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1425 lines
44 KiB
Java
1425 lines
44 KiB
Java
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package eu.dnetlib.dhp.oa.provision.utils;
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import static eu.dnetlib.dhp.oa.provision.utils.GraphMappingUtils.*;
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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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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.*;
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import java.util.stream.Collectors;
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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 org.apache.commons.lang3.StringUtils;
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import org.apache.spark.util.LongAccumulator;
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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 com.fasterxml.jackson.databind.ObjectMapper;
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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.Maps;
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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.oa.provision.model.*;
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import eu.dnetlib.dhp.schema.common.EntityType;
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import eu.dnetlib.dhp.schema.common.MainEntityType;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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import eu.dnetlib.dhp.schema.oaf.*;
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import eu.dnetlib.dhp.schema.oaf.Result;
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public class XmlRecordFactory implements Serializable {
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private static final String REL_SUBTYPE_DEDUP = "dedup";
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private final Map<String, LongAccumulator> accumulators;
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private final Set<String> specialDatasourceTypes;
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private final ContextMapper contextMapper;
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private final String schemaLocation;
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private boolean indent = false;
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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public XmlRecordFactory(
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final ContextMapper contextMapper,
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final boolean indent,
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final String schemaLocation,
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final String otherDatasourceTypesUForUI) {
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this(Maps.newHashMap(), contextMapper, indent, schemaLocation, otherDatasourceTypesUForUI);
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}
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public XmlRecordFactory(
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final Map<String, LongAccumulator> accumulators,
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final ContextMapper contextMapper,
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final boolean indent,
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final String schemaLocation,
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final String otherDatasourceTypesUForUI) {
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this.accumulators = accumulators;
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this.contextMapper = contextMapper;
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this.schemaLocation = schemaLocation;
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this.specialDatasourceTypes = Sets.newHashSet(Splitter.on(",").trimResults().split(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 Set<String> contexts = Sets.newHashSet();
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// final OafEntity entity = toOafEntity(je.getEntity());
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OafEntity entity = je.getEntity();
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TemplateFactory templateFactory = new TemplateFactory();
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try {
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final EntityType type = EntityType.fromClass(entity.getClass());
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final List<String> metadata = metadata(type, entity, contexts);
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// rels has to be processed before the contexts because they enrich the contextMap with
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// the
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// funding info.
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final List<RelatedEntityWrapper> links = je.getLinks();
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final List<String> relations = links
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.stream()
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.filter(link -> !isDuplicate(link))
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.map(link -> mapRelation(contexts, templateFactory, type, link))
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.collect(Collectors.toCollection(ArrayList::new));
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final String mainType = ModelSupport.getMainType(type);
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metadata.addAll(buildContexts(mainType, contexts));
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metadata.add(XmlSerializationUtils.parseDataInfo(entity.getDataInfo()));
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final String body = templateFactory
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.buildBody(
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mainType,
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metadata,
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relations,
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listChildren(entity, je, templateFactory),
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listExtraInfo(entity));
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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 static OafEntity parseOaf(final String json, final String type) {
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try {
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switch (EntityType.valueOf(type)) {
