, project, country from organization_projects op + join organization o on o.id=op.id + join project p on p.id=op.project + where country <> 'UNKNOWN') select f1.funder, f1.country as country1, f2.country as country2, count(distinct f1.project) as collaborations from tmp as f1 -join tmp as f2 on f1.project=f2.project + join tmp as f2 on f1.project=f2.project where f1.country<>f2.country group by f1.funder, f2.country, f1.country; compute stats indi_funder_country_collab; create table indi_result_country_collab stored as parquet as -with tmp as -(select country, ro.id as result,r.type from organization o -join result_organization ro on o.id=ro.organization -join result r on r.id=ro.id) + with tmp as + (select country, ro.id as result,r.type from organization o + join result_organization ro on o.id=ro.organization + join result r on r.id=ro.id where country <> 'UNKNOWN') select o1.country country1, o2.country country2, o1.type, count(distinct o1.result) as collaborations from tmp as o1 -join tmp as o2 on o1.result=o2.result + join tmp as o2 on o1.result=o2.result where o1.country<>o2.country group by o1.country, o2.country, o1.type; @@ -138,255 +170,257 @@ compute stats indi_result_country_collab; create table indi_pub_diamond stored as parquet as select distinct pd.id, coalesce(in_diamond_journal, 0) as in_diamond_journal from publication_datasources pd -left outer join ( -select pd.id, 1 as in_diamond_journal from publication_datasources pd -join datasource d on d.id=pd.datasource -join stats_ext.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_online=d.issn_online) -and (ps.journal_is_in_doaj=true or ps.journal_is_oa=true) and ps.has_apc=false) tmp -on pd.id=tmp.id; + left outer join ( + select pd.id, 1 as in_diamond_journal from publication_datasources pd + join datasource d on d.id=pd.datasource + join stats_ext.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_online=d.issn_online) + and (ps.journal_is_in_doaj=true or ps.journal_is_oa=true) and ps.has_apc=false) tmp + on pd.id=tmp.id; compute stats indi_pub_diamond; create table indi_pub_hybrid stored as parquet as select distinct pd.id, coalesce(is_hybrid, 0) as is_hybrid from publication_datasources pd -left outer join ( -select pd.id, 1 as is_hybrid from publication_datasources pd -join datasource d on d.id=pd.datasource -join stats_ext.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_online=d.issn_online) -and (ps.journal_is_in_doaj=false and ps.journal_is_oa=false)) tmp -on pd.id=tmp.id; + left outer join ( + select pd.id, 1 as is_hybrid from publication_datasources pd + join datasource d on d.id=pd.datasource + join stats_ext.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_online=d.issn_online) + and (ps.journal_is_in_doaj=false and ps.journal_is_oa=false)) tmp + on pd.id=tmp.id; compute stats indi_pub_hybrid; create table indi_pub_in_transformative stored as parquet as select distinct pd.id, coalesce(is_transformative, 0) as is_transformative from publication pd -left outer join ( -select pd.id, 1 as is_transformative from publication_datasources pd -join datasource d on d.id=pd.datasource -join stats_ext.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_online=d.issn_online) -and ps.is_transformative_journal=true) tmp -on pd.id=tmp.id; + left outer join ( + select pd.id, 1 as is_transformative from publication_datasources pd + join datasource d on d.id=pd.datasource + join stats_ext.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_online=d.issn_online) + and ps.is_transformative_journal=true) tmp + on pd.id=tmp.id; compute stats indi_pub_in_transformative; create table indi_pub_closed_other_open stored as parquet as select distinct ri.id, coalesce(pub_closed_other_open, 0) as pub_closed_other_open from result_instance ri -left outer join -(select ri.id, 1 as pub_closed_other_open from result_instance ri -join publication p on p.id=ri.id -join datasource d on ri.hostedby=d.id -where d.type like '%Journal%' and ri.accessright='Closed Access' and -(p.bestlicence='Open Access' or p.bestlicence='Open Source')) tmp -on tmp.id=ri.id; + left outer join + (select ri.id, 1 as pub_closed_other_open from result_instance ri + join publication p on p.id=ri.id + join datasource d on ri.hostedby=d.id + where d.type like '%Journal%' and ri.accessright='Closed Access' and + (p.bestlicence='Open Access' or p.bestlicence='Open Source')) tmp + on tmp.id=ri.id; compute stats indi_pub_closed_other_open; + ---- Sprint 5 ---- create table indi_result_no_of_copies stored as parquet as select id, count(id) as number_of_copies from result_instance group by id; compute stats indi_result_no_of_copies; + ---- Sprint 6 ---- -create table indi_pub_gold_oa stored as parquet as -WITH gold_oa AS ( - SELECT issn_l, journal_is_in_doaj,journal_is_oa, issn_1 as issn - FROM stats_ext.oa_journals - WHERE issn_1 != "" - UNION ALL - SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_2 as issn - FROM stats_ext.oa_journals - WHERE issn_2 != "" ), -issn AS ( - SELECT * FROM - (SELECT id, issn_printed as issn - FROM datasource WHERE issn_printed IS NOT NULL - UNION - SELECT id, issn_online as issn - FROM datasource WHERE issn_online IS NOT NULL) as issn - WHERE LENGTH(issn) > 7) -SELECT DISTINCT pd.id, coalesce(is_gold, 0) as is_gold -FROM publication_datasources pd -LEFT OUTER JOIN ( - SELECT pd.id, 1 as is_gold FROM publication_datasources pd - JOIN issn on issn.id=pd.datasource - JOIN gold_oa on issn.issn = gold_oa.issn) tmp ON pd.id=tmp.id; +--create table indi_pub_gold_oa stored as parquet as +--WITH gold_oa AS ( +-- SELECT issn_l, journal_is_in_doaj,journal_is_oa, issn_1 as issn +-- FROM stats_ext.oa_journals +-- WHERE issn_1 != "" +-- UNION ALL +-- SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_2 as issn +-- FROM stats_ext.oa_journals +-- WHERE issn_2 != "" ), +--issn AS ( +-- SELECT * FROM +-- (SELECT id, issn_printed as issn +-- FROM datasource WHERE issn_printed IS NOT NULL +-- UNION +-- SELECT id, issn_online as issn +-- FROM datasource WHERE issn_online IS NOT NULL) as issn +-- WHERE LENGTH(issn) > 7) +--SELECT DISTINCT pd.id, coalesce(is_gold, 0) as is_gold +--FROM publication_datasources pd +--LEFT OUTER JOIN ( +-- SELECT pd.id, 1 as is_gold FROM publication_datasources pd +-- JOIN issn on issn.id=pd.datasource +-- JOIN gold_oa on issn.issn = gold_oa.issn) tmp ON pd.id=tmp.id; -compute stats indi_pub_gold_oa; +--compute stats indi_pub_gold_oa; +-- +--create table indi_datasets_gold_oa stored as parquet as +--WITH gold_oa AS ( +-- SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_1 as issn +-- FROM stats_ext.oa_journals +-- WHERE issn_1 != "" +-- UNION +-- ALL SELECT issn_l,journal_is_in_doaj,journal_is_oa,issn_2 as issn +-- FROM stats_ext.oa_journals +-- WHERE issn_2 != "" ), +--issn AS ( +-- SELECT * +-- FROM ( +-- SELECT id,issn_printed as issn +-- FROM datasource +-- WHERE issn_printed IS NOT NULL +-- UNION +-- SELECT id, issn_online as issn +-- FROM datasource +-- WHERE issn_online IS NOT NULL ) as issn +-- WHERE LENGTH(issn) > 7) +--SELECT DISTINCT pd.id, coalesce(is_gold, 0) as is_gold +--FROM dataset_datasources pd +--LEFT OUTER JOIN ( +-- SELECT pd.id, 1 as is_gold FROM dataset_datasources pd +-- JOIN issn on issn.id=pd.datasource +-- JOIN gold_oa on issn.issn = gold_oa.issn) tmp ON pd.id=tmp.id; +-- +--compute stats indi_datasets_gold_oa; -create table indi_datasets_gold_oa stored as parquet as -WITH gold_oa AS ( - SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_1 as issn - FROM stats_ext.oa_journals - WHERE issn_1 != "" - UNION - ALL SELECT issn_l,journal_is_in_doaj,journal_is_oa,issn_2 as issn - FROM stats_ext.oa_journals - WHERE issn_2 != "" ), -issn AS ( - SELECT * - FROM ( - SELECT id,issn_printed as issn - FROM datasource - WHERE issn_printed IS NOT NULL - UNION - SELECT id, issn_online as issn - FROM datasource - WHERE issn_online IS NOT NULL ) as issn - WHERE LENGTH(issn) > 7) -SELECT DISTINCT pd.id, coalesce(is_gold, 0) as is_gold -FROM dataset_datasources pd -LEFT OUTER JOIN ( - SELECT pd.id, 1 as is_gold FROM dataset_datasources pd - JOIN issn on issn.id=pd.datasource - JOIN gold_oa on issn.issn = gold_oa.issn) tmp ON pd.id=tmp.id; - -compute stats indi_datasets_gold_oa; - -create table indi_software_gold_oa stored as parquet as -WITH gold_oa AS ( - SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_1 as issn - FROM stats_ext.oa_journals - WHERE issn_1 != "" - UNION - ALL SELECT issn_l,journal_is_in_doaj,journal_is_oa,issn_2 as issn - FROM stats_ext.oa_journals - WHERE issn_2 != "" ), -issn AS ( - SELECT * - FROM ( - SELECT id,issn_printed as issn - FROM datasource - WHERE issn_printed IS NOT NULL - UNION - SELECT id, issn_online as issn - FROM datasource - WHERE issn_online IS NOT NULL ) as issn - WHERE LENGTH(issn) > 7) -SELECT DISTINCT pd.id, coalesce(is_gold, 0) as is_gold -FROM software_datasources pd -LEFT OUTER JOIN ( - SELECT pd.id, 1 as is_gold FROM software_datasources pd - JOIN issn on issn.id=pd.datasource - JOIN gold_oa on issn.issn = gold_oa.issn) tmp ON pd.id=tmp.id; - -compute stats indi_software_gold_oa; - -create table indi_org_findable stored as parquet as -with result_with_pid as ( - select ro.organization organization, count(distinct rp.id) no_result_with_pid from result_organization ro - join result_pids rp on rp.id=ro.id - group by ro.organization), -result_has_abstract as ( - select ro.organization organization, count(distinct rp.id) no_result_with_abstract from result_organization ro - join result rp on rp.id=ro.id where rp.abstract=true - group by ro.organization), -allresults as ( - select organization, count(distinct id) no_allresults from result_organization - group by organization), -result_with_pid_share as ( - select allresults.organization, result_with_pid.no_result_with_pid/allresults.no_allresults pid_share - from allresults - join result_with_pid on result_with_pid.organization=allresults.organization), -result_with_abstract_share as ( - select allresults.organization, result_has_abstract.no_result_with_abstract/allresults.no_allresults abstract_share - from allresults - join result_has_abstract on result_has_abstract.organization=allresults.organization) -select allresults.organization, coalesce((pid_share+abstract_share)/2,pid_share) org_findable -from allresults -join result_with_pid_share on result_with_pid_share.organization=allresults.organization -left outer join ( - select organization, abstract_share from result_with_abstract_share) tmp on tmp.organization=allresults.organization; - -compute stats indi_org_findable; - -create table indi_org_openess stored as parquet as -WITH datasets_oa as ( - SELECT ro.organization, count(dg.id) no_oadatasets FROM indi_datasets_gold_oa dg - join openaire_prod_stats.result_organization ro on dg.id=ro.id - join openaire_prod_stats.dataset ds on dg.id=ds.id - WHERE dg.is_gold=1 - group by ro.organization), -software_oa as ( - SELECT ro.organization, count(dg.id) no_oasoftware FROM indi_software_gold_oa dg - join openaire_prod_stats.result_organization ro on dg.id=ro.id - join openaire_prod_stats.software ds on dg.id=ds.id - WHERE dg.is_gold=1 - group by ro.organization), -pubs_oa as ( - SELECT ro.organization, count(dg.id) no_oapubs FROM indi_pub_gold_oa dg - join openaire_prod_stats.result_organization ro on dg.id=ro.id - join openaire_prod_stats.publication ds on dg.id=ds.id - where dg.is_gold=1 - group by ro.organization), -allpubs as ( - SELECT ro.organization organization, count(ro.id) no_allpubs FROM result_organization ro - join openaire_prod_stats.publication ps on ps.id=ro.id - group by ro.organization), -alldatasets as ( - SELECT ro.organization organization, count(ro.id) no_alldatasets FROM result_organization ro - join openaire_prod_stats.dataset ps on ps.id=ro.id - group by ro.organization), -allsoftware as ( - SELECT ro.organization organization, count(ro.id) no_allsoftware FROM result_organization ro - join openaire_prod_stats.software ps on ps.id=ro.id - group by ro.organization), -allpubsshare as ( - select pubs_oa.organization, pubs_oa.no_oapubs/allpubs.no_allpubs p from allpubs - join pubs_oa on allpubs.organization=pubs_oa.organization), -alldatasetssshare as ( - select datasets_oa.organization, datasets_oa.no_oadatasets/alldatasets.no_alldatasets c - from alldatasets - join datasets_oa on alldatasets.organization=datasets_oa.organization), -allsoftwaresshare as ( - select software_oa.organization, software_oa.no_oasoftware/allsoftware.no_allsoftware s - from allsoftware - join software_oa on allsoftware.organization=software_oa.organization) -select allpubsshare.organization, coalesce((c+p+s)/3, p) org_openess -FROM allpubsshare -left outer join ( - select organization,c from - alldatasetssshare) tmp on tmp.organization=allpubsshare.organization -left outer join ( - select organization,s from allsoftwaresshare) tmp1 on tmp1.organization=allpubsshare.organization; - -compute stats indi_org_openess; +--create table indi_software_gold_oa stored as parquet as +--WITH gold_oa AS ( +-- SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_1 as issn +-- FROM stats_ext.oa_journals +-- WHERE issn_1 != "" +-- UNION +-- ALL SELECT issn_l,journal_is_in_doaj,journal_is_oa,issn_2 as issn +-- FROM stats_ext.oa_journals +-- WHERE issn_2 != "" ), +--issn AS ( +-- SELECT * +-- FROM ( +-- SELECT id,issn_printed as issn +-- FROM datasource +-- WHERE issn_printed IS NOT NULL +-- UNION +-- SELECT id, issn_online as issn +-- FROM datasource +-- WHERE issn_online IS NOT NULL ) as issn +-- WHERE LENGTH(issn) > 7) +--SELECT DISTINCT pd.id, coalesce(is_gold, 0) as is_gold +--FROM software_datasources pd +--LEFT OUTER JOIN ( +-- SELECT pd.id, 1 as is_gold FROM software_datasources pd +-- JOIN issn on issn.id=pd.datasource +-- JOIN gold_oa on issn.issn = gold_oa.issn) tmp ON pd.id=tmp.id; +-- +--compute stats indi_software_gold_oa; +--create table indi_org_findable stored as parquet as +--with result_with_pid as ( +-- select ro.organization organization, count(distinct rp.id) no_result_with_pid from result_organization ro +-- join result_pids rp on rp.id=ro.id +-- group by ro.organization), +--result_has_abstract as ( +-- select ro.organization organization, count(distinct rp.id) no_result_with_abstract from result_organization ro +-- join result rp on rp.id=ro.id where rp.abstract=true +-- group by ro.organization), +--allresults as ( +-- select organization, count(distinct id) no_allresults from result_organization +-- group by organization), +--result_with_pid_share as ( +-- select allresults.organization, result_with_pid.no_result_with_pid/allresults.no_allresults pid_share +-- from allresults +-- join result_with_pid on result_with_pid.organization=allresults.organization), +--result_with_abstract_share as ( +-- select allresults.organization, result_has_abstract.no_result_with_abstract/allresults.no_allresults abstract_share +-- from allresults +-- join result_has_abstract on result_has_abstract.organization=allresults.organization) +--select allresults.organization, coalesce((pid_share+abstract_share)/2,pid_share) org_findable +--from allresults +--join result_with_pid_share on result_with_pid_share.organization=allresults.organization +--left outer join ( +-- select organization, abstract_share from result_with_abstract_share) tmp on tmp.organization=allresults.organization; +-- +--compute stats indi_org_findable; +-- +--create table indi_org_openess stored as parquet as +--WITH datasets_oa as ( +-- SELECT ro.organization, count(dg.id) no_oadatasets FROM indi_datasets_gold_oa dg +-- join result_organization ro on dg.id=ro.id +-- join dataset ds on dg.id=ds.id +-- WHERE dg.is_gold=1 +-- group by ro.organization), +--software_oa as ( +-- SELECT ro.organization, count(dg.id) no_oasoftware FROM indi_software_gold_oa dg +-- join result_organization ro on dg.id=ro.id +-- join software ds on dg.id=ds.id +-- WHERE dg.is_gold=1 +-- group by ro.organization), +--pubs_oa as ( +-- SELECT ro.organization, count(dg.id) no_oapubs FROM indi_pub_gold_oa dg +-- join result_organization ro on dg.id=ro.id +-- join publication ds on dg.id=ds.id +-- where dg.is_gold=1 +-- group by ro.organization), +--allpubs as ( +-- SELECT ro.organization organization, count(ro.id) no_allpubs FROM result_organization ro +-- join publication ps on ps.id=ro.id +-- group by ro.organization), +--alldatasets as ( +-- SELECT ro.organization organization, count(ro.id) no_alldatasets FROM result_organization ro +-- join dataset ps on ps.id=ro.id +-- group by ro.organization), +--allsoftware as ( +-- SELECT ro.organization organization, count(ro.id) no_allsoftware FROM result_organization ro +-- join software ps on ps.id=ro.id +-- group by ro.organization), +--allpubsshare as ( +-- select pubs_oa.organization, pubs_oa.no_oapubs/allpubs.no_allpubs p from allpubs +-- join pubs_oa on allpubs.organization=pubs_oa.organization), +--alldatasetssshare as ( +-- select datasets_oa.organization, datasets_oa.no_oadatasets/alldatasets.no_alldatasets c +-- from alldatasets +-- join datasets_oa on alldatasets.organization=datasets_oa.organization), +--allsoftwaresshare as ( +-- select software_oa.organization, software_oa.no_oasoftware/allsoftware.no_allsoftware s +-- from allsoftware +-- join software_oa on allsoftware.organization=software_oa.organization) +--select allpubsshare.organization, coalesce((c+p+s)/3, p) org_openess +--FROM allpubsshare +--left outer join ( +-- select organization,c from +-- alldatasetssshare) tmp on tmp.organization=allpubsshare.organization +--left outer join ( +-- select organization,s from allsoftwaresshare) tmp1 on tmp1.organization=allpubsshare.organization; +-- +--compute stats indi_org_openess; +-- create table indi_pub_hybrid_oa_with_cc stored as parquet as -WITH hybrid_oa AS ( - SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_print as issn - FROM stats_ext.plan_s_jn - WHERE issn_print != "" - UNION ALL - SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_online as issn - FROM stats_ext.plan_s_jn - WHERE issn_online != "" and (journal_is_in_doaj = FALSE OR journal_is_oa = FALSE)), -issn AS ( - SELECT * - FROM ( - SELECT id, issn_printed as issn - FROM datasource - WHERE issn_printed IS NOT NULL - UNION - SELECT id,issn_online as issn - FROM datasource - WHERE issn_online IS NOT NULL ) as issn + WITH hybrid_oa AS ( + SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_print as issn + FROM stats_ext.plan_s_jn + WHERE issn_print != "" + UNION ALL + SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_online as issn + FROM stats_ext.plan_s_jn + WHERE issn_online != "" and (journal_is_in_doaj = FALSE OR journal_is_oa = FALSE)), + issn AS ( + SELECT * + FROM ( + SELECT id, issn_printed as issn + FROM datasource + WHERE issn_printed IS NOT NULL + UNION + SELECT id,issn_online as issn + FROM datasource + WHERE issn_online IS NOT NULL ) as issn WHERE LENGTH(issn) > 7) SELECT DISTINCT pd.id, coalesce(is_hybrid_oa, 0) as is_hybrid_oa FROM publication_datasources pd -LEFT OUTER JOIN ( + LEFT OUTER JOIN ( SELECT pd.id, 1 as is_hybrid_oa from publication_datasources pd - JOIN datasource d on d.id=pd.datasource - JOIN issn on issn.id=pd.datasource - JOIN hybrid_oa ON issn.issn = hybrid_oa.issn - JOIN indi_result_has_cc_licence cc on pd.id=cc.id + JOIN datasource d on d.id=pd.datasource + JOIN issn on issn.id=pd.datasource + JOIN hybrid_oa ON issn.issn = hybrid_oa.issn + JOIN indi_result_has_cc_licence cc on pd.id=cc.id where cc.has_cc_license=1) tmp on pd.id=tmp.id; compute stats indi_pub_hybrid_oa_with_cc; create table indi_pub_downloads stored as parquet as SELECT result_id, sum(downloads) no_dowloads from openaire_prod_usage_stats.usage_stats -join publication on result_id=id + join publication on result_id=id where downloads>0 GROUP BY result_id order by no_dowloads desc; @@ -395,7 +429,7 @@ compute stats indi_pub_downloads; create table indi_pub_downloads_datasource stored as parquet as SELECT result_id, repository_id, sum(downloads) no_dowloads from openaire_prod_usage_stats.usage_stats -join publication on result_id=id + join publication on result_id=id where downloads>0 GROUP BY result_id, repository_id order by result_id; @@ -404,7 +438,7 @@ compute stats indi_pub_downloads_datasource; create table indi_pub_downloads_year stored as parquet as SELECT result_id, substring(us.`date`, 1,4) as `year`, sum(downloads) no_dowloads from openaire_prod_usage_stats.usage_stats us -join publication on result_id=id where downloads>0 + join publication on result_id=id where downloads>0 GROUP BY result_id, `year` order by `year` asc; @@ -412,9 +446,400 @@ compute stats indi_pub_downloads_year; create table indi_pub_downloads_datasource_year stored as parquet as SELECT result_id, substring(us.`date`, 1,4) as `year`, repository_id, sum(downloads) no_dowloads from openaire_prod_usage_stats.usage_stats us -join publication on result_id=id + join publication on result_id=id where downloads>0 GROUP BY result_id, repository_id, `year` order by `year` asc, result_id; -compute stats indi_pub_downloads_datasource_year; \ No newline at end of file +compute stats indi_pub_downloads_datasource_year; + +---- Sprint 7 ---- +create table indi_pub_gold_oa stored as parquet as + WITH gold_oa AS ( SELECT + issn_l, + journal_is_in_doaj, + journal_is_oa, + issn_1 as issn + FROM + stats_ext.oa_journals + WHERE + issn_1 != "" + UNION + ALL SELECT + issn_l, + journal_is_in_doaj, + journal_is_oa, + issn_2 as issn + FROM + stats_ext.oa_journals + WHERE + issn_2 != "" ), issn AS ( SELECT + * + FROM +( SELECT + id, + issn_printed as issn + FROM + datasource + WHERE + issn_printed IS NOT NULL + UNION + SELECT + id, + issn_online as issn + FROM + datasource + WHERE + issn_online IS NOT NULL or id like '%doajarticles%') as issn + WHERE + LENGTH(issn) > 7) +SELECT + DISTINCT pd.id, coalesce(is_gold, 0) as is_gold +FROM + publication_datasources pd + left outer join( + select pd.id, 1 as is_gold FROM publication_datasources pd + JOIN issn on issn.id=pd.datasource + JOIN gold_oa on issn.issn = gold_oa.issn) tmp + on pd.id=tmp.id; + +compute stats indi_pub_gold_oa; + +create table indi_pub_hybrid stored as parquet as + WITH gold_oa AS ( SELECT + issn_l, + journal_is_in_doaj, + journal_is_oa, + issn_1 as issn, + has_apc + FROM + stats_ext.oa_journals + WHERE + issn_1 != "" + UNION + ALL SELECT + issn_l, + journal_is_in_doaj, + journal_is_oa, + issn_2 as issn, + has_apc + FROM + stats_ext.oa_journals + WHERE + issn_2 != "" ), issn AS ( SELECT + * + FROM +( SELECT + id, + issn_printed as issn + FROM + datasource + WHERE + issn_printed IS NOT NULL + UNION + SELECT + id, + issn_online as issn + FROM + datasource + WHERE + issn_online IS NOT NULL or id like '%doajarticles%') as issn + WHERE + LENGTH(issn) > 7) +select distinct pd.id, coalesce(is_hybrid, 0) as is_hybrid +from publication_datasources pd + left outer join ( + select pd.id, 1 as is_hybrid from publication_datasources pd + join datasource d on d.id=pd.datasource + join issn on issn.id=pd.datasource + join gold_oa on issn.issn=gold_oa.issn + where (gold_oa.journal_is_in_doaj=false or gold_oa.journal_is_oa=false))tmp + on pd.id=tmp.id; + +compute stats indi_pub_hybrid; + +create table indi_org_fairness stored as parquet as +--return results with PIDs, and rich metadata group by organization + with result_fair as + (select ro.organization organization, count(distinct ro.id) no_result_fair from result_organization ro + join result r on r.id=ro.id +--join result_pids rp on r.id=rp.id + where (title is not null) and (publisher is not null) and (abstract is true) and (year is not null) and (authors>0) and year>2003 + group by ro.organization), +--return all results group by organization + allresults as (select organization, count(distinct ro.id) no_allresults from result_organization ro + join result r on r.id=ro.id + where year>2003 + group by organization) +--return results_fair/all_results +select allresults.organization, result_fair.no_result_fair/allresults.no_allresults org_fairness +from allresults + join result_fair on result_fair.organization=allresults.organization; + +compute stats indi_org_fairness; + +create table indi_org_fairness_pub_pr stored as parquet as + with result_fair as + (select ro.organization organization, count(distinct ro.id) no_result_fair + from result_organization ro + join publication p on p.id=ro.id + join indi_pub_doi_from_crossref dc on dc.id=p.id + join indi_pub_grey_lit gl on gl.id=p.id + where (title is not null) and (publisher is not null) and (abstract is true) and (year is not null) + and (authors>0) and cast(year as int)>2003 and dc.doi_from_crossref=1 and gl.grey_lit=0 + group by ro.organization), + allresults as (select organization, count(distinct ro.id) no_allresults from result_organization ro + join publication p on p.id=ro.id + where cast(year as int)>2003 + group by organization) +--return results_fair/all_results +select allresults.organization, result_fair.no_result_fair/allresults.no_allresults org_fairness +from allresults + join result_fair on result_fair.organization=allresults.organization; + +compute stats indi_org_fairness_pub_pr; + +create table indi_org_fairness_pub_year stored as parquet as + with result_fair as + (select year, ro.organization organization, count(distinct ro.id) no_result_fair from result_organization ro + join publication p on p.id=ro.id + where (title is not null) and (publisher is not null) and (abstract is true) and (year is not null) and (authors>0) and cast(year as int)>2003 + group by ro.organization, year), + allresults as (select year, organization, count(distinct ro.id) no_allresults from result_organization ro + join publication p on p.id=ro.id + where cast(year as int)>2003 + group by organization, year) +select allresults.year, allresults.organization, result_fair.no_result_fair/allresults.no_allresults org_fairness +from allresults + join result_fair on result_fair.organization=allresults.organization and result_fair.year=allresults.year; + +compute stats indi_org_fairness_pub_year; + +create table indi_org_fairness_pub as +with result_fair as + (select ro.organization organization, count(distinct ro.id) no_result_fair + from result_organization ro + join publication p on p.id=ro.id + where (title is not null) and (publisher is not null) and (abstract is true) and (year is not null) + and (authors>0) and cast(year as int)>2003 + group by ro.organization), + allresults as (select organization, count(distinct ro.id) no_allresults from result_organization ro + join publication p on p.id=ro.id + where cast(year as int)>2003 + group by organization) +select allresults.organization, result_fair.no_result_fair/allresults.no_allresults org_fairness +from allresults + join result_fair on result_fair.organization=allresults.organization; + +compute stats indi_org_fairness_pub; + +create table indi_org_fairness_year stored as parquet as + with result_fair as + (select year, ro.organization organization, count(distinct ro.id) no_result_fair from result_organization ro + join result r on r.id=ro.id + join result_pids rp on r.id=rp.id + where (title is not null) and (publisher is not null) and (abstract is true) and (year is not null) and (authors>0) and year>2003 + group by ro.organization, year), + allresults as (select year, organization, count(distinct ro.id) no_allresults from result_organization ro + join result r on r.id=ro.id + where year>2003 + group by organization, year) +--return results_fair/all_results +select allresults.year, allresults.organization, result_fair.no_result_fair/allresults.no_allresults org_fairness +from allresults + join result_fair on result_fair.organization=allresults.organization and result_fair.year=allresults.year; + +compute stats indi_org_fairness_year; + +create table indi_org_findable_year stored as parquet as +--return results with PIDs group by organization,year + with result_with_pid as + (select year, ro.organization organization, count(distinct rp.id) no_result_with_pid from result_organization ro + join result_pids rp on rp.id=ro.id + join result r on r.id=rp.id + where year >2003 + group by ro.organization, year), +--return all results group by organization,year + allresults as (select year, organization, count(distinct ro.id) no_allresults from result_organization ro + join result r on r.id=ro.id + where year >2003 + group by organization, year) +--return results_with_pid/all_results +select allresults.year, allresults.organization, result_with_pid.no_result_with_pid/allresults.no_allresults org_findable +from allresults + join result_with_pid on result_with_pid.organization=allresults.organization and result_with_pid.year=allresults.year; + +compute stats indi_org_findable_year; + +create table indi_org_findable stored as parquet as +--return results with PIDs group by organization + with result_with_pid as + (select ro.organization organization, count(distinct rp.id) no_result_with_pid from result_organization ro + join result_pids rp on rp.id=ro.id + join result r on r.id=rp.id + where year >2003 + group by ro.organization), +--return all results group by organization + allresults as (select organization, count(distinct ro.id) no_allresults from result_organization ro + join result r on r.id=ro.id + where year >2003 + group by organization) +--return results_with_pid/all_results +select allresults.organization, result_with_pid.no_result_with_pid/allresults.no_allresults org_findable +from allresults + join result_with_pid on result_with_pid.organization=allresults.organization; + +compute stats indi_org_findable; + +create table indi_org_openess stored as parquet as + WITH pubs_oa as ( + SELECT ro.organization, count(distinct r.id) no_oapubs FROM publication r + join result_organization ro on ro.id=r.id + join result_instance ri on ri.id=r.id + where (ri.accessright = 'Open Access' or ri.accessright = 'Embargo' or ri.accessright = 'Open Source') + and cast(r.year as int)>2003 + group by ro.organization), + datasets_oa as ( + SELECT ro.organization, count(distinct r.id) no_oadatasets FROM dataset r + join result_organization ro on ro.id=r.id + join result_instance ri on ri.id=r.id + where (ri.accessright = 'Open Access' or ri.accessright = 'Embargo' or ri.accessright = 'Open Source') + and cast(r.year as int)>2003 + group by ro.organization), + software_oa as ( + SELECT ro.organization, count(distinct r.id) no_oasoftware FROM software r + join result_organization ro on ro.id=r.id + join result_instance ri on ri.id=r.id + where (ri.accessright = 'Open Access' or ri.accessright = 'Embargo' or ri.accessright = 'Open Source') + and cast(r.year as int)>2003 + group by ro.organization), + allpubs as ( + SELECT ro.organization organization, count(ro.id) no_allpubs FROM result_organization ro + join publication ps on ps.id=ro.id + where cast(ps.year as int)>2003 + group by ro.organization), + alldatasets as ( + SELECT ro.organization organization, count(ro.id) no_alldatasets FROM result_organization ro + join dataset ps on ps.id=ro.id + where cast(ps.year as int)>2003 + group by ro.organization), + allsoftware as ( + SELECT ro.organization organization, count(ro.id) no_allsoftware FROM result_organization ro + join software ps on ps.id=ro.id + where cast(ps.year as int)>2003 + group by ro.organization), + allpubsshare as ( + select pubs_oa.organization, pubs_oa.no_oapubs/allpubs.no_allpubs p from allpubs + join pubs_oa on allpubs.organization=pubs_oa.organization), + alldatasetssshare as ( + select datasets_oa.organization, datasets_oa.no_oadatasets/alldatasets.no_alldatasets d + from alldatasets + join datasets_oa on alldatasets.organization=datasets_oa.organization), + allsoftwaresshare as ( + select software_oa.organization, software_oa.no_oasoftware/allsoftware.no_allsoftware s + from allsoftware + join software_oa on allsoftware.organization=software_oa.organization) +select allpubsshare.organization, + (p+isnull(s,0)+isnull(d,0))/(1+(case when s is null then 0 else 1 end) + +(case when d is null then 0 else 1 end)) + org_openess FROM allpubsshare + left outer join (select organization,d from + alldatasetssshare) tmp1 + on tmp1.organization=allpubsshare.organization + left outer join (select organization,s from + allsoftwaresshare) tmp2 + on tmp2.organization=allpubsshare.organization; + +compute stats indi_org_openess; + +create table indi_org_openess_year stored as parquet as + WITH pubs_oa as ( + SELECT r.year, ro.organization, count(distinct r.id) no_oapubs FROM publication r + join result_organization ro on ro.id=r.id + join result_instance ri on ri.id=r.id + where (ri.accessright = 'Open Access' or ri.accessright = 'Embargo' or ri.accessright = 'Open Source') + and cast(r.year as int)>2003 + group by ro.organization,r.year), + datasets_oa as ( + SELECT r.year,ro.organization, count(distinct r.id) no_oadatasets FROM dataset r + join result_organization ro on ro.id=r.id + join result_instance ri on ri.id=r.id + where (ri.accessright = 'Open Access' or ri.accessright = 'Embargo' or ri.accessright = 'Open Source') + and cast(r.year as int)>2003 + group by ro.organization, r.year), + software_oa as ( + SELECT r.year,ro.organization, count(distinct r.id) no_oasoftware FROM software r + join result_organization ro on ro.id=r.id + join result_instance ri on ri.id=r.id + where (ri.accessright = 'Open Access' or ri.accessright = 'Embargo' or ri.accessright = 'Open Source') + and cast(r.year as int)>2003 + group by ro.organization, r.year), + allpubs as ( + SELECT p.year,ro.organization organization, count(ro.id) no_allpubs FROM result_organization ro + join publication p on p.id=ro.id where cast(p.year as int)>2003 + group by ro.organization, p.year), + alldatasets as ( + SELECT d.year, ro.organization organization, count(ro.id) no_alldatasets FROM result_organization ro + join dataset d on d.id=ro.id where cast(d.year as int)>2003 + group by ro.organization, d.year), + allsoftware as ( + SELECT s.year,ro.organization organization, count(ro.id) no_allsoftware FROM result_organization ro + join software s on s.id=ro.id where cast(s.year as int)>2003 + group by ro.organization, s.year), + allpubsshare as ( + select allpubs.year, pubs_oa.organization, pubs_oa.no_oapubs/allpubs.no_allpubs p from allpubs + join pubs_oa on allpubs.organization=pubs_oa.organization where cast(allpubs.year as INT)=cast(pubs_oa.year as int)), + alldatasetssshare as ( + select alldatasets.year, datasets_oa.organization, datasets_oa.no_oadatasets/alldatasets.no_alldatasets d + from alldatasets + join datasets_oa on alldatasets.organization=datasets_oa.organization where cast(alldatasets.year as INT)=cast(datasets_oa.year as int)), + allsoftwaresshare as ( + select allsoftware.year, software_oa.organization, software_oa.no_oasoftware/allsoftware.no_allsoftware s + from allsoftware + join software_oa on allsoftware.organization=software_oa.organization where cast(allsoftware.year as INT)=cast(software_oa.year as int)) +select allpubsshare.year, allpubsshare.organization, + (p+isnull(s,0)+isnull(d,0))/(1+(case when s is null then 0 else 1 end) + +(case when d is null then 0 else 1 end)) + org_openess FROM allpubsshare + left outer join (select year, organization,d from + alldatasetssshare) tmp1 + on tmp1.organization=allpubsshare.organization and tmp1.year=allpubsshare.year + left outer join (select year, organization,s from + allsoftwaresshare) tmp2 + on tmp2.organization=allpubsshare.organization and tmp2.year=allpubsshare.year; + +compute stats indi_org_openess_year; + +create table indi_pub_has_preprint stored as parquet as +select distinct p.id, coalesce(has_preprint, 0) as has_preprint +from publication_classifications p + left outer join ( + select p.id, 1 as has_preprint + from publication_classifications p + where p.type='Preprint') tmp + on p.id= tmp.id; + +compute stats indi_pub_has_preprint; + +create table indi_pub_in_subscribed stored as parquet as +select distinct p.id, coalesce(is_subscription, 0) as is_subscription +from publication p + left outer join( + select p.id, 1 as is_subscription from publication p + join indi_pub_gold_oa g on p.id=g.id + join indi_pub_hybrid h on p.id=h.id + join indi_pub_in_transformative t on p.id=t.id + where g.is_gold=0 and h.is_hybrid=0 and t.is_transformative=0) tmp + on p.id=tmp.id; + +compute stats indi_pub_in_subscribed; + +create table indi_result_with_pid as +select distinct p.id, coalesce(result_with_pid, 0) as result_with_pid +from result p + left outer join ( + select p.id, 1 as result_with_pid + from result_pids p) tmp + on p.id= tmp.id; + +compute stats indi_result_with_pid; \ No newline at end of file From eb53b52f7c5e1ca1db48171d76379ab9b364b050 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 2 Aug 2022 13:24:47 +0200 Subject: [PATCH 28/33] code formatting --- .../eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala index 0f82ecadf..088a07427 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala @@ -587,7 +587,7 @@ object DataciteToOAFTransformation { val oid = result.getId result.setId(IdentifierFactory.createIdentifier(result)) if (!result.getId.equalsIgnoreCase(oid)) { - result.setOriginalId((oid::List(doi)).asJava) + result.setOriginalId((oid :: List(doi)).asJava) } var relations: List[Relation] = From 8b0407d8ecb8cb793247ec0d72348f78a042d929 Mon Sep 17 00:00:00 2001 From: Antonis Lempesis Date: Wed, 3 Aug 2022 12:26:59 +0300 Subject: [PATCH 29/33] fixed the datasourceOrganization relations --- .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql index 6fa0e6fdf..01bed17cc 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql @@ -93,7 +93,7 @@ where d.datainfo.deletedbyinference=false and d.datainfo.invisible=false; CREATE TABLE ${stats_db_name}.datasource_organizations STORED AS PARQUET AS SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS organization FROM ${openaire_db_name}.relation r -WHERE r.reltype = 'datasourceOrganization' and r.datainfo.deletedbyinference = false and r.target like '20|%' and r.datainfo.invisible=false; +WHERE r.reltype = 'datasourceOrganization' and r.datainfo.deletedbyinference = false and r.source like '20|%' and r.datainfo.invisible=false; -- datasource sources: -- where the datasource info have been collected from. From 499826ead1934f1dbe3f880cdcaa82200ea5f470 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 4 Aug 2022 12:40:48 +0200 Subject: [PATCH 30/33] serialising field eoscifguidelines field in the Solr XML records --- .../dhp/oa/provision/utils/XmlRecordFactory.java | 11 +++++++++++ .../oa/provision/utils/XmlSerializationUtils.java | 13 +++++++++++++ .../dhp/oa/provision/XmlRecordFactoryTest.java | 2 ++ .../eu/dnetlib/dhp/oa/provision/publication.json | 8 ++++++++ 4 files changed, 34 insertions(+) diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java index b34ec9693..45ba840c9 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java @@ -214,6 +214,17 @@ public class XmlRecordFactory implements Serializable { metadata.addAll(measuresAsXml(r.getMeasures())); } + if (r.getEoscifguidelines() != null) { + metadata + .addAll( + r + .getEoscifguidelines() + .stream() + .filter(Objects::nonNull) + .map(e -> XmlSerializationUtils.mapEoscIf(e)) + .collect(Collectors.toList())); + } + if (r.getContext() != null) { contexts.addAll(r.getContext().stream().map(c -> c.getId()).collect(Collectors.toList())); /* FIXME: Workaround for CLARIN mining issue: #3670#note-29 */ diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlSerializationUtils.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlSerializationUtils.java index 73667e056..adf7090d2 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlSerializationUtils.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlSerializationUtils.java @@ -7,6 +7,8 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank; import java.util.List; +import com.google.common.collect.Lists; + import eu.dnetlib.dhp.schema.oaf.*; import scala.Tuple2; @@ -161,4 +163,15 @@ public class XmlSerializationUtils { sb.append("/>"); return sb.toString(); } + + public static String mapEoscIf(EoscIfGuidelines e) { + return asXmlElement( + "eoscifguidelines", Lists + .newArrayList( + new Tuple2<>("code", e.getCode()), + new Tuple2<>("label", e.getLabel()), + new Tuple2<>("url", e.getUrl()), + new Tuple2<>("semanticrelation", e.getSemanticRelation()))); + } + } diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java index 92d9f497f..77d1f9fdb 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java @@ -87,6 +87,8 @@ public class XmlRecordFactoryTest { assertEquals( "C", doc.valueOf("//*[local-name() = 'result']/measure[./@id = 'popularity']/@class")); + assertEquals("EOSC::Jupyter Notebook", doc.valueOf("//*[local-name() = 'result']/eoscifguidelines/@code")); + } @Test diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json index 41ced45ae..5e3f19bd7 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json @@ -1,4 +1,12 @@ { + "eoscifguidelines": [ + { + "code" : "EOSC::Jupyter Notebook", + "label" : "EOSC::Jupyter Notebook", + "url" : "", + "semanticRelation" : "compliesWith" + } + ], "measures": [ { "id": "influence", From a7a18d76306bdae96691a5945ffa84ee32eafcaf Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 4 Aug 2022 17:40:40 +0200 Subject: [PATCH 31/33] [Graph Dump] removed code for the dump from the project. Fixed issues in tests when possible --- .../publication_license_embargo_datetime.json | 4 +- .../graph/datasource/datasource.json | 22 +- .../oa/graph/clean/CleanContextSparkJob.java | 8 - .../dnetlib/dhp/oa/graph/dump/Constants.java | 58 -- .../dhp/oa/graph/dump/DumpProducts.java | 107 -- .../eu/dnetlib/dhp/oa/graph/dump/MakeTar.java | 74 -- .../oa/graph/dump/QueryInformationSystem.java | 74 -- .../dhp/oa/graph/dump/ResultMapper.java | 672 ------------ .../dhp/oa/graph/dump/SaveCommunityMap.java | 99 -- .../dhp/oa/graph/dump/SendToZenodoHDFS.java | 100 -- .../eu/dnetlib/dhp/oa/graph/dump/Utils.java | 77 -- .../oa/graph/dump/community/CommunityMap.java | 8 - .../graph/dump/community/CommunitySplit.java | 81 -- .../graph/dump/community/ResultProject.java | 28 - .../community/SparkDumpCommunityProducts.java | 67 -- .../community/SparkPrepareResultProject.java | 193 ---- .../community/SparkSplitForCommunity.java | 50 - .../community/SparkUpdateProjectInfo.java | 90 -- .../dhp/oa/graph/dump/complete/Constants.java | 26 - .../oa/graph/dump/complete/ContextInfo.java | 84 -- .../dump/complete/CreateContextEntities.java | 110 -- .../dump/complete/CreateContextRelation.java | 128 --- .../dump/complete/DumpGraphEntities.java | 518 ---------- .../dhp/oa/graph/dump/complete/Extractor.java | 201 ---- .../oa/graph/dump/complete/MergedRels.java | 25 - .../graph/dump/complete/OrganizationMap.java | 21 - .../dhp/oa/graph/dump/complete/Process.java | 99 -- .../dump/complete/QueryInformationSystem.java | 195 ---- .../dump/complete/SparkCollectAndSave.java | 122 --- .../dump/complete/SparkDumpEntitiesJob.java | 54 - .../dump/complete/SparkDumpRelationJob.java | 132 --- .../SparkExtractRelationFromEntities.java | 54 - .../complete/SparkOrganizationRelation.java | 176 ---- .../SparkSelectValidRelationsJob.java | 136 --- .../dump/exceptions/MyRuntimeException.java | 30 - .../NoAvailableEntityTypeException.java | 29 - .../funderresults/SparkDumpFunderResults.java | 129 --- .../SparkResultLinkedToProject.java | 118 --- .../ProjectsSubsetSparkJob.java | 82 -- .../graph/raw/PatchRelationsApplication.java | 13 +- .../graph/dump/funder_result_parameters.json | 26 - .../oa/graph/dump/input_cm_parameters.json | 37 - .../oa/graph/dump/input_collect_and_save.json | 30 - .../graph/dump/input_complete_parameters.json | 35 - .../oa/graph/dump/input_entity_parameter.json | 24 - .../graph/dump/input_maketar_parameters.json | 30 - .../dump/input_organization_parameters.json | 36 - .../dump/input_parameter_select_relation.json | 20 - .../dhp/oa/graph/dump/input_parameters.json | 47 - .../graph/dump/input_parameters_link_prj.json | 41 - .../dump/input_relationdump_parameters.json | 32 - .../graph/dump/project_input_parameters.json | 29 - .../graph/dump/project_prep_parameters.json | 20 - .../graph/dump/project_subset_parameters.json | 27 - .../oozie_app/config-default.xml | 30 - .../dump/projectsubset/oozie_app/workflow.xml | 171 ---- .../dhp/oa/graph/dump/split_parameters.json | 37 - .../dhp/oa/graph/dump/upload_zenodo.json | 58 -- .../dump/wf/main/oozie_app/config-default.xml | 30 - .../graph/dump/wf/main/oozie_app/import.txt | 4 - .../graph/dump/wf/main/oozie_app/workflow.xml | 306 ------ .../community/oozie_app/config-default.xml | 30 - .../community/oozie_app/workflow.xml | 362 ------- .../complete/oozie_app/config-default.xml | 30 - .../complete/oozie_app/workflow.xml | 539 ---------- .../funder/oozie_app/config-default.xml | 30 - .../funder/oozie_app/workflow.xml | 255 ----- .../dhp/oa/graph/clean/CleanContextTest.java | 17 +- .../dhp/oa/graph/dump/DumpJobTest.java | 967 ------------------ .../dhp/oa/graph/dump/GenerateJsonSchema.java | 28 - .../dhp/oa/graph/dump/MakeTarTest.java | 60 -- .../dump/PrepareResultProjectJobTest.java | 347 ------- .../dump/QueryInformationSystemTest.java | 117 --- .../oa/graph/dump/SplitForCommunityTest.java | 143 --- .../oa/graph/dump/UpdateProjectInfoTest.java | 236 ----- .../dhp/oa/graph/dump/ZenodoUploadTest.java | 153 --- .../graph/dump/complete/CreateEntityTest.java | 173 ---- .../dump/complete/CreateRelationTest.java | 723 ------------- ...DumpOrganizationProjectDatasourceTest.java | 157 --- .../graph/dump/complete/DumpRelationTest.java | 305 ------ .../ExtractRelationFromEntityTest.java | 172 ---- .../dump/complete/FunderParsingTest.java | 70 -- .../complete/QueryInformationSystemTest.java | 810 --------------- .../RelationFromOrganizationTest.java | 121 --- .../dump/complete/SelectRelationTest.java | 100 -- .../ResultLinkedToProjectTest.java | 142 --- .../dump/funderresult/SplitPerFunderTest.java | 151 --- .../projectssubset/ProjectSubsetTest.java | 125 --- .../oa/graph/dump/addProjectInfo/preparedInfo | 2 - .../dump/addProjectInfo/preparedInfoValidated | 2 - .../addProjectInfo/publication_extendedmodel | 2 - .../graph/dump/addProjectInfo/software.json | 6 - .../dump/communityMapPath/communitymap.json | 1 - .../communitymapservices.json | 1 - .../dump/complete/datasource/datasource.json | 5 - .../complete/organization/organization.json | 34 - .../graph/dump/complete/project/project.json | 12 - .../oa/graph/dump/complete/relation/relation | 6 - .../communityMapPath/communityMap | 1 - .../oa/graph/dump/funderresource/ext/dataset | 0 .../funderresource/ext/otherresearchproduct | 0 .../oa/graph/dump/funderresource/ext/project | 12 - .../graph/dump/funderresource/ext/publication | 13 - .../oa/graph/dump/funderresource/ext/software | 0 .../dump/funderresource/extendeddump/dataset | 0 .../extendeddump/otherresearchproduct | 32 - .../dump/funderresource/extendeddump/project | 12 - .../funderresource/extendeddump/publication | 13 - .../dump/funderresource/extendeddump/software | 0 .../dump/funderresource/fundersList/list | 8 - .../dump/funderresource/match/papers.json | 32 - .../graph/dump/funderresource/match/project | 12 - .../graph/dump/funderresource/match/relation | 30 - .../dump/funderresource/nomatch/papers.json | 32 - .../graph/dump/funderresource/nomatch/project | 12 - .../dump/funderresource/nomatch/relation | 30 - .../funderresource/preparedInfo/resultProject | 1 - .../graph/dump/projectsubset/allnew/projects | 12 - .../dump/projectsubset/matchOne/projects | 12 - .../dhp/oa/graph/dump/projectsubset/projectId | 28 - .../dhp/oa/graph/dump/relation/relation | 30 - .../oa/graph/dump/relation/relation_validated | 30 - .../dhp/oa/graph/dump/resultDump/dataset.json | 90 -- .../oa/graph/dump/resultDump/dataset_cleaned | 7 - .../dump/resultDump/dataset_extendedinstance | 1 - .../dhp/oa/graph/dump/resultDump/orp.json | 3 - .../dump/resultDump/orp_extendedinstance | 1 - .../oa/graph/dump/resultDump/publication.json | 76 -- .../resultDump/publication_extendedinstance | 1 - .../oa/graph/dump/resultDump/publication_pca | 25 - .../dump/resultDump/singelRecord_pub.json | 2 - .../oa/graph/dump/resultDump/software.json | 6 - .../dump/resultDump/software_extendedinstance | 1 - .../oa/graph/dump/resultProject/match/project | 23 - .../graph/dump/resultProject/match/relation | 8 - .../dump/resultProject/match_one/project | 23 - .../dump/resultProject/match_one/relation | 8 - .../resultProject/match_validatedRels/project | 23 - .../match_validatedRels/relation | 8 - .../graph/dump/resultProject/no_match/project | 23 - .../dump/resultProject/no_match/relation | 19 - .../dhp/oa/graph/dump/selectrelations/dataset | 10 - .../oa/graph/dump/selectrelations/datasource | 7 - .../graph/dump/selectrelations/organization | 19 - .../dump/selectrelations/otherresearchproduct | 3 - .../dhp/oa/graph/dump/selectrelations/project | 12 - .../oa/graph/dump/selectrelations/publication | 9 - .../oa/graph/dump/selectrelations/relation | 15 - .../oa/graph/dump/selectrelations/software | 6 - .../oa/graph/dump/splitForCommunity/dataset | 10 - .../dhp/oa/graph/dump/splitForCommunity/orp | 3 - .../graph/dump/splitForCommunity/publication | 10 - .../oa/graph/dump/splitForCommunity/software 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a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/publication_license_embargo_datetime.json b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/publication_license_embargo_datetime.json index c84e16350..c715e44ed 100644 --- a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/publication_license_embargo_datetime.json +++ b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/publication_license_embargo_datetime.json @@ -1443,7 +1443,7 @@ 17 ] ], -"date-time": "2021-05-17T15:08:12Z", +"date-time": "3021-05-17T15:08:12Z", "timestamp": 1621264092000 }, "score": 1.0, @@ -1461,7 +1461,7 @@ 22 ] ], - "date-time": "2021-05-17T15:08:12Z" + "date-time": "3021-05-17T15:08:12Z" }, "references-count": 83, "journal-issue": { diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/countrypropagation/graph/datasource/datasource.json b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/countrypropagation/graph/datasource/datasource.json index 6b71024fd..8e481df4a 100644 --- a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/countrypropagation/graph/datasource/datasource.json +++ b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/countrypropagation/graph/datasource/datasource.json @@ -1,11 +1,11 @@ -{"accessinfopackage":[],"collectedfrom":[{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"}],"contentpolicies":[{"classid":"Journal articles","classname":"Journal 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b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java index 3e9b17f3f..55fdbac59 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java @@ -4,7 +4,6 @@ package eu.dnetlib.dhp.oa.graph.clean; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.io.Serializable; -import java.util.List; import java.util.Optional; import java.util.stream.Collectors; @@ -21,15 +20,8 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.common.HdfsSupport; -import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.oaf.Context; -import eu.dnetlib.dhp.schema.oaf.Oaf; -import eu.dnetlib.dhp.schema.oaf.OafEntity; import eu.dnetlib.dhp.schema.oaf.Result; -import eu.dnetlib.dhp.utils.ISLookupClientFactory; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; public class CleanContextSparkJob implements Serializable { private static final Logger log = LoggerFactory.getLogger(CleanContextSparkJob.class); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java deleted file mode 100644 index 61167639c..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java +++ /dev/null @@ -1,58 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump; - -import java.util.Map; - -import com.google.common.collect.Maps; - -import eu.dnetlib.dhp.schema.common.ModelConstants; - -public class Constants { - - protected static final Map accessRightsCoarMap = Maps.newHashMap(); - protected static final Map coarCodeLabelMap = Maps.newHashMap(); - - public static final String INFERRED = "Inferred by OpenAIRE"; - public static final String CABF2 = "c_abf2"; - - public static final String HARVESTED = "Harvested"; - public static final String DEFAULT_TRUST = "0.9"; - public static final String USER_CLAIM = "Linked by user"; - - public static final String COAR_ACCESS_RIGHT_SCHEMA = "http://vocabularies.coar-repositories.org/documentation/access_rights/"; - - public static final String ZENODO_COMMUNITY_PREFIX = "https://zenodo.org/communities/"; - - public static final String RESEARCH_COMMUNITY = "Research Community"; - - public static final String RESEARCH_INFRASTRUCTURE = "Research Infrastructure/Initiative"; - - static { - accessRightsCoarMap.put(ModelConstants.ACCESS_RIGHT_OPEN, CABF2); - accessRightsCoarMap.put("RESTRICTED", "c_16ec"); - accessRightsCoarMap.put("OPEN SOURCE", CABF2); - accessRightsCoarMap.put(ModelConstants.ACCESS_RIGHT_CLOSED, "c_14cb"); - accessRightsCoarMap.put(ModelConstants.ACCESS_RIGHT_EMBARGO, "c_f1cf"); - } - - static { - coarCodeLabelMap.put(CABF2, ModelConstants.ACCESS_RIGHT_OPEN); - coarCodeLabelMap.put("c_16ec", "RESTRICTED"); - coarCodeLabelMap.put("c_14cb", ModelConstants.ACCESS_RIGHT_CLOSED); - coarCodeLabelMap.put("c_f1cf", "EMBARGO"); - } - - public enum DUMPTYPE { - COMPLETE("complete"), COMMUNITY("community"), FUNDER("funder"); - - private final String type; - - DUMPTYPE(String type) { - this.type = type; - } - - public String getType() { - return type; - } - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java deleted file mode 100644 index a714cea20..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java +++ /dev/null @@ -1,107 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.util.List; -import java.util.Objects; -import java.util.Optional; -import java.util.Set; -import java.util.stream.Collectors; - -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.FilterFunction; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SaveMode; -import org.apache.spark.sql.SparkSession; - -import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; -import eu.dnetlib.dhp.oa.graph.dump.exceptions.NoAvailableEntityTypeException; -import eu.dnetlib.dhp.schema.oaf.*; - -/** - * It fires the execution of the actual dump for result entities. If the dump is for RC/RI products its checks for each - * result its belongingess to at least one RC/RI before "asking" for its mapping. - */ -public class DumpProducts implements Serializable { - - public void run(Boolean isSparkSessionManaged, String inputPath, String outputPath, String communityMapPath, - Class inputClazz, - Class outputClazz, - String dumpType) { - - SparkConf conf = new SparkConf(); - - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - execDump( - spark, inputPath, outputPath, communityMapPath, inputClazz, outputClazz, dumpType); - }); - } - - public static void execDump( - SparkSession spark, - String inputPath, - String outputPath, - String communityMapPath, - Class inputClazz, - Class outputClazz, - String dumpType) { - - CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath); - - Utils - .readPath(spark, inputPath, inputClazz) - .map((MapFunction) value -> execMap(value, communityMap, dumpType), Encoders.bean(outputClazz)) - .filter((FilterFunction) value -> value != null) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); - - } - - private static O execMap(I value, - CommunityMap communityMap, - String dumpType) throws NoAvailableEntityTypeException { - - Optional odInfo = Optional.ofNullable(value.getDataInfo()); - if (odInfo.isPresent()) { - if (odInfo.get().getDeletedbyinference() || odInfo.get().getInvisible()) { - return null; - } - } else { - return null; - } - - if (Constants.DUMPTYPE.COMMUNITY.getType().equals(dumpType)) { - Set communities = communityMap.keySet(); - - Optional> inputContext = Optional - .ofNullable(((eu.dnetlib.dhp.schema.oaf.Result) value).getContext()); - if (!inputContext.isPresent()) { - return null; - } - List toDumpFor = inputContext.get().stream().map(c -> { - if (communities.contains(c.getId())) { - return c.getId(); - } - if (c.getId().contains("::") && communities.contains(c.getId().substring(0, c.getId().indexOf("::")))) { - return c.getId().substring(0, c.getId().indexOf("::")); - } - return null; - }).filter(Objects::nonNull).collect(Collectors.toList()); - if (toDumpFor.isEmpty()) { - return null; - } - } - - return (O) ResultMapper.map(value, communityMap, dumpType); - - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/MakeTar.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/MakeTar.java deleted file mode 100644 index b56849a3a..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/MakeTar.java +++ /dev/null @@ -1,74 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump; - -import java.io.IOException; -import java.io.Serializable; -import java.util.Optional; - -import org.apache.commons.io.IOUtils; -import org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.fs.LocatedFileStatus; -import org.apache.hadoop.fs.Path; -import org.apache.hadoop.fs.RemoteIterator; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.common.MakeTarArchive; - -public class MakeTar implements Serializable { - - private static final Logger log = LoggerFactory.getLogger(MakeTar.class); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - MakeTar.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_maketar_parameters.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - final String outputPath = parser.get("hdfsPath"); - log.info("hdfsPath: {}", outputPath); - - final String hdfsNameNode = parser.get("nameNode"); - log.info("nameNode: {}", hdfsNameNode); - - final String inputPath = parser.get("sourcePath"); - log.info("input path : {}", inputPath); - - final int gBperSplit = Optional - .ofNullable(parser.get("splitSize")) - .map(Integer::valueOf) - .orElse(10); - - Configuration conf = new Configuration(); - conf.set("fs.defaultFS", hdfsNameNode); - - FileSystem fileSystem = FileSystem.get(conf); - - makeTArArchive(fileSystem, inputPath, outputPath, gBperSplit); - - } - - public static void makeTArArchive(FileSystem fileSystem, String inputPath, String outputPath, int gBperSplit) - throws IOException { - - RemoteIterator dirIterator = fileSystem.listLocatedStatus(new Path(inputPath)); - - while (dirIterator.hasNext()) { - LocatedFileStatus fileStatus = dirIterator.next(); - - Path p = fileStatus.getPath(); - String pathString = p.toString(); - String entity = pathString.substring(pathString.lastIndexOf("/") + 1); - - MakeTarArchive.tarMaxSize(fileSystem, pathString, outputPath + "/" + entity, entity, gBperSplit); - } - - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java deleted file mode 100644 index b972de6e9..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java +++ /dev/null @@ -1,74 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump; - -import java.io.StringReader; -import java.util.List; - -import org.dom4j.Document; -import org.dom4j.DocumentException; -import org.dom4j.Element; -import org.dom4j.io.SAXReader; -import org.xml.sax.SAXException; - -import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; - -public class QueryInformationSystem { - - private ISLookUpService isLookUp; - - private static final String XQUERY_ALL = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') " - + - " where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " + - " and ($x//context/param[./@name = 'status']/text() = 'all') " - + - " return " + - " " + - "{$x//CONFIGURATION/context/@id}" + - "{$x//CONFIGURATION/context/@label}" + - ""; - - private static final String XQUERY_CI = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') " - + - " where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " + - " and $x//CONFIGURATION/context[./@id=%s] " - + - " return " + - " " + - "{$x//CONFIGURATION/context/@id}" + - "{$x//CONFIGURATION/context/@label}" + - ""; - - public CommunityMap getCommunityMap(boolean singleCommunity, String communityId) - throws ISLookUpException, DocumentException, SAXException { - if (singleCommunity) - return getMap(isLookUp.quickSearchProfile(XQUERY_CI.replace("%s", "'" + communityId + "'"))); - return getMap(isLookUp.quickSearchProfile(XQUERY_ALL)); - - } - - public ISLookUpService getIsLookUp() { - return isLookUp; - } - - public void setIsLookUp(ISLookUpService isLookUpService) { - this.isLookUp = isLookUpService; - } - - private CommunityMap getMap(List communityMap) throws DocumentException, SAXException { - final CommunityMap map = new CommunityMap(); - - for (String xml : communityMap) { - final Document doc; - final SAXReader reader = new SAXReader(); - reader.setFeature("http://apache.org/xml/features/disallow-doctype-decl", true); - doc = reader.read(new StringReader(xml)); - Element root = doc.getRootElement(); - map.put(root.attribute("id").getValue(), root.attribute("label").getValue()); - } - - return map; - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java deleted file mode 100644 index aad3a8706..