forked from D-Net/dnet-hadoop
extended the logic of the dump to consider the validation date in the relation (also in the dumped result for communities and funders at the level of the project), the extention on the instance for the APC, the pid, the alternate identifiers, and the extention of the AccessRight to store the OpenAccessRoute. Added new resourec for testing and extended the old class to verify the new dump. Fixed also issue on relation dump: only relation whose source and target are entities in the graph are dumped. The same hold for references to projects
This commit is contained in:
parent
6bd1eca7e0
commit
c3931557e3
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@ -37,8 +37,8 @@ public class DumpProducts implements Serializable {
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isSparkSessionManaged,
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spark -> {
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Utils.removeOutputDir(spark, outputPath);
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execDump(
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spark, inputPath, outputPath, communityMapPath, inputClazz, outputClazz, dumpType);
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execDump(
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spark, inputPath, outputPath, communityMapPath, inputClazz, outputClazz, dumpType);
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});
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}
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@ -29,15 +29,15 @@ public class QueryInformationSystem {
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"</community>";
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private static final String XQUERY_CI = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') "
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+
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" where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " +
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" and $x//CONFIGURATION/context[./@id=%s] "
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+
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" return " +
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"<community> " +
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"{$x//CONFIGURATION/context/@id}" +
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"{$x//CONFIGURATION/context/@label}" +
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"</community>";
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+
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" where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " +
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" and $x//CONFIGURATION/context[./@id=%s] "
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+
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" return " +
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"<community> " +
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"{$x//CONFIGURATION/context/@id}" +
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"{$x//CONFIGURATION/context/@label}" +
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"</community>";
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public CommunityMap getCommunityMap(boolean singleCommunity, String community_id)
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throws ISLookUpException, DocumentException {
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@ -5,6 +5,10 @@ import java.io.Serializable;
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import java.util.*;
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import java.util.stream.Collectors;
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import org.apache.commons.lang3.StringUtils;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.dump.oaf.*;
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import eu.dnetlib.dhp.schema.dump.oaf.AccessRight;
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import eu.dnetlib.dhp.schema.dump.oaf.Author;
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import eu.dnetlib.dhp.schema.dump.oaf.Country;
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@ -14,15 +18,13 @@ import eu.dnetlib.dhp.schema.dump.oaf.KeyValue;
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import eu.dnetlib.dhp.schema.dump.oaf.OpenAccessRoute;
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import eu.dnetlib.dhp.schema.dump.oaf.Qualifier;
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import eu.dnetlib.dhp.schema.dump.oaf.Result;
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import eu.dnetlib.dhp.schema.oaf.*;
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import org.apache.commons.lang3.StringUtils;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.dump.oaf.*;
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import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityInstance;
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import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult;
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import eu.dnetlib.dhp.schema.dump.oaf.community.Context;
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import eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult;
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import eu.dnetlib.dhp.schema.oaf.*;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.sql.Encoders;
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public class ResultMapper implements Serializable {
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@ -137,9 +139,12 @@ public class ResultMapper implements Serializable {
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}
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Optional<List<Measure>> mes = Optional.ofNullable(input.getMeasures());
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if(mes.isPresent()){
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if (mes.isPresent()) {
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List<KeyValue> measure = new ArrayList<>();
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mes.get().forEach(m -> m.getUnit().forEach(u -> measure.add(KeyValue.newInstance(u.getKey(), u.getValue()))));
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mes
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.get()
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.forEach(
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m -> m.getUnit().forEach(u -> measure.add(KeyValue.newInstance(m.getId(), u.getValue()))));
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out.setMeasures(measure);
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}
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@ -271,18 +276,17 @@ public class ResultMapper implements Serializable {
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}
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List<ControlledField> pids = new ArrayList<>();
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Optional
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.ofNullable(input.getPid())
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.ifPresent(
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value -> value
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value -> out.setPid(value
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.stream()
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.forEach(
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p -> pids
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.add(
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.map(
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p ->
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ControlledField
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.newInstance(p.getQualifier().getClassid(), p.getValue()))));
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out.setPid(pids);
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.newInstance(p.getQualifier().getClassid(), p.getValue())).collect(Collectors.toList())));
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oStr = Optional.ofNullable(input.getDateofacceptance());
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if (oStr.isPresent()) {
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out.setPublicationdate(oStr.get().getValue());
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@ -292,10 +296,11 @@ public class ResultMapper implements Serializable {
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out.setPublisher(oStr.get().getValue());
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}
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List<String> sourceList = new ArrayList<>();
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Optional
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.ofNullable(input.getSource())
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.ifPresent(value -> value.stream().forEach(s -> sourceList.add(s.getValue())));
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.ifPresent(value -> out.setSource(value.stream().map(s -> s.getValue()).collect(Collectors.toList()) ));
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// value.stream().forEach(s -> sourceList.add(s.getValue())));
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// out.setSource(input.getSource().stream().map(s -> s.getValue()).collect(Collectors.toList()));
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List<Subject> subjectList = new ArrayList<>();
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Optional
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@ -421,8 +426,8 @@ public class ResultMapper implements Serializable {
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code,
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Constants.coarCodeLabelMap.get(code),
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Constants.COAR_ACCESS_RIGHT_SCHEMA));
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if (opAr.get().getOpenAccessRoute() != null){
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switch (opAr.get().getOpenAccessRoute()){
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if (opAr.get().getOpenAccessRoute() != null) {
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switch (opAr.get().getOpenAccessRoute()) {
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case hybrid:
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instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.hybrid);
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break;
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@ -441,14 +446,25 @@ public class ResultMapper implements Serializable {
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}
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}
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Optional.ofNullable(i.getPid())
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.ifPresent(pid -> instance.setPid(
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pid.stream().map(p -> ControlledField.newInstance(p.getQualifier().getClassid(), p.getValue()))
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.collect(Collectors.toList())));
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Optional
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.ofNullable(i.getPid())
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.ifPresent(
