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package eu.dnetlib.data.mapreduce.util;
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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.Map;
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import java.util.Map.Entry;
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import java.util.Set;
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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 com.google.common.base.Joiner;
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import com.google.common.base.Predicate;
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import com.google.common.base.Splitter;
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import com.google.common.collect.Iterables;
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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.google.protobuf.Descriptors.EnumValueDescriptor;
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import com.google.protobuf.Descriptors.FieldDescriptor;
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import com.google.protobuf.GeneratedMessage;
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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.data.mapreduce.hbase.index.config.*;
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import eu.dnetlib.data.proto.FieldTypeProtos.*;
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import eu.dnetlib.data.proto.OafProtos.OafEntity;
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import eu.dnetlib.data.proto.OafProtos.OafRel;
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import eu.dnetlib.data.proto.PersonProtos.Person;
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import eu.dnetlib.data.proto.ProjectProtos.Project;
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import eu.dnetlib.data.proto.RelMetadataProtos.RelMetadata;
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import eu.dnetlib.data.proto.ResultProtos.Result;
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import eu.dnetlib.data.proto.ResultProtos.Result.Context;
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import eu.dnetlib.data.proto.ResultProtos.Result.ExternalReference;
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import eu.dnetlib.data.proto.ResultProtos.Result.Instance;
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import eu.dnetlib.data.proto.ResultProtos.Result.Journal;
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import eu.dnetlib.data.proto.TypeProtos;
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import eu.dnetlib.data.proto.TypeProtos.Type;
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import eu.dnetlib.miscutils.functional.UnaryFunction;
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import org.apache.commons.lang.StringUtils;
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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.SAXReader;
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import static eu.dnetlib.miscutils.collections.MappedCollection.listMap;
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public class XmlRecordFactory {
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// private static final Log log = LogFactory.getLog(XmlRecordFactory.class); // NOPMD by marko on 11/24/08 5:02 PM
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private final Map<String, Integer> relCounters = Maps.newHashMap();
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protected Set<String> specialDatasourceTypes;
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protected TemplateFactory templateFactory = new TemplateFactory();
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protected OafDecoder mainEntity = null;
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protected String key = null;
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protected List<OafDecoder> relations = Lists.newLinkedList();
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protected List<OafDecoder> children = Lists.newLinkedList();
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protected EntityConfigTable entityConfigTable;
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protected ContextMapper contextMapper;
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protected RelClasses relClasses;
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protected String schemaLocation;
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protected boolean entityDefaults;
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protected boolean relDefaults;
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protected boolean childDefaults;
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protected Set<String> contextes = Sets.newHashSet();
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protected List<String> extraInfo = Lists.newArrayList();
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protected Map<String, Integer> counters = Maps.newHashMap();
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protected Transformer transformer;
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protected static Predicate<String> instanceFilter = new Predicate<String>() {
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final Set<String> instanceFieldFilter = Sets.newHashSet("instancetype", "hostedby", "licence");
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@Override
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public boolean apply(final String s) {
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return instanceFieldFilter.contains(s);
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}
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};
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public XmlRecordFactory(final EntityConfigTable entityConfigTable, final ContextMapper contextMapper, final RelClasses relClasses,
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final String schemaLocation, final boolean entityDefaults, final boolean relDefaults, final boolean childDefeaults, final Set<String> otherDatasourceTypesUForUI)
