forked from D-Net/dnet-hadoop
result pids (new xpaths + IS vocabularies)
This commit is contained in:
parent
7a7272d9ec
commit
a25598140a
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@ -64,8 +64,10 @@ public abstract class AbstractMdRecordToOafMapper {
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protected static final String DATACITE_SCHEMA_KERNEL_4 = "http://datacite.org/schema/kernel-4";
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protected static final String DATACITE_SCHEMA_KERNEL_3 = "http://datacite.org/schema/kernel-3";
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protected static final Qualifier ORCID_PID_TYPE = qualifier("ORCID", "Open Researcher and Contributor ID", DNET_PID_TYPES, DNET_PID_TYPES);
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protected static final Qualifier MAG_PID_TYPE = qualifier("MAGIdentifier", "Microsoft Academic Graph Identifier", DNET_PID_TYPES, DNET_PID_TYPES);
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protected static final Qualifier ORCID_PID_TYPE = qualifier(
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"ORCID", "Open Researcher and Contributor ID", DNET_PID_TYPES, DNET_PID_TYPES);
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protected static final Qualifier MAG_PID_TYPE = qualifier(
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"MAGIdentifier", "Microsoft Academic Graph Identifier", DNET_PID_TYPES, DNET_PID_TYPES);
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protected static final Map<String, String> nsContext = new HashMap<>();
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@ -79,7 +81,8 @@ public abstract class AbstractMdRecordToOafMapper {
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nsContext.put("datacite", DATACITE_SCHEMA_KERNEL_3);
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}
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protected static final Qualifier MAIN_TITLE_QUALIFIER = qualifier("main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title");
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protected static final Qualifier MAIN_TITLE_QUALIFIER = qualifier(
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"main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title");
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protected AbstractMdRecordToOafMapper(final Map<String, String> code2name) {
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this.code2name = code2name;
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@ -93,15 +96,20 @@ public abstract class AbstractMdRecordToOafMapper {
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.parseText(xml.replaceAll(DATACITE_SCHEMA_KERNEL_4, DATACITE_SCHEMA_KERNEL_3));
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final String type = doc.valueOf("//dr:CobjCategory/@type");
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final KeyValue collectedFrom = getProvenanceDatasource(doc, "//oaf:collectedFrom/@id", "//oaf:collectedFrom/@name");
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final KeyValue collectedFrom = getProvenanceDatasource(
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doc, "//oaf:collectedFrom/@id", "//oaf:collectedFrom/@name");
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if (collectedFrom == null) { return null; }
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if (collectedFrom == null) {
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return null;
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}
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final KeyValue hostedBy = StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id"))
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? collectedFrom
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: getProvenanceDatasource(doc, "//oaf:hostedBy/@id", "//oaf:hostedBy/@name");
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if (hostedBy == null) { return null; }
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if (hostedBy == null) {
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return null;
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}
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final DataInfo info = prepareDataInfo(doc);
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final long lastUpdateTimestamp = new Date().getTime();
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@ -116,7 +124,9 @@ public abstract class AbstractMdRecordToOafMapper {
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final String dsId = doc.valueOf(xpathId);
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final String dsName = doc.valueOf(xpathName);
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if (StringUtils.isBlank(dsId) | StringUtils.isBlank(dsName)) { return null; }
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if (StringUtils.isBlank(dsId) | StringUtils.isBlank(dsName)) {
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return null;
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}
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return keyValue(createOpenaireId(10, dsId, true), dsName);
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}
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@ -201,9 +211,15 @@ public abstract class AbstractMdRecordToOafMapper {
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final String projectId = createOpenaireId(40, originalId, true);
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res
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.add(getRelation(docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, collectedFrom, info, lastUpdateTimestamp));
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.add(
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getRelation(
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docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, collectedFrom, info,
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lastUpdateTimestamp));
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res
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.add(getRelation(projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, collectedFrom, info, lastUpdateTimestamp));
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.add(
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getRelation(
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projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, collectedFrom, info,
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lastUpdateTimestamp));
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}
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}
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@ -398,7 +414,9 @@ public abstract class AbstractMdRecordToOafMapper {
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final String sp = n.valueOf("@sp");
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final String vol = n.valueOf("@vol");
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final String edition = n.valueOf("@edition");
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if (StringUtils.isNotBlank(name)) { return journal(name, issnPrinted, issnOnline, issnLinking, ep, iss, sp, vol, edition, null, null, info); }
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if (StringUtils.isNotBlank(name)) {
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return journal(name, issnPrinted, issnOnline, issnLinking, ep, iss, sp, vol, edition, null, null, info);
