forked from D-Net/dnet-hadoop
962 lines
45 KiB
Java
962 lines
45 KiB
Java
package eu.dnetlib.dhp.graph.utils;
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import com.google.common.base.Joiner;
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import com.google.common.base.Splitter;
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import com.google.common.collect.Lists;
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import com.google.common.collect.Sets;
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import com.mycila.xmltool.XMLDoc;
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import com.mycila.xmltool.XMLTag;
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import eu.dnetlib.dhp.graph.model.JoinedEntity;
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import eu.dnetlib.dhp.graph.model.RelatedEntity;
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import eu.dnetlib.dhp.graph.model.Tuple2;
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import eu.dnetlib.dhp.schema.oaf.Result;
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import eu.dnetlib.dhp.schema.oaf.*;
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import org.dom4j.Document;
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import org.dom4j.DocumentException;
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import org.dom4j.Element;
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import org.dom4j.Node;
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import org.dom4j.io.OutputFormat;
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import org.dom4j.io.SAXReader;
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import org.dom4j.io.XMLWriter;
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import javax.xml.transform.*;
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import javax.xml.transform.dom.DOMSource;
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import javax.xml.transform.stream.StreamResult;
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import java.io.IOException;
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import java.io.Serializable;
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import java.io.StringReader;
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import java.io.StringWriter;
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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 static eu.dnetlib.dhp.graph.utils.GraphMappingUtils.*;
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import static eu.dnetlib.dhp.graph.utils.XmlSerializationUtils.*;
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import static org.apache.commons.lang3.StringUtils.isNotBlank;
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import static org.apache.commons.lang3.StringUtils.substringBefore;
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public class XmlRecordFactory implements Serializable {
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private Set<String> specialDatasourceTypes;
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private ContextMapper contextMapper;
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private String schemaLocation;
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private Set<String> contextes = Sets.newHashSet();
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private boolean indent = false;
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public XmlRecordFactory(
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final ContextMapper contextMapper, final boolean indent,
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final String schemaLocation, final Set<String> otherDatasourceTypesUForUI) {
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this.contextMapper = contextMapper;
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this.schemaLocation = schemaLocation;
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this.specialDatasourceTypes = otherDatasourceTypesUForUI;
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this.indent = indent;
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}
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public String build(final JoinedEntity je) {
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final OafEntity entity = je.getEntity();
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TemplateFactory templateFactory = new TemplateFactory();
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try {
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final List<String> metadata = metadata(je.getType(), entity);
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// rels has to be processed before the contexts because they enrich the contextMap with the funding info.
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final List<String> relations = listRelations(je, templateFactory);
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metadata.addAll(buildContexts(getMainType(je.getType())));
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metadata.add(parseDataInfo(entity.getDataInfo()));
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final String body = templateFactory.buildBody(
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getMainType(je.getType()),
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metadata,
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relations,
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listChildren(je, templateFactory), listExtraInfo(je));
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return printXML(templateFactory.buildRecord(entity, schemaLocation, body), indent);
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} catch (final Throwable e) {
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throw new RuntimeException(String.format("error building record '%s'", entity.getId()), e);
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}
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}
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private String printXML(String xml, boolean indent) {
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try {
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final Document doc = new SAXReader().read(new StringReader(xml));
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OutputFormat format = indent ? OutputFormat.createPrettyPrint() : OutputFormat.createCompactFormat();
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format.setExpandEmptyElements(false);
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format.setSuppressDeclaration(true);
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StringWriter sw = new StringWriter();
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XMLWriter writer = new XMLWriter(sw, format);
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writer.write(doc);
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return sw.toString();
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} catch (IOException | DocumentException e) {
