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package eu.dnetlib.data.mapreduce.util;
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import static eu.dnetlib.miscutils.collections.MappedCollection.listMap;
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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 java.util.StringTokenizer;
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import javax.xml.transform.OutputKeys;
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import javax.xml.transform.Transformer;
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import javax.xml.transform.TransformerConfigurationException;
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import javax.xml.transform.TransformerException;
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import javax.xml.transform.TransformerFactory;
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import javax.xml.transform.TransformerFactoryConfigurationError;
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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.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.io.SAXReader;
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import org.json.JSONException;
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import org.json.JSONObject;
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import com.google.common.base.Predicate;
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import com.google.common.collect.Iterators;
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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.ContextDef;
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import eu.dnetlib.data.mapreduce.hbase.index.config.ContextMapper;
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import eu.dnetlib.data.mapreduce.hbase.index.config.EntityConfigTable;
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import eu.dnetlib.data.mapreduce.hbase.index.config.LinkDescriptor;
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import eu.dnetlib.data.mapreduce.hbase.index.config.RelClasses;
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import eu.dnetlib.data.proto.FieldTypeProtos.DataInfo;
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import eu.dnetlib.data.proto.FieldTypeProtos.ExtraInfo;
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import eu.dnetlib.data.proto.FieldTypeProtos.KeyValue;
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import eu.dnetlib.data.proto.FieldTypeProtos.Qualifier;
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import eu.dnetlib.data.proto.FieldTypeProtos.StringField;
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import eu.dnetlib.data.proto.FieldTypeProtos.StructuredProperty;
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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.Type;
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import eu.dnetlib.miscutils.functional.UnaryFunction;
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public class XmlRecordFactory {
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protected Set<String> specialDatasourceTypes = Sets.newHashSet("scholarcomminfra", "infospace", "pubsrepository::mock", "entityregistry");
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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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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)
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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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transformer = TransformerFactory.newInstance().newTransformer();
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transformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
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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 OafDecoder rel) {
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addRelOrChild(relations, rel);
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}
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public void addChild(final OafDecoder child) {
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addRelOrChild(children, child);
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}
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private void addRelOrChild(final List<OafDecoder> list, final OafDecoder decoder) {
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list.add(decoder);
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}
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public String build() {
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OafEntityDecoder entity = mainEntity.decodeEntity();
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// System.out.println("building");
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// System.out.println("main: " + mainEntity);
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// System.out.println("rel: " + relations);
