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WIP: using common definitions from ModelConstants

This commit is contained in:
Claudio Atzori 2021-03-31 18:33:57 +02:00
parent 879e8cc7ef
commit 7941d7be29
22 changed files with 112 additions and 121 deletions
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20
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java
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@ -35,10 +35,22 @@ public class ModelConstants {
public static final String DNET_PROVENANCE_ACTIONS = "dnet:provenanceActions";
public static final String DNET_COUNTRY_TYPE = "dnet:countries";
public static final String DNET_REVIEW_LEVELS = "dnet:review_levels";
public static final String DNET_PROGRAMMING_LANGUAGES = "dnet:programming_languages";
public static final String DNET_PROVENANCEACTIONS = "dnet:provenanceActions";
public static final String DNET_EXTERNAL_REF_TYPES = "dnet:externalReference_typologies";
public static final String SYSIMPORT_CROSSWALK_REPOSITORY = "sysimport:crosswalk:repository";
public static final String SYSIMPORT_CROSSWALK_ENTITYREGISTRY = "sysimport:crosswalk:entityregistry";
public static final String SYSIMPORT_ACTIONSET = "sysimport:actionset";
public static final String SYSIMPORT_ORCID_NO_DOI = "sysimport:actionset:orcidworks-no-doi";
public static final String USER_CLAIM = "user:claim";
public static final String HARVESTED = "Harvested";
public static final String PROVENANCE_DEDUP = "sysimport:dedup";
public static final Qualifier PROVENANCE_ACTION_SET_QUALIFIER = qualifier(
SYSIMPORT_ACTIONSET, SYSIMPORT_ACTIONSET, DNET_PROVENANCEACTIONS, DNET_PROVENANCEACTIONS);
public static final String DATASET_RESULTTYPE_CLASSID = "dataset";
public static final String PUBLICATION_RESULTTYPE_CLASSID = "publication";
@ -100,13 +112,6 @@ public class ModelConstants {
public static final String UNKNOWN = "UNKNOWN";
public static final String NOT_AVAILABLE = "not available";
public static final String ACTION_SET_SCHEME = "sysimport:actionset";
public static final String PROVENANCE_VOCABULARY = "dnet:provenanceActions";
public static final Qualifier ACTION_SET_PROVENANCE_QUALIFIER = qualifier(
ACTION_SET_SCHEME, ACTION_SET_SCHEME, PROVENANCE_VOCABULARY, PROVENANCE_VOCABULARY);
public static final Qualifier PUBLICATION_DEFAULT_RESULTTYPE = qualifier(
PUBLICATION_RESULTTYPE_CLASSID, PUBLICATION_RESULTTYPE_CLASSID,
DNET_RESULT_TYPOLOGIES, DNET_RESULT_TYPOLOGIES);
@ -131,6 +136,7 @@ public class ModelConstants {
SYSIMPORT_CROSSWALK_ENTITYREGISTRY, SYSIMPORT_CROSSWALK_ENTITYREGISTRY,
DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS);
public static final String UNKNOWN_REPOSITORY_ORIGINALID = "openaire____::1256f046-bf1f-4afc-8b47-d0b147148b18";
public static final KeyValue UNKNOWN_REPOSITORY = keyValue(
"10|openaire____::55045bd2a65019fd8e6741a755395c8c", "Unknown Repository");

24
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelSupport.java
View File

@ -158,10 +158,10 @@ public class ModelSupport {
relationInverseMap
.put(
"organizationOrganization_dedupSimilarity_isSimilarTo", new RelationInverse()
.setInverse("isSimilarTo")
.setRelation("isSimilarTo")
.setRelType("organizationOrganization")
.setSubReltype("dedupSimilarity"));
.setInverse(ModelConstants.IS_SIMILAR_TO)
.setRelation(ModelConstants.IS_SIMILAR_TO)
.setRelType(ModelConstants.ORG_ORG_RELTYPE)
.setSubReltype(ModelConstants.DEDUP));
relationInverseMap
.put(
@ -215,10 +215,10 @@ public class ModelSupport {
relationInverseMap
.put(
"personPerson_dedupSimilarity_isSimilarTo", new RelationInverse()
.setInverse("isSimilarTo")
.setRelation("isSimilarTo")
.setInverse(ModelConstants.IS_SIMILAR_TO)
.setRelation(ModelConstants.IS_SIMILAR_TO)
.setRelType("personPerson")
.setSubReltype("dedupSimilarity"));
.setSubReltype(ModelConstants.DEDUP));
relationInverseMap
.put(
"datasourceOrganization_provision_isProvidedBy", new RelationInverse()
@ -239,14 +239,14 @@ public class ModelSupport {
.setInverse("isAmongTopNSimilarDocuments")
.setRelation("hasAmongTopNSimilarDocuments")
.setRelType(ModelConstants.RESULT_RESULT)
.setSubReltype("similarity"));
.setSubReltype(ModelConstants.SIMILARITY));
relationInverseMap
.put(
"resultResult_similarity_isAmongTopNSimilarDocuments", new RelationInverse()
.setInverse("hasAmongTopNSimilarDocuments")
.setRelation("isAmongTopNSimilarDocuments")
.setRelType(ModelConstants.RESULT_RESULT)
.setSubReltype("similarity"));
.setSubReltype(ModelConstants.SIMILARITY));
relationInverseMap
.put(
"resultResult_relationship_isRelatedTo", new RelationInverse()
@ -299,10 +299,10 @@ public class ModelSupport {
relationInverseMap
.put(
"resultResult_dedupSimilarity_isSimilarTo", new RelationInverse()
.setInverse("isSimilarTo")
.setRelation("isSimilarTo")
.setInverse(ModelConstants.IS_SIMILAR_TO)
.setRelation(ModelConstants.IS_SIMILAR_TO)
.setRelType(ModelConstants.RESULT_RESULT)
.setSubReltype("dedupSimilarity"));
.setSubReltype(ModelConstants.DEDUP));
}