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throw new IllegalArgumentException("Unable to indent XML. Invalid record:\n" + xml, e);
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}
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}
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private List<String> metadata(final String type, final OafEntity entity) {
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final List<String> metadata = Lists.newArrayList();
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if (entity.getCollectedfrom() != null) {
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metadata.addAll(entity.getCollectedfrom()
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.stream()
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.map(kv -> mapKeyValue("collectedfrom", kv))
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.collect(Collectors.toList()));
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}
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if (entity.getOriginalId() != null) {
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metadata.addAll(entity.getOriginalId()
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.stream()
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.map(s -> asXmlElement("originalId", s))
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.collect(Collectors.toList()));
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}
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if (entity.getPid() != null) {
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metadata.addAll(entity.getPid()
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.stream()
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.map(p -> mapStructuredProperty("pid", p))
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.collect(Collectors.toList()));
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}
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if (GraphMappingUtils.isResult(type)) {
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final Result r = (Result) entity;
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if (r.getTitle() != null) {
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metadata.addAll(r.getTitle()
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.stream()
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.map(t -> mapStructuredProperty("title", t))
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.collect(Collectors.toList()));
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}
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if (r.getBestaccessright() != null) {
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metadata.add(mapQualifier("bestaccessright", r.getBestaccessright()));
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}
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if (r.getAuthor() != null) {
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metadata.addAll(r.getAuthor()
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.stream()
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.map(a -> {
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final StringBuilder sb = new StringBuilder("<creator rank=\"" + a.getRank() + "\"");
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if (isNotBlank(a.getName())) {
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sb.append(" name=\"" + escapeXml(a.getName()) + "\"");
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}
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if (isNotBlank(a.getSurname())) {
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sb.append(" surname=\"" + escapeXml(a.getSurname()) + "\"");
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}
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if (a.getPid() != null) {
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a.getPid().stream()
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.filter(sp -> isNotBlank(sp.getQualifier().getClassid()) && isNotBlank(sp.getValue()))
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.forEach(sp -> {
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String pidType = escapeXml(sp.getQualifier().getClassid()).replaceAll("\\W", "");
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String pidValue = escapeXml(sp.getValue());
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// ugly hack: some records provide swapped pidtype and pidvalue
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if (authorPidTypes.contains(pidValue.toLowerCase().trim())) {
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sb.append(String.format(" %s=\"%s\"", pidValue, pidType));
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} else {
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pidType = pidType.replaceAll("\\W", "").replaceAll("\\d", "");
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if (isNotBlank(pidType)) {
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sb.append(String.format(" %s=\"%s\"",
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pidType,
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pidValue.toLowerCase().replaceAll("orcid", "")));
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}
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}
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});
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}
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sb.append(">" + escapeXml(a.getFullname()) + "</creator>");
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return sb.toString();
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}).collect(Collectors.toList()));
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}
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if (r.getContributor() != null) {
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metadata.addAll(r.getContributor()
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.stream()
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.map(c -> asXmlElement("contributor", c.getValue()))
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.collect(Collectors.toList()));
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}
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if (r.getCountry() != null) {
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metadata.addAll(r.getCountry()
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.stream()
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.map(c -> mapQualifier("country", c))
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.collect(Collectors.toList()));
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}
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if (r.getCoverage() != null) {
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metadata.addAll(r.getCoverage()
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.stream()
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.map(c -> asXmlElement("coverage", c.getValue()))