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case publication:
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return OBJECT_MAPPER.readValue(json, Publication.class);
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case dataset:
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return OBJECT_MAPPER.readValue(json, Dataset.class);
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case otherresearchproduct:
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return OBJECT_MAPPER.readValue(json, OtherResearchProduct.class);
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case software:
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return OBJECT_MAPPER.readValue(json, Software.class);
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case datasource:
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return OBJECT_MAPPER.readValue(json, Datasource.class);
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case organization:
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return OBJECT_MAPPER.readValue(json, Organization.class);
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case project:
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return OBJECT_MAPPER.readValue(json, Project.class);
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default:
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throw new IllegalArgumentException("invalid type: " + type);
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}
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} catch (IOException e) {
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throw new IllegalArgumentException(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(
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final EntityType type, final OafEntity entity, final Set<String> contexts) {
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final List<String> metadata = Lists.newArrayList();
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if (entity.getCollectedfrom() != null) {
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metadata
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.addAll(
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entity
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.getCollectedfrom()
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.stream()
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.filter(XmlRecordFactory::kvNotBlank)
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.map(kv -> XmlSerializationUtils.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
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.addAll(
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entity
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.getOriginalId()
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.stream()
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.filter(Objects::nonNull)
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.map(s -> XmlSerializationUtils.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
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.addAll(
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entity
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.getPid()
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.stream()
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.filter(Objects::nonNull)
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.map(p -> XmlSerializationUtils.mapStructuredProperty("pid", p))
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.collect(Collectors.toList()));
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}
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if (ModelSupport.isResult(type)) {
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final Result r = (Result) entity;
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if (r.getContext() != null) {
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contexts.addAll(r.getContext().stream().map(c -> c.getId()).collect(Collectors.toList()));
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/* FIXME: Workaround for CLARIN mining issue: #3670#note-29 */
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if (contexts.contains("dh-ch::subcommunity::2")) {
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contexts.add("clarin");
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}
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}
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if (r.getTitle() != null) {
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metadata
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.addAll(
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r
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.getTitle()
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.stream()
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.filter(Objects::nonNull)
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.map(t -> XmlSerializationUtils.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(XmlSerializationUtils.mapQualifier("bestaccessright", r.getBestaccessright()));
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}
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if (r.getAuthor() != null) {
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metadata
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.addAll(
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r
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.getAuthor()
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.stream()
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.filter(Objects::nonNull)
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.map(
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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=\"" + XmlSerializationUtils.escapeXml(a.getName()) + "\"");
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}
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if (isNotBlank(a.getSurname())) {
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sb
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.append(
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" surname=\"" + XmlSerializationUtils.escapeXml(a.getSurname()) + "\"");
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}
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if (a.getPid() != null) {
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a
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.getPid()
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.stream()
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.filter(Objects::nonNull)