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throws TransformerConfigurationException, TransformerFactoryConfigurationError {
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this.entityConfigTable = entityConfigTable;
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this.contextMapper = contextMapper;
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this.relClasses = relClasses;
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this.schemaLocation = schemaLocation;
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this.entityDefaults = entityDefaults;
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this.relDefaults = relDefaults;
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this.childDefaults = childDefeaults;
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this.specialDatasourceTypes = otherDatasourceTypesUForUI;
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transformer = TransformerFactory.newInstance().newTransformer();
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transformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
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}
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public static String removePrefix(final String s) {
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if (s.contains("|")) return StringUtils.substringAfter(s, "|");
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return s;
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}
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public static String escapeXml(final String value) {
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return value.replaceAll("&", "&").replaceAll("<", "<").replaceAll(">", ">").replaceAll("\"", """).replaceAll("'", "'");
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}
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public Map<String, Integer> getRelCounters() {
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return relCounters;
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}
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public RelClasses getRelClasses() {
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return relClasses;
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}
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public String getId() {
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return key;
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}
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public boolean isValid() {
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return mainEntity != null;
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}
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public void setMainEntity(final OafDecoder mainEntity) {
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this.mainEntity = mainEntity;
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this.key = mainEntity.decodeEntity().getId();
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}
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public void addRelation(final Type type, final OafDecoder rel) {
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addRelOrChild(type, relations, rel);
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}
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public void addChild(final Type type, final OafDecoder child) {
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addRelOrChild(type, children, child);
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}
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private void addRelOrChild(final Type type, final List<OafDecoder> list, final OafDecoder decoder) {
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final OafRel oafRel = decoder.getOafRel();
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final String rd = oafRel.getRelType().toString() + "_" + oafRel.getSubRelType() + "_" + relClasses.getInverse(oafRel.getRelClass());
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final LinkDescriptor ld = entityConfigTable.getDescriptor(type, new RelDescriptor(rd));
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if (getRelCounters().get(rd) == null) {
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getRelCounters().put(rd, 0);
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}
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if (ld == null) {
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list.add(decoder);
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return;
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}
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if (ld.getMax() < 0) {
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list.add(decoder);
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return;
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}
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if (getRelCounters().get(rd) < ld.getMax()) {
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getRelCounters().put(rd, getRelCounters().get(rd) + 1);
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list.add(decoder);
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}
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}
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public String build() {
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try {
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final OafEntityDecoder entity = mainEntity.decodeEntity();
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// log.info("building");
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// log.info("main: " + mainEntity);
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// log.info("rel: " + relations);
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// log.info("chi: " + children);
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// log.info("=============");
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final Predicate<String> filter = entityConfigTable.getFilter(entity.getType());
