forked from D-Net/dnet-hadoop
fixed a problem with missing instances
This commit is contained in:
parent
9e4d58f505
commit
d920ce501e
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@ -10,19 +10,6 @@ import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.oaiIProvenance;
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import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.qualifier;
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import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.Date;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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import org.apache.commons.lang3.StringUtils;
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import org.dom4j.Document;
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import org.dom4j.DocumentFactory;
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import org.dom4j.DocumentHelper;
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import org.dom4j.Node;
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import eu.dnetlib.dhp.oa.graph.raw.common.MigrationConstants;
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import eu.dnetlib.dhp.schema.oaf.Author;
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import eu.dnetlib.dhp.schema.oaf.DataInfo;
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@ -41,388 +28,439 @@ import eu.dnetlib.dhp.schema.oaf.Relation;
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import eu.dnetlib.dhp.schema.oaf.Result;
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import eu.dnetlib.dhp.schema.oaf.Software;
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import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.Date;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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import org.apache.commons.lang3.StringUtils;
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import org.dom4j.Document;
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import org.dom4j.DocumentFactory;
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import org.dom4j.DocumentHelper;
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import org.dom4j.Node;
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public abstract class AbstractMdRecordToOafMapper {
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protected final Map<String, String> code2name;
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protected static final Qualifier MAIN_TITLE_QUALIFIER =
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qualifier("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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}
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public List<Oaf> processMdRecord(final String xml) {
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try {
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final Map<String, String> nsContext = new HashMap<>();
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nsContext.put("dr", "http://www.driver-repository.eu/namespace/dr");
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nsContext.put("dri", "http://www.driver-repository.eu/namespace/dri");
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nsContext.put("oaf", "http://namespace.openaire.eu/oaf");
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nsContext.put("oai", "http://www.openarchives.org/OAI/2.0/");
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nsContext.put("prov", "http://www.openarchives.org/OAI/2.0/provenance");
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nsContext.put("dc", "http://purl.org/dc/elements/1.1/");
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nsContext.put("datacite", "http://datacite.org/schema/kernel-3");
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DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext);
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final Document doc =
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DocumentHelper.parseText(xml.replaceAll("http://datacite.org/schema/kernel-4", "http://datacite.org/schema/kernel-3"));
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final String type = doc.valueOf("//dr:CobjCategory/@type");
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final KeyValue collectedFrom =
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keyValue(createOpenaireId(10, doc.valueOf("//oaf:collectedFrom/@id"), true), doc.valueOf("//oaf:collectedFrom/@name"));
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final KeyValue hostedBy =
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StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id"))
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? collectedFrom
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: keyValue(createOpenaireId(10, doc.valueOf("//oaf:hostedBy/@id"), true), doc.valueOf("//oaf:hostedBy/@name"));
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final DataInfo info = prepareDataInfo(doc);
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final long lastUpdateTimestamp = new Date().getTime();
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return createOafs(doc, type, collectedFrom, hostedBy, info, lastUpdateTimestamp);
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} catch (final Exception e) {
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throw new RuntimeException(e);
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}
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}
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protected List<Oaf> createOafs(
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final Document doc,
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final String type,
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final KeyValue collectedFrom,
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final KeyValue hostedBy,
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final DataInfo info,
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final long lastUpdateTimestamp) {
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final List<Oaf> oafs = new ArrayList<>();
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switch (type.toLowerCase()) {
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case "":
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case "publication":
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final Publication p = new Publication();
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populateResultFields(p, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
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p.setResulttype(MigrationConstants.PUBLICATION_RESULTTYPE_QUALIFIER);
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p.setJournal(prepareJournal(doc, info));
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oafs.add(p);
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break;