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// System.out.println("chi: " + children);
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// System.out.println("=============");
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final Type type = entity.getType();
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final List<String> metadata = decodeType(entity, null, 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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List<String> rels = listRelations();
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metadata.addAll(buildContexts(type));
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metadata.add(parseDataInfo(mainEntity));
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final String body = templateFactory.buildBody(type, metadata, rels, listChildren(), extraInfo);
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// System.out.println("record id: " + recordId);
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return templateFactory.buildRecord(type, key, entity.getDateOfCollection(), schemaLocation, body, countersAsXml());
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}
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private String parseDataInfo(final OafDecoder decoder) {
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DataInfo dataInfo = decoder.getOaf().getDataInfo();
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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 Set<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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LicenseComparator lc = new LicenseComparator();
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for (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 (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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final List<String> metadata = Lists.newArrayList();
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Type targetType = relDecoder.getTargetType(mainEntity.getEntity().getType());
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Set<String> relFilter = entityConfigTable.getFilter(targetType, relDecoder.getRelDescriptor());
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metadata.addAll(listFields(relDecoder.getSubRel(), relFilter, false, true));
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String semanticclass = "";
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String semanticscheme = "";
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RelDescriptor relDescriptor = relDecoder.getRelDescriptor();
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if (cachedTarget != null && cachedTarget.isInitialized()) {
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final Set<String> filter = entityConfigTable.getFilter(targetType, relDescriptor);
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metadata.addAll(decodeType(OafEntityDecoder.decode(cachedTarget), filter, relDefaults, true));
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}
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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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incrementCounter(relDescriptor.getSubRelType().toString());
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LinkDescriptor ld = entityConfigTable.getDescriptor(relDecoder.getTargetType(mainEntity.getEntity().getType()), relDescriptor);
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String relId = ld != null && !ld.isSymmetric() ? relDecoder.getRelTargetId() : relDecoder.getRelSourceId();
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DataInfo info = decoder.getOaf().getDataInfo();
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rels.add(templateFactory.getRel(targetType, relId, metadata, semanticclass, semanticscheme, info.getInferred(), info.getTrust(),
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info.getInferenceprovenance(), info.getProvenanceaction().getClassid()));
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}
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}
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return rels;
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}
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private List<String> listChildren() {
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final List<String> children = Lists.newArrayList();
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for (OafDecoder decoder : this.children) {
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OafEntity cachedTarget = decoder.getOafRel().getCachedTarget();
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addChildren(children, cachedTarget, decoder.getRelDescriptor());
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}
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OafEntityDecoder entity = mainEntity.decodeEntity();
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if (entity.getType().equals(Type.result)) {