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final List<String> metadata = decodeType(entity, filter, entityDefaults, false);
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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> rels = listRelations();
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metadata.addAll(buildContexts(entity.getType()));
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metadata.add(parseDataInfo(mainEntity));
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final String body = templateFactory.buildBody(entity.getType(), metadata, rels, listChildren(), extraInfo);
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return templateFactory
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.buildRecord(key, entity.getDateOfCollection(), entity.getDateOfTransformation(), schemaLocation, body, countersAsXml());
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} catch (final Throwable e) {
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throw new RuntimeException(String.format("error building record '%s'", this.key), e);
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}
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}
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private String parseDataInfo(final OafDecoder decoder) {
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final DataInfo dataInfo = decoder.getOaf().getDataInfo();
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final StringBuilder sb = new StringBuilder();
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sb.append("<datainfo>");
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sb.append(asXmlElement("inferred", dataInfo.getInferred() + "", null, null));
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sb.append(asXmlElement("deletedbyinference", dataInfo.getDeletedbyinference() + "", null, null));
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sb.append(asXmlElement("trust", dataInfo.getTrust() + "", null, null));
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sb.append(asXmlElement("inferenceprovenance", dataInfo.getInferenceprovenance() + "", null, null));
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sb.append(asXmlElement("provenanceaction", null, dataInfo.getProvenanceaction(), null));
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sb.append("</datainfo>");
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return sb.toString();
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}
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private List<String> decodeType(final OafEntityDecoder decoder, final Predicate<String> filter, final boolean defaults, final boolean expandingRel) {
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final List<String> metadata = Lists.newArrayList();
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metadata.addAll(listFields(decoder.getMetadata(), filter, defaults, expandingRel));
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metadata.addAll(listFields(decoder.getOafEntity(), filter, defaults, expandingRel));
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if ((decoder.getEntity() instanceof Result) && !expandingRel) {
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metadata.add(asXmlElement("bestlicense", "", getBestLicense(), null));
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metadata.addAll(listFields(decoder.getEntity(), filter, defaults, expandingRel));
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}
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if ((decoder.getEntity() instanceof Person) && !expandingRel) {
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metadata.addAll(listFields(decoder.getEntity(), filter, defaults, expandingRel));
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}
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if ((decoder.getEntity() instanceof Project) && !expandingRel) {
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metadata.addAll(listFields(decoder.getEntity(), filter, defaults, expandingRel));
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}
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return metadata;
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}
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private Qualifier getBestLicense() {
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Qualifier bestLicense = getQualifier("UNKNOWN", "not available", "dnet:access_modes");
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final LicenseComparator lc = new LicenseComparator();
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for (final Instance instance : ((Result) mainEntity.decodeEntity().getEntity()).getInstanceList()) {
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if (lc.compare(bestLicense, instance.getLicence()) > 0) {
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bestLicense = instance.getLicence();
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}
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}
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return bestLicense;
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}
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public Qualifier getQualifier(final String classid, final String classname, final String schemename) {
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return Qualifier.newBuilder().setClassid(classid).setClassname(classname).setSchemeid(schemename).setSchemename(schemename).build();
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}
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private List<String> listRelations() {
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final List<String> rels = Lists.newArrayList();
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for (final OafDecoder decoder : this.relations) {
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final OafRel rel = decoder.getOafRel();
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final OafEntity cachedTarget = rel.getCachedTarget();
