387 lines
12 KiB
Java
387 lines
12 KiB
Java
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package eu.dnetlib.dhp.oa.graph.raw;
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import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
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import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.createOpenaireId;
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import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.field;
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import static eu.dnetlib.dhp.schema.oaf.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.HashSet;
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import java.util.List;
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import java.util.Set;
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import java.util.stream.Collectors;
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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.Node;
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import eu.dnetlib.dhp.common.PacePerson;
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import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup;
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import eu.dnetlib.dhp.schema.oaf.*;
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import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
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public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
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public static final String HTTP_DX_DOI_PREIFX = "http://dx.doi.org/";
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public OdfToOafMapper(final VocabularyGroup vocs, final boolean invisible) {
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super(vocs, invisible);
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}
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@Override
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protected List<StructuredProperty> prepareTitles(final Document doc, final DataInfo info) {
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return prepareListStructProps(doc, "//datacite:title", MAIN_TITLE_QUALIFIER, info);
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}
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@Override
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protected List<Author> prepareAuthors(final Document doc, final DataInfo info) {
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final List<Author> res = new ArrayList<>();
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int pos = 1;
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for (final Object o : doc.selectNodes("//datacite:creator")) {
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final Node n = (Node) o;
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final Author author = new Author();
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final String fullname = n.valueOf("./datacite:creatorName");
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author.setFullname(fullname);
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final PacePerson pp = new PacePerson(fullname, false);
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final String name = n.valueOf("./datacite:givenName");
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if (StringUtils.isBlank(name) & pp.isAccurate()) {
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author.setName(pp.getNormalisedFirstName());
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} else {
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author.setName(name);
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}
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final String surname = n.valueOf("./datacite:familyName");
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if (StringUtils.isBlank(surname) & pp.isAccurate()) {
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author.setSurname(pp.getNormalisedSurname());
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} else {
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author.setSurname(surname);
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}
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if (StringUtils.isBlank(author.getFullname())) {
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author.setFullname(String.format("%s, %s", author.getSurname(), author.getName()));
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}
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author.setAffiliation(prepareListFields(n, "./datacite:affiliation", info));
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author.setPid(preparePids(n, info));
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author.setRank(pos++);
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res.add(author);
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}
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return res;
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}
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private List<StructuredProperty> preparePids(final Node n, final DataInfo info) {
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final List<StructuredProperty> res = new ArrayList<>();
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for (final Object o : n.selectNodes("./datacite:nameIdentifier")) {
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final String id = ((Node) o).getText();
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final String type = ((Node) o)
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.valueOf("./@nameIdentifierScheme")
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.trim()
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.toUpperCase()
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.replaceAll(" ", "")
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.replaceAll("_", "");
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if (type.startsWith("ORCID")) {
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final String cleanedId = id.replaceAll("http://orcid.org/", "").replaceAll("https://orcid.org/", "");
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res.add(structuredProperty(cleanedId, ORCID_PID_TYPE, info));
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} else if (type.startsWith("MAGID")) {
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res.add(structuredProperty(id, MAG_PID_TYPE, info));
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}
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}
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return res;
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}
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@Override
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protected List<Instance> prepareInstances(
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final Document doc,
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final DataInfo info,
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final KeyValue collectedfrom,
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final KeyValue hostedby) {
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final Instance instance = new Instance();
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instance
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.setInstancetype(prepareQualifier(doc, "//dr:CobjCategory", DNET_PUBLICATION_RESOURCE));
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instance.setCollectedfrom(collectedfrom);
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instance.setHostedby(hostedby);
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instance.setDateofacceptance(field(doc.valueOf("//oaf:dateAccepted"), info));
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instance.setDistributionlocation(doc.valueOf("//oaf:distributionlocation"));
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instance
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.setAccessright(prepareQualifier(doc, "//oaf:accessrights", DNET_ACCESS_MODES));
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instance.setLicense(field(doc.valueOf("//oaf:license"), info));
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instance.setRefereed(prepareQualifier(doc, "//oaf:refereed", DNET_REVIEW_LEVELS));
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instance.setProcessingchargeamount(field(doc.valueOf("//oaf:processingchargeamount"), info));
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instance
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.setProcessingchargecurrency(field(doc.valueOf("//oaf:processingchargeamount/@currency"), info));
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final Set<String> url = new HashSet<>();
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for (final Object o : doc.selectNodes("//datacite:alternateIdentifier[@alternateIdentifierType='URL']")) {
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url.add(((Node) o).getText().trim());
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}
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for (final Object o : doc
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.selectNodes("//datacite:alternateIdentifier[@alternateIdentifierType='landingPage']")) {
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url.add(((Node) o).getText().trim());
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}
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for (final Object o : doc.selectNodes("//datacite:identifier[@identifierType='URL']")) {
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url.add(((Node) o).getText().trim());
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}
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for (final Object o : doc.selectNodes("//datacite:identifier[@identifierType='landingPage']")) {
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url.add(((Node) o).getText().trim());
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}
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for (final Object o : doc.selectNodes("//datacite:alternateIdentifier[@alternateIdentifierType='DOI']")) {
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url.add(HTTP_DX_DOI_PREIFX + ((Node) o).getText().trim());
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}
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for (final Object o : doc.selectNodes("//datacite:identifier[@identifierType='DOI']")) {
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url.add(HTTP_DX_DOI_PREIFX + ((Node) o).getText().trim());
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}
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if (!url.isEmpty()) {
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instance.setUrl(new ArrayList<>());
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instance.getUrl().addAll(url);
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}
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return Arrays.asList(instance);
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}
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@Override
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protected List<Field<String>> prepareSources(final Document doc, final DataInfo info) {
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return new ArrayList<>(); // Not present in ODF ???