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case "dataset":
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final Dataset d = new Dataset();
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populateResultFields(d, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
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d.setResulttype(MigrationConstants.DATASET_RESULTTYPE_QUALIFIER);
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d.setStoragedate(prepareDatasetStorageDate(doc, info));
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d.setDevice(prepareDatasetDevice(doc, info));
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d.setSize(prepareDatasetSize(doc, info));
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d.setVersion(prepareDatasetVersion(doc, info));
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d.setLastmetadataupdate(prepareDatasetLastMetadataUpdate(doc, info));
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d.setMetadataversionnumber(prepareDatasetMetadataVersionNumber(doc, info));
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d.setGeolocation(prepareDatasetGeoLocations(doc, info));
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oafs.add(d);
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break;
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case "software":
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final Software s = new Software();
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populateResultFields(s, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
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s.setResulttype(MigrationConstants.SOFTWARE_RESULTTYPE_QUALIFIER);
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s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info));
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s.setLicense(prepareSoftwareLicenses(doc, info));
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s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info));
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s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info));
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oafs.add(s);
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break;
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case "otherresearchproducts":
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default:
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final OtherResearchProduct o = new OtherResearchProduct();
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populateResultFields(o, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
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o.setResulttype(MigrationConstants.OTHER_RESULTTYPE_QUALIFIER);
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o.setContactperson(prepareOtherResearchProductContactPersons(doc, info));
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o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info));
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o.setTool(prepareOtherResearchProductTools(doc, info));
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oafs.add(o);
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break;
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}
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if (!oafs.isEmpty()) {
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oafs.addAll(addProjectRels(doc, collectedFrom, info, lastUpdateTimestamp));
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oafs.addAll(addOtherResultRels(doc, collectedFrom, info, lastUpdateTimestamp));
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}
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return oafs;
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}
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private List<Oaf> addProjectRels(
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final Document doc,
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final KeyValue collectedFrom,
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final DataInfo info,
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final long lastUpdateTimestamp) {
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final List<Oaf> res = new ArrayList<>();
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final String docId = createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false);
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for (final Object o : doc.selectNodes("//oaf:projectid")) {
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final String projectId = createOpenaireId(40, ((Node) o).getText(), true);
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final Relation r1 = new Relation();
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r1.setRelType("resultProject");
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r1.setSubRelType("outcome");
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r1.setRelClass("isProducedBy");
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r1.setSource(docId);
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r1.setTarget(projectId);
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r1.setCollectedfrom(Arrays.asList(collectedFrom));
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r1.setDataInfo(info);
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r1.setLastupdatetimestamp(lastUpdateTimestamp);
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res.add(r1);
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final Relation r2 = new Relation();
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r2.setRelType("resultProject");
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r2.setSubRelType("outcome");
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r2.setRelClass("produces");
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r2.setSource(projectId);
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r2.setTarget(docId);
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r2.setCollectedfrom(Arrays.asList(collectedFrom));
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r2.setDataInfo(info);
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r2.setLastupdatetimestamp(lastUpdateTimestamp);
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res.add(r2);
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}
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return res;
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}
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protected abstract List<Oaf> addOtherResultRels(
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final Document doc,
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final KeyValue collectedFrom,
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final DataInfo info,
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final long lastUpdateTimestamp);