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java +++ /dev/null @@ -1,672 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump; - -import java.io.Serializable; -import java.util.*; -import java.util.stream.Collectors; - -import org.apache.commons.lang3.StringUtils; - -import eu.dnetlib.dhp.oa.graph.dump.exceptions.NoAvailableEntityTypeException; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.dump.oaf.*; -import eu.dnetlib.dhp.schema.dump.oaf.AccessRight; -import eu.dnetlib.dhp.schema.dump.oaf.Author; -import eu.dnetlib.dhp.schema.dump.oaf.GeoLocation; -import eu.dnetlib.dhp.schema.dump.oaf.Instance; -import eu.dnetlib.dhp.schema.dump.oaf.Measure; -import eu.dnetlib.dhp.schema.dump.oaf.OpenAccessRoute; -import eu.dnetlib.dhp.schema.dump.oaf.Result; -import eu.dnetlib.dhp.schema.dump.oaf.community.CfHbKeyValue; -import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityInstance; -import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; -import eu.dnetlib.dhp.schema.dump.oaf.community.Context; -import eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult; -import eu.dnetlib.dhp.schema.oaf.*; - -public class ResultMapper implements Serializable { - - public static Result map( - E in, Map communityMap, String dumpType) throws NoAvailableEntityTypeException { - - Result out; - if (Constants.DUMPTYPE.COMPLETE.getType().equals(dumpType)) { - out = new GraphResult(); - } else { - out = new CommunityResult(); - } - - eu.dnetlib.dhp.schema.oaf.Result input = (eu.dnetlib.dhp.schema.oaf.Result) in; - Optional ort = Optional.ofNullable(input.getResulttype()); - if (ort.isPresent()) { - try { - - addTypeSpecificInformation(out, input, ort); - - Optional - .ofNullable(input.getAuthor()) - .ifPresent( - ats -> out.setAuthor(ats.stream().map(ResultMapper::getAuthor).collect(Collectors.toList()))); - - // I do not map Access Right UNKNOWN or OTHER - - Optional oar = Optional.ofNullable(input.getBestaccessright()); - if (oar.isPresent() && Constants.accessRightsCoarMap.containsKey(oar.get().getClassid())) { - String code = Constants.accessRightsCoarMap.get(oar.get().getClassid()); - out - .setBestaccessright( - - BestAccessRight - .newInstance( - code, - Constants.coarCodeLabelMap.get(code), - Constants.COAR_ACCESS_RIGHT_SCHEMA)); - } - - final List contributorList = new ArrayList<>(); - Optional - .ofNullable(input.getContributor()) - .ifPresent(value -> value.stream().forEach(c -> contributorList.add(c.getValue()))); - out.setContributor(contributorList); - - Optional - .ofNullable(input.getCountry()) - .ifPresent( - value -> out - .setCountry( - value - .stream() - .map( - c -> { - if (c.getClassid().equals((ModelConstants.UNKNOWN))) { - return null; - } - ResultCountry country = new ResultCountry(); - country.setCode(c.getClassid()); - country.setLabel(c.getClassname()); - Optional - .ofNullable(c.getDataInfo()) - .ifPresent( - provenance -> country - .setProvenance( - Provenance - .newInstance( - provenance - .getProvenanceaction() - .getClassname(), - c.getDataInfo().getTrust()))); - return country; - }) - .filter(Objects::nonNull) - .collect(Collectors.toList()))); - - final List coverageList = new ArrayList<>(); - Optional - .ofNullable(input.getCoverage()) - .ifPresent(value -> value.stream().forEach(c -> coverageList.add(c.getValue()))); - out.setCoverage(coverageList); - - out.setDateofcollection(input.getDateofcollection()); - - final List descriptionList = new ArrayList<>(); - Optional - .ofNullable(input.getDescription()) - .ifPresent(value -> value.forEach(d -> descriptionList.add(d.getValue()))); - out.setDescription(descriptionList); - Optional> oStr = Optional.ofNullable(input.getEmbargoenddate()); - if (oStr.isPresent()) { - out.setEmbargoenddate(oStr.get().getValue()); - } - - final List formatList = new ArrayList<>(); - Optional - .ofNullable(input.getFormat()) - .ifPresent(value -> value.stream().forEach(f -> formatList.add(f.getValue()))); - out.setFormat(formatList); - out.setId(input.getId()); - out.setOriginalId(new ArrayList<>()); - Optional - .ofNullable(input.getOriginalId()) - .ifPresent( - v -> out - .setOriginalId( - input - .getOriginalId() - .stream() - .filter(s -> !s.startsWith("50|")) - .collect(Collectors.toList()))); - - Optional> oInst = Optional - .ofNullable(input.getInstance()); - - if (oInst.isPresent()) { - if (Constants.DUMPTYPE.COMPLETE.getType().equals(dumpType)) { - ((GraphResult) out) - .setInstance( - oInst.get().stream().map(ResultMapper::getGraphInstance).collect(Collectors.toList())); - } else { - ((CommunityResult) out) - .setInstance( - oInst - .get() - .stream() - .map(ResultMapper::getCommunityInstance) - .collect(Collectors.toList())); - } - } - - Optional oL = Optional.ofNullable(input.getLanguage()); - if (oL.isPresent()) { - eu.dnetlib.dhp.schema.oaf.Qualifier language = oL.get(); - out.setLanguage(Language.newInstance(language.getClassid(), language.getClassname())); - } - Optional oLong = Optional.ofNullable(input.getLastupdatetimestamp()); - if (oLong.isPresent()) { - out.setLastupdatetimestamp(oLong.get()); - } - Optional> otitle = Optional.ofNullable(input.getTitle()); - if (otitle.isPresent()) { - List iTitle = otitle - .get() - .stream() - .filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("main title")) - .collect(Collectors.toList()); - if (!iTitle.isEmpty()) { - out.setMaintitle(iTitle.get(0).getValue()); - } - - iTitle = otitle - .get() - .stream() - .filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("subtitle")) - .collect(Collectors.toList()); - if (!iTitle.isEmpty()) { - out.setSubtitle(iTitle.get(0).getValue()); - } - - } - - Optional - .ofNullable(input.getPid()) - .ifPresent( - value -> out - .setPid( - value - .stream() - .map( - p -> ResultPid - .newInstance(p.getQualifier().getClassid(), p.getValue())) - .collect(Collectors.toList()))); - - oStr = Optional.ofNullable(input.getDateofacceptance()); - if (oStr.isPresent()) { - out.setPublicationdate(oStr.get().getValue()); - } - oStr = Optional.ofNullable(input.getPublisher()); - if (oStr.isPresent()) { - out.setPublisher(oStr.get().getValue()); - } - - Optional - .ofNullable(input.getSource()) - .ifPresent( - value -> out.setSource(value.stream().map(Field::getValue).collect(Collectors.toList()))); - - List subjectList = new ArrayList<>(); - Optional - .ofNullable(input.getSubject()) - .ifPresent( - value -> value - .forEach(s -> subjectList.add(getSubject(s)))); - - out.setSubjects(subjectList); - - out.setType(input.getResulttype().getClassid()); - - if (!Constants.DUMPTYPE.COMPLETE.getType().equals(dumpType)) { - ((CommunityResult) out) - .setCollectedfrom( - input - .getCollectedfrom() - .stream() - .map(cf -> CfHbKeyValue.newInstance(cf.getKey(), cf.getValue())) - .collect(Collectors.toList())); - - Set communities = communityMap.keySet(); - List contextList = Optional - .ofNullable( - input - .getContext()) - .map( - value -> value - .stream() - .map(c -> { - String communityId = c.getId(); - if (communityId.contains("::")) { - communityId = communityId.substring(0, communityId.indexOf("::")); - } - if (communities.contains(communityId)) { - Context context = new Context(); - context.setCode(communityId); - context.setLabel(communityMap.get(communityId)); - Optional> dataInfo = Optional.ofNullable(c.getDataInfo()); - if (dataInfo.isPresent()) { - List provenance = new ArrayList<>(); - provenance - .addAll( - dataInfo - .get() - .stream() - .map( - di -> Optional - .ofNullable(di.getProvenanceaction()) - .map( - provenanceaction -> Provenance - .newInstance( - provenanceaction.getClassname(), - di.getTrust())) - .orElse(null)) - .filter(Objects::nonNull) - .collect(Collectors.toSet())); - - try { - context.setProvenance(getUniqueProvenance(provenance)); - } catch (NoAvailableEntityTypeException e) { - e.printStackTrace(); - } - } - return context; - } - return null; - }) - .filter(Objects::nonNull) - .collect(Collectors.toList())) - .orElse(new ArrayList<>()); - - if (!contextList.isEmpty()) { - Set hashValue = new HashSet<>(); - List remainigContext = new ArrayList<>(); - contextList.forEach(c -> { - if (!hashValue.contains(c.hashCode())) { - remainigContext.add(c); - hashValue.add(c.hashCode()); - } - }); - ((CommunityResult) out).setContext(remainigContext); - } - } - } catch (ClassCastException cce) { - return out; - } - } - - return out; - - } - - private static void addTypeSpecificInformation(Result out, eu.dnetlib.dhp.schema.oaf.Result input, - Optional ort) throws NoAvailableEntityTypeException { - switch (ort.get().getClassid()) { - case "publication": - Optional journal = Optional - .ofNullable(((Publication) input).getJournal()); - if (journal.isPresent()) { - Journal j = journal.get(); - Container c = new Container(); - c.setConferencedate(j.getConferencedate()); - c.setConferenceplace(j.getConferenceplace()); - c.setEdition(j.getEdition()); - c.setEp(j.getEp()); - c.setIss(j.getIss()); - c.setIssnLinking(j.getIssnLinking()); - c.setIssnOnline(j.getIssnOnline()); - c.setIssnPrinted(j.getIssnPrinted()); - c.setName(j.getName()); - c.setSp(j.getSp()); - c.setVol(j.getVol()); - out.setContainer(c); - out.setType(ModelConstants.PUBLICATION_DEFAULT_RESULTTYPE.getClassname()); - } - break; - case "dataset": - Dataset id = (Dataset) input; - Optional.ofNullable(id.getSize()).ifPresent(v -> out.setSize(v.getValue())); - Optional.ofNullable(id.getVersion()).ifPresent(v -> out.setVersion(v.getValue())); - - out - .setGeolocation( - Optional - .ofNullable(id.getGeolocation()) - .map( - igl -> igl - .stream() - .filter(Objects::nonNull) - .map(gli -> { - GeoLocation gl = new GeoLocation(); - gl.setBox(gli.getBox()); - gl.setPlace(gli.getPlace()); - gl.setPoint(gli.getPoint()); - return gl; - }) - .collect(Collectors.toList())) - .orElse(null)); - - out.setType(ModelConstants.DATASET_DEFAULT_RESULTTYPE.getClassname()); - break; - case "software": - - Software is = (Software) input; - Optional - .ofNullable(is.getCodeRepositoryUrl()) - .ifPresent(value -> out.setCodeRepositoryUrl(value.getValue())); - Optional - .ofNullable(is.getDocumentationUrl()) - .ifPresent( - value -> out - .setDocumentationUrl( - value - .stream() - .map(Field::getValue) - .collect(Collectors.toList()))); - - Optional - .ofNullable(is.getProgrammingLanguage()) - .ifPresent(value -> out.setProgrammingLanguage(value.getClassid())); - - out.setType(ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE.getClassname()); - break; - case "other": - - OtherResearchProduct ir = (OtherResearchProduct) input; - out - .setContactgroup( - Optional - .ofNullable(ir.getContactgroup()) - .map(value -> value.stream().map(Field::getValue).collect(Collectors.toList())) - .orElse(null)); - - out - .setContactperson( - Optional - .ofNullable(ir.getContactperson()) - .map(value -> value.stream().map(Field::getValue).collect(Collectors.toList())) - .orElse(null)); - out - .setTool( - Optional - .ofNullable(ir.getTool()) - .map(value -> value.stream().map(Field::getValue).collect(Collectors.toList())) - .orElse(null)); - - out.setType(ModelConstants.ORP_DEFAULT_RESULTTYPE.getClassname()); - - break; - default: - throw new NoAvailableEntityTypeException(); - } - } - - private static Instance getGraphInstance(eu.dnetlib.dhp.schema.oaf.Instance i) { - Instance instance = new Instance(); - - setCommonValue(i, instance); - - return instance; - - } - - private static CommunityInstance getCommunityInstance(eu.dnetlib.dhp.schema.oaf.Instance i) { - CommunityInstance instance = new CommunityInstance(); - - setCommonValue(i, instance); - - instance - .setCollectedfrom( - CfHbKeyValue - .newInstance(i.getCollectedfrom().getKey(), i.getCollectedfrom().getValue())); - - instance - .setHostedby( - CfHbKeyValue.newInstance(i.getHostedby().getKey(), i.getHostedby().getValue())); - - return instance; - - } - - private static void setCommonValue(eu.dnetlib.dhp.schema.oaf.Instance i, I instance) { - Optional opAr = Optional.ofNullable(i.getAccessright()); - - if (opAr.isPresent() && Constants.accessRightsCoarMap.containsKey(opAr.get().getClassid())) { - String code = Constants.accessRightsCoarMap.get(opAr.get().getClassid()); - - instance - .setAccessright( - AccessRight - .newInstance( - code, - Constants.coarCodeLabelMap.get(code), - Constants.COAR_ACCESS_RIGHT_SCHEMA)); - - Optional> mes = Optional.ofNullable(i.getMeasures()); - if (mes.isPresent()) { - List measure = new ArrayList<>(); - mes - .get() - .forEach( - m -> m.getUnit().forEach(u -> measure.add(Measure.newInstance(m.getId(), u.getValue())))); - instance.setMeasures(measure); - } - - if (opAr.get().getOpenAccessRoute() != null) { - switch (opAr.get().getOpenAccessRoute()) { - case hybrid: - instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.hybrid); - break; - case gold: - instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.gold); - break; - case green: - instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.green); - break; - case bronze: - instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.bronze); - break; - - } - } - - } - - Optional - .ofNullable(i.getPid()) - .ifPresent( - pid -> instance - .setPid( - pid - .stream() - .map(p -> ResultPid.newInstance(p.getQualifier().getClassid(), p.getValue())) - .collect(Collectors.toList()))); - - Optional - .ofNullable(i.getAlternateIdentifier()) - .ifPresent( - ai -> instance - .setAlternateIdentifier( - ai - .stream() - .map(p -> AlternateIdentifier.newInstance(p.getQualifier().getClassid(), p.getValue())) - .collect(Collectors.toList()))); - - Optional - .ofNullable(i.getLicense()) - .ifPresent(value -> instance.setLicense(value.getValue())); - Optional - .ofNullable(i.getDateofacceptance()) - .ifPresent(value -> instance.setPublicationdate(value.getValue())); - Optional - .ofNullable(i.getRefereed()) - .ifPresent(value -> instance.setRefereed(value.getClassname())); - Optional - .ofNullable(i.getInstancetype()) - .ifPresent(value -> instance.setType(value.getClassname())); - Optional.ofNullable(i.getUrl()).ifPresent(value -> instance.setUrl(value)); - Optional> oPca = Optional.ofNullable(i.getProcessingchargeamount()); - Optional> oPcc = Optional.ofNullable(i.getProcessingchargecurrency()); - if (oPca.isPresent() && oPcc.isPresent()) { - Field pca = oPca.get(); - Field pcc = oPcc.get(); - if (!pca.getValue().trim().equals("") && !pcc.getValue().trim().equals("")) { - APC apc = new APC(); - apc.setCurrency(oPcc.get().getValue()); - apc.setAmount(oPca.get().getValue()); - instance.setArticleprocessingcharge(apc); - } - - } - Optional.ofNullable(i.getUrl()).ifPresent(instance::setUrl); - - } - - private static List getUniqueProvenance(List provenance) - throws NoAvailableEntityTypeException { - Provenance iProv = new Provenance(); - - Provenance hProv = new Provenance(); - Provenance lProv = new Provenance(); - - for (Provenance p : provenance) { - switch (p.getProvenance()) { - case Constants.HARVESTED: - hProv = getHighestTrust(hProv, p); - break; - case Constants.INFERRED: - iProv = getHighestTrust(iProv, p); - // To be removed as soon as the new beta run has been done - // this fixex issue of not set trust during bulktagging - if (StringUtils.isEmpty(iProv.getTrust())) { - iProv.setTrust(Constants.DEFAULT_TRUST); - } - break; - case Constants.USER_CLAIM: - lProv = getHighestTrust(lProv, p); - break; - default: - throw new NoAvailableEntityTypeException(); - } - - } - - return Arrays - .asList(iProv, hProv, lProv) - .stream() - .filter(p -> !StringUtils.isEmpty(p.getProvenance())) - .collect(Collectors.toList()); - - } - - private static Provenance getHighestTrust(Provenance hProv, Provenance p) { - if (StringUtils.isNoneEmpty(hProv.getTrust(), p.getTrust())) - return hProv.getTrust().compareTo(p.getTrust()) > 0 ? hProv : p; - - return (StringUtils.isEmpty(p.getTrust()) && !StringUtils.isEmpty(hProv.getTrust())) ? hProv : p; - - } - - private static Subject getSubject(StructuredProperty s) { - Subject subject = new Subject(); - subject.setSubject(SubjectSchemeValue.newInstance(s.getQualifier().getClassid(), s.getValue())); - Optional di = Optional.ofNullable(s.getDataInfo()); - if (di.isPresent()) { - Provenance p = new Provenance(); - p.setProvenance(di.get().getProvenanceaction().getClassname()); - p.setTrust(di.get().getTrust()); - subject.setProvenance(p); - } - - return subject; - } - - private static Author getAuthor(eu.dnetlib.dhp.schema.oaf.Author oa) { - Author a = new Author(); - a.setFullname(oa.getFullname()); - a.setName(oa.getName()); - a.setSurname(oa.getSurname()); - a.setRank(oa.getRank()); - - Optional> oPids = Optional - .ofNullable(oa.getPid()); - if (oPids.isPresent()) { - AuthorPid pid = getOrcid(oPids.get()); - if (pid != null) { - a.setPid(pid); - } - } - - return a; - } - - private static AuthorPid getAuthorPid(StructuredProperty pid) { - Optional di = Optional.ofNullable(pid.getDataInfo()); - if (di.isPresent()) { - return AuthorPid - .newInstance( - AuthorPidSchemeValue - .newInstance( - pid.getQualifier().getClassid(), - pid.getValue()), - Provenance - .newInstance( - di.get().getProvenanceaction().getClassname(), - di.get().getTrust())); - } else { - return AuthorPid - .newInstance( - AuthorPidSchemeValue - .newInstance( - pid.getQualifier().getClassid(), - pid.getValue()) - - ); - } - } - - private static AuthorPid getOrcid(List p) { - List pidList = p.stream().map(pid -> { - if (pid.getQualifier().getClassid().equals(ModelConstants.ORCID) || - (pid.getQualifier().getClassid().equals(ModelConstants.ORCID_PENDING))) { - return pid; - } - return null; - }).filter(Objects::nonNull).collect(Collectors.toList()); - - if (pidList.size() == 1) { - return getAuthorPid(pidList.get(0)); - } - - List orcid = pidList - .stream() - .filter( - ap -> ap - .getQualifier() - .getClassid() - .equals(ModelConstants.ORCID)) - .collect(Collectors.toList()); - if (orcid.size() == 1) { - return getAuthorPid(orcid.get(0)); - } - orcid = pidList - .stream() - .filter( - ap -> ap - .getQualifier() - .getClassid() - .equals(ModelConstants.ORCID_PENDING)) - .collect(Collectors.toList()); - if (orcid.size() == 1) { - return getAuthorPid(orcid.get(0)); - } - - return null; - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SaveCommunityMap.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SaveCommunityMap.java deleted file mode 100644 index a6595d756..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SaveCommunityMap.java +++ /dev/null @@ -1,99 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump; - -import java.io.BufferedWriter; -import java.io.IOException; -import java.io.OutputStreamWriter; -import java.io.Serializable; -import java.nio.charset.StandardCharsets; -import java.util.Optional; - -import org.apache.commons.io.IOUtils; -import org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.FSDataOutputStream; -import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.fs.Path; -import org.dom4j.DocumentException; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; -import org.xml.sax.SAXException; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; - -/** - * This class connects with the IS related to the isLookUpUrl got as parameter. It saves the information about the - * context that will guide the dump of the results. The information saved is a HashMap. The key is the id of a community - * - research infrastructure/initiative , the value is the label of the research community - research - * infrastructure/initiative. - */ - -public class SaveCommunityMap implements Serializable { - - private static final Logger log = LoggerFactory.getLogger(SaveCommunityMap.class); - private final transient QueryInformationSystem queryInformationSystem; - - private final transient BufferedWriter writer; - - public SaveCommunityMap(String hdfsPath, String hdfsNameNode, String isLookUpUrl) throws IOException { - final Configuration conf = new Configuration(); - conf.set("fs.defaultFS", hdfsNameNode); - FileSystem fileSystem = FileSystem.get(conf); - Path hdfsWritePath = new Path(hdfsPath); - - if (fileSystem.exists(hdfsWritePath)) { - fileSystem.delete(hdfsWritePath, true); - } - - queryInformationSystem = new QueryInformationSystem(); - queryInformationSystem.setIsLookUp(Utils.getIsLookUpService(isLookUpUrl)); - - FSDataOutputStream fos = fileSystem.create(hdfsWritePath); - writer = new BufferedWriter(new OutputStreamWriter(fos, StandardCharsets.UTF_8)); - } - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SaveCommunityMap.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_cm_parameters.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - final String nameNode = parser.get("nameNode"); - log.info("nameNode: {}", nameNode); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - final String isLookUpUrl = parser.get("isLookUpUrl"); - log.info("isLookUpUrl: {}", isLookUpUrl); - - final Boolean singleCommunity = Optional - .ofNullable(parser.get("singleDeposition")) - .map(Boolean::valueOf) - .orElse(false); - - final String community_id = Optional.ofNullable(parser.get("communityId")).orElse(null); - - final SaveCommunityMap scm = new SaveCommunityMap(outputPath, nameNode, isLookUpUrl); - - scm.saveCommunityMap(singleCommunity, community_id); - - } - - private void saveCommunityMap(boolean singleCommunity, String communityId) - throws ISLookUpException, IOException, DocumentException, SAXException { - final String communityMapString = Utils.OBJECT_MAPPER - .writeValueAsString(queryInformationSystem.getCommunityMap(singleCommunity, communityId)); - log.info("communityMap {} ", communityMapString); - writer - .write( - communityMapString); - writer.close(); - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SendToZenodoHDFS.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SendToZenodoHDFS.java deleted file mode 100644 index a19a3a5b6..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SendToZenodoHDFS.java +++ /dev/null @@ -1,100 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump; - -import java.io.Serializable; -import java.util.Optional; - -import org.apache.commons.io.IOUtils; -import org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.*; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.common.api.MissingConceptDoiException; -import eu.dnetlib.dhp.common.api.ZenodoAPIClient; -import eu.dnetlib.dhp.oa.graph.dump.exceptions.NoAvailableEntityTypeException; - -public class SendToZenodoHDFS implements Serializable { - - private static final String NEW = "new"; // to be used for a brand new deposition in zenodo - private static final String VERSION = "version"; // to be used to upload a new version of a published deposition - private static final String UPDATE = "update"; // to upload content to an open deposition not published - - public static void main(final String[] args) throws Exception, MissingConceptDoiException { - final ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils - .toString( - SendToZenodoHDFS.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/upload_zenodo.json"))); - - parser.parseArgument(args); - - final String hdfsPath = parser.get("hdfsPath"); - final String hdfsNameNode = parser.get("nameNode"); - final String access_token = parser.get("accessToken"); - final String connection_url = parser.get("connectionUrl"); - final String metadata = parser.get("metadata"); - final String depositionType = parser.get("depositionType"); - final String concept_rec_id = Optional - .ofNullable(parser.get("conceptRecordId")) - .orElse(null); - final Boolean publish = Optional - .ofNullable(parser.get("publish")) - .map(Boolean::valueOf) - .orElse(false); - - final String depositionId = Optional.ofNullable(parser.get("depositionId")).orElse(null); - - Configuration conf = new Configuration(); - conf.set("fs.defaultFS", hdfsNameNode); - - FileSystem fileSystem = FileSystem.get(conf); - - RemoteIterator fileStatusListIterator = fileSystem - .listFiles( - new Path(hdfsPath), true); - ZenodoAPIClient zenodoApiClient = new ZenodoAPIClient(connection_url, access_token); - switch (depositionType) { - case NEW: - zenodoApiClient.newDeposition(); - break; - case VERSION: - if (concept_rec_id == null) { - throw new MissingConceptDoiException("No concept record id has been provided"); - } - zenodoApiClient.newVersion(concept_rec_id); - break; - case UPDATE: - if (depositionId == null) { - throw new MissingConceptDoiException("No deposition id has been provided"); - } - zenodoApiClient.uploadOpenDeposition(depositionId); - break; - default: - throw new NoAvailableEntityTypeException(); - } - - while (fileStatusListIterator.hasNext()) { - LocatedFileStatus fileStatus = fileStatusListIterator.next(); - - Path p = fileStatus.getPath(); - String pString = p.toString(); - if (!pString.endsWith("_SUCCESS")) { - String name = pString.substring(pString.lastIndexOf("/") + 1); - - FSDataInputStream inputStream = fileSystem.open(p); - zenodoApiClient.uploadIS(inputStream, name, fileStatus.getLen()); - - } - - } - if (!metadata.equals("")) { - zenodoApiClient.sendMretadata(metadata); - } - - if (Boolean.TRUE.equals(publish)) { - zenodoApiClient.publish(); - } - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Utils.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Utils.java deleted file mode 100644 index 8e75e9d92..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Utils.java +++ /dev/null @@ -1,77 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump; - -import java.io.BufferedReader; -import java.io.IOException; -import java.io.InputStreamReader; - -import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.fs.Path; -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 com.fasterxml.jackson.databind.ObjectMapper; -import com.google.gson.Gson; - -import eu.dnetlib.dhp.common.HdfsSupport; -import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; -import eu.dnetlib.dhp.oa.graph.dump.complete.Constants; -import eu.dnetlib.dhp.utils.DHPUtils; -import eu.dnetlib.dhp.utils.ISLookupClientFactory; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; - -public class Utils { - public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private Utils() { - } - - public static void removeOutputDir(SparkSession spark, String path) { - HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); - } - - public static Dataset readPath( - SparkSession spark, String inputPath, Class clazz) { - return spark - .read() - .textFile(inputPath) - .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz)); - } - - public static ISLookUpService getIsLookUpService(String isLookUpUrl) { - return ISLookupClientFactory.getLookUpService(isLookUpUrl); - } - - public static String getContextId(String id) { - - return String - .format( - "%s|%s::%s", Constants.CONTEXT_ID, Constants.CONTEXT_NS_PREFIX, - DHPUtils.md5(id)); - } - - public static CommunityMap getCommunityMap(SparkSession spark, String communityMapPath) { - - return new Gson().fromJson(spark.read().textFile(communityMapPath).collectAsList().get(0), CommunityMap.class); - - } - - public static CommunityMap readCommunityMap(FileSystem fileSystem, String communityMapPath) throws IOException { - BufferedReader br = new BufferedReader(new InputStreamReader(fileSystem.open(new Path(communityMapPath)))); - StringBuilder sb = new StringBuilder(); - try { - String line; - while ((line = br.readLine()) != null) { - sb.append(line); - } - } finally { - br.close(); - - } - - return new Gson().fromJson(sb.toString(), CommunityMap.class); - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunityMap.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunityMap.java deleted file mode 100644 index d45906337..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunityMap.java +++ /dev/null @@ -1,8 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.community; - -import java.io.Serializable; -import java.util.HashMap; - -public class CommunityMap extends HashMap implements Serializable { -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java deleted file mode 100644 index ee6341f84..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java +++ /dev/null @@ -1,81 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.community; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.util.Optional; -import java.util.stream.Collectors; - -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.FilterFunction; -import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.SaveMode; -import org.apache.spark.sql.SparkSession; - -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; -import eu.dnetlib.dhp.schema.dump.oaf.community.Context; - -/** - * This class splits the dumped results according to the research community - research initiative/infrastructure they - * are related to. The information about the community is found in the element "context.id" in the result. Since the - * context that can be found in the result can be associated not only to communities, a community Map is provided. It - * will guide the splitting process. Note: the repartition(1) just before writing the results related to a community. - * This is a choice due to uploading constraints (just one file for each community) As soon as a better solution will be - * in place remove the repartition - */ -public class CommunitySplit implements Serializable { - - public void run(Boolean isSparkSessionManaged, String inputPath, String outputPath, String communityMapPath) { - SparkConf conf = new SparkConf(); - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath); - execSplit(spark, inputPath, outputPath, communityMap); - }); - } - - private static void execSplit(SparkSession spark, String inputPath, String outputPath, - CommunityMap communities) { - - Dataset result = Utils - .readPath(spark, inputPath + "/publication", CommunityResult.class) - .union(Utils.readPath(spark, inputPath + "/dataset", CommunityResult.class)) - .union(Utils.readPath(spark, inputPath + "/orp", CommunityResult.class)) - .union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class)); - - communities - .keySet() - .stream() - .forEach(c -> printResult(c, result, outputPath + "/" + communities.get(c).replace(" ", "_"))); - - } - - private static void printResult(String c, Dataset result, String outputPath) { - Dataset communityProducts = result - .filter((FilterFunction) r -> containsCommunity(r, c)); - - communityProducts - .write() - .option("compression", "gzip") - .mode(SaveMode.Overwrite) - .json(outputPath); - - } - - private static boolean containsCommunity(CommunityResult r, String c) { - if (Optional.ofNullable(r.getContext()).isPresent()) { - return r - .getContext() - .stream() - .map(Context::getCode) - .collect(Collectors.toList()) - .contains(c); - } - return false; - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/ResultProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/ResultProject.java deleted file mode 100644 index 300af62f3..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/ResultProject.java +++ /dev/null @@ -1,28 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.community; - -import java.io.Serializable; -import java.util.List; - -import eu.dnetlib.dhp.schema.dump.oaf.community.Project; - -public class ResultProject implements Serializable { - private String resultId; - private List projectsList; - - public String getResultId() { - return resultId; - } - - public void setResultId(String resultId) { - this.resultId = resultId; - } - - public List getProjectsList() { - return projectsList; - } - - public void setProjectsList(List projectsList) { - this.projectsList = projectsList; - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkDumpCommunityProducts.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkDumpCommunityProducts.java deleted file mode 100644 index 7ab8a7540..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkDumpCommunityProducts.java +++ /dev/null @@ -1,67 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.community; - -import java.io.Serializable; -import java.util.Optional; - -import org.apache.commons.io.IOUtils; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.DumpProducts; -import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; -import eu.dnetlib.dhp.schema.oaf.Result; - -/** - * Spark action to trigger the dump of results associated to research community - reseach initiative/infrasctructure The - * actual dump if performed via the class DumpProducts that is used also for the entire graph dump - */ -public class SparkDumpCommunityProducts implements Serializable { - - private static final Logger log = LoggerFactory.getLogger(SparkDumpCommunityProducts.class); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkDumpCommunityProducts.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - final String resultClassName = parser.get("resultTableName"); - log.info("resultTableName: {}", resultClassName); - - String communityMapPath = parser.get("communityMapPath"); - - final String dumpType = Optional - .ofNullable(parser.get("dumpType")) - .map(String::valueOf) - .orElse("community"); - - Class inputClazz = (Class) Class.forName(resultClassName); - - DumpProducts dump = new DumpProducts(); - - dump - .run( - isSparkSessionManaged, inputPath, outputPath, communityMapPath, inputClazz, CommunityResult.class, - dumpType); - - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java deleted file mode 100644 index 410feea02..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java +++ /dev/null @@ -1,193 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.community; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.io.StringReader; -import java.util.*; -import java.util.stream.Collectors; - -import org.apache.commons.io.IOUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.FilterFunction; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.api.java.function.MapGroupsFunction; -import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SaveMode; -import org.apache.spark.sql.SparkSession; -import org.dom4j.Document; -import org.dom4j.DocumentException; -import org.dom4j.Node; -import org.dom4j.io.SAXReader; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; -import org.xml.sax.SAXException; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.dump.oaf.Provenance; -import eu.dnetlib.dhp.schema.dump.oaf.community.Funder; -import eu.dnetlib.dhp.schema.dump.oaf.community.Project; -import eu.dnetlib.dhp.schema.dump.oaf.community.Validated; -import eu.dnetlib.dhp.schema.oaf.DataInfo; -import eu.dnetlib.dhp.schema.oaf.Field; -import eu.dnetlib.dhp.schema.oaf.Relation; -import scala.Tuple2; - -/** - * Preparation of the Project information to be added to the dumped results. For each result associated to at least one - * Project, a serialization of an instance af ResultProject class is done. ResultProject contains the resultId, and the - * list of Projects (as in eu.dnetlib.dhp.schema.dump.oaf.community.Project) it is associated to - */ -public class SparkPrepareResultProject implements Serializable { - private static final Logger log = LoggerFactory.getLogger(SparkPrepareResultProject.class); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkPrepareResultProject.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/project_prep_parameters.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - SparkConf conf = new SparkConf(); - - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - prepareResultProjectList(spark, inputPath, outputPath); - }); - } - - private static void prepareResultProjectList(SparkSession spark, String inputPath, String outputPath) { - Dataset relation = Utils - .readPath(spark, inputPath + "/relation", Relation.class) - .filter( - (FilterFunction) r -> !r.getDataInfo().getDeletedbyinference() && - r.getRelClass().equalsIgnoreCase(ModelConstants.IS_PRODUCED_BY)); - - Dataset projects = Utils - .readPath(spark, inputPath + "/project", eu.dnetlib.dhp.schema.oaf.Project.class); - - projects - .joinWith(relation, projects.col("id").equalTo(relation.col("target")), "inner") - .groupByKey( - (MapFunction, String>) value -> value - ._2() - .getSource(), - Encoders.STRING()) - .mapGroups( - (MapGroupsFunction, ResultProject>) (s, - it) -> { - Set projectSet = new HashSet<>(); - Tuple2 first = it.next(); - ResultProject rp = new ResultProject(); - rp.setResultId(s); - eu.dnetlib.dhp.schema.oaf.Project p = first._1(); - projectSet.add(p.getId()); - Project ps = getProject(p, first._2); - - List projList = new ArrayList<>(); - projList.add(ps); - rp.setProjectsList(projList); - it.forEachRemaining(c -> { - eu.dnetlib.dhp.schema.oaf.Project op = c._1(); - if (!projectSet.contains(op.getId())) { - projList - .add(getProject(op, c._2)); - - projectSet.add(op.getId()); - - } - - }); - return rp; - }, Encoders.bean(ResultProject.class)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); - } - - private static Project getProject(eu.dnetlib.dhp.schema.oaf.Project op, Relation relation) { - Project p = Project - .newInstance( - op.getId(), - op.getCode().getValue(), - Optional - .ofNullable(op.getAcronym()) - .map(Field::getValue) - .orElse(null), - Optional - .ofNullable(op.getTitle()) - .map(Field::getValue) - .orElse(null), - Optional - .ofNullable(op.getFundingtree()) - .map(value -> { - List tmp = value - .stream() - .map(ft -> getFunder(ft.getValue())) - .collect(Collectors.toList()); - if (!tmp.isEmpty()) { - return tmp.get(0); - } else { - return null; - } - }) - .orElse(null)); - - Optional di = Optional.ofNullable(op.getDataInfo()); - Provenance provenance = new Provenance(); - if (di.isPresent()) { - provenance.setProvenance(di.get().getProvenanceaction().getClassname()); - provenance.setTrust(di.get().getTrust()); - p.setProvenance(provenance); - } - if (Boolean.TRUE.equals(relation.getValidated())) { - p.setValidated(Validated.newInstance(relation.getValidated(), relation.getValidationDate())); - } - return p; - - } - - private static Funder getFunder(String fundingtree) { - final Funder f = new Funder(); - final Document doc; - try { - final SAXReader reader = new SAXReader(); - reader.setFeature("http://apache.org/xml/features/disallow-doctype-decl", true); - doc = reader.read(new StringReader(fundingtree)); - f.setShortName(((Node) (doc.selectNodes("//funder/shortname").get(0))).getText()); - f.setName(((Node) (doc.selectNodes("//funder/name").get(0))).getText()); - f.setJurisdiction(((Node) (doc.selectNodes("//funder/jurisdiction").get(0))).getText()); - for (Object o : doc.selectNodes("//funding_level_0")) { - List node = ((Node) o).selectNodes("./name"); - f.setFundingStream((node.get(0)).getText()); - } - - return f; - } catch (DocumentException | SAXException e) { - throw new IllegalArgumentException(e); - } - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkSplitForCommunity.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkSplitForCommunity.java deleted file mode 100644 index b62bf18e7..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkSplitForCommunity.java +++ /dev/null @@ -1,50 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.community; - -import java.io.Serializable; -import java.util.Optional; - -import org.apache.commons.io.IOUtils; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; - -/** - * Spark job to trigger the split of results associated to research community - reseach initiative/infrasctructure. The - * actual split is performed by the class CommunitySplit - */ -public class SparkSplitForCommunity implements Serializable { - - private static final Logger log = LoggerFactory.getLogger(SparkSplitForCommunity.class); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkSplitForCommunity.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/split_parameters.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - final String communityMapPath = parser.get("communityMapPath"); - - CommunitySplit split = new CommunitySplit(); - split.run(isSparkSessionManaged, inputPath, outputPath, communityMapPath); - - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkUpdateProjectInfo.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkUpdateProjectInfo.java deleted file mode 100644 index 39ae32053..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkUpdateProjectInfo.java +++ /dev/null @@ -1,90 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.community; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.util.Optional; - -import org.apache.commons.io.IOUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SaveMode; -import org.apache.spark.sql.SparkSession; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; -import scala.Tuple2; - -public class SparkUpdateProjectInfo implements Serializable { - - private static final Logger log = LoggerFactory.getLogger(SparkUpdateProjectInfo.class); - public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkUpdateProjectInfo.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/project_input_parameters.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - final String preparedInfoPath = parser.get("preparedInfoPath"); - log.info("preparedInfoPath: {}", preparedInfoPath); - - SparkConf conf = new SparkConf(); - - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - extend(spark, inputPath, outputPath, preparedInfoPath); - }); - } - - private static void extend( - SparkSession spark, - String inputPath, - String outputPath, - String preparedInfoPath) { - Dataset result = Utils.readPath(spark, inputPath, CommunityResult.class); - Dataset resultProject = Utils.readPath(spark, preparedInfoPath, ResultProject.class); - result - .joinWith( - resultProject, result.col("id").equalTo(resultProject.col("resultId")), - "left") - .map((MapFunction, CommunityResult>) value -> { - CommunityResult r = value._1(); - Optional.ofNullable(value._2()).ifPresent(rp -> r.setProjects(rp.getProjectsList())); - return r; - }, Encoders.bean(CommunityResult.class)) - .write() - .option("compression", "gzip") - .mode(SaveMode.Append) - .json(outputPath); - - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Constants.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Constants.java deleted file mode 100644 index 57708a78d..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Constants.java +++ /dev/null @@ -1,26 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import java.io.Serializable; - -public class Constants implements Serializable { - - public static final String IS_HOSTED_BY = "isHostedBy"; - public static final String HOSTS = "hosts"; - - public static final String IS_FUNDED_BY = "isFundedBy"; - public static final String FUNDS = "funds"; - - public static final String FUNDINGS = "fundings"; - - public static final String RESULT_ENTITY = "result"; - public static final String DATASOURCE_ENTITY = "datasource"; - public static final String CONTEXT_ENTITY = "context"; - public static final String ORGANIZATION_ENTITY = "organization"; - public static final String PROJECT_ENTITY = "project"; - - public static final String CONTEXT_ID = "00"; - public static final String CONTEXT_NS_PREFIX = "context_____"; - public static final String UNKNOWN = "UNKNOWN"; - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/ContextInfo.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/ContextInfo.java deleted file mode 100644 index 982a69afb..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/ContextInfo.java +++ /dev/null @@ -1,84 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import java.io.Serializable; -import java.util.List; - -/** - * Deserialization of the information in the context needed to create Context Entities, and relations between context - * entities and datasources and projects - */ -public class ContextInfo implements Serializable { - private String id; - private String description; - private String type; - private String zenodocommunity; - private String name; - private List projectList; - private List datasourceList; - private List subject; - - public List getSubject() { - return subject; - } - - public void setSubject(List subject) { - this.subject = subject; - } - - public String getName() { - return name; - } - - public void setName(String name) { - this.name = name; - } - - public String getId() { - return id; - } - - public void setId(String id) { - this.id = id; - } - - public String getDescription() { - return description; - } - - public void setDescription(String description) { - this.description = description; - } - - public String getType() { - return type; - } - - public void setType(String type) { - this.type = type; - } - - public String getZenodocommunity() { - return zenodocommunity; - } - - public void setZenodocommunity(String zenodocommunity) { - this.zenodocommunity = zenodocommunity; - } - - public List getProjectList() { - return projectList; - } - - public void setProjectList(List projectList) { - this.projectList = projectList; - } - - public List getDatasourceList() { - return datasourceList; - } - - public void setDatasourceList(List datasourceList) { - this.datasourceList = datasourceList; - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextEntities.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextEntities.java deleted file mode 100644 index c422c3b40..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextEntities.java +++ /dev/null @@ -1,110 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import java.io.BufferedWriter; -import java.io.IOException; -import java.io.OutputStreamWriter; -import java.io.Serializable; -import java.nio.charset.StandardCharsets; -import java.util.function.Consumer; -import java.util.function.Function; - -import org.apache.commons.io.IOUtils; -import org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.FSDataOutputStream; -import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.fs.Path; -import org.apache.hadoop.io.compress.CompressionCodec; -import org.apache.hadoop.io.compress.CompressionCodecFactory; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.schema.dump.oaf.graph.ResearchInitiative; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; - -/** - * Writes on HDFS Context entities. It queries the Information System at the lookup url provided as parameter and - * collects the general information for contexes of type community or ri. The general information is the id of the - * context, its label, the subjects associated to the context, its zenodo community, description and type. This - * information is used to create a new Context Entity - */ -public class CreateContextEntities implements Serializable { - - private static final Logger log = LoggerFactory.getLogger(CreateContextEntities.class); - private final transient Configuration conf; - private final transient BufferedWriter writer; - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - CreateContextEntities.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_entity_parameter.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - final String hdfsPath = parser.get("hdfsPath"); - log.info("hdfsPath: {}", hdfsPath); - - final String hdfsNameNode = parser.get("nameNode"); - log.info("nameNode: {}", hdfsNameNode); - - final String isLookUpUrl = parser.get("isLookUpUrl"); - log.info("isLookUpUrl: {}", isLookUpUrl); - - final CreateContextEntities cce = new CreateContextEntities(hdfsPath, hdfsNameNode); - - log.info("Processing contexts..."); - cce.execute(Process::getEntity, isLookUpUrl); - - cce.close(); - - } - - private void close() throws IOException { - writer.close(); - } - - public CreateContextEntities(String hdfsPath, String hdfsNameNode) throws IOException { - this.conf = new Configuration(); - this.conf.set("fs.defaultFS", hdfsNameNode); - FileSystem fileSystem = FileSystem.get(this.conf); - Path hdfsWritePath = new Path(hdfsPath); - FSDataOutputStream fsDataOutputStream = null; - if (fileSystem.exists(hdfsWritePath)) { - fsDataOutputStream = fileSystem.append(hdfsWritePath); - } else { - fsDataOutputStream = fileSystem.create(hdfsWritePath); - } - CompressionCodecFactory factory = new CompressionCodecFactory(conf); - CompressionCodec codec = factory.getCodecByClassName("org.apache.hadoop.io.compress.GzipCodec"); - - this.writer = new BufferedWriter(new OutputStreamWriter(codec.createOutputStream(fsDataOutputStream), - StandardCharsets.UTF_8)); - - } - - public void execute(final Function producer, String isLookUpUrl) - throws ISLookUpException { - - QueryInformationSystem queryInformationSystem = new QueryInformationSystem(); - queryInformationSystem.setIsLookUp(Utils.getIsLookUpService(isLookUpUrl)); - - final Consumer consumer = ci -> writeEntity(producer.apply(ci)); - - queryInformationSystem.getContextInformation(consumer); - } - - protected void writeEntity(final R r) { - try { - writer.write(Utils.OBJECT_MAPPER.writeValueAsString(r)); - writer.newLine(); - } catch (final IOException e) { - throw new IllegalArgumentException(e); - } - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextRelation.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextRelation.java deleted file mode 100644 index 03f53de64..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextRelation.java +++ /dev/null @@ -1,128 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import java.io.BufferedWriter; -import java.io.IOException; -import java.io.OutputStreamWriter; -import java.io.Serializable; -import java.nio.charset.StandardCharsets; -import java.util.List; -import java.util.Objects; -import java.util.Optional; -import java.util.function.Consumer; -import java.util.function.Function; - -import org.apache.commons.io.IOUtils; -import org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.FSDataOutputStream; -import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.fs.Path; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.oa.graph.dump.exceptions.MyRuntimeException; -import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.dhp.schema.dump.oaf.graph.*; -import eu.dnetlib.dhp.schema.oaf.Datasource; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; - -/** - * Writes the set of new Relation between the context and datasources. At the moment the relation between the context - * and the project is not created because of a low coverage in the profiles of openaire ids related to projects - */ -public class CreateContextRelation implements Serializable { - private static final Logger log = LoggerFactory.getLogger(CreateContextRelation.class); - private final transient Configuration conf; - private final transient BufferedWriter writer; - private final transient QueryInformationSystem queryInformationSystem; - - private static final String CONTEX_RELATION_DATASOURCE = "contentproviders"; - private static final String CONTEX_RELATION_PROJECT = "projects"; - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - Objects - .requireNonNull( - CreateContextRelation.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_entity_parameter.json"))); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String hdfsPath = parser.get("hdfsPath"); - log.info("hdfsPath: {}", hdfsPath); - - final String hdfsNameNode = parser.get("nameNode"); - log.info("nameNode: {}", hdfsNameNode); - - final String isLookUpUrl = parser.get("isLookUpUrl"); - log.info("isLookUpUrl: {}", isLookUpUrl); - - final CreateContextRelation cce = new CreateContextRelation(hdfsPath, hdfsNameNode, isLookUpUrl); - - log.info("Creating relation for datasource..."); - cce.execute(Process::getRelation, CONTEX_RELATION_DATASOURCE, ModelSupport.getIdPrefix(Datasource.class)); - - log.info("Creating relations for projects... "); - cce - .execute( - Process::getRelation, CONTEX_RELATION_PROJECT, - ModelSupport.getIdPrefix(eu.dnetlib.dhp.schema.oaf.Project.class)); - - cce.close(); - - } - - private void close() throws IOException { - writer.close(); - } - - public CreateContextRelation(String hdfsPath, String hdfsNameNode, String isLookUpUrl) - throws IOException, ISLookUpException { - this.conf = new Configuration(); - this.conf.set("fs.defaultFS", hdfsNameNode); - - queryInformationSystem = new QueryInformationSystem(); - queryInformationSystem.setIsLookUp(Utils.getIsLookUpService(isLookUpUrl)); - queryInformationSystem.execContextRelationQuery(); - - FileSystem fileSystem = FileSystem.get(this.conf); - Path hdfsWritePath = new Path(hdfsPath); - FSDataOutputStream fsDataOutputStream = null; - if (fileSystem.exists(hdfsWritePath)) { - fsDataOutputStream = fileSystem.append(hdfsWritePath); - } else { - fsDataOutputStream = fileSystem.create(hdfsWritePath); - } - - this.writer = new BufferedWriter(new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8)); - - } - - public void execute(final Function> producer, String category, String prefix) { - - final Consumer consumer = ci -> producer.apply(ci).forEach(this::writeEntity); - - queryInformationSystem.getContextRelation(consumer, category, prefix); - } - - protected void writeEntity(final Relation r) { - try { - writer.write(Utils.OBJECT_MAPPER.writeValueAsString(r)); - writer.newLine(); - } catch (final Exception e) { - throw new MyRuntimeException(e); - } - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpGraphEntities.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpGraphEntities.java deleted file mode 100644 index c9de86613..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpGraphEntities.java +++ /dev/null @@ -1,518 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.io.StringReader; -import java.util.*; -import java.util.stream.Collectors; - -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.FilterFunction; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SaveMode; -import org.apache.spark.sql.SparkSession; -import org.dom4j.Document; -import org.dom4j.DocumentException; -import org.dom4j.Node; -import org.dom4j.io.SAXReader; - -import eu.dnetlib.dhp.oa.graph.dump.DumpProducts; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.dhp.schema.dump.oaf.*; -import eu.dnetlib.dhp.schema.dump.oaf.graph.