3
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/OafUtils.scala
View File

@ -1,5 +1,6 @@
package eu.dnetlib.dhp.schema.scholexplorer
import eu.dnetlib.dhp.schema.common.ModelConstants
import eu.dnetlib.dhp.schema.oaf.{AccessRight, DataInfo, Field, KeyValue, Qualifier, StructuredProperty}
object OafUtils {
@ -21,7 +22,7 @@ object OafUtils {
di.setInferred(false)
di.setInvisible(invisible)
di.setTrust(trust)
di.setProvenanceaction(createQualifier("sysimport:actionset", "dnet:provenanceActions"))
di.setProvenanceaction(createQualifier(ModelConstants.SYSIMPORT_ACTIONSET, ModelConstants.DNET_PROVENANCE_ACTIONS))
di
}

7
dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/scholexplorer/DLItest.java
View File

@ -12,6 +12,7 @@ import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.SerializationFeature;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
@ -20,7 +21,7 @@ public class DLItest {
@Test
public void testMergePublication() throws JsonProcessingException {
DLIPublication a1 = new DLIPublication();
a1.setPid(Arrays.asList(createSP("123456", "pdb", "dnet:pid_types")));
a1.setPid(Arrays.asList(createSP("123456", "pdb", ModelConstants.DNET_PID_TYPES)));
a1.setTitle(Collections.singletonList(createSP("Un Titolo", "title", "dnetTitle")));
a1.setDlicollectedfrom(Arrays.asList(createCollectedFrom("znd", "Zenodo", "complete")));
a1.setCompletionStatus("complete");
@ -30,8 +31,8 @@ public class DLItest {
.setPid(
Arrays
.asList(
createSP("10.11", "doi", "dnet:pid_types"),
createSP("123456", "pdb", "dnet:pid_types")));
createSP("10.11", "doi", ModelConstants.DNET_PID_TYPES),
createSP("123456", "pdb", ModelConstants.DNET_PID_TYPES)));
a.setTitle(Collections.singletonList(createSP("A Title", "title", "dnetTitle")));
a
.setDlicollectedfrom(

5
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/ProtoConverter.java
View File

@ -15,6 +15,7 @@ import com.google.common.collect.Lists;
import com.googlecode.protobuf.format.JsonFormat;
import eu.dnetlib.data.proto.*;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.*;
public class ProtoConverter implements Serializable {
@ -106,8 +107,8 @@ public class ProtoConverter implements Serializable {
Qualifier q = new Qualifier();
q.setClassid(refereed.getValue());
q.setSchemename(refereed.getValue());
q.setSchemeid("dnet:review_levels");
q.setSchemename("dnet:review_levels");
q.setSchemeid(DNET_REVIEW_LEVELS);
q.setSchemename(DNET_REVIEW_LEVELS);
return q;
}

19
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/DataciteToOAFTransformation.scala
View File

@ -23,8 +23,6 @@ import java.util.regex.Pattern
import scala.collection.JavaConverters._
import scala.io.{Codec, Source}
case class DataciteType(doi:String,timestamp:Long,isActive:Boolean, json:String ){}
case class NameIdentifiersType(nameIdentifierScheme: Option[String], schemeUri: Option[String], nameIdentifier: Option[String]) {}
@ -49,10 +47,7 @@ object DataciteToOAFTransformation {
codec.onMalformedInput(CodingErrorAction.REPLACE)
codec.onUnmappableCharacter(CodingErrorAction.REPLACE)
val ACCESS_MODE_VOCABULARY = "dnet:access_modes"
val DOI_CLASS = "doi"
val SUBJ_CLASS = "keywords"
@ -62,7 +57,7 @@ object DataciteToOAFTransformation {
}
val mapper = new ObjectMapper()
val unknown_repository: HostedByMapType = HostedByMapType("openaire____::1256f046-bf1f-4afc-8b47-d0b147148b18", "Unknown Repository", "Unknown Repository", Some(1.0F))
val unknown_repository: HostedByMapType = HostedByMapType(ModelConstants.UNKNOWN_REPOSITORY_ORIGINALID, ModelConstants.UNKNOWN_REPOSITORY.getValue, ModelConstants.UNKNOWN_REPOSITORY.getValue, Some(1.0F))
val dataInfo: DataInfo = generateDataInfo("0.9")
val DATACITE_COLLECTED_FROM: KeyValue = OafMapperUtils.keyValue(ModelConstants.DATACITE_ID, "Datacite")
@ -244,9 +239,9 @@ object DataciteToOAFTransformation {
val r = new Relation
r.setSource(sourceId)
r.setTarget(targetId)
r.setRelType("resultProject")
r.setRelType(ModelConstants.RESULT_PROJECT)
r.setRelClass(relClass)
r.setSubRelType("outcome")
r.setSubRelType(ModelConstants.OUTCOME)
r.setCollectedfrom(List(cf).asJava)
r.setDataInfo(di)
r
@ -381,7 +376,7 @@ object DataciteToOAFTransformation {
result.setRelevantdate(dates.filter(d => d.date.isDefined && d.dateType.isDefined)
.map(d => (extract_date(d.date.get), d.dateType.get))
.filter(d => d._1.isDefined)
.map(d => (d._1.get, vocabularies.getTermAsQualifier("dnet:dataCite_date", d._2.toLowerCase())))
.map(d => (d._1.get, vocabularies.getTermAsQualifier(ModelConstants.DNET_DATACITE_DATE, d._2.toLowerCase())))
.filter(d => d._2 != null)
.map(d => generateOAFDate(d._1, d._2)).asJava)
@ -413,7 +408,7 @@ object DataciteToOAFTransformation {
val language: String = (json \\ "language").extractOrElse[String](null)
if (language != null)
result.setLanguage(vocabularies.getSynonymAsQualifier("dnet:languages", language))
result.setLanguage(vocabularies.getSynonymAsQualifier(ModelConstants.DNET_LANGUAGES, language))
val instance = result.getInstance().get(0)
@ -437,7 +432,7 @@ object DataciteToOAFTransformation {
})
val access_rights_qualifier = if (aRights.isDefined) aRights.get else OafMapperUtils.accessRight("UNKNOWN", "not available", ModelConstants.DNET_ACCESS_MODES, ModelConstants.DNET_ACCESS_MODES)
val access_rights_qualifier = if (aRights.isDefined) aRights.get else OafMapperUtils.accessRight(ModelConstants.UNKNOWN, ModelConstants.NOT_AVAILABLE, ModelConstants.DNET_ACCESS_MODES, ModelConstants.DNET_ACCESS_MODES)
if (client.isDefined) {
val hb = hostedByMap.getOrElse(client.get.toUpperCase(), unknown_repository)
@ -475,7 +470,7 @@ object DataciteToOAFTransformation {
di.setInferred(false)
di.setInvisible(false)
di.setTrust(trust)
di.setProvenanceaction(ModelConstants.ACTION_SET_PROVENANCE_QUALIFIER)
di.setProvenanceaction(ModelConstants.PROVENANCE_ACTION_SET_QUALIFIER)
di
}