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.collect(Collectors.toList()));
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}
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if (r.getDateofacceptance() != null) {
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metadata.add(asXmlElement("dateofacceptance", r.getDateofacceptance().getValue()));
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}
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if (r.getDescription() != null) {
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metadata.addAll(r.getDescription()
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.stream()
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.map(c -> asXmlElement("description", c.getValue()))
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.collect(Collectors.toList()));
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}
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if (r.getEmbargoenddate() != null) {
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metadata.add(asXmlElement("embargoenddate", r.getEmbargoenddate().getValue()));
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}
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if (r.getSubject() != null) {
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metadata.addAll(r.getSubject()
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.stream()
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.map(s -> mapStructuredProperty("subject", s))
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.collect(Collectors.toList()));
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}
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if (r.getLanguage() != null) {
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metadata.add(mapQualifier("language", r.getLanguage()));
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}
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if (r.getRelevantdate() != null) {
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metadata.addAll(r.getRelevantdate()
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.stream()
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.map(s -> mapStructuredProperty("relevantdate", s))
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.collect(Collectors.toList()));
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}
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if (r.getPublisher() != null) {
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metadata.add(asXmlElement("publisher", r.getPublisher().getValue()));
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}
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if (r.getSource() != null) {
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metadata.addAll(r.getSource()
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.stream()
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.map(c -> asXmlElement("source", c.getValue()))
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.collect(Collectors.toList()));
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}
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if (r.getFormat() != null) {
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metadata.addAll(r.getFormat()
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.stream()
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.map(c -> asXmlElement("format", c.getValue()))
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.collect(Collectors.toList()));
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}
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if (r.getResulttype() != null) {
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metadata.add(mapQualifier("resulttype", r.getResulttype()));
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}
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if (r.getResourcetype() != null) {
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metadata.add(mapQualifier("resourcetype", r.getResourcetype()));
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}
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metadata.add(mapQualifier("bestaccessright", getBestAccessright(r)));
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if (r.getContext() != null) {
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contextes.addAll(r.getContext()
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.stream()
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.map(c -> c.getId())
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.collect(Collectors.toList()));
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if (contextes.contains("dh-ch::subcommunity::2")) {
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contextes.add("clarin");
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}
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}
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}
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switch (EntityType.valueOf(type)) {
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case publication:
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final Publication pub = (Publication) entity;
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if (pub.getJournal() != null) {
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final Journal j = pub.getJournal();
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metadata.add(mapJournal(j));
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}
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break;
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case dataset:
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final Dataset d = (Dataset) entity;
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if (d.getDevice() != null) {
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metadata.add(asXmlElement("device", d.getDevice().getValue()));
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}
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if (d.getLastmetadataupdate() != null) {
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metadata.add(asXmlElement("lastmetadataupdate", d.getLastmetadataupdate().getValue()));
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}
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if (d.getMetadataversionnumber() != null) {
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metadata.add(asXmlElement("metadataversionnumber", d.getMetadataversionnumber().getValue()));
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}
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if (d.getSize() != null) {
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metadata.add(asXmlElement("size", d.getSize().getValue()));
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}
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if (d.getStoragedate() != null) {
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metadata.add(asXmlElement("storagedate", d.getStoragedate().getValue()));