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for (Instance instance : ((Result) entity.getEntity()).getInstanceList()) {
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children.add(templateFactory.getInstance(instance.getHostedby().getKey(), listFields(instance, null, false, false),
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listMap(instance.getUrlList(), new UnaryFunction<String, String>() {
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@Override
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public String evaluate(final String identifier) {
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return templateFactory.getWebResource(identifier);
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}
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})));
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}
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for (ExternalReference er : ((Result) entity.getEntity()).getExternalReferenceList()) {
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// Set<String> filters = entityConfigTable.getFilter(Type.result, RelType.resultResult);
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List<String> fields = listFields(er, null, false, false);
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children.add(templateFactory.getChild("externalreference", null, fields));
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}
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}
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return children;
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}
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private void addChildren(final List<String> children, final OafEntity target, final RelDescriptor relDescriptor) {
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final OafEntityDecoder decoder = OafEntityDecoder.decode(target);
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incrementCounter(relDescriptor.getSubRelType().toString());
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Set<String> filters = entityConfigTable.getFilter(target.getType(), relDescriptor);
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children.add(templateFactory.getChild(decoder.getType().toString(), decoder.getId(), listFields(decoder.getMetadata(), filters, childDefaults, false)));
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}
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// //////////////////////////////////
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304
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private List<String> listFields(final GeneratedMessage fields, final Set<String> filter, final boolean defaults, final boolean expandingRel) {
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final List<String> metadata = Lists.newArrayList();
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if (fields != null) {
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Set<String> seen = Sets.newHashSet();
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for (Entry<FieldDescriptor, Object> e : filterFields(fields, filter)) {
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// final String name = getFieldName(e.getKey().getName());
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final String name = e.getKey().getName();
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seen.add(name);
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addFieldValue(metadata, e.getKey(), e.getValue(), expandingRel);
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}
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if (defaults) {
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for (FieldDescriptor fd : fields.getDescriptorForType().getFields()) {
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if (!seen.contains(fd.getName())) {
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addFieldValue(metadata, fd, getDefault(fd), expandingRel);
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}
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}
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}
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}
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return metadata;
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}
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private Object getDefault(final FieldDescriptor fd) {
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switch (fd.getType()) {
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case BOOL:
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return false;
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case BYTES:
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return "".getBytes();
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case MESSAGE: {
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if (Qualifier.getDescriptor().equals(fd.getMessageType())) { return defaultQualifier(); }
