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merge with upstream

This commit is contained in:
Miriam Baglioni 2020-04-27 10:43:59 +02:00
parent 7b6505ec69 fad94c2155
commit 5dccbe13db
38 changed files with 1242 additions and 683 deletions
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40
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java Normal file
View File

@ -0,0 +1,40 @@
package eu.dnetlib.dhp.schema.common;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
public class ModelConstants {
public static final String DNET_RESULT_TYPOLOGIES = "dnet:result_typologies";
public static final String DATASET_RESULTTYPE_CLASSID = "dataset";
public static final String PUBLICATION_RESULTTYPE_CLASSID = "publication";
public static final String SOFTWARE_RESULTTYPE_CLASSID = "software";
public static final String ORP_RESULTTYPE_CLASSID = "other";
public static Qualifier PUBLICATION_DEFAULT_RESULTTYPE = new Qualifier();
public static Qualifier DATASET_DEFAULT_RESULTTYPE = new Qualifier();
public static Qualifier SOFTWARE_DEFAULT_RESULTTYPE = new Qualifier();
public static Qualifier ORP_DEFAULT_RESULTTYPE = new Qualifier();
static {
PUBLICATION_DEFAULT_RESULTTYPE.setClassid(PUBLICATION_RESULTTYPE_CLASSID);
PUBLICATION_DEFAULT_RESULTTYPE.setClassname(PUBLICATION_RESULTTYPE_CLASSID);
PUBLICATION_DEFAULT_RESULTTYPE.setSchemeid(DNET_RESULT_TYPOLOGIES);
PUBLICATION_DEFAULT_RESULTTYPE.setSchemename(DNET_RESULT_TYPOLOGIES);
DATASET_DEFAULT_RESULTTYPE.setClassid(DATASET_RESULTTYPE_CLASSID);
DATASET_DEFAULT_RESULTTYPE.setClassname(DATASET_RESULTTYPE_CLASSID);
DATASET_DEFAULT_RESULTTYPE.setSchemeid(DNET_RESULT_TYPOLOGIES);
DATASET_DEFAULT_RESULTTYPE.setSchemename(DNET_RESULT_TYPOLOGIES);
SOFTWARE_DEFAULT_RESULTTYPE.setClassid(SOFTWARE_RESULTTYPE_CLASSID);
SOFTWARE_DEFAULT_RESULTTYPE.setClassname(SOFTWARE_RESULTTYPE_CLASSID);
SOFTWARE_DEFAULT_RESULTTYPE.setSchemeid(DNET_RESULT_TYPOLOGIES);
SOFTWARE_DEFAULT_RESULTTYPE.setSchemename(DNET_RESULT_TYPOLOGIES);
ORP_DEFAULT_RESULTTYPE.setClassid(ORP_RESULTTYPE_CLASSID);
ORP_DEFAULT_RESULTTYPE.setClassname(ORP_RESULTTYPE_CLASSID);
ORP_DEFAULT_RESULTTYPE.setSchemeid(DNET_RESULT_TYPOLOGIES);
ORP_DEFAULT_RESULTTYPE.setSchemename(DNET_RESULT_TYPOLOGIES);
}
}

64
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelSupport.java
View File

@ -3,6 +3,8 @@ package eu.dnetlib.dhp.schema.common;
import com.google.common.collect.Maps; import com.google.common.collect.Maps;
import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.*;
import java.util.Map; import java.util.Map;
import java.util.Optional;
import java.util.function.Function;
/** Oaf model utility methods. */ /** Oaf model utility methods. */
public class ModelSupport { public class ModelSupport {
@ -146,4 +148,66 @@ public class ModelSupport {
entityMapping.get(EntityType.valueOf(sourceType)).name(), entityMapping.get(EntityType.valueOf(sourceType)).name(),
entityMapping.get(EntityType.valueOf(targetType)).name()); entityMapping.get(EntityType.valueOf(targetType)).name());
} }
public static <T extends Oaf> Function<T, String> idFn() {
return x -> {
if (isSubClass(x, Relation.class)) {
return idFnForRelation(x);
}
return idFnForOafEntity(x);
};
}
private static <T extends Oaf> String idFnForRelation(T t) {
Relation r = (Relation) t;
return Optional.ofNullable(r.getSource())
.map(
source ->
Optional.ofNullable(r.getTarget())
.map(
target ->
Optional.ofNullable(r.getRelType())
.map(
relType ->
Optional.ofNullable(
r
.getSubRelType())
.map(
subRelType ->
Optional
.ofNullable(
r
.getRelClass())
.map(
relClass ->
String
.join(
source,
target,
relType,
subRelType,
relClass))
.orElse(
String
.join(
source,
target,
relType,
subRelType)))
.orElse(
String
.join(
source,
target,
relType)))
.orElse(
String.join(
source, target)))
.orElse(source))
.orElse(null);
}
private static <T extends Oaf> String idFnForOafEntity(T t) {
return ((OafEntity) t).getId();
}
} }

34
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Dataset.java
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@ -1,8 +1,8 @@
package eu.dnetlib.dhp.schema.oaf; package eu.dnetlib.dhp.schema.oaf;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import java.io.Serializable; import java.io.Serializable;
import java.util.List; import java.util.List;
import java.util.Objects;
public class Dataset extends Result implements Serializable { public class Dataset extends Result implements Serializable {
@ -20,6 +20,10 @@ public class Dataset extends Result implements Serializable {
private List<GeoLocation> geolocation; private List<GeoLocation> geolocation;
public Dataset() {
setResulttype(ModelConstants.DATASET_DEFAULT_RESULTTYPE);
}
public Field<String> getStoragedate() { public Field<String> getStoragedate() {
return storagedate; return storagedate;
} }
@ -111,32 +115,4 @@ public class Dataset extends Result implements Serializable {
mergeOAFDataInfo(d); mergeOAFDataInfo(d);
} }
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
if (!super.equals(o)) return false;
Dataset dataset = (Dataset) o;
return Objects.equals(storagedate, dataset.storagedate)
&& Objects.equals(device, dataset.device)
&& Objects.equals(size, dataset.size)
&& Objects.equals(version, dataset.version)
&& Objects.equals(lastmetadataupdate, dataset.lastmetadataupdate)
&& Objects.equals(metadataversionnumber, dataset.metadataversionnumber)
&& Objects.equals(geolocation, dataset.geolocation);
}
@Override
public int hashCode() {
return Objects.hash(
super.hashCode(),
storagedate,
device,
size,
version,
lastmetadataupdate,
metadataversionnumber,
geolocation);
}
} }

85
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Datasource.java
View File

@ -2,7 +2,6 @@ package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable; import java.io.Serializable;
import java.util.List; import java.util.List;
import java.util.Objects;
public class Datasource extends OafEntity implements Serializable { public class Datasource extends OafEntity implements Serializable {
@ -512,88 +511,4 @@ public class Datasource extends OafEntity implements Serializable {
mergeOAFDataInfo(e); mergeOAFDataInfo(e);
} }
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
if (!super.equals(o)) return false;
Datasource that = (Datasource) o;
return Objects.equals(datasourcetype, that.datasourcetype)
&& Objects.equals(openairecompatibility, that.openairecompatibility)
&& Objects.equals(officialname, that.officialname)
&& Objects.equals(englishname, that.englishname)
&& Objects.equals(websiteurl, that.websiteurl)
&& Objects.equals(logourl, that.logourl)
&& Objects.equals(contactemail, that.contactemail)
&& Objects.equals(namespaceprefix, that.namespaceprefix)
&& Objects.equals(latitude, that.latitude)
&& Objects.equals(longitude, that.longitude)
&& Objects.equals(dateofvalidation, that.dateofvalidation)
&& Objects.equals(description, that.description)
&& Objects.equals(subjects, that.subjects)
&& Objects.equals(odnumberofitems, that.odnumberofitems)
&& Objects.equals(odnumberofitemsdate, that.odnumberofitemsdate)
&& Objects.equals(odpolicies, that.odpolicies)
&& Objects.equals(odlanguages, that.odlanguages)
&& Objects.equals(odcontenttypes, that.odcontenttypes)
&& Objects.equals(accessinfopackage, that.accessinfopackage)
&& Objects.equals(releasestartdate, that.releasestartdate)
&& Objects.equals(releaseenddate, that.releaseenddate)
&& Objects.equals(missionstatementurl, that.missionstatementurl)
&& Objects.equals(dataprovider, that.dataprovider)
&& Objects.equals(serviceprovider, that.serviceprovider)
&& Objects.equals(databaseaccesstype, that.databaseaccesstype)
&& Objects.equals(datauploadtype, that.datauploadtype)
&& Objects.equals(databaseaccessrestriction, that.databaseaccessrestriction)
&& Objects.equals(datauploadrestriction, that.datauploadrestriction)
&& Objects.equals(versioning, that.versioning)
&& Objects.equals(citationguidelineurl, that.citationguidelineurl)
&& Objects.equals(qualitymanagementkind, that.qualitymanagementkind)
&& Objects.equals(pidsystems, that.pidsystems)
&& Objects.equals(certificates, that.certificates)
&& Objects.equals(policies, that.policies)
&& Objects.equals(journal, that.journal);
}
@Override
public int hashCode() {
return Objects.hash(
super.hashCode(),
datasourcetype,
openairecompatibility,
officialname,
englishname,
websiteurl,
logourl,
contactemail,
namespaceprefix,
latitude,
longitude,
dateofvalidation,
description,
subjects,
odnumberofitems,
odnumberofitemsdate,
odpolicies,
odlanguages,
odcontenttypes,
accessinfopackage,
releasestartdate,
releaseenddate,
missionstatementurl,
dataprovider,
serviceprovider,
databaseaccesstype,
datauploadtype,
databaseaccessrestriction,
datauploadrestriction,
versioning,
citationguidelineurl,
qualitymanagementkind,
pidsystems,
certificates,
policies,
journal);
}
} }

20
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java
View File

@ -113,27 +113,11 @@ public abstract class OafEntity extends Oaf implements Serializable {
if (o == null || getClass() != o.getClass()) return false; if (o == null || getClass() != o.getClass()) return false;
if (!super.equals(o)) return false; if (!super.equals(o)) return false;
OafEntity oafEntity = (OafEntity) o; OafEntity oafEntity = (OafEntity) o;
return Objects.equals(id, oafEntity.id) return Objects.equals(id, oafEntity.id);
&& Objects.equals(originalId, oafEntity.originalId)
&& Objects.equals(collectedfrom, oafEntity.collectedfrom)
&& Objects.equals(pid, oafEntity.pid)
&& Objects.equals(dateofcollection, oafEntity.dateofcollection)
&& Objects.equals(dateoftransformation, oafEntity.dateoftransformation)
&& Objects.equals(extraInfo, oafEntity.extraInfo)
&& Objects.equals(oaiprovenance, oafEntity.oaiprovenance);
} }
@Override @Override
public int hashCode() { public int hashCode() {
return Objects.hash( return Objects.hash(super.hashCode(), id);
super.hashCode(),
id,
originalId,
collectedfrom,
pid,
dateofcollection,
dateoftransformation,
extraInfo,
oaiprovenance);
} }
} }