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}
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if (d.getVersion() != null) {
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metadata.add(asXmlElement("version", d.getVersion().getValue()));
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}
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//TODO d.getGeolocation()
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break;
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case otherresearchproduct:
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final OtherResearchProduct orp = (OtherResearchProduct) entity;
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if (orp.getContactperson() != null) {
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metadata.addAll(orp.getContactperson()
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.stream()
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.map(c -> asXmlElement("contactperson", c.getValue()))
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.collect(Collectors.toList()));
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}
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if (orp.getContactgroup() != null) {
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metadata.addAll(orp.getContactgroup()
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.stream()
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.map(c -> asXmlElement("contactgroup", c.getValue()))
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.collect(Collectors.toList()));
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}
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if (orp.getTool() != null) {
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metadata.addAll(orp.getTool()
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.stream()
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.map(c -> asXmlElement("tool", c.getValue()))
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.collect(Collectors.toList()));
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}
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break;
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case software:
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final Software s = (Software) entity;
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if (s.getDocumentationUrl() != null) {
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metadata.addAll(s.getDocumentationUrl()
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.stream()
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.map(c -> asXmlElement("documentationUrl", c.getValue()))
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.collect(Collectors.toList()));
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}
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if (s.getLicense() != null) {
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metadata.addAll(s.getLicense()
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.stream()
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.map(l -> mapStructuredProperty("license", l))
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.collect(Collectors.toList()));
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}
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if (s.getCodeRepositoryUrl() != null) {
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metadata.add(asXmlElement("codeRepositoryUrl", s.getCodeRepositoryUrl().getValue()));
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}
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if (s.getProgrammingLanguage() != null) {
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metadata.add(mapQualifier("programmingLanguage", s.getProgrammingLanguage()));
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}
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break;
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case datasource:
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final Datasource ds = (Datasource) entity;
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if (ds.getDatasourcetype() != null) {
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mapDatasourceType(metadata, ds.getDatasourcetype());
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}
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if (ds.getOpenairecompatibility() != null) {
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metadata.add(mapQualifier("openairecompatibility", ds.getOpenairecompatibility()));
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}
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if (ds.getOfficialname() != null) {
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metadata.add(asXmlElement("officialname", ds.getOfficialname().getValue()));
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}
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if (ds.getEnglishname() != null) {
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metadata.add(asXmlElement("englishname", ds.getEnglishname().getValue()));
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}
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if (ds.getWebsiteurl() != null) {
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metadata.add(asXmlElement("websiteurl", ds.getWebsiteurl().getValue()));
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}
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if (ds.getLogourl() != null) {
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metadata.add(asXmlElement("logourl", ds.getLogourl().getValue()));
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}
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if (ds.getContactemail() != null) {
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metadata.add(asXmlElement("contactemail", ds.getContactemail().getValue()));
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}
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if (ds.getNamespaceprefix() != null) {
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metadata.add(asXmlElement("namespaceprefix", ds.getNamespaceprefix().getValue()));
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}
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if (ds.getLatitude() != null) {
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metadata.add(asXmlElement("latitude", ds.getLatitude().getValue()));
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}
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if (ds.getLongitude() != null) {
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metadata.add(asXmlElement("longitude", ds.getLongitude().getValue()));
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}
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if (ds.getDateofvalidation() != null) {
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metadata.add(asXmlElement("dateofvalidation", ds.getDateofvalidation().getValue()));