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if (StructuredProperty.getDescriptor().equals(fd.getMessageType())) { return StructuredProperty.newBuilder().setValue("")
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.setQualifier(defaultQualifier()).build(); }
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if (KeyValue.getDescriptor().equals(fd.getMessageType())) { return KeyValue.newBuilder().setKey("").setValue("").build(); }
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if (StringField.getDescriptor().equals(fd.getMessageType())) { return StringField.newBuilder().setValue("").build(); }
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return null;
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}
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case SFIXED32:
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case SFIXED64:
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case SINT32:
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348
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case SINT64:
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349
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case INT32:
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350
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case INT64:
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351
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case DOUBLE:
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case FIXED32:
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case FIXED64:
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case FLOAT:
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return 0;
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case STRING:
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return "";
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default:
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return null;
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}
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361
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}
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362
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363
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private Qualifier defaultQualifier() {
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364
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return Qualifier.newBuilder().setClassid("").setClassname("").setSchemeid("").setSchemename("").build();
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365
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}
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366
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367
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@SuppressWarnings("unchecked")
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368
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private void addFieldValue(final List<String> metadata, final FieldDescriptor fd, final Object value, final boolean expandingRel) {
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369
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if (fd.getName().equals("dateofcollection") || fd.getName().equals("id") || fd.getName().equals("url") || value == null) { return; }
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370
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371
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if (fd.getName().equals("datasourcetype")) {
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String classid = ((Qualifier) value).getClassid();
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373
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Qualifier.Builder q = Qualifier.newBuilder((Qualifier) value);
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if (specialDatasourceTypes.contains(classid)) {
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q.setClassid("other").setClassname("other");
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}
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metadata.add(asXmlElement("datasourcetypeui", "", q.build(), null));
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}
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380
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381
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if (fd.isRepeated() && value instanceof List<?>) {
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for (Object o : (List<Object>) value) {
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guessType(metadata, fd, o, expandingRel);
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}
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385
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} else {
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guessType(metadata, fd, value, expandingRel);
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}
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}
