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package eu.dnetlib.data.transform.xml;
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3
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import com.google.common.base.Predicate;
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import com.google.common.base.Predicates;
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import com.google.common.base.Splitter;
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import com.google.common.collect.Iterables;
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import com.google.common.collect.Lists;
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import com.google.protobuf.Descriptors.Descriptor;
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import com.google.protobuf.Descriptors.FieldDescriptor;
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import com.google.protobuf.InvalidProtocolBufferException;
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import com.google.protobuf.Message;
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import com.google.protobuf.Message.Builder;
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import com.google.protobuf.ProtocolMessageEnum;
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import eu.dnetlib.data.proto.DNGFProtos.DNGF;
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import eu.dnetlib.data.proto.DNGFProtos.DNGFEntity;
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import eu.dnetlib.data.proto.DNGFProtos.DNGFRel;
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import eu.dnetlib.data.proto.FieldTypeProtos.*;
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import eu.dnetlib.data.proto.FieldTypeProtos.OAIProvenance.OriginDescription;
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import eu.dnetlib.data.proto.KindProtos.Kind;
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import eu.dnetlib.data.proto.TypeProtos.Type;
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import eu.dnetlib.miscutils.collections.Pair;
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import org.apache.commons.codec.binary.Base64;
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import org.apache.commons.codec.binary.Hex;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.commons.lang3.math.NumberUtils;
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import org.w3c.dom.NamedNodeMap;
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import org.w3c.dom.Node;
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import org.w3c.dom.NodeList;
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import java.nio.charset.Charset;
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import java.security.MessageDigest;
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import java.util.Iterator;
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import java.util.List;
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import java.util.Map;
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public abstract class AbstractDNetXsltFunctions {
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public static final String URL_REGEX = "^(http|https|ftp)\\://.*";
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private static final int MAX_NSPREFIX_LEN = 12;
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public static Predicate<String> urlFilter = s -> s.trim().matches(URL_REGEX);
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// Builder for Entities
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protected static DNGF getOaf(final DNGFEntity.Builder entity, final DataInfo.Builder info) {
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return _getOaf(DNGF.newBuilder(), info).setKind(Kind.entity).setEntity(entity).build();
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}
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// Builder for Rels
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protected static DNGF getOaf(final DNGFRel.Builder rel, final DataInfo.Builder info) {
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return _getOaf(DNGF.newBuilder(), info).setKind(Kind.relation).setRel(rel).build();
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}
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private static DNGF.Builder _getOaf(final DNGF.Builder oaf, final DataInfo.Builder info) {
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if (info != null) {
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return oaf.setDataInfo(ensureDataInfo(info));
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} else return oaf;
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}
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protected static DataInfo.Builder ensureDataInfo(final DataInfo.Builder info) {
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if (info.isInitialized()) return info;
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return getDataInfo(null, "UNKNOWN", "0.9", false, false);
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}
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protected static KeyValue getKV(final String id, final String name) {
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return KeyValue.newBuilder().setKey(id).setValue(name).build();
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}
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protected static DNGFRel.Builder getRel(
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final String sourceId,
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final Type sourceType,
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final String targetId,
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final Type targetType,
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final Qualifier relType,
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final boolean isChild) {
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return DNGFRel.newBuilder().setSource(sourceId).setTarget(targetId).setRelType(relType)
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.setChild(isChild);
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}
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protected static DNGFEntity.Builder getEntity(final Type type,
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final String id,
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final KeyValue collectedFrom,
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final List<String> originalIds,
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final String dateOfCollection,
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final String dateOfTransformation,
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final List<StructuredProperty> pids) {
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final DNGFEntity.Builder builder = DNGFEntity.newBuilder().setType(type).setId(id);
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if (collectedFrom != null) builder.addCollectedfrom(collectedFrom);
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builder.setDateoftransformation(StringUtils.isBlank(dateOfTransformation) ? "" : dateOfTransformation);
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builder.setDateofcollection(StringUtils.isBlank(dateOfCollection) ? "" : dateOfCollection);
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if ((originalIds != null) && !originalIds.isEmpty()) {
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builder.addAllOriginalId(Iterables.filter(originalIds, getPredicateNotBlankString()));
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}
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if ((pids != null) && !pids.isEmpty()) {
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builder.addAllPid(Iterables.filter(pids, Predicates.notNull()));
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}
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return builder;
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}
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public static Predicate<String> getPredicateNotBlankString() {
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return s -> StringUtils.isNotBlank(s);
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}
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public static DataInfo.Builder getDataInfo(final NodeList about,
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final String provenanceaction,
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final String trust,
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final boolean deletedbyinference,
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final boolean inferred) {
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final DataInfo.Builder dataInfoBuilder = DataInfo.newBuilder();
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dataInfoBuilder.setInferred(Boolean.valueOf(inferred));
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dataInfoBuilder.setDeletedbyinference(Boolean.valueOf(deletedbyinference));
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dataInfoBuilder.setTrust(trust);
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dataInfoBuilder.setProvenanceaction(getSimpleQualifier(provenanceaction, "dnet:provenanceActions").build());
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// checking instanceof because when receiving an empty <oaf:datainfo> we don't want to parse it.
