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package eu.dnetlib.data.mapreduce.util;
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import com.google.common.base.Splitter;
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import com.google.common.collect.Sets;
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import com.google.gson.JsonArray;
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import com.google.gson.JsonElement;
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import com.google.gson.JsonObject;
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import com.google.protobuf.Descriptors;
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import com.google.protobuf.GeneratedMessage;
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import eu.dnetlib.data.graph.model.DNGFDecoder;
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import eu.dnetlib.data.graph.model.DNGFEntityDecoder;
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import eu.dnetlib.data.graph.model.DNGFRelDecoder;
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import eu.dnetlib.data.graph.utils.RelDescriptor;
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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.proto.*;
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import eu.dnetlib.data.transform.Ontologies;
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import org.apache.commons.lang3.StringUtils;
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import javax.xml.transform.TransformerException;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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/**
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* Created by sandro on 1/9/17.
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*/
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public class JSONRecordFactory extends AbstractRecordFactory {
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public JSONRecordFactory(EntityConfigTable entityConfigTable, ContextMapper contextMapper, Ontologies ontologies, boolean entityDefaults, boolean relDefaults, boolean childDefaults) {
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super(entityConfigTable, contextMapper, ontologies, entityDefaults, relDefaults, childDefaults);
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}
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@Override
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public String build() {
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try {
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final DNGFEntityDecoder entity = mainEntity.decodeEntity();
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final JsonObject result = new JsonObject();
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final TypeProtos.Type type = entity.getType();
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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 JsonArray rels = listRelations();
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result.add("rels", rels);
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buildContexts(type, result);
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// metadata.add(parseDataInfo(mainEntity));
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//
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// final String body = templateFactory.buildBody(type, metadata, rels, listChildren(), extraInfo);
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result.add("metadata", decodeType(entity, null, entityDefaults, false));
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return result.toString();
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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 JsonObject decodeType(final DNGFEntityDecoder decoder, final Set<String> filter, final boolean defaults, final boolean expandingRel) {
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final JsonObject root = new JsonObject();
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addFields(root, decoder.getMetadata(), filter, defaults, expandingRel);
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if ((decoder.getEntity() instanceof PublicationProtos.Publication) && !expandingRel) {
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asJsonElement("bestlicense", "", getBestLicense(), null, root);
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addFields(root, decoder.getEntity(), filter, defaults, expandingRel);
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}
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if ((decoder.getEntity() instanceof PersonProtos.Person) && !expandingRel) {
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addFields(root, decoder.getEntity(), filter, defaults, expandingRel);
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}
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if ((decoder.getEntity() instanceof ProjectProtos.Project) && !expandingRel) {
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addFields(root, decoder.getEntity(), filter, defaults, expandingRel);
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}
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return root;
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}
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private void addFields(final JsonObject metadata, final GeneratedMessage fields, final Set<String> filter, final boolean defaults, final boolean expandingRel) {
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if (fields != null) {
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final Set<String> seen = Sets.newHashSet();
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for (final Map.Entry<Descriptors.FieldDescriptor, Object> e : filterFields(fields, filter)) {
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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 (final Descriptors.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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}
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private void addFieldValue(final JsonObject metadata, final Descriptors.FieldDescriptor fd, final Object value, final boolean expandingRel) {
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if ("dateofcollection".equals(fd.getName()) ||
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"dateoftransformation".equals(fd.getName()) ||
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"id".equals(fd.getName()) ||
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(value == null)) return;
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if (fd.getName().equals("datasourcetype")) {
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final String classid = ((FieldTypeProtos.Qualifier) value).getClassid();
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final FieldTypeProtos.Qualifier.Builder q = FieldTypeProtos.Qualifier.newBuilder((FieldTypeProtos.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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asJsonElement("datasourcetypeui", "", q.build(), null, metadata);
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}
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if (fd.isRepeated() && (value instanceof List<?>)) {
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for (final Object o : (List<Object>) value) {
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guessType(metadata, fd, o, expandingRel);
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}
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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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private void guessType(JsonObject metadata, Descriptors.FieldDescriptor fd, Object object, boolean expandingRel) {
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if (fd.getType().equals(Descriptors.FieldDescriptor.Type.MESSAGE)) {
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if (FieldTypeProtos.Qualifier.getDescriptor().equals(fd.getMessageType())) {