*; -import eu.dnetlib.dhp.schema.dump.oaf.graph.Funder; -import eu.dnetlib.dhp.schema.dump.oaf.graph.Project; -import eu.dnetlib.dhp.schema.oaf.Field; -import eu.dnetlib.dhp.schema.oaf.Journal; -import eu.dnetlib.dhp.schema.oaf.OafEntity; - -/** - * Dumps of entities in the model defined in eu.dnetlib.dhp.schema.dump.oaf.graph. Results are dumped using the same - * Mapper as for eu.dnetlib.dhp.schema.dump.oaf.community, while for the other entities the mapping is defined below - */ -public class DumpGraphEntities implements Serializable { - - public void run(Boolean isSparkSessionManaged, - String inputPath, - String outputPath, - Class inputClazz, - String communityMapPath) { - - SparkConf conf = new SparkConf(); - - switch (ModelSupport.idPrefixMap.get(inputClazz)) { - case "50": - DumpProducts d = new DumpProducts(); - d - .run( - isSparkSessionManaged, inputPath, outputPath, communityMapPath, inputClazz, GraphResult.class, - eu.dnetlib.dhp.oa.graph.dump.Constants.DUMPTYPE.COMPLETE.getType()); - break; - case "40": - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - projectMap(spark, inputPath, outputPath, inputClazz); - - }); - break; - case "20": - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - organizationMap(spark, inputPath, outputPath, inputClazz); - - }); - break; - case "10": - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - datasourceMap(spark, inputPath, outputPath, inputClazz); - - }); - break; - } - - } - - private static void datasourceMap(SparkSession spark, String inputPath, String outputPath, - Class inputClazz) { - Utils - .readPath(spark, inputPath, inputClazz) - .map( - (MapFunction) d -> mapDatasource((eu.dnetlib.dhp.schema.oaf.Datasource) d), - Encoders.bean(Datasource.class)) - .filter(Objects::nonNull) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); - } - - private static void projectMap(SparkSession spark, String inputPath, String outputPath, - Class inputClazz) { - Utils - .readPath(spark, inputPath, inputClazz) - .map( - (MapFunction) p -> mapProject((eu.dnetlib.dhp.schema.oaf.Project) p), - Encoders.bean(Project.class)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); - } - - private static Datasource mapDatasource(eu.dnetlib.dhp.schema.oaf.Datasource d) { - Datasource datasource = new Datasource(); - - datasource.setId(d.getId()); - - Optional - .ofNullable(d.getOriginalId()) - .ifPresent( - oId -> datasource.setOriginalId(oId.stream().filter(Objects::nonNull).collect(Collectors.toList()))); - - Optional - .ofNullable(d.getPid()) - .ifPresent( - pids -> pids - .stream() - .map(p -> DatasourcePid.newInstance(p.getQualifier().getClassid(), p.getValue())) - .collect(Collectors.toList())); - - Optional - .ofNullable(d.getDatasourcetype()) - .ifPresent( - dsType -> datasource - .setDatasourcetype(DatasourceSchemeValue.newInstance(dsType.getClassid(), dsType.getClassname()))); - - Optional - .ofNullable(d.getOpenairecompatibility()) - .ifPresent(v -> datasource.setOpenairecompatibility(v.getClassname())); - - Optional - .ofNullable(d.getOfficialname()) - .ifPresent(oname -> datasource.setOfficialname(oname.getValue())); - - Optional - .ofNullable(d.getEnglishname()) - .ifPresent(ename -> datasource.setEnglishname(ename.getValue())); - - Optional - .ofNullable(d.getWebsiteurl()) - .ifPresent(wsite -> datasource.setWebsiteurl(wsite.getValue())); - - Optional - .ofNullable(d.getLogourl()) - .ifPresent(lurl -> datasource.setLogourl(lurl.getValue())); - - Optional - .ofNullable(d.getDateofvalidation()) - .ifPresent(dval -> datasource.setDateofvalidation(dval.getValue())); - - Optional - .ofNullable(d.getDescription()) - .ifPresent(dex -> datasource.setDescription(dex.getValue())); - - Optional - .ofNullable(d.getSubjects()) - .ifPresent( - sbjs -> datasource.setSubjects(sbjs.stream().map(sbj -> sbj.getValue()).collect(Collectors.toList()))); - - Optional - .ofNullable(d.getOdpolicies()) - .ifPresent(odp -> datasource.setPolicies(Arrays.asList(odp.getValue()))); - - Optional - .ofNullable(d.getOdlanguages()) - .ifPresent( - langs -> datasource - .setLanguages(langs.stream().map(lang -> lang.getValue()).collect(Collectors.toList()))); - - Optional - .ofNullable(d.getOdcontenttypes()) - .ifPresent( - ctypes -> datasource - .setContenttypes(ctypes.stream().map(ctype -> ctype.getValue()).collect(Collectors.toList()))); - - Optional - .ofNullable(d.getReleasestartdate()) - .ifPresent(rd -> datasource.setReleasestartdate(rd.getValue())); - - Optional - .ofNullable(d.getReleaseenddate()) - .ifPresent(ed -> datasource.setReleaseenddate(ed.getValue())); - - Optional - .ofNullable(d.getMissionstatementurl()) - .ifPresent(ms -> datasource.setMissionstatementurl(ms.getValue())); - - Optional - .ofNullable(d.getDatabaseaccesstype()) - .ifPresent(ar -> datasource.setAccessrights(ar.getValue())); - - Optional - .ofNullable(d.getDatauploadtype()) - .ifPresent(dut -> datasource.setUploadrights(dut.getValue())); - - Optional - .ofNullable(d.getDatabaseaccessrestriction()) - .ifPresent(dar -> datasource.setDatabaseaccessrestriction(dar.getValue())); - - Optional - .ofNullable(d.getDatauploadrestriction()) - .ifPresent(dur -> datasource.setDatauploadrestriction(dur.getValue())); - - Optional - .ofNullable(d.getVersioning()) - .ifPresent(v -> datasource.setVersioning(v.getValue())); - - Optional - .ofNullable(d.getCitationguidelineurl()) - .ifPresent(cu -> datasource.setCitationguidelineurl(cu.getValue())); - - Optional - .ofNullable(d.getPidsystems()) - .ifPresent(ps -> datasource.setPidsystems(ps.getValue())); - - Optional - .ofNullable(d.getCertificates()) - .ifPresent(c -> datasource.setCertificates(c.getValue())); - - Optional - .ofNullable(d.getPolicies()) - .ifPresent(ps -> datasource.setPolicies(ps.stream().map(p -> p.getValue()).collect(Collectors.toList()))); - - Optional - .ofNullable(d.getJournal()) - .ifPresent(j -> datasource.setJournal(getContainer(j))); - - return datasource; - - } - - private static Container getContainer(Journal j) { - Container c = new Container(); - - Optional - .ofNullable(j.getName()) - .ifPresent(n -> c.setName(n)); - - Optional - .ofNullable(j.getIssnPrinted()) - .ifPresent(issnp -> c.setIssnPrinted(issnp)); - - Optional - .ofNullable(j.getIssnOnline()) - .ifPresent(issno -> c.setIssnOnline(issno)); - - Optional - .ofNullable(j.getIssnLinking()) - .ifPresent(isnl -> c.setIssnLinking(isnl)); - - Optional - .ofNullable(j.getEp()) - .ifPresent(ep -> c.setEp(ep)); - - Optional - .ofNullable(j.getIss()) - .ifPresent(iss -> c.setIss(iss)); - - Optional - .ofNullable(j.getSp()) - .ifPresent(sp -> c.setSp(sp)); - - Optional - .ofNullable(j.getVol()) - .ifPresent(vol -> c.setVol(vol)); - - Optional - .ofNullable(j.getEdition()) - .ifPresent(edition -> c.setEdition(edition)); - - Optional - .ofNullable(j.getConferencedate()) - .ifPresent(cdate -> c.setConferencedate(cdate)); - - Optional - .ofNullable(j.getConferenceplace()) - .ifPresent(cplace -> c.setConferenceplace(cplace)); - - return c; - } - - private static Project mapProject(eu.dnetlib.dhp.schema.oaf.Project p) throws DocumentException { - Project project = new Project(); - - Optional - .ofNullable(p.getId()) - .ifPresent(id -> project.setId(id)); - - Optional - .ofNullable(p.getWebsiteurl()) - .ifPresent(w -> project.setWebsiteurl(w.getValue())); - - Optional - .ofNullable(p.getCode()) - .ifPresent(code -> project.setCode(code.getValue())); - - Optional - .ofNullable(p.getAcronym()) - .ifPresent(acronynim -> project.setAcronym(acronynim.getValue())); - - Optional - .ofNullable(p.getTitle()) - .ifPresent(title -> project.setTitle(title.getValue())); - - Optional - .ofNullable(p.getStartdate()) - .ifPresent(sdate -> project.setStartdate(sdate.getValue())); - - Optional - .ofNullable(p.getEnddate()) - .ifPresent(edate -> project.setEnddate(edate.getValue())); - - Optional - .ofNullable(p.getCallidentifier()) - .ifPresent(cide -> project.setCallidentifier(cide.getValue())); - - Optional - .ofNullable(p.getKeywords()) - .ifPresent(key -> project.setKeywords(key.getValue())); - - Optional> omandate = Optional.ofNullable(p.getOamandatepublications()); - Optional> oecsc39 = Optional.ofNullable(p.getEcsc39()); - boolean mandate = false; - if (omandate.isPresent()) { - if (omandate.get().getValue().equals("true")) { - mandate = true; - } - } - if (oecsc39.isPresent()) { - if (oecsc39.get().getValue().equals("true")) { - mandate = true; - } - } - - project.setOpenaccessmandateforpublications(mandate); - project.setOpenaccessmandatefordataset(false); - - Optional - .ofNullable(p.getEcarticle29_3()) - .ifPresent(oamandate -> project.setOpenaccessmandatefordataset(oamandate.getValue().equals("true"))); - - project - .setSubject( - Optional - .ofNullable(p.getSubjects()) - .map(subjs -> subjs.stream().map(s -> s.getValue()).collect(Collectors.toList())) - .orElse(new ArrayList<>())); - - Optional - .ofNullable(p.getSummary()) - .ifPresent(summary -> project.setSummary(summary.getValue())); - - Optional ofundedamount = Optional.ofNullable(p.getFundedamount()); - Optional> ocurrency = Optional.ofNullable(p.getCurrency()); - Optional ototalcost = Optional.ofNullable(p.getTotalcost()); - - if (ocurrency.isPresent()) { - if (ofundedamount.isPresent()) { - if (ototalcost.isPresent()) { - project - .setGranted( - Granted.newInstance(ocurrency.get().getValue(), ototalcost.get(), ofundedamount.get())); - } else { - project.setGranted(Granted.newInstance(ocurrency.get().getValue(), ofundedamount.get())); - } - } - } - - project - .setH2020programme( - Optional - .ofNullable(p.getH2020classification()) - .map( - classification -> classification - .stream() - .map( - c -> Programme - .newInstance( - c.getH2020Programme().getCode(), c.getH2020Programme().getDescription())) - .collect(Collectors.toList())) - .orElse(new ArrayList<>())); - - Optional>> ofundTree = Optional - .ofNullable(p.getFundingtree()); - List funList = new ArrayList<>(); - if (ofundTree.isPresent()) { - for (Field fundingtree : ofundTree.get()) { - funList.add(getFunder(fundingtree.getValue())); - } - } - project.setFunding(funList); - - return project; - } - - public static Funder getFunder(String fundingtree) throws DocumentException { - Funder f = new Funder(); - final Document doc; - - doc = new SAXReader().read(new StringReader(fundingtree)); - f.setShortName(((org.dom4j.Node) (doc.selectNodes("//funder/shortname").get(0))).getText()); - f.setName(((org.dom4j.Node) (doc.selectNodes("//funder/name").get(0))).getText()); - f.setJurisdiction(((org.dom4j.Node) (doc.selectNodes("//funder/jurisdiction").get(0))).getText()); - // f.setId(((org.dom4j.Node) (doc.selectNodes("//funder/id").get(0))).getText()); - - String id = ""; - String description = ""; - // List fundings = new ArrayList<>(); - int level = 0; - List nodes = doc.selectNodes("//funding_level_" + level); - while (nodes.size() > 0) { - for (org.dom4j.Node n : nodes) { - - List node = n.selectNodes("./id"); - id = ((org.dom4j.Node) node.get(0)).getText(); - id = id.substring(id.indexOf("::") + 2); - - node = n.selectNodes("./description"); - description += ((Node) node.get(0)).getText() + " - "; - - } - level += 1; - nodes = doc.selectNodes("//funding_level_" + level); - } - - if (!id.equals("")) { - Fundings fundings = new Fundings(); - fundings.setId(id); - fundings.setDescription(description.substring(0, description.length() - 3).trim()); - f.setFunding_stream(fundings); - } - - return f; - - } - - private static void organizationMap(SparkSession spark, String inputPath, String outputPath, - Class inputClazz) { - Utils - .readPath(spark, inputPath, inputClazz) - .map( - (MapFunction) o -> mapOrganization((eu.dnetlib.dhp.schema.oaf.Organization) o), - Encoders.bean(Organization.class)) - .filter((FilterFunction) o -> o != null) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); - } - - private static eu.dnetlib.dhp.schema.dump.oaf.graph.Organization mapOrganization( - eu.dnetlib.dhp.schema.oaf.Organization org) { - if (org.getDataInfo().getDeletedbyinference()) - return null; - Organization organization = new Organization(); - - Optional - .ofNullable(org.getLegalshortname()) - .ifPresent(value -> organization.setLegalshortname(value.getValue())); - - Optional - .ofNullable(org.getLegalname()) - .ifPresent(value -> organization.setLegalname(value.getValue())); - - Optional - .ofNullable(org.getWebsiteurl()) - .ifPresent(value -> organization.setWebsiteurl(value.getValue())); - - Optional - .ofNullable(org.getAlternativeNames()) - .ifPresent( - value -> organization - .setAlternativenames( - value - .stream() - .map(v -> v.getValue()) - .collect(Collectors.toList()))); - - Optional - .ofNullable(org.getCountry()) - .ifPresent( - value -> { - if (!value.getClassid().equals(Constants.UNKNOWN)) { - organization.setCountry(Country.newInstance(value.getClassid(), value.getClassname())); - } - - }); - - Optional - .ofNullable(org.getId()) - .ifPresent(value -> organization.setId(value)); - - Optional - .ofNullable(org.getPid()) - .ifPresent( - value -> organization - .setPid( - value - .stream() - .map(p -> OrganizationPid.newInstance(p.getQualifier().getClassid(), p.getValue())) - .collect(Collectors.toList()))); - - return organization; - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Extractor.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Extractor.java deleted file mode 100644 index cb4e42ac7..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Extractor.java +++ /dev/null @@ -1,201 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.util.*; - -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.FlatMapFunction; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SaveMode; -import org.apache.spark.sql.SparkSession; - -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.dump.oaf.Provenance; -import eu.dnetlib.dhp.schema.dump.oaf.graph.Node; -import eu.dnetlib.dhp.schema.dump.oaf.graph.RelType; -import eu.dnetlib.dhp.schema.dump.oaf.graph.Relation; -import eu.dnetlib.dhp.schema.oaf.KeyValue; -import eu.dnetlib.dhp.schema.oaf.Result; - -/** - * Creates new Relations (as in eu.dnetlib.dhp.schema.dump.oaf.graph.Relation) from the information in the Entity. The - * new Relations are created for the datasource in the collectedfrom and hostedby elements and for the context related - * to communities and research initiative/infrastructures. For collectedfrom elements it creates: datasource -> provides - * -> result and result -> isProvidedBy -> datasource For hostedby elements it creates: datasource -> hosts -> result - * and result -> isHostedBy -> datasource For context elements it creates: context <-> isRelatedTo <-> result. Note for - * context: it gets the first provenance in the dataInfo. If more than one is present the others are not dumped - */ -public class Extractor implements Serializable { - - public void run(Boolean isSparkSessionManaged, - String inputPath, - String outputPath, - Class inputClazz, - String communityMapPath) { - - SparkConf conf = new SparkConf(); - - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - extractRelationResult( - spark, inputPath, outputPath, inputClazz, Utils.getCommunityMap(spark, communityMapPath)); - }); - } - - private void extractRelationResult(SparkSession spark, - String inputPath, - String outputPath, - Class inputClazz, - CommunityMap communityMap) { - - Set hashCodes = new HashSet<>(); - - Utils - .readPath(spark, inputPath, inputClazz) - .flatMap((FlatMapFunction) value -> { - List relationList = new ArrayList<>(); - extractRelationsFromInstance(hashCodes, value, relationList); - Set communities = communityMap.keySet(); - Optional - .ofNullable(value.getContext()) - .ifPresent(contexts -> contexts.forEach(context -> { - String id = context.getId(); - if (id.contains(":")) { - id = id.substring(0, id.indexOf(":")); - } - if (communities.contains(id)) { - String contextId = Utils.getContextId(id); - Provenance provenance = Optional - .ofNullable(context.getDataInfo()) - .map( - dinfo -> Optional - .ofNullable(dinfo.get(0).getProvenanceaction()) - .map( - paction -> Provenance - .newInstance( - paction.getClassid(), - dinfo.get(0).getTrust())) - .orElse(null)) - .orElse(null); - Relation r = getRelation( - value.getId(), contextId, - Constants.RESULT_ENTITY, - Constants.CONTEXT_ENTITY, - ModelConstants.IS_RELATED_TO, ModelConstants.RELATIONSHIP, provenance); - if (!hashCodes.contains(r.hashCode())) { - relationList - .add(r); - hashCodes.add(r.hashCode()); - } - r = getRelation( - contextId, value.getId(), - Constants.CONTEXT_ENTITY, - Constants.RESULT_ENTITY, - ModelConstants.IS_RELATED_TO, - ModelConstants.RELATIONSHIP, provenance); - if (!hashCodes.contains(r.hashCode())) { - relationList - .add( - r); - hashCodes.add(r.hashCode()); - } - - } - - })); - - return relationList.iterator(); - }, Encoders.bean(Relation.class)) - .write() - .option("compression", "gzip") - .mode(SaveMode.Overwrite) - .json(outputPath); - - } - - private void extractRelationsFromInstance(Set hashCodes, R value, - List relationList) { - Optional - .ofNullable(value.getInstance()) - .ifPresent(inst -> inst.forEach(instance -> { - Optional - .ofNullable(instance.getCollectedfrom()) - .ifPresent( - cf -> getRelatioPair( - value, relationList, cf, - ModelConstants.IS_PROVIDED_BY, ModelConstants.PROVIDES, hashCodes)); - Optional - .ofNullable(instance.getHostedby()) - .ifPresent( - hb -> getRelatioPair( - value, relationList, hb, - Constants.IS_HOSTED_BY, Constants.HOSTS, hashCodes)); - })); - } - - private static void getRelatioPair(R value, List relationList, KeyValue cf, - String resultDatasource, String datasourceResult, - Set hashCodes) { - Provenance provenance = Optional - .ofNullable(cf.getDataInfo()) - .map( - dinfo -> Optional - .ofNullable(dinfo.getProvenanceaction()) - .map( - paction -> Provenance - .newInstance( - paction.getClassname(), - dinfo.getTrust())) - .orElse( - Provenance - .newInstance( - eu.dnetlib.dhp.oa.graph.dump.Constants.HARVESTED, - eu.dnetlib.dhp.oa.graph.dump.Constants.DEFAULT_TRUST))) - .orElse( - Provenance - .newInstance( - eu.dnetlib.dhp.oa.graph.dump.Constants.HARVESTED, - eu.dnetlib.dhp.oa.graph.dump.Constants.DEFAULT_TRUST)); - Relation r = getRelation( - value.getId(), - cf.getKey(), Constants.RESULT_ENTITY, Constants.DATASOURCE_ENTITY, - resultDatasource, ModelConstants.PROVISION, - provenance); - if (!hashCodes.contains(r.hashCode())) { - relationList - .add(r); - hashCodes.add(r.hashCode()); - } - - r = getRelation( - cf.getKey(), value.getId(), - Constants.DATASOURCE_ENTITY, Constants.RESULT_ENTITY, - datasourceResult, ModelConstants.PROVISION, - provenance); - - if (!hashCodes.contains(r.hashCode())) { - relationList - .add(r); - hashCodes.add(r.hashCode()); - } - - } - - private static Relation getRelation(String source, String target, String sourceType, String targetType, - String relName, String relType, Provenance provenance) { - Relation r = new Relation(); - r.setSource(Node.newInstance(source, sourceType)); - r.setTarget(Node.newInstance(target, targetType)); - r.setReltype(RelType.newInstance(relName, relType)); - r.setProvenance(provenance); - return r; - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/MergedRels.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/MergedRels.java deleted file mode 100644 index 30088e8d0..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/MergedRels.java +++ /dev/null @@ -1,25 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import java.io.Serializable; - -public class MergedRels implements Serializable { - private String organizationId; - private String representativeId; - - public String getOrganizationId() { - return organizationId; - } - - public void setOrganizationId(String organizationId) { - this.organizationId = organizationId; - } - - public String getRepresentativeId() { - return representativeId; - } - - public void setRepresentativeId(String representativeId) { - this.representativeId = representativeId; - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/OrganizationMap.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/OrganizationMap.java deleted file mode 100644 index bf6cdbd14..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/OrganizationMap.java +++ /dev/null @@ -1,21 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import java.util.ArrayList; -import java.util.HashMap; -import java.util.List; - -public class OrganizationMap extends HashMap> { - - public OrganizationMap() { - super(); - } - - public List get(String key) { - - if (super.get(key) == null) { - return new ArrayList<>(); - } - return super.get(key); - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Process.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Process.java deleted file mode 100644 index e1cb0e753..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Process.java +++ /dev/null @@ -1,99 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import java.io.Serializable; -import java.util.ArrayList; -import java.util.List; - -import org.apache.commons.lang3.StringUtils; - -import eu.dnetlib.dhp.oa.graph.dump.Constants; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.oa.graph.dump.exceptions.MyRuntimeException; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.dhp.schema.dump.oaf.Provenance; -import eu.dnetlib.dhp.schema.dump.oaf.graph.*; - -/** - * It process the ContextInfo information to produce a new Context Entity or a set of Relations between the generic - * context entity and datasource/projects related to the context. - */ -public class Process implements Serializable { - - @SuppressWarnings("unchecked") - public static R getEntity(ContextInfo ci) { - try { - ResearchInitiative ri; - if (ci.getType().equals("community")) { - ri = new ResearchCommunity(); - ((ResearchCommunity) ri).setSubject(ci.getSubject()); - ri.setType(Constants.RESEARCH_COMMUNITY); - } else { - ri = new ResearchInitiative(); - ri.setType(Constants.RESEARCH_INFRASTRUCTURE); - } - ri.setId(Utils.getContextId(ci.getId())); - ri.setAcronym(ci.getId()); - - ri.setDescription(ci.getDescription()); - ri.setName(ci.getName()); - if (StringUtils.isNotEmpty(ci.getZenodocommunity())) { - ri.setZenodo_community(Constants.ZENODO_COMMUNITY_PREFIX + ci.getZenodocommunity()); - } - return (R) ri; - - } catch (final Exception e) { - throw new MyRuntimeException(e); - } - } - - public static List getRelation(ContextInfo ci) { - try { - - List relationList = new ArrayList<>(); - ci - .getDatasourceList() - .forEach(ds -> { - - String nodeType = ModelSupport.idPrefixEntity.get(ds.substring(0, 2)); - - String contextId = Utils.getContextId(ci.getId()); - relationList - .add( - Relation - .newInstance( - Node - .newInstance( - contextId, eu.dnetlib.dhp.schema.dump.oaf.graph.Constants.CONTEXT_ENTITY), - Node.newInstance(ds, nodeType), - RelType.newInstance(ModelConstants.IS_RELATED_TO, ModelConstants.RELATIONSHIP), - Provenance - .newInstance( - Constants.USER_CLAIM, - Constants.DEFAULT_TRUST))); - - relationList - .add( - Relation - .newInstance( - Node.newInstance(ds, nodeType), - Node - .newInstance( - contextId, eu.dnetlib.dhp.schema.dump.oaf.graph.Constants.CONTEXT_ENTITY), - RelType.newInstance(ModelConstants.IS_RELATED_TO, ModelConstants.RELATIONSHIP), - Provenance - .newInstance( - Constants.USER_CLAIM, - Constants.DEFAULT_TRUST))); - - }); - - return relationList; - - } catch (final Exception e) { - throw new MyRuntimeException(e); - } - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystem.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystem.java deleted file mode 100644 index fcc4bf39c..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystem.java +++ /dev/null @@ -1,195 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import java.io.StringReader; -import java.util.*; -import java.util.function.Consumer; - -import org.dom4j.Document; -import org.dom4j.DocumentException; -import org.dom4j.Element; -import org.dom4j.Node; -import org.dom4j.io.SAXReader; -import org.jetbrains.annotations.NotNull; -import org.xml.sax.SAXException; - -import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.dhp.utils.DHPUtils; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; - -public class QueryInformationSystem { - - private ISLookUpService isLookUp; - private List contextRelationResult; - - private static final String XQUERY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') " - + - " where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " + - " and $x//context/param[./@name = 'status']/text() = 'all' " + - " return " + - "$x//context"; - - private static final String XQUERY_ENTITY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') " - + - "where $x//context[./@type='community' or ./@type = 'ri'] and $x//context/param[./@name = 'status']/text() = 'all' return " - + - "concat(data($x//context/@id) , '@@', $x//context/param[./@name =\"name\"]/text(), '@@', " + - "$x//context/param[./@name=\"description\"]/text(), '@@', $x//context/param[./@name = \"subject\"]/text(), '@@', " - + - "$x//context/param[./@name = \"zenodoCommunity\"]/text(), '@@', $x//context/@type)"; - - public void getContextInformation(final Consumer consumer) throws ISLookUpException { - - isLookUp - .quickSearchProfile(XQUERY_ENTITY) - .forEach(c -> { - ContextInfo cinfo = new ContextInfo(); - String[] cSplit = c.split("@@"); - cinfo.setId(cSplit[0]); - cinfo.setName(cSplit[1]); - cinfo.setDescription(cSplit[2]); - if (!cSplit[3].trim().equals("")) { - cinfo.setSubject(Arrays.asList(cSplit[3].split(","))); - } - cinfo.setZenodocommunity(cSplit[4]); - cinfo.setType(cSplit[5]); - consumer.accept(cinfo); - }); - - } - - public List getContextRelationResult() { - return contextRelationResult; - } - - public void setContextRelationResult(List contextRelationResult) { - this.contextRelationResult = contextRelationResult; - } - - public ISLookUpService getIsLookUp() { - return isLookUp; - } - - public void setIsLookUp(ISLookUpService isLookUpService) { - this.isLookUp = isLookUpService; - } - - public void execContextRelationQuery() throws ISLookUpException { - contextRelationResult = isLookUp.quickSearchProfile(XQUERY); - - } - - public void getContextRelation(final Consumer consumer, String category, String prefix) { - - contextRelationResult.forEach(xml -> { - ContextInfo cinfo = new ContextInfo(); - final Document doc; - - try { - final SAXReader reader = new SAXReader(); - reader.setFeature("http://apache.org/xml/features/disallow-doctype-decl", true); - doc = reader.read(new StringReader(xml)); - Element root = doc.getRootElement(); - cinfo.setId(root.attributeValue("id")); - - Iterator it = root.elementIterator(); - while (it.hasNext()) { - Element el = it.next(); - if (el.getName().equals("category")) { - String categoryId = el.attributeValue("id"); - categoryId = categoryId.substring(categoryId.lastIndexOf("::") + 2); - if (categoryId.equals(category)) { - cinfo.setDatasourceList(getCategoryList(el, prefix)); - } - } - - } - consumer.accept(cinfo); - } catch (DocumentException | SAXException e) { - e.printStackTrace(); - } - - }); - - } - - @NotNull - private List getCategoryList(Element el, String prefix) { - List datasourceList = new ArrayList<>(); - for (Object node : el.selectNodes(".//concept")) { - String oid = getOpenaireId((Node) node, prefix); - if (oid != null) - datasourceList.add(oid); - } - - return datasourceList; - } - - private String getOpenaireId(Node el, String prefix) { - for (Object node : el.selectNodes(".//param")) { - Node n = (Node) node; - if (n.valueOf("./@name").equals("openaireId")) { - return prefix + "|" + n.getText(); - } - } - - return makeOpenaireId(el, prefix); - - } - - private String makeOpenaireId(Node el, String prefix) { - if (!prefix.equals(ModelSupport.entityIdPrefix.get("project"))) { - return null; - } - String funder = ""; - String grantId = null; - String funding = null; - for (Object node : el.selectNodes(".//param")) { - Node n = (Node) node; - switch (n.valueOf("./@name")) { - case "funding": - funding = n.getText(); - break; - case "funder": - funder = n.getText(); - break; - case "CD_PROJECT_NUMBER": - grantId = n.getText(); - break; - default: - break; - } - } - String nsp = null; - - switch (funder.toLowerCase()) { - case "ec": - if (funding == null) { - return null; - } - if (funding.toLowerCase().contains("h2020")) { - nsp = "corda__h2020::"; - } else { - nsp = "corda_______::"; - } - break; - case "tubitak": - nsp = "tubitakf____::"; - break; - case "dfg": - nsp = "dfgf________::"; - break; - default: - StringBuilder bld = new StringBuilder(); - bld.append(funder.toLowerCase()); - for (int i = funder.length(); i < 12; i++) - bld.append("_"); - bld.append("::"); - nsp = bld.toString(); - } - - return prefix + "|" + nsp + DHPUtils.md5(grantId); - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkCollectAndSave.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkCollectAndSave.java deleted file mode 100644 index 1c98ea6cb..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkCollectAndSave.java +++ /dev/null @@ -1,122 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.util.Optional; - -import org.apache.commons.io.IOUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.SaveMode; -import org.apache.spark.sql.SparkSession; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult; -import eu.dnetlib.dhp.schema.dump.oaf.graph.Relation; - -/** - * Reads all the entities of the same type (Relation / Results) and saves them in the same folder - */ -public class SparkCollectAndSave implements Serializable { - - private static final Logger log = LoggerFactory.getLogger(SparkCollectAndSave.class); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkCollectAndSave.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_collect_and_save.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - final Boolean aggregateResult = Optional - .ofNullable(parser.get("resultAggregation")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - - SparkConf conf = new SparkConf(); - - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath + "/result"); - run(spark, inputPath, outputPath, aggregateResult); - - }); - - } - - private static void run(SparkSession spark, String inputPath, String outputPath, boolean aggregate) { - if (aggregate) { - Utils - .readPath(spark, inputPath + "/result/publication", GraphResult.class) - .union(Utils.readPath(spark, inputPath + "/result/dataset", GraphResult.class)) - .union(Utils.readPath(spark, inputPath + "/result/otherresearchproduct", GraphResult.class)) - .union(Utils.readPath(spark, inputPath + "/result/software", GraphResult.class)) - .write() - .option("compression", "gzip") - .mode(SaveMode.Overwrite) - .json(outputPath + "/result"); - } else { - write( - Utils - .readPath(spark, inputPath + "/result/publication", GraphResult.class), - outputPath + "/publication"); - write( - Utils - .readPath(spark, inputPath + "/result/dataset", GraphResult.class), - outputPath + "/dataset"); - write( - Utils - .readPath(spark, inputPath + "/result/otherresearchproduct", GraphResult.class), - outputPath + "/otheresearchproduct"); - write( - Utils - .readPath(spark, inputPath + "/result/software", GraphResult.class), - outputPath + "/software"); - - } - - Utils - .readPath(spark, inputPath + "/relation/publication", Relation.class) - .union(Utils.readPath(spark, inputPath + "/relation/dataset", Relation.class)) - .union(Utils.readPath(spark, inputPath + "/relation/orp", Relation.class)) - .union(Utils.readPath(spark, inputPath + "/relation/software", Relation.class)) - .union(Utils.readPath(spark, inputPath + "/relation/contextOrg", Relation.class)) - .union(Utils.readPath(spark, inputPath + "/relation/context", Relation.class)) - .union(Utils.readPath(spark, inputPath + "/relation/relation", Relation.class)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath + "/relation"); - - } - - private static void write(Dataset dataSet, String outputPath) { - dataSet - .write() - .option("compression", "gzip") - .mode(SaveMode.Overwrite) - .json(outputPath); - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpEntitiesJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpEntitiesJob.java deleted file mode 100644 index 7cc05a821..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpEntitiesJob.java +++ /dev/null @@ -1,54 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import java.io.Serializable; -import java.util.Optional; - -import org.apache.commons.io.IOUtils; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.schema.oaf.OafEntity; - -/** - * Spark Job that fires the dump for the entites - */ -public class SparkDumpEntitiesJob implements Serializable { - private static final Logger log = LoggerFactory.getLogger(SparkDumpEntitiesJob.class); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkDumpEntitiesJob.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - final String resultClassName = parser.get("resultTableName"); - log.info("resultTableName: {}", resultClassName); - - final String communityMapPath = parser.get("communityMapPath"); - - Class inputClazz = (Class) Class.forName(resultClassName); - - DumpGraphEntities dg = new DumpGraphEntities(); - dg.run(isSparkSessionManaged, inputPath, outputPath, inputClazz, communityMapPath); - - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpRelationJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpRelationJob.java deleted file mode 100644 index 0ac97dcb6..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpRelationJob.java +++ /dev/null @@ -1,132 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.util.*; - -import org.apache.commons.io.IOUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.FilterFunction; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SaveMode; -import org.apache.spark.sql.SparkSession; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.dhp.schema.dump.oaf.Provenance; -import eu.dnetlib.dhp.schema.dump.oaf.graph.Node; -import eu.dnetlib.dhp.schema.dump.oaf.graph.RelType; -import eu.dnetlib.dhp.schema.oaf.DataInfo; -import eu.dnetlib.dhp.schema.oaf.Relation; - -/** - * Dumps eu.dnetlib.dhp.schema.oaf.Relation in eu.dnetlib.dhp.schema.dump.oaf.graph.Relation - */ -public class SparkDumpRelationJob implements Serializable { - - private static final Logger log = LoggerFactory.getLogger(SparkDumpRelationJob.class); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkDumpRelationJob.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_relationdump_parameters.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - Optional rs = Optional.ofNullable(parser.get("removeSet")); - final Set removeSet = new HashSet<>(); - if (rs.isPresent()) { - Collections.addAll(removeSet, rs.get().split(";")); - } - - SparkConf conf = new SparkConf(); - - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - dumpRelation(spark, inputPath, outputPath, removeSet); - - }); - - } - - private static void dumpRelation(SparkSession spark, String inputPath, String outputPath, Set removeSet) { - Dataset relations = Utils.readPath(spark, inputPath, Relation.class); - relations - .filter((FilterFunction) r -> !removeSet.contains(r.getRelClass())) - .map((MapFunction) relation -> { - eu.dnetlib.dhp.schema.dump.oaf.graph.Relation relNew = new eu.dnetlib.dhp.schema.dump.oaf.graph.Relation(); - relNew - .setSource( - Node - .newInstance( - relation.getSource(), - ModelSupport.idPrefixEntity.get(relation.getSource().substring(0, 2)))); - - relNew - .setTarget( - Node - .newInstance( - relation.getTarget(), - ModelSupport.idPrefixEntity.get(relation.getTarget().substring(0, 2)))); - - relNew - .setReltype( - RelType - .newInstance( - relation.getRelClass(), - relation.getSubRelType())); - - Optional odInfo = Optional.ofNullable(relation.getDataInfo()); - if (odInfo.isPresent()) { - DataInfo dInfo = odInfo.get(); - if (Optional.ofNullable(dInfo.getProvenanceaction()).isPresent() && - Optional.ofNullable(dInfo.getProvenanceaction().getClassname()).isPresent()) { - relNew - .setProvenance( - Provenance - .newInstance( - dInfo.getProvenanceaction().getClassname(), - dInfo.getTrust())); - } - } - if (Boolean.TRUE.equals(relation.getValidated())) { - relNew.setValidated(relation.getValidated()); - relNew.setValidationDate(relation.getValidationDate()); - } - - return relNew; - - }, Encoders.bean(eu.dnetlib.dhp.schema.dump.oaf.graph.Relation.class)) - .write() - .option("compression", "gzip") - .mode(SaveMode.Overwrite) - .json(outputPath); - - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkExtractRelationFromEntities.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkExtractRelationFromEntities.java deleted file mode 100644 index ec91bd8d6..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkExtractRelationFromEntities.java +++ /dev/null @@ -1,54 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import java.io.Serializable; -import java.util.*; - -import org.apache.commons.io.IOUtils; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.schema.oaf.Result; - -/** - * Spark job that fires the extraction of relations from entities - */ -public class SparkExtractRelationFromEntities implements Serializable { - private static final Logger log = LoggerFactory.getLogger(SparkExtractRelationFromEntities.class); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkExtractRelationFromEntities.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - final String resultClassName = parser.get("resultTableName"); - log.info("resultTableName: {}", resultClassName); - - final String communityMapPath = parser.get("communityMapPath"); - - Class inputClazz = (Class) Class.forName(resultClassName); - - Extractor extractor = new Extractor(); - extractor.run(isSparkSessionManaged, inputPath, outputPath, inputClazz, communityMapPath); - - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkOrganizationRelation.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkOrganizationRelation.java deleted file mode 100644 index dff1a1066..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkOrganizationRelation.java +++ /dev/null @@ -1,176 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.util.*; -import java.util.function.Consumer; - -import org.apache.commons.io.IOUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.*; -import org.jetbrains.annotations.NotNull; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.google.gson.Gson; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.dhp.schema.dump.oaf.Provenance; -import eu.dnetlib.dhp.schema.dump.oaf.graph.Node; -import eu.dnetlib.dhp.schema.dump.oaf.graph.RelType; -import eu.dnetlib.dhp.schema.oaf.Relation; - -/** - * Create new Relations between Context Entities and Organizations whose products are associated to the context. It - * produces relation such as: organization <-> isRelatedTo <-> context - */ -public class SparkOrganizationRelation implements Serializable { - private static final Logger log = LoggerFactory.getLogger(SparkOrganizationRelation.class); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkOrganizationRelation.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_organization_parameters.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - final OrganizationMap organizationMap = new Gson() - .fromJson(parser.get("organizationCommunityMap"), OrganizationMap.class); - final String serializedOrganizationMap = new Gson().toJson(organizationMap); - log.info("organization map : {}", serializedOrganizationMap); - - final String communityMapPath = parser.get("communityMapPath"); - log.info("communityMapPath: {}", communityMapPath); - - SparkConf conf = new SparkConf(); - - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - extractRelation(spark, inputPath, organizationMap, outputPath, communityMapPath); - - }); - - } - - private static void extractRelation(SparkSession spark, String inputPath, OrganizationMap organizationMap, - String outputPath, String communityMapPath) { - - CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath); - - Dataset relationDataset = Utils.readPath(spark, inputPath, Relation.class); - - relationDataset.createOrReplaceTempView("relation"); - - List relList = new ArrayList<>(); - - Dataset mergedRelsDataset = spark - .sql( - "SELECT target organizationId, source representativeId " + - "FROM relation " + - "WHERE datainfo.deletedbyinference = false " + - "AND relclass = 'merges' " + - "AND substr(source, 1, 2) = '20'") - .as(Encoders.bean(MergedRels.class)); - - mergedRelsDataset.map((MapFunction) mergedRels -> { - if (organizationMap.containsKey(mergedRels.getOrganizationId())) { - return mergedRels; - } - return null; - }, Encoders.bean(MergedRels.class)) - .filter(Objects::nonNull) - .collectAsList() - .forEach(getMergedRelsConsumer(organizationMap, relList, communityMap)); - - organizationMap - .keySet() - .forEach( - oId -> organizationMap - .get(oId) - .forEach(community -> { - if (communityMap.containsKey(community)) { - addRelations(relList, community, oId); - } - })); - - spark - .createDataset(relList, Encoders.bean(eu.dnetlib.dhp.schema.dump.oaf.graph.Relation.class)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); - } - - @NotNull - private static Consumer getMergedRelsConsumer(OrganizationMap organizationMap, - List relList, CommunityMap communityMap) { - return mergedRels -> { - String oId = mergedRels.getOrganizationId(); - organizationMap - .get(oId) - .forEach(community -> { - if (communityMap.containsKey(community)) { - addRelations(relList, community, mergedRels.getRepresentativeId()); - } - - }); - organizationMap.remove(oId); - }; - } - - private static void addRelations(List relList, String community, - String organization) { - - String id = Utils.getContextId(community); - log.info("create relation for organization: {}", organization); - relList - .add( - eu.dnetlib.dhp.schema.dump.oaf.graph.Relation - .newInstance( - Node.newInstance(id, Constants.CONTEXT_ENTITY), - Node.newInstance(organization, ModelSupport.idPrefixEntity.get(organization.substring(0, 2))), - RelType.newInstance(ModelConstants.IS_RELATED_TO, ModelConstants.RELATIONSHIP), - Provenance - .newInstance( - eu.dnetlib.dhp.oa.graph.dump.Constants.USER_CLAIM, - eu.dnetlib.dhp.oa.graph.dump.Constants.DEFAULT_TRUST))); - - relList - .add( - eu.dnetlib.dhp.schema.dump.oaf.graph.Relation - .newInstance( - Node.newInstance(organization, ModelSupport.idPrefixEntity.get(organization.substring(0, 2))), - Node.newInstance(id, Constants.CONTEXT_ENTITY), - RelType.newInstance(ModelConstants.IS_RELATED_TO, ModelConstants.RELATIONSHIP), - Provenance - .newInstance( - eu.dnetlib.dhp.oa.graph.dump.Constants.USER_CLAIM, - eu.dnetlib.dhp.oa.graph.dump.Constants.DEFAULT_TRUST))); - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkSelectValidRelationsJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkSelectValidRelationsJob.java deleted file mode 100644 index 1e5675e5f..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkSelectValidRelationsJob.java +++ /dev/null @@ -1,136 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.util.Optional; - -import org.apache.commons.io.IOUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SaveMode; -import org.apache.spark.sql.SparkSession; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.schema.oaf.*; - -/** - * It selects the valid relations among those present in the graph. One relation is valid if it is not deletedbyinference - * and if both the source and the target node are present in the graph and are not deleted by inference nor invisible. - * To check this I made a view of the ids of all the entities in the graph, and select the relations for which a join exists - * with this view for both the source and the target - */ - -public class SparkSelectValidRelationsJob implements Serializable { - - private static final Logger log = LoggerFactory.getLogger(SparkSelectValidRelationsJob.class); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkSelectValidRelationsJob.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_relationdump_parameters.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - SparkConf conf = new SparkConf(); - - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - selectValidRelation(spark, inputPath, outputPath); - - }); - - } - - private static void selectValidRelation(SparkSession spark, String inputPath, String outputPath) { - Dataset relation = Utils.readPath(spark, inputPath + "/relation", Relation.class); - Dataset publication = Utils.readPath(spark, inputPath + "/publication", Publication.class); - Dataset dataset = Utils - .readPath(spark, inputPath + "/dataset", eu.dnetlib.dhp.schema.oaf.Dataset.class); - Dataset software = Utils.readPath(spark, inputPath + "/software", Software.class); - Dataset other = Utils - .readPath(spark, inputPath + "/otherresearchproduct", OtherResearchProduct.class); - Dataset organization = Utils.readPath(spark, inputPath + "/organization", Organization.class); - Dataset project = Utils.readPath(spark, inputPath + "/project", Project.class); - Dataset datasource = Utils.readPath(spark, inputPath + "/datasource", Datasource.class); - - relation.createOrReplaceTempView("relation"); - publication.createOrReplaceTempView("publication"); - dataset.createOrReplaceTempView("dataset"); - other.createOrReplaceTempView("other"); - software.createOrReplaceTempView("software"); - organization.createOrReplaceTempView("organization"); - project.createOrReplaceTempView("project"); - datasource.createOrReplaceTempView("datasource"); - - spark - .sql( - "SELECT id " + - "FROM publication " + - "WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " + - "UNION ALL " + - "SELECT id " + - "FROM dataset " + - "WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " + - "UNION ALL " + - "SELECT id " + - "FROM other " + - "WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " + - "UNION ALL " + - "SELECT id " + - "FROM software " + - "WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " + - "UNION ALL " + - "SELECT id " + - "FROM organization " + - "WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " + - "UNION ALL " + - "SELECT id " + - "FROM project " + - "WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " + - "UNION ALL " + - "SELECT id " + - "FROM datasource " + - "WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false ") - .createOrReplaceTempView("identifiers"); - - spark - .sql( - "SELECT relation.* " + - "FROM relation " + - "JOIN identifiers i1 " + - "ON source = i1.id " + - "JOIN identifiers i2 " + - "ON target = i2.id " + - "WHERE datainfo.deletedbyinference = false") - .as(Encoders.bean(Relation.class)) - .write() - .option("compression", "gzip") - .mode(SaveMode.Overwrite) - .json(outputPath); - - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/MyRuntimeException.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/MyRuntimeException.java deleted file mode 100644 index e325c4334..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/MyRuntimeException.java +++ /dev/null @@ -1,30 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.exceptions; - -public class MyRuntimeException extends RuntimeException { - - public MyRuntimeException() { - super(); - } - - public MyRuntimeException( - final String message, - final Throwable cause, - final boolean enableSuppression, - final boolean writableStackTrace) { - super(message, cause, enableSuppression, writableStackTrace); - } - - public MyRuntimeException(final String message, final Throwable cause) { - super(message, cause); - } - - public MyRuntimeException(final String message) { - super(message); - } - - public MyRuntimeException(final Throwable cause) { - super(cause); - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/NoAvailableEntityTypeException.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/NoAvailableEntityTypeException.java deleted file mode 100644 index f3fbf740a..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/NoAvailableEntityTypeException.java +++ /dev/null @@ -1,29 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.exceptions; - -public class NoAvailableEntityTypeException extends Exception { - public NoAvailableEntityTypeException() { - super(); - } - - public NoAvailableEntityTypeException( - final String message, - final Throwable cause, - final boolean enableSuppression, - final boolean writableStackTrace) { - super(message, cause, enableSuppression, writableStackTrace); - } - - public NoAvailableEntityTypeException(final String message, final Throwable cause) { - super(message, cause); - } - - public NoAvailableEntityTypeException(final String message) { - super(message); - } - - public NoAvailableEntityTypeException(final Throwable cause) { - super(cause); - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java deleted file mode 100644 index 34ca6697c..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java +++ /dev/null @@ -1,129 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.funderresults; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.util.List; -import java.util.Objects; -import java.util.Optional; -import java.util.stream.Collectors; - -import org.apache.commons.io.IOUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.FlatMapFunction; -import org.apache.spark.api.java.function.ForeachFunction; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.*; -import org.jetbrains.annotations.NotNull; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; -import eu.dnetlib.dhp.schema.dump.oaf.community.Funder; -import eu.dnetlib.dhp.schema.dump.oaf.community.Project; - -/** - * Splits the dumped results by funder and stores them in a folder named as the funder nsp (for all the funders, but the EC - * for the EC it specifies also the fundingStream (FP7 or H2020) - */ -public class SparkDumpFunderResults implements Serializable { - private static final Logger log = LoggerFactory.getLogger(SparkDumpFunderResults.class); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkDumpFunderResults.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json")); - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - SparkConf conf = new SparkConf(); - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - writeResultProjectList(spark, inputPath, outputPath); - }); - } - - private static void writeResultProjectList(SparkSession spark, String inputPath, String outputPath) { - Dataset result = Utils - .readPath(spark, inputPath + "/publication", CommunityResult.class) - .union(Utils.readPath(spark, inputPath + "/dataset", CommunityResult.class)) - .union(Utils.readPath(spark, inputPath + "/otherresearchproduct", CommunityResult.class)) - .union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class)); - log.info("Number of result {}", result.count()); - Dataset tmp = result - .flatMap((FlatMapFunction) cr -> cr.getProjects().stream().map(p -> { - return getFunderName(p); - }).collect(Collectors.toList()).iterator(), Encoders.STRING()) - .distinct(); - List funderList = tmp.collectAsList(); - funderList.forEach(funder -> { - dumpResults(funder, result, outputPath); - }); - } - - @NotNull - private static String getFunderName(Project p) { - Optional ofunder = Optional.ofNullable(p.getFunder()); - if (ofunder.isPresent()) { - String fName = ofunder.get().getShortName(); - if (fName.equalsIgnoreCase("ec")) { - fName += "_" + ofunder.get().getFundingStream(); - } - return fName; - } else { - String fName = p.getId().substring(3, p.getId().indexOf("_")).toUpperCase(); - if (fName.equalsIgnoreCase("ec")) { - if (p.getId().contains("h2020")) { - fName += "_H2020"; - } else { - fName += "_FP7"; - } - } else if (fName.equalsIgnoreCase("conicytf")) { - fName = "CONICYT"; - } else if (fName.equalsIgnoreCase("dfgf")) { - fName = "DFG"; - } else if (fName.equalsIgnoreCase("tubitakf")) { - fName = "TUBITAK"; - } else if (fName.equalsIgnoreCase("euenvagency")) { - fName = "EEA"; - } - return fName; - } - } - - private static void dumpResults(String funder, Dataset results, String outputPath) { - results.map((MapFunction) r -> { - if (!Optional.ofNullable(r.getProjects()).isPresent()) { - return null; - } - for (Project p : r.getProjects()) { - String fName = getFunderName(p); - if (fName.equalsIgnoreCase(funder)) { - return r; - } - } - return null; - }, Encoders.bean(CommunityResult.class)) - .filter(Objects::nonNull) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath + "/" + funder); - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java deleted file mode 100644 index 4b0072944..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java +++ /dev/null @@ -1,118 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.funderresults; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.util.Optional; -import java.util.stream.Collectors; - -import org.apache.commons.io.IOUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.FilterFunction; -import org.apache.spark.api.java.function.FlatMapFunction; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.api.java.function.MapGroupsFunction; -import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SaveMode; -import org.apache.spark.sql.SparkSession; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Constants; -import eu.dnetlib.dhp.oa.graph.dump.DumpProducts; -import eu.dnetlib.dhp.oa.graph.dump.ResultMapper; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; -import eu.dnetlib.dhp.oa.graph.dump.community.ResultProject; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; -import eu.dnetlib.dhp.schema.oaf.Project; -import eu.dnetlib.dhp.schema.oaf.Relation; -import eu.dnetlib.dhp.schema.oaf.Result; -import scala.Tuple2; - -/** - * Selects the results linked to projects. Only for these results the dump will be performed. - * The code to perform the dump and to expend the dumped results with the information related to projects - * is the one used for the dump of the community products - */ -public class SparkResultLinkedToProject implements Serializable { - - private static final Logger log = LoggerFactory.getLogger(SparkResultLinkedToProject.class); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - SparkResultLinkedToProject.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - final String resultClassName = parser.get("resultTableName"); - log.info("resultTableName: {}", resultClassName); - - final String resultProjectsPath = parser.get("graphPath"); - log.info("graphPath: {}", resultProjectsPath); - - String communityMapPath = parser.get("communityMapPath"); - - @SuppressWarnings("unchecked") - Class inputClazz = (Class) Class.forName(resultClassName); - SparkConf conf = new SparkConf(); - - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - writeResultsLinkedToProjects( - communityMapPath, spark, inputClazz, inputPath, outputPath, resultProjectsPath); - }); - } - - private static void writeResultsLinkedToProjects(String communityMapPath, SparkSession spark, - Class inputClazz, - String inputPath, String outputPath, String resultProjectsPath) { - - Dataset results = Utils - .readPath(spark, inputPath, inputClazz) - .filter( - (FilterFunction) r -> !r.getDataInfo().getDeletedbyinference() && - !r.getDataInfo().getInvisible()); - Dataset resultProjectDataset = Utils - .readPath(spark, resultProjectsPath, ResultProject.class); - CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath); - results - .joinWith(resultProjectDataset, results.col("id").equalTo(resultProjectDataset.col("resultId"))) - .map((MapFunction, CommunityResult>) t2 -> { - CommunityResult cr = (CommunityResult) ResultMapper - .map( - t2._1(), - communityMap, Constants.DUMPTYPE.FUNDER.getType()); - cr.setProjects(t2._2().getProjectsList()); - return cr; - }, Encoders.bean(CommunityResult.class)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); - - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java deleted file mode 100644 index 38eb3cb37..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java +++ /dev/null @@ -1,82 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.projectssubset; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.util.Objects; -import java.util.Optional; - -import org.apache.commons.io.IOUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SaveMode; -import org.apache.spark.sql.SparkSession; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.schema.dump.oaf.graph.Project; -import scala.Tuple2; - -public class ProjectsSubsetSparkJob implements Serializable { - private static final Logger log = LoggerFactory.getLogger(ProjectsSubsetSparkJob.class); - - public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - ProjectsSubsetSparkJob.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/dump/project_subset_parameters.json")); - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String inputPath = parser.get("sourcePath"); - log.info("inputPath: {}", inputPath); - final String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - final String projectListPath = parser.get("projectListPath"); - log.info("projectListPath: {}", projectListPath); - SparkConf conf = new SparkConf(); - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - Utils.removeOutputDir(spark, outputPath); - getNewProjectList(spark, inputPath, outputPath, projectListPath); - }); - } - - private static void getNewProjectList(SparkSession spark, String inputPath, String outputPath, - String projectListPath) { - Dataset projectList = spark.read().textFile(projectListPath); - Dataset projects; - projects = Utils.readPath(spark, inputPath, Project.class); - projects - .joinWith(projectList, projects.col("id").equalTo(projectList.col("value")), "left") - .map((MapFunction, Project>) t2 -> { - if (Optional.ofNullable(t2._2()).isPresent()) - return null; - return t2._1(); - }, Encoders.bean(Project.class)) - .filter(Objects::nonNull) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); - Utils - .readPath(spark, outputPath, Project.class) - .map((MapFunction) p -> p.getId(), Encoders.STRING()) - .write() - .mode(SaveMode.Append) - .option("compression", "gzip") - .text(projectListPath); - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationsApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationsApplication.java index edfd65299..615b4a824 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationsApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationsApplication.java @@ -19,7 +19,6 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.oa.graph.raw.common.RelationIdMapping; import eu.dnetlib.dhp.schema.oaf.Relation; import scala.Tuple2; @@ -78,8 +77,8 @@ public class PatchRelationsApplication { final String relationPath = graphBasePath + "/relation"; - final Dataset rels = Utils.readPath(spark, relationPath, Relation.class); - final Dataset idMapping = Utils.readPath(spark, idMappingPath, RelationIdMapping.class); + final Dataset rels = readPath(spark, relationPath, Relation.class); + final Dataset idMapping = readPath(spark, idMappingPath, RelationIdMapping.class); log.info("relations: {}", rels.count()); log.info("idMapping: {}", idMapping.count()); @@ -122,4 +121,12 @@ public class PatchRelationsApplication { .text(relationPath); } + public static Dataset readPath( + SparkSession spark, String inputPath, Class clazz) { + return spark + .read() + .textFile(inputPath) + .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz)); + } + } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json deleted file mode 100644 index 5669dca37..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json +++ /dev/null @@ -1,26 +0,0 @@ -[ - { - "paramName":"s", - "paramLongName":"sourcePath", - "paramDescription": "the path of the sequencial file to read", - "paramRequired": true - }, - { - "paramName": "out", - "paramLongName": "outputPath", - "paramDescription": "the path used to store temporary output files", - "paramRequired": true - }, - { - "paramName": "ssm", - "paramLongName": "isSparkSessionManaged", - "paramDescription": "true if the spark session is managed, false otherwise", - "paramRequired": false - }, - { - "paramName": "gp", - "paramLongName": "graphPath", - "paramDescription": "the relationPath", - "paramRequired": false - } -] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_cm_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_cm_parameters.json deleted file mode 100644 index 677715847..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_cm_parameters.json +++ /dev/null @@ -1,37 +0,0 @@ - -[ - - { - "paramName":"is", - "paramLongName":"isLookUpUrl", - "paramDescription": "URL of the isLookUp Service", - "paramRequired": true - }, - { - "paramName":"nn", - "paramLongName":"nameNode", - "paramDescription": "the name node", - "paramRequired": true - }, - { - "paramName": "out", - "paramLongName": "outputPath", - "paramDescription": "the path used to store temporary output files", - "paramRequired": true - }, - { - "paramName": "sd", - "paramLongName": "singleDeposition", - "paramDescription": "true if the dump should be created for a single community", - "paramRequired": true - }, - { - "paramName": "ci", - "paramLongName": "communityId", - "paramDescription": "the id of the community for which to create the dump", - "paramRequired": true - } -] - - - diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_collect_and_save.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_collect_and_save.json deleted file mode 100644 index 2b422176c..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_collect_and_save.json +++ /dev/null @@ -1,30 +0,0 @@ -[ - - { - "paramName":"s", - "paramLongName":"sourcePath", - "paramDescription": "the path of the sequencial file to read", - "paramRequired": true - }, - { - "paramName": "out", - "paramLongName": "outputPath", - "paramDescription": "the path used to store temporary output files", - "paramRequired": true - }, - { - "paramName": "ssm", - "paramLongName": "isSparkSessionManaged", - "paramDescription": "true if the spark session is managed, false otherwise", - "paramRequired": false - }, - { - "paramName": "ra", - "paramLongName": "resultAggregation", - "paramDescription": "true if all the result type should be saved under the generic result name. false to get a different dump for each result type", - "paramRequired": true -} -] - - - diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_complete_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_complete_parameters.json deleted file mode 100644 index bc3e0cd51..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_complete_parameters.json +++ /dev/null @@ -1,35 +0,0 @@ -[ - { - "paramName":"cmp", - "paramLongName":"communityMapPath", - "paramDescription": "the path to the serialization of the community map", - "paramRequired": true - }, - { - "paramName":"s", - "paramLongName":"sourcePath", - "paramDescription": "the path of the sequencial file to read", - "paramRequired": true - }, - { - "paramName": "out", - "paramLongName": "outputPath", - "paramDescription": "the path used to store temporary output files", - "paramRequired": true - }, - { - "paramName": "ssm", - "paramLongName": "isSparkSessionManaged", - "paramDescription": "true if the spark session is managed, false otherwise", - "paramRequired": false - }, - { - "paramName":"tn", - "paramLongName":"resultTableName", - "paramDescription": "the name of the result table we are currently working on", - "paramRequired": true - } -] - - - diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_entity_parameter.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_entity_parameter.json deleted file mode 100644 index 87de13d63..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_entity_parameter.json +++ /dev/null @@ -1,24 +0,0 @@ -[ - - { - "paramName":"is", - "paramLongName":"isLookUpUrl", - "paramDescription": "URL of the isLookUp Service", - "paramRequired": false - }, - { - "paramName": "hdfs", - "paramLongName": "hdfsPath", - "paramDescription": "the path used to store temporary output files", - "paramRequired": true - }, - { - "paramName": "nn", - "paramLongName": "nameNode", - "paramDescription": "the name node", - "paramRequired": true - } -] - - - diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_maketar_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_maketar_parameters.json deleted file mode 100644 index a15318865..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_maketar_parameters.json +++ /dev/null @@ -1,30 +0,0 @@ -[ - - { - "paramName":"s", - "paramLongName":"sourcePath", - "paramDescription": "the path of the sequencial file to read", - "paramRequired": true - }, - { - "paramName": "hdp", - "paramLongName": "hdfsPath", - "paramDescription": "the path used to store the output archive", - "paramRequired": true - }, - { - "paramName":"nn", - "paramLongName":"nameNode", - "paramDescription": "the name node", - "paramRequired": true - }, - { - "paramName":"ss", - "paramLongName":"splitSize", - "paramDescription": "the maximum size of the archive", - "paramRequired": false - } -] - - - diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_organization_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_organization_parameters.json deleted file mode 100644 index c27a9234d..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_organization_parameters.json +++ /dev/null @@ -1,36 +0,0 @@ -[ - - { - "paramName":"ocm", - "paramLongName":"organizationCommunityMap", - "paramDescription": "the organization community map association", - "paramRequired": false - }, - { - "paramName":"s", - "paramLongName":"sourcePath", - "paramDescription": "the path of the sequencial file to read", - "paramRequired": true - }, - { - "paramName": "out", - "paramLongName": "outputPath", - "paramDescription": "the path used to store temporary output files", - "paramRequired": true - }, - { - "paramName": "ssm", - "paramLongName": "isSparkSessionManaged", - "paramDescription": "true if the spark session is managed, false otherwise", - "paramRequired": false - }, - { - "paramName":"cmp", - "paramLongName":"communityMapPath", - "paramDescription": "the path to the serialization of the community map", - "paramRequired": true - } -] - - - diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameter_select_relation.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameter_select_relation.json deleted file mode 100644 index 1a67134a6..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameter_select_relation.json +++ /dev/null @@ -1,20 +0,0 @@ -[ - { - "paramName":"s", - "paramLongName":"sourcePath", - "paramDescription": "the path of the sequencial file to read", - "paramRequired": true - }, - { - "paramName": "out", - "paramLongName": "outputPath", - "paramDescription": "the path used to store temporary output files", - "paramRequired": true - }, - { - "paramName": "ssm", - "paramLongName": "isSparkSessionManaged", - "paramDescription": "true if the spark session is managed, false otherwise", - "paramRequired": false - } -] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json deleted file mode 100644 index e86f6e3d2..