3
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/BrokerConstants.java
View File

@ -7,12 +7,13 @@ import java.util.Set;
import eu.dnetlib.dhp.broker.model.Event;
import eu.dnetlib.dhp.broker.oa.util.aggregators.simple.ResultGroup;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.common.ModelSupport;
public class BrokerConstants {
public static final String OPEN_ACCESS = "OPEN";
public static final String IS_MERGED_IN_CLASS = "isMergedIn";
public static final String IS_MERGED_IN_CLASS = ModelConstants.IS_MERGED_IN;
public static final String COLLECTED_FROM_REL = "collectedFrom";

16
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCopyOpenorgsMergeRels.java
View File

@ -35,8 +35,6 @@ import net.sf.saxon.ma.trie.Tuple2;
public class SparkCopyOpenorgsMergeRels extends AbstractSparkAction {
private static final Logger log = LoggerFactory.getLogger(SparkCopyOpenorgsMergeRels.class);
public static final String PROVENANCE_ACTION_CLASS = "sysimport:dedup";
public static final String DNET_PROVENANCE_ACTIONS = "dnet:provenanceActions";
public SparkCopyOpenorgsMergeRels(ArgumentApplicationParser parser, SparkSession spark) {
super(parser, spark);
@ -93,7 +91,7 @@ public class SparkCopyOpenorgsMergeRels extends AbstractSparkAction {
JavaRDD<Relation> selfRawRels = rawRels
.map(r -> r.getSource())
.distinct()
.map(s -> rel(s, s, "isSimilarTo", dedupConf));
.map(s -> rel(s, s, ModelConstants.IS_SIMILAR_TO, dedupConf));
log.info("Number of raw Openorgs Relations collected: {}", rawRels.count());
@ -109,8 +107,8 @@ public class SparkCopyOpenorgsMergeRels extends AbstractSparkAction {
List<Relation> mergerels = new ArrayList<>();
mergerels.add(rel(rel.getSource(), rel.getTarget(), "merges", dedupConf));
mergerels.add(rel(rel.getTarget(), rel.getSource(), "isMergedIn", dedupConf));
mergerels.add(rel(rel.getSource(), rel.getTarget(), ModelConstants.MERGES, dedupConf));
mergerels.add(rel(rel.getTarget(), rel.getSource(), ModelConstants.IS_MERGED_IN, dedupConf));
return mergerels.iterator();
});
@ -174,10 +172,10 @@ public class SparkCopyOpenorgsMergeRels extends AbstractSparkAction {
info.setInvisible(false);
info.setInferenceprovenance(dedupConf.getWf().getConfigurationId());
Qualifier provenanceAction = new Qualifier();
provenanceAction.setClassid(PROVENANCE_ACTION_CLASS);
provenanceAction.setClassname(PROVENANCE_ACTION_CLASS);
provenanceAction.setSchemeid(DNET_PROVENANCE_ACTIONS);
provenanceAction.setSchemename(DNET_PROVENANCE_ACTIONS);
provenanceAction.setClassid(ModelConstants.PROVENANCE_DEDUP);
provenanceAction.setClassname(ModelConstants.PROVENANCE_DEDUP);
provenanceAction.setSchemeid(ModelConstants.DNET_PROVENANCE_ACTIONS);
provenanceAction.setSchemename(ModelConstants.DNET_PROVENANCE_ACTIONS);
info.setProvenanceaction(provenanceAction);
// TODO calculate the trust value based on the similarity score of the elements in the CC

8
dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateConnectedComponent.java
View File