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pid -> instance
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.setPid(
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pid
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.stream()
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.map(p -> ControlledField.newInstance(p.getQualifier().getClassid(), p.getValue()))
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.collect(Collectors.toList())));
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Optional.ofNullable(i.getAlternateIdentifier())
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.ifPresent(ai -> instance.setAlternateIdentifier(ai.stream().map(p -> ControlledField.
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newInstance(p.getQualifier().getClassid(), p.getValue())).collect(Collectors.toList())));
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Optional
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.ofNullable(i.getAlternateIdentifier())
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.ifPresent(
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ai -> instance
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.setAlternateIdentifier(
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ai
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.stream()
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.map(p -> ControlledField.newInstance(p.getQualifier().getClassid(), p.getValue()))
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.collect(Collectors.toList())));
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Optional
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.ofNullable(i.getLicense())
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@ -554,34 +570,55 @@ public class ResultMapper implements Serializable {
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return a;
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}
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private static Pid getOrcid(List<StructuredProperty> p) {
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for (StructuredProperty pid : p) {
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if (pid.getQualifier().getClassid().equals(ModelConstants.ORCID)) {
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Optional<DataInfo> di = Optional.ofNullable(pid.getDataInfo());
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if (di.isPresent()) {
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return Pid
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.newInstance(
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private static Pid getAuthorPid(StructuredProperty pid) {
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Optional<DataInfo> di = Optional.ofNullable(pid.getDataInfo());
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if (di.isPresent()) {
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return Pid
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.newInstance(
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ControlledField
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.newInstance(
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pid.getQualifier().getClassid(),
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pid.getValue()),
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.newInstance(
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pid.getQualifier().getClassid(),
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pid.getValue()),
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Provenance
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.newInstance(
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di.get().getProvenanceaction().getClassname(),
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di.get().getTrust()));
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} else {
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return Pid
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.newInstance(
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.newInstance(
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di.get().getProvenanceaction().getClassname(),
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di.get().getTrust()));
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} else {
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return Pid
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.newInstance(
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ControlledField
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.newInstance(
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pid.getQualifier().getClassid(),
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pid.getValue())
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.newInstance(
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pid.getQualifier().getClassid(),
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pid.getValue())
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);
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}
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}
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);
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}
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}
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private static Pid getOrcid(List<StructuredProperty> p) {
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List<StructuredProperty> pid_list = p.stream().map(pid -> {
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if (pid.getQualifier().getClassid().equals(ModelConstants.ORCID) ||
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(pid.getQualifier().getClassid().equals(ModelConstants.ORCID_PENDING))){
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return pid;
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}
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return null;
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}).filter(pid -> pid != null).collect(Collectors.toList());
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if(pid_list.size() == 1){
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return getAuthorPid(pid_list.get(0));
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}
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List<StructuredProperty> orcid = pid_list.stream().filter(ap -> ap.getQualifier().getClassid()
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.equals(ModelConstants.ORCID)).collect(Collectors.toList());
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if(orcid.size() == 1){
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return getAuthorPid(orcid.get(0));
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}
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orcid = pid_list.stream().filter(ap -> ap.getQualifier().getClassid()
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.equals(ModelConstants.ORCID_PENDING)).collect(Collectors.toList());
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if(orcid.size() == 1){
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return getAuthorPid(orcid.get(0));
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}
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return null;
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}
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@ -1,3 +1,4 @@
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package eu.dnetlib.dhp.oa.graph.dump;
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import java.io.BufferedWriter;
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@ -54,10 +55,10 @@ public class SaveCommunityMap implements Serializable {
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public static void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils
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.toString(
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SaveCommunityMap.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/graph/dump/input_cm_parameters.json"));
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.toString(
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SaveCommunityMap.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/graph/dump/input_cm_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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@ -71,8 +72,10 @@ public class SaveCommunityMap implements Serializable {
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final String isLookUpUrl = parser.get("isLookUpUrl");
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log.info("isLookUpUrl: {}", isLookUpUrl);
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final Boolean singleCommunity = Optional.ofNullable(parser.get("singleDeposition"))
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.map(Boolean::valueOf).orElse(false);
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final Boolean singleCommunity = Optional
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.ofNullable(parser.get("singleDeposition"))
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.map(Boolean::valueOf)
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.orElse(false);
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final String community_id = Optional.ofNullable(parser.get("communityId")).orElse(null);
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@ -82,8 +85,12 @@ public class SaveCommunityMap implements Serializable {
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}
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private void saveCommunityMap(boolean singleCommunity, String community_id) throws ISLookUpException, IOException, DocumentException {
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writer.write(Utils.OBJECT_MAPPER.writeValueAsString(queryInformationSystem.getCommunityMap(singleCommunity, community_id)));
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private void saveCommunityMap(boolean singleCommunity, String community_id)
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throws ISLookUpException, IOException, DocumentException {
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writer
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.write(
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Utils.OBJECT_MAPPER
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.writeValueAsString(queryInformationSystem.getCommunityMap(singleCommunity, community_id)));
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writer.close();
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}
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}
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|
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@ -48,14 +48,14 @@ public class SendToZenodoHDFS implements Serializable {
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.orElse(false);
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final String depositionId = Optional.ofNullable(parser.get("depositionId")).orElse(null);
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//final String communityMapPath = parser.get("communityMapPath");
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// final String communityMapPath = parser.get("communityMapPath");
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Configuration conf = new Configuration();
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conf.set("fs.defaultFS", hdfsNameNode);
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FileSystem fileSystem = FileSystem.get(conf);