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json +++ /dev/null @@ -1,47 +0,0 @@ -[ - - { - "paramName":"cmp", - "paramLongName":"communityMapPath", - "paramDescription": "the path to the serialization of the community map", - "paramRequired": true - }, - { - "paramName":"s", - "paramLongName":"sourcePath", - "paramDescription": "the path of the sequencial file to read", - "paramRequired": true - }, - { - "paramName": "out", - "paramLongName": "outputPath", - "paramDescription": "the path used to store temporary output files", - "paramRequired": true - }, - { - "paramName": "ssm", - "paramLongName": "isSparkSessionManaged", - "paramDescription": "true if the spark session is managed, false otherwise", - "paramRequired": false - }, - { - "paramName":"tn", - "paramLongName":"resultTableName", - "paramDescription": "the name of the result table we are currently working on", - "paramRequired": true - }, - { - "paramName":"dt", - "paramLongName":"dumpType", - "paramDescription": "the type of the dump (complete for the whole graph, community for the products related to communities, funder for the results with at least a link to project", - "paramRequired": false - }, { - "paramName":"cid", - "paramLongName":"communityId", - "paramDescription": "the id of the community to be dumped", - "paramRequired": false -} -] - - - diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json deleted file mode 100644 index 6c45538cf..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json +++ /dev/null @@ -1,41 +0,0 @@ -[ - { - "paramName":"s", - "paramLongName":"sourcePath", - "paramDescription": "the path of the sequencial file to read", - "paramRequired": true - }, - { - "paramName": "out", - "paramLongName": "outputPath", - "paramDescription": "the path used to store temporary output files", - "paramRequired": true - }, - { - "paramName": "ssm", - "paramLongName": "isSparkSessionManaged", - "paramDescription": "true if the spark session is managed, false otherwise", - "paramRequired": false - }, - { - "paramName":"tn", - "paramLongName":"resultTableName", - "paramDescription": "the name of the result table we are currently working on", - "paramRequired": true - }, - { - "paramName":"gp", - "paramLongName":"graphPath", - "paramDescription": "the path to the relations", - "paramRequired": true - }, - { - "paramName":"cmp", - "paramLongName":"communityMapPath", - "paramDescription": "the path to the relations", - "paramRequired": true - } -] - - - diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_relationdump_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_relationdump_parameters.json deleted file mode 100644 index 5c26ea7d1..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_relationdump_parameters.json +++ /dev/null @@ -1,32 +0,0 @@ - - -[ - - { - "paramName":"s", - "paramLongName":"sourcePath", - "paramDescription": "the path of the sequencial file to read", - "paramRequired": true - }, - { - "paramName": "out", - "paramLongName": "outputPath", - "paramDescription": "the path used to store temporary output files", - "paramRequired": true - }, - { - "paramName": "ssm", - "paramLongName": "isSparkSessionManaged", - "paramDescription": "true if the spark session is managed, false otherwise", - "paramRequired": false - }, - { - "paramName": "rs", - "paramLongName": "removeSet", - "paramDescription": "the list of classname relations, split by ';', not to be dumped", - "paramRequired": false - } -] - - - diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/project_input_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/project_input_parameters.json deleted file mode 100644 index f2dc02ba9..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/project_input_parameters.json +++ /dev/null @@ -1,29 +0,0 @@ -[ - - { - "paramName":"s", - "paramLongName":"sourcePath", - "paramDescription": "the path of the sequencial file to read", - "paramRequired": true - }, - { - "paramName": "out", - "paramLongName": "outputPath", - "paramDescription": "the path used to store temporary output files", - "paramRequired": true - }, - { - "paramName": "ssm", - "paramLongName": "isSparkSessionManaged", - "paramDescription": "true if the spark session is managed, false otherwise", - "paramRequired": false - }, - { - "paramName": "pip", - "paramLongName": "preparedInfoPath", - "paramDescription": "the path of the association result projectlist", - "paramRequired": true - } -] - - diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/project_prep_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/project_prep_parameters.json deleted file mode 100644 index 82714d973..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/project_prep_parameters.json +++ /dev/null @@ -1,20 +0,0 @@ -[ - { - "paramName":"s", - "paramLongName":"sourcePath", - "paramDescription": "the path of the sequencial file to read", - "paramRequired": true - }, - { - "paramName": "out", - "paramLongName": "outputPath", - "paramDescription": "the path used to store temporary output files", - "paramRequired": true - }, - { - "paramName": "ssm", - "paramLongName": "isSparkSessionManaged", - "paramDescription": "true if the spark session is managed, false otherwise", - "paramRequired": false - } -] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/project_subset_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/project_subset_parameters.json deleted file mode 100644 index ed2313680..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/project_subset_parameters.json +++ /dev/null @@ -1,27 +0,0 @@ -[ - { - "paramName":"s", - "paramLongName":"sourcePath", - "paramDescription": "the path of the sequencial file to read", - "paramRequired": true - }, - { - "paramName": "out", - "paramLongName": "outputPath", - "paramDescription": "the path used to store temporary output files", - "paramRequired": true - }, - { - "paramName": "ssm", - "paramLongName": "isSparkSessionManaged", - "paramDescription": "true if the spark session is managed, false otherwise", - "paramRequired": false - }, - { - "paramName": "pl", - "paramLongName": "projectListPath", - "paramDescription": "the path of the association result projectlist", - "paramRequired": true - } -] - diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/oozie_app/config-default.xml deleted file mode 100644 index d262cb6e0..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/oozie_app/config-default.xml +++ /dev/null @@ -1,30 +0,0 @@ - - - jobTracker - yarnRM - - - nameNode - hdfs://nameservice1 - - - oozie.use.system.libpath - true - - - hiveMetastoreUris - thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 - - - hiveJdbcUrl - jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000 - - - hiveDbName - openaire - - - oozie.launcher.mapreduce.user.classpath.first - true - - diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/oozie_app/workflow.xml deleted file mode 100644 index 619e3aa20..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/oozie_app/workflow.xml +++ /dev/null @@ -1,171 +0,0 @@ - - - - sourcePath - the source path - - - projectListPath - the path to the project list - - - outputPath - the output path - - - accessToken - the access token used for the deposition in Zenodo - - - connectionUrl - the connection url for Zenodo - - - metadata - the metadata associated to the deposition - - - depositionType - the type of deposition we want to perform. "new" for brand new deposition, "version" for a new version of a published deposition (in this case the concept record id must be provided), "upload" to upload content to an open deposition for which we already have the deposition id (in this case the deposition id should be provided) - - - conceptRecordId - for new version, the id of the record for the old deposition - - - depositionId - the depositionId of a deposition open that has to be added content - - - sparkDriverMemory - memory for driver process - - - sparkExecutorMemory - memory for individual executor - - - sparkExecutorCores - number of cores used by single executor - - - oozieActionShareLibForSpark2 - oozie action sharelib for spark 2.* - - - spark2ExtraListeners - com.cloudera.spark.lineage.NavigatorAppListener - spark 2.* extra listeners classname - - - spark2SqlQueryExecutionListeners - com.cloudera.spark.lineage.NavigatorQueryListener - spark 2.* sql query execution listeners classname - - - spark2YarnHistoryServerAddress - spark 2.* yarn history server address - - - spark2EventLogDir - spark 2.* event log dir location - - - - ${jobTracker} - ${nameNode} - - - mapreduce.job.queuename - ${queueName} - - - oozie.launcher.mapred.job.queue.name - ${oozieLauncherQueueName} - - - oozie.action.sharelib.for.spark - ${oozieActionShareLibForSpark2} - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - yarn - cluster - Dump table project - eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath}/project - --resultTableNameeu.dnetlib.dhp.schema.oaf.Project - --outputPath${workingDir}/project - --communityMapPathnoneed - - - - - - - yarn - cluster - Dump table project - eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectsSubsetSparkJob - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${workingDir}/project - --outputPath${workingDir}/tar/project - --projectListPath${projectListPath} - - - - - - - eu.dnetlib.dhp.oa.graph.dump.MakeTar - --hdfsPath${outputPath} - --nameNode${nameNode} - --sourcePath${workingDir}/tar - - - - - - - eu.dnetlib.dhp.oa.graph.dump.SendToZenodoHDFS - --hdfsPath${outputPath} - --nameNode${nameNode} - --accessToken${accessToken} - --connectionUrl${connectionUrl} - --metadata${metadata} - --conceptRecordId${conceptRecordId} - --depositionType${depositionType} - --depositionId${depositionId} - - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/split_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/split_parameters.json deleted file mode 100644 index dec82bc97..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/split_parameters.json +++ /dev/null @@ -1,37 +0,0 @@ - -[ - - { - "paramName":"cmp", - "paramLongName":"communityMapPath", - "paramDescription": "the path to the serialization of the community map", - "paramRequired": false - }, - - { - "paramName":"s", - "paramLongName":"sourcePath", - "paramDescription": "the path of the sequencial file to read", - "paramRequired": true - }, - { - "paramName": "out", - "paramLongName": "outputPath", - "paramDescription": "the path used to store temporary output files", - "paramRequired": true - }, - { - "paramName": "ssm", - "paramLongName": "isSparkSessionManaged", - "paramDescription": "true if the spark session is managed, false otherwise", - "paramRequired": false - }, { - "paramName":"cid", - "paramLongName":"communityId", - "paramDescription": "the id of the community to be dumped", - "paramRequired": false -} -] - - - diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/upload_zenodo.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/upload_zenodo.json deleted file mode 100644 index b02062ede..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/upload_zenodo.json +++ /dev/null @@ -1,58 +0,0 @@ - -[ - { - "paramName":"dt", - "paramLongName":"depositionType", - "paramDescription": "the type of the deposition (new, version, update)", - "paramRequired": true - }, - { - "paramName":"cri", - "paramLongName":"conceptRecordId", - "paramDescription": "The id of the concept record for a new version", - "paramRequired": false - }, - - { - "paramName":"di", - "paramLongName":"depositionId", - "paramDescription": "the id of an open deposition which has not been published", - "paramRequired": false - }, -{ -"paramName":"hdfsp", -"paramLongName":"hdfsPath", -"paramDescription": "the path of the folder tofind files to send to Zenodo", -"paramRequired": true -}, -{ -"paramName": "nn", -"paramLongName": "nameNode", -"paramDescription": "the name node", -"paramRequired": true -}, -{ -"paramName": "at", -"paramLongName": "accessToken", -"paramDescription": "the access token for the deposition", -"paramRequired": false -}, -{ -"paramName":"cu", -"paramLongName":"connectionUrl", -"paramDescription": "the url to connect to deposit", -"paramRequired": false -}, -{ -"paramName":"m", -"paramLongName":"metadata", -"paramDescription": "metadata associated to the deposition", -"paramRequired": false -}, - { - "paramName":"p", - "paramLongName":"publish", - "paramDescription": "if to publish the upload", - "paramRequired": false - } -] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/config-default.xml deleted file mode 100644 index d262cb6e0..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/config-default.xml +++ /dev/null @@ -1,30 +0,0 @@ - - - jobTracker - yarnRM - - - nameNode - hdfs://nameservice1 - - - oozie.use.system.libpath - true - - - hiveMetastoreUris - thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 - - - hiveJdbcUrl - jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000 - - - hiveDbName - openaire - - - oozie.launcher.mapreduce.user.classpath.first - true - - diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/import.txt b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/import.txt deleted file mode 100644 index bf55947d1..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/import.txt +++ /dev/null @@ -1,4 +0,0 @@ -## This is a classpath-based import file (this header is required) -dump_complete classpath eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app -dump_funder classpath eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app -dump_community classpath eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/workflow.xml deleted file mode 100644 index 2a612dec5..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/workflow.xml +++ /dev/null @@ -1,306 +0,0 @@ - - - - - singleDeposition - Indicates if it is a single community deposition - - - communityId - the id of the community to be dumped if a dump for a single community should be done - - - dumpType - the type of the dump one of {complete, community, funder} - - - onlyUpload - true if the dump is already done and should only be upload in zenodo - - - upload - true if the dump should be upload in zenodo - - - sourcePath - the source path - - - isLookUpUrl - the isLookup service endpoint - - - outputPath - the output path - - - resultAggregation - true if all the result type have to be dumped under result. false otherwise - - - accessToken - the access token used for the deposition in Zenodo - - - connectionUrl - the connection url for Zenodo - - - metadata - the metadata associated to the deposition - - - depositionType - the type of deposition we want to perform. "new" for brand new deposition, "version" for a new version of a published deposition (in this case the concept record id must be provided), "upload" to upload content to an open deposition for which we already have the deposition id (in this case the deposition id should be provided) - - - conceptRecordId - for new version, the id of the record for the old deposition - - - depositionId - the depositionId of a deposition open that has to be added content - - - organizationCommunityMap - the organization community map - - - - hiveDbName - the target hive database name - - - hiveJdbcUrl - hive server jdbc url - - - hiveMetastoreUris - hive server metastore URIs - - - sparkDriverMemory - memory for driver process - - - sparkExecutorMemory - memory for individual executor - - - sparkExecutorCores - number of cores used by single executor - - - oozieActionShareLibForSpark2 - oozie action sharelib for spark 2.* - - - spark2ExtraListeners - com.cloudera.spark.lineage.NavigatorAppListener - spark 2.* extra listeners classname - - - spark2SqlQueryExecutionListeners - com.cloudera.spark.lineage.NavigatorQueryListener - spark 2.* sql query execution listeners classname - - - spark2YarnHistoryServerAddress - spark 2.* yarn history server address - - - spark2EventLogDir - spark 2.* event log dir location - - - - - ${jobTracker} - ${nameNode} - - - mapreduce.job.queuename - ${queueName} - - - oozie.launcher.mapred.job.queue.name - ${oozieLauncherQueueName} - - - oozie.action.sharelib.for.spark - ${oozieActionShareLibForSpark2} - - - - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - ${wf:conf('onlyUpload') eq true} - - - - - - - - - - - - - - - - eu.dnetlib.dhp.oa.graph.dump.SaveCommunityMap - --outputPath${workingDir}/communityMap - --nameNode${nameNode} - --isLookUpUrl${isLookUpUrl} - --singleDeposition${singleDeposition} - --communityId${communityId} - - - - - - - - ${wf:conf('dumpType') eq "funder"} - ${wf:conf('dumpType') eq "community"} - - - - - - - - ${wf:appPath()}/dump_complete - - - - - communityMapPath - ${workingDir}/communityMap - - - outputPath - ${workingDir}/tar - - - sourcePath - ${sourcePath} - - - organizationCommunityMap - ${organizationCommunityMap} - - - isLookUpUrl - ${isLookUpUrl} - - - resultAggregation - ${resultAggregation} - - - - - - - - - - - ${wf:appPath()}/dump_community - - - - - sourcePath - ${sourcePath} - - - communityMapPath - ${workingDir}/communityMap - - - outputPath - ${workingDir}/tar - - - - - - - - - - ${wf:appPath()}/dump_funder - - - - - communityMapPath - ${workingDir}/communityMap - - - outputPath - ${workingDir}/tar - - - sourcePath - ${sourcePath} - - - dumpType - ${dumpType} - - - - - - - - - - eu.dnetlib.dhp.oa.graph.dump.MakeTar - --hdfsPath${outputPath} - --nameNode${nameNode} - --sourcePath${workingDir}/tar - - - - - - - - ${wf:conf('upload') eq true} - - - - - - - eu.dnetlib.dhp.oa.graph.dump.SendToZenodoHDFS - --hdfsPath${outputPath} - --nameNode${nameNode} - --accessToken${accessToken} - --connectionUrl${connectionUrl} - --metadata${metadata} - --conceptRecordId${conceptRecordId} - --depositionType${depositionType} - --depositionId${depositionId} - - - - - - - - diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/config-default.xml deleted file mode 100644 index e5ec3d0ae..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/config-default.xml +++ /dev/null @@ -1,30 +0,0 @@ - - - jobTracker - yarnRM - - - nameNode - hdfs://nameservice1 - - - oozie.use.system.libpath - true - - - hiveMetastoreUris - thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 - - - hiveJdbcUrl - jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000 - - - hiveDbName - openaire - - - oozie.launcher.mapreduce.user.classpath.first - true - - \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml deleted file mode 100644 index dfbe93b67..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml +++ /dev/null @@ -1,362 +0,0 @@ - - - - - sourcePath - the source path - - - outputPath - the output path - - - hiveDbName - the target hive database name - - - hiveJdbcUrl - hive server jdbc url - - - hiveMetastoreUris - hive server metastore URIs - - - sparkDriverMemory - memory for driver process - - - sparkExecutorMemory - memory for individual executor - - - sparkExecutorCores - number of cores used by single executor - - - oozieActionShareLibForSpark2 - oozie action sharelib for spark 2.* - - - spark2ExtraListeners - com.cloudera.spark.lineage.NavigatorAppListener - spark 2.* extra listeners classname - - - spark2SqlQueryExecutionListeners - com.cloudera.spark.lineage.NavigatorQueryListener - spark 2.* sql query execution listeners classname - - - spark2YarnHistoryServerAddress - spark 2.* yarn history server address - - - spark2EventLogDir - spark 2.* event log dir location - - - - - ${jobTracker} - ${nameNode} - - - mapreduce.job.queuename - ${queueName} - - - oozie.launcher.mapred.job.queue.name - ${oozieLauncherQueueName} - - - oozie.action.sharelib.for.spark - ${oozieActionShareLibForSpark2} - - - - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - - - - - - - - yarn - cluster - Dump table publication for community/funder related products - eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath}/publication - --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication - --outputPath${workingDir}/dump/publication - --communityMapPath${communityMapPath} - --dumpType${dumpType} - - - - - - - - yarn - cluster - Dump table dataset for community/funder related products - eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath}/dataset - --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset - --outputPath${workingDir}/dump/dataset - --communityMapPath${communityMapPath} - - - - - - - - yarn - cluster - Dump table ORP for community related products - eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath}/otherresearchproduct - --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct - --outputPath${workingDir}/dump/otherresearchproduct - --communityMapPath${communityMapPath} - - - - - - - - yarn - cluster - Dump table software for community related products - eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath}/software - --resultTableNameeu.dnetlib.dhp.schema.oaf.Software - --outputPath${workingDir}/dump/software - --communityMapPath${communityMapPath} - - - - - - - - - - yarn - cluster - Prepare association result subset of project info - eu.dnetlib.dhp.oa.graph.dump.community.SparkPrepareResultProject - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath} - --outputPath${workingDir}/preparedInfo - - - - - - - - - - - - - - - yarn - cluster - Extend dumped publications with information about project - eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${workingDir}/dump/publication - --outputPath${workingDir}/ext/publication - --preparedInfoPath${workingDir}/preparedInfo - - - - - - - - yarn - cluster - Extend dumped dataset with information about project - eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${workingDir}/dump/dataset - --outputPath${workingDir}/ext/dataset - --preparedInfoPath${workingDir}/preparedInfo - - - - - - - - yarn - cluster - Extend dumped ORP with information about project - eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${workingDir}/dump/otherresearchproduct - --outputPath${workingDir}/ext/orp - --preparedInfoPath${workingDir}/preparedInfo - - - - - - - - yarn - cluster - Extend dumped software with information about project - eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${workingDir}/dump/software - --outputPath${workingDir}/ext/software - --preparedInfoPath${workingDir}/preparedInfo - - - - - - - - - - yarn - cluster - Split dumped result for community - eu.dnetlib.dhp.oa.graph.dump.community.SparkSplitForCommunity - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${workingDir}/ext - --outputPath${outputPath} - --communityMapPath${communityMapPath} - - - - - - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/config-default.xml deleted file mode 100644 index e5ec3d0ae..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/config-default.xml +++ /dev/null @@ -1,30 +0,0 @@ - - - jobTracker - yarnRM - - - nameNode - hdfs://nameservice1 - - - oozie.use.system.libpath - true - - - hiveMetastoreUris - thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 - - - hiveJdbcUrl - jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000 - - - hiveDbName - openaire - - - oozie.launcher.mapreduce.user.classpath.first - true - - \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/workflow.xml deleted file mode 100644 index 7cc133323..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/workflow.xml +++ /dev/null @@ -1,539 +0,0 @@ - - - - sourcePath - the source path - - - outputPath - the output path - - - resultAggregation - true if all the result type have to be dumped under result. false otherwise - - - organizationCommunityMap - the organization community map - - - - hiveDbName - the target hive database name - - - hiveJdbcUrl - hive server jdbc url - - - hiveMetastoreUris - hive server metastore URIs - - - sparkDriverMemory - memory for driver process - - - sparkExecutorMemory - memory for individual executor - - - sparkExecutorCores - number of cores used by single executor - - - oozieActionShareLibForSpark2 - oozie action sharelib for spark 2.* - - - spark2ExtraListeners - com.cloudera.spark.lineage.NavigatorAppListener - spark 2.* extra listeners classname - - - spark2SqlQueryExecutionListeners - com.cloudera.spark.lineage.NavigatorQueryListener - spark 2.* sql query execution listeners classname - - - spark2YarnHistoryServerAddress - spark 2.* yarn history server address - - - spark2EventLogDir - spark 2.* event log dir location - - - - - ${jobTracker} - ${nameNode} - - - mapreduce.job.queuename - ${queueName} - - - oozie.launcher.mapred.job.queue.name - ${oozieLauncherQueueName} - - - oozie.action.sharelib.for.spark - ${oozieActionShareLibForSpark2} - - - - - - - - - - - - - - - - - - - - - - - yarn - cluster - Dump table publication - eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath}/publication - --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication - --outputPath${workingDir}/result/publication - --communityMapPath${communityMapPath} - - - - - - - - yarn - cluster - Dump table dataset - eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath}/dataset - --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset - --outputPath${workingDir}/result/dataset - --communityMapPath${communityMapPath} - - - - - - - - yarn - cluster - Dump table ORP - eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath}/otherresearchproduct - --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct - --outputPath${workingDir}/result/otherresearchproduct - --communityMapPath${communityMapPath} - - - - - - - - yarn - cluster - Dump table software - eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath}/software - --resultTableNameeu.dnetlib.dhp.schema.oaf.Software - --outputPath${workingDir}/result/software - --communityMapPath${communityMapPath} - - - - - - - - yarn - cluster - Dump table organization - eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath}/organization - --resultTableNameeu.dnetlib.dhp.schema.oaf.Organization - --outputPath${outputPath}/organization - --communityMapPath${communityMapPath} - - - - - - - - yarn - cluster - Dump table project - eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath}/project - --resultTableNameeu.dnetlib.dhp.schema.oaf.Project - --outputPath${outputPath}/project - --communityMapPath${communityMapPath} - - - - - - - - yarn - cluster - Dump table datasource - eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath}/datasource - --resultTableNameeu.dnetlib.dhp.schema.oaf.Datasource - --outputPath${outputPath}/datasource - --communityMapPath${workingDir}/communityMap - - - - - - - - yarn - cluster - Select valid table relation - eu.dnetlib.dhp.oa.graph.dump.complete.SparkSelectValidRelationsJob - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - --conf spark.sql.shuffle.partitions=3840 - - --sourcePath${sourcePath} - --outputPath${workingDir}/validrelation - - - - - - - - yarn - cluster - Dump table relation - eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpRelationJob - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${workingDir}/validrelation - --outputPath${workingDir}/relation/relation - --removeSet${removeSet} - - - - - - - - - - - - - - - - eu.dnetlib.dhp.oa.graph.dump.complete.CreateContextEntities - --hdfsPath${outputPath}/communities_infrastructures/communities_infrastructure.json.gz - --nameNode${nameNode} - --isLookUpUrl${isLookUpUrl} - - - - - - - - eu.dnetlib.dhp.oa.graph.dump.complete.CreateContextRelation - --hdfsPath${workingDir}/relation/context - --nameNode${nameNode} - --isLookUpUrl${isLookUpUrl} - - - - - - - - yarn - cluster - Dump table relation - eu.dnetlib.dhp.oa.graph.dump.complete.SparkOrganizationRelation - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath}/relation - --outputPath${workingDir}/relation/contextOrg - --organizationCommunityMap${organizationCommunityMap} - --communityMapPath${communityMapPath} - - - - - - - - - - - - - - - - - yarn - cluster - Extract Relations from publication - eu.dnetlib.dhp.oa.graph.dump.complete.SparkExtractRelationFromEntities - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath}/publication - --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication - --outputPath${workingDir}/relation/publication - --communityMapPath${communityMapPath} - - - - - - - - yarn - cluster - Dump table dataset - eu.dnetlib.dhp.oa.graph.dump.complete.SparkExtractRelationFromEntities - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath}/dataset - --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset - --outputPath${workingDir}/relation/dataset - --communityMapPath${communityMapPath} - - - - - - - - yarn - cluster - Dump table ORP - eu.dnetlib.dhp.oa.graph.dump.complete.SparkExtractRelationFromEntities - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath}/otherresearchproduct - --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct - --outputPath${workingDir}/relation/orp - --communityMapPath${communityMapPath} - - - - - - - - yarn - cluster - Dump table software - eu.dnetlib.dhp.oa.graph.dump.complete.SparkExtractRelationFromEntities - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath}/software - --resultTableNameeu.dnetlib.dhp.schema.oaf.Software - --outputPath${workingDir}/relation/software - --communityMapPath${communityMapPath} - - - - - - - - - - yarn - cluster - Collect Results and Relations and put them in the right path - eu.dnetlib.dhp.oa.graph.dump.complete.SparkCollectAndSave - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${workingDir} - --outputPath${outputPath} - --resultAggregation${resultAggregation} - - - - - - - - - Sub-workflow dump complete failed with error message ${wf:errorMessage()} - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/config-default.xml deleted file mode 100644 index e5ec3d0ae..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/config-default.xml +++ /dev/null @@ -1,30 +0,0 @@ - - - jobTracker - yarnRM - - - nameNode - hdfs://nameservice1 - - - oozie.use.system.libpath - true - - - hiveMetastoreUris - thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 - - - hiveJdbcUrl - jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000 - - - hiveDbName - openaire - - - oozie.launcher.mapreduce.user.classpath.first - true - - \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/workflow.xml deleted file mode 100644 index 2c05256cf..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/workflow.xml +++ /dev/null @@ -1,255 +0,0 @@ - - - - - sourcePath - the source path - - - outputPath - the output path - - - hiveDbName - the target hive database name - - - hiveJdbcUrl - hive server jdbc url - - - hiveMetastoreUris - hive server metastore URIs - - - sparkDriverMemory - memory for driver process - - - sparkExecutorMemory - memory for individual executor - - - sparkExecutorCores - number of cores used by single executor - - - oozieActionShareLibForSpark2 - oozie action sharelib for spark 2.* - - - spark2ExtraListeners - com.cloudera.spark.lineage.NavigatorAppListener - spark 2.* extra listeners classname - - - spark2SqlQueryExecutionListeners - com.cloudera.spark.lineage.NavigatorQueryListener - spark 2.* sql query execution listeners classname - - - spark2YarnHistoryServerAddress - spark 2.* yarn history server address - - - spark2EventLogDir - spark 2.* event log dir location - - - - - ${jobTracker} - ${nameNode} - - - mapreduce.job.queuename - ${queueName} - - - oozie.launcher.mapred.job.queue.name - ${oozieLauncherQueueName} - - - oozie.action.sharelib.for.spark - ${oozieActionShareLibForSpark2} - - - - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - yarn - cluster - Prepare association result subset of project info - eu.dnetlib.dhp.oa.graph.dump.community.SparkPrepareResultProject - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath} - --outputPath${workingDir}/preparedInfo - - - - - - - - - - - - - - - - yarn - cluster - Dump funder results - eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath}/publication - --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication - --outputPath${workingDir}/result/publication - --graphPath${workingDir}/preparedInfo - --communityMapPath${communityMapPath} - - - - - - - - yarn - cluster - Dump funder results - eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath}/dataset - --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset - --outputPath${workingDir}/result/dataset - --graphPath${workingDir}/preparedInfo - --communityMapPath${communityMapPath} - - - - - - - - yarn - cluster - Dump funder results - eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath}/otherresearchproduct - --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct - --outputPath${workingDir}/result/otherresearchproduct - --graphPath${workingDir}/preparedInfo - --communityMapPath${communityMapPath} - - - - - - - - yarn - cluster - Dump funder results - eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath}/software - --resultTableNameeu.dnetlib.dhp.schema.oaf.Software - --outputPath${workingDir}/result/software - --graphPath${workingDir}/preparedInfo - --communityMapPath${communityMapPath} - - - - - - - - - - yarn - cluster - Dump funder results - eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkDumpFunderResults - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${workingDir}/result - --outputPath${outputPath} - - - - - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java index 472d3781d..e206c7c5a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java @@ -5,7 +5,6 @@ import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; import java.util.List; -import java.util.Locale; import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; @@ -21,19 +20,9 @@ import org.junit.jupiter.api.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import com.fasterxml.jackson.core.JsonProcessingException; import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.oa.graph.dump.Constants; -import eu.dnetlib.dhp.oa.graph.dump.DumpJobTest; -import eu.dnetlib.dhp.oa.graph.dump.DumpProducts; -import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.dump.oaf.Instance; -import eu.dnetlib.dhp.schema.dump.oaf.OpenAccessRoute; -import eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult; import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.Software; import eu.dnetlib.dhp.schema.oaf.StructuredProperty; public class CleanContextTest { @@ -48,11 +37,11 @@ public class CleanContextTest { @BeforeAll public static void beforeAll() throws IOException { - workingDir = Files.createTempDirectory(DumpJobTest.class.getSimpleName()); + workingDir = Files.createTempDirectory(CleanContextTest.class.getSimpleName()); log.info("using work dir {}", workingDir); SparkConf conf = new SparkConf(); - conf.setAppName(DumpJobTest.class.getSimpleName()); + conf.setAppName(CleanContextTest.class.getSimpleName()); conf.setMaster("local[*]"); conf.set("spark.driver.host", "localhost"); @@ -63,7 +52,7 @@ public class CleanContextTest { spark = SparkSession .builder() - .appName(DumpJobTest.class.getSimpleName()) + .appName(CleanContextTest.class.getSimpleName()) .config(conf) .getOrCreate(); } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java deleted file mode 100644 index 7300ce860..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java +++ /dev/null @@ -1,967 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.Arrays; -import java.util.List; - -import org.apache.commons.io.FileUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.Row; -import org.apache.spark.sql.SparkSession; -import org.junit.jupiter.api.*; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.core.JsonProcessingException; -import com.fasterxml.jackson.databind.ObjectMapper; -import com.google.gson.Gson; - -import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.dump.oaf.Instance; -import eu.dnetlib.dhp.schema.dump.oaf.OpenAccessRoute; -import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; -import eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult; -import eu.dnetlib.dhp.schema.oaf.Dataset; -import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.Software; - -//@Disabled -public class DumpJobTest { - - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private static SparkSession spark; - - private static Path workingDir; - - private static final Logger log = LoggerFactory.getLogger(DumpJobTest.class); - - private static final CommunityMap map = new CommunityMap(); - - static { - map.put("egi", "EGI Federation"); - map.put("fet-fp7", "FET FP7"); - map.put("fet-h2020", "FET H2020"); - map.put("clarin", "CLARIN"); - map.put("fam", "Fisheries and Aquaculture Management"); - map.put("ni", "Neuroinformatics"); - map.put("mes", "European Marine Scinece"); - map.put("instruct", "Instruct-Eric"); - map.put("rda", "Research Data Alliance"); - map.put("elixir-gr", "ELIXIR GR"); - map.put("aginfra", "Agricultural and Food Sciences"); - map.put("dariah", "DARIAH EU"); - map.put("risis", "RISI"); - map.put("ee", "SDSN - Greece"); - map.put("oa-pg", "EC Post-Grant Open Access Pilot"); - map.put("beopen", "Transport Research"); - map.put("euromarine", "Euromarine"); - map.put("ifremer", "Ifremer"); - map.put("dh-ch", "Digital Humanities and Cultural Heritage"); - map.put("science-innovation-policy", "Science and Innovation Policy Studies"); - map.put("covid-19", "COVID-19"); - map.put("enrmaps", "Energy Research"); - map.put("epos", "EPOS"); - - } - - List communityMap = Arrays - .asList( - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - ""); - - private static final String XQUERY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') " - + - " where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " + - " return " + - " " + - "{$x//CONFIGURATION/context/@id}" + - "{$x//CONFIGURATION/context/@label}" + - ""; - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files.createTempDirectory(DumpJobTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - - SparkConf conf = new SparkConf(); - conf.setAppName(DumpJobTest.class.getSimpleName()); - - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - - spark = SparkSession - .builder() - .appName(DumpJobTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Test - public void testMap() { - System.out.println(new Gson().toJson(map)); - } - - @Test - public void testPublicationDump() { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication_extendedinstance") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - DumpProducts dump = new DumpProducts(); - dump - .run( - // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, - false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, - GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType()); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(GraphResult.class)); - - Assertions.assertEquals(1, verificationDataset.count()); - - GraphResult gr = verificationDataset.first(); - - Assertions.assertEquals(6, gr.getAuthor().size()); - Assertions - .assertTrue( - gr - .getAuthor() - .stream() - .anyMatch( - a -> a.getFullname().equals("Nikolaidou,Charitini") && - a.getName().equals("Charitini") && a.getSurname().equals("Nikolaidou") - && a.getRank() == 1 && a.getPid() == null)); - - Assertions - .assertTrue( - gr - .getAuthor() - .stream() - .anyMatch( - a -> a.getFullname().equals("Votsi,Nefta") && - a.getName().equals("Nefta") && a.getSurname().equals("Votsi") - && a.getRank() == 2 && a.getPid().getId().getScheme().equals(ModelConstants.ORCID) - && a.getPid().getId().getValue().equals("0000-0001-6651-1178") - && a.getPid().getProvenance() != null)); - - Assertions - .assertTrue( - gr - .getAuthor() - .stream() - .anyMatch( - a -> a.getFullname().equals("Sgardelis,Steanos") && - a.getName().equals("Steanos") && a.getSurname().equals("Sgardelis") - && a.getRank() == 3 && a.getPid().getId().getScheme().equals(ModelConstants.ORCID_PENDING) - && a.getPid().getId().getValue().equals("0000-0001-6651-1178") - && a.getPid().getProvenance() != null)); - - Assertions - .assertTrue( - gr - .getAuthor() - .stream() - .anyMatch( - a -> a.getFullname().equals("Halley,John") && - a.getName().equals("John") && a.getSurname().equals("Halley") - && a.getRank() == 4 && a.getPid() == null)); - - Assertions - .assertTrue( - gr - .getAuthor() - .stream() - .anyMatch( - a -> a.getFullname().equals("Pantis,John") && - a.getName().equals("John") && a.getSurname().equals("Pantis") - && a.getRank() == 5 && a.getPid().getId().getScheme().equals(ModelConstants.ORCID) - && a.getPid().getId().getValue().equals("0000-0001-6651-1178") - && a.getPid().getProvenance() != null)); - - Assertions - .assertTrue( - gr - .getAuthor() - .stream() - .anyMatch( - a -> a.getFullname().equals("Tsiafouli,Maria") && - a.getName().equals("Maria") && a.getSurname().equals("Tsiafouli") - && a.getRank() == 6 && a.getPid().getId().getScheme().equals(ModelConstants.ORCID_PENDING) - && a.getPid().getId().getValue().equals("0000-0001-6651-1178") - && a.getPid().getProvenance() != null)); - - Assertions.assertEquals("publication", gr.getType()); - - Assertions.assertEquals("eng", gr.getLanguage().getCode()); - Assertions.assertEquals("English", gr.getLanguage().getLabel()); - - Assertions.assertEquals(1, gr.getCountry().size()); - Assertions.assertEquals("IT", gr.getCountry().get(0).getCode()); - Assertions.assertEquals("Italy", gr.getCountry().get(0).getLabel()); - Assertions.assertTrue(gr.getCountry().get(0).getProvenance() == null); - - Assertions.assertEquals(12, gr.getSubjects().size()); - Assertions - .assertTrue( - gr - .getSubjects() - .stream() - .anyMatch( - s -> s.getSubject().getValue().equals("Ecosystem Services hotspots") - && s.getSubject().getScheme().equals("ACM") && s.getProvenance() != null && - s.getProvenance().getProvenance().equals("sysimport:crosswalk:repository"))); - Assertions - .assertTrue( - gr - .getSubjects() - .stream() - .anyMatch( - s -> s.getSubject().getValue().equals("Natura 2000") - && s.getSubject().getScheme().equals("") && s.getProvenance() != null && - s.getProvenance().getProvenance().equals("sysimport:crosswalk:repository"))); - - Assertions - .assertEquals( - "Ecosystem Service capacity is higher in areas of multiple designation types", - gr.getMaintitle()); - - Assertions.assertEquals(null, gr.getSubtitle()); - - Assertions.assertEquals(1, gr.getDescription().size()); - - Assertions - .assertTrue( - gr - .getDescription() - .get(0) - .startsWith("The implementation of the Ecosystem Service (ES) concept into practice")); - Assertions - .assertTrue( - gr - .getDescription() - .get(0) - .endsWith( - "start complying with new standards and demands for nature conservation and environmental management.")); - - Assertions.assertEquals("2017-01-01", gr.getPublicationdate()); - - Assertions.assertEquals("Pensoft Publishers", gr.getPublisher()); - - Assertions.assertEquals(null, gr.getEmbargoenddate()); - - Assertions.assertEquals(1, gr.getSource().size()); - Assertions.assertEquals("One Ecosystem 2: e13718", gr.getSource().get(0)); - - Assertions.assertEquals(1, gr.getFormat().size()); - Assertions.assertEquals("text/html", gr.getFormat().get(0)); - - Assertions.assertEquals(0, gr.getContributor().size()); - - Assertions.assertEquals(0, gr.getCoverage().size()); - - Assertions.assertEquals(ModelConstants.ACCESS_RIGHT_OPEN, gr.getBestaccessright().getLabel()); - Assertions - .assertEquals( - Constants.accessRightsCoarMap.get(ModelConstants.ACCESS_RIGHT_OPEN), gr.getBestaccessright().getCode()); - - Assertions.assertEquals("One Ecosystem", gr.getContainer().getName()); - Assertions.assertEquals("2367-8194", gr.getContainer().getIssnOnline()); - Assertions.assertEquals("", gr.getContainer().getIssnPrinted()); - Assertions.assertEquals("", gr.getContainer().getIssnLinking()); - - Assertions.assertTrue(null == gr.getDocumentationUrl() || gr.getDocumentationUrl().size() == 0); - - Assertions.assertTrue(null == gr.getCodeRepositoryUrl()); - - Assertions.assertEquals(null, gr.getProgrammingLanguage()); - - Assertions.assertTrue(null == gr.getContactperson() || gr.getContactperson().size() == 0); - - Assertions.assertTrue(null == gr.getContactgroup() || gr.getContactgroup().size() == 0); - - Assertions.assertTrue(null == gr.getTool() || gr.getTool().size() == 0); - - Assertions.assertEquals(null, gr.getSize()); - - Assertions.assertEquals(null, gr.getVersion()); - - Assertions.assertTrue(null == gr.getGeolocation() || gr.getGeolocation().size() == 0); - - Assertions.assertEquals("50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2", gr.getId()); - - Assertions.assertEquals(1, gr.getOriginalId().size()); - Assertions - .assertTrue( - gr.getOriginalId().contains("10.3897/oneeco.2.e13718")); - - Assertions.assertEquals(1, gr.getPid().size()); - Assertions - .assertTrue( - gr.getPid().get(0).getScheme().equals("doi") - && gr.getPid().get(0).getValue().equals("10.1016/j.triboint.2014.05.004")); - - Assertions.assertEquals("2020-03-23T00:20:51.392Z", gr.getDateofcollection()); - - Assertions.assertEquals(1, gr.getInstance().size()); - - Instance instance = gr.getInstance().get(0); - Assertions.assertEquals(0, instance.getPid().size()); - Assertions.assertEquals(1, instance.getAlternateIdentifier().size()); - Assertions - .assertTrue( - instance.getAlternateIdentifier().get(0).getScheme().equals("doi") - && instance.getAlternateIdentifier().get(0).getValue().equals("10.3897/oneeco.2.e13718")); - Assertions.assertEquals(null, instance.getLicense()); - Assertions - .assertTrue( - instance - .getAccessright() - .getCode() - .equals( - Constants.accessRightsCoarMap - .get(ModelConstants.ACCESS_RIGHT_OPEN))); - Assertions.assertTrue(instance.getAccessright().getLabel().equals(ModelConstants.ACCESS_RIGHT_OPEN)); - Assertions.assertTrue(instance.getAccessright().getOpenAccessRoute().equals(OpenAccessRoute.green)); - Assertions.assertTrue(instance.getType().equals("Article")); - Assertions.assertEquals(2, instance.getUrl().size()); - Assertions - .assertTrue( - instance.getUrl().contains("https://doi.org/10.3897/oneeco.2.e13718") - && instance.getUrl().contains("https://oneecosystem.pensoft.net/article/13718/")); - Assertions.assertEquals("2017-01-01", instance.getPublicationdate()); - Assertions.assertEquals(null, instance.getArticleprocessingcharge()); - Assertions.assertEquals("peerReviewed", instance.getRefereed()); - } - - @Test - public void testDatasetDump() { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/dataset_extendedinstance") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - DumpProducts dump = new DumpProducts(); - dump - .run( - false, sourcePath, workingDir.toString() + "/result", - communityMapPath, Dataset.class, - GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType()); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(GraphResult.class)); - - Assertions.assertEquals(1, verificationDataset.count()); - - Assertions.assertEquals(1, verificationDataset.filter("type = 'dataset'").count()); - - // the common fields in the result have been already checked. Now checking only - // community specific fields - - GraphResult gr = verificationDataset.first(); - - Assertions.assertEquals(2, gr.getGeolocation().size()); - Assertions.assertEquals(2, gr.getGeolocation().stream().filter(gl -> gl.getBox().equals("")).count()); - Assertions.assertEquals(1, gr.getGeolocation().stream().filter(gl -> gl.getPlace().equals("")).count()); - Assertions.assertEquals(1, gr.getGeolocation().stream().filter(gl -> gl.getPoint().equals("")).count()); - Assertions - .assertEquals( - 1, - gr - .getGeolocation() - .stream() - .filter(gl -> gl.getPlace().equals("18 York St, Ottawa, ON K1N 5S6; Ottawa; Ontario; Canada")) - .count()); - Assertions - .assertEquals( - 1, gr.getGeolocation().stream().filter(gl -> gl.getPoint().equals("45.427242 -75.693904")).count()); - Assertions - .assertEquals( - 1, - gr - .getGeolocation() - .stream() - .filter(gl -> gl.getPoint().equals("") && !gl.getPlace().equals("")) - .count()); - Assertions - .assertEquals( - 1, - gr - .getGeolocation() - .stream() - .filter(gl -> !gl.getPoint().equals("") && gl.getPlace().equals("")) - .count()); - - Assertions.assertEquals("1024Gb", gr.getSize()); - - Assertions.assertEquals("1.01", gr.getVersion()); - - Assertions.assertEquals(null, gr.getContainer()); - Assertions.assertEquals(null, gr.getCodeRepositoryUrl()); - Assertions.assertEquals(null, gr.getProgrammingLanguage()); - Assertions.assertEquals(null, gr.getDocumentationUrl()); - Assertions.assertEquals(null, gr.getContactperson()); - Assertions.assertEquals(null, gr.getContactgroup()); - Assertions.assertEquals(null, gr.getTool()); - - } - - @Test - public void testSoftwareDump() { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/software_extendedinstance") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - DumpProducts dump = new DumpProducts(); - dump - .run( - false, sourcePath, workingDir.toString() + "/result", - communityMapPath, Software.class, - GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType()); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(GraphResult.class)); - - Assertions.assertEquals(1, verificationDataset.count()); - - Assertions.assertEquals(1, verificationDataset.filter("type = 'software'").count()); - - GraphResult gr = verificationDataset.first(); - - Assertions.assertEquals(2, gr.getDocumentationUrl().size()); - Assertions.assertTrue(gr.getDocumentationUrl().contains("doc_url_1")); - Assertions.assertTrue(gr.getDocumentationUrl().contains("doc_url_2")); - - Assertions.assertEquals("code_repo", gr.getCodeRepositoryUrl()); - - Assertions.assertEquals("perl", gr.getProgrammingLanguage()); - - Assertions.assertEquals(null, gr.getContainer()); - Assertions.assertEquals(null, gr.getContactperson()); - Assertions.assertEquals(null, gr.getContactgroup()); - Assertions.assertEquals(null, gr.getTool()); - Assertions.assertEquals(null, gr.getGeolocation()); - Assertions.assertEquals(null, gr.getSize()); - Assertions.assertEquals(null, gr.getVersion()); - - } - - @Test - public void testOrpDump() { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/orp_extendedinstance") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - DumpProducts dump = new DumpProducts(); - dump - .run( - false, sourcePath, workingDir.toString() + "/result", - communityMapPath, OtherResearchProduct.class, - GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType()); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(GraphResult.class)); - - Assertions.assertEquals(1, verificationDataset.count()); - - Assertions.assertEquals(1, verificationDataset.filter("type = 'other'").count()); - - GraphResult gr = verificationDataset.first(); - - Assertions.assertEquals(2, gr.getContactperson().size()); - Assertions.assertTrue(gr.getContactperson().contains(("contact_person1"))); - Assertions.assertTrue(gr.getContactperson().contains(("contact_person2"))); - - Assertions.assertEquals(1, gr.getContactgroup().size()); - Assertions.assertTrue(gr.getContactgroup().contains(("contact_group"))); - - Assertions.assertEquals(2, gr.getTool().size()); - Assertions.assertTrue(gr.getTool().contains("tool1")); - Assertions.assertTrue(gr.getTool().contains("tool2")); - - Assertions.assertEquals(null, gr.getContainer()); - Assertions.assertEquals(null, gr.getDocumentationUrl()); - Assertions.assertEquals(null, gr.getCodeRepositoryUrl()); - Assertions.assertEquals(null, gr.getProgrammingLanguage()); - Assertions.assertEquals(null, gr.getGeolocation()); - Assertions.assertEquals(null, gr.getSize()); - Assertions.assertEquals(null, gr.getVersion()); - - } - - @Test - public void testPublicationDumpCommunity() throws JsonProcessingException { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication_extendedinstance") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - DumpProducts dump = new DumpProducts(); - dump - .run( - false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, - CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - Assertions.assertEquals(1, verificationDataset.count()); - - Assertions.assertEquals(1, verificationDataset.filter("type = 'publication'").count()); - - // the common fields in the result have been already checked. Now checking only - // community specific fields - - CommunityResult cr = verificationDataset.first(); - - Assertions.assertEquals(1, cr.getContext().size()); - Assertions.assertEquals("dh-ch", cr.getContext().get(0).getCode()); - Assertions.assertEquals("Digital Humanities and Cultural Heritage", cr.getContext().get(0).getLabel()); - Assertions.assertEquals(1, cr.getContext().get(0).getProvenance().size()); - Assertions.assertEquals("Inferred by OpenAIRE", cr.getContext().get(0).getProvenance().get(0).getProvenance()); - Assertions.assertEquals("0.9", cr.getContext().get(0).getProvenance().get(0).getTrust()); - - Assertions.assertEquals(1, cr.getCollectedfrom().size()); - Assertions - .assertEquals("10|openaire____::fdc7e0400d8c1634cdaf8051dbae23db", cr.getCollectedfrom().get(0).getKey()); - Assertions.assertEquals("Pensoft", cr.getCollectedfrom().get(0).getValue()); - - Assertions.assertEquals(1, cr.getInstance().size()); - Assertions - .assertEquals( - "10|openaire____::fdc7e0400d8c1634cdaf8051dbae23db", - cr.getInstance().get(0).getCollectedfrom().getKey()); - Assertions.assertEquals("Pensoft", cr.getInstance().get(0).getCollectedfrom().getValue()); - Assertions - .assertEquals( - "10|openaire____::e707e544b9a5bd23fc27fbfa65eb60dd", cr.getInstance().get(0).getHostedby().getKey()); - Assertions.assertEquals("One Ecosystem", cr.getInstance().get(0).getHostedby().getValue()); - - } - - @Test - public void testDataset() { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/dataset.json") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - DumpProducts dump = new DumpProducts(); - dump - .run( - false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, - CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - Assertions.assertEquals(90, verificationDataset.count()); - - Assertions - .assertTrue( - verificationDataset.filter("bestAccessright.code = 'c_abf2'").count() == verificationDataset - .filter("bestAccessright.code = 'c_abf2' and bestAccessright.label = 'OPEN'") - .count()); - - Assertions - .assertTrue( - verificationDataset.filter("bestAccessright.code = 'c_16ec'").count() == verificationDataset - .filter("bestAccessright.code = 'c_16ec' and bestAccessright.label = 'RESTRICTED'") - .count()); - - Assertions - .assertTrue( - verificationDataset.filter("bestAccessright.code = 'c_14cb'").count() == verificationDataset - .filter("bestAccessright.code = 'c_14cb' and bestAccessright.label = 'CLOSED'") - .count()); - - Assertions - .assertTrue( - verificationDataset.filter("bestAccessright.code = 'c_f1cf'").count() == verificationDataset - .filter("bestAccessright.code = 'c_f1cf' and bestAccessright.label = 'EMBARGO'") - .count()); - - Assertions.assertTrue(verificationDataset.filter("size(context) > 0").count() == 90); - - Assertions.assertTrue(verificationDataset.filter("type = 'dataset'").count() == 90); - - } - - @Test - public void testDataset2All() { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/dataset_cleaned") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - DumpProducts dump = new DumpProducts(); - dump - .run( - // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, - false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, - GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType()); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult.class)); - - Assertions.assertEquals(5, verificationDataset.count()); - - } - - @Test - public void testDataset2Communities() { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/dataset_cleaned") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - DumpProducts dump = new DumpProducts(); - dump - .run( - false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, - CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - Assertions.assertEquals(0, verificationDataset.count()); - - } - - @Test - public void testPublication() { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication.json") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - DumpProducts dump = new DumpProducts(); - dump - .run( - // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, - false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, - CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - Assertions.assertEquals(74, verificationDataset.count()); - verificationDataset.show(false); - - Assertions.assertEquals(74, verificationDataset.filter("type = 'publication'").count()); - - } - - @Test - public void testSoftware() { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/software.json") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - DumpProducts dump = new DumpProducts(); - dump - .run( - // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Software.class, - false, sourcePath, workingDir.toString() + "/result", communityMapPath, Software.class, - CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - Assertions.assertEquals(6, verificationDataset.count()); - - Assertions.assertEquals(6, verificationDataset.filter("type = 'software'").count()); - - } - - @Test - public void testORP() { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/orp.json") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - DumpProducts dump = new DumpProducts(); - dump - .run( - // false, sourcePath, workingDir.toString() + "/result", communityMapPath, OtherResearchProduct.class, - false, sourcePath, workingDir.toString() + "/result", communityMapPath, OtherResearchProduct.class, - CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - Assertions.assertEquals(3, verificationDataset.count()); - - Assertions.assertEquals(3, verificationDataset.filter("type = 'other'").count()); - - } - - @Test - public void testRecord() { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/singelRecord_pub.json") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - DumpProducts dump = new DumpProducts(); - dump - .run( - false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, - CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - Assertions.assertEquals(2, verificationDataset.count()); - verificationDataset.show(false); - - Assertions.assertEquals(2, verificationDataset.filter("type = 'publication'").count()); - - } - - @Test - public void testArticlePCA() { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication_pca") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - DumpProducts dump = new DumpProducts(); - dump - .run( - false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, - GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType()); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(GraphResult.class)); - - Assertions.assertEquals(23, verificationDataset.count()); - - Assertions.assertEquals(23, verificationDataset.filter("type = 'publication'").count()); - - verificationDataset.createOrReplaceTempView("check"); - - org.apache.spark.sql.Dataset temp = spark - .sql( - "select id " + - "from check " + - "lateral view explode (instance) i as inst " + - "where inst.articleprocessingcharge is not null"); - - Assertions.assertTrue(temp.count() == 2); - - Assertions.assertTrue(temp.filter("id = '50|datacite____::05c611fdfc93d7a2a703d1324e28104a'").count() == 1); - - Assertions.assertTrue(temp.filter("id = '50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8'").count() == 1); - - temp = spark - .sql( - "select id, inst.articleprocessingcharge.amount, inst.articleprocessingcharge.currency " + - "from check " + - "lateral view explode (instance) i as inst " + - "where inst.articleprocessingcharge is not null"); - - Assertions - .assertEquals( - "3131.64", - temp - .filter("id = '50|datacite____::05c611fdfc93d7a2a703d1324e28104a'") - .collectAsList() - .get(0) - .getString(1)); - Assertions - .assertEquals( - "EUR", - temp - .filter("id = '50|datacite____::05c611fdfc93d7a2a703d1324e28104a'") - .collectAsList() - .get(0) - .getString(2)); - - Assertions - .assertEquals( - "2578.35", - temp - .filter("id = '50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8'") - .collectAsList() - .get(0) - .getString(1)); - Assertions - .assertEquals( - "EUR", - temp - .filter("id = '50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8'") - .collectAsList() - .get(0) - .getString(2)); - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/GenerateJsonSchema.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/GenerateJsonSchema.java deleted file mode 100644 index 2cc53027e..