49
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Organization.java
View File

@ -2,7 +2,6 @@ package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable; import java.io.Serializable;
import java.util.List; import java.util.List;
import java.util.Objects;
public class Organization extends OafEntity implements Serializable { public class Organization extends OafEntity implements Serializable {
@ -233,52 +232,4 @@ public class Organization extends OafEntity implements Serializable {
country = o.getCountry() != null && compareTrust(this, e) < 0 ? o.getCountry() : country; country = o.getCountry() != null && compareTrust(this, e) < 0 ? o.getCountry() : country;
mergeOAFDataInfo(o); mergeOAFDataInfo(o);
} }
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
if (!super.equals(o)) return false;
Organization that = (Organization) o;
return Objects.equals(legalshortname, that.legalshortname)
&& Objects.equals(legalname, that.legalname)
&& Objects.equals(alternativeNames, that.alternativeNames)
&& Objects.equals(websiteurl, that.websiteurl)
&& Objects.equals(logourl, that.logourl)
&& Objects.equals(eclegalbody, that.eclegalbody)
&& Objects.equals(eclegalperson, that.eclegalperson)
&& Objects.equals(ecnonprofit, that.ecnonprofit)
&& Objects.equals(ecresearchorganization, that.ecresearchorganization)
&& Objects.equals(echighereducation, that.echighereducation)
&& Objects.equals(
ecinternationalorganizationeurinterests,
that.ecinternationalorganizationeurinterests)
&& Objects.equals(ecinternationalorganization, that.ecinternationalorganization)
&& Objects.equals(ecenterprise, that.ecenterprise)
&& Objects.equals(ecsmevalidated, that.ecsmevalidated)
&& Objects.equals(ecnutscode, that.ecnutscode)
&& Objects.equals(country, that.country);
}
@Override
public int hashCode() {
return Objects.hash(
super.hashCode(),
legalshortname,
legalname,
alternativeNames,
websiteurl,
logourl,
eclegalbody,
eclegalperson,
ecnonprofit,
ecresearchorganization,
echighereducation,
ecinternationalorganizationeurinterests,
ecinternationalorganization,
ecenterprise,
ecsmevalidated,
ecnutscode,
country);
}
} }

22
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OtherResearchProduct.java
View File

@ -1,8 +1,8 @@
package eu.dnetlib.dhp.schema.oaf; package eu.dnetlib.dhp.schema.oaf;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import java.io.Serializable; import java.io.Serializable;
import java.util.List; import java.util.List;
import java.util.Objects;
public class OtherResearchProduct extends Result implements Serializable { public class OtherResearchProduct extends Result implements Serializable {
@ -12,6 +12,10 @@ public class OtherResearchProduct extends Result implements Serializable {
private List<Field<String>> tool; private List<Field<String>> tool;
public OtherResearchProduct() {
setResulttype(ModelConstants.ORP_DEFAULT_RESULTTYPE);
}
public List<Field<String>> getContactperson() { public List<Field<String>> getContactperson() {
return contactperson; return contactperson;
} }
@ -51,20 +55,4 @@ public class OtherResearchProduct extends Result implements Serializable {
tool = mergeLists(tool, o.getTool()); tool = mergeLists(tool, o.getTool());
mergeOAFDataInfo(e); mergeOAFDataInfo(e);
} }
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
if (!super.equals(o)) return false;
OtherResearchProduct that = (OtherResearchProduct) o;
return Objects.equals(contactperson, that.contactperson)
&& Objects.equals(contactgroup, that.contactgroup)
&& Objects.equals(tool, that.tool);
}
@Override
public int hashCode() {
return Objects.hash(super.hashCode(), contactperson, contactgroup, tool);
}
} }

67
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Project.java
View File

@ -2,7 +2,6 @@ package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable; import java.io.Serializable;
import java.util.List; import java.util.List;
import java.util.Objects;
public class Project extends OafEntity implements Serializable { public class Project extends OafEntity implements Serializable {
@ -352,70 +351,4 @@ public class Project extends OafEntity implements Serializable {
: fundedamount; : fundedamount;
mergeOAFDataInfo(e); mergeOAFDataInfo(e);
} }
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
if (!super.equals(o)) return false;
Project project = (Project) o;
return Objects.equals(websiteurl, project.websiteurl)
&& Objects.equals(code, project.code)
&& Objects.equals(acronym, project.acronym)
&& Objects.equals(title, project.title)
&& Objects.equals(startdate, project.startdate)
&& Objects.equals(enddate, project.enddate)
&& Objects.equals(callidentifier, project.callidentifier)
&& Objects.equals(keywords, project.keywords)
&& Objects.equals(duration, project.duration)
&& Objects.equals(ecsc39, project.ecsc39)
&& Objects.equals(oamandatepublications, project.oamandatepublications)
&& Objects.equals(ecarticle29_3, project.ecarticle29_3)
&& Objects.equals(subjects, project.subjects)
&& Objects.equals(fundingtree, project.fundingtree)
&& Objects.equals(contracttype, project.contracttype)
&& Objects.equals(optional1, project.optional1)
&& Objects.equals(optional2, project.optional2)
&& Objects.equals(jsonextrainfo, project.jsonextrainfo)
&& Objects.equals(contactfullname, project.contactfullname)
&& Objects.equals(contactfax, project.contactfax)
&& Objects.equals(contactphone, project.contactphone)
&& Objects.equals(contactemail, project.contactemail)
&& Objects.equals(summary, project.summary)
&& Objects.equals(currency, project.currency)
&& Objects.equals(totalcost, project.totalcost)
&& Objects.equals(fundedamount, project.fundedamount);
}
@Override
public int hashCode() {
return Objects.hash(
super.hashCode(),
websiteurl,
code,
acronym,
title,
startdate,
enddate,
callidentifier,
keywords,
duration,
ecsc39,
oamandatepublications,
ecarticle29_3,
subjects,
fundingtree,
contracttype,
optional1,
optional2,
jsonextrainfo,
contactfullname,
contactfax,
contactphone,
contactemail,
summary,
currency,
totalcost,
fundedamount);
}
} }

20
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Publication.java
View File

@ -1,13 +1,17 @@
package eu.dnetlib.dhp.schema.oaf; package eu.dnetlib.dhp.schema.oaf;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import java.io.Serializable; import java.io.Serializable;
import java.util.Objects;
public class Publication extends Result implements Serializable { public class Publication extends Result implements Serializable {
// publication specific // publication specific
private Journal journal; private Journal journal;
public Publication() {
setResulttype(ModelConstants.PUBLICATION_DEFAULT_RESULTTYPE);
}
public Journal getJournal() { public Journal getJournal() {
return journal; return journal;
} }
@ -29,18 +33,4 @@ public class Publication extends Result implements Serializable {
if (p.getJournal() != null && compareTrust(this, e) < 0) journal = p.getJournal(); if (p.getJournal() != null && compareTrust(this, e) < 0) journal = p.getJournal();
mergeOAFDataInfo(e); mergeOAFDataInfo(e);
} }
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
if (!super.equals(o)) return false;
Publication that = (Publication) o;
return Objects.equals(journal, that.journal);
}
@Override
public int hashCode() {
return Objects.hash(super.hashCode(), journal);
}
} }

60
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java
View File

@ -3,7 +3,6 @@ package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable; import java.io.Serializable;
import java.util.Comparator; import java.util.Comparator;
import java.util.List; import java.util.List;
import java.util.Objects;
public class Result extends OafEntity implements Serializable { public class Result extends OafEntity implements Serializable {
@ -231,6 +230,9 @@ public class Result extends OafEntity implements Serializable {
instance = mergeLists(instance, r.getInstance()); instance = mergeLists(instance, r.getInstance());
if (r.getBestaccessright() != null && compareTrust(this, r) < 0)
bestaccessright = r.getBestaccessright();
if (r.getResulttype() != null && compareTrust(this, r) < 0) resulttype = r.getResulttype(); if (r.getResulttype() != null && compareTrust(this, r) < 0) resulttype = r.getResulttype();
if (r.getLanguage() != null && compareTrust(this, r) < 0) language = r.getLanguage(); if (r.getLanguage() != null && compareTrust(this, r) < 0) language = r.getLanguage();
@ -286,60 +288,4 @@ public class Result extends OafEntity implements Serializable {
} }
return a.size() > b.size() ? a : b; return a.size() > b.size() ? a : b;
} }
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
if (!super.equals(o)) return false;
Result result = (Result) o;
return Objects.equals(author, result.author)
&& Objects.equals(resulttype, result.resulttype)
&& Objects.equals(language, result.language)
&& Objects.equals(country, result.country)
&& Objects.equals(subject, result.subject)
&& Objects.equals(title, result.title)
&& Objects.equals(relevantdate, result.relevantdate)
&& Objects.equals(description, result.description)
&& Objects.equals(dateofacceptance, result.dateofacceptance)
&& Objects.equals(publisher, result.publisher)
&& Objects.equals(embargoenddate, result.embargoenddate)
&& Objects.equals(source, result.source)
&& Objects.equals(fulltext, result.fulltext)
&& Objects.equals(format, result.format)
&& Objects.equals(contributor, result.contributor)
&& Objects.equals(resourcetype, result.resourcetype)
&& Objects.equals(coverage, result.coverage)
&& Objects.equals(bestaccessright, result.bestaccessright)
&& Objects.equals(context, result.context)
&& Objects.equals(externalReference, result.externalReference)
&& Objects.equals(instance, result.instance);
}
@Override
public int hashCode() {
return Objects.hash(
super.hashCode(),
author,
resulttype,
language,
country,
subject,
title,
relevantdate,
description,
dateofacceptance,
publisher,
embargoenddate,
source,
fulltext,
format,
contributor,
resourcetype,
coverage,
bestaccessright,
context,
externalReference,
instance);
}
} }