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//CommunityMap communityMap = Utils.readCommunityMap(fileSystem, communityMapPath);
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// CommunityMap communityMap = Utils.readCommunityMap(fileSystem, communityMapPath);
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RemoteIterator<LocatedFileStatus> fileStatusListIterator = fileSystem
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.listFiles(
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|
|
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|
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@ -49,7 +49,7 @@ public class CommunitySplit implements Serializable {
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.union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class));
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communities
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.keySet()
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.keySet()
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.stream()
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.forEach(c -> printResult(c, result, outputPath + "/" + communities.get(c).replace(" ", "_")));
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|
|
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@ -8,6 +8,8 @@ import java.io.StringReader;
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import java.util.*;
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import java.util.stream.Collectors;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.dump.oaf.community.Validated;
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import org.apache.commons.io.IOUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.function.MapFunction;
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|
@ -76,7 +78,7 @@ public class SparkPrepareResultProject implements Serializable {
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private static void prepareResultProjectList(SparkSession spark, String inputPath, String outputPath) {
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Dataset<Relation> relation = Utils
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.readPath(spark, inputPath + "/relation", Relation.class)
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.filter("dataInfo.deletedbyinference = false and lower(relClass) = 'isproducedby'");
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.filter("dataInfo.deletedbyinference = false and lower(relClass) = '" + ModelConstants.IS_PRODUCED_BY.toLowerCase() + "'");
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Dataset<eu.dnetlib.dhp.schema.oaf.Project> projects = Utils
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.readPath(spark, inputPath + "/project", eu.dnetlib.dhp.schema.oaf.Project.class);
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|
|
@ -96,7 +98,7 @@ public class SparkPrepareResultProject implements Serializable {
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rp.setResultId(s);
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eu.dnetlib.dhp.schema.oaf.Project p = first._1();
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projectSet.add(p.getId());
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Project ps = getProject(p);
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Project ps = getProject(p, first._2);
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List<Project> projList = new ArrayList<>();
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projList.add(ps);
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|
|
@ -105,7 +107,7 @@ public class SparkPrepareResultProject implements Serializable {
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eu.dnetlib.dhp.schema.oaf.Project op = c._1();
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if (!projectSet.contains(op.getId())) {
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projList
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.add(getProject(op));
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.add(getProject(op, c._2));
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|
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projectSet.add(op.getId());
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|
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|
|
@ -120,7 +122,7 @@ public class SparkPrepareResultProject implements Serializable {
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.json(outputPath);
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}
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private static Project getProject(eu.dnetlib.dhp.schema.oaf.Project op) {
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private static Project getProject(eu.dnetlib.dhp.schema.oaf.Project op, Relation relation) {
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Project p = Project
|
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.newInstance(
|
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op.getId(),
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|
|
@ -155,7 +157,9 @@ public class SparkPrepareResultProject implements Serializable {
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provenance.setTrust(di.get().getTrust());
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p.setProvenance(provenance);
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}
|
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|
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if (relation.getValidated()){
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p.setValidated(Validated.newInstance(relation.getValidated(), relation.getValidationDate()));
|
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}
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return p;
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|
||||
}
|
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|
|
|
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|
|
@ -1,6 +1,7 @@
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|||
|
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package eu.dnetlib.dhp.oa.graph.dump.complete;
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|
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import static com.jayway.jsonpath.Filter.filter;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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|
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import java.io.Serializable;
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|
|
@ -8,8 +9,12 @@ import java.io.StringReader;
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import java.util.*;
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import java.util.stream.Collectors;
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|
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import com.fasterxml.jackson.databind.ObjectMapper;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.function.FilterFunction;
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import org.apache.spark.api.java.function.ForeachFunction;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.sql.Dataset;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.SaveMode;
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import org.apache.spark.sql.SparkSession;
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|
|
@ -448,19 +453,18 @@ public class DumpGraphEntities implements Serializable {
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|
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private static <E extends OafEntity> void organizationMap(SparkSession spark, String inputPath, String outputPath,
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Class<E> inputClazz) {
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Utils
|
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.readPath(spark, inputPath, inputClazz)
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.map(
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(MapFunction<E, Organization>) o -> mapOrganization((eu.dnetlib.dhp.schema.oaf.Organization) o),
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Encoders.bean(Organization.class))
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.filter(Objects::nonNull)
|
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.json(outputPath);
|
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Utils.readPath(spark, inputPath, inputClazz)
|
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.map(
|
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(MapFunction<E, Organization>) o -> mapOrganization((eu.dnetlib.dhp.schema.oaf.Organization) o),
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Encoders.bean(Organization.class))
|
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.filter((FilterFunction<Organization>) o -> o!= null)
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.write()
|
||||
.mode(SaveMode.Overwrite)
|
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.option("compression", "gzip")
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.json(outputPath);
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}
|
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|
||||
private static Organization mapOrganization(eu.dnetlib.dhp.schema.oaf.Organization org) {
|
||||
private static eu.dnetlib.dhp.schema.dump.oaf.graph.Organization mapOrganization(eu.dnetlib.dhp.schema.oaf.Organization org) {
|
||||
if (org.getDataInfo().getDeletedbyinference())
|
||||
return null;
|
||||
Organization organization = new Organization();
|
||||
|
|
|
|||
|
|
@ -129,7 +129,7 @@ public class Extractor implements Serializable {
|
|||
|
||||
return relationList.iterator();
|
||||
}, Encoders.bean(Relation.class))
|
||||
.write()
|
||||
.write()
|
||||
.option("compression", "gzip")
|
||||
.mode(SaveMode.Overwrite)
|
||||
.json(outputPath);
|
||||
|
|
|
|||
|
|
@ -5,6 +5,8 @@ import java.io.StringReader;
|
|||
import java.util.*;
|
||||
import java.util.function.Consumer;
|
||||
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||
import org.dom4j.Document;
|
||||
import org.dom4j.DocumentException;
|
||||
import org.dom4j.Element;
|
||||
|
|
@ -12,9 +14,9 @@ import org.dom4j.Node;
|
|||
import org.dom4j.io.SAXReader;
|
||||
import org.jetbrains.annotations.NotNull;
|
||||
|
||||
import eu.dnetlib.dhp.utils.DHPUtils;
|
||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
|
||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
||||
import eu.dnetlib.dhp.utils.DHPUtils;
|
||||
|
||||
public class QueryInformationSystem {
|
||||
|
||||
|
|
@ -136,6 +138,9 @@ public class QueryInformationSystem {
|
|||
}
|
||||
|
||||
private String makeOpenaireId(Node el, String prefix) {
|
||||
if (!prefix.equals(ModelSupport.entityIdPrefix.get("project"))){
|
||||
return null;
|
||||
}
|
||||
String funder = null;
|
||||
String grantId = null;
|
||||
String funding = null;
|
||||
|
|
|
|||
|
|
@ -107,13 +107,10 @@ public class SparkDumpRelationJob implements Serializable {
|
|||
}
|
||||
}
|
||||
}
|
||||
// Optional
|
||||
// .ofNullable(relation.getDataInfo())
|
||||
// .ifPresent(
|
||||
// datainfo -> rel_new
|
||||
// .setProvenance(
|
||||
// Provenance
|
||||
// .newInstance(datainfo.getProvenanceaction().getClassname(), datainfo.getTrust())));
|
||||
if(relation.getValidated()){
|
||||
rel_new.setValidated(relation.getValidated());
|
||||
rel_new.setValidationDate(relation.getValidationDate());
|
||||
}
|
||||
|
||||
return rel_new;
|
||||
|
||||
|
|
|
|||
|
|