@ -22,6 +22,7 @@ import com.google.common.hash.Hashing;
import eu.dnetlib.dedup.graph.ConnectedComponent;
import eu.dnetlib.dedup.graph.GraphProcessor;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.pace.config.DedupConfig;
@ -47,8 +48,7 @@ public class SparkCreateConnectedComponent {
final String inputPath = parser.get("sourcePath");
final String entity = parser.get("entity");
final String targetPath = parser.get("targetPath");
// final DedupConfig dedupConf =
// DedupConfig.load(IOUtils.toString(SparkCreateConnectedComponent.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf2.json")));
final DedupConfig dedupConf = DedupConfig.load(parser.get("dedupConf"));
final JavaPairRDD<Object, String> vertexes = spark
@ -88,12 +88,12 @@ public class SparkCreateConnectedComponent {
Relation r = new Relation();
r.setSource(c.getCcId());
r.setTarget(id);
r.setRelClass("merges");
r.setRelClass(ModelConstants.MERGES);
tmp.add(r);
r = new Relation();
r.setTarget(c.getCcId());
r.setSource(id);
r.setRelClass("isMergedIn");
r.setRelClass(ModelConstants.IS_MERGED_IN);
tmp.add(r);
return tmp.stream();
})

20
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala
View File

@ -30,8 +30,6 @@ object DoiBoostMappingUtil {
//STATIC STRING
val MAG = "microsoft"
val MAG_NAME = "Microsoft Academic Graph"
val ORCID = "orcid"
val ORCID_PENDING = "orcid_pending"
val CROSSREF = "Crossref"
val UNPAYWALL = "UnpayWall"
val GRID_AC = "grid.ac"
@ -39,8 +37,6 @@ object DoiBoostMappingUtil {
val doiBoostNSPREFIX = "doiboost____"
val OPENAIRE_PREFIX = "openaire____"
val SEPARATOR = "::"
val DNET_LANGUAGES = "dnet:languages"
val PID_TYPES = "dnet:pid_types"
val invalidName = List(",", "none none", "none, none", "none &na;", "(:null)", "test test test", "test test", "test", "&na; &na;")
@ -122,12 +118,11 @@ object DoiBoostMappingUtil {
def getOpenAccessQualifier():AccessRight = {
OafUtils.createAccessRight("OPEN","Open Access","dnet:access_modes", "dnet:access_modes")
OafUtils.createAccessRight("OPEN","Open Access", ModelConstants.DNET_ACCESS_MODES, ModelConstants.DNET_ACCESS_MODES)
}
def getRestrictedQualifier():AccessRight = {
OafUtils.createAccessRight("RESTRICTED","Restricted","dnet:access_modes", "dnet:access_modes")
OafUtils.createAccessRight("RESTRICTED","Restricted",ModelConstants.DNET_ACCESS_MODES, ModelConstants.DNET_ACCESS_MODES)
}
@ -141,14 +136,12 @@ object DoiBoostMappingUtil {
val item = if (input._2 != null) input._2._2 else null
val instanceType:Option[Instance] = extractInstance(publication)
if (instanceType.isDefined) {
publication.getInstance().asScala.foreach(i => i.setInstancetype(instanceType.get.getInstancetype))
}
publication.getInstance().asScala.foreach(i => {
var hb = new KeyValue
if (item != null) {
@ -179,7 +172,6 @@ object DoiBoostMappingUtil {
publication
}
def generateDSId(input: String): String = {
val b = StringUtils.substringBefore(input, "::")
@ -187,12 +179,10 @@ object DoiBoostMappingUtil {
s"10|${b}::${DHPUtils.md5(a)}"
}
def generateDataInfo(): DataInfo = {
generateDataInfo("0.9")
}
def filterPublication(publication: Publication): Boolean = {
//Case empty publication
@ -264,7 +254,7 @@ object DoiBoostMappingUtil {
di.setInferred(false)
di.setInvisible(false)
di.setTrust(trust)
di.setProvenanceaction(OafUtils.createQualifier("sysimport:actionset", "dnet:provenanceActions"))
di.setProvenanceaction(OafUtils.createQualifier(ModelConstants.SYSIMPORT_ACTIONSET, ModelConstants.DNET_PROVENANCE_ACTIONS))
di
}
@ -330,8 +320,8 @@ object DoiBoostMappingUtil {
def createORIDCollectedFrom(): KeyValue = {
val cf = new KeyValue
cf.setValue(ORCID)
cf.setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + DHPUtils.md5(ORCID.toLowerCase))
cf.setValue(StringUtils.upperCase(ModelConstants.ORCID))
cf.setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + DHPUtils.md5(ModelConstants.ORCID.toLowerCase))
cf
}