28
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Software.java
View File

@ -1,8 +1,8 @@
package eu.dnetlib.dhp.schema.oaf; package eu.dnetlib.dhp.schema.oaf;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import java.io.Serializable; import java.io.Serializable;
import java.util.List; import java.util.List;
import java.util.Objects;
public class Software extends Result implements Serializable { public class Software extends Result implements Serializable {
@ -14,6 +14,10 @@ public class Software extends Result implements Serializable {
private Qualifier programmingLanguage; private Qualifier programmingLanguage;
public Software() {
setResulttype(ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE);
}
public List<Field<String>> getDocumentationUrl() { public List<Field<String>> getDocumentationUrl() {
return documentationUrl; return documentationUrl;
} }
@ -71,26 +75,4 @@ public class Software extends Result implements Serializable {
mergeOAFDataInfo(e); mergeOAFDataInfo(e);
} }
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
if (!super.equals(o)) return false;
Software software = (Software) o;
return Objects.equals(documentationUrl, software.documentationUrl)
&& Objects.equals(license, software.license)
&& Objects.equals(codeRepositoryUrl, software.codeRepositoryUrl)
&& Objects.equals(programmingLanguage, software.programmingLanguage);
}
@Override
public int hashCode() {
return Objects.hash(
super.hashCode(),
documentationUrl,
license,
codeRepositoryUrl,
programmingLanguage);
}
} }

68
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJob.java
View File

@ -166,10 +166,8 @@ public class PromoteActionPayloadForGraphTableJob {
actionPayloadClazz.getSimpleName(), actionPayloadClazz.getSimpleName(),
rowClazz.getSimpleName()); rowClazz.getSimpleName());
SerializableSupplier<Function<G, String>> rowIdFn = SerializableSupplier<Function<G, String>> rowIdFn = ModelSupport::idFn;
PromoteActionPayloadForGraphTableJob::idFn; SerializableSupplier<Function<A, String>> actionPayloadIdFn = ModelSupport::idFn;
SerializableSupplier<Function<A, String>> actionPayloadIdFn =
PromoteActionPayloadForGraphTableJob::idFn;
SerializableSupplier<BiFunction<G, A, G>> mergeRowWithActionPayloadAndGetFn = SerializableSupplier<BiFunction<G, A, G>> mergeRowWithActionPayloadAndGetFn =
MergeAndGet.functionFor(strategy); MergeAndGet.functionFor(strategy);
SerializableSupplier<BiFunction<G, G, G>> mergeRowsAndGetFn = SerializableSupplier<BiFunction<G, G, G>> mergeRowsAndGetFn =
@ -192,68 +190,6 @@ public class PromoteActionPayloadForGraphTableJob {
joinedAndMerged, rowIdFn, mergeRowsAndGetFn, zeroFn, isNotZeroFn, rowClazz); joinedAndMerged, rowIdFn, mergeRowsAndGetFn, zeroFn, isNotZeroFn, rowClazz);
} }
private static <T extends Oaf> Function<T, String> idFn() {
return x -> {
if (isSubClass(x, Relation.class)) {
return idFnForRelation(x);
}
return idFnForOafEntity(x);
};
}
private static <T extends Oaf> String idFnForRelation(T t) {
Relation r = (Relation) t;
return Optional.ofNullable(r.getSource())
.map(
source ->
Optional.ofNullable(r.getTarget())
.map(
target ->
Optional.ofNullable(r.getRelType())
.map(
relType ->
Optional.ofNullable(
r
.getSubRelType())
.map(
subRelType ->
Optional
.ofNullable(
r
.getRelClass())
.map(
relClass ->
String
.join(
source,
target,
relType,
subRelType,
relClass))
.orElse(
String
.join(
source,
target,
relType,
subRelType)))
.orElse(
String
.join(
source,
target,
relType)))
.orElse(
String.join(
source, target)))
.orElse(source))
.orElse(null);
}
private static <T extends Oaf> String idFnForOafEntity(T t) {
return ((OafEntity) t).getId();
}
private static <T extends Oaf> SerializableSupplier<T> zeroFn(Class<T> clazz) { private static <T extends Oaf> SerializableSupplier<T> zeroFn(Class<T> clazz) {
switch (clazz.getCanonicalName()) { switch (clazz.getCanonicalName()) {
case "eu.dnetlib.dhp.schema.oaf.Dataset": case "eu.dnetlib.dhp.schema.oaf.Dataset":

53
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java
View File

@ -25,6 +25,7 @@ public class DedupRecordFactory {
public static <T extends OafEntity> Dataset<T> createDedupRecord( public static <T extends OafEntity> Dataset<T> createDedupRecord(
final SparkSession spark, final SparkSession spark,
final DataInfo dataInfo,
final String mergeRelsInputPath, final String mergeRelsInputPath,
final String entitiesInputPath, final String entitiesInputPath,
final Class<T> clazz) { final Class<T> clazz) {
@ -67,41 +68,39 @@ public class DedupRecordFactory {
Encoders.STRING()) Encoders.STRING())
.mapGroups( .mapGroups(
(MapGroupsFunction<String, Tuple2<String, T>, T>) (MapGroupsFunction<String, Tuple2<String, T>, T>)
(key, values) -> entityMerger(key, values, ts, clazz), (key, values) -> entityMerger(key, values, ts, dataInfo),
Encoders.bean(clazz)); Encoders.bean(clazz));
} }
private static <T extends OafEntity> T entityMerger( private static <T extends OafEntity> T entityMerger(
String id, Iterator<Tuple2<String, T>> entities, long ts, Class<T> clazz) { String id, Iterator<Tuple2<String, T>> entities, long ts, DataInfo dataInfo) {
try {
T entity = clazz.newInstance();
entity.setId(id);
entity.setDataInfo(new DataInfo());
entity.getDataInfo().setTrust("0.9");
entity.setLastupdatetimestamp(ts);
final Collection<String> dates = Lists.newArrayList(); T entity = entities.next()._2();
entities.forEachRemaining(
t -> {
T duplicate = t._2();
entity.mergeFrom(duplicate);
if (ModelSupport.isSubClass(duplicate, Result.class)) {
Result r1 = (Result) duplicate;
Result er = (Result) entity;
er.setAuthor(DedupUtility.mergeAuthor(er.getAuthor(), r1.getAuthor()));
if (er.getDateofacceptance() != null) { final Collection<String> dates = Lists.newArrayList();
dates.add(r1.getDateofacceptance().getValue()); entities.forEachRemaining(
} t -> {
T duplicate = t._2();
entity.mergeFrom(duplicate);
if (ModelSupport.isSubClass(duplicate, Result.class)) {
Result r1 = (Result) duplicate;
Result er = (Result) entity;
er.setAuthor(DedupUtility.mergeAuthor(er.getAuthor(), r1.getAuthor()));
if (r1.getDateofacceptance() != null) {
dates.add(r1.getDateofacceptance().getValue());
} }
}); }
});
if (ModelSupport.isSubClass(entity, Result.class)) { if (ModelSupport.isSubClass(entity, Result.class)) {
((Result) entity).setDateofacceptance(DatePicker.pick(dates)); ((Result) entity).setDateofacceptance(DatePicker.pick(dates));
}
return entity;
} catch (IllegalAccessException | InstantiationException e) {
throw new RuntimeException(e);
} }
entity.setId(id);
entity.setLastupdatetimestamp(ts);
entity.setDataInfo(dataInfo);
return entity;
} }
} }

29
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java
View File

@ -3,7 +3,9 @@ package eu.dnetlib.dhp.oa.dedup;
import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.common.EntityType; import eu.dnetlib.dhp.schema.common.EntityType;
import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.OafEntity; import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
@ -21,6 +23,10 @@ public class SparkCreateDedupRecord extends AbstractSparkAction {
private static final Logger log = LoggerFactory.getLogger(SparkCreateDedupRecord.class); private static final Logger log = LoggerFactory.getLogger(SparkCreateDedupRecord.class);
public static final String ROOT_TRUST = "0.8";
public static final String PROVENANCE_ACTION_CLASS = "sysimport:dedup";
public static final String PROVENANCE_ACTIONS = "dnet:provenanceActions";
public SparkCreateDedupRecord(ArgumentApplicationParser parser, SparkSession spark) { public SparkCreateDedupRecord(ArgumentApplicationParser parser, SparkSession spark) {
super(parser, spark); super(parser, spark);
} }
@ -67,13 +73,30 @@ public class SparkCreateDedupRecord extends AbstractSparkAction {
DedupUtility.createMergeRelPath(workingPath, actionSetId, subEntity); DedupUtility.createMergeRelPath(workingPath, actionSetId, subEntity);
final String entityPath = DedupUtility.createEntityPath(graphBasePath, subEntity); final String entityPath = DedupUtility.createEntityPath(graphBasePath, subEntity);
Class<OafEntity> clazz = ModelSupport.entityTypes.get(EntityType.valueOf(subEntity)); final Class<OafEntity> clazz =
ModelSupport.entityTypes.get(EntityType.valueOf(subEntity));
DedupRecordFactory.createDedupRecord(spark, mergeRelPath, entityPath, clazz) final DataInfo dataInfo = getDataInfo(dedupConf);
DedupRecordFactory.createDedupRecord(spark, dataInfo, mergeRelPath, entityPath, clazz)
.write() .write()
.mode(SaveMode.Overwrite) .mode(SaveMode.Overwrite)
.option("compression", "gzip") .option("compression", "gzip")
.json(outputPath); .json(outputPath);
} }
} }
private static DataInfo getDataInfo(DedupConfig dedupConf) {
DataInfo info = new DataInfo();
info.setDeletedbyinference(false);
info.setInferred(true);
info.setInvisible(false);
info.setTrust(ROOT_TRUST);
info.setInferenceprovenance(dedupConf.getWf().getConfigurationId());
Qualifier provenance = new Qualifier();
provenance.setClassid(PROVENANCE_ACTION_CLASS);
provenance.setClassname(PROVENANCE_ACTION_CLASS);
provenance.setSchemeid(PROVENANCE_ACTIONS);
provenance.setSchemename(PROVENANCE_ACTIONS);
info.setProvenanceaction(provenance);
return info;
}
} }

2
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/graph/ConnectedComponent.java
View File

@ -25,7 +25,7 @@ public class ConnectedComponent implements Serializable {
if (docIds.size() > 1) { if (docIds.size() > 1) {
final String s = getMin(); final String s = getMin();
String prefix = s.split("\\|")[0]; String prefix = s.split("\\|")[0];
ccId = prefix + "|dedup_______::" + DedupUtility.md5(s); ccId = prefix + "|dedup_wf_001::" + DedupUtility.md5(s);
return ccId; return ccId;
} else { } else {
return docIds.iterator().next(); return docIds.iterator().next();