@ -44,9 +44,9 @@ public class SparkDumpFunderResults implements Serializable {
|
|||
parser.parseArgument(args);
|
||||
|
||||
Boolean isSparkSessionManaged = Optional
|
||||
.ofNullable(parser.get("isSparkSessionManaged"))
|
||||
.map(Boolean::valueOf)
|
||||
.orElse(Boolean.TRUE);
|
||||
.ofNullable(parser.get("isSparkSessionManaged"))
|
||||
.map(Boolean::valueOf)
|
||||
.orElse(Boolean.TRUE);
|
||||
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
|
||||
|
||||
final String inputPath = parser.get("sourcePath");
|
||||
|
|
@ -55,40 +55,38 @@ public class SparkDumpFunderResults implements Serializable {
|
|||
final String outputPath = parser.get("outputPath");
|
||||
log.info("outputPath: {}", outputPath);
|
||||
|
||||
final String relationPath = parser.get("relationPath");
|
||||
log.info("relationPath: {}", relationPath);
|
||||
final String graphPath = parser.get("graphPath");
|
||||
log.info("relationPath: {}", graphPath);
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
|
||||
runWithSparkSession(
|
||||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
Utils.removeOutputDir(spark, outputPath);
|
||||
writeResultProjectList(spark, inputPath, outputPath, relationPath);
|
||||
});
|
||||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
Utils.removeOutputDir(spark, outputPath);
|
||||
writeResultProjectList(spark, inputPath, outputPath, graphPath);
|
||||
});
|
||||
}
|
||||
|
||||
private static void writeResultProjectList(SparkSession spark, String inputPath, String outputPath,
|
||||
String relationPath) {
|
||||
String graphPath) {
|
||||
|
||||
Dataset<Relation> relation = Utils
|
||||
.readPath(spark, relationPath + "/relation", Relation.class)
|
||||
.filter(
|
||||
"dataInfo.deletedbyinference = false and lower(relClass) = '"
|
||||
+ ModelConstants.IS_PRODUCED_BY.toLowerCase() + "'");
|
||||
Dataset<eu.dnetlib.dhp.schema.oaf.Project> project = Utils
|
||||
.readPath(spark, graphPath + "/project", eu.dnetlib.dhp.schema.oaf.Project.class);
|
||||
|
||||
Dataset<CommunityResult> result = Utils
|
||||
.readPath(spark, inputPath + "/publication", CommunityResult.class)
|
||||
.union(Utils.readPath(spark, inputPath + "/dataset", CommunityResult.class))
|
||||
.union(Utils.readPath(spark, inputPath + "/orp", CommunityResult.class))
|
||||
.union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class));
|
||||
.readPath(spark, inputPath + "/publication", CommunityResult.class)
|
||||
.union(Utils.readPath(spark, inputPath + "/dataset", CommunityResult.class))
|
||||
.union(Utils.readPath(spark, inputPath + "/orp", CommunityResult.class))
|
||||
.union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class));
|
||||
|
||||
List<String> funderList = relation
|
||||
.select("target")
|
||||
.map((MapFunction<Row, String>) value -> value.getString(0).substring(0, 15), Encoders.STRING())
|
||||
.distinct()
|
||||
.collectAsList();
|
||||
|
||||
List<String> funderList = project
|
||||
.select("id")
|
||||
.map((MapFunction<Row, String>) value -> value.getString(0).substring(0, 15), Encoders.STRING())
|
||||
.distinct()
|
||||
.collectAsList();
|
||||
|
||||
funderList.forEach(funder -> {
|
||||
String fundernsp = funder.substring(3);
|
||||
|
|
@ -109,7 +107,7 @@ public class SparkDumpFunderResults implements Serializable {
|
|||
}
|
||||
|
||||
private static void dumpResults(String nsp, Dataset<CommunityResult> results, String outputPath,
|
||||
String funderName) {
|
||||
String funderName) {
|
||||
|
||||
results.map((MapFunction<CommunityResult, CommunityResult>) r -> {
|
||||
if (!Optional.ofNullable(r.getProjects()).isPresent()) {
|
||||
|
|
@ -117,7 +115,6 @@ public class SparkDumpFunderResults implements Serializable {
|
|||
}
|
||||
for (Project p : r.getProjects()) {
|
||||
if (p.getId().startsWith(nsp)) {
|
||||
|
||||
if (nsp.startsWith("40|irb")) {
|
||||
if (p.getFunder().getShortName().equals(funderName))
|
||||
return r;
|
||||
|
|
@ -129,15 +126,15 @@ public class SparkDumpFunderResults implements Serializable {
|
|||
}
|
||||
return null;
|
||||
}, Encoders.bean(CommunityResult.class))
|
||||
.filter((FilterFunction<CommunityResult>) r -> r != null)
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.option("compression", "gzip")
|
||||
.json(outputPath + "/" + funderName);
|
||||
.filter(Objects::nonNull)
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.option("compression", "gzip")
|
||||
.json(outputPath + "/" + funderName);
|
||||
}
|
||||
|
||||
private static void writeFunderResult(String funder, Dataset<CommunityResult> results, String outputPath,
|
||||
String funderDump) {
|
||||
String funderDump) {
|
||||
|
||||
if (funder.startsWith("40|irb")) {
|
||||
dumpResults(funder, results, outputPath, "HRZZ");
|
||||
|
|
|
|||
|
|
@ -10,6 +10,7 @@ import org.apache.commons.io.IOUtils;
|
|||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.function.MapFunction;
|
||||
import org.apache.spark.api.java.function.MapGroupsFunction;
|
||||
import org.apache.spark.sql.*;
|
||||
import org.apache.spark.sql.Dataset;
|
||||
import org.apache.spark.sql.Encoders;
|
||||
import org.apache.spark.sql.SaveMode;
|
||||
|
|
@ -21,14 +22,14 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
|||
import eu.dnetlib.dhp.oa.graph.dump.Constants;
|
||||
import eu.dnetlib.dhp.oa.graph.dump.Utils;
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
import eu.dnetlib.dhp.schema.oaf.Project;
|
||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
import scala.Tuple2;
|
||||
import org.apache.spark.sql.*;
|
||||
import eu.dnetlib.dhp.schema.oaf.Project;
|
||||
|
||||
/**
|
||||
* Selects the results linked to projects. Only for these results the dump will be performed.
|
||||
* The code to perform the dump and to expend the dumped results with the informaiton related to projects
|
||||
* The code to perform the dump and to expend the dumped results with the information related to projects
|
||||
* is the one used for the dump of the community products
|
||||
*/
|
||||
public class SparkResultLinkedToProject implements Serializable {
|
||||
|
|
@ -78,6 +79,7 @@ public class SparkResultLinkedToProject implements Serializable {
|
|||
private static <R extends Result> void writeResultsLinkedToProjects(SparkSession spark, Class<R> inputClazz,
|
||||
String inputPath, String outputPath, String graphPath) {
|
||||
|
||||
|
||||
Dataset<R> results = Utils
|
||||
.readPath(spark, inputPath, inputClazz)
|
||||
.filter("dataInfo.deletedbyinference = false and datainfo.invisible = false");
|
||||
|
|
@ -86,25 +88,32 @@ public class SparkResultLinkedToProject implements Serializable {
|
|||
.filter(
|
||||
"dataInfo.deletedbyinference = false and lower(relClass) = '"
|
||||
+ ModelConstants.IS_PRODUCED_BY.toLowerCase() + "'");
|
||||
Dataset<Project> project = Utils.readPath(spark, graphPath + "/project", Project.class);
|
||||
|
||||
spark
|
||||
.sql(
|
||||
"Select res.* " +
|
||||
"from relation rel " +
|
||||
"join result res " +
|
||||
"on rel.source = res.id " +
|
||||
"join project p " +
|
||||
"on rel.target = p.id " +
|
||||
"")
|
||||
.as(Encoders.bean(inputClazz))
|
||||
.groupByKey(
|
||||
(MapFunction< R, String>) value -> value
|
||||
.getId(),
|
||||
results.createOrReplaceTempView("result");
|
||||
relations.createOrReplaceTempView("relation");
|
||||
project.createOrReplaceTempView("project");
|
||||
|
||||
Dataset<R> tmp = spark
|
||||
.sql(
|
||||
"Select res.* " +
|
||||
"from relation rel " +
|
||||
"join result res " +
|
||||
"on rel.source = res.id " +
|
||||
"join project p " +
|
||||
"on rel.target = p.id " +
|
||||
"")
|
||||
.as(Encoders.bean(inputClazz));
|
||||
tmp
|
||||
.groupByKey(
|
||||
(MapFunction<R, String>) value -> value
|
||||
.getId(),
|
||||
Encoders.STRING())
|
||||
.mapGroups((MapGroupsFunction<String, R, R>) (k, it) -> it.next(), Encoders.bean(inputClazz))
|
||||
.mapGroups((MapGroupsFunction<String, R, R>) (k, it) -> it.next(), Encoders.bean(inputClazz))
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.option("compression", "gzip")
|
||||
.json(outputPath);
|
||||
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -18,8 +18,8 @@
|
|||
"paramRequired": false
|
||||
},
|
||||
{
|
||||
"paramName": "rp",
|
||||
"paramLongName": "relationPath",
|
||||
"paramName": "gp",
|
||||
"paramLongName": "graphPath",
|
||||
"paramDescription": "the relationPath",
|
||||
"paramRequired": true
|
||||
}
|
||||
|
|
|
|||
|
|
@ -24,8 +24,8 @@
|
|||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName":"rp",
|
||||
"paramLongName":"relationPath",
|
||||
"paramName":"gp",
|
||||
"paramLongName":"graphPath",
|
||||
"paramDescription": "the path to the relations",
|
||||
"paramRequired": true
|
||||
}
|
||||
|
|
|
|||
|
|
@ -7,7 +7,13 @@ import java.nio.file.Path;
|
|||
import java.util.Arrays;
|
||||
import java.util.List;
|
||||
|
||||
import com.fasterxml.jackson.core.JsonProcessingException;
|
||||
import com.sun.xml.internal.ws.policy.AssertionSet;
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
import eu.dnetlib.dhp.schema.dump.oaf.Instance;
|
||||
import eu.dnetlib.dhp.schema.dump.oaf.OpenAccessRoute;
|
||||
import org.apache.commons.io.FileUtils;
|
||||
import org.apache.neethi.Assertion;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.JavaRDD;
|
||||
import org.apache.spark.api.java.JavaSparkContext;
|
||||
|
|
@ -199,7 +205,7 @@ public class DumpJobTest {
|
|||
|
||||
Assertions.assertTrue(verificationDataset.filter("type = 'dataset'").count() == 90);
|
||||
|
||||
//TODO verify value and name of the fields for vocab related value (i.e. accessright, bestaccessright)
|
||||
|
||||
|
||||
}
|
||||
|
||||
|
|
@ -302,6 +308,178 @@ public class DumpJobTest {
|
|||
|
||||
//TODO verify value and name of the fields for vocab related value (i.e. accessright, bestaccessright)
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testPublicationExtendedInstance(){
|
||||
final String sourcePath = getClass()
|
||||
.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication_extendedinstance")
|
||||
.getPath();
|
||||
|
||||
final String communityMapPath = getClass()
|
||||
.getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json")
|
||||
.getPath();
|
||||
|
||||
DumpProducts dump = new DumpProducts();
|
||||
dump
|
||||
.run(
|
||||
// false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class,
|
||||
false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class,
|
||||
GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType());
|
||||
|
||||
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||
|
||||
JavaRDD<GraphResult> tmp = sc
|
||||
.textFile(workingDir.toString() + "/result")
|
||||
.map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class));
|
||||
|
||||
org.apache.spark.sql.Dataset<GraphResult> verificationDataset = spark
|
||||
.createDataset(tmp.rdd(), Encoders.bean(GraphResult.class));
|
||||
|
||||
Assertions.assertEquals(1, verificationDataset.count());
|
||||
verificationDataset.show(false);
|
||||
|
||||
GraphResult gr = verificationDataset.first();
|
||||
|
||||
|
||||
Assertions.assertEquals(2, gr.getMeasures().size());
|
||||
Assertions.assertTrue(gr.getMeasures().stream().anyMatch(m -> m.getKey().equals("influence")
|
||||
&& m.getValue().equals("1.62759106106e-08")));
|
||||
Assertions.assertTrue(gr.getMeasures().stream().anyMatch(m -> m.getKey().equals("popularity")
|
||||
&& m.getValue().equals("0.22519296")));
|
||||
|
||||
Assertions.assertEquals(6, gr.getAuthor().size());
|
||||
Assertions.assertTrue(gr.getAuthor().stream().anyMatch(a -> a.getFullname().equals("Nikolaidou,Charitini") &&
