forked from D-Net/dnet-hadoop
411 lines
14 KiB
Java
411 lines
14 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 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 com.google.common.collect.Lists;
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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.Author;
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import eu.dnetlib.dhp.schema.oaf.DataInfo;
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import eu.dnetlib.dhp.schema.oaf.Field;
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import eu.dnetlib.dhp.schema.oaf.GeoLocation;
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import eu.dnetlib.dhp.schema.oaf.Instance;
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import eu.dnetlib.dhp.schema.oaf.KeyValue;
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import eu.dnetlib.dhp.schema.oaf.Oaf;
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import eu.dnetlib.dhp.schema.oaf.Qualifier;
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import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
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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(
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doc, "//*[local-name()='titles']/*[local-name()='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("//*[local-name()='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("./*[local-name()='creatorName']");
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final String name = n.valueOf("./*[local-name()='givenName']");
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final String surname = n.valueOf("./*[local-name()='familyName']");
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if (StringUtils.isNotBlank(fullname) || StringUtils.isNotBlank(name) || StringUtils.isNotBlank(surname)) {
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author.setFullname(fullname);
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final PacePerson pp = new PacePerson(fullname, false);
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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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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, "./*[local-name()='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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}
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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("./*[local-name()='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
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.selectNodes("//*[local-name()='alternateIdentifier' and ./@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("//*[local-name()='alternateIdentifier' and ./@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("//*[local-name()='identifier' and ./@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("//*[local-name()='identifier' and ./@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
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.selectNodes("//*[local-name()='alternateIdentifier' and ./@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("//*[local-name()='identifier' and ./@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("//*[local-name()='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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} else {
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res
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.add(
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structuredProperty(
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((Node) o).getText(), dateType, dateType, 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, "//*[local-name()='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, "//*[local-name()=':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, "//*[local-name()=':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, "//*[local-name()='description' and ./@descriptionType='Abstract']", info);
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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, "//*[local-name()='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, "//*[local-name()=':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,
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"//*[local-name()='contributor' and ./@contributorType='ContactGroup']/*[local-name()='contributorName']",
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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,
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"//*[local-name()='contributor' and ./@contributorType='ContactPerson']/*[local-name()='contributorName']",
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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, "//*[local-name()='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,
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"//*[local-name()='relatedIdentifier' and ./@relatedIdentifierType='URL' and @relationType='IsDocumentedBy']",
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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("//*[local-name()='geoLocation']")) {
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final GeoLocation loc = new GeoLocation();
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loc.setBox(((Node) o).valueOf("./*[local-name()=':geoLocationBox']"));
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loc.setPlace(((Node) o).valueOf("./*[local-name()=':geoLocationPlace']"));
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loc.setPoint(((Node) o).valueOf("./*[local-name()=':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, "//*[local-name()='date' and ./@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, "//*[local-name()='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, "//*[local-name()='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, "//*[local-name()='date' and ./@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 KeyValue collectedFrom,
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final DataInfo info,
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final long lastUpdateTimestamp) {
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final String docId = createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false);
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final List<Oaf> res = new ArrayList<>();
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for (final Object o : doc
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.selectNodes("//*[local-name()='relatedIdentifier' and ./@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("IsSupplementTo")) {
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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, 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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otherId, docId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENTED_BY, collectedFrom, info,
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lastUpdateTimestamp));
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} else if (type.equalsIgnoreCase("IsPartOf")) {
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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, 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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otherId, docId, RESULT_RESULT, PART, HAS_PARTS, collectedFrom, info,
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lastUpdateTimestamp));
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} else {
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}
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}
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}
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return res;
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}
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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,
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"//*[local-name()='identifier' and ./@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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"//*[local-name()='alternateIdentifier' and ./@alternateIdentifierType != 'URL' and ./@alternateIdentifierType != 'landingPage']",
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"@alternateIdentifierType", DNET_PID_TYPES, info));
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return Lists.newArrayList(res);
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}
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}
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