102
dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java
View File

@ -57,7 +57,6 @@ public class SparkDedupTest implements Serializable {
.toURI()) .toURI())
.toFile() .toFile()
.getAbsolutePath(); .getAbsolutePath();
testOutputBasePath = testOutputBasePath =
createTempDirectory(SparkDedupTest.class.getSimpleName() + "-") createTempDirectory(SparkDedupTest.class.getSimpleName() + "-")
.toAbsolutePath() .toAbsolutePath()
@ -110,6 +109,22 @@ public class SparkDedupTest implements Serializable {
IOUtils.toString( IOUtils.toString(
SparkDedupTest.class.getResourceAsStream( SparkDedupTest.class.getResourceAsStream(
"/eu/dnetlib/dhp/dedup/conf/sw.curr.conf.json"))); "/eu/dnetlib/dhp/dedup/conf/sw.curr.conf.json")));
lenient()
.when(isLookUpService.getResourceProfileByQuery(Mockito.contains("dataset")))
.thenReturn(
IOUtils.toString(
SparkDedupTest.class.getResourceAsStream(
"/eu/dnetlib/dhp/dedup/conf/ds.curr.conf.json")));
lenient()
.when(
isLookUpService.getResourceProfileByQuery(
Mockito.contains("otherresearchproduct")))
.thenReturn(
IOUtils.toString(
SparkDedupTest.class.getResourceAsStream(
"/eu/dnetlib/dhp/dedup/conf/orp.curr.conf.json")));
} }
@Test @Test
@ -144,9 +159,25 @@ public class SparkDedupTest implements Serializable {
.load(testOutputBasePath + "/" + testActionSetId + "/software_simrel") .load(testOutputBasePath + "/" + testActionSetId + "/software_simrel")
.count(); .count();
long ds_simrel =
spark.read()
.load(testOutputBasePath + "/" + testActionSetId + "/dataset_simrel")
.count();
long orp_simrel =
spark.read()
.load(
testOutputBasePath
+ "/"
+ testActionSetId
+ "/otherresearchproduct_simrel")
.count();
assertEquals(3432, orgs_simrel); assertEquals(3432, orgs_simrel);
assertEquals(7260, pubs_simrel); assertEquals(7260, pubs_simrel);
assertEquals(344, sw_simrel); assertEquals(344, sw_simrel);
assertEquals(458, ds_simrel);
assertEquals(6740, orp_simrel);
} }
@Test @Test
@ -181,9 +212,25 @@ public class SparkDedupTest implements Serializable {
.load(testOutputBasePath + "/" + testActionSetId + "/software_mergerel") .load(testOutputBasePath + "/" + testActionSetId + "/software_mergerel")
.count(); .count();
long ds_mergerel =
spark.read()
.load(testOutputBasePath + "/" + testActionSetId + "/dataset_mergerel")
.count();
long orp_mergerel =
spark.read()
.load(
testOutputBasePath
+ "/"
+ testActionSetId
+ "/otherresearchproduct_mergerel")
.count();
assertEquals(1276, orgs_mergerel); assertEquals(1276, orgs_mergerel);
assertEquals(1460, pubs_mergerel); assertEquals(1460, pubs_mergerel);
assertEquals(288, sw_mergerel); assertEquals(288, sw_mergerel);
assertEquals(472, ds_mergerel);
assertEquals(714, orp_mergerel);
} }
@Test @Test
@ -222,10 +269,22 @@ public class SparkDedupTest implements Serializable {
long sw_deduprecord = long sw_deduprecord =
jsc.textFile(testOutputBasePath + "/" + testActionSetId + "/software_deduprecord") jsc.textFile(testOutputBasePath + "/" + testActionSetId + "/software_deduprecord")
.count(); .count();
long ds_deduprecord =
jsc.textFile(testOutputBasePath + "/" + testActionSetId + "/dataset_deduprecord")
.count();
long orp_deduprecord =
jsc.textFile(
testOutputBasePath
+ "/"
+ testActionSetId
+ "/otherresearchproduct_deduprecord")
.count();
assertEquals(82, orgs_deduprecord); assertEquals(82, orgs_deduprecord);
assertEquals(66, pubs_deduprecord); assertEquals(66, pubs_deduprecord);
assertEquals(51, sw_deduprecord); assertEquals(51, sw_deduprecord);
assertEquals(96, ds_deduprecord);
assertEquals(89, orp_deduprecord);
} }
@Test @Test
@ -251,6 +310,9 @@ public class SparkDedupTest implements Serializable {
long projects = jsc.textFile(testDedupGraphBasePath + "/project").count(); long projects = jsc.textFile(testDedupGraphBasePath + "/project").count();
long datasource = jsc.textFile(testDedupGraphBasePath + "/datasource").count(); long datasource = jsc.textFile(testDedupGraphBasePath + "/datasource").count();
long softwares = jsc.textFile(testDedupGraphBasePath + "/software").count(); long softwares = jsc.textFile(testDedupGraphBasePath + "/software").count();
long dataset = jsc.textFile(testDedupGraphBasePath + "/dataset").count();
long otherresearchproduct =
jsc.textFile(testDedupGraphBasePath + "/otherresearchproduct").count();
long mergedOrgs = long mergedOrgs =
spark.read() spark.read()
@ -282,11 +344,37 @@ public class SparkDedupTest implements Serializable {
.distinct() .distinct()
.count(); .count();
long mergedDs =
spark.read()
.load(testOutputBasePath + "/" + testActionSetId + "/dataset_mergerel")
.as(Encoders.bean(Relation.class))
.where("relClass=='merges'")
.javaRDD()
.map(Relation::getTarget)
.distinct()
.count();
long mergedOrp =
spark.read()
.load(
testOutputBasePath
+ "/"
+ testActionSetId
+ "/otherresearchproduct_mergerel")
.as(Encoders.bean(Relation.class))
.where("relClass=='merges'")
.javaRDD()
.map(Relation::getTarget)
.distinct()
.count();
assertEquals(897, publications); assertEquals(897, publications);
assertEquals(835, organizations); assertEquals(835, organizations);
assertEquals(100, projects); assertEquals(100, projects);
assertEquals(100, datasource); assertEquals(100, datasource);
assertEquals(200, softwares); assertEquals(200, softwares);
assertEquals(388, dataset);
assertEquals(517, otherresearchproduct);
long deletedOrgs = long deletedOrgs =
jsc.textFile(testDedupGraphBasePath + "/organization") jsc.textFile(testDedupGraphBasePath + "/organization")
@ -303,9 +391,21 @@ public class SparkDedupTest implements Serializable {
.filter(this::isDeletedByInference) .filter(this::isDeletedByInference)
.count(); .count();
long deletedDs =
jsc.textFile(testDedupGraphBasePath + "/dataset")
.filter(this::isDeletedByInference)
.count();
long deletedOrp =
jsc.textFile(testDedupGraphBasePath + "/otherresearchproduct")
.filter(this::isDeletedByInference)
.count();
assertEquals(mergedOrgs, deletedOrgs); assertEquals(mergedOrgs, deletedOrgs);
assertEquals(mergedPubs, deletedPubs); assertEquals(mergedPubs, deletedPubs);
assertEquals(mergedSw, deletedSw); assertEquals(mergedSw, deletedSw);
assertEquals(mergedDs, deletedDs);
assertEquals(mergedOrp, deletedOrp);
} }
@Test @Test

11
dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/ds.curr.conf.json
View File

@ -11,7 +11,9 @@
"maxChildren" : "100", "maxChildren" : "100",
"slidingWindowSize" : "200", "slidingWindowSize" : "200",
"rootBuilder" : ["result", "resultProject_outcome_isProducedBy", "resultResult_publicationDataset_isRelatedTo", "resultResult_similarity_isAmongTopNSimilarDocuments", "resultResult_similarity_hasAmongTopNSimilarDocuments", "resultOrganization_affiliation_hasAuthorInstitution", "resultResult_part_hasPart", "resultResult_part_isPartOf", "resultResult_supplement_isSupplementTo", "resultResult_supplement_isSupplementedBy", "resultResult_version_isVersionOf" ], "rootBuilder" : ["result", "resultProject_outcome_isProducedBy", "resultResult_publicationDataset_isRelatedTo", "resultResult_similarity_isAmongTopNSimilarDocuments", "resultResult_similarity_hasAmongTopNSimilarDocuments", "resultOrganization_affiliation_hasAuthorInstitution", "resultResult_part_hasPart", "resultResult_part_isPartOf", "resultResult_supplement_isSupplementTo", "resultResult_supplement_isSupplementedBy", "resultResult_version_isVersionOf" ],
"includeChildren" : "true" "includeChildren" : "true",
"idPath" : "$.id",
"maxIterations" : 20
}, },
"pace" : { "pace" : {
"clustering" : [ "clustering" : [
@ -70,7 +72,8 @@
"field": "title", "field": "title",
"comparator": "levensteinTitle", "comparator": "levensteinTitle",
"weight": 1.0, "weight": 1.0,
"countIfUndefined": "true" "countIfUndefined": "true",
"params": {}
} }
], ],
"threshold": 0.99, "threshold": 0.99,
@ -85,7 +88,7 @@
{ {
"name" : "doi", "name" : "doi",
"type" : "String", "type" : "String",
"path" : "$.pid[@.qualifier.classid = 'doi'].value" "path" : "$.pid[?(@.qualifier.classid == 'doi')].value"
}, },
{ {
"name" : "pid", "name" : "pid",
@ -96,7 +99,7 @@
{ {
"name" : "title", "name" : "title",
"type" : "String", "type" : "String",
"path" : "$.title[@.qualifier.classid = 'main title'].value", "path" : "$.title[?(@.qualifier.classid == 'main title')].value",
"length" : 250, "length" : 250,
"size" : 5 "size" : 5
}, },

11
dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/orp.curr.conf.json
View File