|
||||
a.getName().equals("Charitini") && a.getSurname().equals("Nikolaidou")
|
||||
&& a.getRank() == 1 && a.getPid() == null));
|
||||
|
||||
Assertions.assertTrue(gr.getAuthor().stream().anyMatch(a -> a.getFullname().equals("Votsi,Nefta") &&
|
||||
a.getName().equals("Nefta") && a.getSurname().equals("Votsi")
|
||||
&& a.getRank() == 2 && a.getPid().getId().getScheme().equals(ModelConstants.ORCID)
|
||||
&& a.getPid().getId().getValue().equals("0000-0001-6651-1178") && a.getPid().getProvenance() != null));
|
||||
|
||||
Assertions.assertTrue(gr.getAuthor().stream().anyMatch(a -> a.getFullname().equals("Sgardelis,Steanos") &&
|
||||
a.getName().equals("Steanos") && a.getSurname().equals("Sgardelis")
|
||||
&& a.getRank() == 3 && a.getPid().getId().getScheme().equals(ModelConstants.ORCID_PENDING)
|
||||
&& a.getPid().getId().getValue().equals("0000-0001-6651-1178") && a.getPid().getProvenance() != null));
|
||||
|
||||
Assertions.assertTrue(gr.getAuthor().stream().anyMatch(a -> a.getFullname().equals("Halley,John") &&
|
||||
a.getName().equals("John") && a.getSurname().equals("Halley")
|
||||
&& a.getRank() == 4 && a.getPid() == null));
|
||||
|
||||
Assertions.assertTrue(gr.getAuthor().stream().anyMatch(a -> a.getFullname().equals("Pantis,John") &&
|
||||
a.getName().equals("John") && a.getSurname().equals("Pantis")
|
||||
&& a.getRank() == 5 && a.getPid().getId().getScheme().equals(ModelConstants.ORCID)
|
||||
&& a.getPid().getId().getValue().equals("0000-0001-6651-1178") && a.getPid().getProvenance() != null));
|
||||
|
||||
Assertions.assertTrue(gr.getAuthor().stream().anyMatch(a -> a.getFullname().equals("Tsiafouli,Maria") &&
|
||||
a.getName().equals("Maria") && a.getSurname().equals("Tsiafouli")
|
||||
&& a.getRank() == 6 && a.getPid().getId().getScheme().equals(ModelConstants.ORCID_PENDING)
|
||||
&& a.getPid().getId().getValue().equals("0000-0001-6651-1178") && a.getPid().getProvenance() != null));
|
||||
|
||||
Assertions.assertEquals("publication", gr.getType());
|
||||
|
||||
Assertions.assertEquals("eng", gr.getLanguage().getCode());
|
||||
Assertions.assertEquals("English", gr.getLanguage().getLabel());
|
||||
|
||||
Assertions.assertEquals(1, gr.getCountry().size());
|
||||
Assertions.assertEquals("IT" , gr.getCountry().get(0).getCode());
|
||||
Assertions.assertEquals("Italy" , gr.getCountry().get(0).getLabel());
|
||||
Assertions.assertTrue( gr.getCountry().get(0).getProvenance() == null);
|
||||
|
||||
Assertions.assertEquals(12, gr.getSubjects().size());
|
||||
Assertions.assertTrue(gr.getSubjects().stream().anyMatch(s -> s.getSubject().getValue().equals("Ecosystem Services hotspots")
|
||||
&& s.getSubject().getScheme().equals("ACM") && s.getProvenance() != null &&
|
||||
s.getProvenance().getProvenance().equals("sysimport:crosswalk:repository")));
|
||||
Assertions.assertTrue(gr.getSubjects().stream().anyMatch(s -> s.getSubject().getValue().equals("Natura 2000")
|
||||
&& s.getSubject().getScheme().equals("") && s.getProvenance() != null &&
|
||||
s.getProvenance().getProvenance().equals("sysimport:crosswalk:repository")));
|
||||
|
||||
Assertions.assertEquals("Ecosystem Service capacity is higher in areas of multiple designation types",
|
||||
gr.getMaintitle());
|
||||
|
||||
Assertions.assertEquals(null, gr.getSubtitle());
|
||||
|
||||
Assertions.assertEquals(1, gr.getDescription().size());
|
||||
|
||||
Assertions.assertTrue(gr.getDescription().get(0).startsWith("The implementation of the Ecosystem Service (ES) concept into practice"));
|
||||
Assertions.assertTrue(gr.getDescription().get(0).endsWith("start complying with new standards and demands for nature conservation and environmental management."));
|
||||
|
||||
Assertions.assertEquals("2017-01-01", gr.getPublicationdate());
|
||||
|
||||
Assertions.assertEquals("Pensoft Publishers", gr.getPublisher());
|
||||
|
||||
Assertions.assertEquals(null, gr.getEmbargoenddate());
|
||||
|
||||
Assertions.assertEquals(1, gr.getSource().size());
|
||||
Assertions.assertEquals("One Ecosystem 2: e13718", gr.getSource().get(0));
|
||||
|
||||
Assertions.assertEquals(1, gr.getFormat().size());
|
||||
Assertions.assertEquals("text/html", gr.getFormat().get(0));
|
||||
|
||||
Assertions.assertEquals(0, gr.getContributor().size());
|
||||
|
||||
Assertions.assertEquals(0, gr.getCoverage().size());
|
||||
|
||||
Assertions.assertEquals(ModelConstants.ACCESS_RIGHT_OPEN, gr.getBestaccessright().getLabel());
|
||||
Assertions.assertEquals(Constants.accessRightsCoarMap.get(ModelConstants.ACCESS_RIGHT_OPEN), gr.getBestaccessright().getCode());
|
||||
Assertions.assertEquals(null, gr.getBestaccessright().getOpenAccessRoute());
|
||||
|
||||
Assertions.assertEquals("One Ecosystem", gr.getContainer().getName());
|
||||
Assertions.assertEquals("2367-8194", gr.getContainer().getIssnOnline());
|
||||
Assertions.assertEquals("", gr.getContainer().getIssnPrinted());
|
||||
Assertions.assertEquals("", gr.getContainer().getIssnLinking());
|
||||
|
||||
Assertions.assertTrue(null == gr.getDocumentationUrl() || gr.getDocumentationUrl().size() == 0);
|
||||
|
||||
Assertions.assertTrue(null == gr.getCodeRepositoryUrl());
|
||||
|
||||
Assertions.assertEquals(null, gr.getProgrammingLanguage());
|
||||
|
||||
Assertions.assertTrue(null == gr.getContactperson() || gr.getContactperson().size() == 0);
|
||||
|
||||
Assertions.assertTrue(null == gr.getContactgroup() || gr.getContactgroup().size() == 0);
|
||||
|
||||
Assertions.assertTrue(null == gr.getTool() || gr.getTool().size() == 0);
|
||||
|
||||
Assertions.assertEquals(null, gr.getSize());
|
||||
|
||||
Assertions.assertEquals(null, gr.getVersion());
|
||||
|
||||
Assertions.assertTrue(null == gr.getGeolocation() || gr.getGeolocation().size() == 0);
|
||||
|
||||
Assertions.assertEquals("50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2", gr.getId());
|
||||
|
||||
Assertions.assertEquals(2, gr.getOriginalId().size());
|
||||
Assertions.assertTrue(gr.getOriginalId().contains("50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2")
|
||||
&& gr.getOriginalId().contains("10.3897/oneeco.2.e13718"));
|
||||
|
||||
Assertions.assertEquals(1, gr.getPid().size());
|
||||
Assertions.assertTrue(gr.getPid().get(0).getScheme().equals("doi")
|
||||
&& gr.getPid().get(0).getValue().equals("10.1016/j.triboint.2014.05.004"));
|
||||
|
||||
Assertions.assertEquals("2020-03-23T00:20:51.392Z", gr.getDateofcollection());
|
||||
|
||||
Assertions.assertEquals(1, gr.getInstance().size());
|
||||
|
||||
Instance instance = gr.getInstance().get(0);
|
||||
Assertions.assertEquals(0, instance.getPid().size());
|
||||
Assertions.assertEquals(1, instance.getAlternateIdentifier().size());
|
||||
Assertions.assertTrue(instance.getAlternateIdentifier().get(0).getScheme().equals("doi")
|
||||
&& instance.getAlternateIdentifier().get(0).getValue().equals("10.3897/oneeco.2.e13718"));
|
||||
Assertions.assertEquals(null, instance.getLicense());
|
||||
Assertions.assertTrue(instance.getAccessright().getCode().equals(Constants.accessRightsCoarMap
|
||||
.get(ModelConstants.ACCESS_RIGHT_OPEN)));
|
||||
Assertions.assertTrue(instance.getAccessright().getLabel().equals(ModelConstants.ACCESS_RIGHT_OPEN));
|
||||
Assertions.assertTrue(instance.getAccessright().getOpenAccessRoute().equals(OpenAccessRoute.green));
|
||||
Assertions.assertEquals(2, instance.getUrl().size());
|
||||
Assertions.assertTrue(instance.getUrl().contains("https://doi.org/10.3897/oneeco.2.e13718")
|
||||
&& instance.getUrl().contains("https://oneecosystem.pensoft.net/article/13718/"));
|
||||
Assertions.assertEquals("2017-01-01",instance.getPublicationdate());
|
||||
Assertions.assertEquals(null,instance.getArticleprocessingcharge());
|
||||
Assertions.assertEquals("peerReviewed", instance.getRefereed());
|
||||
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
|
|
@ -455,6 +633,8 @@ public class DumpJobTest {
|
|||
|
||||
Assertions.assertTrue(temp.filter("id = '50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8'").count() == 1);
|
||||
|
||||
|
||||
|
||||
// verificationDataset.filter("bestAccessright.code = 'c_abf2'").count() == verificationDataset
|
||||
// .filter("bestAccessright.code = 'c_abf2' and bestAccessright.label = 'OPEN'")
|
||||
// .count()
|
||||
|
|
|
|||
|
|
@ -7,9 +7,11 @@ import java.nio.file.Path;
|
|||
import java.util.HashMap;
|
||||
|
||||
import org.apache.commons.io.FileUtils;
|
||||
import org.apache.neethi.Assertion;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.JavaRDD;
|
||||
import org.apache.spark.api.java.JavaSparkContext;
|
||||
import org.apache.spark.api.java.function.ForeachFunction;
|
||||
import org.apache.spark.sql.Dataset;
|
||||
import org.apache.spark.sql.Encoders;
|
||||
import org.apache.spark.sql.Row;
|
||||
|
|
@ -236,4 +238,111 @@ public class PrepareResultProjectJobTest {
|
|||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testMatchValidated() throws Exception {
|
||||
|
||||
final String sourcePath = getClass()
|
||||
.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_validatedRels")
|
||||
.getPath();
|
||||
|
||||
SparkPrepareResultProject.main(new String[] {
|
||||
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||
"-outputPath", workingDir.toString() + "/preparedInfo",
|
||||
"-sourcePath", sourcePath
|
||||
});
|
||||
|
||||
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||
|
||||
JavaRDD<ResultProject> tmp = sc
|
||||
.textFile(workingDir.toString() + "/preparedInfo")
|
||||
.map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class));
|
||||
|
||||
org.apache.spark.sql.Dataset<ResultProject> verificationDataset = spark
|
||||
.createDataset(tmp.rdd(), Encoders.bean(ResultProject.class));
|
||||
|
||||
Assertions.assertTrue(verificationDataset.count() == 2);
|
||||
|
||||
Assertions
|
||||
.assertEquals(
|
||||
1,
|
||||
verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count());
|
||||
Assertions
|
||||
.assertEquals(
|
||||
1,
|
||||
verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count());
|
||||
|
||||
verificationDataset.createOrReplaceTempView("dataset");
|
||||
|
||||
String query = "select resultId, MyT.id project , MyT.title title, MyT.acronym acronym , MyT.provenance.provenance provenance, " +
|
||||
"MyT.validated.validatedByFunder, MyT.validated.validationDate "
|
||||
+ "from dataset "
|
||||
+ "lateral view explode(projectsList) p as MyT ";
|
||||
|
||||
org.apache.spark.sql.Dataset<Row> resultExplodedProvenance = spark.sql(query);
|
||||
Assertions.assertEquals(3, resultExplodedProvenance.count());
|
||||
Assertions.assertEquals(3, resultExplodedProvenance.filter("validatedByFunder = true").count());
|
||||
Assertions
|
||||
.assertEquals(
|
||||
2,
|
||||
resultExplodedProvenance
|
||||
.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'")
|
||||
.count());
|
||||
|
||||
Assertions
|
||||
.assertEquals(
|
||||
1,
|
||||
resultExplodedProvenance
|
||||
.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'")
|
||||
.count());
|
||||
|
||||
Assertions
|
||||
.assertEquals(
|
||||
2,
|
||||
resultExplodedProvenance
|
||||
.filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'")
|
||||
.count());
|
||||
|
||||
Assertions
|
||||
.assertEquals(
|
||||
1,
|
||||
resultExplodedProvenance
|
||||
.filter(
|
||||
"project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " +
|
||||
"and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " +
|
||||
"and validatedByFunder = true " +
|
||||
"and validationDate = '2021-08-06'")
|
||||
.count());
|
||||
|
||||
Assertions
|
||||
.assertEquals(
|
||||
1,
|
||||
