forked from D-Net/dnet-hadoop
added generation of Scholix collection
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2ef3705b2c
commit
7936583a3d
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@ -39,19 +39,14 @@ public class SparkGenerateScholix {
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final JavaRDD<String> relationToExport = sc.textFile(graphPath + "/relation").filter(ProvisionUtil::isNotDeleted);
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final JavaPairRDD<String,String> scholixSummary = sc.textFile(workingDirPath + "/summary").mapToPair((PairFunction<String, String, String>) i -> new Tuple2<>(DHPUtils.getJPathString(jsonIDPath, i), i));
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PairFunction<Tuple2<String, String>, String, Scholix> k =
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summaryRelation ->
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new Tuple2<>(
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DHPUtils.getJPathString(targetIDPath,summaryRelation._2()),
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Scholix.generateScholixWithSource(summaryRelation._1(), summaryRelation._2()));
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scholixSummary.join(
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relationToExport
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.mapToPair((PairFunction<String, String, String>) i -> new Tuple2<>(DHPUtils.getJPathString(sourceIDPath, i), i)))
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.map(Tuple2::_2)
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.mapToPair(k)
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.mapToPair(summaryRelation ->
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new Tuple2<>(
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DHPUtils.getJPathString(targetIDPath,summaryRelation._2()),
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Scholix.generateScholixWithSource(summaryRelation._1(), summaryRelation._2())))
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.join(scholixSummary)
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.map(Tuple2::_2)
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.map(i -> i._1().addTarget(i._2()))
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@ -3,10 +3,8 @@ package eu.dnetlib.dhp.provision.scholix;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.provision.scholix.summary.ScholixSummary;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import eu.dnetlib.dhp.utils.DHPUtils;
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import java.io.Serializable;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.Collections;
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import java.util.List;
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import java.util.stream.Collectors;
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@ -32,25 +30,39 @@ public class Scholix implements Serializable {
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try {
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ScholixSummary scholixSummary = mapper.readValue(sourceSummaryJson, ScholixSummary.class);
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Relation rel = mapper.readValue(sourceSummaryJson, Relation.class);
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Relation rel = mapper.readValue(relation, Relation.class);
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final Scholix s = new Scholix();
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if (scholixSummary.getDate() != null)
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s.setPublicationDate(scholixSummary.getDate().stream().findFirst().orElse(null));
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s.setLinkprovider(rel.getCollectedFrom().stream().map(cf ->
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new ScholixEntityId(cf.getValue(), Collections.singletonList(
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new ScholixIdentifier(cf.getKey(), "dnet_identifier")
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))).collect(Collectors.toList()));
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s.setRelationship(new ScholixRelationship(rel.getRelType(),rel.getRelClass(),null ));
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s.setSource(ScholixResource.fromSummary(scholixSummary));
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return s;
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} catch (Throwable e) {
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throw new RuntimeException(e);
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}
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}
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private void generateIdentifier( ) {
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setIdentifier(DHPUtils.md5(String.format("%s::%s::%s",source.getDnetIdentifier(),relationship.getName(), target.getDnetIdentifier())));
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}
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public Scholix addTarget(final String targetSummaryJson) {
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return this;
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final ObjectMapper mapper = new ObjectMapper();
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try {
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ScholixSummary targetSummary = mapper.readValue(targetSummaryJson, ScholixSummary.class);
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setTarget(ScholixResource.fromSummary(targetSummary));
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generateIdentifier();
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return this;
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} catch (Throwable e) {
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throw new RuntimeException(e);
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}
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}
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@ -1,26 +1,70 @@
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package eu.dnetlib.dhp.provision.scholix;
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import eu.dnetlib.dhp.provision.scholix.summary.ScholixSummary;
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import java.io.Serializable;
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import java.util.Arrays;
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import java.util.Collections;
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import java.util.List;
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import java.util.stream.Collectors;
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public class ScholixResource implements Serializable {
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private ScholixIdentifier identifier ;
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private String dnetIdentifier ;
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private String objectType ;
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private String objectSubType ;
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private String title ;
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private List<ScholixEntityId> creator ;
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private String publicationDate ;
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private List<ScholixEntityId> publisher ;
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private List<ScholixCollectedFrom> collectedFrom ;
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private List<ScholixIdentifier> identifier;
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private String dnetIdentifier;
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private String objectType;
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private String objectSubType;
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private String title;
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private List<ScholixEntityId> creator;
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private String publicationDate;
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private List<ScholixEntityId> publisher;
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private List<ScholixCollectedFrom> collectedFrom;
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public ScholixIdentifier getIdentifier() {
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public static ScholixResource fromSummary(ScholixSummary summary) {
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final ScholixResource resource = new ScholixResource();
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resource.setDnetIdentifier(summary.getId());
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resource.setIdentifier(summary.getLocalIdentifier().stream()
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.map(i ->
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new ScholixIdentifier(i.getId(), i.getType()))
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.collect(Collectors.toList()));
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resource.setObjectType(summary.getTypology().toString());
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resource.setTitle(summary.getTitle().stream().findAny().orElse(null));
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if (summary.getAuthor() != null)
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resource.setCreator(summary.getAuthor().stream()
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.map(c -> new ScholixEntityId(c, null))
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.collect(Collectors.toList())
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);
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if (summary.getDate() != null)
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resource.setPublicationDate(summary.getDate().stream().findAny().orElse(null));
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if (summary.getPublisher() != null)
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resource.setPublisher(summary.getPublisher().stream()
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.map(p -> new ScholixEntityId(p, null))
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.collect(Collectors.toList())
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);
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if (summary.getDatasources() != null)
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resource.setCollectedFrom(summary.getDatasources().stream()
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.map(d ->
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new ScholixCollectedFrom(new ScholixEntityId(d.getDatasourceName(),
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Collections.singletonList(new ScholixIdentifier(d.getDatasourceId(), "dnet_identifier"))
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), "collected", d.getCompletionStatus()))
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.collect(Collectors.toList()));
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return resource;
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}
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public List<ScholixIdentifier> getIdentifier() {
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return identifier;
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}
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public ScholixResource setIdentifier(ScholixIdentifier identifier) {
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public ScholixResource setIdentifier(List<ScholixIdentifier> identifier) {
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this.identifier = identifier;
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return this;
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}
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@ -27,7 +27,7 @@
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</parameters>
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<start to="indexSummary"/>
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<start to="generateScholix"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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@ -91,10 +91,29 @@
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<arg>--sourcePath</arg><arg>${workingDirPath}/summary</arg>
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<arg>--index</arg><arg>${index}_object</arg>
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</spark>
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<ok to="End"/>
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<ok to="generateScholix"/>
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<error to="Kill"/>
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</action>
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<action name="generateScholix">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>generate Summary</name>
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<class>eu.dnetlib.dhp.provision.SparkGenerateScholix</class>
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<jar>dhp-graph-provision-${projectVersion}.jar</jar>
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<spark-opts>--executor-memory ${sparkExecutorMemory} --driver-memory=${sparkDriverMemory} ${sparkExtraOPT}</spark-opts>
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<arg>-mt</arg> <arg>yarn-cluster</arg>
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<arg>--workingDirPath</arg><arg>${workingDirPath}</arg>
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<arg>--graphPath</arg><arg>${graphPath}</arg>
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</spark>
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<ok to="indexSummary"/>
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<error to="Kill"/>
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</action>
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<end name="End"/>
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</workflow-app>
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