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.filter(
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sp -> isNotBlank(sp.getQualifier().getClassid())
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&& isNotBlank(sp.getValue()))
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.collect(
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Collectors
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.toMap(
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p -> getAuthorPidType(p.getQualifier().getClassid()),
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p -> p,
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(p1, p2) -> p1))
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.values()
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.stream()
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.collect(
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Collectors
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.groupingBy(
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p -> p.getValue(),
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Collectors
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.mapping(
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p -> p,
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Collectors.minBy(new AuthorPidTypeComparator()))))
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.values()
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.stream()
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.map(op -> op.get())
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.forEach(
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sp -> {
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String pidType = getAuthorPidType(sp.getQualifier().getClassid());
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String pidValue = XmlSerializationUtils.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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if (isNotBlank(pidType)) {
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sb
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.append(
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String
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.format(
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" %s=\"%s\"",
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pidType,
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pidValue
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.toLowerCase()
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.replaceAll("^.*orcid\\.org\\/", "")));
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}
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}
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});
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}
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sb
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.append(
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">" + XmlSerializationUtils.escapeXml(a.getFullname()) + "</creator>");
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return sb.toString();
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})
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.collect(Collectors.toList()));
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}
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if (r.getContributor() != null) {
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metadata
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.addAll(
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r
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.getContributor()
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.stream()
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.filter(Objects::nonNull)
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.map(c -> XmlSerializationUtils.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
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.addAll(
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r
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.getCountry()
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.stream()
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.filter(Objects::nonNull)
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.map(c -> XmlSerializationUtils.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
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.addAll(
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r
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.getCoverage()
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.stream()
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.filter(Objects::nonNull)
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.map(c -> XmlSerializationUtils.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
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.add(
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XmlSerializationUtils
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.asXmlElement(
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"dateofacceptance", r.getDateofacceptance().getValue()));
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}
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if (r.getDescription() != null) {
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metadata
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.addAll(
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r
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.getDescription()
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.stream()
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.filter(Objects::nonNull)
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.map(c -> XmlSerializationUtils.asXmlElement("description", c.getValue()))
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.collect(Collectors.toCollection(HashSet::new)));
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}
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if (r.getEmbargoenddate() != null) {
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metadata
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.add(
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XmlSerializationUtils.asXmlElement("embargoenddate", r.getEmbargoenddate().getValue()));
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}
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if (r.getSubject() != null) {
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metadata
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.addAll(
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r