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/GenerateJsonSchema.java +++ /dev/null @@ -1,28 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump; - -import org.junit.jupiter.api.Disabled; -import org.junit.jupiter.api.Test; - -import com.fasterxml.jackson.databind.JsonNode; -import com.github.victools.jsonschema.generator.*; - -import eu.dnetlib.dhp.schema.dump.oaf.graph.*; - -//@Disabled -class GenerateJsonSchema { - - @Test - void generateSchema() { - SchemaGeneratorConfigBuilder configBuilder = new SchemaGeneratorConfigBuilder(SchemaVersion.DRAFT_7, - OptionPreset.PLAIN_JSON) - .with(Option.SCHEMA_VERSION_INDICATOR) - .without(Option.NONPUBLIC_NONSTATIC_FIELDS_WITHOUT_GETTERS); - configBuilder.forFields().withDescriptionResolver(field -> "Description of " + field.getDeclaredName()); - SchemaGeneratorConfig config = configBuilder.build(); - SchemaGenerator generator = new SchemaGenerator(config); - JsonNode jsonSchema = generator.generateSchema(GraphResult.class); - - System.out.println(jsonSchema.toString()); - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/MakeTarTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/MakeTarTest.java deleted file mode 100644 index 41b906e58..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/MakeTarTest.java +++ /dev/null @@ -1,60 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump; - -import java.io.IOException; -import java.nio.file.Files; - -import org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.*; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.Disabled; -import org.junit.jupiter.api.Test; - -@Disabled -public class MakeTarTest { - private static String workingDir; - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory(MakeTarTest.class.getSimpleName()) - .toString(); - } - - @Test - void testTar() throws IOException { - LocalFileSystem fs = FileSystem.getLocal(new Configuration()); - - fs - .copyFromLocalFile( - false, new Path(getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/ni") - .getPath()), - new Path(workingDir + "/zenodo/ni/part-00000")); - - fs - .copyFromLocalFile( - false, new Path(getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/egi") - .getPath()), - new Path(workingDir + "/zenodo/ni/part-00001")); - - fs - .copyFromLocalFile( - false, new Path(getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/dh-ch") - .getPath()), - new Path(workingDir + "/zenodo/dh-ch/part-00000")); - fs - .copyFromLocalFile( - false, new Path(getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/science-innovation-policy") - .getPath()), - new Path(workingDir + "/zenodo/ni/part-00002")); - - String inputPath = workingDir + "/zenodo/"; - - MakeTar.makeTArArchive(fs, inputPath, "/tmp/out", 0); - - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java deleted file mode 100644 index f3b7246b1..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java +++ /dev/null @@ -1,347 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump; - -import static org.junit.jupiter.api.Assertions.assertEquals; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; - -import org.apache.commons.io.FileUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.Row; -import org.apache.spark.sql.SparkSession; -import org.junit.jupiter.api.AfterAll; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.Test; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.oa.graph.dump.community.ResultProject; -import eu.dnetlib.dhp.oa.graph.dump.community.SparkPrepareResultProject; - -public class PrepareResultProjectJobTest { - - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private static SparkSession spark; - - private static Path workingDir; - - private static final Logger log = LoggerFactory - .getLogger(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class); - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - - SparkConf conf = new SparkConf(); - conf.setAppName(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class.getSimpleName()); - - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - - spark = SparkSession - .builder() - .appName(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Test - void testNoMatch() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/no_match") - .getPath(); - - SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); - - assertEquals(0, verificationDataset.count()); - - } - - @Test - void testMatchOne() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_one") - .getPath(); - - SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); - - assertEquals(1, verificationDataset.count()); - - assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); - - verificationDataset.createOrReplaceTempView("table"); - - Dataset check = spark - .sql( - "Select projList.provenance.provenance " + - "from table " + - "lateral view explode (projectsList) pl as projList"); - - assertEquals(1, check.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); - - verificationDataset.show(false); - - } - - @Test - void testMatch() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match") - .getPath(); - - SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); - - assertEquals(2, verificationDataset.count()); - - assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); - assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); - - verificationDataset.createOrReplaceTempView("dataset"); - - String query = "select resultId, MyT.id project , MyT.title title, MyT.acronym acronym , MyT.provenance.provenance provenance " - + "from dataset " - + "lateral view explode(projectsList) p as MyT "; - - org.apache.spark.sql.Dataset resultExplodedProvenance = spark.sql(query); - assertEquals(3, resultExplodedProvenance.count()); - assertEquals( - 2, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") - .count()); - - assertEquals( - 1, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") - .count()); - - assertEquals( - 2, - resultExplodedProvenance - .filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'") - .count()); - - assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") - .count()); - - assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") - .count()); - - assertEquals( - 1, - resultExplodedProvenance - .filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'") - .count()); - - assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::03376222b28a3aebf2730ac514818d04' and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") - .count()); - - assertEquals( - 3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); - - } - - @Test - public void testMatchValidated() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_validatedRels") - .getPath(); - - SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); - - assertEquals(2, verificationDataset.count()); - - assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); - assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); - - verificationDataset.createOrReplaceTempView("dataset"); - - String query = "select resultId, MyT.id project , MyT.title title, MyT.acronym acronym , MyT.provenance.provenance provenance, " - + - "MyT.validated.validatedByFunder, MyT.validated.validationDate " - + "from dataset " - + "lateral view explode(projectsList) p as MyT "; - - org.apache.spark.sql.Dataset resultExplodedProvenance = spark.sql(query); - assertEquals(3, resultExplodedProvenance.count()); - assertEquals(3, resultExplodedProvenance.filter("validatedByFunder = true").count()); - assertEquals( - 2, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") - .count()); - - assertEquals( - 1, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") - .count()); - - assertEquals( - 2, - resultExplodedProvenance - .filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'") - .count()); - - assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + - "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + - "and validatedByFunder = true " + - "and validationDate = '2021-08-06'") - .count()); - - assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + - "and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80' " + - "and validatedByFunder = true and validationDate = '2021-08-04'") - .count()); - - assertEquals( - 1, - resultExplodedProvenance - .filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'") - .count()); - - assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::03376222b28a3aebf2730ac514818d04' " + - "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + - "and validatedByFunder = true and validationDate = '2021-08-05'") - .count()); - - assertEquals( - 3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); - - } - - @Test - void testMatchx() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match") - .getPath(); - - SparkPrepareResultProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); - - tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r))); - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystemTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystemTest.java deleted file mode 100644 index 8391c8963..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystemTest.java +++ /dev/null @@ -1,117 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump; - -import static org.mockito.Mockito.lenient; - -import java.util.Arrays; -import java.util.List; -import java.util.Map; - -import org.dom4j.DocumentException; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeEach; -import org.junit.jupiter.api.Test; -import org.junit.jupiter.api.extension.ExtendWith; -import org.mockito.Mock; -import org.mockito.junit.jupiter.MockitoExtension; -import org.xml.sax.SAXException; - -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; - -@ExtendWith(MockitoExtension.class) -class QueryInformationSystemTest { - - private static final String XQUERY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') " - + - " where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " + - " and ($x//context/param[./@name = 'status']/text() = 'all') " - + - " return " + - " " + - "{$x//CONFIGURATION/context/@id}" + - "{$x//CONFIGURATION/context/@label}" + - ""; - - List communityMap = Arrays - .asList( - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - ""); - - @Mock - private ISLookUpService isLookUpService; - - private QueryInformationSystem queryInformationSystem; - - private Map map; - - @BeforeEach - public void setUp() throws ISLookUpException, DocumentException, SAXException { - lenient().when(isLookUpService.quickSearchProfile(XQUERY)).thenReturn(communityMap); - queryInformationSystem = new QueryInformationSystem(); - queryInformationSystem.setIsLookUp(isLookUpService); - map = queryInformationSystem.getCommunityMap(false, null); - } - - @Test - void testSize() throws ISLookUpException { - - Assertions.assertEquals(23, map.size()); - } - - @Test - void testContent() { - Assertions.assertTrue(map.containsKey("egi") && map.get("egi").equals("EGI Federation")); - - Assertions.assertTrue(map.containsKey("fet-fp7") && map.get("fet-fp7").equals("FET FP7")); - Assertions.assertTrue(map.containsKey("fet-h2020") && map.get("fet-h2020").equals("FET H2020")); - Assertions.assertTrue(map.containsKey("clarin") && map.get("clarin").equals("CLARIN")); - Assertions.assertTrue(map.containsKey("rda") && map.get("rda").equals("Research Data Alliance")); - Assertions.assertTrue(map.containsKey("ee") && map.get("ee").equals("SDSN - Greece")); - Assertions - .assertTrue( - map.containsKey("dh-ch") && map.get("dh-ch").equals("Digital Humanities and Cultural Heritage")); - Assertions.assertTrue(map.containsKey("fam") && map.get("fam").equals("Fisheries and Aquaculture Management")); - Assertions.assertTrue(map.containsKey("ni") && map.get("ni").equals("Neuroinformatics")); - Assertions.assertTrue(map.containsKey("mes") && map.get("mes").equals("European Marine Science")); - Assertions.assertTrue(map.containsKey("instruct") && map.get("instruct").equals("Instruct-ERIC")); - Assertions.assertTrue(map.containsKey("elixir-gr") && map.get("elixir-gr").equals("ELIXIR GR")); - Assertions - .assertTrue(map.containsKey("aginfra") && map.get("aginfra").equals("Agricultural and Food Sciences")); - Assertions.assertTrue(map.containsKey("dariah") && map.get("dariah").equals("DARIAH EU")); - Assertions.assertTrue(map.containsKey("risis") && map.get("risis").equals("RISIS")); - Assertions.assertTrue(map.containsKey("epos") && map.get("epos").equals("EPOS")); - Assertions.assertTrue(map.containsKey("beopen") && map.get("beopen").equals("Transport Research")); - Assertions.assertTrue(map.containsKey("euromarine") && map.get("euromarine").equals("EuroMarine")); - Assertions.assertTrue(map.containsKey("ifremer") && map.get("ifremer").equals("Ifremer")); - Assertions.assertTrue(map.containsKey("oa-pg") && map.get("oa-pg").equals("EC Post-Grant Open Access Pilot")); - Assertions - .assertTrue( - map.containsKey("science-innovation-policy") - && map.get("science-innovation-policy").equals("Science and Innovation Policy Studies")); - Assertions.assertTrue(map.containsKey("covid-19") && map.get("covid-19").equals("COVID-19")); - Assertions.assertTrue(map.containsKey("enermaps") && map.get("enermaps").equals("Energy Research")); - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/SplitForCommunityTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/SplitForCommunityTest.java deleted file mode 100644 index 4209caad3..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/SplitForCommunityTest.java +++ /dev/null @@ -1,143 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; - -import org.apache.commons.io.FileUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SparkSession; -import org.junit.jupiter.api.AfterAll; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.Test; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.oa.graph.dump.community.CommunitySplit; -import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; - -public class SplitForCommunityTest { - - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private static SparkSession spark; - - private static Path workingDir; - - private static final Logger log = LoggerFactory.getLogger(DumpJobTest.class); - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files.createTempDirectory(SplitForCommunityTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - - SparkConf conf = new SparkConf(); - conf.setAppName(SplitForCommunityTest.class.getSimpleName()); - - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - - spark = SparkSession - .builder() - .appName(SplitForCommunityTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Test - void testCommunitySplit() { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/splitForCommunity") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - CommunitySplit split = new CommunitySplit(); - - split.run(false, sourcePath, workingDir.toString() + "/split", communityMapPath); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/split/Digital_Humanities_and_Cultural_Heritage") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - Assertions.assertEquals(19, verificationDataset.count()); - - Assertions - .assertEquals( - 1, verificationDataset.filter("id = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); - - tmp = sc - .textFile(workingDir.toString() + "/split/EGI_Federation") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - Assertions.assertEquals(1, verificationDataset.count()); - - Assertions - .assertEquals( - 1, verificationDataset.filter("id = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); - - tmp = sc - .textFile(workingDir.toString() + "/split/Neuroinformatics") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - Assertions.assertEquals(5, verificationDataset.count()); - - Assertions - .assertEquals( - 1, verificationDataset.filter("id = '50|datacite____::6b1e3a2fa60ed8c27317a66d6357f795'").count()); - - tmp = sc - .textFile(workingDir.toString() + "/split/Science_and_Innovation_Policy_Studies") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - Assertions.assertEquals(4, verificationDataset.count()); - - Assertions - .assertEquals( - 1, verificationDataset.filter("id = '50|dedup_wf_001::0347b1cd516fc59e41ba92e0d74e4e9f'").count()); - Assertions - .assertEquals( - 1, verificationDataset.filter("id = '50|dedup_wf_001::1432beb6171baa5da8a85a7f99545d69'").count()); - Assertions - .assertEquals( - 1, verificationDataset.filter("id = '50|dedup_wf_001::1c8bd19e633976e314b88ce5c3f92d69'").count()); - Assertions - .assertEquals( - 1, verificationDataset.filter("id = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); - - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/UpdateProjectInfoTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/UpdateProjectInfoTest.java deleted file mode 100644 index 9710e4553..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/UpdateProjectInfoTest.java +++ /dev/null @@ -1,236 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.HashMap; -import java.util.logging.Filter; -import java.util.stream.Collectors; - -import org.apache.commons.io.FileUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.api.java.function.FilterFunction; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.Row; -import org.apache.spark.sql.SparkSession; -import org.junit.jupiter.api.AfterAll; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.Test; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo; -import eu.dnetlib.dhp.schema.dump.oaf.Result; -import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; -import eu.dnetlib.dhp.schema.dump.oaf.community.Funder; -import eu.dnetlib.dhp.schema.dump.oaf.community.Project; - -public class UpdateProjectInfoTest { - - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private static SparkSession spark; - - private static Path workingDir; - - private static final Logger log = LoggerFactory.getLogger(eu.dnetlib.dhp.oa.graph.dump.UpdateProjectInfoTest.class); - - private static final HashMap map = new HashMap<>(); - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory(eu.dnetlib.dhp.oa.graph.dump.UpdateProjectInfoTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - - SparkConf conf = new SparkConf(); - conf.setAppName(eu.dnetlib.dhp.oa.graph.dump.UpdateProjectInfoTest.class.getSimpleName()); - - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - - spark = SparkSession - .builder() - .appName(eu.dnetlib.dhp.oa.graph.dump.UpdateProjectInfoTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Test - void test1() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/addProjectInfo") - .getPath(); - - SparkUpdateProjectInfo.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-preparedInfoPath", sourcePath + "/preparedInfo", - "-outputPath", workingDir.toString() + "/result", - "-sourcePath", sourcePath + "/software.json" - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - verificationDataset.show(false); - - Assertions.assertEquals(6, verificationDataset.count()); - verificationDataset.createOrReplaceTempView("dataset"); - - String query = "select id, MyT.code code, MyT.title title, MyT.funder.name funderName, MyT.funder.shortName funderShortName, " - + - "MyT.funder.jurisdiction funderJurisdiction, MyT.funder.fundingStream fundingStream " - + "from dataset " + - "lateral view explode(projects) p as MyT "; - - org.apache.spark.sql.Dataset resultExplodedProvenance = spark.sql(query); - - Assertions.assertEquals(3, resultExplodedProvenance.count()); - resultExplodedProvenance.show(false); - - Assertions - .assertEquals( - 2, - resultExplodedProvenance.filter("id = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); - - Assertions - .assertEquals( - 1, - resultExplodedProvenance - .filter("id = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' and code = '123455'") - .count()); - - Assertions - .assertEquals( - 1, - resultExplodedProvenance - .filter("id = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' and code = '119027'") - .count()); - - Assertions - .assertEquals( - 1, - resultExplodedProvenance - .filter("id = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80' and code = '123455'") - .count()); - - resultExplodedProvenance.show(false); - } - - @Test - public void testValidatedRelation() throws Exception { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/addProjectInfo") - .getPath(); - - SparkUpdateProjectInfo.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-preparedInfoPath", sourcePath + "/preparedInfoValidated", - "-outputPath", workingDir.toString() + "/result", - "-sourcePath", sourcePath + "/publication_extendedmodel" - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/result") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - verificationDataset.show(false); - - Assertions.assertEquals(2, verificationDataset.count()); - verificationDataset.createOrReplaceTempView("dataset"); - - String query = "select id, MyT.code code, MyT.title title, MyT.funder.name funderName, MyT.funder.shortName funderShortName, " - + - "MyT.funder.jurisdiction funderJurisdiction, MyT.funder.fundingStream fundingStream, MyT.validated " - + "from dataset " + - "lateral view explode(projects) p as MyT "; - - org.apache.spark.sql.Dataset resultExplodedProvenance = spark.sql(query); - - Assertions.assertEquals(2, resultExplodedProvenance.count()); - resultExplodedProvenance.show(false); - - Assertions - .assertEquals( - 2, - resultExplodedProvenance.filter("id = '50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2'").count()); - - Assertions - .assertEquals( - 1, - resultExplodedProvenance - .filter("id = '50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2' and code = '123455'") - .count()); - - Assertions - .assertEquals( - 1, - resultExplodedProvenance - .filter("id = '50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2' and code = '119027'") - .count()); - - Project project = verificationDataset - .map( - (MapFunction) cr -> cr - .getProjects() - .stream() - .filter(p -> p.getValidated() != null) - .collect(Collectors.toList()) - .get(0), - Encoders.bean(Project.class)) - .first(); - - Assertions.assertTrue(project.getFunder().getName().equals("Academy of Finland")); - Assertions.assertTrue(project.getFunder().getShortName().equals("AKA")); - Assertions.assertTrue(project.getFunder().getJurisdiction().equals("FI")); - Assertions.assertTrue(project.getFunder().getFundingStream() == null); - Assertions.assertTrue(project.getValidated().getValidationDate().equals("2021-08-06")); - - project = verificationDataset - .map( - (MapFunction) cr -> cr - .getProjects() - .stream() - .filter(p -> p.getValidated() == null) - .collect(Collectors.toList()) - .get(0), - Encoders.bean(Project.class)) - .first(); - - Assertions.assertTrue(project.getFunder().getName().equals("European Commission")); - Assertions.assertTrue(project.getFunder().getShortName().equals("EC")); - Assertions.assertTrue(project.getFunder().getJurisdiction().equals("EU")); - Assertions.assertTrue(project.getFunder().getFundingStream().equals("H2020")); - - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/ZenodoUploadTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/ZenodoUploadTest.java deleted file mode 100644 index 8d06758a8..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/ZenodoUploadTest.java +++ /dev/null @@ -1,153 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump; - -import java.io.*; -import java.nio.file.Files; - -import org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.*; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.Disabled; -import org.junit.jupiter.api.Test; - -import com.google.gson.Gson; - -import eu.dnetlib.dhp.common.api.MissingConceptDoiException; -import eu.dnetlib.dhp.common.api.ZenodoAPIClient; -import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; - -@Disabled -public class ZenodoUploadTest { - - private static String workingDir; - - private final String URL_STRING = "https://sandbox.zenodo.org/api/deposit/depositions"; - private final String ACCESS_TOKEN = ""; - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory(eu.dnetlib.dhp.oa.graph.dump.UpdateProjectInfoTest.class.getSimpleName()) - .toString(); - } - - @Test - void testNewDeposition() throws IOException { - CommunityMap communityMap = new CommunityMap(); - communityMap.put("ni", "Neuroinformatics"); - communityMap.put("dh-ch", "Digital Humanities and Cultural Heritage"); - LocalFileSystem fs = FileSystem.getLocal(new Configuration()); - - fs - .copyFromLocalFile( - false, new Path(getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/ni") - .getPath()), - new Path(workingDir + "/zenodo/ni/ni")); - fs - .copyFromLocalFile( - false, new Path(getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/dh-ch") - .getPath()), - new Path(workingDir + "/zenodo/dh-ch/dh-ch")); - - ZenodoAPIClient client = new ZenodoAPIClient(URL_STRING, - ACCESS_TOKEN); - client.newDeposition(); - - // the second boolean parameter here sets the recursion to true - RemoteIterator fileStatusListIterator = fs - .listFiles( - new Path(workingDir + "/zenodo"), true); - while (fileStatusListIterator.hasNext()) { - LocatedFileStatus fileStatus = fileStatusListIterator.next(); - - String p_string = fileStatus.getPath().toString(); - - int index = p_string.lastIndexOf("/"); - String community = p_string.substring(0, index); - community = community.substring(community.lastIndexOf("/") + 1); - String community_name = communityMap.get(community).replace(" ", "_"); - // fs.copyToLocalFile(fileStatus.getPath(), new Path("/tmp/" + community_name)); - System.out.println(community); - - // File f = new File("/tmp/" + community_name); - FSDataInputStream inputStream = fs.open(fileStatus.getPath()); - System.out.println(client.uploadIS(inputStream, community_name, fileStatus.getLen())); - - } - - String metadata = "{\"metadata\":{\"access_right\":\"open\",\"communities\":[{\"identifier\":\"openaire-research-graph\"}],\"creators\":[{\"affiliation\":\"CNR - ISTI\",\"name\":\"Manghi, Paolo\",\"orcid\":\"0000-0001-7291-3210\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"Atzori, Claudio\",\"orcid\":\"0000-0001-9613-6639\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"Bardi, Alessia\",\"orcid\":\"0000-0002-1112-1292\"},{\"affiliation\":\"ISTI - CNR\",\"name\":\"Baglioni, Miriam\",\"orcid\":\"0000-0002-2273-9004\"},{\"affiliation\":\"University of Bielefeld\",\"name\":\"Shirrwagen, Jochen\"},{\"affiliation\":\"Athena Research and Innovation Centre\",\"name\":\"Dimitropoulos, Harry\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"La Bruzzo, Sandro\",\"orcid\":\"0000-0003-2855-1245\"},{\"affiliation\":\"Athena Research and Innovation Centre\",\"name\":\"Foufoulas, Ioannis\"},{\"affiliation\":\"University of Bielefeld\",\"name\":\"Löhden, Aenne\"},{\"affiliation\":\"University of Bielefeld\",\"name\":\"Bäcker, Amelie\",\"orcid\":\"0000-0001-6015-2063\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"Mannocci, Andrea\",\"orcid\":\"0000-0002-5193-7851\"},{\"affiliation\":\"University of Warsaw\",\"name\":\"Horst, Marek\"},{\"affiliation\":\"University of Bielefeld\",\"name\":\"Czerniak, Andreas\",\"orcid\":\"0000-0003-3883-4169\"},{\"affiliation\":\"Athena Research and Innovation Centre\",\"name\":\"Kiatropoulou, Katerina\"},{\"affiliation\":\"Athena Research and Innovation Centre\",\"name\":\"Kokogiannaki, Argiro\",\"orcid\":\"0000-0002-3880-0244\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"De Bonis, Michele\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"Artini, Michele\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"Ottonello, Enrico\"},{\"affiliation\":\"Athena Research and Innovation Centre\",\"name\":\"Lempesis, Antonis\"},{\"affiliation\":\"CERN\",\"name\":\"Ioannidis, Alexandros\"},{\"affiliation\":\"University of Bielefeld\",\"name\":\"Summan, Friedrich\"}],\"description\":\"\\u003cp\\u003eThis dataset contains dumps of the OpenAIRE Research Graph containing metadata records relevant for the research communities and initiatives collaborating with OpenAIRE\\u003c/p\\u003e. \\u003cp\\u003eEach dataset is a zip containing a file with one json per line. Each json is compliant to the schema available at XXXX\\u003c/p\\u003e Note that the file that is offered is not a typical json file: each line contains a separate, self-contained json object. For more information please see http://jsonlines.org\",\"grants\":[{\"id\":\"777541\"},{\"id\":\"824091\"},{\"id\":\"824323\"}],\"keywords\":[\"Open Science\",\"Scholarly Communication\",\"Information Science\"],\"language\":\"eng\",\"license\":\"CC-BY-4.0\",\"title\":\"OpenAIRE Research Graph: Dumps for research communities and initiatives.\",\"upload_type\":\"dataset\",\"version\":\"1.0\"}}"; - - System.out.println(client.sendMretadata(metadata)); - - System.out.println(client.publish()); - - } - - @Test - void testNewVersion() throws IOException, MissingConceptDoiException { - - ZenodoAPIClient client = new ZenodoAPIClient(URL_STRING, - ACCESS_TOKEN); - - client.newVersion("656628"); - - CommunityMap communityMap = new CommunityMap(); - communityMap.put("ni", "Neuroinformatics"); - communityMap.put("dh-ch", "Digital Humanities and Cultural Heritage"); - LocalFileSystem fs = FileSystem.getLocal(new Configuration()); - - fs - .copyFromLocalFile( - false, new Path(getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/ni") - .getPath()), - new Path(workingDir + "/zenodo/ni/ni")); - fs - .copyFromLocalFile( - false, new Path(getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/dh-ch") - .getPath()), - new Path(workingDir + "/zenodo/dh-ch/dh-ch")); - - RemoteIterator fileStatusListIterator = fs - .listFiles( - new Path(workingDir + "/zenodo"), true); - while (fileStatusListIterator.hasNext()) { - LocatedFileStatus fileStatus = fileStatusListIterator.next(); - - String p_string = fileStatus.getPath().toString(); - - int index = p_string.lastIndexOf("/"); - String community = p_string.substring(0, index); - community = community.substring(community.lastIndexOf("/") + 1); - String community_name = communityMap.get(community).replace(" ", "_"); - // fs.copyToLocalFile(fileStatus.getPath(), new Path("/tmp/" + community_name)); - System.out.println(community); - - // File f = new File("/tmp/" + community_name); - FSDataInputStream inputStream = fs.open(fileStatus.getPath()); - System.out.println(client.uploadIS(inputStream, community_name, fileStatus.getLen())); - - } - - System.out.println(client.publish()); - - } - - @Test - void readCommunityMap() throws IOException { - LocalFileSystem fs = FileSystem.getLocal(new Configuration()); - System.out - .println( - new Gson() - .toJson( - Utils - .readCommunityMap( - fs, getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath()))); - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java deleted file mode 100644 index b5f73da71..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java +++ /dev/null @@ -1,173 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import static org.mockito.Mockito.lenient; - -import java.io.BufferedWriter; -import java.io.IOException; -import java.io.OutputStreamWriter; -import java.nio.charset.StandardCharsets; -import java.nio.file.Files; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.List; -import java.util.function.Consumer; - -import org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.FSDataOutputStream; -import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.fs.LocalFileSystem; -import org.apache.hadoop.fs.Path; -import org.apache.hadoop.io.compress.CompressionCodec; -import org.apache.hadoop.io.compress.CompressionCodecFactory; -import org.junit.jupiter.api.*; -import org.junit.jupiter.api.extension.ExtendWith; -import org.mockito.Mock; -import org.mockito.junit.jupiter.MockitoExtension; - -import com.google.gson.Gson; - -import eu.dnetlib.dhp.schema.dump.oaf.graph.ResearchCommunity; -import eu.dnetlib.dhp.schema.dump.oaf.graph.ResearchInitiative; -import eu.dnetlib.dhp.utils.DHPUtils; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; - -@ExtendWith(MockitoExtension.class) -public class CreateEntityTest { - - private static final String XQUERY_ENTITY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') " - + - "where $x//context[./@type='community' or ./@type = 'ri'] and $x//context/param[./@name = 'status']/text() = 'all' return " - + - "concat(data($x//context/@id) , '@@', $x//context/param[./@name =\"name\"]/text(), '@@', " + - "$x//context/param[./@name=\"description\"]/text(), '@@', $x//context/param[./@name = \"subject\"]/text(), '@@', " - + - "$x//context/param[./@name = \"zenodoCommunity\"]/text(), '@@', $x//context/@type)"; - - List communityMap = Arrays - .asList( - "clarin@@Common Language Resources and Technology Infrastructure@@CLARIN@@@@oac_clarin@@ri", - "ee@@Sustainable Development Solutions Network - Greece@@The UN Sustainable Development Solutions Network (SDSN) has been operating since 2012 under the auspices of the UN Secretary-General. " - + - "SDSN mobilizes global scientific and technological expertise to promote practical solutions for sustainable development, including the implementation of the Sustainable Development Goals (SDGs) and the Paris Climate Agreement. The Greek hub of SDSN has been included in the SDSN network in 2017 and is co-hosted by ICRE8: International Center for Research on the Environment and the Economy and the Political Economy of Sustainable Development Lab.@@SDG13 - Climate action,SDG8 - Decent work and economic growth,SDG15 - " - + - "Life on land,SDG2 - Zero hunger,SDG17 - Partnerships for the ´goals,SDG10 - Reduced inequalities,SDG5 - Gender equality,SDG12 - Responsible consumption and production,SDG14 - Life below water,SDG6 - Clean water and sanitation,SDG11 - Sustainable cities and communities,SDG1 - No poverty,SDG3 - Good health and well being,SDG7 - Affordable and clean energy,SDG4 - Quality education,SDG9 - Industry innovation and infrastructure,SDG16 - Peace justice and strong institutions@@oac_sdsn-greece@@community", - "dh-ch@@Digital Humanities and Cultural Heritage@@This community gathers research results, data, scientific publications and projects related to the domain of Digital Humanities. This broad definition includes Humanities, Cultural Heritage, History, Archaeology and related fields.@@modern art,monuments,europeana data model,sites,field walking,frescoes,LIDO metadata schema,art history,excavation,Arts and Humanities General,cities,coins,temples,numismatics,lithics,roads,environmental archaeology,digital cultural heritage,archaeological reports,history,CRMba,churches,cultural heritage,archaeological stratigraphy,religious art,buidings,digital humanities,survey,archaeological sites,linguistic studies,bioarchaeology,architectural orders,palaeoanthropology,fine arts,europeana,CIDOC CRM,decorations,classic art,stratigraphy,digital archaeology,intangible cultural heritage,walls,humanities,chapels,CRMtex,Language and Literature,paintings,archaeology,fair data,mosaics,burials,architecture,medieval art,castles,CARARE metadata schema,statues,natural language processing,inscriptions,CRMsci,vaults,contemporary art,Arts and Humanities,CRMarchaeo,pottery,site,architectural,vessels@@oac_dh-ch@@community", - "fam@@Fisheries and Aquaculture Management@@Conservation of marine resources for sustainable development. The Fisheries and Aquaculture community focus on resources (document, data, codes..) which have been produced in the framework of projects (H2020, FP7, ..) related to the domain of fisheries and aquaculture.@@Stock Assessment,pelagic,Acoustic,Fish farming,Fisheries,Fishermen,maximum sustainable yield,trawler,Fishing vessel,Fisherman,Fishing gear,mackerel,RFMO,Fish Aggregating Device,Bycatch,Fishery,common fisheries policy,Fishing fleet,Aquaculture@@fisheries@@community", - "ni@@Neuroinformatics@@The neuroinformatics dashboard gathers research outputs from the 'neuroinformatics' community at large including the fields of: neuroscience, neuroinformatics, brain imaging databases and standards, brain imaging techniques, neuroimaging methods including statistics and machine learning. The dashboard covers a wide range of imaging methods including (but not limited to): MRI, TEP, EEG, MEG, and studies involving human participants as well as animal studies.@@brain mapping,brain imaging,electroencephalography,arterial spin labelling,brain fingerprinting,brain,neuroimaging,Multimodal Brain Image Analysis,fMRI,neuroinformatics,fetal brain,brain ultrasonic imaging,topographic brain mapping,diffusion tensor imaging,computerized knowledge assessment,connectome mapping,brain magnetic resonance imaging,brain abnormalities@@oac_ni@@community", - "mes@@European Marine Science@@This community was initially defined to include a very broad range of topics, with the intention to generate a number of more focused and sustainable dashboards for research communities and initiatives. As outlined in the logo of this community, we intend to setup a community dashboard for EuroMarine (a consortium of 56 research and academic organisations) and monitoring dashboards for marine research initiatives, including infrastructures (e.g. EMBRC & EMSO), advisory boards (e.g. Marine Boards & ICES), and transnational funding bodies (e.g. JPI-Oceans and Tara Foundation).@@marine,ocean,fish,aqua,sea@@oac_mes@@community", - "instruct@@Instruct-ERIC@@Instruct-ERIC is the European Research Infrastructure for Structural Biology@@@@oac_instruct@@community", - "elixir-gr@@The Greek National Node of the ESFRI European RI ELIXIR@@ELIXIR-GR enhances the potential of the Greek bioinformatics community to offer open, easily accessible and state -of- the- art services to the Greek and the international academic community and other stakeholders, such as industry and the health sector. More importantly, by providing these services, the infrastructure facilitates discoveries in the field of the life-sciences, having strong spill over effects in promoting innovation in sectors such as discovery of new drug targets and development of novel therapeutic agents, development of innovative diagnostics, personalized medicine, and development of innovative biotechnological products and processes.@@@@oaa_elixir-gr@@ri", - "aginfra@@Agricultural and Food Sciences@@The scope of this community is to provide access to publications, research data, projects and software that are related to agricultural and food sciences@@animal production and health,fisheries and aquaculture,food safety and human nutrition,information management,food technology,agri-food education and extension,natural resources and environment,food system,engineering technology and Research,agriculture,food safety risk assessment,food security,farming practices and systems,plant production and protection,agri-food economics and policy,Agri-food,food distribution,forestry@@oac_aginfra@@community", - "dariah@@DARIAH EU@@The Digital Research Infrastructure for the Arts and Humanities (DARIAH) aims to enhance and support digitally-enabled research and teaching across the arts and humanities. It develops, maintains and operates an infrastructure in support of ICT-based research practices and sustains researchers in using them to build, analyse and interpret digital resources. DARIAH was established as a European Research Infrastructure Consortium (ERIC) in August 2014. Currently, DARIAH has 18 Members and several cooperating partners in eight non-member countries. Here you will find a growing collection of DARIAH-affiliated research outputs and other documents. @@@@dariah@@ri", - "epos@@European Plate Observing System@@EPOS, the European Plate Observing System, is a long-term plan to facilitate integrated use of data, data products, and facilities from distributed research infrastructures for solid Earth science in Europe.@@@@@@ri", - "covid-19@@Corona Virus Disease@@This portal provides access to publications, research data, projects and software that may be relevant to the Corona Virus Disease (COVID-19). The OpenAIRE COVID-19 Gateway aggregates COVID-19 related records, links them and provides a single access point for discovery and navigation. We tag content from the OpenAIRE Research Graph (10,000+ data sources) and additional sources. All COVID-19 related research results are linked to people, organizations and projects, providing a contextualized navigation.@@COVID19,SARS-CoV,HCoV-19,mesh:C000657245,MERS-CoV,Síndrome Respiratorio Agudo Severo,mesh:COVID-19,COVID2019,COVID-19,SARS-CoV-2,2019 novel coronavirus,severe acute respiratory syndrome coronavirus 2,Orthocoronavirinae,Coronaviridae,mesh:D045169,coronavirus,SARS,coronaviruses,coronavirus disease-19,sars cov 2,Middle East Respiratory Syndrome,Severe acute respiratory syndrome coronavirus 2,Severe Acute Respiratory Syndrome,coronavirus disease 2019,2019-nCoV@@covid-19@@community"); - - @Mock - private ISLookUpService isLookUpService; - - private QueryInformationSystem queryInformationSystem; - - private static String workingDir; - - @BeforeEach - public void setUp() throws ISLookUpException { - lenient().when(isLookUpService.quickSearchProfile(XQUERY_ENTITY)).thenReturn(communityMap); - queryInformationSystem = new QueryInformationSystem(); - queryInformationSystem.setIsLookUp(isLookUpService); - } - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory(eu.dnetlib.dhp.oa.graph.dump.complete.CreateEntityTest.class.getSimpleName()) - .toString(); - } - - @Test - void test1() throws ISLookUpException, IOException { - List cInfoList = new ArrayList<>(); - final Consumer consumer = ci -> cInfoList.add(ci); - queryInformationSystem.getContextInformation(consumer); - - List riList = new ArrayList<>(); - cInfoList.forEach(cInfo -> riList.add(Process.getEntity(cInfo))); - - Assertions.assertEquals(12, riList.size()); - - riList.stream().forEach(c -> { - switch (c.getAcronym()) { - case "mes": - Assertions - .assertTrue(c.getType().equals(eu.dnetlib.dhp.oa.graph.dump.Constants.RESEARCH_COMMUNITY)); - Assertions.assertTrue(((ResearchCommunity) c).getSubject().size() == 5); - Assertions.assertTrue(((ResearchCommunity) c).getSubject().contains("marine")); - Assertions.assertTrue(((ResearchCommunity) c).getSubject().contains("ocean")); - Assertions.assertTrue(((ResearchCommunity) c).getSubject().contains("fish")); - Assertions.assertTrue(((ResearchCommunity) c).getSubject().contains("aqua")); - Assertions.assertTrue(((ResearchCommunity) c).getSubject().contains("sea")); - Assertions - .assertTrue( - c - .getId() - .equals( - String - .format( - "%s|%s::%s", Constants.CONTEXT_ID, Constants.CONTEXT_NS_PREFIX, - DHPUtils.md5(c.getAcronym())))); - Assertions.assertTrue(c.getZenodo_community().equals("https://zenodo.org/communities/oac_mes")); - Assertions.assertTrue("mes".equals(c.getAcronym())); - break; - case "clarin": - Assertions - .assertTrue(c.getType().equals(eu.dnetlib.dhp.oa.graph.dump.Constants.RESEARCH_INFRASTRUCTURE)); - Assertions - .assertTrue( - c - .getId() - .equals( - String - .format( - "%s|%s::%s", Constants.CONTEXT_ID, Constants.CONTEXT_NS_PREFIX, - DHPUtils.md5(c.getAcronym())))); - Assertions.assertTrue(c.getZenodo_community().equals("https://zenodo.org/communities/oac_clarin")); - Assertions.assertTrue("clarin".equals(c.getAcronym())); - break; - } - // TODO add check for all the others Entities - - }); - - riList.forEach(c -> System.out.println(new Gson().toJson(c))); - } - - @Test - @Disabled - void test2() throws IOException, ISLookUpException { - LocalFileSystem fs = FileSystem.getLocal(new Configuration()); - - Path hdfsWritePath = new Path(workingDir + "/prova"); - FSDataOutputStream fsDataOutputStream = null; - if (fs.exists(hdfsWritePath)) { - fsDataOutputStream = fs.append(hdfsWritePath); - } else { - fsDataOutputStream = fs.create(hdfsWritePath); - } - CompressionCodecFactory factory = new CompressionCodecFactory(fs.getConf()); - CompressionCodec codec = factory.getCodecByClassName("org.apache.hadoop.io.compress.GzipCodec"); - - BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(codec.createOutputStream(fsDataOutputStream), - StandardCharsets.UTF_8)); - - List cInfoList = new ArrayList<>(); - final Consumer consumer = ci -> cInfoList.add(ci); - queryInformationSystem.getContextInformation(consumer); - - for (ContextInfo cInfo : cInfoList) { - writer.write(new Gson().toJson(Process.getEntity(cInfo))); - } - writer.close(); - - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateRelationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateRelationTest.java deleted file mode 100644 index d2343d274..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateRelationTest.java +++ /dev/null @@ -1,723 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import java.util.*; -import java.util.function.Consumer; -import java.util.stream.Collectors; - -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeEach; -import org.junit.jupiter.api.Test; - -import com.google.gson.Gson; - -import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.dhp.schema.dump.oaf.graph.Relation; -import eu.dnetlib.dhp.schema.oaf.Datasource; -import eu.dnetlib.dhp.schema.oaf.Project; -import eu.dnetlib.dhp.utils.DHPUtils; - -class CreateRelationTest { - - List communityContext = Arrays - .asList( - "\n" + - " all\n" + - " CLARIN\n" + - " https://www.clarin.eu/sites/default/files/clarin-frontpage-logo.jpg\n" - + - " Common Language Resources and Technology Infrastructure\n" + - " maria@clarin.eu,dieter@clarin.eu,f.m.g.dejong@uu.nl,paolo.manghi@isti.cnr.it\n" - + - " \n" + - " (Part of) the work reported here was made possible by using the CLARIN infrastructure.\n" - + - " The work reported here has received funding through <CLARIN national consortium member, e.g. CLARIN.SI>, <XYZ> project, grant no. <XYZ>.\n" - + - " The work reported here has received funding (through CLARIN ERIC) from the European Union’s Horizon 2020 research and innovation programme under grant agreement No <0-9> for project <XYZ>.\n" - + - " (E.g. No 676529 for project CLARIN-PLUS.)\n" + - " oac_clarin\n" + - " 2018-03-01T12:00:00\n" + - " \n" + - " \n" + - " CLARIN-PLUS\n" + - " \n" + - " \n" + - " 676529\n" + - " http://www.clarin.eu\n" + - " EC\n" + - " H2020-INFRADEV-1-2015-1\n" + - " CLARIN+\n" + - " \n" + - " \n" + - " Common Language Resources and Technology Infrastructure\n" - + - " CLARIN\n" + - " 212230\n" + - " EC\n" + - " corda_______::ef782b2d85676aa3e5a907427feb18c4\n" + - " \n" + - " \n" + - " " + - "\n" + - " \n" + - " LINDAT/CLARIN repository\n" + - " LINDAT/CLARIN repository\n" + - " true\n" + - " \n" + - " \n" + - " \n" + - " \n" + - " CLARIN-D\n" + - " https://www.clarin-d.de/en/\n" + - " \n" + - " http://www.lrec-conf.org/proceedings/lrec2018/pdf/504.pdf\n" - + - " Germany\n" + - " \n" + - " \n" + - " \n" - + - " \n" + - "", - "\n" + - " all\n" + - " This community gathers research results, data, scientific publications and projects related to the domain of Digital Humanities. This broad definition includes Humanities, Cultural Heritage, History, Archaeology and related fields.\n" - + - " http://sanmamante.org/DH_CH_logo.png\n" + - " Digital Humanities and Cultural Heritage\n" + - " ileniagalluccio87@gmail.com,achille.felicetti@gmail.com,paolo.manghi@isti.cnr.it,tim.evans@york.ac.uk\n" - + - " modern art,monuments,europeana data model,sites,field walking,frescoes,LIDO metadata schema,art history,excavation,Arts and Humanities General,cities,coins,temples,numismatics,lithics,roads,environmental archaeology,digital cultural heritage,archaeological reports,history,CRMba,churches,cultural heritage,archaeological stratigraphy,religious art,buidings,digital humanities,survey,archaeological sites,linguistic studies,bioarchaeology,architectural orders,palaeoanthropology,fine arts,europeana,CIDOC CRM,decorations,classic art,stratigraphy,digital archaeology,intangible cultural heritage,walls,humanities,chapels,CRMtex,Language and Literature,paintings,archaeology,fair data,mosaics,burials,architecture,medieval art,castles,CARARE metadata schema,statues,natural language processing,inscriptions,CRMsci,vaults,contemporary art,Arts and Humanities,CRMarchaeo,pottery,site,architectural,vessels\n" - + - " The present work has been partially supported by the PARTHENOS project, funded by the European Commission (Grant Agreement No. 654119) under the HORIZON 2020 - INFRADEV-4-2014/2015 call\n" - + - " oac_dh-ch\n" + - " 2018-03-01T12:00:00\n" + - " \n" + - " \n" - + - " Pooling Activities, Resources and Tools for Heritage E-research Networking, Optimization and Synergies\n" - + - " The present work has been partially supported by the PARTHENOS project, funded by the European Commission (Grant Agreement No. 654119) under the HORIZON 2020 - INFRADEV-4-2014/2015 call\n" - + - " \n" + - " 654119\n" + - " http://www.parthenos-project.eu\n" + - " EC\n" + - " PARTHENOS\n" + - " \n" + - " \n" + - " \n" + - " \n" - + - " re3data_____::9ebe127e5f3a0bf401875690f3bb6b81\n" + - " The UK's largest collection of digital research data in the social sciences and humanities\n" - + - " UK Data Archive\n" + - " true\n" + - " \n" + - " \n" - + - " doajarticles::c6cd4b532e12868c1d760a8d7cda6815\n" + - " Journal of Data Mining and Digital Humanities\n" + - " Journal of Data Mining and Digital Humanities\n" + - " true\n" + - " \n" + - " \n" - + - " doajarticles::a6de4499bb87bf3c01add0a9e2c9ed0b\n" + - " Frontiers in Digital Humanities\n" + - " Frontiers in Digital Humanities\n" + - " true\n" + - " \n" + - " \n" - + - " doajarticles::6eb31d13b12bc06bbac06aef63cf33c9\n" + - " Il Capitale Culturale: Studies on the Value of Cultural Heritage\n" - + - " Il Capitale Culturale: Studies on the Value of Cultural Heritage\n" - + - " true\n" + - " \n" + - " \n" - + - " doajarticles::0da84e9dfdc8419576169e027baa8028\n" + - " Conservation Science in Cultural Heritage\n" + - " Conservation Science in Cultural Heritage\n" + - " true\n" + - " \n" + - " \n" - + - " re3data_____::84e123776089ce3c7a33db98d9cd15a8\n" + - " Electronic Archiving System\n" + - " EASY\n" + - " true\n" + - " \n" + - " \n" + - " openaire____::c5502a43e76feab55dd00cf50f519125\n" + - " DANS-KB Harvester\n" + - " Gemeenschappelijke Harvester DANS-KB\n" + - " true\n" + - " \n" + - " \n" + - " re3data_____::a48f09c562b247a9919acfe195549b47\n" + - " ads\n" + - " Archaeology Data Service\n" + - " true\n" + - " \n" + - " \n" + - " opendoar____::97275a23ca44226c9964043c8462be96\n" + - " KNAW Repository\n" + - " KNAW Repository\n" + - " true\n" + - " \n" + - " \n" - + - " doajarticles::2899208a99aa7d142646e0a80bfeef05\n" + - " Internet Archaeology\n" + - " Internet Archaeology\n" + - " true\n" + - " \n" + - " \n" + - " \n" + - "\n", - "\n" + - " all\n" + - " The neuroinformatics dashboard gathers research outputs from the 'neuroinformatics' community at large including the fields of: neuroscience, neuroinformatics, brain imaging databases and standards, brain imaging techniques, neuroimaging methods including statistics and machine learning. The dashboard covers a wide range of imaging methods including (but not limited to): MRI, TEP, EEG, MEG, and studies involving human participants as well as animal studies.\n" - + - " https://docs.google.com/drawings/u/0/d/10e191xGoGf4uaRluMqbt_7cCj6LSCs2a29im4CmWjqU/export/png\n" - + - " Neuroinformatics\n" + - " sorina.pop@creatis.insa-lyon.fr,camille.maumet@inria.fr,christian.barillot@irisa.fr,xavier.rolland@irisa.fr,axel.bonnet@creatis.insa-lyon.fr,paolo.manghi@isti.cnr.it\n" - + - " brain mapping,brain imaging,electroencephalography,arterial spin labelling,brain fingerprinting,brain,neuroimaging,Multimodal Brain Image Analysis,fMRI,neuroinformatics,fetal brain,brain ultrasonic imaging,topographic brain mapping,diffusion tensor imaging,computerized knowledge assessment,connectome mapping,brain magnetic resonance imaging,brain abnormalities\n" - + - " \n" + - " oac_ni\n" + - " 2018-03-01T12:00:00\n" + - " \n" + - " \n" + - " \n" + - " re3data_____::5b9bf9171d92df854cf3c520692e9122\n" + - " Formerly:OpenFMRI\n" + - " OpenNeuro\n" + - " true\n" + - " \n" + - " \n" + - " doajarticles::c7d3de67dc77af72f6747157441252ec\n" + - " Research Ideas and Outcomes\n" + - " Research Ideas and Outcomes\n" + - " true\n" + - " \n" + - " \n" + - " re3data_____::8515794670370f49c1d176c399c714f5\n" + - " Neuroimaging Informatics Tools and Resources Clearinghouse\n" - + - " NITRC\n" + - " true\n" + - " \n" + - " \n" + - " doajarticles::d640648c84b10d425f96f11c3de468f3\n" + - " Frontiers in Neuroinformatics\n" + - " Frontiers in Neuroinformatics\n" + - " true\n" + - " \n" + - " \n" + - " doajarticles::0c0e74daa5d95504eade9c81ebbd5b8a\n" + - " NeuroImage: Clinical\n" + - " NeuroImage: Clinical\n" + - " true\n" + - " \n" + - " \n" + - " rest________::fb1a3d4523c95e63496e3bc7ba36244b\n" + - " NeuroVault\n" + - " NeuroVault\n" + - " true\n" + - " \n" + - " \n" + - "\n", - "\n" + - " all\n" + - " Instruct-ERIC is the European Research Infrastructure for Structural Biology\n" - + - " https://instruct-eric.eu/templates/instructeric/images/logos/instruct-eric-logo-noline.png\n" - + - " Instruct-ERIC\n" + - " claudia@instruct-eric.eu,carazo@cnb.csic.es,echrysina@eie.gr,susan@instruct-eric.eu,naomi@instruct-eric.eu,natalie@instruct-eric.eu,pmarie@igbmc.fr,darren.hart@ibs.fr,claudia@strubi.ox.ac.uk,paolo.manghi@isti.cnr.it\n" - + - " \n" + - " The authors acknowledge the support and the use of resources of Instruct-ERIC.\n" - + - " The authors acknowledge the support and the use of resources of Instruct (PID # or APPID #), a Landmark ESFRI project\n" - + - " oac_instruct\n" + - " 2018-03-01T12:00:00\n" + - " \n" + - " \n" - + - " Authentication and Authorisation For Research and Collaboration\n" - + - " \n" + - " 730941\n" + - " \n" + - " H2020-EINFRA-2016-1\n" + - " AARC2\n" + - " EC\n" + - " \n" + - " \n" - + - " Building data bridges between biological and medical infrastructures in Europe\n" - + - " \n" + - " 284209\n" + - " \n" + - " FP7-INFRASTRUCTURES-2011-1\n" + - " EC\n" + - " BioMedBridges\n" + - " \n" + - " \n" - + - " Transnational access and enhancement of integrated Biological Structure determination at synchrotron X-ray radiation facilities\n" - + - " \n" + - " 283570\n" + - " \n" + - " FP7-INFRASTRUCTURES-2011-1\n" + - " EC\n" + - " BioStruct-X\n" + - " \n" + - " \n" - + - " Coordinated Research Infrastructures Building Enduring Life-science services\n" - + - " \n" + - " 654248\n" + - " \n" + - " H2020-INFRADEV-1-2014-1\n" + - " EC\n" + - " CORBEL\n" + - " \n" + - " \n" - + - " Infrastructure for NMR, EM and X-rays for translational research\n" - + - " \n" + - " 653706\n" + - " \n" + - " H2020-INFRAIA-2014-2015\n" + - " EC\n" + - " iNEXT\n" + - " \n" + - " \n" - + - " Integrated Structural Biology Infrastructure\n" + - " \n" + - " 211252\n" + - " \n" + - " FP7-INFRASTRUCTURES-2007-1\n" + - " EC\n" + - " INSTRUCT\n" + - " \n" + - " \n" - + - " Releasing the full potential of Instruct to expand and consolidate infrastructure services for integrated structural life science research\n" - + - " \n" + - " 731005\n" + - " \n" + - " H2020-INFRADEV-2016-1\n" + - " EC\n" + - " INSTRUCT-ULTRA\n" + - " \n" + - " \n" - + - " Opening Synchrotron Light for Experimental Science and Applications in the Middle East\n" - + - " \n" + - " 730943\n" + - " \n" + - " H2020-INFRASUPP-2016-1\n" + - " EC\n" + - " OPEN SESAME\n" + - " \n" + - " \n" - + - " Infrastructure for Protein Production Platforms\n" - + - " \n" + - " 227764\n" + - " \n" + - " FP7-INFRASTRUCTURES-2008-1\n" + - " EC\n" + - " PCUBE\n" + - " \n" + - " \n" - + - " European Vaccine Research and Development Infrastructure\n" - + - " \n" + - " 730964\n" + - " \n" + - " H2020-INFRAIA-2016-1\n" + - " EC\n" + - " TRAMSVAC2\n" + - " \n" + - " \n" - + - " World-wide E-infrastructure for structural biology\n" - + - " \n" + - " 675858\n" + - " \n" + - " EC | H2020 | RIA\n" + - " EC\n" + - " West-Life\n" + - " \n" + - " \n" + - " Expanding research infrastructure visibility to strengthen strategic partnerships\n" - + - " RI-VIS\n" + - " 824063\n" + - " EC\n" + - " corda__h2020::af93b591b76991d8437993a8f6fc6538\n" + - " \n" + - " \n" + - " \n" - + - " \n" - + - " \n" + - " instruct\n" + - " \n" + - " \n" + - " \n" - + - " west-life\n" + - " \n" + - " \n" + - " \n" + - " \n" - + - " \n" + - " FRISBI\n" + - " aHR0cDovL2ZyaXNiaS5ldS9zdGF0aWMvaW1hZ2VzL2xvZ29zL2xvZ28tZnJpc2JpLnBuZw==\n" - + - " aHR0cDovL2ZyaXNiaS5ldS8=\n" + - " \n" + - " \n" + - " RI-VIS\n" + - " aHR0cHM6Ly9yaS12aXMuZXUvbmV0d29yay9yaXZpcy90ZW1wbGF0ZXMvcml2aXMvaW1hZ2VzL1JJLVZJU0xvZ29GaW5hbC0wNi5wbmc=\n" - + - " aHR0cHM6Ly9yaS12aXMuZXU=\n" + - " \n" + - " \n" + - " CIISB\n" + - " aHR0cDovL2JpYy5jZWl0ZWMuY3ovZmlsZXMvMjkyLzEyNS5KUEc=\n" + - " aHR0cHM6Ly93d3cuY2lpc2Iub3Jn\n" + - " \n" + - " \n" + - "\n", - "\n" + - " all\n" + - " ELIXIR-GR enhances the potential of the Greek bioinformatics community to offer open, easily accessible and state -of- the- art services to the Greek and the international academic community and other stakeholders, such as industry and the health sector. More importantly, by providing these services, the infrastructure facilitates discoveries in the field of the life-sciences, having strong spill over effects in promoting innovation in sectors such as discovery of new drug targets and development of novel therapeutic agents, development of innovative diagnostics, personalized medicine, and development of innovative biotechnological products and processes.\n" - + - " https://elixir-greece.org/sites/default/files/ELIXIR_GREECE_white_background.png\n" - + - " The Greek National Node of the ESFRI European RI ELIXIR\n" + - " vergoulis@imis.athena-innovation.gr,schatz@imis.athena-innovation.gr,paolo.manghi@isti.cnr.it\n" - + - " \n" + - " \n" + - " oaa_elixir-gr\n" + - " 2018-03-01T12:00:00\n" + - " \n" + - " \n" + - " BIO-INFORMATICS RESEARCH NETWORK COORDINATING CENTER (BIRN-CC)\n" - + - " \n" + - " 1U24RR025736-01\n" + - " NIH\n" + - " \n" + - " \n" + - " COLLABORATIVE RESEARCH: The Cognitive Neuroscience of Category Learning\n" - + - " \n" + - " 0223843\n" + - " NSF\n" + - " \n" + - " \n" + - " The Cognitive Atlas: Developing an Interdisciplinary Knowledge Base Through Socia\n" - + - " \n" + - " 5R01MH082795-05\n" + - " NIH\n" + - " \n" + - " \n" + - " Fragmented early life environmental and emotional / cognitive vulnerabilities\n" - + - " \n" + - " 1P50MH096889-01A1\n" + - " NIH\n" + - " \n" + - " \n" + - " Enhancement of the 1000 Functional Connectome Project\n" - + - " \n" + - " 1R03MH096321-01A1\n" + - " TUBITAK\n" + - " \n" + - " \n" + - " CRCNS Data Sharing: An open data repository for cognitive neuroscience: The OpenfMRI Project\n" - + - " \n" + - " 1131441\n" + - " NSF\n" + - " \n" + - " \n" + - " Enhancing Human Cortical Plasticity: Visual Psychophysics and fMRI\n" - + - " \n" + - " 0121950\n" + - " NSF\n" + - " \n" + - " \n" + - " Transforming statistical methodology for neuroimaging meta-analysis.