@ -11,7 +11,9 @@
"maxChildren" : "100", "maxChildren" : "100",
"slidingWindowSize" : "200", "slidingWindowSize" : "200",
"rootBuilder" : [ "result", "resultProject_outcome_isProducedBy", "resultResult_publicationDataset_isRelatedTo", "resultResult_similarity_isAmongTopNSimilarDocuments", "resultResult_similarity_hasAmongTopNSimilarDocuments", "resultOrganization_affiliation_hasAuthorInstitution", "resultResult_part_hasPart", "resultResult_part_isPartOf", "resultResult_supplement_isSupplementTo", "resultResult_supplement_isSupplementedBy", "resultResult_version_isVersionOf" ], "rootBuilder" : [ "result", "resultProject_outcome_isProducedBy", "resultResult_publicationDataset_isRelatedTo", "resultResult_similarity_isAmongTopNSimilarDocuments", "resultResult_similarity_hasAmongTopNSimilarDocuments", "resultOrganization_affiliation_hasAuthorInstitution", "resultResult_part_hasPart", "resultResult_part_isPartOf", "resultResult_supplement_isSupplementTo", "resultResult_supplement_isSupplementedBy", "resultResult_version_isVersionOf" ],
"includeChildren" : "true" "includeChildren" : "true",
"idPath" : "$.id",
"maxIterations" : 20
}, },
"pace" : { "pace" : {
"clustering" : [ "clustering" : [
@ -70,7 +72,8 @@
"field": "title", "field": "title",
"comparator": "levensteinTitle", "comparator": "levensteinTitle",
"weight": 1.0, "weight": 1.0,
"countIfUndefined": "true" "countIfUndefined": "true",
"params": {}
} }
], ],
"threshold": 0.99, "threshold": 0.99,
@ -85,7 +88,7 @@
{ {
"name" : "doi", "name" : "doi",
"type" : "String", "type" : "String",
"path" : "$.pid[@.qualifier.classid = 'doi'}].value" "path" : "$.pid[?(@.qualifier.classid == 'doi')].value"
}, },
{ {
"name" : "pid", "name" : "pid",
@ -96,7 +99,7 @@
{ {
"name" : "title", "name" : "title",
"type" : "String", "type" : "String",
"path" : "$.title[@.qualifier.classid = 'main title'].value", "path" : "$.title[?(@.qualifier.classid == 'main title')].value",
"length" : 250, "length" : 250,
"size" : 5 "size" : 5
}, },

4
dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/sw.curr.conf.json
View File

@ -11,7 +11,9 @@
"maxChildren" : "100", "maxChildren" : "100",
"slidingWindowSize" : "200", "slidingWindowSize" : "200",
"rootBuilder" : [ "result", "resultProject_outcome_isProducedBy", "resultResult_publicationDataset_isRelatedTo", "resultResult_similarity_isAmongTopNSimilarDocuments", "resultResult_similarity_hasAmongTopNSimilarDocuments", "resultOrganization_affiliation_hasAuthorInstitution", "resultResult_part_hasPart", "resultResult_part_isPartOf", "resultResult_supplement_isSupplementTo", "resultResult_supplement_isSupplementedBy", "resultResult_version_isVersionOf" ], "rootBuilder" : [ "result", "resultProject_outcome_isProducedBy", "resultResult_publicationDataset_isRelatedTo", "resultResult_similarity_isAmongTopNSimilarDocuments", "resultResult_similarity_hasAmongTopNSimilarDocuments", "resultOrganization_affiliation_hasAuthorInstitution", "resultResult_part_hasPart", "resultResult_part_isPartOf", "resultResult_supplement_isSupplementTo", "resultResult_supplement_isSupplementedBy", "resultResult_version_isVersionOf" ],
"includeChildren" : "true" "includeChildren" : "true",
"idPath" : "$.id",
"maxIterations" : 20
}, },
"pace" : { "pace" : {
"clustering" : [ "clustering" : [

292
dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/dataset
View File

File diff suppressed because one or more lines are too long

428
dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/otherresearchproduct
View File

File diff suppressed because one or more lines are too long

2
dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml
View File

@ -15,6 +15,8 @@
<SCAN id="organization"/> <SCAN id="organization"/>
<SCAN id="publication"/> <SCAN id="publication"/>
<SCAN id="software"/> <SCAN id="software"/>
<SCAN id="dataset"/>
<SCAN id="otherresearchproduct"/>
</SCAN_SEQUENCE> </SCAN_SEQUENCE>
</DEDUPLICATION> </DEDUPLICATION>
</CONFIGURATION> </CONFIGURATION>

2
dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/graph/ConnectedComponent.java
View File

@ -25,7 +25,7 @@ public class ConnectedComponent implements Serializable {
if (docIds.size() > 1) { if (docIds.size() > 1) {
final String s = getMin(); final String s = getMin();
String prefix = s.split("\\|")[0]; String prefix = s.split("\\|")[0];
ccId = prefix + "|dedup_______::" + DedupUtility.md5(s); ccId = prefix + "|dedup_wf_001::" + DedupUtility.md5(s);
return ccId; return ccId;
} else { } else {
return docIds.iterator().next(); return docIds.iterator().next();

14
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/GraphHiveImporterJob.java → dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hive/GraphHiveImporterJob.java
View File

@ -1,4 +1,4 @@
package eu.dnetlib.dhp.oa.graph; package eu.dnetlib.dhp.oa.graph.hive;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
@ -19,6 +19,8 @@ public class GraphHiveImporterJob {
private static final Logger log = LoggerFactory.getLogger(GraphHiveImporterJob.class); private static final Logger log = LoggerFactory.getLogger(GraphHiveImporterJob.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static void main(String[] args) throws Exception { public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser = final ArgumentApplicationParser parser =
@ -37,12 +39,12 @@ public class GraphHiveImporterJob {
String inputPath = parser.get("inputPath"); String inputPath = parser.get("inputPath");
log.info("inputPath: {}", inputPath); log.info("inputPath: {}", inputPath);
String hiveMetastoreUris = parser.get("hiveMetastoreUris");
log.info("hiveMetastoreUris: {}", hiveMetastoreUris);
String hiveDbName = parser.get("hiveDbName"); String hiveDbName = parser.get("hiveDbName");
log.info("hiveDbName: {}", hiveDbName); log.info("hiveDbName: {}", hiveDbName);
String hiveMetastoreUris = parser.get("hiveMetastoreUris");
log.info("hiveMetastoreUris: {}", hiveMetastoreUris);
SparkConf conf = new SparkConf(); SparkConf conf = new SparkConf();
conf.set("hive.metastore.uris", hiveMetastoreUris); conf.set("hive.metastore.uris", hiveMetastoreUris);
@ -58,13 +60,13 @@ public class GraphHiveImporterJob {
spark.sql(String.format("DROP DATABASE IF EXISTS %s CASCADE", hiveDbName)); spark.sql(String.format("DROP DATABASE IF EXISTS %s CASCADE", hiveDbName));
spark.sql(String.format("CREATE DATABASE IF NOT EXISTS %s", hiveDbName)); spark.sql(String.format("CREATE DATABASE IF NOT EXISTS %s", hiveDbName));
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
// Read the input file and convert it into RDD of serializable object // Read the input file and convert it into RDD of serializable object
ModelSupport.oafTypes.forEach( ModelSupport.oafTypes.forEach(
(name, clazz) -> (name, clazz) ->
spark.createDataset( spark.createDataset(
sc.textFile(inputPath + "/" + name) sc.textFile(inputPath + "/" + name)
.map(s -> new ObjectMapper().readValue(s, clazz)) .map(s -> OBJECT_MAPPER.readValue(s, clazz))
.rdd(), .rdd(),
Encoders.bean(clazz)) Encoders.bean(clazz))
.write() .write()

53
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java
View File

@ -10,7 +10,9 @@ import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.oaiIProvenance;
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.qualifier; import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.qualifier;
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty; import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty;
import eu.dnetlib.dhp.oa.graph.raw.common.MigrationConstants;
import eu.dnetlib.dhp.schema.oaf.Author; import eu.dnetlib.dhp.schema.oaf.Author;
import eu.dnetlib.dhp.schema.oaf.Context;
import eu.dnetlib.dhp.schema.oaf.DataInfo; import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.Dataset; import eu.dnetlib.dhp.schema.oaf.Dataset;
import eu.dnetlib.dhp.schema.oaf.Field; import eu.dnetlib.dhp.schema.oaf.Field;
@ -46,25 +48,6 @@ public abstract class AbstractMdRecordToOafMapper {
protected static final Qualifier MAIN_TITLE_QUALIFIER = protected static final Qualifier MAIN_TITLE_QUALIFIER =
qualifier("main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title"); qualifier("main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title");
protected static final Qualifier PUBLICATION_RESULTTYPE_QUALIFIER =
qualifier(
"publication",
"publication",
"dnet:result_typologies",
"dnet:result_typologies");
protected static final Qualifier DATASET_RESULTTYPE_QUALIFIER =
qualifier("dataset", "dataset", "dnet:result_typologies", "dnet:result_typologies");
protected static final Qualifier SOFTWARE_RESULTTYPE_QUALIFIER =
qualifier("software", "software", "dnet:result_typologies", "dnet:result_typologies");
protected static final Qualifier OTHER_RESULTTYPE_QUALIFIER =
qualifier("other", "other", "dnet:result_typologies", "dnet:result_typologies");
protected static final Qualifier REPOSITORY_QUALIFIER =
qualifier(
"sysimport:crosswalk:repository",
"sysimport:crosswalk:repository",
"dnet:provenanceActions",
"dnet:provenanceActions");
protected AbstractMdRecordToOafMapper(final Map<String, String> code2name) { protected AbstractMdRecordToOafMapper(final Map<String, String> code2name) {
this.code2name = code2name; this.code2name = code2name;
} }
@ -123,14 +106,14 @@ public abstract class AbstractMdRecordToOafMapper {
case "publication": case "publication":
final Publication p = new Publication(); final Publication p = new Publication();
populateResultFields(p, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); populateResultFields(p, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
p.setResulttype(PUBLICATION_RESULTTYPE_QUALIFIER); p.setResulttype(MigrationConstants.PUBLICATION_RESULTTYPE_QUALIFIER);
p.setJournal(prepareJournal(doc, info)); p.setJournal(prepareJournal(doc, info));
oafs.add(p); oafs.add(p);
break; break;
case "dataset": case "dataset":
final Dataset d = new Dataset(); final Dataset d = new Dataset();
populateResultFields(d, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); populateResultFields(d, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
d.setResulttype(DATASET_RESULTTYPE_QUALIFIER); d.setResulttype(MigrationConstants.DATASET_RESULTTYPE_QUALIFIER);
d.setStoragedate(prepareDatasetStorageDate(doc, info)); d.setStoragedate(prepareDatasetStorageDate(doc, info));
d.setDevice(prepareDatasetDevice(doc, info)); d.setDevice(prepareDatasetDevice(doc, info));
d.setSize(prepareDatasetSize(doc, info)); d.setSize(prepareDatasetSize(doc, info));
@ -143,7 +126,7 @@ public abstract class AbstractMdRecordToOafMapper {
case "software": case "software":
final Software s = new Software(); final Software s = new Software();
populateResultFields(s, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); populateResultFields(s, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
s.setResulttype(SOFTWARE_RESULTTYPE_QUALIFIER); s.setResulttype(MigrationConstants.SOFTWARE_RESULTTYPE_QUALIFIER);
s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info)); s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info));
s.setLicense(prepareSoftwareLicenses(doc, info)); s.setLicense(prepareSoftwareLicenses(doc, info));
s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info)); s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info));
@ -154,7 +137,7 @@ public abstract class AbstractMdRecordToOafMapper {
default: default:
final OtherResearchProduct o = new OtherResearchProduct(); final OtherResearchProduct o = new OtherResearchProduct();
populateResultFields(o, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); populateResultFields(o, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
o.setResulttype(OTHER_RESULTTYPE_QUALIFIER); o.setResulttype(MigrationConstants.OTHER_RESULTTYPE_QUALIFIER);
o.setContactperson(prepareOtherResearchProductContactPersons(doc, info)); o.setContactperson(prepareOtherResearchProductContactPersons(doc, info));
o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info)); o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info));
o.setTool(prepareOtherResearchProductTools(doc, info)); o.setTool(prepareOtherResearchProductTools(doc, info));
@ -255,11 +238,25 @@ public abstract class AbstractMdRecordToOafMapper {
r.setContributor(prepareContributors(doc, info)); r.setContributor(prepareContributors(doc, info));
r.setResourcetype(prepareResourceType(doc, info)); r.setResourcetype(prepareResourceType(doc, info));
r.setCoverage(prepareCoverages(doc, info)); r.setCoverage(prepareCoverages(doc, info));
r.setContext(new ArrayList<>()); // NOT PRESENT IN MDSTORES r.setContext(prepareContexts(doc, info));
r.setExternalReference(new ArrayList<>()); // NOT PRESENT IN MDSTORES r.setExternalReference(new ArrayList<>()); // NOT PRESENT IN MDSTORES
r.setInstance(prepareInstances(doc, info, collectedFrom, hostedBy)); r.setInstance(prepareInstances(doc, info, collectedFrom, hostedBy));
} }
private List<Context> prepareContexts(final Document doc, final DataInfo info) {
final List<Context> list = new ArrayList<>();
for (final Object o : doc.selectNodes("//oaf:concept")) {
final String cid = ((Node) o).valueOf("@id");
if (StringUtils.isNotBlank(cid)) {
final Context c = new Context();
c.setId(cid);
c.setDataInfo(Arrays.asList(info));
list.add(c);
}
}
return list;
}
protected abstract Qualifier prepareResourceType(Document doc, DataInfo info); protected abstract Qualifier prepareResourceType(Document doc, DataInfo info);
protected abstract List<Instance> prepareInstances( protected abstract List<Instance> prepareInstances(
@ -433,7 +430,13 @@ public abstract class AbstractMdRecordToOafMapper {
final Node n = doc.selectSingleNode("//oaf:datainfo"); final Node n = doc.selectSingleNode("//oaf:datainfo");
if (n == null) { if (n == null) {
return dataInfo(false, null, false, false, REPOSITORY_QUALIFIER, "0.9"); return dataInfo(
false,
null,
false,
false,
MigrationConstants.REPOSITORY_PROVENANCE_ACTIONS,
"0.9");
} }
final String paClassId = n.valueOf("./oaf:provenanceaction/@classid"); final String paClassId = n.valueOf("./oaf:provenanceaction/@classid");