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.getSubject()
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.stream()
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.filter(Objects::nonNull)
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.map(s -> XmlSerializationUtils.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(XmlSerializationUtils.mapQualifier("language", r.getLanguage()));
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}
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if (r.getRelevantdate() != null) {
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metadata
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.addAll(
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r
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.getRelevantdate()
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.stream()
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.filter(Objects::nonNull)
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.map(s -> XmlSerializationUtils.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(XmlSerializationUtils.asXmlElement("publisher", r.getPublisher().getValue()));
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}
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if (r.getSource() != null) {
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metadata
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.addAll(
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r
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.getSource()
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.stream()
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.filter(Objects::nonNull)
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.map(c -> XmlSerializationUtils.asXmlElement("source", c.getValue()))
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.collect(Collectors.toCollection(HashSet::new)));
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}
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if (r.getFormat() != null) {
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metadata
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.addAll(
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r
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.getFormat()
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.stream()
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.filter(Objects::nonNull)
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.map(c -> XmlSerializationUtils.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(XmlSerializationUtils.mapQualifier("resulttype", r.getResulttype()));
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}
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if (r.getResourcetype() != null) {
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metadata.add(XmlSerializationUtils.mapQualifier("resourcetype", r.getResourcetype()));
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}
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}
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switch (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(XmlSerializationUtils.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(XmlSerializationUtils.asXmlElement("device", d.getDevice().getValue()));
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}
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if (d.getLastmetadataupdate() != null) {
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metadata
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.add(
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XmlSerializationUtils
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.asXmlElement(
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"lastmetadataupdate", d.getLastmetadataupdate().getValue()));
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}
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if (d.getMetadataversionnumber() != null) {
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metadata
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.add(
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XmlSerializationUtils
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.asXmlElement(
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"metadataversionnumber", d.getMetadataversionnumber().getValue()));
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}
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if (d.getSize() != null) {
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metadata.add(XmlSerializationUtils.asXmlElement("size", d.getSize().getValue()));
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}
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if (d.getStoragedate() != null) {
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metadata
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.add(
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XmlSerializationUtils.asXmlElement("storagedate", d.getStoragedate().getValue()));
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}
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if (d.getVersion() != null) {
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metadata.add(XmlSerializationUtils.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
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.addAll(
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orp
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.getContactperson()
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.stream()
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.filter(Objects::nonNull)
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.map(c -> XmlSerializationUtils.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
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.addAll(
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orp
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.getContactgroup()
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.stream()
|
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.filter(Objects::nonNull)
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.map(c -> XmlSerializationUtils.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
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.addAll(
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orp
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.getTool()
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.stream()
|
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.filter(Objects::nonNull)
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.map(c -> XmlSerializationUtils.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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|