resultExplodedProvenance
|
||||
.filter(
|
||||
"project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " +
|
||||
"and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80' " +
|
||||
"and validatedByFunder = true and validationDate = '2021-08-04'")
|
||||
.count());
|
||||
|
||||
Assertions
|
||||
.assertEquals(
|
||||
1,
|
||||
resultExplodedProvenance
|
||||
.filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'")
|
||||
.count());
|
||||
|
||||
Assertions
|
||||
.assertEquals(
|
||||
1,
|
||||
resultExplodedProvenance
|
||||
.filter(
|
||||
"project = '40|aka_________::03376222b28a3aebf2730ac514818d04' " +
|
||||
"and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " +
|
||||
"and validatedByFunder = true and validationDate = '2021-08-05'")
|
||||
.count());
|
||||
|
||||
Assertions
|
||||
.assertEquals(
|
||||
3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count());
|
||||
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -24,7 +24,7 @@ public class QueryInformationSystemTest {
|
|||
private static final String XQUERY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') "
|
||||
+
|
||||
" where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " +
|
||||
" and ($x//context/param[./@name = 'status']/text() = 'manager' or $x//context/param[./@name = 'status']/text() = 'all') "
|
||||
" and ($x//context/param[./@name = 'status']/text() = 'all') "
|
||||
+
|
||||
" return " +
|
||||
"<community> " +
|
||||
|
|
|
|||
|
|
@ -79,7 +79,7 @@ public class SplitForCommunityTest {
|
|||
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||
|
||||
JavaRDD<CommunityResult> tmp = sc
|
||||
.textFile(workingDir.toString() + "/split/dh-ch")
|
||||
.textFile(workingDir.toString() + "/split/Digital_Humanities_and_Cultural_Heritage")
|
||||
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
|
||||
|
||||
org.apache.spark.sql.Dataset<CommunityResult> verificationDataset = spark
|
||||
|
|
@ -92,7 +92,7 @@ public class SplitForCommunityTest {
|
|||
1, verificationDataset.filter("id = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count());
|
||||
|
||||
tmp = sc
|
||||
.textFile(workingDir.toString() + "/split/egi")
|
||||
.textFile(workingDir.toString() + "/split/EGI_Federation")
|
||||
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
|
||||
|
||||
verificationDataset = spark
|
||||
|
|
@ -105,7 +105,7 @@ public class SplitForCommunityTest {
|
|||
1, verificationDataset.filter("id = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count());
|
||||
|
||||
tmp = sc
|
||||
.textFile(workingDir.toString() + "/split/ni")
|
||||
.textFile(workingDir.toString() + "/split/Neuroinformatics")
|
||||
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
|
||||
|
||||
verificationDataset = spark
|
||||
|
|
@ -118,7 +118,7 @@ public class SplitForCommunityTest {
|
|||
1, verificationDataset.filter("id = '50|datacite____::6b1e3a2fa60ed8c27317a66d6357f795'").count());
|
||||
|
||||
tmp = sc
|
||||
.textFile(workingDir.toString() + "/split/science-innovation-policy")
|
||||
.textFile(workingDir.toString() + "/split/Science_and_Innovation_Policy_Studies")
|
||||
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
|
||||
|
||||
verificationDataset = spark
|
||||
|
|
|
|||
|
|
@ -1,8 +1,6 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.graph.dump.complete;
|
||||
|
||||
|
||||
import eu.dnetlib.dhp.schema.oaf.Project;
|
||||
import java.util.*;
|
||||
import java.util.function.Consumer;
|
||||
import java.util.stream.Collectors;
|
||||
|
|
@ -16,6 +14,7 @@ import com.google.gson.Gson;
|
|||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||
import eu.dnetlib.dhp.schema.dump.oaf.graph.Relation;
|
||||
import eu.dnetlib.dhp.schema.oaf.Datasource;
|
||||
import eu.dnetlib.dhp.schema.oaf.Project;
|
||||
import eu.dnetlib.dhp.utils.DHPUtils;
|
||||
|
||||
public class CreateRelationTest {
|
||||
|
|
@ -205,7 +204,7 @@ public class CreateRelationTest {
|
|||
" <param name=\"suggestedAcknowledgement\"/>\n" +
|
||||
" <param name=\"zenodoCommunity\">oac_ni</param>\n" +
|
||||
" <param name=\"creationdate\">2018-03-01T12:00:00</param>\n" +
|
||||
" <category claim=\"false\" id=\"ni::projects\" label=\"NI Content providers\"/>\n" +
|
||||
" <category claim=\"false\" id=\"ni::projects\" label=\"NI Content providers\"/>\n" +
|
||||
" <category claim=\"false\" id=\"ni::contentproviders\" label=\"NI Content providers\">\n" +
|
||||
" <concept claim=\"false\" id=\"ni::contentproviders::1\" label=\"OpenNeuro\">\n" +
|
||||
" <param name=\"openaireId\">re3data_____::5b9bf9171d92df854cf3c520692e9122</param>\n" +
|
||||
|
|
@ -441,57 +440,65 @@ public class CreateRelationTest {
|
|||
" <param name=\"zenodoCommunity\">oaa_elixir-gr</param>\n" +
|
||||
" <param name=\"creationdate\">2018-03-01T12:00:00</param>\n" +
|
||||
" <category claim=\"false\" id=\"elixir-gr::projects\" label=\"ELIXIR GR Projects\">\n" +
|
||||
" <concept claim=\"false\" id=\"ni::projects::12\" label=\"\">\n" +
|
||||
" <param name=\"projectfullname\">BIO-INFORMATICS RESEARCH NETWORK COORDINATING CENTER (BIRN-CC)</param>\n" +
|
||||
" <param name=\"acronym\"/>\n" +
|
||||
" <param name=\"CD_PROJECT_NUMBER\">1U24RR025736-01</param>\n" +
|
||||
" <param name=\"funder\">NIH</param>\n" +
|
||||
" </concept>\n" +
|
||||
" <concept claim=\"false\" id=\"ni::projects::13\" label=\"\">\n" +
|
||||
" <param name=\"projectfullname\">COLLABORATIVE RESEARCH: The Cognitive Neuroscience of Category Learning</param>\n" +
|
||||
" <param name=\"acronym\"/>\n" +
|
||||
" <param name=\"CD_PROJECT_NUMBER\">0223843</param>\n" +
|
||||
" <param name=\"funder\">NSF</param>\n" +
|
||||
" </concept>\n" +
|
||||
" <concept claim=\"false\" id=\"ni::projects::14\" label=\"\">\n" +
|
||||
" <param name=\"projectfullname\">The Cognitive Atlas: Developing an Interdisciplinary Knowledge Base Through Socia</param>\n" +
|
||||
" <param name=\"acronym\"/>\n" +
|
||||
" <param name=\"CD_PROJECT_NUMBER\">5R01MH082795-05</param>\n" +
|
||||
" <param name=\"funder\">NIH</param>\n" +
|
||||
" </concept>\n" +
|
||||
" <concept claim=\"false\" id=\"ni::projects::15\" label=\"\">\n" +
|
||||
" <param name=\"projectfullname\">Fragmented early life environmental and emotional / cognitive vulnerabilities</param>\n" +
|
||||
" <param name=\"acronym\"/>\n" +
|
||||
" <param name=\"CD_PROJECT_NUMBER\">1P50MH096889-01A1</param>\n" +
|
||||
" <param name=\"funder\">NIH</param>\n" +
|
||||
" </concept>\n" +
|
||||
" <concept claim=\"false\" id=\"ni::projects::16\" label=\"\">\n" +
|
||||
" <param name=\"projectfullname\">Enhancement of the 1000 Functional Connectome Project</param>\n" +
|
||||
" <param name=\"acronym\"/>\n" +
|
||||
" <param name=\"CD_PROJECT_NUMBER\">1R03MH096321-01A1</param>\n" +
|
||||
" <param name=\"funder\">TUBITAK</param>\n" +
|
||||
" </concept>\n" +
|
||||
" <concept claim=\"false\" id=\"ni::projects::17\" label=\"\">\n" +
|
||||
" <param name=\"projectfullname\">CRCNS Data Sharing: An open data repository for cognitive neuroscience: The OpenfMRI Project</param>\n" +
|
||||
" <param name=\"acronym\"/>\n" +
|
||||
" <param name=\"CD_PROJECT_NUMBER\">1131441</param>\n" +
|
||||
" <param name=\"funder\">NSF</param>\n" +
|
||||
" </concept>\n" +
|
||||
" <concept claim=\"false\" id=\"ni::projects::18\" label=\"\">\n" +
|
||||
" <param name=\"projectfullname\">Enhancing Human Cortical Plasticity: Visual Psychophysics and fMRI</param>\n" +
|
||||
" <param name=\"acronym\"/>\n" +
|
||||
" <param name=\"CD_PROJECT_NUMBER\">0121950</param>\n" +
|
||||
" <param name=\"funder\">NSF</param>\n" +
|
||||
" </concept>\n" +
|
||||
" <concept claim=\"false\" id=\"ni::projects::18\" label=\"\">\n" +
|
||||
" <param name=\"projectfullname\">Transforming statistical methodology for neuroimaging meta-analysis.</param>\n" +
|
||||
" <param name=\"acronym\"/>\n" +
|
||||
" <param name=\"CD_PROJECT_NUMBER\">100309</param>\n" +
|
||||
" <param name=\"funder\">WT</param>\n" +
|
||||
" </concept>\n" +
|
||||
" </category>" +
|
||||
" <concept claim=\"false\" id=\"ni::projects::12\" label=\"\">\n" +
|
||||
" <param name=\"projectfullname\">BIO-INFORMATICS RESEARCH NETWORK COORDINATING CENTER (BIRN-CC)</param>\n"
|
||||
+
|
||||
" <param name=\"acronym\"/>\n" +
|
||||
" <param name=\"CD_PROJECT_NUMBER\">1U24RR025736-01</param>\n" +
|
||||
" <param name=\"funder\">NIH</param>\n" +
|
||||
" </concept>\n" +
|
||||
" <concept claim=\"false\" id=\"ni::projects::13\" label=\"\">\n" +
|
||||
" <param name=\"projectfullname\">COLLABORATIVE RESEARCH: The Cognitive Neuroscience of Category Learning</param>\n"
|
||||
+
|
||||
" <param name=\"acronym\"/>\n" +
|
||||
" <param name=\"CD_PROJECT_NUMBER\">0223843</param>\n" +
|
||||
" <param name=\"funder\">NSF</param>\n" +
|
||||
" </concept>\n" +
|
||||
" <concept claim=\"false\" id=\"ni::projects::14\" label=\"\">\n" +
|
||||
" <param name=\"projectfullname\">The Cognitive Atlas: Developing an Interdisciplinary Knowledge Base Through Socia</param>\n"
|
||||
+
|
||||
" <param name=\"acronym\"/>\n" +
|
||||
" <param name=\"CD_PROJECT_NUMBER\">5R01MH082795-05</param>\n" +
|
||||
" <param name=\"funder\">NIH</param>\n" +
|
||||
" </concept>\n" +
|
||||
" <concept claim=\"false\" id=\"ni::projects::15\" label=\"\">\n" +
|
||||
" <param name=\"projectfullname\">Fragmented early life environmental and emotional / cognitive vulnerabilities</param>\n"
|
||||
+
|
||||
" <param name=\"acronym\"/>\n" +
|
||||
" <param name=\"CD_PROJECT_NUMBER\">1P50MH096889-01A1</param>\n" +
|
||||
" <param name=\"funder\">NIH</param>\n" +
|
||||
" </concept>\n" +
|
||||
" <concept claim=\"false\" id=\"ni::projects::16\" label=\"\">\n" +
|
||||
" <param name=\"projectfullname\">Enhancement of the 1000 Functional Connectome Project</param>\n"
|
||||
+
|
||||
" <param name=\"acronym\"/>\n" +
|
||||
" <param name=\"CD_PROJECT_NUMBER\">1R03MH096321-01A1</param>\n" +
|
||||
" <param name=\"funder\">TUBITAK</param>\n" +
|
||||
" </concept>\n" +
|
||||
" <concept claim=\"false\" id=\"ni::projects::17\" label=\"\">\n" +
|
||||
" <param name=\"projectfullname\">CRCNS Data Sharing: An open data repository for cognitive neuroscience: The OpenfMRI Project</param>\n"
|
||||
+
|
||||
" <param name=\"acronym\"/>\n" +
|
||||
" <param name=\"CD_PROJECT_NUMBER\">1131441</param>\n" +
|
||||
" <param name=\"funder\">NSF</param>\n" +
|
||||
" </concept>\n" +
|
||||
" <concept claim=\"false\" id=\"ni::projects::18\" label=\"\">\n" +
|
||||
" <param name=\"projectfullname\">Enhancing Human Cortical Plasticity: Visual Psychophysics and fMRI</param>\n"
|
||||
+
|
||||
" <param name=\"acronym\"/>\n" +
|
||||
" <param name=\"CD_PROJECT_NUMBER\">0121950</param>\n" +
|
||||
" <param name=\"funder\">NSF</param>\n" +
|
||||
" </concept>\n" +
|
||||
" <concept claim=\"false\" id=\"ni::projects::18\" label=\"\">\n" +
|
||||
" <param name=\"projectfullname\">Transforming statistical methodology for neuroimaging meta-analysis.</param>\n"
|
||||
+
|
||||
" <param name=\"acronym\"/>\n" +
|
||||
" <param name=\"CD_PROJECT_NUMBER\">100309</param>\n" +
|
||||
" <param name=\"funder\">WT</param>\n" +
|
||||
" </concept>\n" +
|
||||
" </category>" +
|
||||
|
||||
" <category claim=\"false\" id=\"elixir-gr::contentproviders\" label=\"Elixir-GR Content providers\">\n"
|
||||
" <category claim=\"false\" id=\"elixir-gr::contentproviders\" label=\"Elixir-GR Content providers\">\n"
|
||||
+
|
||||
" <concept claim=\"false\" id=\"elixir-gr::contentproviders::1\" label=\"bio.tools\">\n" +
|
||||
" <param name=\"openaireId\">rest________::b8e502674c3c3499d5374e9b2ea6d8d5</param>\n" +
|
||||
|
|