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private void populateResultFields(
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final Result r,
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final Document doc,
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final KeyValue collectedFrom,
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final KeyValue hostedBy,
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final DataInfo info,
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final long lastUpdateTimestamp) {
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r.setDataInfo(info);
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r.setLastupdatetimestamp(lastUpdateTimestamp);
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r.setId(createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false));
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r.setOriginalId(Arrays.asList(doc.valueOf("//dri:objIdentifier")));
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r.setCollectedfrom(Arrays.asList(collectedFrom));
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r.setPid(prepareListStructProps(doc, "//oaf:identifier", "@identifierType", "dnet:pid_types", "dnet:pid_types", info));
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r.setDateofcollection(doc.valueOf("//dr:dateOfCollection"));
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r.setDateoftransformation(doc.valueOf("//dr:dateOfTransformation"));
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r.setExtraInfo(new ArrayList<>()); // NOT PRESENT IN MDSTORES
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r.setOaiprovenance(prepareOAIprovenance(doc));
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r.setAuthor(prepareAuthors(doc, info));
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r.setLanguage(prepareLanguages(doc));
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r.setCountry(new ArrayList<>()); // NOT PRESENT IN MDSTORES
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r.setSubject(prepareSubjects(doc, info));
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r.setTitle(prepareTitles(doc, info));
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r.setRelevantdate(prepareRelevantDates(doc, info));
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r.setDescription(prepareDescriptions(doc, info));
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r.setDateofacceptance(prepareField(doc, "//oaf:dateAccepted", info));
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r.setPublisher(preparePublisher(doc, info));
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r.setEmbargoenddate(prepareField(doc, "//oaf:embargoenddate", info));
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r.setSource(prepareSources(doc, info));
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r.setFulltext(new ArrayList<>()); // NOT PRESENT IN MDSTORES
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r.setFormat(prepareFormats(doc, info));
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r.setContributor(prepareContributors(doc, info));
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r.setResourcetype(prepareResourceType(doc, info));
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r.setCoverage(prepareCoverages(doc, info));
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r.setContext(new ArrayList<>()); // NOT PRESENT IN MDSTORES
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r.setExternalReference(new ArrayList<>()); // NOT PRESENT IN MDSTORES
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r.setInstance(prepareInstances(doc, info, collectedFrom, hostedBy));
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}
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protected abstract Qualifier prepareResourceType(Document doc, DataInfo info);
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protected abstract List<Instance> prepareInstances(
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Document doc,
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DataInfo info,
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KeyValue collectedfrom,
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KeyValue hostedby);
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protected abstract List<Field<String>> prepareSources(Document doc, DataInfo info);
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protected abstract List<StructuredProperty> prepareRelevantDates(Document doc, DataInfo info);
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protected abstract List<Field<String>> prepareCoverages(Document doc, DataInfo info);
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protected abstract List<Field<String>> prepareContributors(Document doc, DataInfo info);
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protected abstract List<Field<String>> prepareFormats(Document doc, DataInfo info);
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protected abstract Field<String> preparePublisher(Document doc, DataInfo info);
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protected abstract List<Field<String>> prepareDescriptions(Document doc, DataInfo info);
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protected abstract List<StructuredProperty> prepareTitles(Document doc, DataInfo info);
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protected abstract List<StructuredProperty> prepareSubjects(Document doc, DataInfo info);
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protected abstract Qualifier prepareLanguages(Document doc);
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protected abstract List<Author> prepareAuthors(Document doc, DataInfo info);
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protected abstract List<Field<String>> prepareOtherResearchProductTools(
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Document doc,
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DataInfo info);
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protected abstract List<Field<String>> prepareOtherResearchProductContactGroups(
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Document doc,
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DataInfo info);
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protected abstract List<Field<String>> prepareOtherResearchProductContactPersons(
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Document doc,
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DataInfo info);
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protected abstract Qualifier prepareSoftwareProgrammingLanguage(Document doc, DataInfo info);
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protected abstract Field<String> prepareSoftwareCodeRepositoryUrl(Document doc, DataInfo info);
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protected abstract List<StructuredProperty> prepareSoftwareLicenses(