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389
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390
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private void guessType(final List<String> metadata, final FieldDescriptor fd, final Object o, final boolean expandingRel) {
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391
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392
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if (fd.getType().equals(FieldDescriptor.Type.MESSAGE)) {
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393
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394
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if (Qualifier.getDescriptor().equals(fd.getMessageType())) {
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Qualifier qualifier = (Qualifier) o;
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396
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metadata.add(asXmlElement(fd.getName(), "", qualifier, null));
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}
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398
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399
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if (StructuredProperty.getDescriptor().equals(fd.getMessageType())) {
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400
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StructuredProperty sp = (StructuredProperty) o;
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401
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metadata.add(asXmlElement(fd.getName(), sp.getValue(), sp.getQualifier(), sp.hasDataInfo() ? sp.getDataInfo() : null));
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402
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}
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403
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404
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if (KeyValue.getDescriptor().equals(fd.getMessageType())) {
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405
|
KeyValue kv = (KeyValue) o;
|
406
|
metadata.add("<" + fd.getName() + " name=\"" + escapeXml(kv.getValue()) + "\" id=\"" + escapeXml(removePrefix(kv.getKey())) + "\"/>");
|
407
|
}
|
408
|
|
409
|
if (StringField.getDescriptor().equals(fd.getMessageType())) {
|
410
|
if (fd.getName().contains("fundingtree")) {
|
411
|
handleFundingTree(metadata, fd, o, expandingRel);
|
412
|
} else {
|
413
|
StringField sf = (StringField) o;
|
414
|
StringBuilder sb = new StringBuilder("<" + fd.getName());
|
415
|
if (sf.hasDataInfo()) {
|
416
|
DataInfo dataInfo = sf.getDataInfo();
|
417
|
dataInfoAsAttributes(sb, dataInfo);
|
418
|
}
|
419
|
sb.append(">" + escapeXml(sf.getValue()) + "</" + fd.getName() + ">");
|
420
|
metadata.add(sb.toString());
|
421
|
}
|
422
|
}
|
423
|
|
424
|
if (Journal.getDescriptor().equals(fd.getMessageType()) && o != null) {
|
425
|
Journal j = (Journal) o;
|
426
|
metadata.add("<journal " + "issn=\"" + escapeXml(j.getIssnPrinted()) + "\" " + "eissn=\"" + escapeXml(j.getIssnOnline()) + "\" " + "lissn=\""
|
427
|
+ escapeXml(j.getIssnLinking()) + "\">" + escapeXml(j.getName()) + "</journal>");
|
428
|
}
|
429
|
|
430
|
if (Context.getDescriptor().equals(fd.getMessageType()) && o != null) {
|
431
|
contextes.add(((Result.Context) o).getId());
|
432
|
}
|
433
|
|
434
|
if (ExtraInfo.getDescriptor().equals(fd.getMessageType()) && o != null) {
|
435
|
|
436
|
ExtraInfo e = (ExtraInfo) o;
|
437
|
StringBuilder sb = new StringBuilder("<" + fd.getName() + " ");
|
438
|
|
439
|
sb.append("name=\"" + e.getName() + "\" ");
|
440
|
sb.append("typology=\"" + e.getTypology() + "\" ");
|
441
|
sb.append("provenance=\"" + e.getProvenance() + "\" ");
|
442
|
sb.append("trust=\"" + e.getTrust() + "\"");
|
443
|
sb.append(">");
|
444
|
sb.append(e.getValue());
|
445
|
sb.append("</" + fd.getName() + ">");
|
446
|
|
447
|
extraInfo.add(sb.toString());
|
448
|
}
|
449
|
|
450
|
} else if (fd.getType().equals(FieldDescriptor.Type.ENUM)) {
|
451
|
if (fd.getFullName().equals("eu.dnetlib.data.proto.OafEntity.type")) { return; }
|
452
|
metadata.add(asXmlElement(fd.getName(), ((EnumValueDescriptor) o).getName(), null, null));
|
453
|
} else {
|
454
|
metadata.add(asXmlElement(fd.getName(), o.toString(), null, null));
|
455
|
}
|
456
|
}
|
457
|
|
458
|
private StringBuilder dataInfoAsAttributes(final StringBuilder sb, final DataInfo dataInfo) {
|
459
|
sb.append(" inferred=\"" + dataInfo.getInferred() + "\"");
|
460
|
sb.append(" inferenceprovenance=\"" + dataInfo.getInferenceprovenance() + "\"");
|
461
|
sb.append(" provenanceaction=\"" + dataInfo.getProvenanceaction().getClassid() + "\"");
|
462
|
sb.append(" trust=\"" + dataInfo.getTrust() + "\" ");
|
463
|
return sb;
|
464
|
}
|
465
|
|
466
|
private List<String> buildContexts(final Type type) {
|
467
|
final List<String> res = Lists.newArrayList();
|
468
|
|
469
|
if (contextMapper != null && !contextMapper.isEmpty() && type.equals(Type.result)) {
|
470
|
|
471
|