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}
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@Override
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protected List<StructuredProperty> prepareRelevantDates(final Document doc, final DataInfo info) {
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final List<StructuredProperty> res = new ArrayList<>();
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for (final Object o : doc.selectNodes("//datacite:date")) {
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final String dateType = ((Node) o).valueOf("@dateType");
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if (StringUtils.isBlank(dateType)
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&& !dateType.equalsIgnoreCase("Accepted")
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&& !dateType.equalsIgnoreCase("Issued")
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&& !dateType.equalsIgnoreCase("Updated")
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&& !dateType.equalsIgnoreCase("Available")) {
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res
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.add(
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structuredProperty(
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((Node) o).getText(), "UNKNOWN", "UNKNOWN", DNET_DATA_CITE_DATE, DNET_DATA_CITE_DATE,
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info));
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}
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}
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return res;
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}
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@Override
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protected List<Field<String>> prepareCoverages(final Document doc, final DataInfo info) {
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return new ArrayList<>(); // Not present in ODF ???
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}
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@Override
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protected List<Field<String>> prepareContributors(final Document doc, final DataInfo info) {
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return prepareListFields(doc, "//datacite:contributorName", info);
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}
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@Override
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protected List<Field<String>> prepareFormats(final Document doc, final DataInfo info) {
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return prepareListFields(doc, "//datacite:format", info);
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}
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@Override
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protected Field<String> preparePublisher(final Document doc, final DataInfo info) {
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return prepareField(doc, "//datacite:publisher", info);
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}
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@Override
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protected List<Field<String>> prepareDescriptions(final Document doc, final DataInfo info) {
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return prepareListFields(doc, "//datacite:description[@descriptionType='Abstract']", info)
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.stream()
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.map(d -> {
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d.setValue(StringUtils.left(d.getValue(), ModelHardLimits.MAX_ABSTRACT_LENGTH));
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return d;
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})
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.collect(Collectors.toList());
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}
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@Override
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protected List<StructuredProperty> prepareSubjects(final Document doc, final DataInfo info) {
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return prepareListStructProps(doc, "//datacite:subject", info);
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}
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@Override
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protected Qualifier prepareLanguages(final Document doc) {
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return prepareQualifier(doc, "//datacite:language", DNET_LANGUAGES);
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}
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@Override
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protected List<Field<String>> prepareOtherResearchProductTools(
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final Document doc,
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final DataInfo info) {
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return new ArrayList<>(); // Not present in ODF ???
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}
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@Override
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protected List<Field<String>> prepareOtherResearchProductContactGroups(
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final Document doc,
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final DataInfo info) {
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return prepareListFields(
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doc, "//datacite:contributor[@contributorType='ContactGroup']/datacite:contributorName", info);
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}
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@Override
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protected List<Field<String>> prepareOtherResearchProductContactPersons(
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final Document doc,
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final DataInfo info) {
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return prepareListFields(
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doc, "//datacite:contributor[@contributorType='ContactPerson']/datacite:contributorName", info);
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}
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@Override
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protected Qualifier prepareSoftwareProgrammingLanguage(final Document doc, final DataInfo info) {
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return prepareQualifier(doc, "//datacite:format", "dnet:programming_languages");
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}
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@Override
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protected Field<String> prepareSoftwareCodeRepositoryUrl(
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final Document doc,
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final DataInfo info) {
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return null; // Not present in ODF ???