@ -626,88 +633,87 @@ public class CreateRelationTest {
|
|||
final Consumer<ContextInfo> consumer = ci -> cInfoList.add(ci);
|
||||
|
||||
queryInformationSystem
|
||||
.getContextRelation(consumer, "projects", ModelSupport.getIdPrefix(Project.class));
|
||||
.getContextRelation(consumer, "projects", ModelSupport.getIdPrefix(Project.class));
|
||||
|
||||
cInfoList.forEach(c -> System.out.println(new Gson().toJson(c)));
|
||||
|
||||
|
||||
List<Relation> rList = new ArrayList<>();
|
||||
|
||||
cInfoList.forEach(cInfo -> Process.getRelation(cInfo).forEach(rList::add));
|
||||
|
||||
Assertions.assertEquals(44 , rList.size());
|
||||
Assertions.assertEquals(44, rList.size());
|
||||
|
||||
Assertions
|
||||
.assertFalse(
|
||||
rList
|
||||
.stream()
|
||||
.map(r -> r.getSource().getId())
|
||||
.collect(Collectors.toSet())
|
||||
.contains(
|
||||
String
|
||||
.format(
|
||||
"%s|%s::%s", Constants.CONTEXT_ID,
|
||||
Constants.CONTEXT_NS_PREFIX,
|
||||
DHPUtils.md5("dh-ch"))));
|
||||
.assertFalse(
|
||||
rList
|
||||
.stream()
|
||||
.map(r -> r.getSource().getId())
|
||||
.collect(Collectors.toSet())
|
||||
.contains(
|
||||
String
|
||||
.format(
|
||||
"%s|%s::%s", Constants.CONTEXT_ID,
|
||||
Constants.CONTEXT_NS_PREFIX,
|
||||
DHPUtils.md5("dh-ch"))));
|
||||
|
||||
Assertions
|
||||
.assertEquals(
|
||||
2,
|
||||
rList
|
||||
.stream()
|
||||
.filter(
|
||||
r -> r
|
||||
.getSource()
|
||||
.getId()
|
||||
.equals(
|
||||
String
|
||||
.format(
|
||||
"%s|%s::%s", Constants.CONTEXT_ID,
|
||||
Constants.CONTEXT_NS_PREFIX,
|
||||
DHPUtils.md5("clarin"))))
|
||||
.collect(Collectors.toList())
|
||||
.size());
|
||||
.assertEquals(
|
||||
2,
|
||||
rList
|
||||
.stream()
|
||||
.filter(
|
||||
r -> r
|
||||
.getSource()
|
||||
.getId()
|
||||
.equals(
|
||||
String
|
||||
.format(
|
||||
"%s|%s::%s", Constants.CONTEXT_ID,
|
||||
Constants.CONTEXT_NS_PREFIX,
|
||||
DHPUtils.md5("clarin"))))
|
||||
.collect(Collectors.toList())
|
||||
.size());
|
||||
|
||||
Assertions
|
||||
.assertEquals(
|
||||
2,
|
||||
rList
|
||||
.stream()
|
||||
.filter(
|
||||
r -> r
|
||||
.getTarget()
|
||||
.getId()
|
||||
.equals(
|
||||
String
|
||||
.format(
|
||||
"%s|%s::%s", Constants.CONTEXT_ID,
|
||||
Constants.CONTEXT_NS_PREFIX,
|
||||
DHPUtils.md5("clarin"))))
|
||||
.collect(Collectors.toList())
|
||||
.size());
|
||||
.assertEquals(
|
||||
2,
|
||||
rList
|
||||
.stream()
|
||||
.filter(
|
||||
r -> r
|
||||
.getTarget()
|
||||
.getId()
|
||||
.equals(
|
||||
String
|
||||
.format(
|
||||
"%s|%s::%s", Constants.CONTEXT_ID,
|
||||
Constants.CONTEXT_NS_PREFIX,
|
||||
DHPUtils.md5("clarin"))))
|
||||
.collect(Collectors.toList())
|
||||
.size());
|
||||
|
||||
Set<String> tmp = rList
|
||||
.stream()
|
||||
.filter(
|
||||
r -> r
|
||||
.getSource()
|
||||
.getId()
|
||||
.equals(
|
||||
String
|
||||
.format(
|
||||
"%s|%s::%s", Constants.CONTEXT_ID,
|
||||
Constants.CONTEXT_NS_PREFIX,
|
||||
DHPUtils.md5("clarin"))))
|
||||
.map(r -> r.getTarget().getId())
|
||||
.collect(Collectors.toSet());
|
||||
.stream()
|
||||
.filter(
|
||||
r -> r
|
||||
.getSource()
|
||||
.getId()
|
||||
.equals(
|
||||
String
|
||||
.format(
|
||||
"%s|%s::%s", Constants.CONTEXT_ID,
|
||||
Constants.CONTEXT_NS_PREFIX,
|
||||
DHPUtils.md5("clarin"))))
|
||||
.map(r -> r.getTarget().getId())
|
||||
.collect(Collectors.toSet());
|
||||
|
||||
Assertions
|
||||
.assertTrue(
|
||||
tmp.contains("40|corda__h2020::b5a4eb56bf84bef2ebc193306b4d423f") &&
|
||||
tmp.contains("40|corda_______::ef782b2d85676aa3e5a907427feb18c4") );
|
||||
.assertTrue(
|
||||
tmp.contains("40|corda__h2020::b5a4eb56bf84bef2ebc193306b4d423f") &&
|
||||
tmp.contains("40|corda_______::ef782b2d85676aa3e5a907427feb18c4"));
|
||||
|
||||
rList.forEach(rel -> {
|
||||
if (rel.getSource().getId().startsWith("40|")){
|
||||
if (rel.getSource().getId().startsWith("40|")) {
|
||||
String proj = rel.getSource().getId().substring(3);
|
||||
Assertions.assertTrue(proj.substring(0, proj.indexOf("::")).length() == 12);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -10,6 +10,7 @@ import org.apache.commons.io.FileUtils;
|
|||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.JavaRDD;
|
||||
import org.apache.spark.api.java.JavaSparkContext;
|
||||
import org.apache.spark.api.java.function.ForeachFunction;
|
||||
import org.apache.spark.sql.Dataset;
|
||||
import org.apache.spark.sql.Encoders;
|
||||
import org.apache.spark.sql.Row;
|
||||
|
|
@ -71,7 +72,7 @@ public class DumpRelationTest {
|
|||
public void test1() throws Exception {
|
||||
|
||||
final String sourcePath = getClass()
|
||||
.getResource("/eu/dnetlib/dhp/oa/graph/dump/relation")
|
||||
.getResource("/eu/dnetlib/dhp/oa/graph/dump/relation/relation")
|
||||
.getPath();
|
||||
|
||||
SparkDumpRelationJob.main(new String[] {
|
||||
|
|
@ -93,6 +94,8 @@ public class DumpRelationTest {
|
|||
|
||||
verificationDataset.createOrReplaceTempView("table");
|
||||
|
||||
verificationDataset.foreach((ForeachFunction<Relation>)r -> System.out.println(new ObjectMapper().writeValueAsString(r)));
|
||||
|
||||
Dataset<Row> check = spark
|
||||
.sql(
|
||||
"SELECT reltype.name, source.id source, source.type stype, target.id target,target.type ttype, provenance.provenance "
|
||||
|
|
@ -127,4 +130,75 @@ public class DumpRelationTest {
|
|||
.count());
|
||||
}
|
||||
|
||||
@Test
|
||||
public void test2() throws Exception {
|
||||
|
||||
final String sourcePath = getClass()
|
||||
.getResource("/eu/dnetlib/dhp/oa/graph/dump/relation/relation_validated")
|
||||
.getPath();
|
||||
|
||||
SparkDumpRelationJob.main(new String[] {
|
||||
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||
"-outputPath", workingDir.toString() + "/relation",
|
||||
"-sourcePath", sourcePath
|
||||
});
|
||||
|
||||
// dumpCommunityProducts.exec(MOCK_IS_LOOK_UP_URL,Boolean.FALSE, workingDir.toString()+"/dataset",sourcePath,"eu.dnetlib.dhp.schema.oaf.Dataset","eu.dnetlib.dhp.schema.dump.oaf.Dataset");
|
||||
|
||||
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||
|
||||
JavaRDD<Relation> tmp = sc
|
||||
.textFile(workingDir.toString() + "/relation")
|
||||
.map(item -> OBJECT_MAPPER.readValue(item, Relation.class));
|
||||
|
||||
org.apache.spark.sql.Dataset<Relation> verificationDataset = spark
|
||||
.createDataset(tmp.rdd(), Encoders.bean(Relation.class));
|
||||
|
||||
verificationDataset.createOrReplaceTempView("table");
|
||||
|
||||
verificationDataset.foreach((ForeachFunction<Relation>)r -> System.out.println(new ObjectMapper().writeValueAsString(r)));
|
||||
|
||||
Dataset<Row> check = spark
|
||||
.sql(
|
||||
"SELECT reltype.name, source.id source, source.type stype, target.id target,target.type ttype, provenance.provenance "
|
||||
+
|
||||
"from table ");
|
||||
|
||||
Assertions.assertEquals(20, check.filter("name = 'isProvidedBy'").count());
|
||||
Assertions
|
||||
.assertEquals(
|
||||
20, check
|
||||
.filter(
|
||||
"name = 'isProvidedBy' and stype = 'datasource' and ttype = 'organization' and " +
|
||||
"provenance = 'Harvested'")
|
||||
.count());
|
||||
|
||||
Assertions.assertEquals(7, check.filter("name = 'isParticipant'").count());
|
||||
Assertions
|
||||
.assertEquals(
|
||||
7, check
|
||||
.filter(
|
||||
"name = 'isParticipant' and stype = 'organization' and ttype = 'project' " +
|
||||
"and provenance = 'Harvested'")
|
||||
.count());
|
||||
|
||||
Assertions.assertEquals(1, check.filter("name = 'isAuthorInstitutionOf'").count());
|
||||
Assertions
|
||||
.assertEquals(
|
||||
1, check
|
||||
.filter(
|
||||
"name = 'isAuthorInstitutionOf' and stype = 'organization' and ttype = 'result' " +
|
||||
"and provenance = 'Inferred by OpenAIRE'")
|
||||
.count());
|
||||
|
||||
Assertions.assertEquals(2, check.filter("name = 'isProducedBy'").count());
|
||||
Assertions
|
||||
.assertEquals(
|
||||
2, check
|
||||
.filter(
|
||||
"name = 'isProducedBy' and stype = 'project' and ttype = 'result' " +
|
||||
"and provenance = 'Harvested' and validated = true " +
|
||||
"and validationDate = '2021-08-06'")
|
||||
.count());
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -6,6 +6,7 @@ import static org.mockito.Mockito.lenient;
|
|||
import java.util.*;
|
||||
import java.util.function.Consumer;
|
||||
|
||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||
import org.junit.jupiter.api.Assertions;
|
||||
import org.junit.jupiter.api.BeforeEach;
|
||||
import org.junit.jupiter.api.Test;
|
||||
|
|
@ -528,7 +529,7 @@ public class QueryInformationSystemTest {
|
|||
List<ContextInfo> cInfoList = new ArrayList<>();
|
||||
final Consumer<ContextInfo> consumer = ci -> cInfoList.add(ci);
|
||||
queryInformationSystem.execContextRelationQuery();
|
||||
queryInformationSystem.getContextRelation(consumer, "contentproviders", "10|");
|
||||
queryInformationSystem.getContextRelation(consumer, "contentproviders", ModelSupport.entityIdPrefix.get("datasource"));
|
||||
|
||||
Assertions.assertEquals(5, cInfoList.size());
|
||||
}
|
||||
|
|
@ -539,7 +540,7 @@ public class QueryInformationSystemTest {
|
|||
List<ContextInfo> cInfoList = new ArrayList<>();
|
||||
final Consumer<ContextInfo> consumer = ci -> cInfoList.add(ci);
|
||||
queryInformationSystem.execContextRelationQuery();
|
||||
queryInformationSystem.getContextRelation(consumer, "contentproviders", "10");
|
||||
queryInformationSystem.getContextRelation(consumer, "contentproviders", ModelSupport.entityIdPrefix.get("datasource"));
|
||||
|
||||
cInfoList.forEach(contextInfo -> {
|
||||
switch (contextInfo.getId()) {
|
||||
|
|
|
|||
|
|
@ -75,8 +75,8 @@ public class ResultLinkedToProjectTest {
|
|||
.getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json")
|
||||
.getPath();
|
||||
|
||||
final String relationPath = getClass()
|
||||
.getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/relations.json")
|
||||
final String graphPath = getClass()
|
||||
.getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch")
|
||||
.getPath();
|
||||
|
||||
SparkResultLinkedToProject.main(new String[] {
|
||||
|
|
@ -84,7 +84,7 @@ public class ResultLinkedToProjectTest {
|
|||
"-outputPath", workingDir.toString() + "/preparedInfo",
|
||||
"-sourcePath", sourcePath,
|
||||
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication",
|
||||
"-relationPath", relationPath
|
||||
"-graphPath", graphPath
|
||||
|
||||
});
|
||||
|
||||
|
|
@ -109,7 +109,7 @@ public class ResultLinkedToProjectTest {
|
|||
.getPath();
|
||||
|
||||
final String relationPath = getClass()
|
||||
.getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/relations.json")
|
||||
.getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match")
|
||||
.getPath();
|
||||
|
||||
SparkResultLinkedToProject.main(new String[] {
|
||||
|
|
@ -117,7 +117,7 @@ public class ResultLinkedToProjectTest {
|
|||
"-outputPath", workingDir.toString() + "/preparedInfo",
|
||||
"-sourcePath", sourcePath,
|
||||
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication",
|
||||
"-relationPath", relationPath
|
||||
"-graphPath", relationPath
|
||||
|
||||
});
|
||||
|
||||
|
|
|
|||
|
|
@ -75,7 +75,7 @@ public class SplitPerFunderTest {
|
|||
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||
"-outputPath", workingDir.toString() + "/split",
|
||||
"-sourcePath", sourcePath,
|
||||
"-relationPath", sourcePath
|
||||
"-graphPath", sourcePath
|
||||
|
||||
});
|
||||
|
||||
|
|
@ -143,5 +143,11 @@ public class SplitPerFunderTest {
|
|||
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
|
||||
Assertions.assertEquals(1, tmp.count());
|
||||
|
||||
// CONICYT 0
|
||||
tmp = sc
|
||||
.textFile(workingDir.toString() + "/split/CONICYTF")