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}
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}
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return null;
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}
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@ -451,7 +469,10 @@ public abstract class AbstractMdRecordToOafMapper {
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for (final Object o : node.selectNodes(xpath)) {
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final Node n = (Node) o;
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res
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.add(structuredProperty(n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"), n.valueOf("@schemename"), info));
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.add(
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structuredProperty(
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n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"),
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n.valueOf("@schemename"), info));
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}
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return res;
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}
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@ -459,7 +480,9 @@ public abstract class AbstractMdRecordToOafMapper {
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protected OAIProvenance prepareOAIprovenance(final Document doc) {
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final Node n = doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']");
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if (n == null) { return null; }
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if (n == null) {
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return null;
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}
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final String identifier = n.valueOf("./*[local-name()='identifier']");
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final String baseURL = n.valueOf("./*[local-name()='baseURL']");
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@ -474,7 +497,9 @@ public abstract class AbstractMdRecordToOafMapper {
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protected DataInfo prepareDataInfo(final Document doc) {
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final Node n = doc.selectSingleNode("//oaf:datainfo");
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if (n == null) { return dataInfo(false, null, false, false, REPOSITORY_PROVENANCE_ACTIONS, "0.9"); }
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if (n == null) {
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return dataInfo(false, null, false, false, REPOSITORY_PROVENANCE_ACTIONS, "0.9");
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}
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final String paClassId = n.valueOf("./oaf:provenanceaction/@classid");
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final String paClassName = n.valueOf("./oaf:provenanceaction/@classname");
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@ -486,7 +511,9 @@ public abstract class AbstractMdRecordToOafMapper {
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final Boolean inferred = Boolean.parseBoolean(n.valueOf("./oaf:inferred"));
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final String trust = n.valueOf("./oaf:trust");
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return dataInfo(deletedbyinference, inferenceprovenance, inferred, false, qualifier(paClassId, paClassName, paSchemeId, paSchemeName), trust);
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return dataInfo(
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deletedbyinference, inferenceprovenance, inferred, false,
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qualifier(paClassId, paClassName, paSchemeId, paSchemeName), trust);
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}
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protected Field<String> prepareField(final Node node, final String xpath, final DataInfo info) {
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@ -56,7 +56,8 @@ public class GenerateEntitiesApplication {
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public static void main(final String[] args) throws Exception {
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(GenerateEntitiesApplication.class
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.toString(
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GenerateEntitiesApplication.class
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.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/generate_entities_parameters.json")));
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parser.parseArgument(args);
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@ -105,7 +106,8 @@ public class GenerateEntitiesApplication {
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for (final String sp : existingSourcePaths) {
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inputRdd = inputRdd
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.union(sc
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.union(
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sc
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.sequenceFile(sp, Text.class, Text.class)
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.map(k -> new Tuple2<>(k._1().toString(), k._2().toString()))
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.map(k -> convertToListOaf(k._1(), k._2(), code2name))
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@ -117,7 +119,8 @@ public class GenerateEntitiesApplication {
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.mapToPair(oaf -> new Tuple2<>(ModelSupport.idFn().apply(oaf), oaf))
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.reduceByKey((o1, o2) -> merge(o1, o2))
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.map(Tuple2::_2)
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.map(oaf -> oaf.getClass().getSimpleName().toLowerCase()
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.map(
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oaf -> oaf.getClass().getSimpleName().toLowerCase()
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+ "|"
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+ OBJECT_MAPPER.writeValueAsString(oaf))
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.saveAsTextFile(targetPath, GzipCodec.class);
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@ -194,8 +197,10 @@ public class GenerateEntitiesApplication {
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private static Map<String, String> loadVocsFromIS(final String isLookupUrl) throws IOException, ISLookUpException {
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final ISLookUpService isLookUpService = ISLookupClientFactory.getLookUpService(isLookupUrl);
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final String xquery =
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IOUtils.toString(GenerateEntitiesApplication.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/xquery/load_vocabularies.xquery"));
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final String xquery = IOUtils
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.toString(
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GenerateEntitiesApplication.class
