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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) {
|
| 296 |
26600
|
sandro.lab
|
final OafEntityDecoder decoder = OafEntityDecoder.decode(target);
|
| 297 |
30968
|
claudio.at
|
incrementCounter(relDescriptor.getSubRelType().toString());
|
| 298 |
28094
|
claudio.at
|
Set<String> filters = entityConfigTable.getFilter(target.getType(), relDescriptor);
|
| 299 |
26600
|
sandro.lab
|
children.add(templateFactory.getChild(decoder.getType().toString(), decoder.getId(), listFields(decoder.getMetadata(), filters, childDefaults, false)));
|
| 300 |
|
|
}
|
| 301 |
|
|
|
| 302 |
|
|
// //////////////////////////////////
|
| 303 |
|
|
|
| 304 |
|
|
private List<String> listFields(final GeneratedMessage fields, final Set<String> filter, final boolean defaults, final boolean expandingRel) {
|
| 305 |
|
|
|
| 306 |
|
|
final List<String> metadata = Lists.newArrayList();
|
| 307 |
|
|
|
| 308 |
|
|
if (fields != null) {
|
| 309 |
|
|
|
| 310 |
|
|
Set<String> seen = Sets.newHashSet();
|
| 311 |
|
|
for (Entry<FieldDescriptor, Object> e : filterFields(fields, filter)) {
|
| 312 |
|
|
|
| 313 |
|
|
// final String name = getFieldName(e.getKey().getName());
|
| 314 |
|
|
final String name = e.getKey().getName();
|
| 315 |
|
|
seen.add(name);
|
| 316 |
|
|
|
| 317 |
|
|
addFieldValue(metadata, e.getKey(), e.getValue(), expandingRel);
|
| 318 |
|
|
}
|
| 319 |
|
|
|
| 320 |
|
|
if (defaults) {
|
| 321 |
|
|
for (FieldDescriptor fd : fields.getDescriptorForType().getFields()) {
|
| 322 |
|
|
if (!seen.contains(fd.getName())) {
|
| 323 |
|
|
addFieldValue(metadata, fd, getDefault(fd), expandingRel);
|
| 324 |
|
|
}
|
| 325 |
|
|
}
|
| 326 |
|
|
}
|
| 327 |
|
|
}
|
| 328 |
|
|
return metadata;
|
| 329 |
|
|
}
|
| 330 |
|
|
|
| 331 |
|
|
private Object getDefault(final FieldDescriptor fd) {
|
| 332 |
|
|
switch (fd.getType()) {
|
| 333 |
|
|
case BOOL:
|
| 334 |
|
|
return false;
|
| 335 |
|
|
case BYTES:
|
| 336 |
|
|
return "".getBytes();
|
| 337 |
|
|
case MESSAGE: {
|
| 338 |
33382
|
claudio.at
|
if (Qualifier.getDescriptor().equals(fd.getMessageType())) { return defaultQualifier(); }
|
| 339 |
|
|
if (StructuredProperty.getDescriptor().equals(fd.getMessageType())) { return StructuredProperty.newBuilder().setValue("")
|
| 340 |
|
|
.setQualifier(defaultQualifier()).build(); }
|
| 341 |
|
|
if (KeyValue.getDescriptor().equals(fd.getMessageType())) { return KeyValue.newBuilder().setKey("").setValue("").build(); }
|
| 342 |
|
|
if (StringField.getDescriptor().equals(fd.getMessageType())) { return StringField.newBuilder().setValue("").build(); }
|
| 343 |
26600
|
sandro.lab
|
return null;
|
| 344 |
|
|
}
|
| 345 |
|
|
case SFIXED32:
|
| 346 |
|
|
case SFIXED64:
|
| 347 |
|
|
case SINT32:
|
| 348 |
|
|
case SINT64:
|
| 349 |
|
|
case INT32:
|
| 350 |
|
|
case INT64:
|
| 351 |
|
|
case DOUBLE:
|
| 352 |
|
|
case FIXED32:
|
| 353 |
|
|
case FIXED64:
|
| 354 |
|
|
case FLOAT:
|
| 355 |
|
|
return 0;
|
| 356 |
|
|
case STRING:
|
| 357 |
|
|
return "";
|
| 358 |
|
|
default:
|
| 359 |
|
|
return null;
|
| 360 |
|
|
}
|
| 361 |
|
|
}
|
| 362 |
|
|
|
| 363 |
|
|
private Qualifier defaultQualifier() {
|
| 364 |
|
|
return Qualifier.newBuilder().setClassid("").setClassname("").setSchemeid("").setSchemename("").build();
|
| 365 |
|
|
}
|
| 366 |
|
|
|
| 367 |
|
|
@SuppressWarnings("unchecked")
|
| 368 |
|
|
private void addFieldValue(final List<String> metadata, final FieldDescriptor fd, final Object value, final boolean expandingRel) {
|
| 369 |
33382
|
claudio.at
|
if (fd.getName().equals("dateofcollection") || fd.getName().equals("id") || fd.getName().equals("url") || value == null) { return; }
|
| 370 |
26600
|
sandro.lab
|
|
| 371 |