|
||||
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
|
||||
Assertions.assertEquals(0, tmp.count());
|
||||
|
||||
}
|
||||
}
|
||||
|
|
|
|||
File diff suppressed because one or more lines are too long
File diff suppressed because one or more lines are too long
|
|
@ -1,9 +0,0 @@
|
|||
{"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1603715146539,"properties":[],"relClass":"isProducedBy","relType":"datasourceOrganization","source":"10|doajarticles::2baa9032dc058d3c8ff780c426b0c19f","subRelType":"provision","target":"40|cihr________::1e5e62235d094afd01cd56e65112fc63"}
|
||||
{"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1603715146539,"properties":[],"relClass":"isProducedBy","relType":"datasourceOrganization","source":"10|doajarticles::5ac587eb28411c351c2e357eb097fd3d","subRelType":"provision","target":"40|nwo_________::dc69ada721bf21ed51055b6421850d73"}
|
||||
{"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1603715146539,"properties":[],"relClass":"isProducedBy","relType":"datasourceOrganization","source":"10|doajarticles::690b3aaf177a4c70b81bacd8d023cbdc","subRelType":"provision","target":"40|nih_________::031bb5f2f70239b3210eda38b2079f67"}
|
||||
{"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1603715146539,"properties":[],"relClass":"isProducedBy","relType":"datasourceOrganization","source":"10|doajarticles::7a71f278237d1ab35088efda03fa007a","subRelType":"provision","target":"40|nsf_________::03748bcb5d754c951efec9700e18a56d"}
|
||||
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{"collectedfrom":[{"key":"10|openaire____::21f8a223b9925c2f87c404096080b046","value":"Registry of Research Data Repository"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1592688952862,"properties":[],"relClass":"isProvidedBy","relType":"datasourceOrganization","source":"10|re3data_____::b26c86eba2b3ad8b242a93b581e6ec8e","subRelType":"provision","target":"20|re3data_____::e841a40265d8d0a6739ac71f56328da3"}
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||||
{"collectedfrom":[{"key":"10|openaire____::21f8a223b9925c2f87c404096080b046","value":"Registry of Research Data Repository"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1592688952862,"properties":[],"relClass":"isProvidedBy","relType":"datasourceOrganization","source":"10|re3data_____::cafe7980294aa5f935f433e7c8aab844","subRelType":"provision","target":"20|dedup_wf_001::2806db65ba8029ee196679cad067eff2"}
|
||||
{"collectedfrom":[{"key":"10|openaire____::6ac933301a3933c8a22ceebea7000326","value":"Academy of Finland"}],"dataInfo":{"deletedbyinference":true,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900000000000000022"},"lastupdatetimestamp":1592688952862,"properties":[],"relClass":"isParticipant","relType":"projectOrganization","source":"20|aka_________::0cd5965141113df5739f1ac7ac7f6d37","subRelType":"participation","target":"40|aka_________::1bc716a1763110da3eb1af867de718a8"}
|
||||
{"collectedfrom":[{"key":"10|openaire____::6ac933301a3933c8a22ceebea7000326","value":"Academy of Finland"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900000000000000022"},"lastupdatetimestamp":1592688952862,"properties":[],"relClass":"isParticipant","relType":"projectOrganization","source":"20|aka_________::1e2df822bf0932ad0f77565789f22e17","subRelType":"participation","target":"40|aka_________::a6c805bcfd383bae043d8df38e79db78"}
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||||
{"collectedfrom":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"iis::document_affiliations","inferred":true,"invisible":false,"provenanceaction":{"classid":"iis","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.8966"},"lastupdatetimestamp":1595258695262,"properties":[],"relClass":"isAuthorInstitutionOf","relType":"resultOrganization","source":"20|aka_________::2c3aab6bce7516338b4dbfb4f6f86db7","subRelType":"affiliation","target":"50|dedup_wf_001::02859c30f6c8bfbdd8c427068a6ec684"}
|
||||
{"collectedfrom":[{"key":"10|openaire____::6ac933301a3933c8a22ceebea7000326","value":"Academy of Finland"}],"dataInfo":{"deletedbyinference":true,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900000000000000022"},"lastupdatetimestamp":1592688952862,"properties":[],"relClass":"isParticipant","relType":"projectOrganization","source":"20|aka_________::8bcd11b6bffc76f4d4f88d7a6728d614","subRelType":"participation","target":"40|aka_________::645123c3fe7bab557c36f0f9bb02a4cd"}
|
||||
{"collectedfrom":[{"key":"10|openaire____::6ac933301a3933c8a22ceebea7000326","value":"Academy of Finland"}],"dataInfo":{"deletedbyinference":true,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900000000000000022"},"lastupdatetimestamp":1592688952862,"properties":[],"relClass":"isParticipant","relType":"projectOrganization","source":"20|aka_________::8bcd11b6bffc76f4d4f88d7a6728d614","subRelType":"participation","target":"40|aka_________::fecf4f862a6b40dd2ccb1abc8fed5bc5"}
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||||
{"collectedfrom":[{"key":"10|openaire____::6ac933301a3933c8a22ceebea7000326","value":"Academy of Finland"}],"dataInfo":{"deletedbyinference":true,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900000000000000022"},"lastupdatetimestamp":1592688952862,"properties":[],"relClass":"isParticipant","relType":"projectOrganization","source":"20|aka_________::a30b9a45766293af38951d767e77a471","subRelType":"participation","target":"40|aka_________::b733217d1cd609001dd3c75af419d872"}
|
||||
{"collectedfrom":[{"key":"10|openaire____::6ac933301a3933c8a22ceebea7000326","value":"Academy of Finland"}],"dataInfo":{"deletedbyinference":true,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900000000000000022"},"lastupdatetimestamp":1592688952862,"properties":[],"relClass":"isParticipant","relType":"projectOrganization","source":"20|aka_________::a30b9a45766293af38951d767e77a471","subRelType":"participation","target":"40|aka_________::c33dee8231ad0374caf93e52c5a473e5"}
|
||||
{"collectedfrom":[{"key":"10|openaire____::6ac933301a3933c8a22ceebea7000326","value":"Academy of Finland"}],"dataInfo":{"deletedbyinference":true,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900000000000000022"},"lastupdatetimestamp":1592688952862,"properties":[],"relClass":"isParticipant","relType":"projectOrganization","source":"20|aka_________::ddcb6d65425e4531a11c610488d42d81","subRelType":"participation","target":"40|aka_________::4d7027ac28c8ac9cc72b062ac4992b4e"}
|
||||
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File diff suppressed because one or more lines are too long
|
|
@ -0,0 +1,8 @@
|
|||
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"iis::document_referencedProjects","inferred":true,"invisible":false,"provenanceaction":{"classid":"iis","classname":"iis","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.6573"},"lastupdatetimestamp":1590395831891,"properties":[],"relClass":"isProducedBy","relType":"resultProject","target":"40|aka_________::0f7d119de1f656b5763a16acf876fed6","subRelType":"outcome","source":"50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb","validated":true, "validationDate":"2021-08-06"}
|
||||
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"iis::document_referencedProjects","inferred":true,"invisible":false,"provenanceaction":{"classid":"iis","classname":"iis","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.6573"},"lastupdatetimestamp":1590395831891,"properties":[],"relClass":"isProducedBy","relType":"resultProject","target":"40|aka_________::03376222b28a3aebf2730ac514818d04","subRelType":"outcome","source":"50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb","validated":true, "validationDate":"2021-08-05"}
|
||||
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"iis::document_referencedProjects","inferred":true,"invisible":false,"provenanceaction":{"classid":"iis","classname":"iis","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.6573"},"lastupdatetimestamp":1590395839728,"properties":[],"relClass":"isProducedBy","relType":"resultProject","target":"40|aka_________::0f7d119de1f656b5763a16acf876fed6","subRelType":"outcome","source":"50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80","validated":true, "validationDate":"2021-08-04"}
|
||||
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"iis::document_referencedProjects","inferred":true,"invisible":false,"provenanceaction":{"classid":"iis","classname":"iis","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.6573"},"lastupdatetimestamp":1590395836359,"properties":[],"relClass":"isProducedBy","relType":"resultProject","target":"40|aka_________::7713935a3e4c65f30fcc6b064f212051","subRelType":"outcome","source":"50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80","validated":true, "validationDate":"2021-08-03"}
|
||||
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"iis::document_referencedProjects","inferred":true,"invisible":false,"provenanceaction":{"classid":"iis","classname":"iis","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.6573"},"lastupdatetimestamp":1590395834612,"properties":[],"relClass":"isProducedBy","relType":"resultProject","target":"40|aka_________::7a1099637c8ec85097e185a00bd4f877","subRelType":"outcome","source":"50|dedup_wf_001::400872751d497a6ff9c7e7aba67d327e","validated":true, "validationDate":"2021-08-02"}
|
||||
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"iis::document_referencedProjects","inferred":true,"invisible":false,"provenanceaction":{"classid":"iis","classname":"iis","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.6573"},"lastupdatetimestamp":1590395834612,"properties":[],"relClass":"isProducedBy","relType":"resultProject","target":"40|aka_________::7a1099637c8ec85097e185a00bd4f877","subRelType":"outcome","source":"50|dedup_wf_001::400872751d497a6ff9c7e7aba67d327e","validated":true, "validationDate":"2021-08-01"}
|
||||
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"iis::document_referencedProjects","inferred":true,"invisible":false,"provenanceaction":{"classid":"iis","classname":"iis","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.6573"},"lastupdatetimestamp":1590395828225,"properties":[],"relClass":"isProducedBy","relType":"resultProject","target":"40|aka_________::87bc20a437817d73c2d64555d225e85b","subRelType":"outcome","source":"50|dedup_wf_001::bc92b920df0f280041a512a7912130cf","validated":true, "validationDate":"2021-07-31"}
|
||||
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"iis::document_referencedProjects","inferred":true,"invisible":false,"provenanceaction":{"classid":"iis","classname":"iis","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.6573"},"lastupdatetimestamp":1590395828225,"properties":[],"relClass":"isProducedBy","relType":"resultProject","target":"40|aka_________::87bc20a437817d73c2d64555d225e85b","subRelType":"outcome","source":"50|dedup_wf_001::bc92b920df0f280041a512a7912130cf","validated":true, "validationDate":"2021-07-30"}
|
||||
2
pom.xml
2
pom.xml
|
|
@ -741,7 +741,7 @@
|
|||
<mockito-core.version>3.3.3</mockito-core.version>
|
||||
<mongodb.driver.version>3.4.2</mongodb.driver.version>
|
||||
<vtd.version>[2.12,3.0)</vtd.version>
|
||||
<dhp-schemas.version>[2.7.15]</dhp-schemas.version>
|
||||
<dhp-schemas.version>2.7.17-SNAPSHOT</dhp-schemas.version>
|
||||
<dnet-actionmanager-api.version>[4.0.3]</dnet-actionmanager-api.version>
|
||||
<dnet-actionmanager-common.version>[6.0.5]</dnet-actionmanager-common.version>
|
||||
<dnet-openaire-broker-common.version>[3.1.6]</dnet-openaire-broker-common.version>
|
||||
|
|
|
|||
Loading…
Reference in New Issue