\n" - + - " \n" + - " 100309\n" + - " WT\n" + - " \n" + - " " + - - " \n" - + - " \n" + - " rest________::b8e502674c3c3499d5374e9b2ea6d8d5\n" + - " bio.tools\n" + - " bio.tools\n" + - " false\n" + - " \n" + - " \n" + - " \n" + - " \n" - + - " \n" + - " \n" + - " ATHENA RC\n" + - " aHR0cHM6Ly9lbGl4aXItZ3JlZWNlLm9yZy9zaXRlcy9kZWZhdWx0L2ZpbGVzL3N0eWxlcy90aHVtYm5haWwvcHVibGljL3BhcnRuZXJfbG9nb3MvYXRoZW5hX2xvZ28uanBnP2l0b2s9VXdGWFNpZng=\n" - + - " aHR0cHM6Ly93d3cuYXRoZW5hLWlubm92YXRpb24uZ3IvZW4=\n" + - " \n" + - " \n" - + - ""); - - private QueryInformationSystem queryInformationSystem; - - private Map map; - - @BeforeEach - public void setUp() { - - queryInformationSystem = new QueryInformationSystem(); - queryInformationSystem.setContextRelationResult(communityContext); - } - - @Test - void test1() { - List cInfoList = new ArrayList<>(); - final Consumer consumer = ci -> cInfoList.add(ci); - - queryInformationSystem - .getContextRelation(consumer, "contentproviders", ModelSupport.getIdPrefix(Datasource.class)); - - cInfoList.forEach(c -> System.out.println(new Gson().toJson(c))); - - List rList = new ArrayList<>(); - - cInfoList.forEach(cInfo -> Process.getRelation(cInfo).forEach(rList::add)); - - Assertions.assertEquals(34, rList.size()); - - Assertions - .assertTrue( - rList - .stream() - .map(r -> r.getSource().getId()) - .collect(Collectors.toSet()) - .contains( - String - .format( - "%s|%s::%s", Constants.CONTEXT_ID, - Constants.CONTEXT_NS_PREFIX, - DHPUtils.md5("dh-ch")))); - - Assertions - .assertEquals( - 10, - rList - .stream() - .filter( - r -> r - .getSource() - .getId() - .equals( - String - .format( - "%s|%s::%s", Constants.CONTEXT_ID, - Constants.CONTEXT_NS_PREFIX, - DHPUtils.md5("dh-ch")))) - .collect(Collectors.toList()) - .size()); - - Assertions - .assertEquals( - 10, - rList - .stream() - .filter( - r -> r - .getTarget() - .getId() - .equals( - String - .format( - "%s|%s::%s", Constants.CONTEXT_ID, - Constants.CONTEXT_NS_PREFIX, - DHPUtils.md5("dh-ch")))) - .collect(Collectors.toList()) - .size()); - - Set tmp = rList - .stream() - .filter( - r -> r - .getSource() - .getId() - .equals( - String - .format( - "%s|%s::%s", Constants.CONTEXT_ID, - Constants.CONTEXT_NS_PREFIX, - DHPUtils.md5("dh-ch")))) - .map(r -> r.getTarget().getId()) - .collect(Collectors.toSet()); - - Assertions - .assertTrue( - tmp.contains("10|re3data_____::9ebe127e5f3a0bf401875690f3bb6b81") && - tmp.contains("10|doajarticles::c6cd4b532e12868c1d760a8d7cda6815") && - tmp.contains("10|doajarticles::a6de4499bb87bf3c01add0a9e2c9ed0b") && - tmp.contains("10|doajarticles::6eb31d13b12bc06bbac06aef63cf33c9") && - tmp.contains("10|doajarticles::0da84e9dfdc8419576169e027baa8028") && - tmp.contains("10|re3data_____::84e123776089ce3c7a33db98d9cd15a8") && - tmp.contains("10|openaire____::c5502a43e76feab55dd00cf50f519125") && - tmp.contains("10|re3data_____::a48f09c562b247a9919acfe195549b47") && - tmp.contains("10|opendoar____::97275a23ca44226c9964043c8462be96") && - tmp.contains("10|doajarticles::2899208a99aa7d142646e0a80bfeef05")); - - } - - @Test - public void test2() { - List cInfoList = new ArrayList<>(); - final Consumer consumer = ci -> cInfoList.add(ci); - - queryInformationSystem - .getContextRelation(consumer, "projects", ModelSupport.getIdPrefix(Project.class)); - - cInfoList.forEach(c -> System.out.println(new Gson().toJson(c))); - - List rList = new ArrayList<>(); - - cInfoList.forEach(cInfo -> Process.getRelation(cInfo).forEach(rList::add)); - - Assertions.assertEquals(44, rList.size()); - - Assertions - .assertFalse( - rList - .stream() - .map(r -> r.getSource().getId()) - .collect(Collectors.toSet()) - .contains( - String - .format( - "%s|%s::%s", Constants.CONTEXT_ID, - Constants.CONTEXT_NS_PREFIX, - DHPUtils.md5("dh-ch")))); - - Assertions - .assertEquals( - 2, - rList - .stream() - .filter( - r -> r - .getSource() - .getId() - .equals( - String - .format( - "%s|%s::%s", Constants.CONTEXT_ID, - Constants.CONTEXT_NS_PREFIX, - DHPUtils.md5("clarin")))) - .collect(Collectors.toList()) - .size()); - - Assertions - .assertEquals( - 2, - rList - .stream() - .filter( - r -> r - .getTarget() - .getId() - .equals( - String - .format( - "%s|%s::%s", Constants.CONTEXT_ID, - Constants.CONTEXT_NS_PREFIX, - DHPUtils.md5("clarin")))) - .collect(Collectors.toList()) - .size()); - - Set tmp = rList - .stream() - .filter( - r -> r - .getSource() - .getId() - .equals( - String - .format( - "%s|%s::%s", Constants.CONTEXT_ID, - Constants.CONTEXT_NS_PREFIX, - DHPUtils.md5("clarin")))) - .map(r -> r.getTarget().getId()) - .collect(Collectors.toSet()); - - Assertions - .assertTrue( - tmp.contains("40|corda__h2020::b5a4eb56bf84bef2ebc193306b4d423f") && - tmp.contains("40|corda_______::ef782b2d85676aa3e5a907427feb18c4")); - - rList.forEach(rel -> { - if (rel.getSource().getId().startsWith("40|")) { - String proj = rel.getSource().getId().substring(3); - Assertions.assertTrue(proj.substring(0, proj.indexOf("::")).length() == 12); - } - }); - - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpOrganizationProjectDatasourceTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpOrganizationProjectDatasourceTest.java deleted file mode 100644 index 80b5fd89e..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpOrganizationProjectDatasourceTest.java +++ /dev/null @@ -1,157 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.HashMap; - -import org.apache.commons.io.FileUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.api.java.function.ForeachFunction; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SparkSession; -import org.junit.jupiter.api.AfterAll; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.Test; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.oa.graph.dump.exceptions.NoAvailableEntityTypeException; -import eu.dnetlib.dhp.schema.oaf.Datasource; -import eu.dnetlib.dhp.schema.oaf.Organization; -import eu.dnetlib.dhp.schema.oaf.Project; - -public class DumpOrganizationProjectDatasourceTest { - - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private static SparkSession spark; - - private static Path workingDir; - - private static final Logger log = LoggerFactory - .getLogger(DumpOrganizationProjectDatasourceTest.class); - - private static final HashMap map = new HashMap<>(); - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory(DumpOrganizationProjectDatasourceTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - - SparkConf conf = new SparkConf(); - conf.setAppName(DumpOrganizationProjectDatasourceTest.class.getSimpleName()); - - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - - spark = SparkSession - .builder() - .appName(DumpOrganizationProjectDatasourceTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Test - public void dumpOrganizationTest() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/complete/organization") - .getPath(); - - DumpGraphEntities dg = new DumpGraphEntities(); - - dg.run(false, sourcePath, workingDir.toString() + "/dump", Organization.class, null); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/dump") - .map(item -> OBJECT_MAPPER.readValue(item, eu.dnetlib.dhp.schema.dump.oaf.graph.Organization.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(eu.dnetlib.dhp.schema.dump.oaf.graph.Organization.class)); - - Assertions.assertEquals(15, verificationDataset.count()); - - verificationDataset - .foreach( - (ForeachFunction) o -> System.out - .println(OBJECT_MAPPER.writeValueAsString(o))); - - } - - @Test - public void dumpProjectTest() throws NoAvailableEntityTypeException { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/complete/project") - .getPath(); - - DumpGraphEntities dg = new DumpGraphEntities(); - - dg.run(false, sourcePath, workingDir.toString() + "/dump", Project.class, null); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/dump") - .map(item -> OBJECT_MAPPER.readValue(item, eu.dnetlib.dhp.schema.dump.oaf.graph.Project.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(eu.dnetlib.dhp.schema.dump.oaf.graph.Project.class)); - - Assertions.assertEquals(12, verificationDataset.count()); - - verificationDataset - .foreach( - (ForeachFunction) o -> System.out - .println(OBJECT_MAPPER.writeValueAsString(o))); - - } - - @Test - public void dumpDatasourceTest() throws NoAvailableEntityTypeException { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/complete/datasource") - .getPath(); - - DumpGraphEntities dg = new DumpGraphEntities(); - - dg.run(false, sourcePath, workingDir.toString() + "/dump", Datasource.class, null); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/dump") - .map(item -> OBJECT_MAPPER.readValue(item, eu.dnetlib.dhp.schema.dump.oaf.graph.Datasource.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(eu.dnetlib.dhp.schema.dump.oaf.graph.Datasource.class)); - - Assertions.assertEquals(5, verificationDataset.count()); - - verificationDataset - .foreach( - (ForeachFunction) o -> System.out - .println(OBJECT_MAPPER.writeValueAsString(o))); - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpRelationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpRelationTest.java deleted file mode 100644 index 763318ae4..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpRelationTest.java +++ /dev/null @@ -1,305 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.HashMap; - -import org.apache.commons.io.FileUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.api.java.function.ForeachFunction; -import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.Row; -import org.apache.spark.sql.SparkSession; -import org.junit.jupiter.api.AfterAll; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.Test; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.schema.dump.oaf.graph.Relation; - -public class DumpRelationTest { - - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private static SparkSession spark; - - private static Path workingDir; - - private static final Logger log = LoggerFactory - .getLogger(DumpRelationTest.class); - - private static final HashMap map = new HashMap<>(); - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory(DumpRelationTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - - SparkConf conf = new SparkConf(); - conf.setAppName(DumpRelationTest.class.getSimpleName()); - - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - - spark = SparkSession - .builder() - .appName(DumpRelationTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Test - public void test1() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/relation/relation") - .getPath(); - - SparkDumpRelationJob.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/relation", - "-sourcePath", sourcePath - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/relation") - .map(item -> OBJECT_MAPPER.readValue(item, Relation.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Relation.class)); - - verificationDataset.createOrReplaceTempView("table"); - - verificationDataset - .foreach((ForeachFunction) r -> System.out.println(new ObjectMapper().writeValueAsString(r))); - - Dataset check = spark - .sql( - "SELECT reltype.name, source.id source, source.type stype, target.id target,target.type ttype, provenance.provenance " - + - "from table "); - - Assertions.assertEquals(22, check.filter("name = 'isProvidedBy'").count()); - Assertions - .assertEquals( - 22, check - .filter( - "name = 'isProvidedBy' and stype = 'datasource' and ttype = 'organization' and " + - "provenance = 'Harvested'") - .count()); - - Assertions.assertEquals(7, check.filter("name = 'isParticipant'").count()); - Assertions - .assertEquals( - 7, check - .filter( - "name = 'isParticipant' and stype = 'organization' and ttype = 'project' " + - "and provenance = 'Harvested'") - .count()); - - Assertions.assertEquals(1, check.filter("name = 'isAuthorInstitutionOf'").count()); - Assertions - .assertEquals( - 1, check - .filter( - "name = 'isAuthorInstitutionOf' and stype = 'organization' and ttype = 'result' " + - "and provenance = 'Inferred by OpenAIRE'") - .count()); - } - - @Test - public void test2() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/relation/relation_validated") - .getPath(); - - SparkDumpRelationJob.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/relation", - "-sourcePath", sourcePath - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/relation") - .map(item -> OBJECT_MAPPER.readValue(item, Relation.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Relation.class)); - - verificationDataset.createOrReplaceTempView("table"); - - verificationDataset - .foreach((ForeachFunction) r -> System.out.println(new ObjectMapper().writeValueAsString(r))); - - Dataset check = spark - .sql( - "SELECT reltype.name, source.id source, source.type stype, target.id target,target.type ttype, provenance.provenance " - + - "from table "); - - Assertions.assertEquals(20, check.filter("name = 'isProvidedBy'").count()); - Assertions - .assertEquals( - 20, check - .filter( - "name = 'isProvidedBy' and stype = 'datasource' and ttype = 'organization' and " + - "provenance = 'Harvested'") - .count()); - - Assertions.assertEquals(7, check.filter("name = 'isParticipant'").count()); - Assertions - .assertEquals( - 7, check - .filter( - "name = 'isParticipant' and stype = 'organization' and ttype = 'project' " + - "and provenance = 'Harvested'") - .count()); - - Assertions.assertEquals(1, check.filter("name = 'isAuthorInstitutionOf'").count()); - Assertions - .assertEquals( - 1, check - .filter( - "name = 'isAuthorInstitutionOf' and stype = 'organization' and ttype = 'result' " + - "and provenance = 'Inferred by OpenAIRE'") - .count()); - - Assertions.assertEquals(2, check.filter("name = 'isProducedBy'").count()); - Assertions - .assertEquals( - 2, check - .filter( - "name = 'isProducedBy' and stype = 'project' and ttype = 'result' " + - "and provenance = 'Harvested' and validated = true " + - "and validationDate = '2021-08-06'") - .count()); - } - - @Test - public void test3() throws Exception {// - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/relation/relation") - .getPath(); - - SparkDumpRelationJob.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/relation", - "-sourcePath", sourcePath, - "-removeSet", "isParticipant" - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/relation") - .map(item -> OBJECT_MAPPER.readValue(item, Relation.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Relation.class)); - - verificationDataset.createOrReplaceTempView("table"); - - verificationDataset - .foreach((ForeachFunction) r -> System.out.println(new ObjectMapper().writeValueAsString(r))); - - Dataset check = spark - .sql( - "SELECT reltype.name, source.id source, source.type stype, target.id target,target.type ttype, provenance.provenance " - + - "from table "); - - Assertions.assertEquals(22, check.filter("name = 'isProvidedBy'").count()); - Assertions - .assertEquals( - 22, check - .filter( - "name = 'isProvidedBy' and stype = 'datasource' and ttype = 'organization' and " + - "provenance = 'Harvested'") - .count()); - - Assertions.assertEquals(0, check.filter("name = 'isParticipant'").count()); - - Assertions.assertEquals(1, check.filter("name = 'isAuthorInstitutionOf'").count()); - Assertions - .assertEquals( - 1, check - .filter( - "name = 'isAuthorInstitutionOf' and stype = 'organization' and ttype = 'result' " + - "and provenance = 'Inferred by OpenAIRE'") - .count()); - } - - @Test - public void test4() throws Exception {// - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/relation/relation") - .getPath(); - - SparkDumpRelationJob.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/relation", - "-sourcePath", sourcePath, - "-removeSet", "isParticipant;isAuthorInstitutionOf" - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/relation") - .map(item -> OBJECT_MAPPER.readValue(item, Relation.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Relation.class)); - - verificationDataset.createOrReplaceTempView("table"); - - verificationDataset - .foreach((ForeachFunction) r -> System.out.println(new ObjectMapper().writeValueAsString(r))); - - Dataset check = spark - .sql( - "SELECT reltype.name, source.id source, source.type stype, target.id target,target.type ttype, provenance.provenance " - + - "from table "); - - Assertions.assertEquals(22, check.filter("name = 'isProvidedBy'").count()); - Assertions - .assertEquals( - 22, check - .filter( - "name = 'isProvidedBy' and stype = 'datasource' and ttype = 'organization' and " + - "provenance = 'Harvested'") - .count()); - - Assertions.assertEquals(0, check.filter("name = 'isParticipant'").count()); - - Assertions.assertEquals(0, check.filter("name = 'isAuthorInstitutionOf'").count()); - - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/ExtractRelationFromEntityTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/ExtractRelationFromEntityTest.java deleted file mode 100644 index 27573bb32..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/ExtractRelationFromEntityTest.java +++ /dev/null @@ -1,172 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; - -import org.apache.commons.io.FileUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.api.java.function.FilterFunction; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SparkSession; -import org.junit.jupiter.api.*; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.schema.dump.oaf.graph.Relation; - -public class ExtractRelationFromEntityTest { - - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private static SparkSession spark; - - private static Path workingDir; - - private static final Logger log = LoggerFactory - .getLogger(ExtractRelationFromEntityTest.class); - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory(ExtractRelationFromEntityTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - - SparkConf conf = new SparkConf(); - conf.setAppName(ExtractRelationFromEntityTest.class.getSimpleName()); - - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - - spark = SparkSession - .builder() - .appName(ExtractRelationFromEntityTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Test - void test1() { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/singelRecord_pub.json") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") - .getPath(); - - Extractor ex = new Extractor(); - ex - .run( - false, sourcePath, workingDir.toString() + "/relation", - // eu.dnetlib.dhp.schema.oaf.Publication.class, communityMapPath); - eu.dnetlib.dhp.schema.oaf.Publication.class, communityMapPath); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/relation") - .map(item -> OBJECT_MAPPER.readValue(item, Relation.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Relation.class)); - - Assertions - .assertEquals( - 9, - verificationDataset.filter("source.id = '50|dedup_wf_001::15270b996fa8fd2fb5723daeab3685c3'").count()); - - Assertions - .assertEquals( - 9, - verificationDataset.filter("source.id = '50|dedup_wf_001::15270b996fa8fd2fb5723daxab3685c3'").count()); - - Assertions - .assertEquals( - "IsRelatedTo", verificationDataset - .filter((FilterFunction) row -> row.getSource().getId().startsWith("00")) - .collectAsList() - .get(0) - .getReltype() - .getName()); - - Assertions - .assertEquals( - "relationship", verificationDataset - .filter((FilterFunction) row -> row.getSource().getId().startsWith("00")) - .collectAsList() - .get(0) - .getReltype() - .getType()); - - Assertions - .assertEquals( - "context", verificationDataset - .filter((FilterFunction) row -> row.getSource().getId().startsWith("00")) - .collectAsList() - .get(0) - .getSource() - .getType()); - - Assertions - .assertEquals( - "result", verificationDataset - .filter((FilterFunction) row -> row.getSource().getId().startsWith("00")) - .collectAsList() - .get(0) - .getTarget() - .getType()); - Assertions - .assertEquals( - "IsRelatedTo", verificationDataset - .filter((FilterFunction) row -> row.getTarget().getId().startsWith("00")) - .collectAsList() - .get(0) - .getReltype() - .getName()); - - Assertions - .assertEquals( - "relationship", verificationDataset - .filter((FilterFunction) row -> row.getTarget().getId().startsWith("00")) - .collectAsList() - .get(0) - .getReltype() - .getType()); - - Assertions - .assertEquals( - "context", verificationDataset - .filter((FilterFunction) row -> row.getTarget().getId().startsWith("00")) - .collectAsList() - .get(0) - .getTarget() - .getType()); - - Assertions - .assertEquals( - "result", verificationDataset - .filter((FilterFunction) row -> row.getTarget().getId().startsWith("00")) - .collectAsList() - .get(0) - .getSource() - .getType()); - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/FunderParsingTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/FunderParsingTest.java deleted file mode 100644 index eb5919fd5..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/FunderParsingTest.java +++ /dev/null @@ -1,70 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import org.dom4j.DocumentException; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.Test; -import org.xml.sax.SAXException; - -import eu.dnetlib.dhp.schema.dump.oaf.graph.Funder; - -class FunderParsingTest { - - @Test - void testFunderTwoLevels() throws DocumentException { - - String funding_Stream = "nsf_________::NSFNSFNational Science " - + - "FoundationUSnsf_________::NSF::CISE/OAD::CISE/CCFDivision " - + - "of Computing and Communication FoundationsDivision of Computing and Communication " + - "Foundationsnsf_________::NSF::CISE/OADDirectorate for " - + - "Computer & Information Science & EngineeringDirectorate for Computer & " + - "Information Science & Engineeringnsf:fundingStream"; - - Funder f = DumpGraphEntities.getFunder(funding_Stream); - - Assertions.assertEquals("NSF", f.getShortName()); - Assertions.assertEquals("National Science Foundation", f.getName()); - Assertions.assertEquals("US", f.getJurisdiction()); - - Assertions.assertEquals("NSF::CISE/OAD::CISE/CCF", f.getFunding_stream().getId()); - Assertions - .assertEquals( - "Directorate for Computer & Information Science & Engineering - Division of Computing and Communication Foundations", - f.getFunding_stream().getDescription()); - - } - - @Test - void testFunderThreeeLevels() throws DocumentException, SAXException { - String funding_stream = "ec__________::EC" + - "EC" + - "European Commission" + - "EU" + - "" + - "ec__________::EC::H2020::ERC::ERC-COG" + - "Consolidator Grant" + - "ERC-COGec:h2020toas" + - "ec__________::EC::H2020::ERC" + - "European Research Council" + - "ERCec:h2020fundings" + - "ec__________::EC::H2020H2020" + - "Horizon 2020 Framework Programme" + - "ec:h2020fundings"; - - Funder f = DumpGraphEntities.getFunder(funding_stream); - - Assertions.assertEquals("EC", f.getShortName()); - Assertions.assertEquals("European Commission", f.getName()); - Assertions.assertEquals("EU", f.getJurisdiction()); - - Assertions.assertEquals("EC::H2020::ERC::ERC-COG", f.getFunding_stream().getId()); - Assertions - .assertEquals( - "Horizon 2020 Framework Programme - European Research Council - Consolidator Grant", - f.getFunding_stream().getDescription()); - - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystemTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystemTest.java deleted file mode 100644 index 08fcd49a8..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystemTest.java +++ /dev/null @@ -1,810 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import static org.mockito.Mockito.lenient; - -import java.util.*; -import java.util.function.Consumer; - -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeEach; -import org.junit.jupiter.api.Test; -import org.junit.jupiter.api.extension.ExtendWith; -import org.mockito.Mock; -import org.mockito.junit.jupiter.MockitoExtension; - -import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; - -@ExtendWith(MockitoExtension.class) -class QueryInformationSystemTest { - - private static final String XQUERY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') " - + - " where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " + - " and $x//context/param[./@name = 'status']/text() = 'all' " + - " return " + - "$x//context"; - - private static final String XQUERY_ENTITY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') " - + - "where $x//context[./@type='community' or ./@type = 'ri'] and $x//context/param[./@name = 'status']/text() = 'all' return " - + - "concat(data($x//context/@id) , '@@', $x//context/param[./@name =\"name\"]/text(), '@@', " + - "$x//context/param[./@name=\"description\"]/text(), '@@', $x//context/param[./@name = \"subject\"]/text(), '@@', " - + - "$x//context/param[./@name = \"zenodoCommunity\"]/text(), '@@', $x//context/@type)"; - - List communityMap = Arrays - .asList( - "clarin@@Common Language Resources and Technology Infrastructure@@CLARIN@@@@oac_clarin@@ri", - "ee@@Sustainable Development Solutions Network - Greece@@The UN Sustainable Development Solutions Network (SDSN) has been operating since 2012 under the auspices of the UN Secretary-General. " - + - "SDSN mobilizes global scientific and technological expertise to promote practical solutions for sustainable development, including the implementation of the Sustainable Development Goals (SDGs) and the Paris Climate Agreement. The Greek hub of SDSN has been included in the SDSN network in 2017 and is co-hosted by ICRE8: International Center for Research on the Environment and the Economy and the Political Economy of Sustainable Development Lab.@@SDG13 - Climate action,SDG8 - Decent work and economic growth,SDG15 - " - + - "Life on land,SDG2 - Zero hunger,SDG17 - Partnerships for the ´goals,SDG10 - Reduced inequalities,SDG5 - Gender equality,SDG12 - Responsible consumption and production,SDG14 - Life below water,SDG6 - Clean water and sanitation,SDG11 - Sustainable cities and communities,SDG1 - No poverty,SDG3 - Good health and well being,SDG7 - Affordable and clean energy,SDG4 - Quality education,SDG9 - Industry innovation and infrastructure,SDG16 - Peace justice and strong institutions@@oac_sdsn-greece@@community", - "dh-ch@@Digital Humanities and Cultural Heritage@@This community gathers research results, data, scientific publications and projects related to the domain of Digital Humanities. This broad definition includes Humanities, Cultural Heritage, History, Archaeology and related fields.@@modern art,monuments,europeana data model,sites,field walking,frescoes,LIDO metadata schema,art history,excavation,Arts and Humanities General,cities,coins,temples,numismatics,lithics,roads,environmental archaeology,digital cultural heritage,archaeological reports,history,CRMba,churches,cultural heritage,archaeological stratigraphy,religious art,buidings,digital humanities,survey,archaeological sites,linguistic studies,bioarchaeology,architectural orders,palaeoanthropology,fine arts,europeana,CIDOC CRM,decorations,classic art,stratigraphy,digital archaeology,intangible cultural heritage,walls,humanities,chapels,CRMtex,Language and Literature,paintings,archaeology,fair data,mosaics,burials,architecture,medieval art,castles,CARARE metadata schema,statues,natural language processing,inscriptions,CRMsci,vaults,contemporary art,Arts and Humanities,CRMarchaeo,pottery,site,architectural,vessels@@oac_dh-ch@@community", - "fam@@Fisheries and Aquaculture Management@@Conservation of marine resources for sustainable development. The Fisheries and Aquaculture community focus on resources (document, data, codes..) which have been produced in the framework of projects (H2020, FP7, ..) related to the domain of fisheries and aquaculture.@@Stock Assessment,pelagic,Acoustic,Fish farming,Fisheries,Fishermen,maximum sustainable yield,trawler,Fishing vessel,Fisherman,Fishing gear,mackerel,RFMO,Fish Aggregating Device,Bycatch,Fishery,common fisheries policy,Fishing fleet,Aquaculture@@fisheries@@community", - "ni@@Neuroinformatics@@The neuroinformatics dashboard gathers research outputs from the 'neuroinformatics' community at large including the fields of: neuroscience, neuroinformatics, brain imaging databases and standards, brain imaging techniques, neuroimaging methods including statistics and machine learning. The dashboard covers a wide range of imaging methods including (but not limited to): MRI, TEP, EEG, MEG, and studies involving human participants as well as animal studies.@@brain mapping,brain imaging,electroencephalography,arterial spin labelling,brain fingerprinting,brain,neuroimaging,Multimodal Brain Image Analysis,fMRI,neuroinformatics,fetal brain,brain ultrasonic imaging,topographic brain mapping,diffusion tensor imaging,computerized knowledge assessment,connectome mapping,brain magnetic resonance imaging,brain abnormalities@@oac_ni@@community", - "mes@@European Marine Science@@This community was initially defined to include a very broad range of topics, with the intention to generate a number of more focused and sustainable dashboards for research communities and initiatives. As outlined in the logo of this community, we intend to setup a community dashboard for EuroMarine (a consortium of 56 research and academic organisations) and monitoring dashboards for marine research initiatives, including infrastructures (e.g. EMBRC & EMSO), advisory boards (e.g. Marine Boards & ICES), and transnational funding bodies (e.g. JPI-Oceans and Tara Foundation).@@marine,ocean,fish,aqua,sea@@oac_mes@@community", - "instruct@@Instruct-ERIC@@Instruct-ERIC is the European Research Infrastructure for Structural Biology@@@@oac_instruct@@community", - "elixir-gr@@The Greek National Node of the ESFRI European RI ELIXIR@@ELIXIR-GR enhances the potential of the Greek bioinformatics community to offer open, easily accessible and state -of- the- art services to the Greek and the international academic community and other stakeholders, such as industry and the health sector. More importantly, by providing these services, the infrastructure facilitates discoveries in the field of the life-sciences, having strong spill over effects in promoting innovation in sectors such as discovery of new drug targets and development of novel therapeutic agents, development of innovative diagnostics, personalized medicine, and development of innovative biotechnological products and processes.@@@@oaa_elixir-gr@@ri", - "aginfra@@Agricultural and Food Sciences@@The scope of this community is to provide access to publications, research data, projects and software that are related to agricultural and food sciences@@animal production and health,fisheries and aquaculture,food safety and human nutrition,information management,food technology,agri-food education and extension,natural resources and environment,food system,engineering technology and Research,agriculture,food safety risk assessment,food security,farming practices and systems,plant production and protection,agri-food economics and policy,Agri-food,food distribution,forestry@@oac_aginfra@@community", - "dariah@@DARIAH EU@@The Digital Research Infrastructure for the Arts and Humanities (DARIAH) aims to enhance and support digitally-enabled research and teaching across the arts and humanities. It develops, maintains and operates an infrastructure in support of ICT-based research practices and sustains researchers in using them to build, analyse and interpret digital resources. DARIAH was established as a European Research Infrastructure Consortium (ERIC) in August 2014. Currently, DARIAH has 18 Members and several cooperating partners in eight non-member countries. Here you will find a growing collection of DARIAH-affiliated research outputs and other documents. @@@@dariah@@ri", - "epos@@European Plate Observing System@@EPOS, the European Plate Observing System, is a long-term plan to facilitate integrated use of data, data products, and facilities from distributed research infrastructures for solid Earth science in Europe.@@@@@@ri", - "covid-19@@Corona Virus Disease@@This portal provides access to publications, research data, projects and software that may be relevant to the Corona Virus Disease (COVID-19). The OpenAIRE COVID-19 Gateway aggregates COVID-19 related records, links them and provides a single access point for discovery and navigation. We tag content from the OpenAIRE Research Graph (10,000+ data sources) and additional sources. All COVID-19 related research results are linked to people, organizations and projects, providing a contextualized navigation.@@COVID19,SARS-CoV,HCoV-19,mesh:C000657245,MERS-CoV,Síndrome Respiratorio Agudo Severo,mesh:COVID-19,COVID2019,COVID-19,SARS-CoV-2,2019 novel coronavirus,severe acute respiratory syndrome coronavirus 2,Orthocoronavirinae,Coronaviridae,mesh:D045169,coronavirus,SARS,coronaviruses,coronavirus disease-19,sars cov 2,Middle East Respiratory Syndrome,Severe acute respiratory syndrome coronavirus 2,Severe Acute Respiratory Syndrome,coronavirus disease 2019,2019-nCoV@@covid-19@@community"); - - List communityContext = Arrays - .asList( - "\n" + - " all\n" + - " CLARIN\n" + - " https://www.clarin.eu/sites/default/files/clarin-frontpage-logo.jpg\n" - + - " Common Language Resources and Technology Infrastructure\n" + - " maria@clarin.eu,dieter@clarin.eu,f.m.g.dejong@uu.nl,paolo.manghi@isti.cnr.it\n" - + - " \n" + - " (Part of) the work reported here was made possible by using the CLARIN infrastructure.\n" - + - " The work reported here has received funding through <CLARIN national consortium member, e.g. CLARIN.SI>, <XYZ> project, grant no. <XYZ>.\n" - + - " The work reported here has received funding (through CLARIN ERIC) from the European Union’s Horizon 2020 research and innovation programme under grant agreement No <0-9> for project <XYZ>.\n" - + - " (E.g. No 676529 for project CLARIN-PLUS.)\n" + - " oac_clarin\n" + - " 2018-03-01T12:00:00\n" + - " \n" + - " \n" + - " CLARIN-PLUS\n" + - " \n" + - " \n" + - " 676529\n" + - " http://www.clarin.eu\n" + - " EC\n" + - " H2020-INFRADEV-1-2015-1\n" + - " CLARIN+\n" + - " \n" + - " \n" + - " Common Language Resources and Technology Infrastructure\n" - + - " CLARIN\n" + - " 212230\n" + - " EC\n" + - " corda_______::ef782b2d85676aa3e5a907427feb18c4\n" + - " \n" + - " \n" + - " " + - "\n" + - " \n" + - " LINDAT/CLARIN repository\n" + - " LINDAT/CLARIN repository\n" + - " true\n" + - " \n" + - " \n" + - " \n" + - " \n" + - " CLARIN-D\n" + - " https://www.clarin-d.de/en/\n" + - " \n" + - " http://www.lrec-conf.org/proceedings/lrec2018/pdf/504.pdf\n" - + - " Germany\n" + - " \n" + - " \n" + - " \n" - + - " \n" + - "", - "\n" + - " all\n" + - " This community gathers research results, data, scientific publications and projects related to the domain of Digital Humanities. This broad definition includes Humanities, Cultural Heritage, History, Archaeology and related fields.\n" - + - " http://sanmamante.org/DH_CH_logo.png\n" + - " Digital Humanities and Cultural Heritage\n" + - " ileniagalluccio87@gmail.com,achille.felicetti@gmail.com,paolo.manghi@isti.cnr.it,tim.evans@york.ac.uk\n" - + - " modern art,monuments,europeana data model,sites,field walking,frescoes,LIDO metadata schema,art history,excavation,Arts and Humanities General,cities,coins,temples,numismatics,lithics,roads,environmental archaeology,digital cultural heritage,archaeological reports,history,CRMba,churches,cultural heritage,archaeological stratigraphy,religious art,buidings,digital humanities,survey,archaeological sites,linguistic studies,bioarchaeology,architectural orders,palaeoanthropology,fine arts,europeana,CIDOC CRM,decorations,classic art,stratigraphy,digital archaeology,intangible cultural heritage,walls,humanities,chapels,CRMtex,Language and Literature,paintings,archaeology,fair data,mosaics,burials,architecture,medieval art,castles,CARARE metadata schema,statues,natural language processing,inscriptions,CRMsci,vaults,contemporary art,Arts and Humanities,CRMarchaeo,pottery,site,architectural,vessels\n" - + - " The present work has been partially supported by the PARTHENOS project, funded by the European Commission (Grant Agreement No. 654119) under the HORIZON 2020 - INFRADEV-4-2014/2015 call\n" - + - " oac_dh-ch\n" + - " 2018-03-01T12:00:00\n" + - " \n" + - " \n" - + - " Pooling Activities, Resources and Tools for Heritage E-research Networking, Optimization and Synergies\n" - + - " The present work has been partially supported by the PARTHENOS project, funded by the European Commission (Grant Agreement No. 654119) under the HORIZON 2020 - INFRADEV-4-2014/2015 call\n" - + - " \n" + - " 654119\n" + - " http://www.parthenos-project.eu\n" + - " EC\n" + - " PARTHENOS\n" + - " \n" + - " \n" + - " \n" + - " \n" - + - " re3data_____::9ebe127e5f3a0bf401875690f3bb6b81\n" + - " The UK's largest collection of digital research data in the social sciences and humanities\n" - + - " UK Data Archive\n" + - " true\n" + - " \n" + - " \n" - + - " doajarticles::c6cd4b532e12868c1d760a8d7cda6815\n" + - " Journal of Data Mining and Digital Humanities\n" + - " Journal of Data Mining and Digital Humanities\n" + - " true\n" + - " \n" + - " \n" - + - " doajarticles::a6de4499bb87bf3c01add0a9e2c9ed0b\n" + - " Frontiers in Digital Humanities\n" + - " Frontiers in Digital Humanities\n" + - " true\n" + - " \n" + - " \n" - + - " doajarticles::6eb31d13b12bc06bbac06aef63cf33c9\n" + - " Il Capitale Culturale: Studies on the Value of Cultural Heritage\n" - + - " Il Capitale Culturale: Studies on the Value of Cultural Heritage\n" - + - " true\n" + - " \n" + - " \n" - + - " doajarticles::0da84e9dfdc8419576169e027baa8028\n" + - " Conservation Science in Cultural Heritage\n" + - " Conservation Science in Cultural Heritage\n" + - " true\n" + - " \n" + - " \n" - + - " re3data_____::84e123776089ce3c7a33db98d9cd15a8\n" + - " Electronic Archiving System\n" + - " EASY\n" + - " true\n" + - " \n" + - " \n" + - " openaire____::c5502a43e76feab55dd00cf50f519125\n" + - " DANS-KB Harvester\n" + - " Gemeenschappelijke Harvester DANS-KB\n" + - " true\n" + - " \n" + - " \n" + - " re3data_____::a48f09c562b247a9919acfe195549b47\n" + - " ads\n" + - " Archaeology Data Service\n" + - " true\n" + - " \n" + - " \n" + - " opendoar____::97275a23ca44226c9964043c8462be96\n" + - " KNAW Repository\n" + - " KNAW Repository\n" + - " true\n" + - " \n" + - " \n" - + - " doajarticles::2899208a99aa7d142646e0a80bfeef05\n" + - " Internet Archaeology\n" + - " Internet Archaeology\n" + - " true\n" + - " \n" + - " \n" + - " \n" + - "\n", - "\n" + - " all\n" + - " The neuroinformatics dashboard gathers research outputs from the 'neuroinformatics' community at large including the fields of: neuroscience, neuroinformatics, brain imaging databases and standards, brain imaging techniques, neuroimaging methods including statistics and machine learning. The dashboard covers a wide range of imaging methods including (but not limited to): MRI, TEP, EEG, MEG, and studies involving human participants as well as animal studies.\n" - + - " https://docs.google.com/drawings/u/0/d/10e191xGoGf4uaRluMqbt_7cCj6LSCs2a29im4CmWjqU/export/png\n" - + - " Neuroinformatics\n" + - " sorina.pop@creatis.insa-lyon.fr,camille.maumet@inria.fr,christian.barillot@irisa.fr,xavier.rolland@irisa.fr,axel.bonnet@creatis.insa-lyon.fr,paolo.manghi@isti.cnr.it\n" - + - " brain mapping,brain imaging,electroencephalography,arterial spin labelling,brain fingerprinting,brain,neuroimaging,Multimodal Brain Image Analysis,fMRI,neuroinformatics,fetal brain,brain ultrasonic imaging,topographic brain mapping,diffusion tensor imaging,computerized knowledge assessment,connectome mapping,brain magnetic resonance imaging,brain abnormalities\n" - + - " \n" + - " oac_ni\n" + - " 2018-03-01T12:00:00\n" + - " \n" + - " \n" + - " re3data_____::5b9bf9171d92df854cf3c520692e9122\n" + - " Formerly:OpenFMRI\n" + - " OpenNeuro\n" + - " true\n" + - " \n" + - " \n" + - " doajarticles::c7d3de67dc77af72f6747157441252ec\n" + - " Research Ideas and Outcomes\n" + - " Research Ideas and Outcomes\n" + - " true\n" + - " \n" + - " \n" + - " re3data_____::8515794670370f49c1d176c399c714f5\n" + - " Neuroimaging Informatics Tools and Resources Clearinghouse\n" - + - " NITRC\n" + - " true\n" + - " \n" + - " \n" + - " doajarticles::d640648c84b10d425f96f11c3de468f3\n" + - " Frontiers in Neuroinformatics\n" + - " Frontiers in Neuroinformatics\n" + - " true\n" + - " \n" + - " \n" + - " doajarticles::0c0e74daa5d95504eade9c81ebbd5b8a\n" + - " NeuroImage: Clinical\n" + - " NeuroImage: Clinical\n" + - " true\n" + - " \n" + - " \n" + - " rest________::fb1a3d4523c95e63496e3bc7ba36244b\n" + - " NeuroVault\n" + - " NeuroVault\n" + - " true\n" + - " \n" + - " \n" + - "\n", - "\n" + - " all\n" + - " Instruct-ERIC is the European Research Infrastructure for Structural Biology\n" - + - " https://instruct-eric.eu/templates/instructeric/images/logos/instruct-eric-logo-noline.png\n" - + - " Instruct-ERIC\n" + - " claudia@instruct-eric.eu,carazo@cnb.csic.es,echrysina@eie.gr,susan@instruct-eric.eu,naomi@instruct-eric.eu,natalie@instruct-eric.eu,pmarie@igbmc.fr,darren.hart@ibs.fr,claudia@strubi.ox.ac.uk,paolo.manghi@isti.cnr.it\n" - + - " \n" + - " The authors acknowledge the support and the use of resources of Instruct-ERIC.\n" - + - " The authors acknowledge the support and the use of resources of Instruct (PID # or APPID #), a Landmark ESFRI project\n" - + - " oac_instruct\n" + - " 2018-03-01T12:00:00\n" + - " \n" + - " \n" - + - " Authentication and Authorisation For Research and Collaboration\n" - + - " \n" + - " 730941\n" + - " \n" + - " H2020-EINFRA-2016-1\n" + - " AARC2\n" + - " EC\n" + - " \n" + - " \n" - + - " Building data bridges between biological and medical infrastructures in Europe\n" - + - " \n" + - " 284209\n" + - " \n" + - " FP7-INFRASTRUCTURES-2011-1\n" + - " EC\n" + - " BioMedBridges\n" + - " \n" + - " \n" - + - " Transnational access and enhancement of integrated Biological Structure determination at synchrotron X-ray radiation facilities\n" - + - " \n" + - " 283570\n" + - " \n" + - " FP7-INFRASTRUCTURES-2011-1\n" + - " EC\n" + - " BioStruct-X\n" + - " \n" + - " \n" - + - " Coordinated Research Infrastructures Building Enduring Life-science services\n" - + - " \n" + - " 654248\n" + - " \n" + - " H2020-INFRADEV-1-2014-1\n" + - " EC\n" + - " CORBEL\n" + - " \n" + - " \n" - + - " Infrastructure for NMR, EM and X-rays for translational research\n" - + - " \n" + - " 653706\n" + - " \n" + - " H2020-INFRAIA-2014-2015\n" + - " EC\n" + - " iNEXT\n" + - " \n" + - " \n" - + - " Integrated Structural Biology Infrastructure\n" + - " \n" + - " 211252\n" + - " \n" + - " FP7-INFRASTRUCTURES-2007-1\n" + - " EC\n" + - " INSTRUCT\n" + - " \n" + - " \n" - + - " Releasing the full potential of Instruct to expand and consolidate infrastructure services for integrated structural life science research\n" - + - " \n" + - " 731005\n" + - " \n" + - " H2020-INFRADEV-2016-1\n" + - " EC\n" + - " INSTRUCT-ULTRA\n" + - " \n" + - " \n" - + - " Opening Synchrotron Light for Experimental Science and Applications in the Middle East\n" - + - " \n" + - " 730943\n" + - " \n" + - " H2020-INFRASUPP-2016-1\n" + - " EC\n" + - " OPEN SESAME\n" + - " \n" + - " \n" - + - " Infrastructure for Protein Production Platforms\n" - + - " \n" + - " 227764\n" + - " \n" + - " FP7-INFRASTRUCTURES-2008-1\n" + - " EC\n" + - " PCUBE\n" + - " \n" + - " \n" - + - " European Vaccine Research and Development Infrastructure\n" - + - " \n" + - " 730964\n" + - " \n" + - " H2020-INFRAIA-2016-1\n" + - " EC\n" + - " TRAMSVAC2\n" + - " \n" + - " \n" - + - " World-wide E-infrastructure for structural biology\n" - + - " \n" + - " 675858\n" + - " \n" + - " H2020-EINFRA-2015-1\n" + - " EC\n" + - " West-Life\n" + - " \n" + - " \n" + - " Expanding research infrastructure visibility to strengthen strategic partnerships\n" - + - " RI-VIS\n" + - " 824063\n" + - " EC\n" + - " corda__h2020::af93b591b76991d8437993a8f6fc6538\n" + - " \n" + - " \n" + - " \n" - + - " \n" - + - " \n" + - " instruct\n" + - " \n" + - " \n" + - " \n" - + - " west-life\n" + - " \n" + - " \n" + - " \n" + - " \n" - + - " \n" + - " FRISBI\n" + - " aHR0cDovL2ZyaXNiaS5ldS9zdGF0aWMvaW1hZ2VzL2xvZ29zL2xvZ28tZnJpc2JpLnBuZw==\n" - + - " aHR0cDovL2ZyaXNiaS5ldS8=\n" + - " \n" + - " \n" + - " RI-VIS\n" + - " aHR0cHM6Ly9yaS12aXMuZXUvbmV0d29yay9yaXZpcy90ZW1wbGF0ZXMvcml2aXMvaW1hZ2VzL1JJLVZJU0xvZ29GaW5hbC0wNi5wbmc=\n" - + - " aHR0cHM6Ly9yaS12aXMuZXU=\n" + - " \n" + - " \n" + - " CIISB\n" + - " aHR0cDovL2JpYy5jZWl0ZWMuY3ovZmlsZXMvMjkyLzEyNS5KUEc=\n" + - " aHR0cHM6Ly93d3cuY2lpc2Iub3Jn\n" + - " \n" + - " \n" + - "\n", - "\n" + - " all\n" + - " ELIXIR-GR enhances the potential of the Greek bioinformatics community to offer open, easily accessible and state -of- the- art services to the Greek and the international academic community and other stakeholders, such as industry and the health sector. More importantly, by providing these services, the infrastructure facilitates discoveries in the field of the life-sciences, having strong spill over effects in promoting innovation in sectors such as discovery of new drug targets and development of novel therapeutic agents, development of innovative diagnostics, personalized medicine, and development of innovative biotechnological products and processes.\n" - + - " https://elixir-greece.org/sites/default/files/ELIXIR_GREECE_white_background.png\n" - + - " The Greek National Node of the ESFRI European RI ELIXIR\n" + - " vergoulis@imis.athena-innovation.gr,schatz@imis.athena-innovation.gr,paolo.manghi@isti.cnr.it\n" - + - " \n" + - " \n" + - " oaa_elixir-gr\n" + - " 2018-03-01T12:00:00\n" + - " \n" + - " \n" - + - " \n" + - " rest________::b8e502674c3c3499d5374e9b2ea6d8d5\n" + - " bio.tools\n" + - " bio.tools\n" + - " false\n" + - " \n" + - " \n" + - " \n" + - " \n" - + - " \n" + - " \n" + - " ATHENA RC\n" + - " aHR0cHM6Ly9lbGl4aXItZ3JlZWNlLm9yZy9zaXRlcy9kZWZhdWx0L2ZpbGVzL3N0eWxlcy90aHVtYm5haWwvcHVibGljL3BhcnRuZXJfbG9nb3MvYXRoZW5hX2xvZ28uanBnP2l0b2s9VXdGWFNpZng=\n" - + - " aHR0cHM6Ly93d3cuYXRoZW5hLWlubm92YXRpb24uZ3IvZW4=\n" + - " \n" + - " \n" - + - ""); - - @Mock - private ISLookUpService isLookUpService; - - private QueryInformationSystem queryInformationSystem; - - private Map map; - - @BeforeEach - public void setUp() throws ISLookUpException { - lenient().when(isLookUpService.quickSearchProfile(XQUERY_ENTITY)).thenReturn(communityMap); - lenient().when(isLookUpService.quickSearchProfile(XQUERY)).thenReturn(communityContext); - queryInformationSystem = new QueryInformationSystem(); - queryInformationSystem.setIsLookUp(isLookUpService); - } - - @Test - void testSizeEntity() throws ISLookUpException { - - List cInfoList = new ArrayList<>(); - final Consumer consumer = ci -> cInfoList.add(ci); - queryInformationSystem.getContextInformation(consumer); - - Assertions.assertEquals(12, cInfoList.size()); - } - - @Test - void testSizeRelation() throws ISLookUpException { - - List cInfoList = new ArrayList<>(); - final Consumer consumer = ci -> cInfoList.add(ci); - queryInformationSystem.execContextRelationQuery(); - queryInformationSystem - .getContextRelation(consumer, "contentproviders", ModelSupport.entityIdPrefix.get("datasource")); - - Assertions.assertEquals(5, cInfoList.size()); - } - - @Test - void testContentRelation() throws ISLookUpException { - - List cInfoList = new ArrayList<>(); - final Consumer consumer = ci -> cInfoList.add(ci); - queryInformationSystem.execContextRelationQuery(); - queryInformationSystem - .getContextRelation(consumer, "contentproviders", ModelSupport.entityIdPrefix.get("datasource")); - - cInfoList.forEach(contextInfo -> { - switch (contextInfo.getId()) { - case "elixir-gr": - Assertions.assertEquals(1, contextInfo.getDatasourceList().size()); - Assertions - .assertEquals( - "10|rest________::b8e502674c3c3499d5374e9b2ea6d8d5", - contextInfo.getDatasourceList().get(0)); - break; - case "instruct": - Assertions.assertEquals(0, contextInfo.getDatasourceList().size()); - break; - case "ni": - Assertions.assertEquals(6, contextInfo.getDatasourceList().size()); - Assertions - .assertTrue( - contextInfo - .getDatasourceList() - .contains("10|rest________::fb1a3d4523c95e63496e3bc7ba36244b")); - break; - case "dh-ch": - Assertions.assertEquals(10, contextInfo.getDatasourceList().size()); - break; - case "clarin": - Assertions.assertEquals(0, contextInfo.getDatasourceList().size()); - break; - } - }); - } - - @Test - void testContentEntity() throws ISLookUpException { - - List cInfoList = new ArrayList<>(); - final Consumer consumer = ci -> cInfoList.add(ci); - queryInformationSystem.getContextInformation(consumer); - - cInfoList.forEach(context -> { - switch (context.getId()) { - case "clarin":// clarin@@Common Language Resources and Technology Infrastructure@@CLARIN@@@@oac_clarin", - Assertions - .assertEquals("Common Language Resources and Technology Infrastructure", context.getName()); - Assertions.assertEquals("CLARIN", context.getDescription()); - Assertions - .assertTrue( - Optional - .ofNullable(context.getSubject()) - .map(value -> false) - .orElse(true)); - Assertions.assertEquals("oac_clarin", context.getZenodocommunity()); - Assertions.assertEquals("ri", context.getType()); - break; - case "ee": - Assertions.assertEquals("Sustainable Development Solutions Network - Greece", context.getName()); - Assertions.assertTrue(context.getDescription().length() > 0); - Assertions - .assertFalse( - Optional - .ofNullable(context.getSubject()) - .map(value -> false) - .orElse(true)); - Assertions.assertEquals(17, context.getSubject().size()); - Assertions.assertEquals("oac_sdsn-greece", context.getZenodocommunity()); - Assertions.assertEquals("community", context.getType()); - break; - case "dh-ch": - Assertions.assertEquals("Digital Humanities and Cultural Heritage", context.getName()); - Assertions.assertTrue(context.getDescription().length() > 0); - Assertions - .assertFalse( - Optional - .ofNullable(context.getSubject()) - .map(value -> false) - .orElse(true)); - Assertions.assertEquals(67, context.getSubject().size()); - Assertions.assertEquals("oac_dh-ch", context.getZenodocommunity()); - Assertions.assertEquals("community", context.getType()); - break; - case "fam": - Assertions.assertEquals("Fisheries and Aquaculture Management", context.getName()); - Assertions.assertTrue(context.getDescription().length() > 0); - Assertions - .assertTrue( - context - .getDescription() - .startsWith("Conservation of marine resources for sustainable development")); - Assertions - .assertFalse( - Optional - .ofNullable(context.getSubject()) - .map(value -> false) - .orElse(true)); - Assertions.assertEquals(19, context.getSubject().size()); - Assertions.assertEquals("fisheries", context.getZenodocommunity()); - Assertions.assertEquals("community", context.getType()); - break; - case "ni": - Assertions.assertEquals("Neuroinformatics", context.getName()); - Assertions.assertTrue(context.getDescription().length() > 0); - Assertions - .assertTrue( - context - .getDescription() - .startsWith("The neuroinformatics dashboard gathers research outputs from the")); - Assertions - .assertFalse( - Optional - .ofNullable(context.getSubject()) - .map(value -> false) - .orElse(true)); - Assertions.assertEquals(18, context.getSubject().size()); - Assertions.assertEquals("oac_ni", context.getZenodocommunity()); - Assertions.assertEquals("community", context.getType()); - Assertions.assertTrue(context.getSubject().contains("brain")); - break; - case "mes": - Assertions.assertEquals("European Marine Science", context.getName()); - Assertions.assertTrue(context.getDescription().length() > 0); - Assertions - .assertTrue( - context - .getDescription() - .startsWith( - "This community was initially defined to include a very broad range of topics")); - Assertions - .assertFalse( - Optional - .ofNullable(context.getSubject()) - .map(value -> false) - .orElse(true)); - Assertions.assertEquals(5, context.getSubject().size()); - Assertions.assertEquals("oac_mes", context.getZenodocommunity()); - Assertions.assertEquals("community", context.getType()); - Assertions.assertTrue(context.getSubject().contains("sea")); - Assertions.assertTrue(context.getSubject().contains("fish")); - Assertions.assertTrue(context.getSubject().contains("ocean")); - Assertions.assertTrue(context.getSubject().contains("aqua")); - Assertions.assertTrue(context.getSubject().contains("marine")); - break; - case "instruct": - Assertions.assertEquals("Instruct-ERIC", context.getName()); - Assertions.assertTrue(context.getDescription().length() > 0); - Assertions - .assertTrue( - context - .getDescription() - .equals( - "Instruct-ERIC is the European Research Infrastructure for Structural Biology")); - Assertions - .assertTrue( - Optional - .ofNullable(context.getSubject()) - .map(value -> false) - .orElse(true)); - Assertions.assertEquals("oac_instruct", context.getZenodocommunity()); - Assertions.assertEquals("community", context.getType()); - - break; - case "elixir-gr": - Assertions - .assertEquals("The Greek National Node of the ESFRI European RI ELIXIR", context.getName()); - Assertions.assertTrue(context.getDescription().length() > 0); - Assertions - .assertTrue( - context - .getDescription() - .startsWith( - "ELIXIR-GR enhances the potential of the Greek bioinformatics community to offer open")); - Assertions - .assertTrue( - Optional - .ofNullable(context.getSubject()) - .map(value -> false) - .orElse(true)); - Assertions.assertEquals("oaa_elixir-gr", context.getZenodocommunity()); - Assertions.assertEquals("ri", context.getType()); - - break; - case "aginfra": - Assertions.assertEquals("Agricultural and Food Sciences", context.getName()); - Assertions.assertTrue(context.getDescription().length() > 0); - Assertions - .assertTrue( - context - .getDescription() - .startsWith( - "The scope of this community is to provide access to publications, research data, projects and software")); - Assertions - .assertFalse( - Optional - .ofNullable(context.getSubject()) - .map(value -> false) - .orElse(true)); - Assertions.assertEquals(18, context.getSubject().size()); - Assertions.assertEquals("oac_aginfra", context.getZenodocommunity()); - Assertions.assertEquals("community", context.getType()); - Assertions.assertTrue(context.getSubject().contains("food distribution")); - break; - case "dariah": - Assertions.assertEquals("DARIAH EU", context.getName()); - Assertions.assertTrue(context.getDescription().length() > 0); - Assertions - .assertTrue( - context - .getDescription() - .startsWith( - "The Digital Research Infrastructure for the Arts and Humanities (DARIAH) aims to enhance and support ")); - Assertions - .assertTrue( - Optional - .ofNullable(context.getSubject()) - .map(value -> false) - .orElse(true)); - - Assertions.assertEquals("dariah", context.getZenodocommunity()); - Assertions.assertEquals("ri", context.getType()); - - break; - case "epos": - Assertions.assertEquals("European Plate Observing System", context.getName()); - Assertions.assertTrue(context.getDescription().length() > 0); - Assertions - .assertTrue( - context - .getDescription() - .startsWith( - "EPOS, the European Plate Observing System, is a long-term plan to facilitate integrated use of ")); - Assertions - .assertTrue( - Optional - .ofNullable(context.getSubject()) - .map(value -> false) - .orElse(true)); - - Assertions.assertEquals("", context.getZenodocommunity()); - Assertions.assertEquals("ri", context.getType()); - - break; - case "covid-19": - Assertions.assertEquals("Corona Virus Disease", context.getName()); - Assertions.assertTrue(context.getDescription().length() > 0); - Assertions - .assertTrue( - context - .getDescription() - .startsWith( - "This portal provides access to publications, research data, projects and ")); - Assertions - .assertFalse( - Optional - .ofNullable(context.getSubject()) - .map(value -> false) - .orElse(true)); - Assertions.assertEquals(25, context.getSubject().size()); - Assertions.assertEquals("covid-19", context.getZenodocommunity()); - Assertions.assertEquals("community", context.getType()); - Assertions.assertTrue(context.getSubject().contains("coronavirus disease 2019")); - break; - - } - }); - - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/RelationFromOrganizationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/RelationFromOrganizationTest.java deleted file mode 100644 index 50a9f26b4..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/RelationFromOrganizationTest.java +++ /dev/null @@ -1,121 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.HashMap; - -import org.apache.commons.io.FileUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SparkSession; -import org.junit.jupiter.api.AfterAll; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.Test; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.schema.dump.oaf.graph.Relation; - -public class RelationFromOrganizationTest { - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private static SparkSession spark; - - private static Path workingDir; - - private static final Logger log = LoggerFactory - .getLogger(RelationFromOrganizationTest.class); - - private static final HashMap map = new HashMap<>(); - - String organizationCommunityMap = "{\"20|grid________::afaa39865943381c51f76c08725ffa75\":[\"mes\",\"euromarine\"], \"20|corda__h2020::e8dbe14cca9bf6fce09d468872f813f8\":[\"mes\",\"euromarine\"], \"20|snsf________::9b253f265e3bef5cae6d881fdf61aceb\":[\"mes\",\"euromarine\"],\"20|rcuk________::e054eea0a47665af8c3656b5785ccf76\":[\"mes\",\"euromarine\"],\"20|corda__h2020::edc18d67c9b11fb616ca9f6e1db1b151\":[\"mes\",\"euromarine\"],\"20|rcuk________::d5736d9da90521ddcdc7828a05a85e9a\":[\"mes\",\"euromarine\"],\"20|corda__h2020::f5d418d3aa1cf817ddefcc3fdc039f27\":[\"mes\",\"euromarine\"],\"20|snsf________::8fa091f8f25a846779acb4ea97b50aef\":[\"mes\",\"euromarine\"],\"20|corda__h2020::81e020977211c2c40fae2e1a50bffd71\":[\"mes\",\"euromarine\"],\"20|corda_______::81e020977211c2c40fae2e1a50bffd71\":[\"mes\",\"euromarine\"],\"20|snsf________::31d0a100e54e3cdb3c6f52d91e638c78\":[\"mes\",\"euromarine\"],\"20|corda__h2020::ea379ef91b8cc86f9ac5edc4169292db\":[\"mes\",\"euromarine\"],\"20|corda__h2020::f75ee2ee48e5cb0ec8c8d30aaa8fef70\":[\"mes\",\"euromarine\"],\"20|rcuk________::e16010089551a1a9182a94604fc0ea59\":[\"mes\",\"euromarine\"],\"20|corda__h2020::38531a2cce7c5c347ffc439b07c1f43b\":[\"mes\",\"euromarine\"],\"20|corda_______::38531a2cce7c5c347ffc439b07c1f43b\":[\"mes\",\"euromarine\"],\"20|grid________::b2cbbf5eadbbf87d534b022bad3191d7\":[\"mes\",\"euromarine\"],\"20|snsf________::74730ef1439d7f7636a8be58a6b471b8\":[\"mes\",\"euromarine\"],\"20|nsf_________::ad72e19043a5a467e35f9b444d11563e\":[\"mes\",\"euromarine\"],\"20|rcuk________::0fc3e92500290902a2d38ec2445e74c3\":[\"mes\",\"euromarine\"],\"20|grid________::ad2c29905da0eb3c06b3fa80cacd89ea\":[\"mes\",\"euromarine\"],\"20|corda__h2020::30b53e4d63d3724f00acb9cbaca40860\":[\"mes\",\"euromarine\"],\"20|corda__h2020::f60f84bee14ad93f0db0e49af1d5c317\":[\"mes\",\"euromarine\"], \"20|corda__h2020::7bf251ac3765b5e89d82270a1763d09f\":[\"mes\",\"euromarine\"], \"20|corda__h2020::65531bd11be9935948c7f2f4db1c1832\":[\"mes\",\"euromarine\"], \"20|corda__h2020::e0e98f86bbc76638bbb72a8fe2302946\":[\"mes\",\"euromarine\"], \"20|snsf________::3eb43582ac27601459a8d8b3e195724b\":[\"mes\",\"euromarine\"], \"20|corda__h2020::af2481dab65d06c8ea0ae02b5517b9b6\":[\"mes\",\"euromarine\"], \"20|corda__h2020::c19d05cfde69a50d3ebc89bd0ee49929\":[\"mes\",\"euromarine\"], \"20|corda__h2020::af0bfd9fc09f80d9488f56d71a9832f0\":[\"mes\",\"euromarine\"], \"20|rcuk________::f33c02afb0dc66c49d0ed97ca5dd5cb0\":[\"beopen\"], " - + - "\"20|grid________::a867f78acdc5041b34acfe4f9a349157\":[\"beopen\"], \"20|grid________::7bb116a1a9f95ab812bf9d2dea2be1ff\":[\"beopen\"], \"20|corda__h2020::6ab0e0739dbe625b99a2ae45842164ad\":[\"beopen\"], \"20|corda__h2020::8ba50792bc5f4d51d79fca47d860c602\":[\"beopen\"], \"20|corda_______::8ba50792bc5f4d51d79fca47d860c602\":[\"beopen\"], \"20|corda__h2020::e70e9114979e963eef24666657b807c3\":[\"beopen\"], \"20|corda_______::e70e9114979e963eef24666657b807c3\":[\"beopen\"], \"20|corda_______::15911e01e9744d57205825d77c218737\":[\"beopen\"], \"20|opendoar____::056a41e24e2a9a67215e87bbee6a80ab\":[\"beopen\"], \"20|opendoar____::7f67f2e6c6fbb0628f8160fcd3d92ae3\":[\"beopen\"], \"20|grid________::a8ecfd7c084e561168bcbe6bf0daf3e3\":[\"beopen\"], \"20|corda_______::7bbe6cc5d8ec1864739a04b0d020c9e9\":[\"beopen\"], \"20|corda_______::3ff558e30c2e434d688539548300b050\":[\"beopen\"], \"20|corda__h2020::5ffee5b3b83b33a8cf0e046877bd3a39\":[\"beopen\"], \"20|corda__h2020::5187217e2e806a6df3579c46f82401bc\":[\"beopen\"], \"20|grid________::5fa7e2709bcd945e26bfa18689adeec1\":[\"beopen\"], \"20|corda_______::d8696683c53027438031a96ad27c3c07\":[\"beopen\"], \"20|corda__h2020::d8696683c53027438031a96ad27c3c07\":[\"beopen\"], \"20|rcuk________::23a79ebdfa59790864e4a485881568c1\":[\"beopen\"], \"20|corda__h2020::b76cf8fe49590a966953c37e18608af9\":[\"beopen\"], \"20|grid________::d2f0204126ee709244a488a4cd3b91c2\":[\"beopen\"], \"20|corda__h2020::05aba9d2ed17533d15221e5655ac11e6\":[\"beopen\"], \"20|grid________::802401579481dc32062bdee69f5e6a34\":[\"beopen\"], \"20|corda__h2020::3f6d9d54cac975a517ba6b252c81582d\":[\"beopen\"]}"; - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory(RelationFromOrganizationTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - - SparkConf conf = new SparkConf(); - conf.setAppName(RelationFromOrganizationTest.class.getSimpleName()); - - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - - spark = SparkSession - .builder() - .appName(RelationFromOrganizationTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Test - void test1() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/relation") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymapservices.json") - .getPath(); - - SparkOrganizationRelation.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/relation", - "-sourcePath", sourcePath, - "-organizationCommunityMap", organizationCommunityMap, - "-communityMapPath", communityMapPath - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/relation") - .map(item -> OBJECT_MAPPER.readValue(item, Relation.