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555 lines
19 KiB
Java
555 lines
19 KiB
Java
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package eu.dnetlib.dhp.oa.graph.raw;
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import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.*;
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import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
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import java.util.*;
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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.VocabularyGroup;
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import eu.dnetlib.dhp.schema.common.LicenseComparator;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.oaf.*;
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public abstract class AbstractMdRecordToOafMapper {
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protected final VocabularyGroup vocs;
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private final boolean invisible;
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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(
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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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static {
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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", DATACITE_SCHEMA_KERNEL_3);
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}
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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 VocabularyGroup vocs, final boolean invisible) {
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this.vocs = vocs;
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this.invisible = invisible;
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}
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public List<Oaf> processMdRecord(final String xml) {
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try {
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DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext);
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final Document doc = DocumentHelper
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.parseText(xml.replaceAll(DATACITE_SCHEMA_KERNEL_4, DATACITE_SCHEMA_KERNEL_3));
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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) {
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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) {
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return null;
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}
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final DataInfo info = prepareDataInfo(doc, invisible);
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final long lastUpdateTimestamp = new Date().getTime();
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final List<Instance> instances = prepareInstances(doc, info, collectedFrom, hostedBy);
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final String type = getResultType(doc, instances);
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return createOafs(doc, type, instances, collectedFrom, 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 String getResultType(final Document doc, final List<Instance> instances) {
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String type = doc.valueOf("//dr:CobjCategory/@type");
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if (StringUtils.isBlank(type) & vocs.vocabularyExists(ModelConstants.DNET_RESULT_TYPOLOGIES)) {
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String instanceType = instances
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.stream()
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.map(i -> i.getInstancetype().getClassid())
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.findFirst()
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.orElse("0000"); // Unknown
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Qualifier resultType = vocs.getSynonymAsQualifier(ModelConstants.DNET_RESULT_TYPOLOGIES, instanceType);
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return resultType.getClassid();
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}
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return type;
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}
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private KeyValue getProvenanceDatasource(final Document doc, final String xpathId, final String xpathName) {
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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)) {
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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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protected List<Oaf> createOafs(
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final Document doc,
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final String type,
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final List<Instance> instances,
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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> oafs = new ArrayList<>();
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switch (type.toLowerCase()) {
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case "publication":
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final Publication p = new Publication();
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populateResultFields(p, doc, instances, collectedFrom, info, lastUpdateTimestamp);
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p.setResulttype(PUBLICATION_DEFAULT_RESULTTYPE);
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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, instances, collectedFrom, info, lastUpdateTimestamp);
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d.setResulttype(DATASET_DEFAULT_RESULTTYPE);
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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, instances, collectedFrom, info, lastUpdateTimestamp);
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s.setResulttype(SOFTWARE_DEFAULT_RESULTTYPE);
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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 "":
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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, instances, collectedFrom, info, lastUpdateTimestamp);
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o.setResulttype(ORP_DEFAULT_RESULTTYPE);
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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 originalId = ((Node) o).getText();
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if (StringUtils.isNotBlank(originalId)) {
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final String projectId = createOpenaireId(40, originalId, true);
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res
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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(
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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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return res;
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}
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protected Relation getRelation(final String source,
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final String target,
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final String relType,
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final String subRelType,
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final String relClass,
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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 Relation rel = new Relation();
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rel.setRelType(relType);
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rel.setSubRelType(subRelType);
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rel.setRelClass(relClass);
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rel.setSource(source);
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rel.setTarget(target);
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rel.setCollectedfrom(Arrays.asList(collectedFrom));
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rel.setDataInfo(info);
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rel.setLastupdatetimestamp(lastUpdateTimestamp);
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return rel;
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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 List<Instance> instances,
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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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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(findOriginalId(doc)));
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r.setCollectedfrom(Arrays.asList(collectedFrom));
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r.setPid(prepareResultPids(doc, 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(prepareContexts(doc, info));
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r.setExternalReference(new ArrayList<>()); // NOT PRESENT IN MDSTORES
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r.setInstance(instances);
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r.setBestaccessright(getBestAccessRights(instances));
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}
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protected abstract List<StructuredProperty> prepareResultPids(Document doc, DataInfo info);
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private List<Context> prepareContexts(final Document doc, final DataInfo info) {
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final List<Context> list = new ArrayList<>();
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for (final Object o : doc.selectNodes("//oaf:concept")) {
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final String cid = ((Node) o).valueOf("@id");
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if (StringUtils.isNotBlank(cid)) {
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final Context c = new Context();
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c.setId(cid);
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c.setDataInfo(Arrays.asList(info));
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list.add(c);
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}
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}
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return list;
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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(Document doc, 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(Document doc, 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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public static Qualifier createBestAccessRights(final List<Instance> instanceList) {
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return getBestAccessRights(instanceList);
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}
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protected static Qualifier getBestAccessRights(final List<Instance> instanceList) {
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if (instanceList != null) {
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final Optional<Qualifier> min = instanceList
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.stream()
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.map(i -> i.getAccessright())
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.min(new LicenseComparator());
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final Qualifier rights = min.isPresent() ? min.get() : new Qualifier();
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if (StringUtils.isBlank(rights.getClassid())) {
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rights.setClassid(UNKNOWN);
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}
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if (StringUtils.isBlank(rights.getClassname())
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|| UNKNOWN.equalsIgnoreCase(rights.getClassname())) {
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rights.setClassname(NOT_AVAILABLE);
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}
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if (StringUtils.isBlank(rights.getSchemeid())) {
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rights.setSchemeid(DNET_ACCESS_MODES);
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}
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if (StringUtils.isBlank(rights.getSchemename())) {
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rights.setSchemename(DNET_ACCESS_MODES);
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}
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return rights;
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}
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return null;
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}
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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)) {
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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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private String findOriginalId(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) {
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final String id = n.valueOf("./*[local-name()='identifier']");
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if (StringUtils.isNotBlank(id)) {
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return id;
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}
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}
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return doc.valueOf("//*[local-name()='header']/*[local-name()='identifier']");
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}
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protected Qualifier prepareQualifier(final Node node, final String xpath, final String schemeId) {
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return prepareQualifier(node.valueOf(xpath).trim(), schemeId);
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}
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protected Qualifier prepareQualifier(final String classId, final String schemeId) {
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return vocs.getTermAsQualifier(schemeId, classId);
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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 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).trim();
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res.add(structuredProperty(n.getText(), prepareQualifier(classId, schemeId), info));
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}
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return res;
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}
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protected List<StructuredProperty> prepareListStructPropsWithValidQualifier(
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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 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).trim();
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if (vocs.termExists(schemeId, classId)) {
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res.add(structuredProperty(n.getText(), vocs.getTermAsQualifier(schemeId, classId), info));
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}
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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
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.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 boolean invisible) {
|
|
final Node n = doc.selectSingleNode("//oaf:datainfo");
|
|
|
|
if (n == null) {
|
|
return dataInfo(false, null, false, invisible, 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, invisible,
|
|
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;
|
|
}
|
|
}
|