48
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/DispatchEntitiesApplication.java
View File

@ -2,16 +2,18 @@ package eu.dnetlib.dhp.oa.graph.raw;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.*;
import java.util.Optional; import java.util.Optional;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.StringUtils;
import org.apache.hadoop.io.compress.GzipCodec;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession; import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger; import org.slf4j.Logger;
import org.slf4j.LoggerFactory; import org.slf4j.LoggerFactory;
@ -20,8 +22,6 @@ public class DispatchEntitiesApplication {
private static final Logger log = LoggerFactory.getLogger(DispatchEntitiesApplication.class); private static final Logger log = LoggerFactory.getLogger(DispatchEntitiesApplication.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static void main(final String[] args) throws Exception { public static void main(final String[] args) throws Exception {
final ArgumentApplicationParser parser = final ArgumentApplicationParser parser =
new ArgumentApplicationParser( new ArgumentApplicationParser(
@ -45,15 +45,9 @@ public class DispatchEntitiesApplication {
isSparkSessionManaged, isSparkSessionManaged,
spark -> { spark -> {
removeOutputDir(spark, targetPath); removeOutputDir(spark, targetPath);
ModelSupport.oafTypes
processEntity(spark, Publication.class, sourcePath, targetPath); .values()
processEntity(spark, Dataset.class, sourcePath, targetPath); .forEach(clazz -> processEntity(spark, clazz, sourcePath, targetPath));
processEntity(spark, Software.class, sourcePath, targetPath);
processEntity(spark, OtherResearchProduct.class, sourcePath, targetPath);
processEntity(spark, Datasource.class, sourcePath, targetPath);
processEntity(spark, Organization.class, sourcePath, targetPath);
processEntity(spark, Project.class, sourcePath, targetPath);
processEntity(spark, Relation.class, sourcePath, targetPath);
}); });
} }
@ -64,26 +58,18 @@ public class DispatchEntitiesApplication {
final String targetPath) { final String targetPath) {
final String type = clazz.getSimpleName().toLowerCase(); final String type = clazz.getSimpleName().toLowerCase();
log.info(String.format("Processing entities (%s) in file: %s", type, sourcePath)); log.info("Processing entities ({}) in file: {}", type, sourcePath);
/*
spark.read() spark.read()
.textFile(sourcePath)
.filter((FilterFunction<String>) value -> isEntityType(value, type))
.map((MapFunction<String, String>) value -> StringUtils.substringAfter(value, "|"), Encoders.STRING())
.map((MapFunction<String, T>) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz))
.write()
.mode(SaveMode.Overwrite)
.parquet(targetPath + "/" + type);
*/
JavaSparkContext.fromSparkContext(spark.sparkContext())
.textFile(sourcePath) .textFile(sourcePath)
.filter(l -> isEntityType(l, type)) .filter((FilterFunction<String>) value -> isEntityType(value, type))
.map(l -> StringUtils.substringAfter(l, "|")) .map(
.saveAsTextFile( (MapFunction<String, String>) l -> StringUtils.substringAfter(l, "|"),
targetPath + "/" + type, GzipCodec.class); // use repartition(XXX) ??? Encoders.STRING())
.write()
.option("compression", "gzip")
.mode(SaveMode.Overwrite)
.text(targetPath + "/" + type);
} }
private static boolean isEntityType(final String line, final String type) { private static boolean isEntityType(final String line, final String type) {

48
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java
View File

@ -6,6 +6,7 @@ import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.oa.graph.raw.common.DbClient; import eu.dnetlib.dhp.oa.graph.raw.common.DbClient;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.*;
import java.io.IOException; import java.io.IOException;
import java.sql.SQLException; import java.sql.SQLException;
@ -29,6 +30,8 @@ public class GenerateEntitiesApplication {
private static final Logger log = LoggerFactory.getLogger(GenerateEntitiesApplication.class); private static final Logger log = LoggerFactory.getLogger(GenerateEntitiesApplication.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static void main(final String[] args) throws Exception { public static void main(final String[] args) throws Exception {
final ArgumentApplicationParser parser = final ArgumentApplicationParser parser =
new ArgumentApplicationParser( new ArgumentApplicationParser(
@ -78,7 +81,7 @@ public class GenerateEntitiesApplication {
log.info("Generate entities from files:"); log.info("Generate entities from files:");
existingSourcePaths.forEach(log::info); existingSourcePaths.forEach(log::info);
JavaRDD<String> inputRdd = sc.emptyRDD(); JavaRDD<Oaf> inputRdd = sc.emptyRDD();
for (final String sp : existingSourcePaths) { for (final String sp : existingSourcePaths) {
inputRdd = inputRdd =
@ -86,15 +89,29 @@ public class GenerateEntitiesApplication {
sc.sequenceFile(sp, Text.class, Text.class) sc.sequenceFile(sp, Text.class, Text.class)
.map(k -> new Tuple2<>(k._1().toString(), k._2().toString())) .map(k -> new Tuple2<>(k._1().toString(), k._2().toString()))
.map(k -> convertToListOaf(k._1(), k._2(), code2name)) .map(k -> convertToListOaf(k._1(), k._2(), code2name))
.flatMap(list -> list.iterator()) .flatMap(list -> list.iterator()));
.map(
oaf ->
oaf.getClass().getSimpleName().toLowerCase()
+ "|"
+ convertToJson(oaf)));
} }
inputRdd.saveAsTextFile(targetPath, GzipCodec.class); inputRdd.mapToPair(oaf -> new Tuple2<>(ModelSupport.idFn().apply(oaf), oaf))
.reduceByKey((o1, o2) -> merge(o1, o2))
.map(Tuple2::_2)
.map(
oaf ->
oaf.getClass().getSimpleName().toLowerCase()
+ "|"
+ OBJECT_MAPPER.writeValueAsString(oaf))
.saveAsTextFile(targetPath, GzipCodec.class);
}
private static Oaf merge(Oaf o1, Oaf o2) {
if (ModelSupport.isSubClass(o1, OafEntity.class)) {
((OafEntity) o1).mergeFrom((OafEntity) o2);
} else if (ModelSupport.isSubClass(o1, Relation.class)) {
((Relation) o1).mergeFrom((Relation) o2);
} else {
throw new RuntimeException("invalid Oaf type:" + o1.getClass().getCanonicalName());
}
return o1;
} }
private static List<Oaf> convertToListOaf( private static List<Oaf> convertToListOaf(
@ -120,9 +137,10 @@ public class GenerateEntitiesApplication {
return Arrays.asList(convertFromJson(s, Dataset.class)); return Arrays.asList(convertFromJson(s, Dataset.class));
case "software": case "software":
return Arrays.asList(convertFromJson(s, Software.class)); return Arrays.asList(convertFromJson(s, Software.class));
case "otherresearchproducts": case "otherresearchproduct":
default:
return Arrays.asList(convertFromJson(s, OtherResearchProduct.class)); return Arrays.asList(convertFromJson(s, OtherResearchProduct.class));
default:
throw new RuntimeException("type not managed: " + type.toLowerCase());
} }
} }
@ -150,17 +168,9 @@ public class GenerateEntitiesApplication {
return map; return map;
} }
private static String convertToJson(final Oaf oaf) {
try {
return new ObjectMapper().writeValueAsString(oaf);
} catch (final Exception e) {
throw new RuntimeException(e);
}
}
private static Oaf convertFromJson(final String s, final Class<? extends Oaf> clazz) { private static Oaf convertFromJson(final String s, final Class<? extends Oaf> clazz) {
try { try {
return new ObjectMapper().readValue(s, clazz); return OBJECT_MAPPER.readValue(s, clazz);
} catch (final Exception e) { } catch (final Exception e) {
log.error("Error parsing object of class: " + clazz); log.error("Error parsing object of class: " + clazz);
log.error(s); log.error(s);