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Relation.class)); - - verificationDataset.createOrReplaceTempView("table"); - - // Assertions.assertEquals(170, verificationDataset.count()); - Assertions.assertEquals(0, verificationDataset.count()); - -// Dataset checkDs = spark -// .sql( -// "Select source.id, source.type " + -// "from table "); -// -// Assertions.assertEquals(2, checkDs.filter("substr(id, 4, 5) = 'dedup' ").count()); -// -// Assertions.assertEquals(0, checkDs.filter("id = '20|grid________::afaa39865943381c51f76c08725ffa75'").count()); -// -// Assertions.assertEquals(25, checkDs.filter("id = '00|context_____::" + DHPUtils.md5("beopen") + "'").count()); -// -// Assertions -// .assertEquals(30, checkDs.filter("id = '00|context_____::" + DHPUtils.md5("euromarine") + "'").count()); -// -// Assertions.assertEquals(30, checkDs.filter("id = '00|context_____::" + DHPUtils.md5("mes") + "'").count()); - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/SelectRelationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/SelectRelationTest.java deleted file mode 100644 index 3e4ab93c5..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/SelectRelationTest.java +++ /dev/null @@ -1,100 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.complete; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.HashMap; - -import org.apache.commons.io.FileUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.api.java.function.ForeachFunction; -import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.Row; -import org.apache.spark.sql.SparkSession; -import org.junit.jupiter.api.AfterAll; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.Test; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.schema.oaf.Relation; -import net.sf.saxon.expr.instruct.ForEach; - -public class SelectRelationTest { - - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private static SparkSession spark; - - private static Path workingDir; - - private static final Logger log = LoggerFactory - .getLogger(SelectRelationTest.class); - - private static HashMap map = new HashMap<>(); - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory(SelectRelationTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - - SparkConf conf = new SparkConf(); - conf.setAppName(SelectRelationTest.class.getSimpleName()); - - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - - spark = SparkSession - .builder() - .appName(SelectRelationTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Test - public void test1() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/selectrelations") - .getPath(); - - SparkSelectValidRelationsJob.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/relation", - "-sourcePath", sourcePath - }); - -// dumpCommunityProducts.exec(MOCK_IS_LOOK_UP_URL,Boolean.FALSE, workingDir.toString()+"/dataset",sourcePath,"eu.dnetlib.dhp.schema.oaf.Dataset","eu.dnetlib.dhp.schema.dump.oaf.Dataset"); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/relation") - .map(item -> OBJECT_MAPPER.readValue(item, eu.dnetlib.dhp.schema.oaf.Relation.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(eu.dnetlib.dhp.schema.oaf.Relation.class)); - - Assertions.assertTrue(verificationDataset.count() == 7); - - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java deleted file mode 100644 index 7046b02c2..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java +++ /dev/null @@ -1,142 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.funderresult; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.HashMap; - -import org.apache.commons.io.FileUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SparkSession; -import org.junit.jupiter.api.AfterAll; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.Test; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject; -import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.Result; - -public class ResultLinkedToProjectTest { - - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private static SparkSession spark; - - private static Path workingDir; - - private static final Logger log = LoggerFactory - .getLogger(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class); - - private static final HashMap map = new HashMap<>(); - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory( - eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - - SparkConf conf = new SparkConf(); - conf.setAppName(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()); - - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - - spark = SparkSession - .builder() - .appName(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Test - void testNoMatch() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json") - .getPath(); - - final String graphPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/communityMapPath") - .getPath(); - - SparkResultLinkedToProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-graphPath", graphPath, - "-communityMapPath", communityMapPath - - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - Assertions.assertEquals(0, tmp.count()); - - } - - @Test - void testMatchOne() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/papers.json") - .getPath(); - - final String graphPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo") - .getPath(); - - final String communityMapPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/communityMapPath") - .getPath(); - - SparkResultLinkedToProject.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/preparedInfo", - "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-graphPath", graphPath, - "-communityMapPath", communityMapPath - - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - Assertions.assertEquals(1, tmp.count()); - - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java deleted file mode 100644 index e9d739db2..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java +++ /dev/null @@ -1,151 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.funderresult; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; - -// import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkDumpFunderResults2; -// import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkGetFunderList; -import org.apache.commons.io.FileUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.api.java.function.ForeachFunction; -import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SparkSession; -import org.junit.jupiter.api.AfterAll; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.Test; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.oa.graph.dump.DumpJobTest; -import eu.dnetlib.dhp.oa.graph.dump.SplitForCommunityTest; -import eu.dnetlib.dhp.oa.graph.dump.community.CommunitySplit; -import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkDumpFunderResults; -import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; - -public class SplitPerFunderTest { - - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - private static SparkSession spark; - - private static Path workingDir; - - private static final Logger log = LoggerFactory.getLogger(SplitPerFunderTest.class); - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files.createTempDirectory(SplitPerFunderTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - - SparkConf conf = new SparkConf(); - conf.setAppName(SplitPerFunderTest.class.getSimpleName()); - - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - - spark = SparkSession - .builder() - .appName(SplitPerFunderTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Test - void test1() throws Exception { - - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext") - .getPath(); - - SparkDumpFunderResults.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/split", - "-sourcePath", sourcePath - - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - // FP7 3 and H2020 3 - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/split/EC_FP7") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); - - Assertions.assertEquals(3, verificationDataset.count()); - - Assertions - .assertEquals( - 1, verificationDataset.filter("id = '50|dedup_wf_001::0d16b1714ab3077df73893a8ea57d776'").count()); - - // CIHR 2 - tmp = sc - .textFile(workingDir.toString() + "/split/CIHR") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - Assertions.assertEquals(2, tmp.count()); - - // NWO 1 - tmp = sc - .textFile(workingDir.toString() + "/split/NWO") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - Assertions.assertEquals(1, tmp.count()); - - // NIH 3 - tmp = sc - .textFile(workingDir.toString() + "/split/NIH") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - Assertions.assertEquals(2, tmp.count()); - - // NSF 1 - tmp = sc - .textFile(workingDir.toString() + "/split/NSF") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - Assertions.assertEquals(1, tmp.count()); - - // SNSF 1 - tmp = sc - .textFile(workingDir.toString() + "/split/SNSF") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - Assertions.assertEquals(1, tmp.count()); - - // NHMRC 1 - tmp = sc - .textFile(workingDir.toString() + "/split/NHMRC") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - Assertions.assertEquals(1, tmp.count()); - - // H2020 3 - tmp = sc - .textFile(workingDir.toString() + "/split/EC_H2020") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - Assertions.assertEquals(3, tmp.count()); - - // MZOS 1 - tmp = sc - .textFile(workingDir.toString() + "/split/MZOS") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - Assertions.assertEquals(1, tmp.count()); - - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java deleted file mode 100644 index 8cdb285e4..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java +++ /dev/null @@ -1,125 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.dump.projectssubset; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.HashMap; - -import org.apache.commons.io.FileUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.sql.SaveMode; -import org.apache.spark.sql.SparkSession; -import org.junit.jupiter.api.AfterAll; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.Test; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.schema.dump.oaf.graph.Project; - -public class ProjectSubsetTest { - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - private static SparkSession spark; - private static Path workingDir; - private static final Logger log = LoggerFactory - .getLogger(eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class); - - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files - .createTempDirectory( - eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class.getSimpleName()); - log.info("using work dir {}", workingDir); - SparkConf conf = new SparkConf(); - conf.setAppName(eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class.getSimpleName()); - conf.setMaster("local[*]"); - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("spark.ui.enabled", "false"); - conf.set("spark.sql.warehouse.dir", workingDir.toString()); - conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); - spark = SparkSession - .builder() - .appName(eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class.getSimpleName()) - .config(conf) - .getOrCreate(); - } - - @AfterAll - public static void afterAll() throws IOException { - FileUtils.deleteDirectory(workingDir.toFile()); - spark.stop(); - } - - @Test - void testAllNew() throws Exception { - final String projectListPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/projectId") - .getPath(); - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/allnew/projects") - .getPath(); - spark - .read() - .textFile(projectListPath) - .write() - .mode(SaveMode.Overwrite) - .text(workingDir.toString() + "/projectIds"); - ProjectsSubsetSparkJob.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/projects", - "-sourcePath", sourcePath, - "-projectListPath", workingDir.toString() + "/projectIds" - }); - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/projects") - .map(item -> OBJECT_MAPPER.readValue(item, Project.class)); - Assertions.assertEquals(12, tmp.count()); - Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("aka_________")).count()); - Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("anr_________")).count()); - Assertions.assertEquals(4, tmp.filter(p -> p.getId().substring(3, 15).equals("arc_________")).count()); - Assertions.assertEquals(3, tmp.filter(p -> p.getId().substring(3, 15).equals("conicytf____")).count()); - Assertions.assertEquals(1, tmp.filter(p -> p.getId().substring(3, 15).equals("corda_______")).count()); - Assertions.assertEquals(40, sc.textFile(workingDir.toString() + "/projectIds").count()); - } - - @Test - void testMatchOne() throws Exception { - final String projectListPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/projectId") - .getPath(); - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/matchOne/projects") - .getPath(); - spark - .read() - .textFile(projectListPath) - .write() - .mode(SaveMode.Overwrite) - .text(workingDir.toString() + "/projectIds"); - ProjectsSubsetSparkJob.main(new String[] { - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-outputPath", workingDir.toString() + "/projects", - "-sourcePath", sourcePath, - "-projectListPath", workingDir.toString() + "/projectIds" - }); - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/projects") - .map(item -> OBJECT_MAPPER.readValue(item, Project.class)); - Assertions.assertEquals(11, tmp.count()); - Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("aka_________")).count()); - Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("anr_________")).count()); - Assertions.assertEquals(4, tmp.filter(p -> p.getId().substring(3, 15).equals("arc_________")).count()); - Assertions.assertEquals(3, tmp.filter(p -> p.getId().substring(3, 15).equals("conicytf____")).count()); - Assertions.assertEquals(0, tmp.filter(p -> p.getId().substring(3, 15).equals("corda__h2020")).count()); - Assertions.assertEquals(39, sc.textFile(workingDir.toString() + "/projectIds").count()); - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/addProjectInfo/preparedInfo b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/addProjectInfo/preparedInfo deleted file mode 100644 index 7f35634f5..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/addProjectInfo/preparedInfo +++ /dev/null @@ -1,2 +0,0 @@ -{"projectsList":[{"code":"123455","funder":{"jurisdiction":"FI","name":"Academy of Finland","shortName":"AKA"},"id":"40|aka_________::0f7d119de1f656b5763a16acf876fed6","provenance":{"provenance":"sysimport:crosswalk:entityregistry","trust":"0.900000000000000022"},"title":"Business services for rural bioenergy entrepreneurship in Finland: a network analysis approach"},{"code":"119027","funder":{"fundingStream":"H2020","jurisdiction":"EU","name":"European Commission","shortName":"EC"},"id":"40|aka_________::03376222b28a3aebf2730ac514818d04","provenance":{"provenance":"sysimport:crosswalk:entityregistry","trust":"0.900000000000000022"},"title":"EGFR Tyrosine Kinase Inhibitors and LKB1 Tumor Suppressor in Non-Small-Cell Lung Cancer"}],"resultId":"50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb"} -{"projectsList":[{"code":"123455","funder":{"jurisdiction":"FI","name":"Academy of Finland","shortName":"AKA"},"id":"40|aka_________::0f7d119de1f656b5763a16acf876fed6","provenance":{"provenance":"sysimport:crosswalk:entityregistry","trust":"0.900000000000000022"},"title":"Business services for rural bioenergy entrepreneurship in Finland: a network analysis approach"}],"resultId":"50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80"} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/addProjectInfo/preparedInfoValidated b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/addProjectInfo/preparedInfoValidated deleted file mode 100644 index 588bec804..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/addProjectInfo/preparedInfoValidated +++ /dev/null @@ -1,2 +0,0 @@ -{"resultId":"50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2","projectsList":[{"id":"40|aka_________::0f7d119de1f656b5763a16acf876fed6","code":"123455","acronym":null,"title":"Business services for rural bioenergy entrepreneurship in Finland: a network analysis approach","funder":{"shortName":"AKA","name":"Academy of Finland","jurisdiction":"FI","fundingStream":null},"provenance":{"provenance":"sysimport:crosswalk:entityregistry","trust":"0.900000000000000022"},"validated":{"validationDate":"2021-08-06","validatedByFunder":true}},{"id":"40|aka_________::03376222b28a3aebf2730ac514818d04","code":"119027","acronym":null,"title":"EGFR Tyrosine Kinase Inhibitors and LKB1 Tumor Suppressor in Non-Small-Cell Lung Cancer","funder":{"shortName":"EC","name":"European Commission","jurisdiction":"EU","fundingStream":"H2020"},"provenance":{"provenance":"sysimport:crosswalk:entityregistry","trust":"0.900000000000000022"},"validated":null}]} -{"resultId":"50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80","projectsList":[{"id":"40|aka_________::0f7d119de1f656b5763a16acf876fed6","code":"123455","acronym":null,"title":"Business services for rural bioenergy entrepreneurship in Finland: a network analysis approach","funder":{"shortName":"AKA","name":"Academy of Finland","jurisdiction":"FI","fundingStream":null},"provenance":{"provenance":"sysimport:crosswalk:entityregistry","trust":"0.900000000000000022"},"validated":{"validationDate":"2021-08-04","validatedByFunder":true}}]} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/addProjectInfo/publication_extendedmodel b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/addProjectInfo/publication_extendedmodel deleted file mode 100644 index 979cbf168..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/addProjectInfo/publication_extendedmodel +++ /dev/null @@ -1,2 +0,0 @@ -{"author":[{"fullname":"Nikolaidou,Charitini","name":"Charitini","surname":"Nikolaidou","rank":1,"pid":null},{"fullname":"Votsi,Nefta","name":"Nefta","surname":"Votsi","rank":2,"pid":{"id":{"scheme":"orcid","value":"0000-0001-6651-1178"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}}},{"fullname":"Sgardelis,Steanos","name":"Steanos","surname":"Sgardelis","rank":3,"pid":{"id":{"scheme":"orcid_pending","value":"0000-0001-6651-1178"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}}},{"fullname":"Halley,John","name":"John","surname":"Halley","rank":4,"pid":null},{"fullname":"Pantis,John","name":"John","surname":"Pantis","rank":5,"pid":{"id":{"scheme":"orcid","value":"0000-0001-6651-1178"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}}},{"fullname":"Tsiafouli,Maria","name":"Maria","surname":"Tsiafouli","rank":6,"pid":{"id":{"scheme":"orcid_pending","value":"0000-0001-6651-1178"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}}}],"type":"publication","language":{"code":"eng","label":"English"},"country":[{"code":"IT","label":"Italy","provenance":null}],"subjects":[{"subject":{"scheme":"ACM","value":"Ecosystem Services hotspots"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":"Natura 2000"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":"Quiet Protected Areas"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":"Biodiversity"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":"Agriculture"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":"Elevation"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":"Slope"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":"Ecosystem Service trade-offs and synergies"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":" cultural services"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":"provisioning services"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":"regulating services"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":"supporting services"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}}],"maintitle":"Ecosystem Service capacity is higher in areas of multiple designation types","subtitle":null,"description":["The implementation of the Ecosystem Service (ES) concept into practice might be a challenging task as it has to take into account previous “traditional” policies and approaches that have evaluated nature and biodiversity differently. Among them the Habitat (92/43/EC) and Bird Directives (79/409/EC), the Water Framework Directive (2000/60/EC), and the Noise Directive (2002/49/EC) have led to the evaluation/designation of areas in Europe with different criteria. In this study our goal was to understand how the ES capacity of an area is related to its designation and if areas with multiple designations have higher capacity in providing ES. We selected four catchments in Greece with a great variety of characteristics covering over 25% of the national territory. Inside the catchments we assessed the ES capacity (following the methodology of Burkhard et al. 2009) of areas designated as Natura 2000 sites, Quiet areas and Wetlands or Water bodies and found those areas that have multiple designations. Data were analyzed by GLM to reveal differences regarding the ES capacity among the different types of areas. We also investigated by PCA synergies and trade-offs among different kinds of ES and tested for correlations among landscape properties, such as elevation, aspect and slope and the ES potential. Our results show that areas with different types or multiple designations have a different capacity in providing ES. Areas of one designation type (Protected or Quiet Areas) had in general intermediate scores in most ES but scores were higher compared to areas with no designation, which displayed stronger capacity in provisioning services. Among Protected Areas and Quiet Areas the latter scored better in general. Areas that combined both designation types (Protected and Quiet Areas) showed the highest capacity in 13 out of 29 ES, that were mostly linked with natural and forest ecosystems. We found significant synergies among most regulating, supporting and cultural ES which in turn display trade-offs with provisioning services. The different ES are spatially related and display strong correlation with landscape properties, such as elevation and slope. We suggest that the designation status of an area can be used as an alternative tool for environmental policy, indicating the capacity for ES provision. Multiple designations of areas can be used as proxies for locating ES “hotspots”. This integration of “traditional” evaluation and designation and the “newer” ES concept forms a time- and cost-effective way to be adopted by stakeholders and policy-makers in order to start complying with new standards and demands for nature conservation and environmental management."],"publicationdate":"2017-01-01","publisher":"Pensoft Publishers","embargoenddate":null,"source":["One Ecosystem 2: e13718"],"format":["text/html"],"contributor":[],"coverage":[],"bestaccessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"container":{"name":"One 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synergies"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":" cultural services"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":"provisioning services"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":"regulating services"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":"supporting services"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}}],"maintitle":"Ecosystem Service capacity is higher in areas of multiple designation types","subtitle":null,"description":["The implementation of the Ecosystem Service (ES) concept into practice might be a challenging task as it has to take into account previous “traditional” policies and approaches that have evaluated nature and biodiversity differently. Among them the Habitat (92/43/EC) and Bird Directives (79/409/EC), the Water Framework Directive (2000/60/EC), and the Noise Directive (2002/49/EC) have led to the evaluation/designation of areas in Europe with different criteria. In this study our goal was to understand how the ES capacity of an area is related to its designation and if areas with multiple designations have higher capacity in providing ES. We selected four catchments in Greece with a great variety of characteristics covering over 25% of the national territory. Inside the catchments we assessed the ES capacity (following the methodology of Burkhard et al. 2009) of areas designated as Natura 2000 sites, Quiet areas and Wetlands or Water bodies and found those areas that have multiple designations. Data were analyzed by GLM to reveal differences regarding the ES capacity among the different types of areas. 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KNAW","name":"NIOO-KNAW","pid":{"id":{"scheme":"orcid","value":"0000-0002-3835-159X"}},"rank":1,"surname":"KNAW"}],"bestaccessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":[{"key":"10|opendoar____::e820a45f1dfc7b95282d10b6087e11c0","value":"Repositorio Institucional de la Universidad de Alicante"},{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"},{"key":"10|openaire____::fdb035c8b3e0540a8d9a561a6c44f4de","value":"NARCIS"},{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"},{"key":"10|openaire____::8ac8380272269217cb09a928c8caa993","value":"UnpayWall"},{"key":"10|openaire____::806360c771262b4d6770e7cdf04b5c5a","value":"ORCID"},{"key":"10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a","value":"Microsoft Academic 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Departamento de Ciencias Ambientales y Recursos Naturales","Universidad de Alicante. Centro Iberoamericano de la Biodiversidad","Biodiversidad y Biotecnología aplicadas a la Biología de la Conservación","Terrestrial Ecology (TE)"],"country":[{"code":"NL","label":"Netherlands","provenance":{"provenance":"Propagation of country to result collected from datasources of type institutional repositories","trust":"0.85"}},{"code":"ES","label":"Spain","provenance":{"provenance":"Propagation of country to result collected from datasources of type institutional repositories","trust":"0.85"}}],"coverage":[],"dateofcollection":"2018-10-03T06:57:46.116Z","description":["Herbivory affects subsequent herbivores, mainly regulated by the phytohormones jasmonic (JA) and salicylic acid (SA). Additionally, organisms such as soil microbes belowground or parasitoids that develop inside their herbivorous hosts aboveground, can change plant responses to herbivory. However, it is not yet well known how organisms of trophic levels other than herbivores, below- and above-ground, alter the interactions between insect species sharing a host plant. Here, we investigated whether the parasitoid Aphidius colemani and different soil microbial communities (created through plant-soil feedbacks) affect the JA and SA signalling pathways in response to the aphid Myzus persicae and the thrips Frankliniella occidentalis, as well as subsequent thrips performance. Our results show that the expression of the JA-responsive gene CaPINII in sweet pepper was more suppressed by aphids than by parasitised aphids. However, parasitism did not affect the expression of CaPAL1, a biosynthetic gene of SA. Furthermore, aphid feeding enhanced thrips performance compared with uninfested plants, but this was not observed when aphids were parasitised. Soils where different plant species were previously grown, did not affect plant responses or the interaction between herbivores. Our study shows that members of the third trophic level can modify herbivore interactions by altering plant physiology.\nThis work and T.V.’s activities were supported by Spanish Ministry of Science and Innovation, (CGL2016-79054), the Open Technology Program of NWO (TTW-13848), and the STSM Cost Action FA1405 funded by the European Union. A.P. research activities were supported by the Netherlands Organisation for Scientific Research (NWO, project no. 870.15.080)."],"format":["application/pdf","application/octet-stream"],"id":"50|dedup_wf_001::01644aebfe64e809f593492e515bc070","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::e820a45f1dfc7b95282d10b6087e11c0","value":"Repositorio Institucional de la Universidad de Alicante"},"hostedby":{"key":"10|opendoar____::e820a45f1dfc7b95282d10b6087e11c0","value":"Repositorio Institucional de la Universidad de Alicante"},"license":"Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.","publicationdate":"2018-09-26","refereed":"UNKNOWN","type":"Article","url":["http://hdl.handle.net/10045/80968"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"},"hostedby":{"key":"10|doajarticles::70703810b20723fe33cba6ffd7128212","value":"Scientific 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(NWO)","shortName":"NWO"},"id":"40|nwo_________::dc69ada721bf21ed51055b6421850d73","provenance":{"provenance":"Harvested","trust":"0.900000000000000022"},"title":"Exploring and exploiting phytochemicals to lure hyperparasitoids away from beneficial biocontrol agents"},{"code":"2300189714","funder":{"jurisdiction":"NL","name":"Netherlands Organisation for Scientific Research (NWO)","shortName":"NWO"},"id":"40|nwo_________::39d892199c3b3d3b5ae9869a79e5bba8","provenance":{"provenance":"Harvested","trust":"0.900000000000000022"},"title":"Linking aboveground-belowground interactions and plant-soil feedback to improve pest control and sustainability in greenhouse cut-flowers"}],"publicationdate":"2018-09-26","publisher":"Springer Nature","subjects":[{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Plant-mediated interactions"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Herbivores"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Feeding guilds"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Parasitism"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Belowground interactions"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Zoología"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Medicine"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"R"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Science"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Q"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"international"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Laboratorium voor Entomologie"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"PE&RC"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Laboratory of Entomology"}},{"subject":{"scheme":"keywords","value":"Multidisciplinary"}}],"type":"publication"} -{"author":[{"fullname":"Bonnie Berger","name":"Bonnie","pid":{"id":{"scheme":"orcid","value":"0000-0002-2724-7228"}},"rank":1,"surname":"Berger"}],"bestaccessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":[{"key":"10|opendoar____::958adb57686c2fdec5796398de5f317a","value":"MPG.PuRe"},{"key":"10|share_______::bbd802baad85d1fd440f32a7a3a2c2b1","value":"bioRxiv"},{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"},{"key":"10|openaire____::8ac8380272269217cb09a928c8caa993","value":"UnpayWall"},{"key":"10|openaire____::806360c771262b4d6770e7cdf04b5c5a","value":"ORCID"},{"key":"10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a","value":"Microsoft Academic Graph"},{"key":"10|opendoar____::89f0fd5c927d466d6ec9a21b9ac34ffa","value":"eScholarship - University of California"},{"key":"10|openaire____::9e3be59865b2c1c335d32dae2fe7b254","value":"Datacite"},{"key":"10|opendoar____::eda80a3d5b344bc40f3bc04f65b7a357","value":"PubMed Central"},{"key":"10|opendoar____::8f19793b2671094e63a15ab883d50137","value":"Digital Access to Scholarship at Harvard"},{"key":"10|opendoar____::2a38a4a9316c49e5a833517c45d31070","value":"DSpace@MIT"}],"context":[{"code":"dh-ch","label":"Digital Humanities and Cultural Heritage","provenance":[{"provenance":"Inferred by OpenAIRE","trust":"0.8"}]}],"contributor":["Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory","Massachusetts Institute of Technology. Department of Mathematics","Lipson, Mark","Loh, Po-Ru","Berger, Bonnie"],"country":[{"code":"DZ","label":"Algeria","provenance":{"provenance":"Propagation of country to result collected from datasources of type institutional repositories","trust":"0.85"}},{"code":"US","label":"United States","provenance":{"provenance":"Propagation of country to result collected from datasources of type institutional repositories","trust":"0.85"}}],"coverage":[],"dateofcollection":"2020-09-12T07:56:34.334Z","description":["Austronesian languages are spread across half the globe, from Easter Island to Madagascar. Evidence from linguistics and archaeology indicates that the ‘Austronesian expansion,’ which began 4,000–5,000 years ago, likely had roots in Taiwan, but the ancestry of present-day Austronesian-speaking populations remains controversial. Here, we analyse genome-wide data from 56 populations using new methods for tracing ancestral gene flow, focusing primarily on Island Southeast Asia. We show that all sampled Austronesian groups harbour ancestry that is more closely related to aboriginal Taiwanese than to any present-day mainland population. Surprisingly, western Island Southeast Asian populations have also inherited ancestry from a source nested within the variation of present-day populations speaking Austro-Asiatic languages, which have historically been nearly exclusive to the mainland. Thus, either there was once a substantial Austro-Asiatic presence in Island Southeast Asia, or Austronesian speakers migrated to and through the mainland, admixing there before continuing to western Indonesia.","National Science Foundation (U.S.). Graduate Research Fellowship Program","Simons Foundation","National Institutes of Health (U.S.) (Grant R01GM108348)","National Institutes of Health (U.S.) (Training Grant 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In this paper the first results from the proton–lead collision data taken in early 2013 are presented. The Z boson production cross section is measured in the muon decay channel in bins of transverse momentum and rapidity together with the forward–backward ratio. The W production is studied in the muon and electron decay channels and the differential cross sections, lepton-charge and forward–backward asymmetries are computed as a function of the lepton pseudorapidity. All results are compared with theory predictions with and without nuclear modification of the parton distribution functions showing hints of nuclear effects."],"format":[],"id":"50|dedup_wf_001::02cb7e7397a1f775e53ed38b38aba680","instance":[{"accessright":{"code":"c_14cb","label":"CLOSED","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::666894f04637d4dd1861ad117e1c4a66","value":"SNSF P3 Database"},"hostedby":{"key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c","value":"Unknown Repository"},"publicationdate":"2014-01-01","refereed":"peerReviewed","type":"Conference object","url":["http://dx.doi.org/doi:10.1016/j.nuclphysa.2014.07.039"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::fc490ca45c00b1249bbe3554a4fdf6fb","value":"CERN Document 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prognostic accuracy in patients with disorders of consciousness. Due to the portability and relative inexpensiveness of electroencephalography, the N400 event-related potential component has been proposed as a clinically valid means to identify preserved linguistic function in non-communicative patients. Across three experiments, we show that changes in both stimuli and task demands significantly influence the probability of detecting statistically significant N400 effects — that is, the difference in N400 amplitudes caused by the experimental manipulation. In terms of task demands, passively heard linguistic stimuli were significantly less likely to elicit N400 effects than task-relevant stimuli. Due to the inability of the majority of patients with disorders of consciousness to follow task commands, the insensitivity of passive listening would impede the identification of residual language abilities even when such abilities exist. In terms of stimuli, passively heard normatively associated word pairs produced the highest detection rate of N400 effects (50% of the participants), compared with semantically-similar word pairs (0%) and high-cloze sentences (17%). This result is consistent with a prediction error account of N400 magnitude, with highly predictable targets leading to smaller N400 waves, and therefore larger N400 effects. Overall, our data indicate that non-repeating normatively associated word pairs provide the highest probability of detecting single-subject N400s during passive listening, and may thereby provide a clinically viable means of assessing residual linguistic function. We also show that more liberal analyses may further increase the detection-rate, but at the potential cost of increased false alarms.","Highlights • The N400 is a candidate marker of linguistic function after severe brain injury. • The probability of detecting N400s is dependent on task demands. • Passive listening is less sensitive than command-following. • The probability of detecting N400s is dependent on stimuli choices. • Word-pairs generated from association norms provide the highest sensitivity."],"format":["application/pdf"],"id":"50|dedup_wf_001::03d1b1b04480058e646b34c174e61082","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"},"hostedby":{"key":"10|doajarticles::0c0e74daa5d95504eade9c81ebbd5b8a","value":"NeuroImage: 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New polyethers, such as iubol (2), 22-hydroxy-15(28)- dehydrovenustatriol (3), 1,2-dehydropseudodehydrothyrsiferol (4), and secodehydrothyrsiferol (5) have been isolated and characterized from this alga. The structures were determined through the interpretation of NMR spectroscopic data and the relative configuration was proposed on the basis of NOESY spectrum and biogenetic considerations. All new compounds exhibited significant cytotoxic activity against a panel of cancer cell lines. © 2011 by the authors.","Financial support was provided by the grants MAREX (FP 7; KBBE-3-245137) (EU), CTQ2008-06754-C04-01 and SAF2008-02251 (MICINN); C2008000145 and EXMAR (ACISII); RD06/0020/1037 from Red Temática de Investigación Cooperativa en Cáncer, Instituto de Salud Carlos III, co-funded by the Fondo Europeo de Desarrollo Regional of the European Union, and Junta de Castilla y León (CSI052A11-2, and GR15-Experimental Therapeutics and Translational Oncology Program). F.C.P. is the recipient of a SEGAI-ULL fellowship.","Peer Reviewed"],"format":["application/pdf"],"id":"50|dedup_wf_001::06496bbae2934f9443037f3df7293791","instance":[{"accessright":{"code":"c_14cb","label":"CLOSED","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::4e99a7004945b3f6298b66c2b8dd4fc6","value":"SESAM Publication Database - FP7 KBBE"},"hostedby":{"key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c","value":"Unknown 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The validity and utility of standard measures of childhood maltreatment requires clarification in order to inform the design of future studies investigating the mental health consequences of maltreatment. The present study assessed agreement between prospective informant-reports and retrospective self-reports of childhood maltreatment, as well as the comparative utility of both reports for predicting a range of psychiatric problems at age 18. Data were obtained from the Environmental Risk (E-Risk) Longitudinal Twin Study, a nationally-representative birth cohort of 2232 children followed to 18 years of age (with 93% retention). Childhood maltreatment was assessed in two ways: (i) prospective informant-reports from caregivers, researchers, and clinicians when children were aged 5, 7, 10 and 12; and (ii) retrospective self-reports of maltreatment experiences occurring up to age 12, obtained at age 18 using the Childhood Trauma Questionnaire. Participants were privately interviewed at age 18 concerning several psychiatric problems including depression, anxiety, self-injury, alcohol/cannabis dependence, and conduct disorder. There was only slight to fair agreement between prospective and retrospective reports of childhood maltreatment (all Kappa's ≤ 0.31). Both prospective and retrospective reports of maltreatment were associated with age-18 psychiatric problems, though the strongest associations were found when maltreatment was retrospectively self-reported. These findings indicate that prospective and retrospective reports of childhood maltreatment capture largely non-overlapping groups of individuals. Young adults who recall being maltreated have a particularly elevated risk for psychopathology."],"format":["application/pdf","text"],"id":"50|dedup_wf_001::085f9efc74e1192abca87031fb573d70","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::566a9968b43628588e76be5a85a0f9e8","value":"King's Research Portal"},"hostedby":{"key":"10|opendoar____::566a9968b43628588e76be5a85a0f9e8","value":"King's Research 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Here, we focused on tomato (Solanum lycopersicum), testing the hypothesis that plants grown on native soils display different responses to soil microbiotas.\r\nUsing transcriptomics, proteomics, and biochemistry, we describe the responses of two tomato genotypes (susceptible or resistant to Fusarium oxysporum f. sp. lycopersici) grown on an artificial growth substrate and two native soils (conducive and suppressive to Fusarium).\r\nNative soils affected tomato responses by modulating pathways involved in responses to oxidative stress, phenol biosynthesis, lignin deposition, and innate immunity, particularly in the suppressive soil. In tomato plants grown on steam-disinfected soils, total phenols and lignin decreased significantly. The inoculation of a mycorrhizal fungus partly rescued this response locally and systemically. Plants inoculated with the fungal pathogen showed reduced disease symptoms in the resistant genotype in both soils, but the susceptible genotype was partially protected from the pathogen only when grown on the suppressive soil.\r\nThe ‘state of alert’ detected in tomatoes reveals novel mechanisms operating in plants in native soils and the soil microbiota appears to be one of the drivers of these plant responses."],"format":[],"id":"50|dedup_wf_001::09e54cbad6670d8f40a7de2704e2d2a4","instance":[{"accessright":{"code":"c_16ec","label":"RESTRICTED","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"},"hostedby":{"key":"10|issn___print::35ee75a5ad42581d604be113a8f56427","value":"New Phytologist"},"license":"http://doi.wiley.com/10.1002/tdm_license_1.1","publicationdate":"2018-02-09","refereed":"UNKNOWN","type":"Article","url":["https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2Fnph.15014","http://onlinelibrary.wiley.com/wol1/doi/10.1111/nph.15014/fullpdf","http://dx.doi.org/10.1111/nph.15014"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::8ac8380272269217cb09a928c8caa993","value":"UnpayWall"},"hostedby":{"key":"10|issn___print::35ee75a5ad42581d604be113a8f56427","value":"New Phytologist"},"refereed":"UNKNOWN","type":"Article","url":["https://nph.onlinelibrary.wiley.com/doi/pdfdirect/10.1111/nph.15014"]},{"collectedfrom":{"key":"10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a","value":"Microsoft Academic Graph"},"hostedby":{"key":"10|issn___print::35ee75a5ad42581d604be113a8f56427","value":"New Phytologist"},"refereed":"UNKNOWN","type":"Article","url":["https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.15014","https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.15014","http://onlinelibrary.wiley.com/doi/10.1111/nph.15014/abstract","https://aperto.unito.it/handle/2318/1660820","https://academic.microsoft.com/#/detail/2793208206"]},{"accessright":{"code":"c_16ec","label":"RESTRICTED","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::89fcd07f20b6785b92134bd6c1d0fa42","value":"Archivio Istituzionale"},"hostedby":{"key":"10|opendoar____::89fcd07f20b6785b92134bd6c1d0fa42","value":"Archivio Istituzionale"},"publicationdate":"2018-01-01","refereed":"UNKNOWN","type":"Article","url":["http://hdl.handle.net/2318/1660820"]},{"collectedfrom":{"key":"10|openaire____::9e3be59865b2c1c335d32dae2fe7b254","value":"Datacite"},"hostedby":{"key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c","value":"Unknown Repository"},"publicationdate":"2018-12-01","refereed":"UNKNOWN","type":"Other literature type","url":["http://dx.doi.org/10.1111/nph.15014"]}],"language":{"code":"und","label":"Undetermined"},"lastupdatetimestamp":1603727328518,"maintitle":"Native soils with their microbiotas elicit a state of alert in tomato plants","originalId":["10.1111/nph.15014","2793208206","oai:iris.unito.it:2318/1660820"],"pid":[{"scheme":"doi","value":"10.1111/nph.15014"},{"scheme":"pmid","value":"29424928"}],"projects":[{"acronym":"TomRes","code":"727929","funder":{"fundingStream":"H2020","jurisdiction":"EU","name":"European Commission","shortName":"EC"},"id":"40|corda__h2020::94c4a066401e22002c4811a301bb4655","provenance":{"provenance":"Harvested","trust":"0.900000000000000022"},"title":"A NOVEL AND INTEGRATED APPROACH TO INCREASE MULTIPLE AND COMBINED STRESS TOLERANCE IN PLANTS USING TOMATO AS A MODEL"}],"publicationdate":"2018-12-01","publisher":"Wiley","subjects":[{"subject":{"scheme":"keywords","value":"Plant Science"}},{"subject":{"scheme":"keywords","value":"Physiology"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Arbuscular mycorrhizal fungi; Defence responses; Lignin biosynthesis; Microbiota; Suppressive and conducive soils; Susceptible and resistant genotypes; Tomato; Physiology; Plant Science"}},{"provenance":{"provenance":"Inferred by OpenAIRE","trust":"0.891"},"subject":{"scheme":"mesheuropmc","value":"food and beverages"}},{"provenance":{"provenance":"Inferred by OpenAIRE","trust":"0.891"},"subject":{"scheme":"mesheuropmc","value":"fungi"}},{"provenance":{"provenance":"Inferred by OpenAIRE","trust":"0.8739"},"subject":{"scheme":"mesheuropmc","value":"complex mixtures"}}],"type":"publication"} -{"author":[{"fullname":"K.P. 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To this end, the main objective of this work is the prognosis of the mean, maximum and minimum hourly wind power (WP) 8hours ahead. For this purpose, Artificial Neural Networks (ANN) modeling is applied. For the appropriate training of the developed ANN models hourly meteorological data are used. These data have been recorded by a meteorological mast in Tilos Island, Greece.\n\nFor the evaluation of the developed ANN forecasting models proper statistical evaluation indices are used. According to the results, the coefficient of the determination ranges from 0.285 up to 0.768 (mean hourly WP), from 0.227 up to 0.798 (maximum hourly WP) and from 0.025 up to 0.398 (minimum hourly WP). Furthermore, the proposed forecasting methodology shows that is able to give sufficient and adequate prognosis of WP by a wind turbine in a specific location 8 hours ahead. This will be a useful tool for the operator of a RES system in order to achieve a better monitoring and a better management of the whole system."],"format":[],"id":"50|dedup_wf_001::0a6525f420fd1f922125c3a1a280c8df","instance":[{"accessright":{"code":"c_16ec","label":"RESTRICTED","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"},"hostedby":{"key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c","value":"Unknown Repository"},"publicationdate":"2017-02-23T20:11:53Z","refereed":"UNKNOWN","type":"Conference object","url":["http://digital-library.theiet.org/content/conferences/10.1049/cp.2016.1094?crawler=true","http://dx.doi.org/10.1049/cp.2016.1094"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::8ac8380272269217cb09a928c8caa993","value":"UnpayWall"},"hostedby":{"key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c","value":"Unknown Repository"},"license":"cc-by","refereed":"UNKNOWN","type":"Conference object","url":["https://zenodo.org/record/887339/files/Wind%20power%20forecasting%20using%20historical%20data%20and%20artificial%20neural%20networks%20modeling.pdf"]},{"collectedfrom":{"key":"10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a","value":"Microsoft Academic Graph"},"hostedby":{"key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c","value":"Unknown Repository"},"refereed":"UNKNOWN","type":"Conference object","url":["http://digital-library.theiet.org/content/conferences/10.1049/cp.2016.1094","https://core.ac.uk/display/144851191","http://jglobal.jst.go.jp/public/20090422/201702260673071390","https://academic.microsoft.com/#/detail/2590295725"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::358aee4cc897452c00244351e4d91f69","value":"ZENODO"},"hostedby":{"key":"10|opendoar____::358aee4cc897452c00244351e4d91f69","value":"ZENODO"},"license":"http://creativecommons.org/licenses/by/4.0/legalcode","publicationdate":"2016-11-07","refereed":"UNKNOWN","type":"Conference object","url":["https://zenodo.org/record/887339"]}],"language":{"code":"und","label":"Undetermined"},"lastupdatetimestamp":1603727328518,"maintitle":"Wind power forecasting using historical data and artificial neural networks modeling","originalId":["10.1049/cp.2016.1094","2590295725","oai:zenodo.org:887339"],"pid":[{"scheme":"doi","value":"10.1049/cp.2016.1094"}],"projects":[{"acronym":"TILOS","code":"646529","funder":{"fundingStream":"H2020","jurisdiction":"EU","name":"European Commission","shortName":"EC"},"id":"40|corda__h2020::64c901e621f90b9a38badb1d78902205","provenance":{"provenance":"Harvested","trust":"0.900000000000000022"},"title":"Technology Innovation for the Local Scale, Optimum Integration of Battery Energy Storage"}],"publicationdate":"2016-11-07","publisher":"Institution of Engineering and Technology","subjects":[{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Wind Power, Forecasting, Artificial Neural Networks"}}],"type":"publication"} -{"author":[{"fullname":"Juan M. 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Vertical velocities can be estimated indirectly from in situ observations by theoretical frameworks like the-equation. Direct measures of vertical exchanges are challenging due to their typically ephemeral spatiotemporal scales. In this study we address this problem with an adaptive sampling strategy coupling various biophysical instruments. We analyze the 3-D organization of a cyclonic mesoscale structure finely sampled during the Observing Submesoscale Coupling At High Resolution cruise in the Ligurian Sea during fall 2015. The observations, acquired with a moving vessel profiler, highlight a subsurface low-salinity layer (≃50 m), as well as rising isopycnals, generated by geostrophic cyclonic circulation, in the structure's center. Reconstructed 3-D fields of density and horizontal velocities are used to estimate the vertical velocity field down to 250 m by applying the adiabatic QG-equation, for the first time in this region. The vertical motions are characterized by multipolar patterns of downward and upward velocities on the edges of the structure and significantly smaller vertical velocities in its center. Both the 3-D distribution of particles (size ≥100 μm), measured with a laser optical plankton counter, and the Synechococcus and Prochlorococcus abundances (cell per cubic meter) measured by flow cytometry are consistent with the 3-D velocity field. In particular, a secondary vertical recirculation is identified that upwells particles (from 250 to 100 m) along isohalines to the structure's center. Besides demonstrating the effect of vertical patterns on biogeochemical distributions, this case study suggests to use particle matter as a tracer to assess physical dynamics."],"format":["application/pdf"],"id":"50|dedup_wf_001::0d16b1714ab3077df73893a8ea57d776","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::7e7757b1e12abcb736ab9a754ffb617a","value":"Hyper Article en Ligne"},"hostedby":{"key":"10|opendoar____::7e7757b1e12abcb736ab9a754ffb617a","value":"Hyper Article en 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Personality traits, affective status and stress are some of the relevant factors contributing to lower quality of life and symptom exacerbation in IBS patients. In order to examine the role of stress in IBS symptom exacerbation, the aims of this study were to explore the relationship of daily stressful events and symptom severity in a prospective manner and to explore the roles of neuroticism, anxiety, depression and stress in the vicious circle of symptom perpetuation. A total of 49 patients with IBS reported their symptom severity and daily stressful events intensity each day for 14 consecutive days. They also completed the Big five personality inventory, the Beck Depression Inventory and the State-trait anxiety inventory. Cross-correlation analyses were performed on the time series data for daily stress and symptom severity for each participant separately. Four different patterns of relationships were found in different subgroups of participants: positive cross-correlations of symptom severity and stress intensity on the same day; higher symptom severity on days following stressful days; lower symptom severity on days following stressful days; and lower stress intensity on days following severe symptoms. Using average scores for daily stress and symptom severity, as well as scores for neuroticism, anxiety and depression, we performed a path analysis to test a model of symptom exacerbation. It showed that, on the group level, average stress intensity predicts average symptom severity. Neuroticism and anxiety were not significant predictors of symptom severity, while depression showed a marginally significant relationship with symptom severity, mediated by stress intensity. In conclusion, depression and daily stress seem to be important contributors to the vicious circle of IBS symptom perpetuation.","Síndrome del intestino irritable se considera un trastorno biopsicosocial, el resultado de la combinación compleja de factores predisponentes, precipitantes y perpetuos. Rasgos de personalidad, estado afectivo y estrés son algunos de los factores relevantes que contribuyen a la calidad de vida más baja y la exacerbación sintomática de los pacientes con SII. Para examinar el papel del estrés en la exacerbación sintomática de SII, el objetivo de este estudio era explorar la relación entre los acontecimientos cotidianos estresantes y la intensidad de los síntomas de forma prospectiva, tanto como explorar los papeles del neuroticismo, ansiedad, depresión y estrés en el círculo vicioso de perpetuación de los síntomas. Todos los 49 pacientes con SII informaron sobre la intensidad de los síntomas y la intensidad de los acontecimientos cotidianos estresantes cada día durante 14 días consecutivos. Además, completaron el Test de personalidad de los cinco grandes, Inventario de depresión de Beck e Inventario de ansiedad estado-rasgo. En los datos de series temporales se hizo el análisis de correlación cruzada para la intensidad del estrés diario y de los síntomas para cada participante por separado. Se encontraron cuatro patrones de relación diferentes en diferentes subgrupos de participantes: correlación cruzada positiva de la intensidad de los síntomas y del estrés el mismo día; intensidad de los síntomas más alta en los días después de los días estresantes; intensidad de los síntomas más baja en los días después de los días estresantes e intensidad del estrés más baja en los días después de los síntomas graves. Usando resultados promedios para el estrés diario y la intensidad de los síntomas, tanto como resultados para el neuroticismo, ansiedad y depresión, realizamos un análisis del camino para examinar el modelo de la exacerbación de los síntomas. Mostró que, al nivel de grupo, la intensidad del estrés promedia predice la intensidad de los síntomas promedia. Neuroticismo y ansiedad no eran predictores significativos de la intensidad de los síntomas, mientras que la depresión demostró una relación marginalmente significante con la intensidad de los síntomas, mediada por la intensidad del estrés. En conclusión, la depresión y el estrés diario parecen ser contribuidores importantes al círculo vicioso de la perpetuación de los síntomas SII."],"format":["application/pdf"],"id":"50|dedup_wf_001::054ea3bc3ccc386d150d900776e1070d","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::2e3d2c4f33a7a1f58bc6c81cacd21e9c","value":"Repository of the University of Rijeka, Faculty of Humanities and Social Sciences"},"hostedby":{"key":"10|opendoar____::2e3d2c4f33a7a1f58bc6c81cacd21e9c","value":"Repository of the University of Rijeka, Faculty of Humanities and Social Sciences"},"license":"http://creativecommons.org/licenses/by/4.0/","publicationdate":"2016-04-01","refereed":"UNKNOWN","type":"Article","url":["https://repository.ffri.uniri.hr/islandora/object/ffri:1182","https://urn.nsk.hr/urn:nbn:hr:186:701987","https://repository.ffri.uniri.hr/islandora/object/ffri:1182/datastream/FILE0"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::1c1d4df596d01da60385f0bb17a4a9e0","value":"HRČAK - Portal of scientific journals of Croatia"},"hostedby":{"key":"10|opendoar____::1c1d4df596d01da60385f0bb17a4a9e0","value":"HRČAK - Portal of scientific journals of Croatia"},"publicationdate":"2016-01-01","refereed":"UNKNOWN","type":"Other literature type","url":["https://hrcak.srce.hr/156331","https://hrcak.srce.hr/file/230444"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"},"hostedby":{"key":"10|doajarticles::23738aeeb586d9f9b652c75aaff54dd4","value":"Psychological Topics"},"publicationdate":"2016-04-01","refereed":"UNKNOWN","type":"Article","url":["http://pt.ffri.hr/index.php/pt/article/view/317","https://doaj.org/toc/1332-0742"]}],"language":{"code":"eng","label":"English"},"lastupdatetimestamp":1603727328518,"maintitle":"The role of stress in IBS symptom severity","originalId":["oai:repository.ffri.uniri.hr:ffri_1182","oai:hrcak.srce.hr:156331","oai:doaj.org/article:4394c5a4f62849ffac7ea485a91540a3"],"pid":[],"projects":[{"code":"009-0092660-2655","funder":{"jurisdiction":"HR","name":"Ministry of Science, Education and Sports of the Republic of Croatia (MSES)","shortName":"MZOS"},"id":"40|irb_hr______::ad496254144c27606e4058841e060fa0","provenance":{"provenance":"Harvested","trust":"0.900000000000000022"},"title":"Psychosomatic aspects of chronic functional and inflammatory bowel diseases"}],"publicationdate":"2016-04-01","subjects":[{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"irritable bowel syndrome"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"symptom severity"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"daily stress"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"depression"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"DRUŠTVENE ZNANOSTI. 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dependence of the recovery of the transition temperature shift after annealing (475 °C, 100 h) on copper and phosphorus contents has been studied on irradiated reactor pressure vessel (RPV) materials. A set of model alloys with low nickel content, lower than 0.2 mass%, was used for the study. Copper and phosphorus contents were varied in a wide range: 0.005–0.99 and 0.002–0.039 mass%, respectively. Recovery efficiency has been estimated by the value of residual embrittlement after annealing, measured in terms of a shift in transition temperature (ΔTKres). A comparison of the results obtained on model alloys with data for VVER-440 RPV materials has also been carried out. Comparative analysis has confirmed the conclusion that ΔTKres is independent of phosphorus content while the effect of copper on ΔTKres is not significant for typical VVER-440 RPV materials with a typical range of Cu contents between 0.10 and 0.24 mass%. 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The bi-functionality of the protein also allowed the binding of hydrophobic solid drug nanoparticles to cellulose nanofibrils and thereby improving their long-term stability under physiological conditions."}],"externalReference":[],"extraInfo":[],"format":[],"fulltext":[],"id":"50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb","instance":[{"accessright":{"classid":"CLOSED","classname":"Closed Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"collectedfrom":{"key":"10|openaire____::4692342f0992d91f9e705c26959f09e0","value":"VTT Research Information 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Ce qui nous frappe en premier lieu dans le roman de Melchior Mbonimpa, Le Totem des Baranda, c'est l'efficacité de sa fonction didactique. Le livre est porteur d'un message, d'une vision sur l'histoire de l'Afrique des Grands Lacs qu'on rencontre rarement dans l'actualité ou l'histoire immédiate que nous livrent les médias.