10
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala
View File

@ -1,5 +1,6 @@
package eu.dnetlib.doiboost.crossref
import eu.dnetlib.dhp.schema.common.ModelConstants
import eu.dnetlib.dhp.schema.oaf._
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory
import eu.dnetlib.dhp.utils.DHPUtils
@ -14,7 +15,6 @@ import org.slf4j.{Logger, LoggerFactory}
import scala.collection.JavaConverters._
import scala.collection.mutable
import scala.util.matching.Regex
import eu.dnetlib.dhp.schema.scholexplorer.OafUtils
case class CrossrefDT(doi: String, json:String, timestamp: Long) {}
@ -88,7 +88,7 @@ case object Crossref2Oaf {
//MAPPING Crossref DOI into PID
val doi: String = (json \ "DOI").extract[String]
result.setPid(List(createSP(doi, "doi", PID_TYPES)).asJava)
result.setPid(List(createSP(doi, "doi", ModelConstants.DNET_PID_TYPES)).asJava)
//MAPPING Crossref DOI into OriginalId
//and Other Original Identifier of dataset like clinical-trial-number
@ -186,13 +186,13 @@ case object Crossref2Oaf {
if(has_review != JNothing) {
instance.setRefereed(
OafUtils.createQualifier("0001", "peerReviewed", "dnet:review_levels", "dnet:review_levels"))
OafUtils.createQualifier("0001", "peerReviewed", ModelConstants.DNET_REVIEW_LEVELS, ModelConstants.DNET_REVIEW_LEVELS))
}
instance.setAccessright(getRestrictedQualifier())
result.setInstance(List(instance).asJava)
instance.setInstancetype(OafUtils.createQualifier(cobjCategory.substring(0, 4), cobjCategory.substring(5), "dnet:publication_resource", "dnet:publication_resource"))
instance.setInstancetype(OafUtils.createQualifier(cobjCategory.substring(0, 4), cobjCategory.substring(5), ModelConstants.DNET_PUBLICATION_RESOURCE, ModelConstants.DNET_PUBLICATION_RESOURCE))
result.setResourcetype(OafUtils.createQualifier(cobjCategory.substring(0, 4),"dnet:dataCite_resource"))
instance.setCollectedfrom(createCrossrefCollectedFrom())
@ -221,7 +221,7 @@ case object Crossref2Oaf {
a.setFullname(s"$given $family")
a.setRank(index+1)
if (StringUtils.isNotBlank(orcid))
a.setPid(List(createSP(orcid, ORCID_PENDING, PID_TYPES, generateDataInfo())).asJava)
a.setPid(List(createSP(orcid, ModelConstants.ORCID_PENDING, ModelConstants.DNET_PID_TYPES, generateDataInfo())).asJava)
a
}

17
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/MagDataModel.scala
View File

@ -1,6 +1,7 @@
package eu.dnetlib.doiboost.mag
import eu.dnetlib.dhp.schema.common.ModelConstants
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory
import eu.dnetlib.dhp.schema.oaf.{Instance, Journal, Publication, StructuredProperty}
import eu.dnetlib.doiboost.DoiBoostMappingUtil
@ -191,7 +192,7 @@ case object ConversionUtil {
val authors = inputParams._2
val pub = new Publication
pub.setPid(List(createSP(paper.Doi.toLowerCase, "doi", PID_TYPES)).asJava)
pub.setPid(List(createSP(paper.Doi.toLowerCase, "doi", ModelConstants.DNET_PID_TYPES)).asJava)
pub.setOriginalId(List(paper.PaperId.toString, paper.Doi.toLowerCase).asJava)
//IMPORTANT
@ -200,8 +201,8 @@ case object ConversionUtil {
pub.setId(IdentifierFactory.createDOIBoostIdentifier(pub))
val mainTitles = createSP(paper.PaperTitle, "main title", "dnet:dataCite_title")
val originalTitles = createSP(paper.OriginalTitle, "alternative title", "dnet:dataCite_title")
val mainTitles = createSP(paper.PaperTitle, "main title", ModelConstants.DNET_DATACITE_TITLE)
val originalTitles = createSP(paper.OriginalTitle, "alternative title", ModelConstants.DNET_DATACITE_TITLE)
pub.setTitle(List(mainTitles, originalTitles).asJava)
pub.setSource(List(asField(paper.BookTitle)).asJava)
@ -214,7 +215,7 @@ case object ConversionUtil {
a.setFullname(f.author.DisplayName.get)
if(f.affiliation!= null)
a.setAffiliation(List(asField(f.affiliation)).asJava)
a.setPid(List(createSP(s"https://academic.microsoft.com/#/detail/${f.author.AuthorId}", "URL", PID_TYPES)).asJava)
a.setPid(List(createSP(s"https://academic.microsoft.com/#/detail/${f.author.AuthorId}", "URL", ModelConstants.DNET_PID_TYPES)).asJava)
a
}
pub.setAuthor(authorsOAF.asJava)
@ -253,14 +254,14 @@ case object ConversionUtil {
val description = inputParams._2
val pub = new Publication
pub.setPid(List(createSP(paper.Doi.toLowerCase, "doi", PID_TYPES)).asJava)
pub.setPid(List(createSP(paper.Doi.toLowerCase, "doi", ModelConstants.DNET_PID_TYPES)).asJava)
pub.setOriginalId(List(paper.PaperId.toString, paper.Doi.toLowerCase).asJava)
//Set identifier as 50 | doiboost____::md5(DOI)
pub.setId(generateIdentifier(pub, paper.Doi.toLowerCase))
val mainTitles = createSP(paper.PaperTitle, "main title", "dnet:dataCite_title")
val originalTitles = createSP(paper.OriginalTitle, "alternative title", "dnet:dataCite_title")
val mainTitles = createSP(paper.PaperTitle, "main title", ModelConstants.DNET_DATACITE_TITLE)
val originalTitles = createSP(paper.OriginalTitle, "alternative title", ModelConstants.DNET_DATACITE_TITLE)
pub.setTitle(List(mainTitles, originalTitles).asJava)
pub.setSource(List(asField(paper.BookTitle)).asJava)
@ -281,7 +282,7 @@ case object ConversionUtil {
a.setAffiliation(List(asField(f.affiliation)).asJava)
a.setPid(List(createSP(s"https://academic.microsoft.com/#/detail/${f.author.AuthorId}", "URL", PID_TYPES)).asJava)
a.setPid(List(createSP(s"https://academic.microsoft.com/#/detail/${f.author.AuthorId}", "URL", ModelConstants.DNET_PID_TYPES)).asJava)
a

11
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ORCIDToOAF.scala
View File