|
|
if (fd.getName().equals("datasourcetype")) {
|
| 372 |
|
|
String classid = ((Qualifier) value).getClassid();
|
| 373 |
|
|
|
| 374 |
|
|
Qualifier.Builder q = Qualifier.newBuilder((Qualifier) value);
|
| 375 |
|
|
if (specialDatasourceTypes.contains(classid)) {
|
| 376 |
|
|
q.setClassid("other").setClassname("other");
|
| 377 |
|
|
}
|
| 378 |
28094
|
claudio.at
|
metadata.add(asXmlElement("datasourcetypeui", "", q.build(), null));
|
| 379 |
26600
|
sandro.lab
|
}
|
| 380 |
|
|
|
| 381 |
33382
|
claudio.at
|
if (fd.isRepeated() && value instanceof List<?>) {
|
| 382 |
26600
|
sandro.lab
|
for (Object o : (List<Object>) value) {
|
| 383 |
|
|
guessType(metadata, fd, o, expandingRel);
|
| 384 |
|
|
}
|
| 385 |
|
|
} else {
|
| 386 |
|
|
guessType(metadata, fd, value, expandingRel);
|
| 387 |
|
|
}
|
| 388 |
|
|
}
|
| 389 |
|
|
|
| 390 |
|
|
private void guessType(final List<String> metadata, final FieldDescriptor fd, final Object o, final boolean expandingRel) {
|
| 391 |
|
|
|
| 392 |
|
|
if (fd.getType().equals(FieldDescriptor.Type.MESSAGE)) {
|
| 393 |
|
|
|
| 394 |
|
|
if (Qualifier.getDescriptor().equals(fd.getMessageType())) {
|
| 395 |
|
|
Qualifier qualifier = (Qualifier) o;
|
| 396 |
28094
|
claudio.at
|
metadata.add(asXmlElement(fd.getName(), "", qualifier, null));
|
| 397 |
26600
|
sandro.lab
|
}
|
| 398 |
|
|
|
| 399 |
|
|
if (StructuredProperty.getDescriptor().equals(fd.getMessageType())) {
|
| 400 |
|
|
StructuredProperty sp = (StructuredProperty) o;
|
| 401 |
28094
|
claudio.at
|
metadata.add(asXmlElement(fd.getName(), sp.getValue(), sp.getQualifier(), sp.hasDataInfo() ? sp.getDataInfo() : null));
|
| 402 |
26600
|
sandro.lab
|
}
|
| 403 |
|
|
|
| 404 |
|
|
if (KeyValue.getDescriptor().equals(fd.getMessageType())) {
|
| 405 |
|
|
KeyValue kv = (KeyValue) o;
|
| 406 |
|
|
metadata.add("<" + fd.getName() + " name=\"" + escapeXml(kv.getValue()) + "\" id=\"" + escapeXml(removePrefix(kv.getKey())) + "\"/>");
|
| 407 |
|
|
}
|
| 408 |
|
|
|
| 409 |
28094
|
claudio.at
|
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 |
33382
|
claudio.at
|
if (Journal.getDescriptor().equals(fd.getMessageType()) && o != null) {
|
| 425 |
26600
|
sandro.lab
|
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 |
33382
|
claudio.at
|
if (Context.getDescriptor().equals(fd.getMessageType()) && o != null) {
|
| 431 |
26600
|
sandro.lab
|
contextes.add(((Result.Context) o).getId());
|
| 432 |
|
|
}
|
| 433 |
|
|
|
| 434 |
33382
|
claudio.at
|
if (ExtraInfo.getDescriptor().equals(fd.getMessageType()) && o != null) {
|
| 435 |
26600
|
sandro.lab
|
|
| 436 |
28094
|
claudio.at
|
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 |
30827
|
claudio.at
|
sb.append(e.getValue());
|
| 445 |
26600
|
sandro.lab
|
sb.append("</" + fd.getName() + ">");
|
| 446 |
28094
|
claudio.at
|
|
| 447 |
|
|
extraInfo.add(sb.toString());
|
| 448 |
26600
|
sandro.lab
|
}
|
| 449 |
|
|
|
| 450 |
|
|
} else if (fd.getType().equals(FieldDescriptor.Type.ENUM)) {
|
| 451 |
33382
|
claudio.at
|
if (fd.getFullName().equals("eu.dnetlib.data.proto.OafEntity.type")) { return; }
|
| 452 |
28094
|
claudio.at
|
metadata.add(asXmlElement(fd.getName(), ((EnumValueDescriptor) o).getName(), null, null));
|
| 453 |
26600
|
sandro.lab
|
} else {
|
| 454 |
28094
|
claudio.at
|
metadata.add(asXmlElement(fd.getName(), o.toString(), null, null));
|
| 455 |
26600
|
sandro.lab
|
}
|
| 456 |
|
|
}
|
| 457 |
|
|
|
| 458 |
28226
|
claudio.at
|
private StringBuilder dataInfoAsAttributes(final StringBuilder sb, final DataInfo dataInfo) {
|
| 459 |
28094
|
claudio.at
|
sb.append(" inferred=\"" + dataInfo.getInferred() + "\"");
|
| 460 |
|
|
sb.append(" inferenceprovenance=\"" + dataInfo.getInferenceprovenance() + "\"");