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.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/xquery/load_vocabularies.xquery"));
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final Map<String, String> map = new HashMap<>();
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@ -130,7 +130,8 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
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final Instance instance = new Instance();
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instance
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.setInstancetype(prepareQualifier(doc, "//dr:CobjCategory", DNET_PUBLICATION_RESOURCE, DNET_PUBLICATION_RESOURCE));
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.setInstancetype(
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prepareQualifier(doc, "//dr:CobjCategory", DNET_PUBLICATION_RESOURCE, DNET_PUBLICATION_RESOURCE));
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instance.setCollectedfrom(collectedfrom);
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instance.setHostedby(hostedby);
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instance.setDateofacceptance(field(doc.valueOf("//oaf:dateAccepted"), info));
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@ -146,7 +147,8 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
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final List<Node> nodes = Lists.newArrayList(doc.selectNodes("//dc:identifier"));
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instance
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.setUrl(nodes
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.setUrl(
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nodes
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.stream()
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.filter(n -> StringUtils.isNotBlank(n.getText()))
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.map(n -> n.getText().trim())
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@ -277,9 +279,15 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
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final String otherId = createOpenaireId(50, originalId, false);
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res
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.add(getRelation(docId, otherId, RESULT_RESULT, PUBLICATION_DATASET, IS_RELATED_TO, collectedFrom, info, lastUpdateTimestamp));
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.add(
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getRelation(
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docId, otherId, RESULT_RESULT, PUBLICATION_DATASET, IS_RELATED_TO, collectedFrom, info,
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lastUpdateTimestamp));
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res
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.add(getRelation(otherId, docId, RESULT_RESULT, PUBLICATION_DATASET, IS_RELATED_TO, collectedFrom, info, lastUpdateTimestamp));
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.add(
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getRelation(
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otherId, docId, RESULT_RESULT, PUBLICATION_DATASET, IS_RELATED_TO, collectedFrom, info,
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lastUpdateTimestamp));
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}
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}
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return res;
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@ -292,6 +300,7 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
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@Override
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protected List<StructuredProperty> prepareResultPids(final Document doc, final DataInfo info) {
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return prepareListStructProps(doc, "//oaf:identifier", "@identifierType", "dnet:pid_types", "dnet:pid_types", info);
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return prepareListStructProps(
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doc, "//oaf:identifier", "@identifierType", "dnet:pid_types", "dnet:pid_types", info);
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}
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}
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@ -120,7 +120,8 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
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final Instance instance = new Instance();
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instance
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.setInstancetype(prepareQualifier(doc, "//dr:CobjCategory", DNET_PUBLICATION_RESOURCE, DNET_PUBLICATION_RESOURCE));
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.setInstancetype(
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prepareQualifier(doc, "//dr:CobjCategory", DNET_PUBLICATION_RESOURCE, DNET_PUBLICATION_RESOURCE));
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instance.setCollectedfrom(collectedfrom);
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instance.setHostedby(hostedby);
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instance.setDateofacceptance(field(doc.valueOf("//oaf:dateAccepted"), info));
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@ -169,7 +170,10 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
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&& !dateType.equalsIgnoreCase("Updated")
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&& !dateType.equalsIgnoreCase("Available")) {
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res
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.add(structuredProperty(((Node) o).getText(), "UNKNOWN", "UNKNOWN", DNET_DATA_CITE_DATE, DNET_DATA_CITE_DATE, info));
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.add(
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structuredProperty(
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((Node) o).getText(), "UNKNOWN", "UNKNOWN", DNET_DATA_CITE_DATE, DNET_DATA_CITE_DATE,
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info));
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}
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}
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return res;
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@ -221,14 +225,16 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
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protected List<Field<String>> prepareOtherResearchProductContactGroups(
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final Document doc,
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final DataInfo info) {
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return prepareListFields(doc, "//datacite:contributor[@contributorType='ContactGroup']/datacite:contributorName", info);
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return prepareListFields(
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doc, "//datacite:contributor[@contributorType='ContactGroup']/datacite:contributorName", info);
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}
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@Override
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protected List<Field<String>> prepareOtherResearchProductContactPersons(
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final Document doc,
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final DataInfo info) {