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if (s.getDocumentationUrl() != null) {
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metadata
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.addAll(
|
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s
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.getDocumentationUrl()
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.stream()
|
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.filter(Objects::nonNull)
|
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.map(c -> XmlSerializationUtils.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
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|
.addAll(
|
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s
|
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.getLicense()
|
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.stream()
|
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.filter(Objects::nonNull)
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.map(l -> XmlSerializationUtils.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
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.add(
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XmlSerializationUtils
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.asXmlElement(
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"codeRepositoryUrl", s.getCodeRepositoryUrl().getValue()));
|
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}
|
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if (s.getProgrammingLanguage() != null) {
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metadata
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.add(
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XmlSerializationUtils
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.mapQualifier(
|
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"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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|
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if (ds.getDatasourcetype() != null) {
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mapDatasourceType(metadata, ds.getDatasourcetype());
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}
|
|
if (ds.getOpenairecompatibility() != null) {
|
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metadata
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.add(
|
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XmlSerializationUtils
|
|
.mapQualifier(
|
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"openairecompatibility", ds.getOpenairecompatibility()));
|
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}
|
|
if (ds.getOfficialname() != null) {
|
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metadata
|
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.add(
|
|
XmlSerializationUtils.asXmlElement("officialname", ds.getOfficialname().getValue()));
|
|
}
|
|
if (ds.getEnglishname() != null) {
|
|
metadata
|
|
.add(
|
|
XmlSerializationUtils.asXmlElement("englishname", ds.getEnglishname().getValue()));
|
|
}
|
|
if (ds.getWebsiteurl() != null) {
|
|
metadata
|
|
.add(
|
|
XmlSerializationUtils.asXmlElement("websiteurl", ds.getWebsiteurl().getValue()));
|
|
}
|
|
if (ds.getLogourl() != null) {
|
|
metadata.add(XmlSerializationUtils.asXmlElement("logourl", ds.getLogourl().getValue()));
|
|
}
|
|
if (ds.getContactemail() != null) {
|
|
metadata
|
|
.add(
|
|
XmlSerializationUtils.asXmlElement("contactemail", ds.getContactemail().getValue()));
|
|
}
|
|
if (ds.getNamespaceprefix() != null) {
|
|
metadata
|
|
.add(
|
|
XmlSerializationUtils
|
|
.asXmlElement(
|
|
"namespaceprefix", ds.getNamespaceprefix().getValue()));
|
|
}
|
|
if (ds.getLatitude() != null) {
|
|
metadata.add(XmlSerializationUtils.asXmlElement("latitude", ds.getLatitude().getValue()));
|
|
}
|
|
if (ds.getLongitude() != null) {
|
|
metadata
|
|
.add(
|
|
XmlSerializationUtils.asXmlElement("longitude", ds.getLongitude().getValue()));
|
|
}
|
|
if (ds.getDateofvalidation() != null) {
|
|
metadata
|
|
.add(
|
|
XmlSerializationUtils
|
|
.asXmlElement(
|
|
"dateofvalidation", ds.getDateofvalidation().getValue()));
|
|
}
|
|
if (ds.getDescription() != null) {
|
|
metadata
|
|
.add(
|
|
XmlSerializationUtils.asXmlElement("description", ds.getDescription().getValue()));
|
|
}
|
|
if (ds.getOdnumberofitems() != null) {
|
|
metadata
|
|
.add(
|
|
XmlSerializationUtils
|
|
.asXmlElement(
|
|
"odnumberofitems", ds.getOdnumberofitems().getValue()));
|
|
}
|
|
if (ds.getOdnumberofitemsdate() != null) {
|
|
metadata
|
|
.add(
|
|
XmlSerializationUtils
|
|
.asXmlElement(
|
|
"odnumberofitemsdate", ds.getOdnumberofitemsdate().getValue()));
|
|
}
|
|
if (ds.getOdpolicies() != null) {
|
|
metadata
|
|
.add(
|
|
XmlSerializationUtils.asXmlElement("odpolicies", ds.getOdpolicies().getValue()));
|
|
}
|
|
if (ds.getOdlanguages() != null) {
|
|
metadata
|
|
.addAll(
|
|
ds
|
|
.getOdlanguages()
|
|
.stream()
|
|
.filter(Objects::nonNull)
|
|
.map(c -> XmlSerializationUtils.asXmlElement("odlanguages", c.getValue()))
|
|
.collect(Collectors.toList()));
|
|
}
|
|
if (ds.getOdcontenttypes() != null) {
|
|
metadata
|
|
.addAll(
|
|
ds
|
|
.getOdcontenttypes()
|
|
.stream()
|
|
.filter(Objects::nonNull)
|
|
.map(c -> XmlSerializationUtils.asXmlElement("odcontenttypes", c.getValue()))
|
|
.collect(Collectors.toList()));
|
|
}
|
|
if (ds.getAccessinfopackage() != null) {
|
|
metadata
|
|
.addAll(
|
|
ds
|
|
.getAccessinfopackage()
|
|
.stream()
|
|
.map(c -> XmlSerializationUtils.asXmlElement("accessinfopackage", c.getValue()))
|
|
.collect(Collectors.toList()));
|
|
}
|
|
if (ds.getReleaseenddate() != null) {
|
|
metadata
|
|
.add(
|
|
XmlSerializationUtils
|
|
.asXmlElement(
|
|
"releasestartdate", ds.getReleaseenddate().getValue()));
|
|
}
|
|
if (ds.getReleaseenddate() != null) {
|
|
metadata
|
|
.add(
|
|
XmlSerializationUtils
|
|
.asXmlElement(
|
|
"releaseenddate", ds.getReleaseenddate().getValue()));
|
|
}
|
|
if (ds.getMissionstatementurl() != null) {
|
|
metadata
|
|
.add(
|
|
XmlSerializationUtils
|
|
.asXmlElement(
|
|
"missionstatementurl", ds.getMissionstatementurl().getValue()));
|
|
}
|
|
if (ds.getDataprovider() != null) {
|
|
metadata
|
|
.add(
|
|
XmlSerializationUtils
|
|
.asXmlElement(
|
|
"dataprovider", ds.getDataprovider().getValue().toString()));
|
|
}
|
|
if (ds.getServiceprovider() != null) {
|
|
metadata
|
|
.add(
|
|
XmlSerializationUtils
|
|
.asXmlElement(
|
|
"serviceprovider", ds.getServiceprovider().getValue().toString()));
|
|
}
|
|
if (ds.getDatabaseaccesstype() != null) {
|
|
metadata
|
|
.add(
|
|