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Document doc,
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DataInfo info);
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protected abstract List<Field<String>> prepareSoftwareDocumentationUrls(
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Document doc,
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DataInfo info);
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protected abstract List<GeoLocation> prepareDatasetGeoLocations(Document doc, DataInfo info);
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protected abstract Field<String> prepareDatasetMetadataVersionNumber(
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Document doc,
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DataInfo info);
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protected abstract Field<String> prepareDatasetLastMetadataUpdate(Document doc, DataInfo info);
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protected abstract Field<String> prepareDatasetVersion(Document doc, DataInfo info);
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protected abstract Field<String> prepareDatasetSize(Document doc, DataInfo info);
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protected abstract Field<String> prepareDatasetDevice(Document doc, DataInfo info);
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protected abstract Field<String> prepareDatasetStorageDate(Document doc, DataInfo info);
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private Journal prepareJournal(final Document doc, final DataInfo info) {
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final Node n = doc.selectSingleNode("//oaf:journal");
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if (n != null) {
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final String name = n.getText();
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final String issnPrinted = n.valueOf("@issn");
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final String issnOnline = n.valueOf("@eissn");
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final String issnLinking = n.valueOf("@lissn");
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final String ep = n.valueOf("@ep");
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final String iss = n.valueOf("@iss");
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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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}
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return null;
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}
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protected Qualifier prepareQualifier(
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final Node node,
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final String xpath,
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final String schemeId,
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final String schemeName) {
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final String classId = node.valueOf(xpath);
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final String className = code2name.get(classId);
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return qualifier(classId, className, schemeId, schemeName);
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}
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protected List<StructuredProperty> prepareListStructProps(
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final Node node,
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final String xpath,
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final String xpathClassId,
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final String schemeId,
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final String schemeName,
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final DataInfo info) {
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final List<StructuredProperty> res = new ArrayList<>();
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for (final Object o : node.selectNodes(xpath)) {
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final Node n = (Node) o;
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final String classId = n.valueOf(xpathClassId);
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final String className = code2name.get(classId);
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res.add(structuredProperty(n.getText(), classId, className, schemeId, schemeName, info));
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}
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return res;
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}
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protected List<StructuredProperty> prepareListStructProps(
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final Node node,
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final String xpath,
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final Qualifier qualifier,
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final DataInfo info) {
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final List<StructuredProperty> res = new ArrayList<>();
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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.add(structuredProperty(n.getText(), qualifier, info));
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}
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return res;
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}
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protected List<StructuredProperty> prepareListStructProps(
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final Node node,
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final String xpath,
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final DataInfo info) {
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final List<StructuredProperty> res = new ArrayList<>();
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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.add(structuredProperty(n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"), n.valueOf("@schemename"), info));
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}
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return res;
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}
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protected OAIProvenance prepareOAIprovenance(final Document doc) {
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final Node n =
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doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']");
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if (n == null) { return null; }
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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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final String metadataNamespace = n.valueOf("./*[local-name()='metadataNamespace']");;