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final OafRelDecoder relDecoder = OafRelDecoder.decode(rel);
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// if (!relDecoder.getRelType().equals(RelType.personResult) || relDecoder.getRelTargetId().equals(key)) {
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if (relDecoder.getRelSourceId().equals(key) || relDecoder.getRelTargetId().equals(key)) {
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250
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final List<String> metadata = Lists.newArrayList();
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final TypeProtos.Type targetType = relDecoder.getTargetType(mainEntity.getEntity().getType());
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//final Set<String> relFilter = entityConfigTable.getFilter(targetType, relDecoder.getRelDescriptor());
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metadata.addAll(listFields(relDecoder.getSubRel(), entityConfigTable.getIncludeFilter(targetType, relDecoder.getRelDescriptor()), false, true));
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String semanticclass = "";
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String semanticscheme = "";
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257
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258
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final RelDescriptor relDescriptor = relDecoder.getRelDescriptor();
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259
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260
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if ((cachedTarget != null) && cachedTarget.isInitialized()) {
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262
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//final Set<String> filter = entityConfigTable.getFilter(targetType, relDescriptor);
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final OafEntityDecoder d = OafEntityDecoder.decode(cachedTarget);
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metadata.addAll(decodeType(d, entityConfigTable.getIncludeFilter(targetType, relDescriptor), relDefaults, true));
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if (d.getType().equals(Type.result)) {
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for(Instance i : cachedTarget.getResult().getInstanceList()) {
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metadata.addAll(listFields(i, entityConfigTable.getIncludeFilter(targetType, relDecoder.getRelDescriptor()), false, true));
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}
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}
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}
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271
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272
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final RelMetadata relMetadata = relDecoder.getRelMetadata();
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// debug
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if (relMetadata == null) {
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// System.err.println(this);
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semanticclass = semanticscheme = "UNKNOWN";
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} else {
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semanticclass = relClasses.getInverse(relMetadata.getSemantics().getClassname());
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semanticscheme = relMetadata.getSemantics().getSchemename();
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}
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281
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282
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final String rd = relDescriptor.getSubRelType().toString();
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incrementCounter(rd);
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284
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285
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final DataInfo info = decoder.getOaf().getDataInfo();
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286
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if (info.getInferred()) {
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incrementCounter(rd + "_inferred");
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288
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} else if(StringUtils.startsWith(info.getProvenanceaction().getClassid(), "sysimport:crosswalk")) {
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incrementCounter(rd + "_collected");
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} else if(StringUtils.startsWith(info.getProvenanceaction().getClassid(), "user:")) {
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291
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incrementCounter(rd + "_claimed");
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292
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}
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293
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294
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final LinkDescriptor ld = entityConfigTable.getDescriptor(relDecoder.getTargetType(mainEntity.getEntity().getType()), relDescriptor);
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295
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296
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final String relId = (ld != null) && !ld.isSymmetric() ? relDecoder.getRelTargetId() : relDecoder.getRelSourceId();
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297
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298
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rels.add(templateFactory.getRel(targetType, relId, metadata, semanticclass, semanticscheme, info.getInferred(), info.getTrust(),
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299
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info.getInferenceprovenance(), info.getProvenanceaction().getClassid()));