XmlSerializationUtils
|
|
.asXmlElement(
|
|
"databaseaccesstype", ds.getDatabaseaccesstype().getValue()));
|
|
}
|
|
if (ds.getDatauploadtype() != null) {
|
|
metadata
|
|
.add(
|
|
XmlSerializationUtils
|
|
.asXmlElement(
|
|
"datauploadtype", ds.getDatauploadtype().getValue()));
|
|
}
|
|
if (ds.getDatabaseaccessrestriction() != null) {
|
|
metadata
|
|
.add(
|
|
XmlSerializationUtils
|
|
.asXmlElement(
|
|
"databaseaccessrestriction", ds.getDatabaseaccessrestriction().getValue()));
|
|
}
|
|
if (ds.getDatauploadrestriction() != null) {
|
|
metadata
|
|
.add(
|
|
XmlSerializationUtils
|
|
.asXmlElement(
|
|
"datauploadrestriction", ds.getDatauploadrestriction().getValue()));
|
|
}
|
|
if (ds.getVersioning() != null) {
|
|
metadata
|
|
.add(
|
|
XmlSerializationUtils
|
|
.asXmlElement(
|
|
"versioning", ds.getVersioning().getValue().toString()));
|
|
}
|
|
if (ds.getCitationguidelineurl() != null) {
|
|
metadata
|
|
.add(
|
|
XmlSerializationUtils
|
|
.asXmlElement(
|
|
"citationguidelineurl", ds.getCitationguidelineurl().getValue()));
|
|
}
|
|
if (ds.getQualitymanagementkind() != null) {
|
|
metadata
|
|
.add(
|
|
XmlSerializationUtils
|
|
.asXmlElement(
|
|
"qualitymanagementkind", ds.getQualitymanagementkind().getValue()));
|
|
}
|
|
if (ds.getPidsystems() != null) {
|
|
metadata
|
|
.add(
|
|
XmlSerializationUtils.asXmlElement("pidsystems", ds.getPidsystems().getValue()));
|
|
}
|
|
if (ds.getCertificates() != null) {
|
|
metadata
|
|
.add(
|
|
XmlSerializationUtils.asXmlElement("certificates", ds.getCertificates().getValue()));
|
|
}
|
|
if (ds.getPolicies() != null) {
|
|
metadata
|
|
.addAll(
|
|
ds
|
|
.getPolicies()
|
|
.stream()
|
|
.filter(XmlRecordFactory::kvNotBlank)
|
|
.map(kv -> XmlSerializationUtils.mapKeyValue("policies", kv))
|
|
.collect(Collectors.toList()));
|
|
}
|
|
if (ds.getJournal() != null) {
|
|
metadata.add(XmlSerializationUtils.mapJournal(ds.getJournal()));
|
|
}
|
|
if (ds.getSubjects() != null) {
|
|
metadata
|
|
.addAll(
|
|
ds
|
|
.getSubjects()
|
|
.stream()
|
|
.filter(Objects::nonNull)
|
|
.map(sp -> XmlSerializationUtils.mapStructuredProperty("subjects", sp))
|
|
.collect(Collectors.toList()));
|
|
}
|
|
|
|
break;
|
|
case organization:
|
|
final Organization o = (Organization) entity;
|
|
|
|
if (o.getLegalshortname() != null) {
|
|
metadata
|
|
.add(
|
|
XmlSerializationUtils
|
|
.asXmlElement(
|
|
"legalshortname", o.getLegalshortname().getValue()));
|
|
}
|
|
if (o.getLegalname() != null) {
|
|
metadata
|
|
.add(
|
|
XmlSerializationUtils.asXmlElement("legalname", o.getLegalname().getValue()));
|
|
}
|
|
if (o.getAlternativeNames() != null) {
|
|
metadata
|
|
.addAll(
|
|
o
|
|
.getAlternativeNames()
|
|
.stream()
|
|
.filter(Objects::nonNull)
|
|
.map(c -> XmlSerializationUtils.asXmlElement("alternativeNames", c.getValue()))
|
|
.collect(Collectors.toList()));
|
|
}
|
|
if (o.getWebsiteurl() != null) {
|
|
metadata
|
|
.add(
|
|
XmlSerializationUtils.asXmlElement("websiteurl", o.getWebsiteurl().getValue()));
|
|
}
|
|
if (o.getLogourl() != null) {
|
|
metadata.add(XmlSerializationUtils.asXmlElement("logourl", o.getLogourl().getValue()));
|
|
}
|
|
|
|
if (o.getEclegalbody() != null) {
|
|
metadata
|
|
.add(
|
|
XmlSerializationUtils.asXmlElement("eclegalbody", o.getEclegalbody().getValue()));
|
|
}
|
|
if (o.getEclegalperson() != null) {
|
|
metadata
|
|
.add(
|
|
XmlSerializationUtils.asXmlElement("eclegalperson", o.getEclegalperson().getValue()));
|
|
}
|
|
if (o.getEcnonprofit() != null) {
|
|
metadata
|
|
.add(
|
|
XmlSerializationUtils.asXmlElement("ecnonprofit", o.getEcnonprofit().getValue()));
|
|
}
|
|
if (o.getEcresearchorganization() != null) {
|
|
metadata
|
|
.add(
|
|
XmlSerializationUtils
|
|
.asXmlElement(
|
|
"ecresearchorganization", o.getEcresearchorganization().getValue()));
|
|
}
|
|
if (o.getEchighereducation() != null) {
|
|
metadata
|
|
.add(
|
|
XmlSerializationUtils
|
|
.asXmlElement(
|
|
"echighereducation", o.getEchighereducation().getValue()));
|
|
}
|
|
if (o.getEcinternationalorganizationeurinterests() != null) {
|
|
metadata
|
|
.add(
|
|
XmlSerializationUtils
|
|
.asXmlElement(
|
|
"ecinternationalorganizationeurinterests",
|
|
o.getEcinternationalorganizationeurinterests().getValue()));
|
|
}
|
|
if (o.getEcinternationalorganization() != null) {
|
|
metadata
|
|
.add(
|
|
XmlSerializationUtils
|
|
.asXmlElement(
|
|
"ecinternationalorganization", o.getEcinternationalorganization().getValue()));
|
|
}
|
|
if (o.getEcenterprise() != null) {
|
|
metadata
|
|
.add(
|
|
XmlSerializationUtils.asXmlElement("ecenterprise", o.getEcenterprise().getValue()));
|
|
}
|
|
if (o.getEcsmevalidated() != null) {
|
|
metadata
|
|
.add(
|
|
XmlSerializationUtils
|
|
.asXmlElement(
|
|
"ecsmevalidated", o.getEcsmevalidated().getValue()));
|
|
}
|
|
if (o.getEcnutscode() != null) {
|
|
metadata
|
|
.add(
|
|
XmlSerializationUtils.asXmlElement("ecnutscode", o.getEcnutscode().getValue()));
|
|
}
|
|
if (o.getCountry() != null) {
|
|
metadata.add(XmlSerializationUtils.mapQualifier("country", o.getCountry()));
|
|
}
|
|
|
|
break;
|
|
case project:
|
|
final Project p = (Project) entity;
|
|
|
|
if (p.getWebsiteurl() != null) {
|
|
metadata
|
|
.add(
|
|
XmlSerializationUtils.asXmlElement("websiteurl", p.getWebsiteurl().getValue()));
|
|
}
|
|
if (p.getCode() != null) {
|
|
metadata.add(XmlSerializationUtils.asXmlElement("code", p.getCode().getValue()));
|
|
}
|
|
if (p.getAcronym() != null) {
|
|
metadata.add(XmlSerializationUtils.asXmlElement("acronym", p.getAcronym().getValue()));
|
|
}
|
|
if (p.getTitle() != null) {
|
|
metadata.add(XmlSerializationUtils.asXmlElement("title", p.getTitle().getValue()));
|
|
}
|
|
if (p.getStartdate() != null) {
|
|
metadata
|
|
.add(
|
|
XmlSerializationUtils.asXmlElement("startdate", p.getStartdate().getValue()));
|
|
}
|
|
if (p.getEnddate() != null) {
|
|
metadata.add(XmlSerializationUtils.asXmlElement("enddate", p.getEnddate().getValue()));
|
|
}
|
|
if (p.getCallidentifier() != null) {
|
|
metadata
|
|
.add(
|
|
XmlSerializationUtils
|
|
.asXmlElement(
|
|
"callidentifier", p.getCallidentifier().getValue()));
|
|
}
|
|
if (p.getKeywords() != null) {
|
|
metadata.add(XmlSerializationUtils.asXmlElement("keywords", p.getKeywords().getValue()));
|
|
}
|
|
if (p.getDuration() != null) {
|
|
metadata.add(XmlSerializationUtils.asXmlElement("duration", p.getDuration().getValue()));
|
|
}
|
|
if (p.getEcarticle29_3() != null) {
|
|
metadata
|
|
.add(
|
|
XmlSerializationUtils.asXmlElement("ecarticle29_3", p.getEcarticle29_3().getValue()));
|
|
}
|
|
if (p.getSubjects() != null) {
|
|
metadata
|
|
.addAll(
|
|
p
|
|
.getSubjects()
|
|
.stream()
|
|
.filter(Objects::nonNull)
|
|