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final boolean altered = n.valueOf("@altered").equalsIgnoreCase("true");
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final String datestamp = n.valueOf("./*[local-name()='datestamp']");;
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final String harvestDate = n.valueOf("@harvestDate");;
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return oaiIProvenance(identifier, baseURL, metadataNamespace, altered, datestamp, harvestDate);
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}
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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, MigrationConstants.REPOSITORY_PROVENANCE_ACTIONS, "0.9"); }
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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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final String paSchemeId = n.valueOf("./oaf:provenanceaction/@schemeid");
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final String paSchemeName = n.valueOf("./oaf:provenanceaction/@schemename");
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final boolean deletedbyinference =
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Boolean.parseBoolean(n.valueOf("./oaf:deletedbyinference"));
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final String inferenceprovenance = n.valueOf("./oaf:inferenceprovenance");
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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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}
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protected Field<String> prepareField(final Node node, final String xpath, final DataInfo info) {
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return field(node.valueOf(xpath), info);
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}
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protected List<Field<String>> prepareListFields(
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final Node node,
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final String xpath,
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final DataInfo info) {
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return listFields(info, prepareListString(node, xpath));
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}
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protected List<String> prepareListString(final Node node, final String xpath) {
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final List<String> res = new ArrayList<>();
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for (final Object o : node.selectNodes(xpath)) {
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final String s = ((Node) o).getText().trim();
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if (StringUtils.isNotBlank(s)) {
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res.add(s);
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}
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}
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return res;
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}
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protected final Map<String, String> code2name;
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protected static final Qualifier MAIN_TITLE_QUALIFIER =
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qualifier("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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}
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public List<Oaf> processMdRecord(final String xml) {
|
||||
try {
|
||||
final Map<String, String> nsContext = new HashMap<>();
|
||||
nsContext.put("dr", "http://www.driver-repository.eu/namespace/dr");
|
||||
nsContext.put("dri", "http://www.driver-repository.eu/namespace/dri");
|
||||
nsContext.put("oaf", "http://namespace.openaire.eu/oaf");
|
||||
nsContext.put("oai", "http://www.openarchives.org/OAI/2.0/");
|
||||
nsContext.put("prov", "http://www.openarchives.org/OAI/2.0/provenance");
|
||||
nsContext.put("dc", "http://purl.org/dc/elements/1.1/");
|
||||
nsContext.put("datacite", "http://datacite.org/schema/kernel-3");
|
||||
DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext);
|
||||
|
||||
final Document doc =
|
||||
DocumentHelper.parseText(
|
||||
xml.replaceAll(
|
||||
"http://datacite.org/schema/kernel-4",
|
||||
"http://datacite.org/schema/kernel-3"));
|
||||
|
||||
final String type = doc.valueOf("//dr:CobjCategory/@type");
|
||||
final KeyValue collectedFrom =
|
||||
keyValue(
|
||||
createOpenaireId(10, doc.valueOf("//oaf:collectedFrom/@id"), true),
|
||||
doc.valueOf("//oaf:collectedFrom/@name"));
|
||||
final KeyValue hostedBy =
|
||||
StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id"))
|
||||
? collectedFrom
|
||||
: keyValue(
|
||||
createOpenaireId(10, doc.valueOf("//oaf:hostedBy/@id"), true),
|
||||
doc.valueOf("//oaf:hostedBy/@name"));
|
||||
|
||||
final DataInfo info = prepareDataInfo(doc);
|
||||
final long lastUpdateTimestamp = new Date().getTime();
|
||||
|
||||
return createOafs(doc, type, collectedFrom, hostedBy, info, lastUpdateTimestamp);
|
||||
} catch (final Exception e) {
|
||||
throw new RuntimeException(e);
|
||||
}
|
||||
}
|
||||
|
||||
protected List<Oaf> createOafs(
|
||||
final Document doc,
|
||||
final String type,
|
||||
final KeyValue collectedFrom,
|
||||
final KeyValue hostedBy,
|
||||
final DataInfo info,
|
||||
final long lastUpdateTimestamp) {
|
||||
|
||||
final List<Oaf> oafs = new ArrayList<>();
|
||||
|
||||
switch (type.toLowerCase()) {
|
||||
case "":
|
||||
case "publication":
|
||||
final Publication p = new Publication();
|
||||
populateResultFields(p, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
|
||||
p.setResulttype(MigrationConstants.PUBLICATION_RESULTTYPE_QUALIFIER);
|
||||
p.setJournal(prepareJournal(doc, info));
|
||||
oafs.add(p);
|
||||
break;
|
||||
case "dataset":
|
||||
final Dataset d = new Dataset();
|
||||
populateResultFields(d, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
|
||||
d.setResulttype(MigrationConstants.DATASET_RESULTTYPE_QUALIFIER);
|
||||
d.setStoragedate(prepareDatasetStorageDate(doc, info));
|
||||
d.setDevice(prepareDatasetDevice(doc, info));
|
||||
d.setSize(prepareDatasetSize(doc, info));
|
||||
d.setVersion(prepareDatasetVersion(doc, info));
|
||||
d.setLastmetadataupdate(prepareDatasetLastMetadataUpdate(doc, info));
|
||||
d.setMetadataversionnumber(prepareDatasetMetadataVersionNumber(doc, info));
|
||||
d.setGeolocation(prepareDatasetGeoLocations(doc, info));
|
||||
oafs.add(d);
|
||||
break;
|
||||
case "software":
|
||||
final Software s = new Software();
|
||||
populateResultFields(s, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
|
||||
s.setResulttype(MigrationConstants.SOFTWARE_RESULTTYPE_QUALIFIER);