XMLTag document = XMLDoc.newDocument(true).addRoot("contextRoot");
|
472
|
|
473
|
for (String id : contextes) {
|
474
|
|
475
|
StringTokenizer st = new StringTokenizer(id, "::");
|
476
|
String token = "";
|
477
|
while (st.hasMoreTokens()) {
|
478
|
token += st.nextToken();
|
479
|
|
480
|
final ContextDef def = contextMapper.get(token);
|
481
|
|
482
|
if (def == null) { throw new IllegalStateException("cannot find context for id: " + token); }
|
483
|
|
484
|
if (def.getName().equals("context")) {
|
485
|
String xpath = "//context/@id='" + def.getId() + "'";
|
486
|
if (!document.gotoRoot().rawXpathBoolean(xpath, new Object())) {
|
487
|
document = addContextDef(document.gotoRoot(), def);
|
488
|
}
|
489
|
}
|
490
|
|
491
|
if (def.getName().equals("category")) {
|
492
|
String rootId = StringUtils.substringBefore(def.getId(), "::");
|
493
|
document = addContextDef(document.gotoRoot().gotoTag("//context[./@id='" + rootId + "']", new Object()), def);
|
494
|
}
|
495
|
|
496
|
if (def.getName().equals("concept")) {
|
497
|
document = addContextDef(document, def).gotoParent();
|
498
|
}
|
499
|
token += "::";
|
500
|
}
|
501
|
}
|
502
|
|
503
|
for (org.w3c.dom.Element x : document.gotoRoot().getChildElement()) {
|
504
|
try {
|
505
|
res.add(asStringElement(x));
|
506
|
} catch (TransformerException e) {
|
507
|
throw new RuntimeException(e);
|
508
|
}
|
509
|
}
|
510
|
}
|
511
|
|
512
|
return res;
|
513
|
}
|
514
|
|
515
|
private XMLTag addContextDef(final XMLTag tag, final ContextDef def) {
|
516
|
tag.addTag(def.getName()).addAttribute("id", def.getId()).addAttribute("label", def.getLabel());
|
517
|
if (def.getType() != null && !def.getType().isEmpty()) {
|
518
|
tag.addAttribute("type", def.getType());
|
519
|
}
|
520
|
return tag;
|
521
|
}
|
522
|
|
523
|
private String asStringElement(final org.w3c.dom.Element element) throws TransformerException {
|
524
|
StringWriter buffer = new StringWriter();
|
525
|
transformer.transform(new DOMSource(element), new StreamResult(buffer));
|
526
|
return buffer.toString();
|
527
|
}
|
528
|
|
529
|
@SuppressWarnings("unchecked")
|
530
|
private void handleFundingTree(final List<String> metadata, final FieldDescriptor fd, final Object o, final boolean expandingRel) {
|
531
|
String xmlTree = asXmlJSon(fd.getName(), o instanceof StringField ? ((StringField) o).getValue() : o.toString());
|
532
|
if (expandingRel) {
|
533
|
try {
|
534
|
Document ftree = new SAXReader().read(new StringReader(xmlTree));
|
535
|
|
536
|
int i = 0;
|
537
|
String funding = "<funding>";
|
538
|
String _id = "";
|
539
|
|
540
|
for (Object id : Lists.reverse(ftree.selectNodes("//fundingtree//name"))) {
|
541
|
_id += ((Element) id).getText();
|
542
|
funding += "<funding_level_" + i + ">" + escapeXml(_id) + "</funding_level_" + i + ">";
|
543
|
_id += "::";
|
544
|
i++;
|
545
|
}
|
546
|
funding += "</funding>";
|
547
|
// System.out.println("-------------------------------\n" + xmlTree + "\n" + funding);
|
548
|
metadata.add(funding);
|
549
|
} catch (DocumentException e) {
|
550
|
System.err.println("unable to parse funding tree: " + xmlTree + "\n" + e.getMessage());
|
551
|
}
|
552
|
} else {
|
553
|
metadata.add(xmlTree);
|
554
|
}
|
555
|
}
|
556
|
|
557
|
private String asXmlJSon(final String root, final String json) {
|
558
|
try {
|
559
|
if (json == null || json.isEmpty()) { return "<" + root + "/>"; }
|
560
|
JSONObject o = new JSONObject(json.replace("'", ""));
|
561
|
|
562
|
String contextId = parseFundingJson(o).toLowerCase();
|
563
|
contextes.add(contextId);
|
564
|
|
565
|
String xml = org.json.XML.toString(o, root);
|
566
|
return xml;
|
567
|
} catch (Exception e) {
|
568
|
System.err.println("unable to parse json: " + json + "\n" + e.getMessage());
|
569
|
return "<" + root + "/>";
|
570
|
}
|
571
|
}
|
572
|
|
573
|
private String parseFundingJson(final JSONObject o) {
|
574
|
try {
|
575
|
String key = (String) Iterators.getOnlyElement(o.keys());
|
576
|
JSONObject obj = o.getJSONObject(key);
|
577
|
|
578
|
String id = obj.getString("id").toLowerCase();
|
579
|
if (id.startsWith("welcometrust::")) {
|
580
|
id = StringUtils.substringBeforeLast("uk::" + id.replace("welcometrust", "wt"), "::") + "::" + cleanup(id);
|
581
|
} else if (id.startsWith("wt::wt")) {
|
582
|
id = StringUtils.substringBeforeLast(id.replaceFirst("wt", "uk"), "::") + "::" + cleanup(id);
|
583
|
} else if (id.startsWith("corda_______::")) {
|
584
|
id = id.replace("corda_______::", "ec::");
|
585
|
} else if (id.startsWith("fct_________::")) {
|
586
|
id = "pt::" + id.replace("fct_________", "fct");
|
587
|
if (id.endsWith("::fct")) {
|
588
|
id = StringUtils.substringBeforeLast(id, "::fct");
|
589
|
}
|
590
|
}
|
591
|
|
592
|
String label = obj.getString("name");
|
593
|
|
594
|
if (key.endsWith("level_0")) {
|
595
|
|
596
|
if (id.equals("uk::wt")) {
|
597
|
label = "Wellcome Trust Funding Stream";
|
598
|
}
|
599
|
contextMapper.put(id, new ContextDef(id, label, "category", ""));
|
600
|
|
601
|
if (id.startsWith("ec::")) {
|
602
|