@ -1,11 +1,12 @@
package eu.dnetlib.doiboost.orcid
import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.schema.common.ModelConstants
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory
import eu.dnetlib.dhp.schema.oaf.{Author, DataInfo, Publication}
import eu.dnetlib.dhp.schema.orcid.OrcidDOI
import eu.dnetlib.doiboost.DoiBoostMappingUtil
import eu.dnetlib.doiboost.DoiBoostMappingUtil.{ORCID, PID_TYPES, createSP, generateDataInfo, generateIdentifier}
import eu.dnetlib.doiboost.DoiBoostMappingUtil.{createSP, generateDataInfo}
import org.apache.commons.lang.StringUtils
import org.slf4j.{Logger, LoggerFactory}
@ -48,7 +49,7 @@ object ORCIDToOAF {
def convertTOOAF(input:OrcidDOI) :Publication = {
val doi = input.getDoi
val pub:Publication = new Publication
pub.setPid(List(createSP(doi.toLowerCase, "doi", PID_TYPES)).asJava)
pub.setPid(List(createSP(doi.toLowerCase, "doi", ModelConstants.DNET_PID_TYPES)).asJava)
pub.setDataInfo(generateDataInfo())
pub.setId(IdentifierFactory.createDOIBoostIdentifier(pub))
@ -74,8 +75,8 @@ object ORCIDToOAF {
def generateOricPIDDatainfo():DataInfo = {
val di =DoiBoostMappingUtil.generateDataInfo("0.91")
di.getProvenanceaction.setClassid("sysimport:crosswalk:entityregistry")
di.getProvenanceaction.setClassname("Harvested")
di.getProvenanceaction.setClassid(ModelConstants.SYSIMPORT_CROSSWALK_ENTITYREGISTRY)
di.getProvenanceaction.setClassname(ModelConstants.HARVESTED)
di
}
@ -88,7 +89,7 @@ object ORCIDToOAF {
else
a.setFullname(s"$given $family")
if (StringUtils.isNotBlank(orcid))
a.setPid(List(createSP(orcid, ORCID, PID_TYPES, generateOricPIDDatainfo())).asJava)
a.setPid(List(createSP(orcid, ModelConstants.ORCID, ModelConstants.DNET_PID_TYPES, generateOricPIDDatainfo())).asJava)
a
}

15
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java
View File

@ -26,12 +26,11 @@ import eu.dnetlib.doiboost.orcidnodoi.util.Pair;
/**
* This class converts an orcid publication from json format to oaf
*/
public class PublicationToOaf implements Serializable {
static Logger logger = LoggerFactory.getLogger(PublicationToOaf.class);
public static final String ORCID = "ORCID";
public static final String ORCID = StringUtils.upperCase(ModelConstants.ORCID);
public final static String orcidPREFIX = "orcid_______";
public static final String OPENAIRE_PREFIX = "openaire____";
public static final String SEPARATOR = "::";
@ -70,7 +69,7 @@ public class PublicationToOaf implements Serializable {
private static Map<String, Pair<String, String>> datasources = new HashMap<String, Pair<String, String>>() {
{
put(ORCID.toLowerCase(), new Pair<>(ORCID, OPENAIRE_PREFIX + SEPARATOR + "orcid"));
put(ORCID.toLowerCase(), new Pair<>(ORCID, OPENAIRE_PREFIX + SEPARATOR + ModelConstants.ORCID));
}
};
@ -135,8 +134,8 @@ public class PublicationToOaf implements Serializable {
dataInfo
.setProvenanceaction(
mapQualifier(
"sysimport:actionset:orcidworks-no-doi",
"sysimport:actionset:orcidworks-no-doi",
ModelConstants.SYSIMPORT_ORCID_NO_DOI,
ModelConstants.SYSIMPORT_ORCID_NO_DOI,
ModelConstants.DNET_PROVENANCE_ACTIONS,
ModelConstants.DNET_PROVENANCE_ACTIONS));
publication.setDataInfo(dataInfo);
@ -183,15 +182,11 @@ public class PublicationToOaf implements Serializable {
}
return null;
}
Qualifier q = mapQualifier(
"main title", "main title", ModelConstants.DNET_DATACITE_TITLE, ModelConstants.DNET_DATACITE_TITLE);
publication
.setTitle(
titles
.stream()
.map(t -> {
return mapStructuredProperty(t, q, null);
})
.map(t -> mapStructuredProperty(t, ModelConstants.MAIN_TITLE_QUALIFIER, null))
.filter(s -> s != null)
.collect(Collectors.toList()));
// Adding identifier

4
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/uw/UnpayWallToOAF.scala
View File

@ -79,7 +79,7 @@ object UnpayWallToOAF {
if (oaLocation.license.isDefined)
i.setLicense(asField(oaLocation.license.get))
pub.setPid(List(createSP(doi, "doi", PID_TYPES)).asJava)
pub.setPid(List(createSP(doi, "doi", ModelConstants.DNET_PID_TYPES)).asJava)
// Ticket #6282 Adding open Access Colour
if (colour.isDefined) {
@ -90,7 +90,7 @@ object UnpayWallToOAF {
a.setSchemename(ModelConstants.DNET_ACCESS_MODES)
a.setOpenAccessRoute(colour.get)
i.setAccessright(a)
i.setPid(List(createSP(doi, "doi", PID_TYPES)).asJava)
i.setPid(List(createSP(doi, "doi", ModelConstants.DNET_PID_TYPES)).asJava)
}
pub.setInstance(List(i).asJava)

3
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/merge/MergeGraphTableSparkJob.java
View File

@ -25,6 +25,7 @@ import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.oa.graph.clean.CleanGraphSparkJob;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*;
import scala.Tuple2;
@ -46,7 +47,7 @@ public class MergeGraphTableSparkJob {
static {
Qualifier compatibility = new Qualifier();
compatibility.setClassid("UNKNOWN");
compatibility.setClassid(ModelConstants.UNKNOWN);
DATASOURCE.setOpenairecompatibility(compatibility);
}