|
||||
s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info));
|
||||
s.setLicense(prepareSoftwareLicenses(doc, info));
|
||||
s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info));
|
||||
s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info));
|
||||
oafs.add(s);
|
||||
break;
|
||||
case "otherresearchproducts":
|
||||
default:
|
||||
final OtherResearchProduct o = new OtherResearchProduct();
|
||||
populateResultFields(o, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
|
||||
o.setResulttype(MigrationConstants.OTHER_RESULTTYPE_QUALIFIER);
|
||||
o.setContactperson(prepareOtherResearchProductContactPersons(doc, info));
|
||||
o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info));
|
||||
o.setTool(prepareOtherResearchProductTools(doc, info));
|
||||
oafs.add(o);
|
||||
break;
|
||||
}
|
||||
|
||||
if (!oafs.isEmpty()) {
|
||||
oafs.addAll(addProjectRels(doc, collectedFrom, info, lastUpdateTimestamp));
|
||||
oafs.addAll(addOtherResultRels(doc, collectedFrom, info, lastUpdateTimestamp));
|
||||
}
|
||||
|
||||
return oafs;
|
||||
}
|
||||
|
||||
private List<Oaf> addProjectRels(
|
||||
final Document doc,
|
||||
final KeyValue collectedFrom,
|
||||
final DataInfo info,
|
||||
final long lastUpdateTimestamp) {
|
||||
|
||||
final List<Oaf> res = new ArrayList<>();
|
||||
|
||||
final String docId = createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false);
|
||||
|
||||
for (final Object o : doc.selectNodes("//oaf:projectid")) {
|
||||
final String projectId = createOpenaireId(40, ((Node) o).getText(), true);
|
||||
|
||||
final Relation r1 = new Relation();
|
||||
r1.setRelType("resultProject");
|
||||
r1.setSubRelType("outcome");
|
||||
r1.setRelClass("isProducedBy");
|
||||
r1.setSource(docId);
|
||||
r1.setTarget(projectId);
|
||||
r1.setCollectedfrom(Arrays.asList(collectedFrom));
|
||||
r1.setDataInfo(info);
|
||||
r1.setLastupdatetimestamp(lastUpdateTimestamp);
|
||||
res.add(r1);
|
||||
|
||||
final Relation r2 = new Relation();
|
||||
r2.setRelType("resultProject");
|
||||
r2.setSubRelType("outcome");
|
||||
r2.setRelClass("produces");
|
||||
r2.setSource(projectId);
|
||||
r2.setTarget(docId);
|
||||
r2.setCollectedfrom(Arrays.asList(collectedFrom));
|
||||
r2.setDataInfo(info);
|
||||
r2.setLastupdatetimestamp(lastUpdateTimestamp);
|
||||
res.add(r2);
|
||||
}
|
||||
|
||||
return res;
|
||||
}
|
||||
|
||||
protected abstract List<Oaf> addOtherResultRels(
|
||||
final Document doc,
|
||||
final KeyValue collectedFrom,
|
||||
final DataInfo info,
|
||||
final long lastUpdateTimestamp);
|
||||
|
||||
private void populateResultFields(
|
||||
final Result r,
|
||||
final Document doc,
|
||||
final KeyValue collectedFrom,
|
||||
final KeyValue hostedBy,
|
||||
final DataInfo info,
|
||||
final long lastUpdateTimestamp) {
|
||||
r.setDataInfo(info);
|
||||
r.setLastupdatetimestamp(lastUpdateTimestamp);
|
||||
r.setId(createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false));
|
||||
r.setOriginalId(Arrays.asList(doc.valueOf("//dri:objIdentifier")));
|
||||
r.setCollectedfrom(Arrays.asList(collectedFrom));
|
||||
r.setPid(
|
||||
prepareListStructProps(
|
||||
doc,
|
||||
"//oaf:identifier",
|
||||
"@identifierType",
|
||||
"dnet:pid_types",
|
||||
"dnet:pid_types",
|
||||
info));
|
||||
r.setDateofcollection(doc.valueOf("//dr:dateOfCollection"));
|
||||
r.setDateoftransformation(doc.valueOf("//dr:dateOfTransformation"));
|
||||
r.setExtraInfo(new ArrayList<>()); // NOT PRESENT IN MDSTORES
|
||||
r.setOaiprovenance(prepareOAIprovenance(doc));
|
||||
r.setAuthor(prepareAuthors(doc, info));
|
||||
r.setLanguage(prepareLanguages(doc));
|
||||
r.setCountry(new ArrayList<>()); // NOT PRESENT IN MDSTORES
|
||||
r.setSubject(prepareSubjects(doc, info));
|
||||
r.setTitle(prepareTitles(doc, info));
|
||||
r.setRelevantdate(prepareRelevantDates(doc, info));
|
||||
r.setDescription(prepareDescriptions(doc, info));
|
||||
r.setDateofacceptance(prepareField(doc, "//oaf:dateAccepted", info));
|
||||
r.setPublisher(preparePublisher(doc, info));
|
||||
r.setEmbargoenddate(prepareField(doc, "//oaf:embargoenddate", info));
|
||||
r.setSource(prepareSources(doc, info));
|
||||
r.setFulltext(new ArrayList<>()); // NOT PRESENT IN MDSTORES
|
||||
r.setFormat(prepareFormats(doc, info));
|
||||
r.setContributor(prepareContributors(doc, info));
|
||||
r.setResourcetype(prepareResourceType(doc, info));
|
||||
r.setCoverage(prepareCoverages(doc, info));
|
||||
r.setContext(new ArrayList<>()); // NOT PRESENT IN MDSTORES
|
||||
r.setExternalReference(new ArrayList<>()); // NOT PRESENT IN MDSTORES
|
||||
r.setInstance(prepareInstances(doc, info, collectedFrom, hostedBy));
|
||||
}
|
||||
|
||||
protected abstract Qualifier prepareResourceType(Document doc, DataInfo info);
|
||||
|
||||
protected abstract List<Instance> prepareInstances(
|
||||
Document doc, DataInfo info, KeyValue collectedfrom, KeyValue hostedby);
|
||||
|
||||
protected abstract List<Field<String>> prepareSources(Document doc, DataInfo info);
|
||||
|
||||
protected abstract List<StructuredProperty> prepareRelevantDates(Document doc, DataInfo info);
|
||||
|
||||
protected abstract List<Field<String>> prepareCoverages(Document doc, DataInfo info);
|
||||
|
||||
protected abstract List<Field<String>> prepareContributors(Document doc, DataInfo info);
|
||||
|
||||
protected abstract List<Field<String>> prepareFormats(Document doc, DataInfo info);
|
||||
|
||||
protected abstract Field<String> preparePublisher(Document doc, DataInfo info);
|
||||
|
||||
protected abstract List<Field<String>> prepareDescriptions(Document doc, DataInfo info);
|
||||
|
||||
protected abstract List<StructuredProperty> prepareTitles(Document doc, DataInfo info);
|
||||
|
||||
protected abstract List<StructuredProperty> prepareSubjects(Document doc, DataInfo info);
|
||||
|
||||
protected abstract Qualifier prepareLanguages(Document doc);
|
||||
|
||||
protected abstract List<Author> prepareAuthors(Document doc, DataInfo info);
|
||||
|
||||
protected abstract List<Field<String>> prepareOtherResearchProductTools(
|
||||
Document doc, DataInfo info);
|
||||
|
||||
protected abstract List<Field<String>> prepareOtherResearchProductContactGroups(
|
||||
Document doc, DataInfo info);
|
||||
|
||||
protected abstract List<Field<String>> prepareOtherResearchProductContactPersons(
|
||||
Document doc, DataInfo info);
|
||||
|
||||
protected abstract Qualifier prepareSoftwareProgrammingLanguage(Document doc, DataInfo info);
|
||||
|
||||
protected abstract Field<String> prepareSoftwareCodeRepositoryUrl(Document doc, DataInfo info);
|
||||
|
||||
protected abstract List<StructuredProperty> prepareSoftwareLicenses(
|
||||
Document doc, DataInfo info);
|
||||
|
||||
protected abstract List<Field<String>> prepareSoftwareDocumentationUrls(
|
||||
Document doc, DataInfo info);
|
||||
|
||||
protected abstract List<GeoLocation> prepareDatasetGeoLocations(Document doc, DataInfo info);
|
||||
|
||||