contextMapper.put("ec", new ContextDef("ec", "European Community", "context", "funding"));
|
603
|
} else if (id.startsWith("uk::")) {
|
604
|
contextMapper.put("uk", new ContextDef("uk", "United Kingdom", "context", "funding"));
|
605
|
} else if (id.startsWith("pt::")) {
|
606
|
contextMapper.put("pt", new ContextDef("pt", "Portugal", "context", "funding"));
|
607
|
}
|
608
|
} else {
|
609
|
contextMapper.put(id, new ContextDef(id, label, "concept", ""));
|
610
|
parseFundingJson(obj.getJSONObject("parent"));
|
611
|
}
|
612
|
|
613
|
return id;
|
614
|
} catch (JSONException e) {
|
615
|
throw new RuntimeException(e);
|
616
|
}
|
617
|
}
|
618
|
|
619
|
private String cleanup(final String id) {
|
620
|
return StringUtils.substring(StringUtils.deleteWhitespace(StringUtils.substringAfterLast(id, "::").replaceAll("[^a-zA-Z]", "")), 0, 20);
|
621
|
}
|
622
|
|
623
|
private String asXmlElement(final String name, final String value, final Qualifier q, final DataInfo dataInfo) {
|
624
|
StringBuilder sb = new StringBuilder();
|
625
|
sb.append("<");
|
626
|
sb.append(name);
|
627
|
if (q != null) {
|
628
|
sb.append(getAttributes(q));
|
629
|
}
|
630
|
if (dataInfo != null) {
|
631
|
sb = dataInfoAsAttributes(sb, dataInfo);
|
632
|
}
|
633
|
if (value == null || value.isEmpty()) {
|
634
|
sb.append("/>");
|
635
|
return sb.toString();
|
636
|
// return "<" + name + getAttributes(q) + "/>";
|
637
|
}
|
638
|
|
639
|
sb.append(">");
|
640
|
// sb.append(escapeXml(Normalizer.normalize(value, Normalizer.Form.NFD)));
|
641
|
sb.append(escapeXml(value));
|
642
|
sb.append("</");
|
643
|
sb.append(name);
|
644
|
sb.append(">");
|
645
|
|
646
|
return sb.toString();
|
647
|
// return "<" + name + getAttributes(q) + ">" + escapeXml(value) + "</" + name + ">";
|
648
|
}
|
649
|
|
650
|
private String getAttributes(final Qualifier q) {
|
651
|
if (q == null) { return ""; }
|
652
|
|
653
|
StringBuilder sb = new StringBuilder();
|
654
|
for (Entry<FieldDescriptor, Object> e : q.getAllFields().entrySet()) {
|
655
|
// sb.append(" " + e.getKey().getName() + "=\"" + escapeXml(e.getValue().toString()) + "\"");
|
656
|
sb.append(" ");
|
657
|
sb.append(e.getKey().getName());
|
658
|
sb.append("=\"");
|
659
|
sb.append(escapeXml(e.getValue().toString()));
|
660
|
sb.append("\"");
|
661
|
}
|
662
|
return sb.toString();
|
663
|
}
|
664
|
|
665
|
private Set<Entry<FieldDescriptor, Object>> filterFields(final GeneratedMessage fields, final Set<String> filter) {
|
666
|
|
667
|
if (filter != null) {
|
668
|
Predicate<FieldDescriptor> p = new Predicate<FieldDescriptor>() {
|
669
|
|
670
|
@Override
|
671
|
public boolean apply(final FieldDescriptor descriptor) {
|
672
|
if (fields == null) {
|
673
|
return false;
|
674
|
}
|
675
|
String name = descriptor.getName();
|
676
|
return filter.contains(name);
|
677
|
}
|
678
|
};
|
679
|
Map<FieldDescriptor, Object> filtered = Maps.filterKeys(fields.getAllFields(), p);
|
680
|
// System.out.println(
|
681
|
// "filtered " + type.toString() + ": " + toString(filterEntries.keySet()) + "\n" +
|
682
|
// "builder " + fields.getDescriptorForType().getFullName() + ": " + toString(fields.getAllFields().keySet()));
|
683
|
return filtered.entrySet();
|
684
|
}
|
685
|
return fields.getAllFields().entrySet();
|
686
|
}
|
687
|
|
688
|
public static String removePrefix(final String s) {
|
689
|
if (s.contains("|")) { return StringUtils.substringAfter(s, "|"); }
|
690
|
return s;
|
691
|
}
|
692
|
|
693
|
public static String escapeXml(final String value) {
|
694
|
// return StringEscapeUtils.escapeXml(value).replaceAll("&", "&").replaceAll("<", "<").replaceAll(">", ">");
|
695
|
return value.replaceAll("&", "&").replaceAll("<", "<").replaceAll(">", ">");
|
696
|
}
|
697
|
|
698
|
private List<String> countersAsXml() {
|
699
|
List<String> out = Lists.newArrayList();
|
700
|
for (Entry<String, Integer> e : counters.entrySet()) {
|
701
|
out.add(String.format("<counter_%s value=\"%s\"/>", e.getKey(), e.getValue()));
|
702
|
}
|
703
|
return out;
|
704
|
}
|
705
|
|
706
|
private void incrementCounter(final String type) {
|
707
|
if (!counters.containsKey(type)) {
|
708
|
counters.put(type, 1);
|
709
|
} else {
|
710
|
counters.put(type, counters.get(type) + 1);
|
711
|
}
|
712
|
}
|
713
|
|
714
|
@Override
|
715
|
public String toString() {
|
716
|
StringBuilder sb = new StringBuilder();
|
717
|
sb.append("################################################\n");
|
718
|
sb.append("ID: ").append(key).append("\n");
|
719
|
if (mainEntity != null) {
|
720
|
sb.append("MAIN ENTITY:\n").append(mainEntity.getEntity().toString() + "\n");
|
721
|
}
|
722
|
if (relations != null) {
|
723
|
sb.append("\nRELATIONS:\n");
|
724
|
for (OafDecoder decoder : relations) {
|
725
|
sb.append(decoder.getOafRel().toString() + "\n");
|
726
|
}
|
727
|
}
|
728
|
if (children != null) {
|
729
|
sb.append("\nCHILDREN:\n");
|
730
|
for (OafDecoder decoder : children) {
|
731
|
sb.append(decoder.getOafRel().toString() + "\n");
|
732
|
}
|
733
|
}
|
734
|
return sb.toString();
|
735
|
}
|
736
|
|
737
|
}
|