87
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MergeClaimsApplication.java
View File

@ -1,7 +1,6 @@
package eu.dnetlib.dhp.oa.graph.raw; package eu.dnetlib.dhp.oa.graph.raw;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import static eu.dnetlib.dhp.schema.common.ModelSupport.isSubClass;
import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.application.ArgumentApplicationParser;
@ -10,7 +9,6 @@ import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.*;
import java.util.Objects; import java.util.Objects;
import java.util.Optional; import java.util.Optional;
import java.util.function.Function;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.api.java.JavaSparkContext;
@ -83,7 +81,9 @@ public class MergeClaimsApplication {
readFromPath(spark, rawPath, clazz) readFromPath(spark, rawPath, clazz)
.map( .map(
(MapFunction<T, Tuple2<String, T>>) (MapFunction<T, Tuple2<String, T>>)
value -> new Tuple2<>(idFn().apply(value), value), value ->
new Tuple2<>(
ModelSupport.idFn().apply(value), value),
Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz))); Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz)));
final JavaSparkContext jsc = JavaSparkContext.fromSparkContext(spark.sparkContext()); final JavaSparkContext jsc = JavaSparkContext.fromSparkContext(spark.sparkContext());
@ -92,14 +92,11 @@ public class MergeClaimsApplication {
.getValue() .getValue()
.map( .map(
(MapFunction<T, Tuple2<String, T>>) (MapFunction<T, Tuple2<String, T>>)
value -> new Tuple2<>(idFn().apply(value), value), value ->
new Tuple2<>(
ModelSupport.idFn().apply(value), value),
Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz))); Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz)));
/*
Dataset<Tuple2<String, T>> claim = readFromPath(spark, claimPath, clazz)
.map((MapFunction<T, Tuple2<String, T>>) value -> new Tuple2<>(idFn().apply(value), value), Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz)));
*/
raw.joinWith(claim, raw.col("_1").equalTo(claim.col("_1")), "full_outer") raw.joinWith(claim, raw.col("_1").equalTo(claim.col("_1")), "full_outer")
.map( .map(
(MapFunction<Tuple2<Tuple2<String, T>, Tuple2<String, T>>, T>) (MapFunction<Tuple2<Tuple2<String, T>, Tuple2<String, T>>, T>)
@ -131,78 +128,12 @@ public class MergeClaimsApplication {
.map( .map(
(MapFunction<String, T>) value -> OBJECT_MAPPER.readValue(value, clazz), (MapFunction<String, T>) value -> OBJECT_MAPPER.readValue(value, clazz),
Encoders.bean(clazz)) Encoders.bean(clazz))
.filter((FilterFunction<T>) value -> Objects.nonNull(idFn().apply(value))); .filter(
/* (FilterFunction<T>)
return spark.read() value -> Objects.nonNull(ModelSupport.idFn().apply(value)));
.load(path)
.as(Encoders.bean(clazz))
.filter((FilterFunction<T>) value -> Objects.nonNull(idFn().apply(value)));
*/
} }
private static void removeOutputDir(SparkSession spark, String path) { private static void removeOutputDir(SparkSession spark, String path) {
HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
} }
private static <T extends Oaf> Function<T, String> idFn() {
return x -> {
if (isSubClass(x, Relation.class)) {
return idFnForRelation(x);
}
return idFnForOafEntity(x);
};
}
private static <T extends Oaf> String idFnForRelation(T t) {
Relation r = (Relation) t;
return Optional.ofNullable(r.getSource())
.map(
source ->
Optional.ofNullable(r.getTarget())
.map(
target ->
Optional.ofNullable(r.getRelType())
.map(
relType ->
Optional.ofNullable(
r
.getSubRelType())
.map(
subRelType ->
Optional
.ofNullable(
r
.getRelClass())
.map(
relClass ->
String
.join(
source,
target,
relType,
subRelType,
relClass))
.orElse(
String
.join(
source,
target,
relType,
subRelType)))
.orElse(
String
.join(
source,
target,
relType)))
.orElse(
String.join(
source, target)))
.orElse(source))
.orElse(null);
}
private static <T extends Oaf> String idFnForOafEntity(T t) {
return ((OafEntity) t).getId();
}
} }

14
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java
View File

@ -13,6 +13,7 @@ import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProper
import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.graph.raw.common.AbstractMigrationApplication; import eu.dnetlib.dhp.oa.graph.raw.common.AbstractMigrationApplication;
import eu.dnetlib.dhp.oa.graph.raw.common.DbClient; import eu.dnetlib.dhp.oa.graph.raw.common.DbClient;
import eu.dnetlib.dhp.oa.graph.raw.common.MigrationConstants;
import eu.dnetlib.dhp.schema.oaf.Context; import eu.dnetlib.dhp.schema.oaf.Context;
import eu.dnetlib.dhp.schema.oaf.DataInfo; import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.Dataset; import eu.dnetlib.dhp.schema.oaf.Dataset;
@ -49,13 +50,6 @@ import org.apache.commons.logging.LogFactory;
public class MigrateDbEntitiesApplication extends AbstractMigrationApplication public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
implements Closeable { implements Closeable {
private static final Qualifier ENTITYREGISTRY_PROVENANCE_ACTION =
qualifier(
"sysimport:crosswalk:entityregistry",
"sysimport:crosswalk:entityregistry",
"dnet:provenance_actions",
"dnet:provenance_actions");
private static final Log log = LogFactory.getLog(MigrateDbEntitiesApplication.class); private static final Log log = LogFactory.getLog(MigrateDbEntitiesApplication.class);
private final DbClient dbClient; private final DbClient dbClient;
@ -402,12 +396,16 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
if (rs.getString("target_type").equals("dataset")) { if (rs.getString("target_type").equals("dataset")) {
r = new Dataset(); r = new Dataset();
r.setResulttype(MigrationConstants.DATASET_RESULTTYPE_QUALIFIER);
} else if (rs.getString("target_type").equals("software")) { } else if (rs.getString("target_type").equals("software")) {
r = new Software(); r = new Software();
r.setResulttype(MigrationConstants.SOFTWARE_RESULTTYPE_QUALIFIER);
} else if (rs.getString("target_type").equals("other")) { } else if (rs.getString("target_type").equals("other")) {
r = new OtherResearchProduct(); r = new OtherResearchProduct();
r.setResulttype(MigrationConstants.OTHER_RESULTTYPE_QUALIFIER);
} else { } else {
r = new Publication(); r = new Publication();
r.setResulttype(MigrationConstants.PUBLICATION_RESULTTYPE_QUALIFIER);
} }
r.setId(createOpenaireId(50, rs.getString("target_id"), false)); r.setId(createOpenaireId(50, rs.getString("target_id"), false));
r.setLastupdatetimestamp(lastUpdateTimestamp); r.setLastupdatetimestamp(lastUpdateTimestamp);
@ -484,7 +482,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
inferenceprovenance, inferenceprovenance,
inferred, inferred,
false, false,
ENTITYREGISTRY_PROVENANCE_ACTION, MigrationConstants.ENTITYREGISTRY_PROVENANCE_ACTION,
trust); trust);
} }

74
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java
View File

@ -1,8 +1,19 @@
package eu.dnetlib.dhp.oa.graph.raw; package eu.dnetlib.dhp.oa.graph.raw;
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.*; import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.createOpenaireId;
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.field;
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty;
import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.Author;
import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.Field;
import eu.dnetlib.dhp.schema.oaf.GeoLocation;
import eu.dnetlib.dhp.schema.oaf.Instance;
import eu.dnetlib.dhp.schema.oaf.KeyValue;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Arrays; import java.util.Arrays;
import java.util.List; import java.util.List;
@ -62,33 +73,44 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
final DataInfo info, final DataInfo info,
final KeyValue collectedfrom, final KeyValue collectedfrom,
final KeyValue hostedby) { final KeyValue hostedby) {
final List<Instance> res = new ArrayList<>();
final Instance instance = new Instance();
instance.setUrl(new ArrayList<>());
instance.setInstancetype(
prepareQualifier(
doc,
"//dr:CobjCategory",
"dnet:publication_resource",
"dnet:publication_resource"));
instance.setCollectedfrom(collectedfrom);
instance.setHostedby(hostedby);
instance.setDateofacceptance(field(doc.valueOf("//oaf:dateAccepted"), info));
instance.setDistributionlocation(doc.valueOf("//oaf:distributionlocation"));
instance.setAccessright(
prepareQualifier(
doc, "//oaf:accessrights", "dnet:access_modes", "dnet:access_modes"));
instance.setLicense(field(doc.valueOf("//oaf:license"), info));
instance.setRefereed(field(doc.valueOf("//oaf:refereed"), info));
instance.setProcessingchargeamount(
field(doc.valueOf("//oaf:processingchargeamount"), info));
instance.setProcessingchargecurrency(
field(doc.valueOf("//oaf:processingchargeamount/@currency"), info));
for (final Object o : for (final Object o :
doc.selectNodes("//datacite:alternateIdentifier[@alternateIdentifierType='URL']")) { doc.selectNodes("//datacite:alternateIdentifier[@alternateIdentifierType='URL']")) {
final Instance instance = new Instance(); instance.getUrl().add(((Node) o).getText().trim());
instance.setUrl(Arrays.asList(((Node) o).getText().trim()));
instance.setInstancetype(
prepareQualifier(
doc,
"//dr:CobjCategory",
"dnet:publication_resource",
"dnet:publication_resource"));
instance.setCollectedfrom(collectedfrom);
instance.setHostedby(hostedby);
instance.setDateofacceptance(field(doc.valueOf("//oaf:dateAccepted"), info));
instance.setDistributionlocation(doc.valueOf("//oaf:distributionlocation"));
instance.setAccessright(
prepareQualifier(
doc, "//oaf:accessrights", "dnet:access_modes", "dnet:access_modes"));
instance.setLicense(field(doc.valueOf("//oaf:license"), info));
instance.setRefereed(field(doc.valueOf("//oaf:refereed"), info));
instance.setProcessingchargeamount(
field(doc.valueOf("//oaf:processingchargeamount"), info));
instance.setProcessingchargecurrency(
field(doc.valueOf("//oaf:processingchargeamount/@currency"), info));
res.add(instance);
} }
return res; for (final Object o : doc.selectNodes("//datacite:identifier[@identifierType='URL']")) {
instance.getUrl().add(((Node) o).getText().trim());
}
for (final Object o :
doc.selectNodes("//datacite:alternateIdentifier[@alternateIdentifierType='DOI']")) {
instance.getUrl().add("http://dx.doi.org/" + ((Node) o).getText().trim());
}
for (final Object o : doc.selectNodes("//datacite:identifier[@identifierType='DOI']")) {
instance.getUrl().add("http://dx.doi.org/" + ((Node) o).getText().trim());
}
return Arrays.asList(instance);
} }
@Override @Override