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}
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if (ds.getDescription() != null) {
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metadata.add(asXmlElement("description", ds.getDescription().getValue()));
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}
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if (ds.getOdnumberofitems() != null) {
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metadata.add(asXmlElement("odnumberofitems", ds.getOdnumberofitems().getValue()));
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}
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if (ds.getOdnumberofitemsdate() != null) {
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metadata.add(asXmlElement("odnumberofitemsdate", ds.getOdnumberofitemsdate().getValue()));
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}
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if (ds.getOdpolicies() != null) {
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metadata.add(asXmlElement("odpolicies", ds.getOdpolicies().getValue()));
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}
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if (ds.getOdlanguages() != null) {
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metadata.addAll(ds.getOdlanguages()
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.stream()
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.map(c -> asXmlElement("odlanguages", c.getValue()))
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.collect(Collectors.toList()));
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}
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if (ds.getOdcontenttypes() != null) {
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metadata.addAll(ds.getOdcontenttypes()
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.stream()
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.map(c -> asXmlElement("odcontenttypes", c.getValue()))
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.collect(Collectors.toList()));
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}
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if (ds.getAccessinfopackage() != null) {
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metadata.addAll(ds.getAccessinfopackage()
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.stream()
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.map(c -> asXmlElement("accessinfopackage", c.getValue()))
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.collect(Collectors.toList()));
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}
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if (ds.getReleaseenddate() != null) {
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metadata.add(asXmlElement("releasestartdate", ds.getReleaseenddate().getValue()));
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}
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if (ds.getReleaseenddate() != null) {
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metadata.add(asXmlElement("releaseenddate", ds.getReleaseenddate().getValue()));
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}
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if (ds.getMissionstatementurl() != null) {
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metadata.add(asXmlElement("missionstatementurl", ds.getMissionstatementurl().getValue()));
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}
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if (ds.getDataprovider() != null) {
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metadata.add(asXmlElement("dataprovider", ds.getDataprovider().getValue().toString()));
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}
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if (ds.getServiceprovider() != null) {
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metadata.add(asXmlElement("serviceprovider", ds.getServiceprovider().getValue().toString()));
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}
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if (ds.getDatabaseaccesstype() != null) {
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metadata.add(asXmlElement("databaseaccesstype", ds.getDatabaseaccesstype().getValue()));
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}
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if (ds.getDatauploadtype() != null) {
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metadata.add(asXmlElement("datauploadtype", ds.getDatauploadtype().getValue()));
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}
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if (ds.getDatabaseaccessrestriction() != null) {
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metadata.add(asXmlElement("databaseaccessrestriction", ds.getDatabaseaccessrestriction().getValue()));
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}
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if (ds.getDatauploadrestriction() != null) {
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metadata.add(asXmlElement("datauploadrestriction", ds.getDatauploadrestriction().getValue()));
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}
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if (ds.getVersioning() != null) {
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metadata.add(asXmlElement("versioning", ds.getVersioning().getValue().toString()));
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}
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if (ds.getCitationguidelineurl() != null) {
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metadata.add(asXmlElement("citationguidelineurl", ds.getCitationguidelineurl().getValue()));
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}
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if (ds.getQualitymanagementkind() != null) {
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metadata.add(asXmlElement("qualitymanagementkind", ds.getQualitymanagementkind().getValue()));
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}
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if (ds.getPidsystems() != null) {
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metadata.add(asXmlElement("pidsystems", ds.getPidsystems().getValue()));
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}
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if (ds.getCertificates() != null) {
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metadata.add(asXmlElement("certificates", ds.getCertificates().getValue()));
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}
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if (ds.getPolicies() != null) {
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metadata.addAll(ds.getPolicies()
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.stream()
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.map(kv -> mapKeyValue("policies", kv))