.map(sp -> XmlSerializationUtils.mapStructuredProperty("subject", sp))
|
|
.collect(Collectors.toList()));
|
|
}
|
|
if (p.getContracttype() != null) {
|
|
metadata.add(XmlSerializationUtils.mapQualifier("contracttype", p.getContracttype()));
|
|
}
|
|
if (p.getOamandatepublications() != null) {
|
|
metadata
|
|
.add(
|
|
XmlSerializationUtils
|
|
.asXmlElement("oamandatepublications", p.getOamandatepublications().getValue()));
|
|
}
|
|
if (p.getEcsc39() != null) {
|
|
metadata.add(XmlSerializationUtils.asXmlElement("ecsc39", p.getEcsc39().getValue()));
|
|
}
|
|
if (p.getSummary() != null) {
|
|
metadata.add(XmlSerializationUtils.asXmlElement("summary", p.getSummary().getValue()));
|
|
}
|
|
if (p.getCurrency() != null) {
|
|
metadata.add(XmlSerializationUtils.asXmlElement("currency", p.getCurrency().getValue()));
|
|
}
|
|
if (p.getTotalcost() != null) {
|
|
metadata
|
|
.add(
|
|
XmlSerializationUtils.asXmlElement("totalcost", p.getTotalcost().toString()));
|
|
}
|
|
if (p.getFundedamount() != null) {
|
|
metadata
|
|
.add(
|
|
XmlSerializationUtils.asXmlElement("fundedamount", p.getFundedamount().toString()));
|
|
}
|
|
if (p.getFundingtree() != null) {
|
|
metadata
|
|
.addAll(
|
|
p
|
|
.getFundingtree()
|
|
.stream()
|
|
.filter(Objects::nonNull)
|
|
.map(ft -> ft.getValue())
|
|
.collect(Collectors.toList()));
|
|
}
|
|
|
|
break;
|
|
default:
|
|
throw new IllegalArgumentException("invalid entity type: " + type);
|
|
}
|
|
|
|
return metadata;
|
|
}
|
|
|
|
private String getAuthorPidType(String s) {
|
|
return XmlSerializationUtils
|
|
.escapeXml(s)
|
|
.replaceAll("\\W", "")
|
|
.replaceAll("\\d", "");
|
|
}
|
|
|
|
private static boolean kvNotBlank(KeyValue kv) {
|
|
return kv != null && StringUtils.isNotBlank(kv.getKey()) && StringUtils.isNotBlank(kv.getValue());
|
|
}
|
|
|
|
private void mapDatasourceType(List<String> metadata, final Qualifier dsType) {
|
|
metadata.add(XmlSerializationUtils.mapQualifier("datasourcetype", dsType));
|
|
|
|
if (specialDatasourceTypes.contains(dsType.getClassid())) {
|
|
dsType.setClassid("other");
|
|
dsType.setClassname("other");
|
|
}
|
|
metadata.add(XmlSerializationUtils.mapQualifier("datasourcetypeui", dsType));
|
|
}
|
|
|
|
private List<String> mapFields(RelatedEntityWrapper link, Set<String> contexts) {
|
|
final Relation rel = link.getRelation();
|
|
final RelatedEntity re = link.getTarget();
|
|
final String targetType = link.getTarget().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(XmlSerializationUtils.mapStructuredProperty("title", re.getTitle()));
|
|
}
|
|
if (isNotBlank(re.getDateofacceptance())) {
|
|
metadata
|
|
.add(
|
|
XmlSerializationUtils.asXmlElement("dateofacceptance", re.getDateofacceptance()));
|
|
}
|
|
if (isNotBlank(re.getPublisher())) {
|
|
metadata.add(XmlSerializationUtils.asXmlElement("publisher", re.getPublisher()));
|
|
}
|
|
if (isNotBlank(re.getCodeRepositoryUrl())) {
|
|
metadata
|
|
.add(
|
|
XmlSerializationUtils.asXmlElement("coderepositoryurl", re.getCodeRepositoryUrl()));
|
|
}
|
|
if (re.getResulttype() != null && re.getResulttype().isBlank()) {
|
|
metadata.add(XmlSerializationUtils.mapQualifier("resulttype", re.getResulttype()));
|
|
}
|
|
if (re.getCollectedfrom() != null) {
|
|
metadata
|
|
.addAll(
|
|
re
|
|
.getCollectedfrom()
|
|
.stream()
|
|
.filter(XmlRecordFactory::kvNotBlank)
|
|
.map(kv -> XmlSerializationUtils.mapKeyValue("collectedfrom", kv))
|
|
.collect(Collectors.toList()));
|
|
}
|
|
if (re.getPid() != null) {
|
|
metadata
|
|
.addAll(
|
|
re
|
|
.getPid()
|
|
.stream()
|
|
.map(p -> XmlSerializationUtils.mapStructuredProperty("pid", p))
|
|
.collect(Collectors.toList()));
|
|
}
|
|
break;
|
|
case datasource:
|
|
if (isNotBlank(re.getOfficialname())) {
|
|
metadata.add(XmlSerializationUtils.asXmlElement("officialname", re.getOfficialname()));
|
|
}
|
|
if (re.getDatasourcetype() != null && !re.getDatasourcetype().isBlank()) {
|
|
mapDatasourceType(metadata, re.getDatasourcetype());
|
|
}
|
|
if (re.getOpenairecompatibility() != null && !re.getOpenairecompatibility().isBlank()) {
|
|
metadata
|
|
.add(
|
|
XmlSerializationUtils
|
|
.mapQualifier(
|
|
"openairecompatibility", re.getOpenairecompatibility()));
|
|
}
|
|
break;
|
|
case organization:
|
|
if (isNotBlank(re.getLegalname())) {
|
|
metadata.add(XmlSerializationUtils.asXmlElement("legalname", re.getLegalname()));
|
|
}
|
|
if (isNotBlank(re.getLegalshortname())) {
|
|
metadata
|
|
.add(
|
|
XmlSerializationUtils.asXmlElement("legalshortname", re.getLegalshortname()));
|
|
}
|
|
if (re.getCountry() != null && !re.getCountry().isBlank()) {
|
|
metadata.add(XmlSerializationUtils.mapQualifier("country", re.getCountry()));
|
|
}
|
|
break;
|
|
case project:
|
|
if (isNotBlank(re.getProjectTitle())) {
|
|
metadata.add(XmlSerializationUtils.asXmlElement("title", re.getProjectTitle()));
|
|
}
|
|
if (isNotBlank(re.getCode())) {
|
|
metadata.add(XmlSerializationUtils.asXmlElement("code", re.getCode()));
|
|
}
|
|
if (isNotBlank(re.getAcronym())) {
|
|
metadata.add(XmlSerializationUtils.asXmlElement("acronym", re.getAcronym()));
|
|
}
|
|
if (re.getContracttype() != null && !re.getContracttype().isBlank()) {
|
|
metadata.add(XmlSerializationUtils.mapQualifier("contracttype", re.getContracttype()));
|
|
}
|
|
if (re.getFundingtree() != null && contexts != null) {
|
|
metadata
|
|
.addAll(
|
|
re
|
|
.getFundingtree()
|
|
.stream()
|
|
.peek(ft -> fillContextMap(ft, contexts))
|
|
.map(ft -> getRelFundingTree(ft))
|
|
.collect(Collectors.toList()));
|
|
}
|
|
break;
|
|
default:
|
|
throw new IllegalArgumentException("invalid target type: " + targetType);
|
|
}
|
|
|
|
final String accumulatorName = getRelDescriptor(rel.getRelType(), rel.getSubRelType(), rel.getRelClass());
|
|
if (accumulators.containsKey(accumulatorName)) {
|
|
accumulators.get(accumulatorName).add(1);
|
|
}
|
|
|
|
return metadata;
|
|
}
|
|
|
|
private String mapRelation(Set<String> contexts, TemplateFactory templateFactory, EntityType type,
|
|
RelatedEntityWrapper link) {
|
|
final Relation rel = link.getRelation();
|
|
final String targetType = link.getTarget().getType();
|
|
final String scheme = ModelSupport.getScheme(type.toString(), targetType);
|
|
|
|
if (StringUtils.isBlank(scheme)) {
|
|
throw new IllegalArgumentException(
|
|
String.format("missing scheme for: <%s - %s>", type.toString(), targetType));
|
|
}
|
|
final HashSet<String> fields = Sets.newHashSet(mapFields(link, contexts));
|
|
return templateFactory
|
|
.getRel(
|
|
targetType, rel.getTarget(), fields, rel.getRelClass(), scheme, rel.getDataInfo(), rel.getValidated(),
|
|
rel.getValidationDate());
|
|
}
|
|
|
|
private List<String> listChildren(
|
|
final OafEntity entity, JoinedEntity je, TemplateFactory templateFactory) {