protected abstract Field<String> prepareDatasetMetadataVersionNumber(
|
||||
Document doc, DataInfo info);
|
||||
|
||||
protected abstract Field<String> prepareDatasetLastMetadataUpdate(Document doc, DataInfo info);
|
||||
|
||||
protected abstract Field<String> prepareDatasetVersion(Document doc, DataInfo info);
|
||||
|
||||
protected abstract Field<String> prepareDatasetSize(Document doc, DataInfo info);
|
||||
|
||||
protected abstract Field<String> prepareDatasetDevice(Document doc, DataInfo info);
|
||||
|
||||
protected abstract Field<String> prepareDatasetStorageDate(Document doc, DataInfo info);
|
||||
|
||||
private Journal prepareJournal(final Document doc, final DataInfo info) {
|
||||
final Node n = doc.selectSingleNode("//oaf:journal");
|
||||
if (n != null) {
|
||||
final String name = n.getText();
|
||||
final String issnPrinted = n.valueOf("@issn");
|
||||
final String issnOnline = n.valueOf("@eissn");
|
||||
final String issnLinking = n.valueOf("@lissn");
|
||||
final String ep = n.valueOf("@ep");
|
||||
final String iss = n.valueOf("@iss");
|
||||
final String sp = n.valueOf("@sp");
|
||||
final String vol = n.valueOf("@vol");
|
||||
final String edition = n.valueOf("@edition");
|
||||
if (StringUtils.isNotBlank(name)) {
|
||||
return journal(
|
||||
name,
|
||||
issnPrinted,
|
||||
issnOnline,
|
||||
issnLinking,
|
||||
ep,
|
||||
iss,
|
||||
sp,
|
||||
vol,
|
||||
edition,
|
||||
null,
|
||||
null,
|
||||
info);
|
||||
}
|
||||
}
|
||||
return null;
|
||||
}
|
||||
|
||||
protected Qualifier prepareQualifier(
|
||||
final Node node, final String xpath, final String schemeId, final String schemeName) {
|
||||
final String classId = node.valueOf(xpath);
|
||||
final String className = code2name.get(classId);
|
||||
return qualifier(classId, className, schemeId, schemeName);
|
||||
}
|
||||
|
||||
protected List<StructuredProperty> prepareListStructProps(
|
||||
final Node node,
|
||||
final String xpath,
|
||||
final String xpathClassId,
|
||||
final String schemeId,
|
||||
final String schemeName,
|
||||
final DataInfo info) {
|
||||
final List<StructuredProperty> res = new ArrayList<>();
|
||||
for (final Object o : node.selectNodes(xpath)) {
|
||||
final Node n = (Node) o;
|
||||
final String classId = n.valueOf(xpathClassId);
|
||||
final String className = code2name.get(classId);
|
||||
res.add(
|
||||
structuredProperty(
|
||||
n.getText(), classId, className, schemeId, schemeName, info));
|
||||
}
|
||||
return res;
|
||||
}
|
||||
|
||||
protected List<StructuredProperty> prepareListStructProps(
|
||||
final Node node, final String xpath, final Qualifier qualifier, final DataInfo info) {
|
||||
final List<StructuredProperty> res = new ArrayList<>();
|
||||
for (final Object o : node.selectNodes(xpath)) {
|
||||
final Node n = (Node) o;
|
||||
res.add(structuredProperty(n.getText(), qualifier, info));
|
||||
}
|
||||
return res;
|
||||
}
|
||||
|
||||
protected List<StructuredProperty> prepareListStructProps(
|
||||
final Node node, final String xpath, final DataInfo info) {
|
||||
final List<StructuredProperty> res = new ArrayList<>();
|
||||
for (final Object o : node.selectNodes(xpath)) {
|
||||
final Node n = (Node) o;
|
||||
res.add(
|
||||
structuredProperty(
|
||||
n.getText(),
|
||||
n.valueOf("@classid"),
|
||||
n.valueOf("@classname"),
|
||||
n.valueOf("@schemeid"),
|
||||
n.valueOf("@schemename"),
|
||||
info));
|
||||
}
|
||||
return res;
|
||||
}
|
||||
|
||||
protected OAIProvenance prepareOAIprovenance(final Document doc) {
|
||||
final Node n =
|
||||
doc.selectSingleNode(
|
||||
"//*[local-name()='provenance']/*[local-name()='originDescription']");
|
||||
|
||||
if (n == null) {
|
||||
return null;
|
||||
}
|
||||
|
||||
final String identifier = n.valueOf("./*[local-name()='identifier']");
|
||||
final String baseURL = n.valueOf("./*[local-name()='baseURL']");
|
||||
;
|
||||
final String metadataNamespace = n.valueOf("./*[local-name()='metadataNamespace']");
|
||||
;
|
||||
final boolean altered = n.valueOf("@altered").equalsIgnoreCase("true");
|
||||
final String datestamp = n.valueOf("./*[local-name()='datestamp']");
|
||||
;
|
||||
final String harvestDate = n.valueOf("@harvestDate");
|
||||
;
|
||||
|
||||
return oaiIProvenance(
|
||||
identifier, baseURL, metadataNamespace, altered, datestamp, harvestDate);
|
||||
}
|
||||
|
||||
protected DataInfo prepareDataInfo(final Document doc) {
|
||||
final Node n = doc.selectSingleNode("//oaf:datainfo");
|
||||
|
||||
if (n == null) {
|
||||
return dataInfo(
|
||||
false,
|
||||
null,
|
||||
false,
|
||||
false,
|
||||
MigrationConstants.REPOSITORY_PROVENANCE_ACTIONS,
|
||||
"0.9");
|
||||
}
|
||||
|
||||
final String paClassId = n.valueOf("./oaf:provenanceaction/@classid");
|
||||
final String paClassName = n.valueOf("./oaf:provenanceaction/@classname");
|
||||
final String paSchemeId = n.valueOf("./oaf:provenanceaction/@schemeid");
|
||||
final String paSchemeName = n.valueOf("./oaf:provenanceaction/@schemename");
|
||||
|
||||
final boolean deletedbyinference =
|
||||
Boolean.parseBoolean(n.valueOf("./oaf:deletedbyinference"));
|
||||
final String inferenceprovenance = n.valueOf("./oaf:inferenceprovenance");
|
||||
final Boolean inferred = Boolean.parseBoolean(n.valueOf("./oaf:inferred"));
|
||||
final String trust = n.valueOf("./oaf:trust");
|
||||
|
||||
return dataInfo(
|
||||
deletedbyinference,
|
||||
inferenceprovenance,
|
||||
inferred,
|
||||
false,
|
||||
qualifier(paClassId, paClassName, paSchemeId, paSchemeName),
|
||||
trust);
|
||||
}
|
||||
|
||||
protected Field<String> prepareField(final Node node, final String xpath, final DataInfo info) {
|
||||
return field(node.valueOf(xpath), info);
|
||||
}
|
||||
|
||||
protected List<Field<String>> prepareListFields(
|
||||
final Node node, final String xpath, final DataInfo info) {
|
||||
return listFields(info, prepareListString(node, xpath));
|
||||
}
|
||||
|
||||
protected List<String> prepareListString(final Node node, final String xpath) {
|
||||
final List<String> res = new ArrayList<>();
|
||||
for (final Object o : node.selectNodes(xpath)) {
|
||||
final String s = ((Node) o).getText().trim();
|
||||
if (StringUtils.isNotBlank(s)) {
|
||||
res.add(s);
|
||||
}
|
||||
}
|
||||
return res;
|
||||
}
|
||||
}
|
||||
|
|
|
|||
File diff suppressed because it is too large
Load Diff
|
|
@ -1,8 +1,19 @@
|
|||
package eu.dnetlib.dhp.oa.graph.raw;
|
||||
|
||||
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.*;
|
||||
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.createOpenaireId;
|
||||
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.field;
|
||||
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty;
|
||||
|
||||
import eu.dnetlib.dhp.schema.oaf.*;
|
||||
import eu.dnetlib.dhp.schema.oaf.Author;
|
||||
import eu.dnetlib.dhp.schema.oaf.DataInfo;
|
||||
import eu.dnetlib.dhp.schema.oaf.Field;
|
||||
import eu.dnetlib.dhp.schema.oaf.GeoLocation;
|
||||
import eu.dnetlib.dhp.schema.oaf.Instance;
|
||||