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.collect(Collectors.toList()));
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}
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if (ds.getJournal() != null) {
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metadata.add(mapJournal(ds.getJournal()));
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}
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if (ds.getSubjects() != null) {
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metadata.addAll(ds.getSubjects()
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.stream()
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.map(sp -> mapStructuredProperty("subject", sp))
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.collect(Collectors.toList()));
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}
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break;
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case organization:
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final Organization o = (Organization) entity;
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if (o.getLegalshortname() != null) {
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metadata.add(asXmlElement("legalshortname", o.getLegalshortname().getValue()));
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}
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if (o.getLegalname() != null) {
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metadata.add(asXmlElement("legalname", o.getLegalname().getValue()));
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}
|
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if (o.getAlternativeNames() != null) {
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metadata.addAll(o.getAlternativeNames()
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.stream()
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.map(c -> asXmlElement("alternativeNames", c.getValue()))
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.collect(Collectors.toList()));
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}
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if (o.getWebsiteurl() != null) {
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metadata.add(asXmlElement("websiteurl", o.getWebsiteurl().getValue()));
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}
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if (o.getLogourl() != null) {
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metadata.add(asXmlElement("websiteurl", o.getLogourl().getValue()));
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}
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|
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if (o.getEclegalbody() != null) {
|
|
metadata.add(asXmlElement("eclegalbody", o.getEclegalbody().getValue()));
|
|
}
|
|
if (o.getEclegalperson() != null) {
|
|
metadata.add(asXmlElement("eclegalperson", o.getEclegalperson().getValue()));
|
|
}
|
|
if (o.getEcnonprofit() != null) {
|
|
metadata.add(asXmlElement("ecnonprofit", o.getEcnonprofit().getValue()));
|
|
}
|
|
if (o.getEcresearchorganization() != null) {
|
|
metadata.add(asXmlElement("ecresearchorganization", o.getEcresearchorganization().getValue()));
|
|
}
|
|
if (o.getEchighereducation() != null) {
|
|
metadata.add(asXmlElement("echighereducation", o.getEchighereducation().getValue()));
|
|
}
|
|
if (o.getEcinternationalorganization() != null) {
|
|
metadata.add(asXmlElement("ecinternationalorganizationeurinterests", o.getEcinternationalorganization().getValue()));
|
|
}
|
|
if (o.getEcinternationalorganization() != null) {
|
|
metadata.add(asXmlElement("ecinternationalorganization", o.getEcinternationalorganization().getValue()));
|
|
}
|
|
if (o.getEcenterprise() != null) {
|
|
metadata.add(asXmlElement("ecenterprise", o.getEcenterprise().getValue()));
|
|
}
|
|
if (o.getEcsmevalidated() != null) {
|
|
metadata.add(asXmlElement("ecsmevalidated", o.getEcsmevalidated().getValue()));
|
|
}
|
|
if (o.getEcnutscode() != null) {
|
|
metadata.add(asXmlElement("ecnutscode", o.getEcnutscode().getValue()));
|
|
}
|
|
if (o.getCountry() != null) {
|
|
metadata.add(mapQualifier("country", o.getCountry()));
|
|
}
|
|
|
|
break;
|
|
case project:
|
|
|
|
final Project p = (Project) entity;
|
|
|
|
if (p.getWebsiteurl() != null) {
|
|
metadata.add(asXmlElement("websiteurl", p.getWebsiteurl().getValue()));
|
|
}
|
|
if (p.getCode() != null) {
|
|
metadata.add(asXmlElement("code", p.getCode().getValue()));
|
|
}
|
|
if (p.getAcronym() != null) {
|
|
metadata.add(asXmlElement("acronym", p.getAcronym().getValue()));
|
|
}
|
|
if (p.getTitle() != null) {
|
|
metadata.add(asXmlElement("title", p.getTitle().getValue()));
|
|
}
|
|
if (p.getStartdate() != null) {
|
|
metadata.add(asXmlElement("startdate", p.getStartdate().getValue()));
|
|
}
|
|
if (p.getEnddate() != null) {
|
|
metadata.add(asXmlElement("enddate", p.getEnddate().getValue()));
|
|
}
|
|
if (p.getCallidentifier() != null) {
|
|
metadata.add(asXmlElement("callidentifier", p.getCallidentifier().getValue()));
|
|
}
|
|
if (p.getKeywords() != null) {
|
|
metadata.add(asXmlElement("keywords", p.getKeywords().getValue()));
|
|
}
|
|
if (p.getDuration() != null) {
|
|
metadata.add(asXmlElement("duration", p.getDuration().getValue()));
|
|
}
|
|
if (p.getEcarticle29_3() != null) {
|
|
metadata.add(asXmlElement("ecarticle29_3", p.getEcarticle29_3().getValue()));
|
|
}
|
|
if (p.getSubjects() != null) {
|
|
metadata.addAll(p.getSubjects()
|
|
.stream()
|
|
.map(sp -> mapStructuredProperty("subject", sp))
|
|
.collect(Collectors.toList()));
|
|
}
|
|
if (p.getContracttype() != null) {
|
|
metadata.add(mapQualifier("contracttype", p.getContracttype()));
|
|
}
|
|
if (p.getEcsc39() != null) {
|
|
metadata.add(asXmlElement("ecsc39", p.getEcsc39().getValue()));
|
|
}
|
|
if (p.getContactfullname() != null) {
|
|
metadata.add(asXmlElement("contactfullname", p.getContactfullname().getValue()));
|
|
}
|
|
if (p.getContactfax() != null) {
|
|
metadata.add(asXmlElement("contactfax", p.getContactfax().getValue()));
|
|
}
|
|
if (p.getContactphone() != null) {
|
|
metadata.add(asXmlElement("contactphone", p.getContactphone().getValue()));
|
|
}
|
|
if (p.getContactemail() != null) {
|
|
metadata.add(asXmlElement("contactemail", p.getContactemail().getValue()));
|
|
}
|
|
if (p.getSummary() != null) {
|
|
metadata.add(asXmlElement("summary", p.getSummary().getValue()));
|
|
}
|
|
if (p.getCurrency() != null) {
|
|
metadata.add(asXmlElement("currency", p.getCurrency().getValue()));
|
|
}
|
|
if (p.getTotalcost() != null) {
|
|
metadata.add(asXmlElement("totalcost", p.getTotalcost().toString()));
|
|
}
|
|
if (p.getFundedamount() != null) {
|
|
metadata.add(asXmlElement("fundedamount", p.getFundedamount().toString()));
|
|
}
|
|
if (p.getFundingtree() != null) {
|
|
metadata.addAll(p.getFundingtree()
|
|
.stream()
|
|
.map(ft -> asXmlElement("fundingtree", ft.getValue()))
|
|
.collect(Collectors.toList()));
|
|
}
|
|