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final FieldTypeProtos.Qualifier qualifier = (FieldTypeProtos.Qualifier) object;
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asJsonElement(fd.getName(), "", qualifier, null, metadata);
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} else if (FieldTypeProtos.StructuredProperty.getDescriptor().equals(fd.getMessageType())) {
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final FieldTypeProtos.StructuredProperty sp = (FieldTypeProtos.StructuredProperty) object;
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asJsonElement(fd.getName(), sp.getValue(), sp.getQualifier(), sp.hasDataInfo() ? sp.getDataInfo() : null, metadata);
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if (!expandingRel && fd.getName().equals("pid")) {
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if (sp.getQualifier().getClassid().equalsIgnoreCase("doi")) {
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incrementCounter("doi");
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}
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}
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} else if (FieldTypeProtos.KeyValue.getDescriptor().equals(fd.getMessageType())) {
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final FieldTypeProtos.KeyValue kv = (FieldTypeProtos.KeyValue) object;
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JsonObject tmp = new JsonObject();
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tmp.addProperty("name", kv.getValue());
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tmp.addProperty("id", removePrefix(kv.getValue()));
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metadata.add(fd.getName(), tmp);
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} else if (FieldTypeProtos.StringField.getDescriptor().equals(fd.getMessageType())) {
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final String fieldName = fd.getName();
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final FieldTypeProtos.StringField sf = (FieldTypeProtos.StringField) object;
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final JsonObject sb = new JsonObject();
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if (sf.hasDataInfo()) {
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final FieldTypeProtos.DataInfo dataInfo = sf.getDataInfo();
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dataInfoAsAttributes(sb, dataInfo);
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if (!StringUtils.isEmpty(sf.getValue()))
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sb.addProperty("value", sf.getValue());
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if (sb.entrySet().size() > 0)
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metadata.add(fieldName, sb);
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} else {
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if (!StringUtils.isEmpty(sf.getValue()))
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metadata.addProperty(fd.getName(), sf.getValue());
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}
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} else if (FieldTypeProtos.BoolField.getDescriptor().equals(fd.getMessageType())) {
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final FieldTypeProtos.BoolField bf = (FieldTypeProtos.BoolField) object;
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if (bf.hasDataInfo()) {
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final JsonObject sb = new JsonObject();
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final FieldTypeProtos.DataInfo dataInfo = bf.getDataInfo();
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dataInfoAsAttributes(sb, dataInfo);
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sb.addProperty("value", bf.getValue());
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metadata.add(fd.getName(), sb);
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} else
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metadata.addProperty(fd.getName(), bf.getValue());
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} else if (FieldTypeProtos.Journal.getDescriptor().equals(fd.getMessageType()) && (object != null)) {
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final FieldTypeProtos.Journal j = (FieldTypeProtos.Journal) object;
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JsonObject journal = new JsonObject();
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journal.addProperty("issn", j.getIssnPrinted());
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journal.addProperty("eissn", j.getIssnOnline());
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journal.addProperty("lissn", j.getIssnLinking());
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journal.addProperty("value", j.getName());
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metadata.add("journal", journal);
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} else if (FieldTypeProtos.Context.getDescriptor().equals(fd.getMessageType()) && (object != null)) {
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contextes.add(((FieldTypeProtos.Context) object).getId());
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} else if (FieldTypeProtos.ExtraInfo.getDescriptor().equals(fd.getMessageType()) && (object != null)) {
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final FieldTypeProtos.ExtraInfo e = (FieldTypeProtos.ExtraInfo) object;
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final JsonObject sb = new JsonObject();
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sb.addProperty("name", e.getName());
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sb.addProperty("typology", e.getTypology());
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sb.addProperty("provenance", e.getProvenance());
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sb.addProperty("trust", e.getTrust());
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sb.addProperty("value", e.getValue());
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metadata.add(fd.getName(), sb);
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}
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} else if (fd.getType().equals(Descriptors.FieldDescriptor.Type.ENUM)) {
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if (fd.getFullName().equals("eu.dnetlib.data.proto.DNGFEntity.type")) return;
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asJsonElement(fd.getName(), ((Descriptors.EnumValueDescriptor) object).getName(), null, null, metadata);
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} else {
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asJsonElement(fd.getName(), object.toString(), null, null, metadata);
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}
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}
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private JsonArray listRelations() {
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JsonArray relations = new JsonArray();
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for (final DNGFDecoder decoder : this.relations) {
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JsonObject root = new JsonObject();
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final DNGFProtos.DNGFRel rel = decoder.getDNGFRel();
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final DNGFProtos.DNGFEntity cachedTarget = rel.getCachedTarget();
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final DNGFRelDecoder relDecoder = DNGFRelDecoder.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 TypeProtos.Type targetType = relDecoder.getTargetType();
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final Set<String> relFilter = entityConfigTable.getFilter(targetType, relDecoder.getRelDescriptor());
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addFields(root, relDecoder.getDngfRel(), relFilter, false, true);