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

@ -13,6 +13,7 @@ import org.dom4j.Node;
import eu.dnetlib.dhp.common.PacePerson;
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.IdentifierFactory;
@ -169,7 +170,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
res
.add(
structuredProperty(
((Node) o).getText(), "UNKNOWN", "UNKNOWN", DNET_DATACITE_DATE, DNET_DATACITE_DATE,
((Node) o).getText(), UNKNOWN, UNKNOWN, DNET_DATACITE_DATE, DNET_DATACITE_DATE,
info));
} else {
res
@ -242,7 +243,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
@Override
protected Qualifier prepareSoftwareProgrammingLanguage(final Document doc, final DataInfo info) {
return prepareQualifier(doc, "//datacite:format", "dnet:programming_languages");
return prepareQualifier(doc, "//datacite:format", DNET_PROGRAMMING_LANGUAGES);
}
@Override

13
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/SparkAddLinkUpdates.scala
View File

@ -1,5 +1,6 @@
package eu.dnetlib.dhp.sx.ebi
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.common.ModelConstants
import eu.dnetlib.dhp.schema.oaf.{Author, Instance, Journal, KeyValue, Oaf, Publication, Relation, Dataset => OafDataset}
import eu.dnetlib.dhp.schema.scholexplorer.OafUtils.createQualifier
import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication, OafUtils, ProvenaceInfo}
@ -50,7 +51,7 @@ case class EBILinks(relation:String, pubdate:String, tpid:String, tpidType:Strin
val p = new DLIPublication
p.setId(dnetPublicationId)
p.setDataInfo(OafUtils.generateDataInfo())
p.setPid(List(OafUtils.createSP(input.getPmid.toLowerCase.trim, "pmid", "dnet:pid_types")).asJava)
p.setPid(List(OafUtils.createSP(input.getPmid.toLowerCase.trim, "pmid", ModelConstants.DNET_PID_TYPES)).asJava)
p.setCompletionStatus("complete")
val pi = new ProvenaceInfo
pi.setId("dli_________::europe_pmc__")
@ -76,13 +77,13 @@ case class EBILinks(relation:String, pubdate:String, tpid:String, tpidType:Strin
if (input.getJournal != null)
p.setJournal(journalToOAF(input.getJournal))
p.setTitle(List(OafUtils.createSP(input.getTitle, "main title", "dnet:dataCite_title")).asJava)
p.setTitle(List(OafUtils.createSP(input.getTitle, "main title", ModelConstants.DNET_DATACITE_TITLE)).asJava)
p.setDateofacceptance(OafUtils.asField(input.getDate))
val i = new Instance
i.setCollectedfrom(generatePubmedDLICollectedFrom())
i.setDateofacceptance(p.getDateofacceptance)
i.setUrl(List(s"https://pubmed.ncbi.nlm.nih.gov/${input.getPmid}").asJava)
i.setInstancetype(createQualifier("0001", "Article", "dnet:publication_resource", "dnet:publication_resource"))
i.setInstancetype(createQualifier("0001", "Article", ModelConstants.DNET_PUBLICATION_RESOURCE, ModelConstants.DNET_PUBLICATION_RESOURCE))
p.setInstance(List(i).asJava)
p
}
@ -139,7 +140,7 @@ case class EBILinks(relation:String, pubdate:String, tpid:String, tpidType:Strin
val d = new DLIDataset
d.setId(targetDnetId)
d.setDataInfo(OafUtils.generateDataInfo())
d.setPid(List(OafUtils.createSP(l.tpid.toLowerCase.trim, l.tpidType.toLowerCase.trim, "dnet:pid_types")).asJava)
d.setPid(List(OafUtils.createSP(l.tpid.toLowerCase.trim, l.tpidType.toLowerCase.trim, ModelConstants.DNET_PID_TYPES)).asJava)
d.setCompletionStatus("complete")
val pi = new ProvenaceInfo
pi.setId("dli_________::europe_pmc__")
@ -149,13 +150,13 @@ case class EBILinks(relation:String, pubdate:String, tpid:String, tpidType:Strin
d.setDlicollectedfrom(List(pi).asJava)
d.setCollectedfrom(List(generatePubmedDLICollectedFrom()).asJava)
d.setPublisher(OafUtils.asField(l.publisher))
d.setTitle(List(OafUtils.createSP(l.title, "main title", "dnet:dataCite_title")).asJava)
d.setTitle(List(OafUtils.createSP(l.title, "main title", ModelConstants.DNET_DATACITE_TITLE)).asJava)
d.setDateofacceptance(OafUtils.asField(l.pubdate))
val i = new Instance
i.setCollectedfrom(generatePubmedDLICollectedFrom())
i.setDateofacceptance(d.getDateofacceptance)
i.setUrl(List(l.turl).asJava)
i.setInstancetype(createQualifier("0021", "Dataset", "dnet:publication_resource", "dnet:publication_resource"))
i.setInstancetype(createQualifier("0021", "Dataset", ModelConstants.DNET_PUBLICATION_RESOURCE, ModelConstants.DNET_PUBLICATION_RESOURCE))
d.setInstance(List(i).asJava)
List(relation, inverseRelation, d)
})

13
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/AbstractScholexplorerParser.java
View File