|
|
break;
|
|
default:
|
|
throw new IllegalArgumentException("invalid entity type: " + type);
|
|
}
|
|
|
|
return metadata;
|
|
}
|
|
|
|
private void mapDatasourceType(List<String> metadata, final Qualifier dsType) {
|
|
metadata.add(mapQualifier("datasourcetype", dsType));
|
|
|
|
if (specialDatasourceTypes.contains(dsType.getClassid())) {
|
|
dsType.setClassid("other");
|
|
dsType.setClassname("other");
|
|
}
|
|
metadata.add(mapQualifier("datasourcetypeui", dsType));
|
|
}
|
|
|
|
private Qualifier getBestAccessright(final Result r) {
|
|
Qualifier bestAccessRight = new Qualifier();
|
|
bestAccessRight.setClassid("UNKNOWN");
|
|
bestAccessRight.setClassname("not available");
|
|
bestAccessRight.setSchemeid("dnet:access_modes");
|
|
bestAccessRight.setSchemename("dnet:access_modes");
|
|
|
|
final LicenseComparator lc = new LicenseComparator();
|
|
for (final Instance instance : r.getInstance()) {
|
|
if (lc.compare(bestAccessRight, instance.getAccessright()) > 0) {
|
|
bestAccessRight = instance.getAccessright();
|
|
}
|
|
}
|
|
return bestAccessRight;
|
|
}
|
|
|
|
private List<String> listRelations(final JoinedEntity je, TemplateFactory templateFactory) {
|
|
final List<String> rels = Lists.newArrayList();
|
|
|
|
for (final Tuple2 link : je.getLinks()) {
|
|
|
|
final Relation rel = link.getRelation();
|
|
final RelatedEntity re = link.getRelatedEntity();
|
|
final String targetType = link.getRelatedEntity().getType();
|
|
|
|
final List<String> metadata = Lists.newArrayList();
|
|
switch (EntityType.valueOf(targetType)) {
|
|
case publication:
|
|
case dataset:
|
|
case otherresearchproduct:
|
|
case software:
|
|
if (re.getTitle() != null && isNotBlank(re.getTitle().getValue())) {
|
|
metadata.add(mapStructuredProperty("title", re.getTitle()));
|
|
}
|
|
if (isNotBlank(re.getDateofacceptance())) {
|
|
metadata.add(asXmlElement("dateofacceptance", re.getDateofacceptance()));
|
|
}
|
|
if (isNotBlank(re.getPublisher())) {
|
|
metadata.add(asXmlElement("publisher", re.getPublisher()));
|
|
}
|
|
if (isNotBlank(re.getCodeRepositoryUrl())) {
|
|
metadata.add(asXmlElement("coderepositoryurl", re.getCodeRepositoryUrl()));
|
|
}
|
|
if (re.getResulttype() != null & !re.getResulttype().isBlank()) {
|
|
metadata.add(mapQualifier("resulttype", re.getResulttype()));
|
|
}
|
|
if (re.getCollectedfrom() != null) {
|
|
metadata.addAll(re.getCollectedfrom()
|
|
.stream()
|
|
.map(kv -> mapKeyValue("collectedfrom", kv))
|
|
.collect(Collectors.toList()));
|
|
}
|
|
if (re.getPid() != null) {
|
|
metadata.addAll(re.getPid()
|
|
.stream()
|
|
.map(p -> mapStructuredProperty("pid", p))
|
|
.collect(Collectors.toList()));
|
|
}
|
|
break;
|
|
case datasource:
|
|
if (isNotBlank(re.getOfficialname())) {
|
|
metadata.add(asXmlElement("officialname", re.getOfficialname()));
|
|
}
|
|
if (re.getDatasourcetype() != null & !re.getDatasourcetype().isBlank()) {
|
|
mapDatasourceType(metadata, re.getDatasourcetype());
|
|
}
|
|
if (re.getOpenairecompatibility() != null & !re.getOpenairecompatibility().isBlank()) {
|
|
metadata.add(mapQualifier("openairecompatibility", re.getOpenairecompatibility()));
|
|
}
|
|
break;
|
|
case organization:
|
|
if (isNotBlank(re.getLegalname())) {
|
|
metadata.add(asXmlElement("legalname", re.getLegalname()));
|
|
}
|
|
if (isNotBlank(re.getLegalshortname())) {
|
|
metadata.add(asXmlElement("legalshortname", re.getLegalshortname()));
|
|
}
|
|
if (re.getCountry() != null & !re.getCountry().isBlank()) {
|
|
metadata.add(mapQualifier("country", re.getCountry()));
|
|
}
|
|
break;
|
|
case project:
|
|
if (isNotBlank(re.getProjectTitle())) {
|
|
metadata.add(asXmlElement("title", re.getProjectTitle()));
|
|
}
|
|
if (isNotBlank(re.getCode())) {
|
|
metadata.add(asXmlElement("code", re.getCode()));
|
|
}
|
|
if (isNotBlank(re.getAcronym())) {
|
|
metadata.add(asXmlElement("acronym", re.getAcronym()));
|
|
}
|
|
if (re.getContracttype() != null & !re.getContracttype().isBlank()) {
|
|
metadata.add(mapQualifier("contracttype", re.getContracttype()));
|
|
}
|
|
if (re.getFundingtree() != null) {
|
|
metadata.addAll(re.getFundingtree()
|
|
.stream()
|
|
.peek(ft -> fillContextMap(ft))
|
|
.map(ft -> getRelFundingTree(ft))
|
|
.collect(Collectors.toList()));
|
|
}
|
|
break;
|
|
default:
|
|
throw new IllegalArgumentException("invalid target type: " + targetType);
|
|
|
|
}
|
|
final DataInfo info = rel.getDataInfo();
|
|
|
|
rels.add(templateFactory.getRel(
|
|
targetType,
|
|
rel.getTarget(),
|
|
Sets.newHashSet(metadata),
|
|
getInverseRelClass(rel.getRelClass()),
|
|
getScheme(targetType, re.getType()),
|
|
info));
|
|
}
|
|
return rels;
|
|
}
|
|
|
|
private List<String> listChildren(final JoinedEntity je, TemplateFactory templateFactory) {
|
|
|
|
final List<String> children = Lists.newArrayList();
|
|
|
|
if (MainEntityType.result.toString().equals(getMainType(je.getType()))) {
|
|
final List<Instance> instances = ((Result) je.getEntity()).getInstance();
|
|
if (instances != null) {
|
|
for (final Instance instance : ((Result) je.getEntity()).getInstance()) {
|
|
|
|
final List<String> fields = Lists.newArrayList();
|
|
|
|
if (instance.getAccessright() != null && !instance.getAccessright().isBlank()) {
|
|
fields.add(mapQualifier("accessright", instance.getAccessright()));
|
|
}
|
|
if (instance.getCollectedfrom() != null) {
|
|
fields.add(mapKeyValue("collectedfrom", instance.getCollectedfrom()));
|
|
}
|
|
if (instance.getHostedby() != null) {
|
|
fields.add(mapKeyValue("hostedby", instance.getHostedby()));
|
|
}
|
|
if (instance.getDateofacceptance() != null && isNotBlank(instance.getDateofacceptance().getValue())) {
|
|
fields.add(asXmlElement("dateofacceptance", instance.getDateofacceptance().getValue()));
|
|
}
|
|
if (instance.getInstancetype() != null && !instance.getInstancetype().isBlank()) {
|
|
fields.add(mapQualifier("instancetype", instance.getInstancetype()));
|
|
}
|
|
if (isNotBlank(instance.getDistributionlocation())) {
|
|
fields.add(asXmlElement("distributionlocation", instance.getDistributionlocation()));
|
|
}
|
|
if (instance.getRefereed() != null && isNotBlank(instance.getRefereed().getValue())) {
|
|
fields.add(asXmlElement("refereed", instance.getRefereed().getValue()));
|
|
}
|
|
if (instance.getProcessingchargeamount() != null && isNotBlank(instance.getProcessingchargeamount().getValue())) {
|
|
fields.add(asXmlElement("processingchargeamount", instance.getProcessingchargeamount().getValue()));
|
|
}
|
|
if (instance.getProcessingchargecurrency() != null && isNotBlank(instance.getProcessingchargecurrency().getValue())) {
|
|
fields.add(asXmlElement("processingchargecurrency", instance.getProcessingchargecurrency().getValue()));
|
|
}
|
|
|
|
children.add(templateFactory.getInstance(instance.getHostedby().getKey(), fields, instance.getUrl()));
|
|
}
|
|
}
|
|
final List<ExternalReference> ext = ((Result) je.getEntity()).getExternalReference();
|
|
if (ext != null) {
|
|
for (final ExternalReference er : ((Result) je.getEntity()).getExternalReference()) {
|
|
|
|