33
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/MigrationConstants.java Normal file
View File

@ -0,0 +1,33 @@
package eu.dnetlib.dhp.oa.graph.raw.common;
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.qualifier;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
public class MigrationConstants {
public static final Qualifier PUBLICATION_RESULTTYPE_QUALIFIER =
qualifier(
"publication",
"publication",
"dnet:result_typologies",
"dnet:result_typologies");
public static final Qualifier DATASET_RESULTTYPE_QUALIFIER =
qualifier("dataset", "dataset", "dnet:result_typologies", "dnet:result_typologies");
public static final Qualifier SOFTWARE_RESULTTYPE_QUALIFIER =
qualifier("software", "software", "dnet:result_typologies", "dnet:result_typologies");
public static final Qualifier OTHER_RESULTTYPE_QUALIFIER =
qualifier("other", "other", "dnet:result_typologies", "dnet:result_typologies");
public static final Qualifier REPOSITORY_PROVENANCE_ACTIONS =
qualifier(
"sysimport:crosswalk:repository",
"sysimport:crosswalk:repository",
"dnet:provenanceActions",
"dnet:provenanceActions");
public static final Qualifier ENTITYREGISTRY_PROVENANCE_ACTION =
qualifier(
"sysimport:crosswalk:entityregistry",
"sysimport:crosswalk:entityregistry",
"dnet:provenanceActions",
"dnet:provenanceActions");
}

10
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/config-default.xml
View File

@ -12,19 +12,15 @@
<value>true</value> <value>true</value>
</property> </property>
<property> <property>
<name>oozie.action.sharelib.for.spark</name> <name>hiveMetastoreUris</name>
<value>spark2</value>
</property>
<property>
<name>hive_metastore_uris</name>
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value> <value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
</property> </property>
<property> <property>
<name>hive_jdbc_url</name> <name>hiveJdbcUrl</name>
<value>jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000</value> <value>jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000</value>
</property> </property>
<property> <property>
<name>hive_db_name</name> <name>hiveDbName</name>
<value>openaire</value> <value>openaire</value>
</property> </property>
</configuration> </configuration>

10
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/lib/scripts/postprocessing.sql
View File

@ -1,10 +1,10 @@
DROP VIEW IF EXISTS ${hive_db_name}.result; DROP VIEW IF EXISTS ${hiveDbName}.result;
CREATE VIEW IF NOT EXISTS result as CREATE VIEW IF NOT EXISTS result as
select id, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, embargoenddate, resourcetype, context, instance from ${hive_db_name}.publication p select id, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, embargoenddate, resourcetype, context, instance from ${hiveDbName}.publication p
union all union all
select id, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, embargoenddate, resourcetype, context, instance from ${hive_db_name}.dataset d select id, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, embargoenddate, resourcetype, context, instance from ${hiveDbName}.dataset d
union all union all
select id, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, embargoenddate, resourcetype, context, instance from ${hive_db_name}.software s select id, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, embargoenddate, resourcetype, context, instance from ${hiveDbName}.software s
union all union all
select id, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, embargoenddate, resourcetype, context, instance from ${hive_db_name}.otherresearchproduct o; select id, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, embargoenddate, resourcetype, context, instance from ${hiveDbName}.otherresearchproduct o;

26
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/workflow.xml
View File

@ -2,13 +2,21 @@
<parameters> <parameters>
<property> <property>
<name>sourcePath</name> <name>inputPath</name>
<description>the source path</description> <description>the source path</description>
</property> </property>
<property> <property>
<name>hive_db_name</name> <name>hiveDbName</name>
<description>the target hive database name</description> <description>the target hive database name</description>
</property> </property>
<property>
<name>hiveJdbcUrl</name>
<description>hive server jdbc url</description>
</property>
<property>
<name>hiveMetastoreUris</name>
<description>hive server metastore URIs</description>
</property>
<property> <property>
<name>sparkDriverMemory</name> <name>sparkDriverMemory</name>
<description>memory for driver process</description> <description>memory for driver process</description>
@ -75,7 +83,7 @@
<master>yarn</master> <master>yarn</master>
<mode>cluster</mode> <mode>cluster</mode>
<name>MapGraphAsHiveDB</name> <name>MapGraphAsHiveDB</name>
<class>eu.dnetlib.dhp.oa.graph.GraphHiveImporterJob</class> <class>eu.dnetlib.dhp.oa.graph.hive.GraphHiveImporterJob</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar> <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts> <spark-opts>
--executor-memory=${sparkExecutorMemory} --executor-memory=${sparkExecutorMemory}
@ -87,9 +95,9 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts> </spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}</arg> <arg>--inputPath</arg><arg>${inputPath}</arg>
<arg>--hive_db_name</arg><arg>${hive_db_name}</arg> <arg>--hiveDbName</arg><arg>${hiveDbName}</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg> <arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
</spark> </spark>
<ok to="PostProcessing"/> <ok to="PostProcessing"/>
<error to="Kill"/> <error to="Kill"/>
@ -102,12 +110,12 @@
<configuration> <configuration>
<property> <property>
<name>hive.metastore.uris</name> <name>hive.metastore.uris</name>
<value>${hive_metastore_uris}</value> <value>${hiveMetastoreUris}</value>
</property> </property>
</configuration> </configuration>
<jdbc-url>${hive_jdbc_url}/${hive_db_name}</jdbc-url> <jdbc-url>${hiveJdbcUrl}/${hiveDbName}</jdbc-url>
<script>lib/scripts/postprocessing.sql</script> <script>lib/scripts/postprocessing.sql</script>
<param>hive_db_name=${hive_db_name}</param> <param>hiveDbName=${hiveDbName}</param>
</hive2> </hive2>
<ok to="End"/> <ok to="End"/>
<error to="Kill"/> <error to="Kill"/>

1
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/GraphHiveImporterJobTest.java
View File

@ -1,5 +1,6 @@
package eu.dnetlib.dhp.oa.graph; package eu.dnetlib.dhp.oa.graph;
import eu.dnetlib.dhp.oa.graph.hive.GraphHiveImporterJob;
import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.common.ModelSupport;
import java.io.IOException; import java.io.IOException;
import java.nio.file.Files; import java.nio.file.Files;

5
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java
View File

@ -54,6 +54,7 @@ public class MappersTest {
assertTrue(p.getSubject().size() > 0); assertTrue(p.getSubject().size() > 0);
assertTrue(StringUtils.isNotBlank(p.getJournal().getIssnOnline())); assertTrue(StringUtils.isNotBlank(p.getJournal().getIssnOnline()));
assertTrue(StringUtils.isNotBlank(p.getJournal().getName())); assertTrue(StringUtils.isNotBlank(p.getJournal().getName()));
assertTrue(p.getInstance().size() > 0);
assertValidId(r1.getSource()); assertValidId(r1.getSource());
assertValidId(r1.getTarget()); assertValidId(r1.getTarget());
@ -96,6 +97,9 @@ public class MappersTest {
assertTrue(StringUtils.isNotBlank(d.getTitle().get(0).getValue())); assertTrue(StringUtils.isNotBlank(d.getTitle().get(0).getValue()));
assertTrue(d.getAuthor().size() > 0); assertTrue(d.getAuthor().size() > 0);
assertTrue(d.getSubject().size() > 0); assertTrue(d.getSubject().size() > 0);
assertTrue(d.getInstance().size() > 0);
assertTrue(d.getContext().size() > 0);
assertTrue(d.getContext().get(0).getId().length() > 0);
assertValidId(r1.getSource()); assertValidId(r1.getSource());
assertValidId(r1.getTarget()); assertValidId(r1.getTarget());
@ -129,6 +133,7 @@ public class MappersTest {
assertTrue(StringUtils.isNotBlank(s.getTitle().get(0).getValue())); assertTrue(StringUtils.isNotBlank(s.getTitle().get(0).getValue()));
assertTrue(s.getAuthor().size() > 0); assertTrue(s.getAuthor().size() > 0);
assertTrue(s.getSubject().size() > 0); assertTrue(s.getSubject().size() > 0);
assertTrue(s.getInstance().size() > 0);
} }
private void assertValidId(final String id) { private void assertValidId(final String id) {

1
dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase2.java
View File

@ -216,6 +216,7 @@ public class CreateRelatedEntitiesJob_phase2 {
(MapFunction<String, E>) (MapFunction<String, E>)
value -> OBJECT_MAPPER.readValue(value, entityClazz), value -> OBJECT_MAPPER.readValue(value, entityClazz),
Encoders.bean(entityClazz)) Encoders.bean(entityClazz))
.filter("dataInfo.invisible == false")
.map( .map(
(MapFunction<E, TypedRow>) (MapFunction<E, TypedRow>)
value -> value ->

8
pom.xml
View File

@ -292,6 +292,12 @@
<groupId>eu.dnetlib</groupId> <groupId>eu.dnetlib</groupId>
<artifactId>dnet-actionmanager-common</artifactId> <artifactId>dnet-actionmanager-common</artifactId>
<version>6.0.5</version> <version>6.0.5</version>
<exclusions>
<exclusion>
<groupId>org.apache.hadoop</groupId>
<artifactId>hadoop-common</artifactId>
</exclusion>
</exclusions>
</dependency> </dependency>
<dependency> <dependency>
<groupId>eu.dnetlib</groupId> <groupId>eu.dnetlib</groupId>
@ -307,7 +313,7 @@
<dependency> <dependency>
<groupId>eu.dnetlib</groupId> <groupId>eu.dnetlib</groupId>
<artifactId>dnet-pace-core</artifactId> <artifactId>dnet-pace-core</artifactId>
<version>4.0.0</version> <version>4.0.1</version>
</dependency> </dependency>
<dependency> <dependency>
<groupId>eu.dnetlib</groupId> <groupId>eu.dnetlib</groupId>