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300
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}
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301
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}
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302
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return rels;
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303
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}
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304
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305
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// //////////////////////////////////
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306
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307
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private List<String> listChildren() {
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308
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309
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final List<String> children = Lists.newArrayList();
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310
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for (final OafDecoder decoder : this.children) {
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311
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final OafEntity cachedTarget = decoder.getOafRel().getCachedTarget();
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312
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addChildren(children, cachedTarget, decoder.getRelDescriptor());
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313
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}
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314
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final OafEntityDecoder entity = mainEntity.decodeEntity();
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315
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if (entity.getType().equals(Type.result)) {
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316
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for (final Instance instance : ((Result) entity.getEntity()).getInstanceList()) {
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317
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318
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319
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children.add(templateFactory.getInstance(instance.getHostedby().getKey(), listFields(instance, instanceFilter, false, false),
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320
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listMap(instance.getUrlList(), new UnaryFunction<String, String>() {
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321
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322
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@Override
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323
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public String evaluate(final String identifier) {
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324
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return templateFactory.getWebResource(identifier);
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325
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}
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326
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})));
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327
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}
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328
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for (final ExternalReference er : ((Result) entity.getEntity()).getExternalReferenceList()) {
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329
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// Set<String> filters = entityConfigTable.getFilter(Type.result, RelType.resultResult);
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330
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final List<String> fields = listFields(er, null, false, false);
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331
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children.add(templateFactory.getChild("externalreference", null, fields));
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332
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}
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333
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}
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334
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335
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return children;
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336
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}
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337
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338
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private void addChildren(final List<String> children, final OafEntity target, final RelDescriptor relDescriptor) {
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339
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final OafEntityDecoder decoder = OafEntityDecoder.decode(target);
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340
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incrementCounter(relDescriptor.getSubRelType().toString());
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341
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final Predicate<String> filter = entityConfigTable.getIncludeFilter(target.getType(), relDescriptor);
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342
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children.add(templateFactory.getChild(decoder.getType().toString(), decoder.getId(), listFields(decoder.getMetadata(), filter, childDefaults, false)));
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343
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}
|
|
344
|
|
|
345
|