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return prepareListFields(doc, "//datacite:contributor[@contributorType='ContactPerson']/datacite:contributorName", info);
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return prepareListFields(
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doc, "//datacite:contributor[@contributorType='ContactPerson']/datacite:contributorName", info);
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}
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@Override
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@ -254,7 +260,8 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
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protected List<Field<String>> prepareSoftwareDocumentationUrls(
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final Document doc,
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final DataInfo info) {
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return prepareListFields(doc, "//datacite:relatedIdentifier[@relatedIdentifierType='URL' and @relationType='IsDocumentedBy']", info);
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return prepareListFields(
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doc, "//datacite:relatedIdentifier[@relatedIdentifierType='URL' and @relationType='IsDocumentedBy']", info);
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}
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// DATASETS
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@ -328,16 +335,29 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
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if (type.equalsIgnoreCase("IsSupplementTo")) {
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res
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.add(getRelation(docId, otherId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENT_TO, collectedFrom, info, lastUpdateTimestamp));
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.add(
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getRelation(
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docId, otherId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENT_TO, collectedFrom, info,
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lastUpdateTimestamp));
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res
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.add(getRelation(otherId, docId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENTED_BY, collectedFrom, info, lastUpdateTimestamp));
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.add(
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getRelation(
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otherId, docId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENTED_BY, collectedFrom, info,
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lastUpdateTimestamp));
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} else if (type.equals("IsPartOf")) {
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res
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.add(getRelation(docId, otherId, RESULT_RESULT, PART, IS_PART_OF, collectedFrom, info, lastUpdateTimestamp));
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.add(
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getRelation(
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docId, otherId, RESULT_RESULT, PART, IS_PART_OF, collectedFrom, info,
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lastUpdateTimestamp));
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res
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.add(getRelation(otherId, docId, RESULT_RESULT, PART, HAS_PARTS, collectedFrom, info, lastUpdateTimestamp));
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} else {}
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.add(
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getRelation(
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otherId, docId, RESULT_RESULT, PART, HAS_PARTS, collectedFrom, info,
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lastUpdateTimestamp));
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} else {
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}
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}
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}
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return res;
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@ -345,15 +365,28 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
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@Override
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protected Qualifier prepareResourceType(final Document doc, final DataInfo info) {
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return prepareQualifier(doc, "//*[local-name() = 'resource']//*[local-name() = 'resourceType']", DNET_DATA_CITE_RESOURCE, DNET_DATA_CITE_RESOURCE);
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return prepareQualifier(
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doc, "//*[local-name() = 'resource']//*[local-name() = 'resourceType']", DNET_DATA_CITE_RESOURCE,
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DNET_DATA_CITE_RESOURCE);
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}
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@Override
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protected List<StructuredProperty> prepareResultPids(final Document doc, final DataInfo info) {
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final List<StructuredProperty> res = new ArrayList<>();
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res.addAll(prepareListStructProps(doc, "//oaf:identifier", "@identifierType", "dnet:pid_types", "dnet:pid_types", info));
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res.addAll(prepareListStructProps(doc, "//datacite:identifier[@identifierType != 'URL']", "@identifierType", "dnet:pid_types", "dnet:pid_types", info));
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res.addAll(prepareListStructProps(doc, "//datacite:alternateIdentifier[@alternateIdentifierType != 'URL']", "@alternateIdentifierType", "dnet:pid_types", "dnet:pid_types", info));
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res
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.addAll(
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prepareListStructProps(
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doc, "//oaf:identifier", "@identifierType", "dnet:pid_types", "dnet:pid_types", info));
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res
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.addAll(
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prepareListStructProps(
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doc, "//datacite:identifier[@identifierType != 'URL']", "@identifierType", "dnet:pid_types",
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"dnet:pid_types", info));
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res
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.addAll(
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prepareListStructProps(
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doc, "//datacite:alternateIdentifier[@alternateIdentifierType != 'URL']",
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"@alternateIdentifierType", "dnet:pid_types", "dnet:pid_types", info));
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return res;
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}
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