final List<String> fields = Lists.newArrayList();
|
|
|
|
if (isNotBlank(er.getSitename())) {
|
|
fields.add(asXmlElement("sitename", er.getSitename()));
|
|
}
|
|
if (isNotBlank(er.getLabel())) {
|
|
fields.add(asXmlElement("label", er.getLabel()));
|
|
}
|
|
if (isNotBlank(er.getUrl())) {
|
|
fields.add(asXmlElement("url", er.getUrl()));
|
|
}
|
|
if (isNotBlank(er.getDescription())) {
|
|
fields.add(asXmlElement("description", er.getDescription()));
|
|
}
|
|
if (isNotBlank(er.getUrl())) {
|
|
fields.add(mapQualifier("qualifier", er.getQualifier()));
|
|
}
|
|
if (isNotBlank(er.getRefidentifier())) {
|
|
fields.add(asXmlElement("refidentifier", er.getRefidentifier()));
|
|
}
|
|
if (isNotBlank(er.getQuery())) {
|
|
fields.add(asXmlElement("query", er.getQuery()));
|
|
}
|
|
|
|
children.add(templateFactory.getChild("externalreference", null, fields));
|
|
}
|
|
}
|
|
}
|
|
|
|
return children;
|
|
}
|
|
|
|
private List<String> listExtraInfo(JoinedEntity je) {
|
|
final List<ExtraInfo> extraInfo = je.getEntity().getExtraInfo();
|
|
return extraInfo != null ? extraInfo
|
|
.stream()
|
|
.map(e -> mapExtraInfo(e))
|
|
.collect(Collectors.toList()) : Lists.newArrayList();
|
|
}
|
|
|
|
private List<String> buildContexts(final String type) {
|
|
final List<String> res = Lists.newArrayList();
|
|
|
|
if ((contextMapper != null) && !contextMapper.isEmpty() && MainEntityType.result.toString().equals(type)) {
|
|
|
|
XMLTag document = XMLDoc.newDocument(true).addRoot("contextRoot");
|
|
|
|
for (final String context : contextes) {
|
|
|
|
String id = "";
|
|
for (final String token : Splitter.on("::").split(context)) {
|
|
id += token;
|
|
|
|
final ContextDef def = contextMapper.get(id);
|
|
|
|
if (def == null) {
|
|
continue;
|
|
// throw new IllegalStateException(String.format("cannot find context for id '%s'", id));
|
|
}
|
|
|
|
if (def.getName().equals("context")) {
|
|
final String xpath = "//context/@id='" + def.getId() + "'";
|
|
if (!document.gotoRoot().rawXpathBoolean(xpath, new Object())) {
|
|
document = addContextDef(document.gotoRoot(), def);
|
|
}
|
|
}
|
|
|
|
if (def.getName().equals("category")) {
|
|
final String rootId = substringBefore(def.getId(), "::");
|
|
document = addContextDef(document.gotoRoot().gotoTag("//context[./@id='" + rootId + "']", new Object()), def);
|
|
}
|
|
|
|
if (def.getName().equals("concept")) {
|
|
document = addContextDef(document, def).gotoParent();
|
|
}
|
|
id += "::";
|
|
}
|
|
}
|
|
final Transformer transformer = getTransformer();
|
|
for (final org.w3c.dom.Element x : document.gotoRoot().getChildElement()) {
|
|
try {
|
|
res.add(asStringElement(x, transformer));
|
|
} catch (final TransformerException e) {
|
|
throw new RuntimeException(e);
|
|
}
|
|
}
|
|
}
|
|
|
|
return res;
|
|
}
|
|
|
|
private Transformer getTransformer() {
|
|
try {
|
|
Transformer transformer = TransformerFactory.newInstance().newTransformer();
|
|
transformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
|
|
return transformer;
|
|
} catch (TransformerConfigurationException e) {
|
|
throw new IllegalStateException("unable to create javax.xml.transform.Transformer", e);
|
|
}
|
|
}
|
|
|
|
private XMLTag addContextDef(final XMLTag tag, final ContextDef def) {
|
|
tag.addTag(def.getName()).addAttribute("id", def.getId()).addAttribute("label", def.getLabel());
|
|
if ((def.getType() != null) && !def.getType().isEmpty()) {
|
|
tag.addAttribute("type", def.getType());
|
|
}
|
|
return tag;
|
|
}
|
|
|
|
private String asStringElement(final org.w3c.dom.Element element, final Transformer transformer) throws TransformerException {
|
|
final StringWriter buffer = new StringWriter();
|
|
transformer.transform(new DOMSource(element), new StreamResult(buffer));
|
|
return buffer.toString();
|
|
}
|
|
|
|
private void fillContextMap(final String xmlTree) {
|
|
|
|
Document fundingPath;
|
|
try {
|
|
fundingPath = new SAXReader().read(new StringReader(xmlTree));
|
|
} catch (final DocumentException e) {
|
|
throw new RuntimeException(e);
|
|
}
|
|
try {
|
|
final Node funder = fundingPath.selectSingleNode("//funder");
|
|
|
|
if (funder != null) {
|
|
|
|
final String funderShortName = funder.valueOf("./shortname");
|
|
contextes.add(funderShortName);
|
|
|
|
contextMapper.put(funderShortName, new ContextDef(funderShortName, funder.valueOf("./name"), "context", "funding"));
|
|
final Node level0 = fundingPath.selectSingleNode("//funding_level_0");
|
|
if (level0 != null) {
|
|
final String level0Id = Joiner.on("::").join(funderShortName, level0.valueOf("./name"));
|
|
contextMapper.put(level0Id, new ContextDef(level0Id, level0.valueOf("./description"), "category", ""));
|
|
final Node level1 = fundingPath.selectSingleNode("//funding_level_1");
|
|
if (level1 == null) {
|
|
contextes.add(level0Id);
|
|
} else {
|
|
final String level1Id = Joiner.on("::").join(level0Id, level1.valueOf("./name"));
|
|
contextMapper.put(level1Id, new ContextDef(level1Id, level1.valueOf("./description"), "concept", ""));
|
|
final Node level2 = fundingPath.selectSingleNode("//funding_level_2");
|
|
if (level2 == null) {
|
|
contextes.add(level1Id);
|
|
} else {
|
|
final String level2Id = Joiner.on("::").join(level1Id, level2.valueOf("./name"));
|
|
contextMapper.put(level2Id, new ContextDef(level2Id, level2.valueOf("./description"), "concept", ""));
|
|
contextes.add(level2Id);
|
|
}
|
|
}
|
|
}
|
|
}
|
|
} catch (final NullPointerException e) {
|
|
throw new IllegalArgumentException("malformed funding path: " + xmlTree, e);
|
|
}
|
|
}
|
|
|
|
|
|
|
|
@SuppressWarnings("unchecked")
|
|
private String getRelFundingTree(final String xmlTree) {
|
|
String funding = "<funding>";
|
|
try {
|
|
final Document ftree = new SAXReader().read(new StringReader(xmlTree));
|
|
funding = "<funding>";
|
|
|
|
funding += getFunderElement(ftree);
|
|
|
|
for (final Object o : Lists.reverse(ftree.selectNodes("//fundingtree//*[starts-with(local-name(),'funding_level_')]"))) {
|
|
final Element e = (Element) o;
|
|
final String _id = e.valueOf("./id");
|
|
funding += "<" + e.getName() + " name=\"" + escapeXml(e.valueOf("./name")) + "\">" + escapeXml(_id) + "</" + e.getName() + ">";
|
|
}
|
|
} catch (final DocumentException e) {
|
|
throw new IllegalArgumentException("unable to parse funding tree: " + xmlTree + "\n" + e.getMessage());
|
|
} finally {
|
|
funding += "</funding>";
|
|
}
|
|
return funding;
|
|
}
|
|
|
|
private String getFunderElement(final Document ftree) {
|
|
final String funderId = ftree.valueOf("//fundingtree/funder/id/text()");
|
|
final String funderShortName = ftree.valueOf("//fundingtree/funder/shortname/text()");
|
|
final String funderName = ftree.valueOf("//fundingtree/funder/name/text()");
|
|
final String funderJurisdiction = ftree.valueOf("//fundingtree/funder/jurisdiction/text()");
|
|
|
|
return "<funder id=\"" + escapeXml(funderId) + "\" shortname=\"" + escapeXml(funderShortName) + "\" name=\"" + escapeXml(funderName)
|
|
+ "\" jurisdiction=\"" + escapeXml(funderJurisdiction) + "\" />";
|
|
}
|
|
|
|
} |