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}
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@Override
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protected List<StructuredProperty> prepareSoftwareLicenses(
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final Document doc,
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final DataInfo info) {
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return new ArrayList<>(); // Not present in ODF ???
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}
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@Override
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protected List<Field<String>> prepareSoftwareDocumentationUrls(
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final Document doc,
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final DataInfo info) {
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return prepareListFields(
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doc, "//datacite:relatedIdentifier[@relatedIdentifierType='URL' and @relationType='IsDocumentedBy']", info);
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}
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// DATASETS
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@Override
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protected List<GeoLocation> prepareDatasetGeoLocations(final Document doc, final DataInfo info) {
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final List<GeoLocation> res = new ArrayList<>();
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for (final Object o : doc.selectNodes("//datacite:geoLocation")) {
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final GeoLocation loc = new GeoLocation();
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loc.setBox(((Node) o).valueOf("./datacite:geoLocationBox"));
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loc.setPlace(((Node) o).valueOf("./datacite:geoLocationPlace"));
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loc.setPoint(((Node) o).valueOf("./datacite:geoLocationPoint"));
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res.add(loc);
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}
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return res;
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}
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@Override
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protected Field<String> prepareDatasetMetadataVersionNumber(
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final Document doc,
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final DataInfo info) {
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return null; // Not present in ODF ???
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}
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@Override
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protected Field<String> prepareDatasetLastMetadataUpdate(
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final Document doc,
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final DataInfo info) {
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return prepareField(doc, "//datacite:date[@dateType='Updated']", info);
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}
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@Override
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protected Field<String> prepareDatasetVersion(final Document doc, final DataInfo info) {
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return prepareField(doc, "//datacite:version", info);
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}
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@Override
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protected Field<String> prepareDatasetSize(final Document doc, final DataInfo info) {
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return prepareField(doc, "//datacite:size", info);
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}
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@Override
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protected Field<String> prepareDatasetDevice(final Document doc, final DataInfo info) {
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return null; // Not present in ODF ???
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}
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@Override
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protected Field<String> prepareDatasetStorageDate(final Document doc, final DataInfo info) {
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return prepareField(doc, "//datacite:date[@dateType='Issued']", info);
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}
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@Override
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protected List<Oaf> addOtherResultRels(
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final Document doc,
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final OafEntity entity) {
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final String docId = entity.getId();
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final List<Oaf> res = new ArrayList<>();
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for (final Object o : doc.selectNodes("//datacite:relatedIdentifier[@relatedIdentifierType='OPENAIRE']")) {
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final String originalId = ((Node) o).getText();
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if (StringUtils.isNotBlank(originalId)) {
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final String otherId = createOpenaireId(50, originalId, false);
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final String type = ((Node) o).valueOf("@relationType");
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if (type.equalsIgnoreCase(IS_SUPPLEMENT_TO)) {
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res
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.add(
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getRelation(
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docId, otherId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENT_TO, entity));
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res
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.add(
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getRelation(
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otherId, docId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENTED_BY, entity));
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} else if (type.equalsIgnoreCase(IS_PART_OF)) {
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res
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.add(
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getRelation(
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docId, otherId, RESULT_RESULT, PART, IS_PART_OF, entity));
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res
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.add(
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getRelation(
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otherId, docId, RESULT_RESULT, PART, HAS_PARTS, entity));
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} else {
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// TODO catch more semantics
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}
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}
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}
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return res;
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}
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@Override
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protected Qualifier prepareResourceType(final Document doc, final DataInfo info) {
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return prepareQualifier(
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doc, "//*[local-name() = 'resource']//*[local-name() = 'resourceType']", DNET_DATA_CITE_RESOURCE);
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}
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@Override
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protected List<StructuredProperty> prepareResultPids(final Document doc, final DataInfo info) {
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final Set<StructuredProperty> res = new HashSet();
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res
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.addAll(
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prepareListStructPropsWithValidQualifier(
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doc, "//oaf:identifier", "@identifierType", DNET_PID_TYPES, info));
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res
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.addAll(
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prepareListStructPropsWithValidQualifier(
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doc, "//datacite:identifier[@identifierType != 'URL' and @identifierType != 'landingPage']",
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"@identifierType", DNET_PID_TYPES, info));
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res
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.addAll(
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prepareListStructPropsWithValidQualifier(
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doc,
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"//datacite:alternateIdentifier[@alternateIdentifierType != 'URL' and @alternateIdentifierType != 'landingPage']",
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"@alternateIdentifierType", DNET_PID_TYPES, info));
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return res
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.stream()
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.map(CleaningFunctions::normalizePidValue)
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.collect(Collectors.toList());
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}
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}
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