|
|
|
|
final EntityType entityType = EntityType.fromClass(je.getEntity().getClass());
|
|
|
|
final List<RelatedEntityWrapper> links = je.getLinks();
|
|
List<String> children = links
|
|
.stream()
|
|
.filter(link -> isDuplicate(link))
|
|
.map(link -> {
|
|
final String targetType = link.getTarget().getType();
|
|
final String name = ModelSupport.getMainType(EntityType.valueOf(targetType));
|
|
final HashSet<String> fields = Sets.newHashSet(mapFields(link, null));
|
|
return templateFactory
|
|
.getChild(name, link.getTarget().getId(), Lists.newArrayList(fields));
|
|
})
|
|
.collect(Collectors.toCollection(ArrayList::new));
|
|
|
|
if (MainEntityType.result.toString().equals(ModelSupport.getMainType(entityType))) {
|
|
final List<Instance> instances = ((Result) entity).getInstance();
|
|
if (instances != null) {
|
|
for (final Instance instance : ((Result) entity).getInstance()) {
|
|
|
|
final List<String> fields = Lists.newArrayList();
|
|
|
|
if (instance.getAccessright() != null && !instance.getAccessright().isBlank()) {
|
|
fields
|
|
.add(
|
|
XmlSerializationUtils.mapQualifier("accessright", instance.getAccessright()));
|
|
}
|
|
if (instance.getCollectedfrom() != null && kvNotBlank(instance.getCollectedfrom())) {
|
|
fields
|
|
.add(
|
|
XmlSerializationUtils.mapKeyValue("collectedfrom", instance.getCollectedfrom()));
|
|
}
|
|
if (instance.getHostedby() != null && kvNotBlank(instance.getHostedby())) {
|
|
fields.add(XmlSerializationUtils.mapKeyValue("hostedby", instance.getHostedby()));
|
|
}
|
|
if (instance.getDateofacceptance() != null
|
|
&& isNotBlank(instance.getDateofacceptance().getValue())) {
|
|
fields
|
|
.add(
|
|
XmlSerializationUtils
|
|
.asXmlElement(
|
|
"dateofacceptance", instance.getDateofacceptance().getValue()));
|
|
}
|
|
if (instance.getInstancetype() != null && !instance.getInstancetype().isBlank()) {
|
|
fields
|
|
.add(
|
|
XmlSerializationUtils.mapQualifier("instancetype", instance.getInstancetype()));
|
|
}
|
|
if (isNotBlank(instance.getDistributionlocation())) {
|
|
fields
|
|
.add(
|
|
XmlSerializationUtils
|
|
.asXmlElement(
|
|
"distributionlocation", instance.getDistributionlocation()));
|
|
}
|
|
if (instance.getRefereed() != null && !instance.getRefereed().isBlank()) {
|
|
fields
|
|
.add(
|
|
XmlSerializationUtils.mapQualifier("refereed", instance.getRefereed()));
|
|
}
|
|
if (instance.getProcessingchargeamount() != null
|
|
&& isNotBlank(instance.getProcessingchargeamount().getValue())) {
|
|
fields
|
|
.add(
|
|
XmlSerializationUtils
|
|
.asXmlElement(
|
|
"processingchargeamount", instance.getProcessingchargeamount().getValue()));
|
|
}
|
|
if (instance.getProcessingchargecurrency() != null
|
|
&& isNotBlank(instance.getProcessingchargecurrency().getValue())) {
|
|
fields
|
|
.add(
|
|
XmlSerializationUtils
|
|
.asXmlElement(
|
|
"processingchargecurrency", instance.getProcessingchargecurrency().getValue()));
|
|
}
|
|
|
|
children
|
|
.add(
|
|
templateFactory
|
|
.getInstance(
|
|
instance.getHostedby().getKey(), fields, instance.getUrl()));
|
|
}
|
|
}
|
|
final List<ExternalReference> ext = ((Result) entity).getExternalReference();
|
|
if (ext != null) {
|
|
for (final ExternalReference er : ((Result) entity).getExternalReference()) {
|
|
|
|
final List<String> fields = Lists.newArrayList();
|
|
|
|
if (isNotBlank(er.getSitename())) {
|
|
fields.add(XmlSerializationUtils.asXmlElement("sitename", er.getSitename()));
|
|
}
|
|
if (isNotBlank(er.getLabel())) {
|
|
fields.add(XmlSerializationUtils.asXmlElement("label", er.getLabel()));
|
|
}
|
|
if (isNotBlank(er.getUrl())) {
|
|
fields.add(XmlSerializationUtils.asXmlElement("url", er.getUrl()));
|
|
}
|
|
if (isNotBlank(er.getDescription())) {
|
|
fields.add(XmlSerializationUtils.asXmlElement("description", er.getDescription()));
|
|
}
|
|
if (isNotBlank(er.getUrl())) {
|
|
fields.add(XmlSerializationUtils.mapQualifier("qualifier", er.getQualifier()));
|
|
}
|
|
if (isNotBlank(er.getRefidentifier())) {
|
|
fields.add(XmlSerializationUtils.asXmlElement("refidentifier", er.getRefidentifier()));
|
|
}
|
|
if (isNotBlank(er.getQuery())) {
|
|
fields.add(XmlSerializationUtils.asXmlElement("query", er.getQuery()));
|
|
}
|
|
|
|
children.add(templateFactory.getChild("externalreference", null, fields));
|
|
}
|
|
}
|
|
}
|
|
|
|
return children;
|
|
}
|
|
|
|
private boolean isDuplicate(RelatedEntityWrapper link) {
|
|
return REL_SUBTYPE_DEDUP.equalsIgnoreCase(link.getRelation().getSubRelType());
|
|
}
|
|
|
|
private List<String> listExtraInfo(OafEntity entity) {
|
|
final List<ExtraInfo> extraInfo = entity.getExtraInfo();
|
|
return extraInfo != null
|
|
? extraInfo
|
|
.stream()
|
|
.map(e -> XmlSerializationUtils.mapExtraInfo(e))
|
|
.collect(Collectors.toList())
|
|
: Lists.newArrayList();
|
|
}
|
|
|
|
private List<String> buildContexts(final String type, final Set<String> contexts) {
|
|
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 : contexts) {
|
|
|
|
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, final Set<String> contexts) {
|
|
|
|
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");
|
|
contexts.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) {
|
|
contexts.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) {
|
|
contexts.add(level1Id);
|
|
} else {
|
|
final String level2Id = Joiner.on("::").join(level1Id, level2.valueOf("./name"));
|
|
contextMapper
|
|
.put(
|
|
level2Id,
|
|
new ContextDef(level2Id, level2.valueOf("./description"), "concept", ""));
|
|
contexts.add(level2Id);
|
|
}
|
|
}
|
|
}
|
|
}
|
|
} catch (final NullPointerException e) {
|
|
throw new IllegalArgumentException("malformed funding path: " + xmlTree, e);
|
|
}
|
|
}
|
|
|
|
@SuppressWarnings("unchecked")
|
|
protected static 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=\""
|
|
+ XmlSerializationUtils.escapeXml(e.valueOf("./name"))
|
|
+ "\">"
|
|
+ XmlSerializationUtils.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 static String getFunderElement(final Document ftree) {
|
|
final String funderId = ftree.valueOf("//fundingtree/funder/id");
|
|
final String funderShortName = ftree.valueOf("//fundingtree/funder/shortname");
|
|
final String funderName = ftree.valueOf("//fundingtree/funder/name");
|
|
final String funderJurisdiction = ftree.valueOf("//fundingtree/funder/jurisdiction");
|
|
|
|
return "<funder id=\""
|
|
+ XmlSerializationUtils.escapeXml(funderId)
|
|
+ "\" shortname=\""
|
|
+ XmlSerializationUtils.escapeXml(funderShortName)
|
|
+ "\" name=\""
|
|
+ XmlSerializationUtils.escapeXml(funderName)
|
|
+ "\" jurisdiction=\""
|
|
+ XmlSerializationUtils.escapeXml(funderJurisdiction)
|
|
+ "\" />";
|
|
}
|
|
}
|