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final 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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root.add("cachedTarget", decodeType(DNGFEntityDecoder.decode(cachedTarget), filter, relDefaults, true));
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}
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final String semanticclass = ontologies.inverseOf(relDescriptor);
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final String semanticscheme = relDescriptor.getOntologyCode();
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final String rd = semanticscheme + "_" + semanticclass;
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incrementCounter(rd);
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final FieldTypeProtos.DataInfo info = decoder.getDNGF().getDataInfo();
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manageInferred(rd, info);
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final LinkDescriptor ld = entityConfigTable.getDescriptor(relDecoder.getTargetType(), relDescriptor);
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final String relId = (ld != null) && !ld.isSymmetric() ? relDecoder.getRelTargetId() : relDecoder.getRelSourceId();
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relations.add(root);
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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 relations;
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}
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private void buildContexts(final TypeProtos.Type type, final JsonObject metadata) {
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if ((contextMapper != null) && !contextMapper.isEmpty() && type.equals(TypeProtos.Type.publication)) {
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JsonObject contextRoot = new JsonObject();
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JsonArray contexts = new JsonArray();
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contextRoot.add("contextRoot", contexts);
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for (final String context : contextes) {
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String id = "";
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for (final String token : Splitter.on("::").split(context)) {
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id += token;
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final ContextDef def = contextMapper.get(id);
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if (def == null)
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throw new IllegalStateException(String.format("cannot find context for id '%s'", id));
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if (def.getName().equals("context")) {
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if (!findExistingContext(contexts,def.getId()))
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addContextDef(contexts,def);
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}
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if (def.getName().equals("category")) {
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final String rootId = StringUtils.substringBefore(def.getId(), "::");
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addContextDef(contexts, def);
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}
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if (def.getName().equals("concept")) {
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addContextDef(contexts, def);
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}
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id += "::";
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}
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}
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}
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}
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private boolean findExistingContext(JsonArray contexes, String id) {
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for(JsonElement item:contexes) {
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if(item.getAsJsonObject().has("context")) {
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if (item.getAsJsonObject().get("context").getAsJsonObject().get("id").getAsString().equals(id)) {
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return true;
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}
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}
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}
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return false;
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}
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private void addContextDef(final JsonArray tags, final ContextDef def) {
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final JsonObject defContext = new JsonObject();
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defContext.addProperty("id",def.getId());
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defContext.addProperty("label", def.getLabel());
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if ((def.getType() != null) && !def.getType().isEmpty()) {
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defContext.addProperty("type", def.getType());
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}
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final JsonObject result = new JsonObject();
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result.add(def.getName(),defContext);
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tags.add(result);
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}
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private void asJsonElement(final String name, final String value, final FieldTypeProtos.Qualifier q, final FieldTypeProtos.DataInfo dataInfo, final JsonObject metadata) {
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335
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JsonObject root = new JsonObject();
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getAttributes(q, root);
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if (dataInfo != null) {
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dataInfoAsAttributes(root, dataInfo);
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}
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if (value != null && !StringUtils.isEmpty(value))
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root.addProperty("value", value);
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343
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344
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if (root.entrySet().size() > 0)
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metadata.add(name, root);
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}
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348
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349
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private void getAttributes(final FieldTypeProtos.Qualifier q, JsonObject root) {
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350
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if (q == null) return;
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q.getAllFields().entrySet().forEach(e -> root.addProperty(e.getKey().getName(), e.getValue().toString()));
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352
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353
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}
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356
|
private void dataInfoAsAttributes(final JsonObject root, final FieldTypeProtos.DataInfo dataInfo) {
|
|
357
|
root.addProperty("inferred", dataInfo.getInferred());
|
|
358
|
root.addProperty("inferenceprovenance", dataInfo.getInferenceprovenance());
|
|
359
|
root.addProperty("provenanceaction", dataInfo.getProvenanceaction().getClassid());
|
|
360
|
root.addProperty("trust", dataInfo.getTrust());
|
|
361
|
|
|
362
|
}
|
|
363
|
|
|
364
|
|
|
365
|
}
|