import eu.dnetlib.dhp.schema.oaf.KeyValue;
|
||||
import eu.dnetlib.dhp.schema.oaf.Oaf;
|
||||
import eu.dnetlib.dhp.schema.oaf.Qualifier;
|
||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
|
||||
import java.util.ArrayList;
|
||||
import java.util.Arrays;
|
||||
import java.util.List;
|
||||
|
|
@ -62,33 +73,44 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
|
|||
final DataInfo info,
|
||||
final KeyValue collectedfrom,
|
||||
final KeyValue hostedby) {
|
||||
final List<Instance> res = new ArrayList<>();
|
||||
|
||||
final Instance instance = new Instance();
|
||||
instance.setUrl(new ArrayList<>());
|
||||
instance.setInstancetype(
|
||||
prepareQualifier(
|
||||
doc,
|
||||
"//dr:CobjCategory",
|
||||
"dnet:publication_resource",
|
||||
"dnet:publication_resource"));
|
||||
instance.setCollectedfrom(collectedfrom);
|
||||
instance.setHostedby(hostedby);
|
||||
instance.setDateofacceptance(field(doc.valueOf("//oaf:dateAccepted"), info));
|
||||
instance.setDistributionlocation(doc.valueOf("//oaf:distributionlocation"));
|
||||
instance.setAccessright(
|
||||
prepareQualifier(
|
||||
doc, "//oaf:accessrights", "dnet:access_modes", "dnet:access_modes"));
|
||||
instance.setLicense(field(doc.valueOf("//oaf:license"), info));
|
||||
instance.setRefereed(field(doc.valueOf("//oaf:refereed"), info));
|
||||
instance.setProcessingchargeamount(
|
||||
field(doc.valueOf("//oaf:processingchargeamount"), info));
|
||||
instance.setProcessingchargecurrency(
|
||||
field(doc.valueOf("//oaf:processingchargeamount/@currency"), info));
|
||||
|
||||
for (final Object o :
|
||||
doc.selectNodes("//datacite:alternateIdentifier[@alternateIdentifierType='URL']")) {
|
||||
final Instance instance = new Instance();
|
||||
instance.setUrl(Arrays.asList(((Node) o).getText().trim()));
|
||||
instance.setInstancetype(
|
||||
prepareQualifier(
|
||||
doc,
|
||||
"//dr:CobjCategory",
|
||||
"dnet:publication_resource",
|
||||
"dnet:publication_resource"));
|
||||
instance.setCollectedfrom(collectedfrom);
|
||||
instance.setHostedby(hostedby);
|
||||
instance.setDateofacceptance(field(doc.valueOf("//oaf:dateAccepted"), info));
|
||||
instance.setDistributionlocation(doc.valueOf("//oaf:distributionlocation"));
|
||||
instance.setAccessright(
|
||||
prepareQualifier(
|
||||
doc, "//oaf:accessrights", "dnet:access_modes", "dnet:access_modes"));
|
||||
instance.setLicense(field(doc.valueOf("//oaf:license"), info));
|
||||
instance.setRefereed(field(doc.valueOf("//oaf:refereed"), info));
|
||||
instance.setProcessingchargeamount(
|
||||
field(doc.valueOf("//oaf:processingchargeamount"), info));
|
||||
instance.setProcessingchargecurrency(
|
||||
field(doc.valueOf("//oaf:processingchargeamount/@currency"), info));
|
||||
res.add(instance);
|
||||
instance.getUrl().add(((Node) o).getText().trim());
|
||||
}
|
||||
return res;
|
||||
for (final Object o : doc.selectNodes("//datacite:identifier[@identifierType='URL']")) {
|
||||
instance.getUrl().add(((Node) o).getText().trim());
|
||||
}
|
||||
for (final Object o :
|
||||
doc.selectNodes("//datacite:alternateIdentifier[@alternateIdentifierType='DOI']")) {
|
||||
instance.getUrl().add("http://dx.doi.org/" + ((Node) o).getText().trim());
|
||||
}
|
||||
for (final Object o : doc.selectNodes("//datacite:identifier[@identifierType='DOI']")) {
|
||||
instance.getUrl().add("http://dx.doi.org/" + ((Node) o).getText().trim());
|
||||
}
|
||||
return Arrays.asList(instance);
|
||||
}
|
||||
|
||||
@Override
|
||||
|
|
|
|||
|
|
@ -6,17 +6,28 @@ import eu.dnetlib.dhp.schema.oaf.Qualifier;
|
|||
|
||||
public class MigrationConstants {
|
||||
|
||||
public static final Qualifier PUBLICATION_RESULTTYPE_QUALIFIER =
|
||||
qualifier("publication", "publication", "dnet:result_typologies", "dnet:result_typologies");
|
||||
public static final Qualifier DATASET_RESULTTYPE_QUALIFIER =
|
||||
qualifier("dataset", "dataset", "dnet:result_typologies", "dnet:result_typologies");
|
||||
public static final Qualifier SOFTWARE_RESULTTYPE_QUALIFIER =
|
||||
qualifier("software", "software", "dnet:result_typologies", "dnet:result_typologies");
|
||||
public static final Qualifier OTHER_RESULTTYPE_QUALIFIER =
|
||||
qualifier("other", "other", "dnet:result_typologies", "dnet:result_typologies");
|
||||
public static final Qualifier REPOSITORY_PROVENANCE_ACTIONS =
|
||||
qualifier("sysimport:crosswalk:repository", "sysimport:crosswalk:repository", "dnet:provenanceActions", "dnet:provenanceActions");
|
||||
public static final Qualifier ENTITYREGISTRY_PROVENANCE_ACTION =
|
||||
qualifier("sysimport:crosswalk:entityregistry", "sysimport:crosswalk:entityregistry", "dnet:provenanceActions", "dnet:provenanceActions");
|
||||
|
||||
public static final Qualifier PUBLICATION_RESULTTYPE_QUALIFIER =
|
||||
qualifier(
|
||||
"publication",
|
||||
"publication",
|
||||
"dnet:result_typologies",
|
||||
"dnet:result_typologies");
|
||||
public static final Qualifier DATASET_RESULTTYPE_QUALIFIER =
|
||||
qualifier("dataset", "dataset", "dnet:result_typologies", "dnet:result_typologies");
|
||||
public static final Qualifier SOFTWARE_RESULTTYPE_QUALIFIER =
|
||||
qualifier("software", "software", "dnet:result_typologies", "dnet:result_typologies");
|
||||
public static final Qualifier OTHER_RESULTTYPE_QUALIFIER =
|
||||
qualifier("other", "other", "dnet:result_typologies", "dnet:result_typologies");
|
||||
public static final Qualifier REPOSITORY_PROVENANCE_ACTIONS =
|
||||
qualifier(
|
||||
"sysimport:crosswalk:repository",
|
||||
"sysimport:crosswalk:repository",
|
||||
"dnet:provenanceActions",
|
||||
"dnet:provenanceActions");
|
||||
public static final Qualifier ENTITYREGISTRY_PROVENANCE_ACTION =
|
||||
qualifier(
|
||||
"sysimport:crosswalk:entityregistry",
|
||||
"sysimport:crosswalk:entityregistry",
|
||||
"dnet:provenanceActions",
|
||||
"dnet:provenanceActions");
|
||||
}
|
||||
|
|
|
|||
|
|
@ -54,6 +54,7 @@ public class MappersTest {
|
|||
assertTrue(p.getSubject().size() > 0);
|
||||
assertTrue(StringUtils.isNotBlank(p.getJournal().getIssnOnline()));
|
||||
assertTrue(StringUtils.isNotBlank(p.getJournal().getName()));
|
||||
assertTrue(p.getInstance().size() > 0);
|
||||
|
||||
assertValidId(r1.getSource());
|
||||
assertValidId(r1.getTarget());
|
||||
|
|
@ -96,6 +97,7 @@ public class MappersTest {
|
|||
assertTrue(StringUtils.isNotBlank(d.getTitle().get(0).getValue()));
|
||||
assertTrue(d.getAuthor().size() > 0);
|
||||
assertTrue(d.getSubject().size() > 0);
|
||||
assertTrue(d.getInstance().size() > 0);
|
||||
|
||||
assertValidId(r1.getSource());
|
||||
assertValidId(r1.getTarget());
|
||||
|
|
@ -129,6 +131,7 @@ public class MappersTest {
|
|||
assertTrue(StringUtils.isNotBlank(s.getTitle().get(0).getValue()));
|
||||
assertTrue(s.getAuthor().size() > 0);
|
||||
assertTrue(s.getSubject().size() > 0);
|
||||
assertTrue(s.getInstance().size() > 0);
|
||||
}
|
||||
|
||||
private void assertValidId(final String id) {
|
||||
|
|
|
|||
Loading…
Reference in New Issue