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

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

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

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

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La NDI a été étudiée dans le cas de diverses applications, y compris en aéronautique et en aérospatiale. Elle permet de calculer des lois de contrôle capables de linéariser et de découpler un modèle non-linéaire à tout point de fonctionnement de son enveloppe d'état. Cependant cette méthode est intrinsèquement non-robuste aux erreurs de modélisation et aux saturations en entrée. En outre, dans un contexte non-linéaire, l'obtention d'une garantie quantifiable du domaine de stabilité atteint reste à l'heure actuelle complexe. Contrairement aux approches classiques de la NDI, notre méthodologie peut être considérée comme un cadre de compensation non-linéaire généralisé qui permet d'intégrer les incertitudes et les saturations en entrée dans le processus de conception. En utilisant des stratégies de contrôle antiwindup, la loi de pilotage peut être calculée grâce à un simple processus en deux phases. Dans ce cadre de travail généralisé des transformations linéaires fractionnaires (LFT - Linear Fractional Transformations) de la boucle fermée non-linéaire peuvent être facilement déduites pour l'analyse de la stabilité robuste en utilisant des outils standards pour de systèmes linéaires. La méthode proposée est testée pour le pilotage d'un véhicule de rentrée atmosphérique de type aile delta lors de ses phases hypersonique, transsonique et subsonique. Pour cette thèse, un simulateur du vol incluant divers facteurs externes ainsi que des erreurs de modélisation a été développé dans Simulink.\n\nThis thesis work is devoted to extending Nonlinear Dynamic Inversion (NDI) for a large scale of\nnonlinear systems while guaranteeing sufficient stability conditions. NDI has been studied in a wide range of applications, including aeronautics and aerospace. It allows to compute nonlinear control laws able to decouple and linearize a model at any operating point of its state envelope. 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Departamento de Ciencias Ambientales y Recursos Naturales","Universidad de Alicante. Centro Iberoamericano de la Biodiversidad","Biodiversidad y Biotecnología aplicadas a la Biología de la Conservación","Terrestrial Ecology (TE)"],"country":[{"code":"NL","label":"Netherlands","provenance":{"provenance":"Propagation of country to result collected from datasources of type institutional repositories","trust":"0.85"}},{"code":"ES","label":"Spain","provenance":{"provenance":"Propagation of country to result collected from datasources of type institutional repositories","trust":"0.85"}}],"coverage":[],"dateofcollection":"2018-10-03T06:57:46.116Z","description":["Herbivory affects subsequent herbivores, mainly regulated by the phytohormones jasmonic (JA) and salicylic acid (SA). Additionally, organisms such as soil microbes belowground or parasitoids that develop inside their herbivorous hosts aboveground, can change plant responses to herbivory. However, it is not yet well known how organisms of trophic levels other than herbivores, below- and above-ground, alter the interactions between insect species sharing a host plant. Here, we investigated whether the parasitoid Aphidius colemani and different soil microbial communities (created through plant-soil feedbacks) affect the JA and SA signalling pathways in response to the aphid Myzus persicae and the thrips Frankliniella occidentalis, as well as subsequent thrips performance. Our results show that the expression of the JA-responsive gene CaPINII in sweet pepper was more suppressed by aphids than by parasitised aphids. However, parasitism did not affect the expression of CaPAL1, a biosynthetic gene of SA. Furthermore, aphid feeding enhanced thrips performance compared with uninfested plants, but this was not observed when aphids were parasitised. Soils where different plant species were previously grown, did not affect plant responses or the interaction between herbivores. Our study shows that members of the third trophic level can modify herbivore interactions by altering plant physiology.\nThis work and T.V.’s activities were supported by Spanish Ministry of Science and Innovation, (CGL2016-79054), the Open Technology Program of NWO (TTW-13848), and the STSM Cost Action FA1405 funded by the European Union. A.P. research activities were supported by the Netherlands Organisation for Scientific Research (NWO, project no. 870.15.080)."],"format":["application/pdf","application/octet-stream"],"id":"50|dedup_wf_001::01644aebfe64e809f593492e515bc070","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::e820a45f1dfc7b95282d10b6087e11c0","value":"Repositorio Institucional de la Universidad de Alicante"},"hostedby":{"key":"10|opendoar____::e820a45f1dfc7b95282d10b6087e11c0","value":"Repositorio Institucional de la Universidad de Alicante"},"license":"Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.","publicationdate":"2018-09-26","refereed":"UNKNOWN","type":"Article","url":["http://hdl.handle.net/10045/80968"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"},"hostedby":{"key":"10|doajarticles::70703810b20723fe33cba6ffd7128212","value":"Scientific 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(NWO)","shortName":"NWO"},"id":"40|nwo_________::dc69ada721bf21ed51055b6421850d73","provenance":{"provenance":"Harvested","trust":"0.900000000000000022"},"title":"Exploring and exploiting phytochemicals to lure hyperparasitoids away from beneficial biocontrol agents"},{"code":"2300189714","funder":{"jurisdiction":"NL","name":"Netherlands Organisation for Scientific Research (NWO)","shortName":"NWO"},"id":"40|nwo_________::39d892199c3b3d3b5ae9869a79e5bba8","provenance":{"provenance":"Harvested","trust":"0.900000000000000022"},"title":"Linking aboveground-belowground interactions and plant-soil feedback to improve pest control and sustainability in greenhouse cut-flowers"}],"publicationdate":"2018-09-26","publisher":"Springer Nature","subjects":[{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Plant-mediated interactions"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Herbivores"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Feeding guilds"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Parasitism"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Belowground interactions"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Zoología"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Medicine"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"R"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Science"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Q"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"international"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Laboratorium voor Entomologie"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"PE&RC"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Laboratory of Entomology"}},{"subject":{"scheme":"keywords","value":"Multidisciplinary"}}],"type":"publication"} -{"author":[{"fullname":"Bonnie Berger","name":"Bonnie","pid":{"id":{"scheme":"orcid","value":"0000-0002-2724-7228"}},"rank":1,"surname":"Berger"}],"bestaccessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":[{"key":"10|opendoar____::958adb57686c2fdec5796398de5f317a","value":"MPG.PuRe"},{"key":"10|share_______::bbd802baad85d1fd440f32a7a3a2c2b1","value":"bioRxiv"},{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"},{"key":"10|openaire____::8ac8380272269217cb09a928c8caa993","value":"UnpayWall"},{"key":"10|openaire____::806360c771262b4d6770e7cdf04b5c5a","value":"ORCID"},{"key":"10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a","value":"Microsoft Academic Graph"},{"key":"10|opendoar____::89f0fd5c927d466d6ec9a21b9ac34ffa","value":"eScholarship - University of 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Computer Science and Artificial Intelligence Laboratory","Massachusetts Institute of Technology. Department of Mathematics","Lipson, Mark","Loh, Po-Ru","Berger, Bonnie"],"country":[{"code":"DZ","label":"Algeria","provenance":{"provenance":"Propagation of country to result collected from datasources of type institutional repositories","trust":"0.85"}},{"code":"US","label":"United States","provenance":{"provenance":"Propagation of country to result collected from datasources of type institutional repositories","trust":"0.85"}}],"coverage":[],"dateofcollection":"2020-09-12T07:56:34.334Z","description":["Austronesian languages are spread across half the globe, from Easter Island to Madagascar. Evidence from linguistics and archaeology indicates that the ‘Austronesian expansion,’ which began 4,000–5,000 years ago, likely had roots in Taiwan, but the ancestry of present-day Austronesian-speaking populations remains controversial. Here, we analyse genome-wide data from 56 populations using new methods for tracing ancestral gene flow, focusing primarily on Island Southeast Asia. We show that all sampled Austronesian groups harbour ancestry that is more closely related to aboriginal Taiwanese than to any present-day mainland population. Surprisingly, western Island Southeast Asian populations have also inherited ancestry from a source nested within the variation of present-day populations speaking Austro-Asiatic languages, which have historically been nearly exclusive to the mainland. Thus, either there was once a substantial Austro-Asiatic presence in Island Southeast Asia, or Austronesian speakers migrated to and through the mainland, admixing there before continuing to western Indonesia.","National Science Foundation (U.S.). Graduate Research Fellowship Program","Simons Foundation","National Institutes of Health (U.S.) (Grant R01GM108348)","National Institutes of Health (U.S.) (Training Grant 5T32HG004947-04)"],"format":["application/pdf"],"id":"50|dedup_wf_001::025dff86cc73c1c865ed35e5b7646e73","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::958adb57686c2fdec5796398de5f317a","value":"MPG.PuRe"},"hostedby":{"key":"10|opendoar____::958adb57686c2fdec5796398de5f317a","value":"MPG.PuRe"},"license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","publicationdate":"2014-01-01","refereed":"UNKNOWN","type":"Article","url":["http://hdl.handle.net/11858/00-001M-0000-0024-1F46-B","http://hdl.handle.net/11858/00-001M-0000-0024-1F8F-7","http://hdl.handle.net/11858/00-001M-0000-0024-1F90-1"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|share_______::bbd802baad85d1fd440f32a7a3a2c2b1","value":"bioRxiv"},"hostedby":{"key":"10|share_______::bbd802baad85d1fd440f32a7a3a2c2b1","value":"bioRxiv"},"publicationdate":"2014-05-27","refereed":"nonPeerReviewed","type":"Preprint","url":["http://dx.doi.org/10.1101/005603"]},{"accessright":{"code":"c_16ec","label":"RESTRICTED","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"},"hostedby":{"key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c","value":"Unknown 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Due to the portability and relative inexpensiveness of electroencephalography, the N400 event-related potential component has been proposed as a clinically valid means to identify preserved linguistic function in non-communicative patients. Across three experiments, we show that changes in both stimuli and task demands significantly influence the probability of detecting statistically significant N400 effects — that is, the difference in N400 amplitudes caused by the experimental manipulation. In terms of task demands, passively heard linguistic stimuli were significantly less likely to elicit N400 effects than task-relevant stimuli. Due to the inability of the majority of patients with disorders of consciousness to follow task commands, the insensitivity of passive listening would impede the identification of residual language abilities even when such abilities exist. In terms of stimuli, passively heard normatively associated word pairs produced the highest detection rate of N400 effects (50% of the participants), compared with semantically-similar word pairs (0%) and high-cloze sentences (17%). This result is consistent with a prediction error account of N400 magnitude, with highly predictable targets leading to smaller N400 waves, and therefore larger N400 effects. Overall, our data indicate that non-repeating normatively associated word pairs provide the highest probability of detecting single-subject N400s during passive listening, and may thereby provide a clinically viable means of assessing residual linguistic function. 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New polyethers, such as iubol (2), 22-hydroxy-15(28)- dehydrovenustatriol (3), 1,2-dehydropseudodehydrothyrsiferol (4), and secodehydrothyrsiferol (5) have been isolated and characterized from this alga. The structures were determined through the interpretation of NMR spectroscopic data and the relative configuration was proposed on the basis of NOESY spectrum and biogenetic considerations. All new compounds exhibited significant cytotoxic activity against a panel of cancer cell lines. © 2011 by the authors.","Financial support was provided by the grants MAREX (FP 7; KBBE-3-245137) (EU), CTQ2008-06754-C04-01 and SAF2008-02251 (MICINN); C2008000145 and EXMAR (ACISII); RD06/0020/1037 from Red Temática de Investigación Cooperativa en Cáncer, Instituto de Salud Carlos III, co-funded by the Fondo Europeo de Desarrollo Regional of the European Union, and Junta de Castilla y León (CSI052A11-2, and GR15-Experimental Therapeutics and Translational Oncology Program). 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The validity and utility of standard measures of childhood maltreatment requires clarification in order to inform the design of future studies investigating the mental health consequences of maltreatment. The present study assessed agreement between prospective informant-reports and retrospective self-reports of childhood maltreatment, as well as the comparative utility of both reports for predicting a range of psychiatric problems at age 18. Data were obtained from the Environmental Risk (E-Risk) Longitudinal Twin Study, a nationally-representative birth cohort of 2232 children followed to 18 years of age (with 93% retention). Childhood maltreatment was assessed in two ways: (i) prospective informant-reports from caregivers, researchers, and clinicians when children were aged 5, 7, 10 and 12; and (ii) retrospective self-reports of maltreatment experiences occurring up to age 12, obtained at age 18 using the Childhood Trauma Questionnaire. Participants were privately interviewed at age 18 concerning several psychiatric problems including depression, anxiety, self-injury, alcohol/cannabis dependence, and conduct disorder. There was only slight to fair agreement between prospective and retrospective reports of childhood maltreatment (all Kappa's ≤ 0.31). Both prospective and retrospective reports of maltreatment were associated with age-18 psychiatric problems, though the strongest associations were found when maltreatment was retrospectively self-reported. These findings indicate that prospective and retrospective reports of childhood maltreatment capture largely non-overlapping groups of individuals. Young adults who recall being maltreated have a particularly elevated risk for psychopathology."],"format":["application/pdf","text"],"id":"50|dedup_wf_001::085f9efc74e1192abca87031fb573d70","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::566a9968b43628588e76be5a85a0f9e8","value":"King's Research Portal"},"hostedby":{"key":"10|opendoar____::566a9968b43628588e76be5a85a0f9e8","value":"King's Research 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Plants inoculated with the fungal pathogen showed reduced disease symptoms in the resistant genotype in both soils, but the susceptible genotype was partially protected from the pathogen only when grown on the suppressive soil.\r\nThe ‘state of alert’ detected in tomatoes reveals novel mechanisms operating in plants in native soils and the soil microbiota appears to be one of the drivers of these plant responses."],"format":[],"id":"50|dedup_wf_001::09e54cbad6670d8f40a7de2704e2d2a4","instance":[{"accessright":{"code":"c_16ec","label":"RESTRICTED","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"},"hostedby":{"key":"10|issn___print::35ee75a5ad42581d604be113a8f56427","value":"New Phytologist"},"license":"http://doi.wiley.com/10.1002/tdm_license_1.1","publicationdate":"2018-02-09","refereed":"UNKNOWN","type":"Article","url":["https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2Fnph.15014","http://onlinelibrary.wiley.com/wol1/doi/10.1111/nph.15014/fullpdf","http://dx.doi.org/10.1111/nph.15014"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::8ac8380272269217cb09a928c8caa993","value":"UnpayWall"},"hostedby":{"key":"10|issn___print::35ee75a5ad42581d604be113a8f56427","value":"New Phytologist"},"refereed":"UNKNOWN","type":"Article","url":["https://nph.onlinelibrary.wiley.com/doi/pdfdirect/10.1111/nph.15014"]},{"collectedfrom":{"key":"10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a","value":"Microsoft Academic Graph"},"hostedby":{"key":"10|issn___print::35ee75a5ad42581d604be113a8f56427","value":"New Phytologist"},"refereed":"UNKNOWN","type":"Article","url":["https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.15014","https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.15014","http://onlinelibrary.wiley.com/doi/10.1111/nph.15014/abstract","https://aperto.unito.it/handle/2318/1660820","https://academic.microsoft.com/#/detail/2793208206"]},{"accessright":{"code":"c_16ec","label":"RESTRICTED","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::89fcd07f20b6785b92134bd6c1d0fa42","value":"Archivio Istituzionale"},"hostedby":{"key":"10|opendoar____::89fcd07f20b6785b92134bd6c1d0fa42","value":"Archivio Istituzionale"},"publicationdate":"2018-01-01","refereed":"UNKNOWN","type":"Article","url":["http://hdl.handle.net/2318/1660820"]},{"collectedfrom":{"key":"10|openaire____::9e3be59865b2c1c335d32dae2fe7b254","value":"Datacite"},"hostedby":{"key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c","value":"Unknown Repository"},"publicationdate":"2018-12-01","refereed":"UNKNOWN","type":"Other literature type","url":["http://dx.doi.org/10.1111/nph.15014"]}],"language":{"code":"und","label":"Undetermined"},"lastupdatetimestamp":1603727328518,"maintitle":"Native soils with their microbiotas elicit a state of alert in tomato plants","originalId":["10.1111/nph.15014","2793208206","oai:iris.unito.it:2318/1660820"],"pid":[{"scheme":"doi","value":"10.1111/nph.15014"},{"scheme":"pmid","value":"29424928"}],"projects":[{"acronym":"TomRes","code":"727929","funder":{"fundingStream":"H2020","jurisdiction":"EU","name":"European Commission","shortName":"EC"},"id":"40|corda__h2020::94c4a066401e22002c4811a301bb4655","provenance":{"provenance":"Harvested","trust":"0.900000000000000022"},"title":"A NOVEL AND INTEGRATED APPROACH TO INCREASE MULTIPLE AND COMBINED STRESS TOLERANCE IN PLANTS USING TOMATO AS A MODEL"}],"publicationdate":"2018-12-01","publisher":"Wiley","subjects":[{"subject":{"scheme":"keywords","value":"Plant Science"}},{"subject":{"scheme":"keywords","value":"Physiology"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Arbuscular mycorrhizal fungi; Defence responses; Lignin biosynthesis; Microbiota; Suppressive and conducive soils; Susceptible and resistant genotypes; Tomato; Physiology; Plant Science"}},{"provenance":{"provenance":"Inferred by OpenAIRE","trust":"0.891"},"subject":{"scheme":"mesheuropmc","value":"food and beverages"}},{"provenance":{"provenance":"Inferred by OpenAIRE","trust":"0.891"},"subject":{"scheme":"mesheuropmc","value":"fungi"}},{"provenance":{"provenance":"Inferred by OpenAIRE","trust":"0.8739"},"subject":{"scheme":"mesheuropmc","value":"complex mixtures"}}],"type":"publication"} -{"author":[{"fullname":"K.P. 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This study focuses on estimating the evapotranspiration and crop coefficients of table grapes vineyards trained on overhead “tendone” systems in the Apulia region (Italy). Maximum vineyard transpiration was estimated by adopting the “direct” methodology for ETp proposed by the Food and Agriculture Organization in Irrigation and Drainage Paper No. 56, with crop parameters estimated from Landsat 8 and RapidEye satellite data in combination with ground-based meteorological data. The modeling results of two growing seasons (2013 and 2014) indicated that canopy growth, seasonal and 10-day sums evapotranspiration values were strictly related to thermal requirements and rainfall events. The estimated values of mean seasonal daily evapotranspiration ranged between 4.2 and 4.1 mm·d−1, while midseason estimated values of crop coefficients ranged from 0.88 to 0.93 in 2013, and 1.02 to 1.04 in 2014, respectively. The experimental evapotranspiration values calculated represent the maximum value in absence of stress, so the resulting crop coefficients should be used with some caution. It is concluded that the retrieval of crop parameters and evapotranspiration derived from remotely-sensed data could be helpful for downscaling to the field the local weather conditions and agronomic practices and thus may be the basis for supporting grape growers and irrigation managers."],"format":["application/pdf"],"id":"50|dedup_wf_001::0bc332de35b4eb0cc3d0c54b3ff22dd3","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::a8db6f6b2ce4fe72e8b2314a9a93e7d9","value":"Sygma"},"hostedby":{"key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c","value":"Unknown Repository"},"license":"https://creativecommons.org/licenses/by/4.0/","refereed":"UNKNOWN","type":"Article","url":["http://dx.doi.org/10.3390/rs71114708"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"},"hostedby":{"key":"10|doajarticles::f7180a75ef642fcf5309759e0d2c431a","value":"Remote Sensing"},"license":"https://creativecommons.org/licenses/by/4.0/","publicationdate":"2015-11-05","refereed":"UNKNOWN","type":"Article","url":["http://www.mdpi.com/2072-4292/7/11/14708/pdf","http://dx.doi.org/10.3390/rs71114708"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::8ac8380272269217cb09a928c8caa993","value":"UnpayWall"},"hostedby":{"key":"10|doajarticles::f7180a75ef642fcf5309759e0d2c431a","value":"Remote Sensing"},"license":"cc-by","refereed":"UNKNOWN","type":"Article","url":["https://www.mdpi.com/2072-4292/7/11/14708/pdf"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a","value":"Microsoft Academic Graph"},"hostedby":{"key":"10|doajarticles::f7180a75ef642fcf5309759e0d2c431a","value":"Remote Sensing"},"refereed":"UNKNOWN","type":"Article","url":["https://dblp.uni-trier.de/db/journals/remotesensing/remotesensing7.html#VaninoPNMBD15","https://doi.org/10.3390/rs71114708","https://core.ac.uk/display/55147144","http://doi.org/10.3390/rs71114708","https://academic.microsoft.com/#/detail/2149946514"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::c2cdfa5866e03cdd07d313cbc8fb8311","value":"Multidisciplinary Digital Publishing Institute"},"hostedby":{"key":"10|doajarticles::f7180a75ef642fcf5309759e0d2c431a","value":"Remote Sensing"},"license":"http://creativecommons.org/licenses/by/3.0/","publicationdate":"2015-11-05","refereed":"UNKNOWN","type":"Other literature type","url":["http://dx.doi.org/10.3390/rs71114708"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"},"hostedby":{"key":"10|doajarticles::f7180a75ef642fcf5309759e0d2c431a","value":"Remote Sensing"},"publicationdate":"2015-11-01","refereed":"UNKNOWN","type":"Article","url":["http://www.mdpi.com/2072-4292/7/11/14708","https://doaj.org/toc/2072-4292"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::d8c24ca8f23c562a5600876ca2a550ce","value":"Archivio della ricerca - 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Vertical velocities can be estimated indirectly from in situ observations by theoretical frameworks like the-equation. Direct measures of vertical exchanges are challenging due to their typically ephemeral spatiotemporal scales. In this study we address this problem with an adaptive sampling strategy coupling various biophysical instruments. We analyze the 3-D organization of a cyclonic mesoscale structure finely sampled during the Observing Submesoscale Coupling At High Resolution cruise in the Ligurian Sea during fall 2015. The observations, acquired with a moving vessel profiler, highlight a subsurface low-salinity layer (≃50 m), as well as rising isopycnals, generated by geostrophic cyclonic circulation, in the structure's center. Reconstructed 3-D fields of density and horizontal velocities are used to estimate the vertical velocity field down to 250 m by applying the adiabatic QG-equation, for the first time in this region. The vertical motions are characterized by multipolar patterns of downward and upward velocities on the edges of the structure and significantly smaller vertical velocities in its center. Both the 3-D distribution of particles (size ≥100 μm), measured with a laser optical plankton counter, and the Synechococcus and Prochlorococcus abundances (cell per cubic meter) measured by flow cytometry are consistent with the 3-D velocity field. In particular, a secondary vertical recirculation is identified that upwells particles (from 250 to 100 m) along isohalines to the structure's center. Besides demonstrating the effect of vertical patterns on biogeochemical distributions, this case study suggests to use particle matter as a tracer to assess physical dynamics."],"format":["application/pdf"],"id":"50|dedup_wf_001::0d16b1714ab3077df73893a8ea57d776","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::7e7757b1e12abcb736ab9a754ffb617a","value":"Hyper Article en Ligne"},"hostedby":{"key":"10|opendoar____::7e7757b1e12abcb736ab9a754ffb617a","value":"Hyper Article en 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Personality traits, affective status and stress are some of the relevant factors contributing to lower quality of life and symptom exacerbation in IBS patients. In order to examine the role of stress in IBS symptom exacerbation, the aims of this study were to explore the relationship of daily stressful events and symptom severity in a prospective manner and to explore the roles of neuroticism, anxiety, depression and stress in the vicious circle of symptom perpetuation. A total of 49 patients with IBS reported their symptom severity and daily stressful events intensity each day for 14 consecutive days. They also completed the Big five personality inventory, the Beck Depression Inventory and the State-trait anxiety inventory. Cross-correlation analyses were performed on the time series data for daily stress and symptom severity for each participant separately. Four different patterns of relationships were found in different subgroups of participants: positive cross-correlations of symptom severity and stress intensity on the same day; higher symptom severity on days following stressful days; lower symptom severity on days following stressful days; and lower stress intensity on days following severe symptoms. Using average scores for daily stress and symptom severity, as well as scores for neuroticism, anxiety and depression, we performed a path analysis to test a model of symptom exacerbation. It showed that, on the group level, average stress intensity predicts average symptom severity. Neuroticism and anxiety were not significant predictors of symptom severity, while depression showed a marginally significant relationship with symptom severity, mediated by stress intensity. In conclusion, depression and daily stress seem to be important contributors to the vicious circle of IBS symptom perpetuation.","Síndrome del intestino irritable se considera un trastorno biopsicosocial, el resultado de la combinación compleja de factores predisponentes, precipitantes y perpetuos. Rasgos de personalidad, estado afectivo y estrés son algunos de los factores relevantes que contribuyen a la calidad de vida más baja y la exacerbación sintomática de los pacientes con SII. Para examinar el papel del estrés en la exacerbación sintomática de SII, el objetivo de este estudio era explorar la relación entre los acontecimientos cotidianos estresantes y la intensidad de los síntomas de forma prospectiva, tanto como explorar los papeles del neuroticismo, ansiedad, depresión y estrés en el círculo vicioso de perpetuación de los síntomas. Todos los 49 pacientes con SII informaron sobre la intensidad de los síntomas y la intensidad de los acontecimientos cotidianos estresantes cada día durante 14 días consecutivos. Además, completaron el Test de personalidad de los cinco grandes, Inventario de depresión de Beck e Inventario de ansiedad estado-rasgo. En los datos de series temporales se hizo el análisis de correlación cruzada para la intensidad del estrés diario y de los síntomas para cada participante por separado. Se encontraron cuatro patrones de relación diferentes en diferentes subgrupos de participantes: correlación cruzada positiva de la intensidad de los síntomas y del estrés el mismo día; intensidad de los síntomas más alta en los días después de los días estresantes; intensidad de los síntomas más baja en los días después de los días estresantes e intensidad del estrés más baja en los días después de los síntomas graves. Usando resultados promedios para el estrés diario y la intensidad de los síntomas, tanto como resultados para el neuroticismo, ansiedad y depresión, realizamos un análisis del camino para examinar el modelo de la exacerbación de los síntomas. Mostró que, al nivel de grupo, la intensidad del estrés promedia predice la intensidad de los síntomas promedia. Neuroticismo y ansiedad no eran predictores significativos de la intensidad de los síntomas, mientras que la depresión demostró una relación marginalmente significante con la intensidad de los síntomas, mediada por la intensidad del estrés. En conclusión, la depresión y el estrés diario parecen ser contribuidores importantes al círculo vicioso de la perpetuación de los síntomas SII."],"format":["application/pdf"],"id":"50|dedup_wf_001::054ea3bc3ccc386d150d900776e1070d","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::2e3d2c4f33a7a1f58bc6c81cacd21e9c","value":"Repository of the University of Rijeka, Faculty of Humanities and Social Sciences"},"hostedby":{"key":"10|opendoar____::2e3d2c4f33a7a1f58bc6c81cacd21e9c","value":"Repository of the University of Rijeka, Faculty of Humanities and Social Sciences"},"license":"http://creativecommons.org/licenses/by/4.0/","publicationdate":"2016-04-01","refereed":"UNKNOWN","type":"Article","url":["https://repository.ffri.uniri.hr/islandora/object/ffri:1182","https://urn.nsk.hr/urn:nbn:hr:186:701987","https://repository.ffri.uniri.hr/islandora/object/ffri:1182/datastream/FILE0"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::1c1d4df596d01da60385f0bb17a4a9e0","value":"HRČAK - Portal of scientific journals of Croatia"},"hostedby":{"key":"10|opendoar____::1c1d4df596d01da60385f0bb17a4a9e0","value":"HRČAK - Portal of scientific journals of Croatia"},"publicationdate":"2016-01-01","refereed":"UNKNOWN","type":"Other literature type","url":["https://hrcak.srce.hr/156331","https://hrcak.srce.hr/file/230444"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"},"hostedby":{"key":"10|doajarticles::23738aeeb586d9f9b652c75aaff54dd4","value":"Psychological Topics"},"publicationdate":"2016-04-01","refereed":"UNKNOWN","type":"Article","url":["http://pt.ffri.hr/index.php/pt/article/view/317","https://doaj.org/toc/1332-0742"]}],"language":{"code":"eng","label":"English"},"lastupdatetimestamp":1603727328518,"maintitle":"The role of stress in IBS symptom severity","originalId":["oai:repository.ffri.uniri.hr:ffri_1182","oai:hrcak.srce.hr:156331","oai:doaj.org/article:4394c5a4f62849ffac7ea485a91540a3"],"pid":[],"projects":[{"code":"009-0092660-2655","funder":{"jurisdiction":"HR","name":"Ministry of Science, Education and Sports of the Republic of Croatia (MSES)","shortName":"MZOS"},"id":"40|irb_hr______::ad496254144c27606e4058841e060fa0","provenance":{"provenance":"Harvested","trust":"0.900000000000000022"},"title":"Psychosomatic aspects of chronic functional and inflammatory bowel diseases"}],"publicationdate":"2016-04-01","subjects":[{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"irritable bowel syndrome"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"symptom severity"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"daily stress"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"depression"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"DRUŠTVENE ZNANOSTI. 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A set of model alloys with low nickel content, lower than 0.2 mass%, was used for the study. Copper and phosphorus contents were varied in a wide range: 0.005–0.99 and 0.002–0.039 mass%, respectively. Recovery efficiency has been estimated by the value of residual embrittlement after annealing, measured in terms of a shift in transition temperature (ΔTKres). A comparison of the results obtained on model alloys with data for VVER-440 RPV materials has also been carried out. Comparative analysis has confirmed the conclusion that ΔTKres is independent of phosphorus content while the effect of copper on ΔTKres is not significant for typical VVER-440 RPV materials with a typical range of Cu contents between 0.10 and 0.24 mass%. 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central problem for the function and manufacture of materials where performance relies on nanoscale structure is to control the compatibility and interactions of the building blocks. In natural materials, such as nacre, there are examples of multifunctional macromolecules that have combined binding affinities for different materials within the same molecule, thereby bridging these materials and acting as a molecular glue. Here, we describe the use of a designed multifunctional protein that is used for self-assembly of nanofibrillar cellulose. Recent advances in the production of cellulose nanofibrils have given inspiration for new uses of cellulosic materials. Cellulose nanofibrils have mechanical and structural features that open new possibilities for performance in composites and other nanoscale materials. Functionalisation was realised through a bi-functional fusion protein having both an ability to bind to cellulose and a second functionality of surface activity. The cellulose-binding function was obtained using cellulose-binding domains from cellulolytic enzymes and the surface activity through the use of a surface active protein called hydrophobin. Using the bi-functional protein, cellulose nanofibrils could be assembled into tightly packed thin films at the air/water interface and at the oil/water interface. It was shown that the combination of protein and cellulose nanofibrils resulted in a synergistic improvement in the formation and stability of oil-in-water emulsions resulting in emulsions that were stable for several months. The bi-functionality of the protein also allowed the binding of hydrophobic solid drug nanoparticles to cellulose nanofibrils and thereby improving their long-term stability under physiological conditions."}],"externalReference":[],"extraInfo":[],"format":[],"fulltext":[],"id":"50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb","instance":[{"accessright":{"classid":"CLOSED","classname":"Closed Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"collectedfrom":{"key":"10|openaire____::4692342f0992d91f9e705c26959f09e0","value":"VTT Research Information 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Ce qui nous frappe en premier lieu dans le roman de Melchior Mbonimpa, Le Totem des Baranda, c'est l'efficacité de sa fonction didactique. Le livre est porteur d'un message, d'une vision sur l'histoire de l'Afrique des Grands Lacs qu'on rencontre rarement dans l'actualité ou l'histoire immédiate que nous livrent les médias.

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

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

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

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

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dependence of the recovery of the transition temperature shift after annealing (475 °C, 100 h) on copper and phosphorus contents has been studied on irradiated reactor pressure vessel (RPV) materials. A set of model alloys with low nickel content, lower than 0.2 mass%, was used for the study. Copper and phosphorus contents were varied in a wide range: 0.005–0.99 and 0.002–0.039 mass%, respectively. Recovery efficiency has been estimated by the value of residual embrittlement after annealing, measured in terms of a shift in transition temperature (ΔTKres). A comparison of the results obtained on model alloys with data for VVER-440 RPV materials has also been carried out. Comparative analysis has confirmed the conclusion that ΔTKres is independent of phosphorus content while the effect of copper on ΔTKres is not significant for typical VVER-440 RPV materials with a typical range of Cu contents between 0.10 and 0.24 mass%. 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The bi-functionality of the protein also allowed the binding of hydrophobic solid drug nanoparticles to cellulose nanofibrils and thereby improving their long-term stability under physiological conditions."}],"externalReference":[],"extraInfo":[],"format":[],"fulltext":[],"id":"50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb","instance":[{"accessright":{"classid":"CLOSED","classname":"Closed Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"collectedfrom":{"key":"10|openaire____::4692342f0992d91f9e705c26959f09e0","value":"VTT Research Information 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Ce qui nous frappe en premier lieu dans le roman de Melchior Mbonimpa, Le Totem des Baranda, c'est l'efficacité de sa fonction didactique. Le livre est porteur d'un message, d'une vision sur l'histoire de l'Afrique des Grands Lacs qu'on rencontre rarement dans l'actualité ou l'histoire immédiate que nous livrent les médias.

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

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

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

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

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La NDI a été étudiée dans le cas de diverses applications, y compris en aéronautique et en aérospatiale. Elle permet de calculer des lois de contrôle capables de linéariser et de découpler un modèle non-linéaire à tout point de fonctionnement de son enveloppe d'état. Cependant cette méthode est intrinsèquement non-robuste aux erreurs de modélisation et aux saturations en entrée. En outre, dans un contexte non-linéaire, l'obtention d'une garantie quantifiable du domaine de stabilité atteint reste à l'heure actuelle complexe. Contrairement aux approches classiques de la NDI, notre méthodologie peut être considérée comme un cadre de compensation non-linéaire généralisé qui permet d'intégrer les incertitudes et les saturations en entrée dans le processus de conception. En utilisant des stratégies de contrôle antiwindup, la loi de pilotage peut être calculée grâce à un simple processus en deux phases. Dans ce cadre de travail généralisé des transformations linéaires fractionnaires (LFT - Linear Fractional Transformations) de la boucle fermée non-linéaire peuvent être facilement déduites pour l'analyse de la stabilité robuste en utilisant des outils standards pour de systèmes linéaires. La méthode proposée est testée pour le pilotage d'un véhicule de rentrée atmosphérique de type aile delta lors de ses phases hypersonique, transsonique et subsonique. Pour cette thèse, un simulateur du vol incluant divers facteurs externes ainsi que des erreurs de modélisation a été développé dans Simulink.\n\nThis thesis work is devoted to extending Nonlinear Dynamic Inversion (NDI) for a large scale of\nnonlinear systems while guaranteeing sufficient stability conditions. NDI has been studied in a wide range of applications, including aeronautics and aerospace. It allows to compute nonlinear control laws able to decouple and linearize a model at any operating point of its state envelope. 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Among them the Habitat (92/43/EC) and Bird Directives (79/409/EC), the Water Framework Directive (2000/60/EC), and the Noise Directive (2002/49/EC) have led to the evaluation/designation of areas in Europe with different criteria. In this study our goal was to understand how the ES capacity of an area is related to its designation and if areas with multiple designations have higher capacity in providing ES. We selected four catchments in Greece with a great variety of characteristics covering over 25% of the national territory. Inside the catchments we assessed the ES capacity (following the methodology of Burkhard et al. 2009) of areas designated as Natura 2000 sites, Quiet areas and Wetlands or Water bodies and found those areas that have multiple designations. Data were analyzed by GLM to reveal differences regarding the ES capacity among the different types of areas. We also investigated by PCA synergies and trade-offs among different kinds of ES and tested for correlations among landscape properties, such as elevation, aspect and slope and the ES potential. Our results show that areas with different types or multiple designations have a different capacity in providing ES. Areas of one designation type (Protected or Quiet Areas) had in general intermediate scores in most ES but scores were higher compared to areas with no designation, which displayed stronger capacity in provisioning services. Among Protected Areas and Quiet Areas the latter scored better in general. Areas that combined both designation types (Protected and Quiet Areas) showed the highest capacity in 13 out of 29 ES, that were mostly linked with natural and forest ecosystems. We found significant synergies among most regulating, supporting and cultural ES which in turn display trade-offs with provisioning services. The different ES are spatially related and display strong correlation with landscape properties, such as elevation and slope. We suggest that the designation status of an area can be used as an alternative tool for environmental policy, indicating the capacity for ES provision. Multiple designations of areas can be used as proxies for locating ES “hotspots”. 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Whereas there are several different web-based predictors for \u03b1-helical membrane proteins, currently there is no freely available prediction method for \u03b2-barrel membrane proteins, at least with an acceptable level of accuracy. We present here a web server (PRED-TMBB, http://bioinformatics.biol.uoa.gr/PRED-TMBB) which is capable of predicting the transmembrane strands and the topology of \u03b2-barrel outer membrane proteins of Gram-negative bacteria. The method is based on a Hidden Markov Model, trained according to the Conditional Maximum Likelihood criterion. The model was retrained and the training set now includes 16 non-homologous outer membrane proteins with structures known at atomic resolution. The user may submit one sequence at a time and has the option of choosing between three different decoding methods. 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tight-binding parameters via Slatet-Koster method with a very little effort. TBFIT is a scientific Fortran program for numerical tight-binding parameter fitting mainly based on Slater-Koster scheme and tight-binding calculations for the electronic band structures of given atomic and electronic configurations with a simple input interfaces. Basically TBFIT fits Slater-Koster parameters including scaling factors to your target first-principles band structure. For the fitting algorithm, Levenberg–Marquardt algorithm is used (implemented by modifying MINPACK library). You can taste how TBFIT works and its performance in Example section. Once you get proper tight-binding parameters, you can also calculate various Berry phase related quantities, such as Berry curvature, Zak phase, Wilson's loop (Z2 index, Wannier charge center), first Chern number, and so on. In addition, density of states, eigenstate charge density or wavefunction plot, STM simulations (integerated eigenstate density within certain energy window), band structures for edge/surface geometries, E-field effects, etc. You do not need to specify all the bond connections, instead, just provide hopping classes (whether it is 1st-, 2nd-, or 3rd-nearest-neighbor hopping) between atomic species and corresponding hopping parameter names in your input file. Then TBFIT automatically set up tight-binding hamiltonian based on your input geometry and tight-binding parameter setup as defined in input interfaces. In the future release, I will add some routines for the Green function approach to get the surface state (or edge spectrum as well) and the routines for the spin/mirror Chern number evaluation within the given tight-binding parameter and model hamiltonian. 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The result has largely been an unhappy marriage with uncertainties blamed more on the data than the process, although the data collection generally is detailed and comprehensive on catch and effort parameters. An extensive literature review of primary and grey literature on ecosystem drivers, exploitation pressures, and fish population and community states shows that Malawi has the necessary knowledge base for expanding their assessment into multi-causal and exploratory indicator-based methods that can assist in better understanding and more disciplined use of existing data and monitoring systems. Selection and ranking of a suite of indicators focusing on the major fisheries in the Southeast arm of Lake Malawi and Lake Malombe were done by a group of Malawian fisheries researchers and management advisers, thereby testing a framework of scoring criteria assessing an indicator's acceptability, observability, and relatedness to management. 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A visualization project that researches trends in military, healthcare, and education expenditures by government. This project uses the Google Charts API.

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b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql index 25776316b..da344d132 100755 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql @@ -84,87 +84,87 @@ from project_results r compute stats indi_funded_result_with_fundref; -create table indi_result_org_collab stored as parquet as -select o1.organization org1, o2.organization org2, count(distinct o1.id) as collaborations -from result_organization as o1 - join result_organization as o2 on o1.id=o2.id and o1.organization!=o2.organization -group by o1.organization, o2.organization; - -compute stats indi_result_org_collab; - -create table indi_result_org_country_collab stored as parquet as - with tmp as - (select o.id as id, o.country , ro.id as result,r.type from organization o - join result_organization ro on o.id=ro.organization - join result r on r.id=ro.id where o.country <> 'UNKNOWN') -select o1.id org1,o2.country country2, o1.type, count(distinct o1.result) as collaborations -from tmp as o1 - join tmp as o2 on o1.result=o2.result -where o1.id<>o2.id and o1.country<>o2.country -group by o1.id, o1.type,o2.country; - -compute stats indi_result_org_country_collab; - -create table indi_result_org_collab stored as parquet as - with tmp as - (select o.id, ro.id as result,r.type from organization o - join result_organization ro on o.id=ro.organization - join result r on r.id=ro.id) -select o1.id org1,o2.id org2, o1.type, count(distinct o1.result) as collaborations -from tmp as o1 - join tmp as o2 on o1.result=o2.result -where o1.id<>o2.id -group by o1.id, o2.id, o1.type; - -compute stats indi_result_org_collab; - -create table indi_project_collab_org stored as parquet as -select o1.id org1,o2.id org2, count(distinct o1.project) as collaborations -from organization_projects as o1 - join organization_projects as o2 on o1.project=o2.project -where o1.id!=o2.id -group by o1.id, o2.id; - -compute stats indi_project_collab_org; - -create table indi_project_collab_org_country stored as parquet as - with tmp as - (select o.id organization, o.country , ro.project as project from organization o - join organization_projects ro on o.id=ro.id - and o.country <> 'UNKNOWN') -select o1.organization org1,o2.country country2, count(distinct o1.project) as collaborations -from tmp as o1 - join tmp as o2 on o1.project=o2.project -where o1.organization<>o2.organization and o1.country<>o2.country -group by o1.organization, o2.country; - -compute stats indi_project_collab_org_country; - -create table indi_funder_country_collab stored as parquet as - with tmp as (select funder, project, country from organization_projects op - join organization o on o.id=op.id - join project p on p.id=op.project - where country <> 'UNKNOWN') -select f1.funder, f1.country as country1, f2.country as country2, count(distinct f1.project) as collaborations -from tmp as f1 - join tmp as f2 on f1.project=f2.project -where f1.country<>f2.country -group by f1.funder, f2.country, f1.country; - -compute stats indi_funder_country_collab; - -create table indi_result_country_collab stored as parquet as - with tmp as - (select country, ro.id as result,r.type from organization o - join result_organization ro on o.id=ro.organization - join result r on r.id=ro.id where country <> 'UNKNOWN') -select o1.country country1, o2.country country2, o1.type, count(distinct o1.result) as collaborations -from tmp as o1 - join tmp as o2 on o1.result=o2.result -where o1.country<>o2.country -group by o1.country, o2.country, o1.type; - -compute stats indi_result_country_collab; +-- create table indi_result_org_collab stored as parquet as +-- select o1.organization org1, o2.organization org2, count(distinct o1.id) as collaborations +-- from result_organization as o1 +-- join result_organization as o2 on o1.id=o2.id and o1.organization!=o2.organization +-- group by o1.organization, o2.organization; +-- +-- compute stats indi_result_org_collab; +-- +-- create table indi_result_org_country_collab stored as parquet as +-- with tmp as +-- (select o.id as id, o.country , ro.id as result,r.type from organization o +-- join result_organization ro on o.id=ro.organization +-- join result r on r.id=ro.id where o.country <> 'UNKNOWN') +-- select o1.id org1,o2.country country2, o1.type, count(distinct o1.result) as collaborations +-- from tmp as o1 +-- join tmp as o2 on o1.result=o2.result +-- where o1.id<>o2.id and o1.country<>o2.country +-- group by o1.id, o1.type,o2.country; +-- +-- compute stats indi_result_org_country_collab; +-- +-- create table indi_result_org_collab stored as parquet as +-- with tmp as +-- (select o.id, ro.id as result,r.type from organization o +-- join result_organization ro on o.id=ro.organization +-- join result r on r.id=ro.id) +-- select o1.id org1,o2.id org2, o1.type, count(distinct o1.result) as collaborations +-- from tmp as o1 +-- join tmp as o2 on o1.result=o2.result +-- where o1.id<>o2.id +-- group by o1.id, o2.id, o1.type; +-- +-- compute stats indi_result_org_collab; +-- +-- create table indi_project_collab_org stored as parquet as +-- select o1.id org1,o2.id org2, count(distinct o1.project) as collaborations +-- from organization_projects as o1 +-- join organization_projects as o2 on o1.project=o2.project +-- where o1.id!=o2.id +-- group by o1.id, o2.id; +-- +-- compute stats indi_project_collab_org; +-- +-- create table indi_project_collab_org_country stored as parquet as +-- with tmp as +-- (select o.id organization, o.country , ro.project as project from organization o +-- join organization_projects ro on o.id=ro.id +-- and o.country <> 'UNKNOWN') +-- select o1.organization org1,o2.country country2, count(distinct o1.project) as collaborations +-- from tmp as o1 +-- join tmp as o2 on o1.project=o2.project +-- where o1.organization<>o2.organization and o1.country<>o2.country +-- group by o1.organization, o2.country; +-- +-- compute stats indi_project_collab_org_country; +-- +-- create table indi_funder_country_collab stored as parquet as +-- with tmp as (select funder, project, country from organization_projects op +-- join organization o on o.id=op.id +-- join project p on p.id=op.project +-- where country <> 'UNKNOWN') +-- select f1.funder, f1.country as country1, f2.country as country2, count(distinct f1.project) as collaborations +-- from tmp as f1 +-- join tmp as f2 on f1.project=f2.project +-- where f1.country<>f2.country +-- group by f1.funder, f2.country, f1.country; +-- +-- compute stats indi_funder_country_collab; +-- +-- create table indi_result_country_collab stored as parquet as +-- with tmp as +-- (select country, ro.id as result,r.type from organization o +-- join result_organization ro on o.id=ro.organization +-- join result r on r.id=ro.id where country <> 'UNKNOWN') +-- select o1.country country1, o2.country country2, o1.type, count(distinct o1.result) as collaborations +-- from tmp as o1 +-- join tmp as o2 on o1.result=o2.result +-- where o1.country<>o2.country +-- group by o1.country, o2.country, o1.type; +-- +-- compute stats indi_result_country_collab; ---- Sprint 4 ---- create table indi_pub_diamond stored as parquet as 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 cc6b69e34..5aca19f6e 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 @@ -170,7 +170,7 @@ compute stats TARGET.indi_result_has_cc_licence; create table TARGET.indi_result_has_cc_licence_url stored as parquet as select * from SOURCE.indi_result_has_cc_licence_url orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_result_has_cc_licence_url; -create view TARGET.indi_funder_country_collab as select * from SOURCE.indi_funder_country_collab; +-- create view TARGET.indi_funder_country_collab as select * from SOURCE.indi_funder_country_collab; create table TARGET.indi_result_with_orcid stored as parquet as select * from SOURCE.indi_result_with_orcid orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_result_with_orcid; From fcef5294e21c8a0c5ba4afcae03a460f8e1ea6fb Mon Sep 17 00:00:00 2001 From: Antonis Lempesis Date: Fri, 5 Aug 2022 13:45:01 +0300 Subject: [PATCH 33/33] restored some collab indicators --- .../scripts/step16-createIndicatorsTables.sql | 68 +++++++++---------- .../scripts/step20-createMonitorDB.sql | 4 +- 2 files changed, 37 insertions(+), 35 deletions(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql index da344d132..2581f1d64 100755 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql @@ -118,40 +118,40 @@ compute stats indi_funded_result_with_fundref; -- -- compute stats indi_result_org_collab; -- --- create table indi_project_collab_org stored as parquet as --- select o1.id org1,o2.id org2, count(distinct o1.project) as collaborations --- from organization_projects as o1 --- join organization_projects as o2 on o1.project=o2.project --- where o1.id!=o2.id --- group by o1.id, o2.id; --- --- compute stats indi_project_collab_org; --- --- create table indi_project_collab_org_country stored as parquet as --- with tmp as --- (select o.id organization, o.country , ro.project as project from organization o --- join organization_projects ro on o.id=ro.id --- and o.country <> 'UNKNOWN') --- select o1.organization org1,o2.country country2, count(distinct o1.project) as collaborations --- from tmp as o1 --- join tmp as o2 on o1.project=o2.project --- where o1.organization<>o2.organization and o1.country<>o2.country --- group by o1.organization, o2.country; --- --- compute stats indi_project_collab_org_country; --- --- create table indi_funder_country_collab stored as parquet as --- with tmp as (select funder, project, country from organization_projects op --- join organization o on o.id=op.id --- join project p on p.id=op.project --- where country <> 'UNKNOWN') --- select f1.funder, f1.country as country1, f2.country as country2, count(distinct f1.project) as collaborations --- from tmp as f1 --- join tmp as f2 on f1.project=f2.project --- where f1.country<>f2.country --- group by f1.funder, f2.country, f1.country; --- --- compute stats indi_funder_country_collab; +create table indi_project_collab_org stored as parquet as +select o1.id org1,o2.id org2, count(distinct o1.project) as collaborations +from organization_projects as o1 + join organization_projects as o2 on o1.project=o2.project +where o1.id!=o2.id +group by o1.id, o2.id; + +compute stats indi_project_collab_org; + +create table indi_project_collab_org_country stored as parquet as + with tmp as + (select o.id organization, o.country , ro.project as project from organization o + join organization_projects ro on o.id=ro.id + and o.country <> 'UNKNOWN') +select o1.organization org1,o2.country country2, count(distinct o1.project) as collaborations +from tmp as o1 + join tmp as o2 on o1.project=o2.project +where o1.organization<>o2.organization and o1.country<>o2.country +group by o1.organization, o2.country; + +compute stats indi_project_collab_org_country; + +create table indi_funder_country_collab stored as parquet as + with tmp as (select funder, project, country from organization_projects op + join organization o on o.id=op.id + join project p on p.id=op.project + where country <> 'UNKNOWN') +select f1.funder, f1.country as country1, f2.country as country2, count(distinct f1.project) as collaborations +from tmp as f1 + join tmp as f2 on f1.project=f2.project +where f1.country<>f2.country +group by f1.funder, f2.country, f1.country; + +compute stats indi_funder_country_collab; -- -- create table indi_result_country_collab stored as parquet as -- with tmp as 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 5aca19f6e..d78895198 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 @@ -170,7 +170,9 @@ compute stats TARGET.indi_result_has_cc_licence; create table TARGET.indi_result_has_cc_licence_url stored as parquet as select * from SOURCE.indi_result_has_cc_licence_url orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_result_has_cc_licence_url; --- create view TARGET.indi_funder_country_collab as select * from SOURCE.indi_funder_country_collab; +create view TARGET.indi_funder_country_collab as select * from SOURCE.indi_funder_country_collab; +create view TARGET.indi_project_collab_org as select * from SOURCE.indi_project_collab_org; +create view TARGET.indi_project_collab_org_country as select * from SOURCE.indi_project_collab_org_country; create table TARGET.indi_result_with_orcid stored as parquet as select * from SOURCE.indi_result_with_orcid orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_result_with_orcid;