private List<String> listFields(final GeneratedMessage fields, final Predicate<String> filter, final boolean defaults, final boolean expandingRel) {
|
|
346
|
|
|
347
|
final List<String> metadata = Lists.newArrayList();
|
|
348
|
|
|
349
|
if (fields != null) {
|
|
350
|
|
|
351
|
final Set<String> seen = Sets.newHashSet();
|
|
352
|
|
|
353
|
final Map<FieldDescriptor, Object> filtered = filterFields(fields, filter);
|
|
354
|
for (final Entry<FieldDescriptor, Object> e : filtered.entrySet()) {
|
|
355
|
|
|
356
|
final String name = e.getKey().getName();
|
|
357
|
seen.add(name);
|
|
358
|
addFieldValue(metadata, e.getKey(), e.getValue(), expandingRel);
|
|
359
|
}
|
|
360
|
|
|
361
|
if (defaults) {
|
|
362
|
final Iterable<FieldDescriptor> unseen = Iterables.filter(fields.getDescriptorForType().getFields(), new Predicate<FieldDescriptor>() {
|
|
363
|
@Override
|
|
364
|
public boolean apply(final FieldDescriptor fd) {
|
|
365
|
return !seen.contains(fd.getName()) && filter.apply(fd.getName());
|
|
366
|
}
|
|
367
|
});
|
|
368
|
for(FieldDescriptor fd : unseen){
|
|
369
|
addFieldValue(metadata, fd, getDefault(fd), expandingRel);
|
|
370
|
}
|
|
371
|
}
|
|
372
|
}
|
|
373
|
return metadata;
|
|
374
|
}
|
|
375
|
|
|
376
|
private Object getDefault(final FieldDescriptor fd) {
|
|
377
|
switch (fd.getType()) {
|
|
378
|
case BOOL:
|
|
379
|
return false;
|
|
380
|
case BYTES:
|
|
381
|
return "".getBytes();
|
|
382
|
case MESSAGE: {
|
|
383
|
if (Qualifier.getDescriptor().equals(fd.getMessageType())) return defaultQualifier();
|
|
384
|
if (StructuredProperty.getDescriptor().equals(fd.getMessageType()))
|
|
385
|
return StructuredProperty.newBuilder().setValue("").setQualifier(defaultQualifier()).build();
|
|
386
|
if (KeyValue.getDescriptor().equals(fd.getMessageType())) return KeyValue.newBuilder().setKey("").setValue("").build();
|
|
387
|
if (StringField.getDescriptor().equals(fd.getMessageType())) return StringField.newBuilder().setValue("").build();
|
|
388
|
if (BoolField.getDescriptor().equals(fd.getMessageType())) return BoolField.newBuilder().buildPartial();
|
|
389
|
return null;
|
|
390
|
}
|
|
391
|
case SFIXED32:
|
|
392
|
case SFIXED64:
|
|
393
|
case SINT32:
|
|
394
|
case SINT64:
|
|
395
|
case INT32:
|
|
396
|
case INT64:
|
|
397
|
case DOUBLE:
|
|
398
|
case FIXED32:
|
|
399
|
case FIXED64:
|
|
400
|
case FLOAT:
|
|
401
|
return 0;
|
|
402
|
case STRING:
|
|
403
|
return "";
|
|
404
|
default:
|
|
405
|
return null;
|
|
406
|
}
|
|
407
|
}
|
|
408
|
|
|
409
|
private Qualifier defaultQualifier() {
|
|
410
|
return Qualifier.newBuilder().setClassid("").setClassname("").setSchemeid("").setSchemename("").build();
|
|
411
|
}
|
|
412
|
|
|
413
|
@SuppressWarnings("unchecked")
|
|
414
|
private void addFieldValue(final List<String> metadata, final FieldDescriptor fd, final Object value, final boolean expandingRel) {
|
|
415
|
if ("dateofcollection".equals(fd.getName()) ||
|
|
416
|
"dateoftransformation".equals(fd.getName()) ||
|
|
417
|
"id".equals(fd.getName()) ||
|
|
418
|
(value == null)) return;
|
|
419
|
|
|
420
|
if (fd.getName().equals("datasourcetype")) {
|
|
421
|
final String classid = ((Qualifier) value).getClassid();
|
|
422
|
|
|
423
|
final Qualifier.Builder q = Qualifier.newBuilder((Qualifier) value);
|
|
424
|
if (specialDatasourceTypes.contains(classid)) {
|
|
425
|
q.setClassid("other").setClassname("other");
|
|
426
|
}
|
|
427
|
metadata.add(asXmlElement("datasourcetypeui", "", q.build(), null));
|
|
428
|
}
|
|
429
|
|
|
430
|
if (fd.isRepeated() && (value instanceof List<?>)) {
|
|
431
|
for (final Object o : (List<Object>) value) {
|
|
432
|
guessType(metadata, fd, o, expandingRel);
|
|
433
|
}
|
|
434
|
} else {
|
|
435
|
guessType(metadata, fd, value, expandingRel);
|
|
436
|
}
|
|
437
|
}
|
|
438
|
|
|
439
|
private void guessType(final List<String> metadata, final FieldDescriptor fd, final Object o, final boolean expandingRel) {
|
|
440
|
|
|
441
|
if (fd.getType().equals(FieldDescriptor.Type.MESSAGE)) {
|
|
442
|
|
|
443
|
if (Qualifier.getDescriptor().equals(fd.getMessageType())) {
|
|
444
|
final Qualifier qualifier = (Qualifier) o;
|
|
445
|
metadata.add(asXmlElement(fd.getName(), "", qualifier, null));
|
|
446
|
}
|
|
447
|
|
|
448
|
if (StructuredProperty.getDescriptor().equals(fd.getMessageType())) {
|
|
449
|
final StructuredProperty sp = (StructuredProperty) o;
|
|
450
|
metadata.add(asXmlElement(fd.getName(), sp.getValue(), sp.getQualifier(), sp.hasDataInfo() ? sp.getDataInfo() : null));
|
|
451
|
|
|
452
|
if (!expandingRel && fd.getName().equals("pid")) {
|
|
453
|
if (sp.getQualifier().getClassid().equalsIgnoreCase("doi")) {
|
|
454
|
incrementCounter("doi");
|
|
455
|
}
|
|
456
|
}
|
|
457
|
}
|
|
458
|
|
|
459
|
if (KeyValue.getDescriptor().equals(fd.getMessageType())) {
|
|
460
|
final KeyValue kv = (KeyValue) o;
|
|
461
|
metadata.add("<" + fd.getName() + " name=\"" + escapeXml(kv.getValue()) + "\" id=\"" + escapeXml(removePrefix(kv.getKey())) + "\"/>");
|
|
462
|
}
|
|
463
|
|
|
464
|
if (StringField.getDescriptor().equals(fd.getMessageType())) {
|
|
465
|
final String fieldName = fd.getName();
|
|
466
|
|
|
467
|
if (fieldName.equals("fundingtree")) {
|
|
468
|
final String xmlTree = o instanceof StringField ? ((StringField) o).getValue() : o.toString();
|
|
469
|
|
|
470
|
if (expandingRel) {
|
|
471
|
metadata.add(getRelFundingTree(xmlTree));
|
|
472
|
fillContextMap(xmlTree);
|
|
473
|
} else {
|
|
474
|
metadata.add(xmlTree);
|
|
475
|
}
|
|
476
|
} else {
|
|
477
|
final StringField sf = (StringField) o;
|
|
478
|
final StringBuilder sb = new StringBuilder("<" + fd.getName());
|
|
479
|
if (sf.hasDataInfo()) {
|
|
480
|
final DataInfo dataInfo = sf.getDataInfo();
|
|
481
|
dataInfoAsAttributes(sb, dataInfo);
|
|
482
|
}
|
|
483
|
sb.append(">" + escapeXml(sf.getValue()) + "</" + fd.getName() + ">");
|
|
484
|
metadata.add(sb.toString());
|
|
485
|
}
|
|
486
|
}
|
|
487
|
|
|
488
|
if (BoolField.getDescriptor().equals(fd.getMessageType())) {
|
|
489
|
final BoolField bf = (BoolField) o;
|
|
490
|
final StringBuilder sb = new StringBuilder("<" + fd.getName());
|
|
491
|
if (bf.hasDataInfo()) {
|