|
| 461 |
30863
|
claudio.at
|
sb.append(" provenanceaction=\"" + dataInfo.getProvenanceaction().getClassid() + "\"");
|
| 462 |
28094
|
claudio.at
|
sb.append(" trust=\"" + dataInfo.getTrust() + "\" ");
|
| 463 |
|
|
return sb;
|
| 464 |
26600
|
sandro.lab
|
}
|
| 465 |
|
|
|
| 466 |
|
|
private List<String> buildContexts(final Type type) {
|
| 467 |
|
|
final List<String> res = Lists.newArrayList();
|
| 468 |
|
|
|
| 469 |
33382
|
claudio.at
|
if (contextMapper != null && !contextMapper.isEmpty() && type.equals(Type.result)) {
|
| 470 |
26600
|
sandro.lab
|
|
| 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 |
33382
|
claudio.at
|
if (def == null) { throw new IllegalStateException("cannot find context for id: " + token); }
|
| 483 |
26600
|
sandro.lab
|
|
| 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 |
33382
|
claudio.at
|
if (def.getType() != null && !def.getType().isEmpty()) {
|
| 518 |
26600
|
sandro.lab
|
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 |
28094
|
claudio.at
|
String xmlTree = asXmlJSon(fd.getName(), o instanceof StringField ? ((StringField) o).getValue() : o.toString());
|
| 532 |
26600
|
sandro.lab
|
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 |
33382
|
claudio.at
|
if (json == null || json.isEmpty()) { return "<" + root + "/>"; }
|
| 560 |
26600
|
sandro.lab
|
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 |
33382
|
claudio.at
|
} 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 |
26600
|
sandro.lab
|
}
|
| 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 |
33382
|
claudio.at
|
} else if (id.startsWith("pt::")) {
|
| 606 |
|
|
contextMapper.put("pt", new ContextDef("pt", "Portugal", "context", "funding"));
|
| 607 |
26600
|
sandro.lab
|
}
|
| 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 |
28094
|
claudio.at
|
private String asXmlElement(final String name, final String value, final Qualifier q, final DataInfo dataInfo) {
|
| 624 |
26600
|
sandro.lab
|
StringBuilder sb = new StringBuilder();
|
| 625 |
|
|
sb.append("<");
|
| 626 |
|
|
sb.append(name);
|
| 627 |
|
|
if (q != null) {
|
| 628 |
|
|
sb.append(getAttributes(q));
|
| 629 |
|
|
}
|
| 630 |
28094
|
claudio.at
|
if (dataInfo != null) {
|
| 631 |
|
|
sb = dataInfoAsAttributes(sb, dataInfo);
|
| 632 |
|
|
}
|
| 633 |
33382
|
claudio.at
|
if (value == null || value.isEmpty()) {
|
| 634 |
26600
|
sandro.lab
|
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 |
33382
|
claudio.at
|
if (q == null) { return ""; }
|
| 652 |
26600
|
sandro.lab
|
|
| 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 |
33382
|
claudio.at
|
if (fields == null) {
|
| 673 |
|
|
return false;
|
| 674 |
|
|
}
|
| 675 |
28094
|
claudio.at
|
String name = descriptor.getName();
|
| 676 |
|
|
return filter.contains(name);
|
| 677 |
26600
|
sandro.lab
|
}
|
| 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 |
33382
|
claudio.at
|
if (s.contains("|")) { return StringUtils.substringAfter(s, "|"); }
|
| 690 |
26600
|
sandro.lab
|
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 |
30968
|
claudio.at
|
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 |
26600
|
sandro.lab
|
@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 |
28226
|
claudio.at
|
for (OafDecoder decoder : relations) {
|
| 725 |
26600
|
sandro.lab
|
sb.append(decoder.getOafRel().toString() + "\n");
|
| 726 |
|
|
}
|
| 727 |
|
|
}
|
| 728 |
|
|
if (children != null) {
|
| 729 |
|
|
sb.append("\nCHILDREN:\n");
|
| 730 |
28226
|
claudio.at
|
for (OafDecoder decoder : children) {
|
| 731 |
26600
|
sandro.lab
|
sb.append(decoder.getOafRel().toString() + "\n");
|
| 732 |
|
|
}
|
| 733 |
|
|
}
|
| 734 |
|
|
return sb.toString();
|
| 735 |
|
|
}
|
| 736 |
|
|
|
| 737 |
|
|
}
|