@ -13,6 +13,7 @@ import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import eu.dnetlib.dhp.parser.utility.VtdUtilityParser;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.scholexplorer.DLIUnknown;
import eu.dnetlib.dhp.schema.scholexplorer.ProvenaceInfo;
@ -76,8 +77,8 @@ public abstract class AbstractScholexplorerParser {
final Qualifier pidType = new Qualifier();
pidType.setClassname(result.getAttributes().get(fieldName));
pidType.setClassid(result.getAttributes().get(fieldName));
pidType.setSchemename("dnet:pid_types");
pidType.setSchemeid("dnet:pid_types");
pidType.setSchemename(ModelConstants.DNET_PID_TYPES);
pidType.setSchemeid(ModelConstants.DNET_PID_TYPES);
pid.setQualifier(pidType);
return pid;
}
@ -90,8 +91,8 @@ public abstract class AbstractScholexplorerParser {
input.setValue(matcher.group());
if (input.getQualifier() == null) {
input.setQualifier(new Qualifier());
input.getQualifier().setSchemename("dnet:pid_types");
input.getQualifier().setSchemeid("dnet:pid_types");
input.getQualifier().setSchemename(ModelConstants.DNET_PID_TYPES);
input.getQualifier().setSchemeid(ModelConstants.DNET_PID_TYPES);
}
input.getQualifier().setClassid("doi");
input.getQualifier().setClassname("doi");
@ -141,8 +142,8 @@ public abstract class AbstractScholexplorerParser {
final Qualifier pt = new Qualifier();
pt.setClassname(pidType);
pt.setClassid(pidType);
pt.setSchemename("dnet:pid_types");
pt.setSchemeid("dnet:pid_types");
pt.setSchemename(ModelConstants.DNET_PID_TYPES);
pt.setSchemeid(ModelConstants.DNET_PID_TYPES);
sourcePid.setQualifier(pt);
uk.setPid(Collections.singletonList(sourcePid));
uk.setDateofcollection(dateOfCollection);

7
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/DatasetScholexplorerParser.java
View File

@ -15,6 +15,7 @@ import com.ximpleware.VTDNav;
import eu.dnetlib.dhp.parser.utility.VtdUtilityParser;
import eu.dnetlib.dhp.parser.utility.VtdUtilityParser.Node;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.scholexplorer.DLIDataset;
import eu.dnetlib.dhp.schema.scholexplorer.ProvenaceInfo;
@ -281,11 +282,7 @@ public class DatasetScholexplorerParser extends AbstractScholexplorerParser {
t -> {
final StructuredProperty st = new StructuredProperty();
st.setValue(t);
st
.setQualifier(
generateQualifier(
"main title", "main title", "dnet:dataCite_title",
"dnet:dataCite_title"));
st.setQualifier(ModelConstants.MAIN_TITLE_QUALIFIER);
return st;
})
.collect(Collectors.toList()));

8
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/DLIToOAF.scala
View File

@ -159,7 +159,7 @@ object DLIToOAF {
result.setUrl(e.url)
result.setRefidentifier(e.pid)
result.setDataInfo(generateDataInfo())
result.setQualifier(createQualifier(e.classId, "dnet:externalReference_typologies"))
result.setQualifier(createQualifier(e.classId, ModelConstants.DNET_EXTERNAL_REF_TYPES))
result
})
publication.setExternalReference(eRefs.asJava)
@ -238,7 +238,7 @@ object DLIToOAF {
if (inputPublication.getAuthor == null || inputPublication.getAuthor.isEmpty)
return null
result.setAuthor(inputPublication.getAuthor.asScala.map(convertAuthor).asJava)
result.setResulttype(createQualifier(inputPublication.getResulttype.getClassid, inputPublication.getResulttype.getClassname, "dnet:result_typologies", "dnet:result_typologies"))
result.setResulttype(createQualifier(inputPublication.getResulttype.getClassid, inputPublication.getResulttype.getClassname, ModelConstants.DNET_RESULT_TYPOLOGIES, ModelConstants.DNET_RESULT_TYPOLOGIES))
if (inputPublication.getSubject != null)
result.setSubject(inputPublication.getSubject.asScala.map(convertSubject).asJava)
@ -259,7 +259,7 @@ object DLIToOAF {
result.setDateofacceptance(asField(inputPublication.getRelevantdate.get(0).getValue))
result.setPublisher(inputPublication.getPublisher)
result.setSource(inputPublication.getSource)
result.setBestaccessright(createAccessRight("UNKNOWN", "not available", "dnet:access_modes", "dnet:access_modes"))
result.setBestaccessright(createAccessRight(ModelConstants.UNKNOWN, ModelConstants.NOT_AVAILABLE, ModelConstants.DNET_ACCESS_MODES, ModelConstants.DNET_ACCESS_MODES))
val dois = result.getPid.asScala.filter(p => "doi".equalsIgnoreCase(p.getQualifier.getClassname)).map(p => p.getValue)
if (dois.isEmpty)
@ -390,7 +390,7 @@ object DLIToOAF {
}
def patchTitle(t: StructuredProperty): StructuredProperty = {
t.setQualifier(createQualifier("main title", ModelConstants.DNET_DATACITE_TITLE))
t.setQualifier(ModelConstants.MAIN_TITLE_QUALIFIER)
t
}

2
dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/RelationComparator.java
View File

@ -18,7 +18,7 @@ public class RelationComparator implements Comparator<Relation> {
static {
weights.put(ModelConstants.OUTCOME, 0);
weights.put(ModelConstants.SUPPLEMENT, 1);
weights.put(ModelConstants.REVIEWS, 2);
weights.put(ModelConstants.REVIEW, 2);
weights.put(ModelConstants.CITATION, 3);
weights.put(ModelConstants.AFFILIATION, 4);
weights.put(ModelConstants.RELATIONSHIP, 5);