|
492
|
final DataInfo dataInfo = bf.getDataInfo();
|
|
493
|
dataInfoAsAttributes(sb, dataInfo);
|
|
494
|
}
|
|
495
|
|
|
496
|
sb.append(">" + (bf.hasValue() ? bf.getValue() : "") + "</" + fd.getName() + ">");
|
|
497
|
metadata.add(sb.toString());
|
|
498
|
}
|
|
499
|
|
|
500
|
if (Journal.getDescriptor().equals(fd.getMessageType()) && (o != null)) {
|
|
501
|
final Journal j = (Journal) o;
|
|
502
|
metadata.add("<journal " + "issn=\"" + escapeXml(j.getIssnPrinted()) + "\" " + "eissn=\"" + escapeXml(j.getIssnOnline()) + "\" " + "lissn=\""
|
|
503
|
+ escapeXml(j.getIssnLinking()) + "\" " + "ep=\"" + escapeXml(j.getEp()) + "\" " + "iss=\"" + escapeXml(j.getIss()) + "\" " + "sp=\""
|
|
504
|
+ escapeXml(j.getSp()) + "\" " + "vol=\"" + escapeXml(j.getVol()) + "\">" + escapeXml(j.getName()) + "</journal>");
|
|
505
|
}
|
|
506
|
|
|
507
|
if (Context.getDescriptor().equals(fd.getMessageType()) && (o != null)) {
|
|
508
|
contextes.add(((Result.Context) o).getId());
|
|
509
|
}
|
|
510
|
|
|
511
|
if (ExtraInfo.getDescriptor().equals(fd.getMessageType()) && (o != null)) {
|
|
512
|
|
|
513
|
final ExtraInfo e = (ExtraInfo) o;
|
|
514
|
final StringBuilder sb = new StringBuilder("<" + fd.getName() + " ");
|
|
515
|
|
|
516
|
sb.append("name=\"" + e.getName() + "\" ");
|
|
517
|
sb.append("typology=\"" + e.getTypology() + "\" ");
|
|
518
|
sb.append("provenance=\"" + e.getProvenance() + "\" ");
|
|
519
|
sb.append("trust=\"" + e.getTrust() + "\"");
|
|
520
|
sb.append(">");
|
|
521
|
sb.append(e.getValue());
|
|
522
|
sb.append("</" + fd.getName() + ">");
|
|
523
|
|
|
524
|
extraInfo.add(sb.toString());
|
|
525
|
}
|
|
526
|
|
|
527
|
} else if (fd.getType().equals(FieldDescriptor.Type.ENUM)) {
|
|
528
|
if (fd.getFullName().equals("eu.dnetlib.data.proto.OafEntity.type")) return;
|
|
529
|
metadata.add(asXmlElement(fd.getName(), ((EnumValueDescriptor) o).getName(), null, null));
|
|
530
|
} else {
|
|
531
|
metadata.add(asXmlElement(fd.getName(), o.toString(), null, null));
|
|
532
|
}
|
|
533
|
}
|
|
534
|
|
|
535
|
private StringBuilder dataInfoAsAttributes(final StringBuilder sb, final DataInfo dataInfo) {
|
|
536
|
sb.append(" inferred=\"" + dataInfo.getInferred() + "\"");
|
|
537
|
sb.append(" inferenceprovenance=\"" + dataInfo.getInferenceprovenance() + "\"");
|
|
538
|
sb.append(" provenanceaction=\"" + dataInfo.getProvenanceaction().getClassid() + "\"");
|
|
539
|
sb.append(" trust=\"" + dataInfo.getTrust() + "\" ");
|
|
540
|
return sb;
|
|
541
|
}
|
|
542
|
|
|
543
|
private List<String> buildContexts(final Type type) {
|
|
544
|
final List<String> res = Lists.newArrayList();
|
|
545
|
|
|
546
|
if ((contextMapper != null) && !contextMapper.isEmpty() && type.equals(Type.result)) {
|
|
547
|
|
|
548
|
XMLTag document = XMLDoc.newDocument(true).addRoot("contextRoot");
|
|
549
|
|
|
550
|
for (final String context : contextes) {
|
|
551
|
|
|
552
|
String id = "";
|
|
553
|
for (final String token : Splitter.on("::").split(context)) {
|
|
554
|
id += token;
|
|
555
|
|
|
556
|
final ContextDef def = contextMapper.get(id);
|
|
557
|
|
|
558
|
if (def == null) throw new IllegalStateException(String.format("cannot find context for id '%s'", id));
|
|
559
|
|
|
560
|
if (def.getName().equals("context")) {
|
|
561
|
final String xpath = "//context/@id='" + def.getId() + "'";
|
|
562
|
if (!document.gotoRoot().rawXpathBoolean(xpath, new Object())) {
|
|
563
|
document = addContextDef(document.gotoRoot(), def);
|
|
564
|
}
|
|
565
|
}
|
|
566
|
|
|
567
|
if (def.getName().equals("category")) {
|
|
568
|
final String rootId = StringUtils.substringBefore(def.getId(), "::");
|
|
569
|
document = addContextDef(document.gotoRoot().gotoTag("//context[./@id='" + rootId + "']", new Object()), def);
|
|
570
|
}
|
|
571
|
|
|
572
|
if (def.getName().equals("concept")) {
|
|
573
|
document = addContextDef(document, def).gotoParent();
|
|
574
|
}
|
|
575
|
id += "::";
|
|
576
|
}
|
|
577
|
}
|
|
578
|
|
|
579
|
for (final org.w3c.dom.Element x : document.gotoRoot().getChildElement()) {
|
|
580
|
try {
|
|
581
|
res.add(asStringElement(x));
|
|
582
|
} catch (final TransformerException e) {
|
|
583
|
throw new RuntimeException(e);
|
|
584
|
}
|
|
585
|
}
|
|
586
|
}
|
|
587
|
|
|
588
|
return res;
|
|
589
|
}
|
|
590
|
|
|
591
|
private XMLTag addContextDef(final XMLTag tag, final ContextDef def) {
|
|
592
|
tag.addTag(def.getName()).addAttribute("id", def.getId()).addAttribute("label", def.getLabel());
|
|
593
|
if ((def.getType() != null) && !def.getType().isEmpty()) {
|
|
594
|
tag.addAttribute("type", def.getType());
|
|
595
|
}
|
|
596
|
return tag;
|
|
597
|
}
|
|
598
|
|
|
599
|
private String asStringElement(final org.w3c.dom.Element element) throws TransformerException {
|
|
600
|
final StringWriter buffer = new StringWriter();
|
|
601
|
transformer.transform(new DOMSource(element), new StreamResult(buffer));
|
|
602
|
return buffer.toString();
|
|
603
|
}
|
|
604
|
|
|
605
|
@SuppressWarnings("unchecked")
|
|
606
|
private String getRelFundingTree(final String xmlTree) {
|
|
607
|
String funding = "<funding>";
|
|
608
|
try {
|
|
609
|
final Document ftree = new SAXReader().read(new StringReader(xmlTree));
|
|
610
|
funding = "<funding>";
|
|
611
|
// String _id = "";
|
|
612
|
|
|
613
|
funding += getFunderElement(ftree);
|
|
614
|
|
|
615
|
for (final Object o : Lists.reverse(ftree.selectNodes("//fundingtree//*[starts-with(local-name(),'funding_level_')]"))) {
|
|
616
|
final Element e = (Element) o;
|
|
617
|
final String _id = e.valueOf("./id");
|
|
618
|
funding += "<" + e.getName() + " name=\"" + escapeXml(e.valueOf("./name")) + "\">" + escapeXml(_id) + "</" + e.getName() + ">";
|
|
619
|
// _id += "::";
|
|
620
|
}
|
|
621
|
} catch (final DocumentException e) {
|
|
622
|
throw new IllegalArgumentException("unable to parse funding tree: " + xmlTree + "\n" + e.getMessage());
|
|
623
|
} finally {
|
|
624
|
funding += "</funding>";
|
|
625
|
}
|
|
626
|
return funding;
|
|
627
|
}
|
|
628
|
|
|
629
|
private String getFunderElement(final Document ftree) {
|
|
630
|
final String funderId = ftree.valueOf("//fundingtree/funder/id/text()");
|
|
631
|
final String funderShortName = ftree.valueOf("//fundingtree/funder/shortname/text()");
|
|
632
|
final String funderName = ftree.valueOf("//fundingtree/funder/name/text()");
|
|
633
|
final String funderJurisdiction = ftree.valueOf("//fundingtree/funder/jurisdiction/text()");
|
|
634
|
|
|
635
|
return "<funder id=\"" + escapeXml(funderId) + "\" shortname=\"" + escapeXml(funderShortName) + "\" name=\"" + escapeXml(funderName)
|
|
636
|
+ "\" jurisdiction=\"" + escapeXml(funderJurisdiction) + "\" />";
|
|
637
|
}
|
|
638
|
|
|
639
|
private void fillContextMap(final String xmlTree) {
|
|
640
|
|
|
641
|
Document fundingPath;
|
|
642
|
try {
|
|
643
|
fundingPath = new SAXReader().read(new StringReader(xmlTree));
|
|
644
|
} catch (final DocumentException e) {
|
|
645
|
throw new RuntimeException(e);
|
|
646
|
}
|
|
647
|
try {
|
|
648
|
final Node funder = fundingPath.selectSingleNode("//funder");
|
|
649
|
|
|
650
|
if (funder != null) {
|
|
651
|
|
|
652
|
final String funderShortName = funder.valueOf("./shortname");
|
|
653
|
contextes.add(funderShortName);
|
|
654
|
|
|
655
|
contextMapper.put(funderShortName, new ContextDef(funderShortName, funder.valueOf("./name"), "context", "funding"));
|
|
656
|
final Node level0 = fundingPath.selectSingleNode("//funding_level_0");
|
|
657
|
if (level0 != null) {
|
|
658
|
final String level0Id = Joiner.on("::").join(funderShortName, level0.valueOf("./name"));
|
|
659
|
contextMapper.put(level0Id, new ContextDef(level0Id, level0.valueOf("./description"), "category", ""));
|
|
660
|
final Node level1 = fundingPath.selectSingleNode("//funding_level_1");
|
|
661
|
if (level1 == null) {
|
|
662
|
contextes.add(level0Id);
|
|
663
|
} else {
|
|
664
|
final String level1Id = Joiner.on("::").join(level0Id, level1.valueOf("./name"));
|
|
665
|
contextMapper.put(level1Id, new ContextDef(level1Id, level1.valueOf("./description"), "concept", ""));
|
|
666
|
final Node level2 = fundingPath.selectSingleNode("//funding_level_2");
|
|
667
|
if (level2 == null) {
|
|
668
|
contextes.add(level1Id);
|
|
669
|
} else {
|
|
670
|
final String level2Id = Joiner.on("::").join(level1Id, level2.valueOf("./name"));
|
|
671
|
contextMapper.put(level2Id, new ContextDef(level2Id, level2.valueOf("./description"), "concept", ""));
|
|
672
|
contextes.add(level2Id);
|
|
673
|
}
|
|
674
|
}
|
|
675
|
}
|
|
676
|
}
|
|
677
|
} catch (final NullPointerException e) {
|
|
678
|
throw new IllegalArgumentException("malformed funding path: " + xmlTree, e);
|
|
679
|
}
|
|
680
|
}
|
|
681
|
|
|
682
|
private String asXmlElement(final String name, final String value, final Qualifier q, final DataInfo dataInfo) {
|
|
683
|
StringBuilder sb = new StringBuilder();
|
|
684
|
sb.append("<");
|
|
685
|
sb.append(name);
|
|
686
|
if (q != null) {
|
|
687
|
sb.append(getAttributes(q));
|
|
688
|
}
|
|
689
|
if (dataInfo != null) {
|
|
690
|
sb = dataInfoAsAttributes(sb, dataInfo);
|
|
691
|
}
|
|
692
|
if ((value == null) || value.isEmpty()) {
|
|
693
|
sb.append("/>");
|
|
694
|
return sb.toString();
|
|
695
|
// return "<" + name + getAttributes(q) + "/>";
|
|
696
|
}
|
|
697
|
|
|
698
|
sb.append(">");
|
|
699
|
// sb.append(escapeXml(Normalizer.normalize(value, Normalizer.Form.NFD)));
|
|
700
|
sb.append(escapeXml(value));
|
|
701
|
sb.append("</");
|
|
702
|
sb.append(name);
|
|
703
|
sb.append(">");
|
|
704
|
|
|
705
|
return sb.toString();
|
|
706
|
// return "<" + name + getAttributes(q) + ">" + escapeXml(value) + "</" + name + ">";
|
|
707
|
}
|
|
708
|
|
|
709
|
private String getAttributes(final Qualifier q) {
|
|
710
|
if (q == null) return "";
|
|
711
|
|
|
712
|
final StringBuilder sb = new StringBuilder();
|
|
713
|
for (final Entry<FieldDescriptor, Object> e : q.getAllFields().entrySet()) {
|
|
714
|
// sb.append(" " + e.getKey().getName() + "=\"" + escapeXml(e.getValue().toString()) + "\"");
|
|
715
|
sb.append(" ");
|
|
716
|
sb.append(e.getKey().getName());
|
|
717
|
sb.append("=\"");
|
|
718
|
sb.append(escapeXml(e.getValue().toString()));
|
|
719
|
sb.append("\"");
|
|
720
|
}
|
|
721
|
return sb.toString();
|
|
722
|
}
|
|
723
|
|
|
724
|
|
|
725
|
private Map<FieldDescriptor, Object> filterFields(final GeneratedMessage fields, final Predicate<String> acceptFilter) {
|
|
726
|
if(acceptFilter == null) return fields.getAllFields();
|
|
727
|
final Map<FieldDescriptor, Object> res = Maps.newHashMap();
|
|
728
|
for(Entry<FieldDescriptor, Object> e : fields.getAllFields().entrySet()) {
|
|
729
|
if (acceptFilter.apply(e.getKey().getName())) {
|
|
730
|
res.put(e.getKey(), e.getValue());
|
|
731
|
}
|
|
732
|
}
|
|
733
|
return res;
|
|
734
|
}
|
|
735
|
|
|
736
|
|
|
737
|
|
|
738
|
private List<String> countersAsXml() {
|
|
739
|
final List<String> out = Lists.newArrayList();
|
|
740
|
for (final Entry<String, Integer> e : counters.entrySet()) {
|
|
741
|
out.add(String.format("<counter_%s value=\"%s\"/>", e.getKey(), e.getValue()));
|
|
742
|
}
|
|
743
|
return out;
|
|
744
|
}
|
|
745
|
|
|
746
|
private void incrementCounter(final String type) {
|
|
747
|
if (!counters.containsKey(type)) {
|
|
748
|
counters.put(type, 1);
|
|
749
|
} else {
|
|
750
|
counters.put(type, counters.get(type) + 1);
|
|
751
|
}
|
|
752
|
}
|
|
753
|
|
|
754
|
@Override
|
|
755
|
public String toString() {
|
|
756
|
final StringBuilder sb = new StringBuilder();
|
|
757
|
sb.append("################################################\n");
|
|
758
|
sb.append("ID: ").append(key).append("\n");
|
|
759
|
if (mainEntity != null) {
|
|
760
|
sb.append("MAIN ENTITY:\n").append(mainEntity.getEntity().toString() + "\n");
|
|
761
|
}
|
|
762
|
if (relations != null) {
|
|
763
|
sb.append("\nRELATIONS:\n");
|
|
764
|
for (final OafDecoder decoder : relations) {
|
|
765
|
sb.append(decoder.getOafRel().toString() + "\n");
|
|
766
|
}
|
|
767
|
}
|
|
768
|
if (children != null) {
|
|
769
|
sb.append("\nCHILDREN:\n");
|
|
770
|
for (final OafDecoder decoder : children) {
|
|
771
|
sb.append(decoder.getOafRel().toString() + "\n");
|
|
772
|
}
|
|
773
|
}
|
|
774
|
return sb.toString();
|
|
775
|
}
|
|
776
|
|
|
777
|
}
|