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if (((about != null) && (about.getLength() > 0)) /* && (dataInfo instanceof org.w3c.dom.Element) */) {
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final org.w3c.dom.Element dataInfoElement = getDirectChild((org.w3c.dom.Element) about.item(0), "datainfo");
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if (dataInfoElement != null) {
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org.w3c.dom.Element elem = getDirectChild(dataInfoElement, "inferred");
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dataInfoBuilder.setInferred(Boolean.valueOf(getStringValue(elem, String.valueOf(inferred))));
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elem = getDirectChild(dataInfoElement, "deletedbyinference");
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dataInfoBuilder.setDeletedbyinference(Boolean.valueOf(getStringValue(elem, String.valueOf(deletedbyinference))));
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elem = getDirectChild(dataInfoElement, "trust");
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dataInfoBuilder.setTrust(getStringValue(elem, trust));
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elem = getDirectChild(dataInfoElement, "inferenceprovenance");
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dataInfoBuilder.setInferenceprovenance(getStringValue(elem));
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elem = getDirectChild(dataInfoElement, "provenanceaction");
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final Qualifier.Builder pBuilder = Qualifier.newBuilder();
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if (elem != null && elem.hasAttributes()) {
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final NamedNodeMap attributes = elem.getAttributes();
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pBuilder.setClassid(getAttributeValue(attributes, "classid"));
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pBuilder.setClassname(getAttributeValue(attributes, "classname"));
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pBuilder.setSchemeid(getAttributeValue(attributes, "schemeid"));
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pBuilder.setSchemename(getAttributeValue(attributes, "schemename"));
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} else {
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pBuilder.mergeFrom(getSimpleQualifier(provenanceaction, "dnet:provenanceActions").build());
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}
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dataInfoBuilder.setProvenanceaction(pBuilder);
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}
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}
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return dataInfoBuilder;
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}
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protected static OAIProvenance getOAIProvenance(final NodeList about) {
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OAIProvenance.Builder oaiProv = OAIProvenance.newBuilder();
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if (((about != null) && (about.getLength() > 0))) {
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final org.w3c.dom.Element provenance = getDirectChild((org.w3c.dom.Element) about.item(0), "provenance");
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if (provenance != null) {
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final org.w3c.dom.Element origDesc = getDirectChild(provenance, "originDescription");
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oaiProv.setOriginDescription(buildOriginDescription(origDesc, OriginDescription.newBuilder()));
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}
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}
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return oaiProv.build();
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}
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private static OriginDescription buildOriginDescription(final org.w3c.dom.Element origDesc, final OriginDescription.Builder od) {
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od.setHarvestDate(origDesc.getAttribute("harvestDate")).setAltered(Boolean.valueOf(origDesc.getAttribute("altered")));
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org.w3c.dom.Element elem = getDirectChild(origDesc, "baseURL");
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od.setBaseURL(getStringValue(elem));
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elem = getDirectChild(origDesc, "identifier");
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od.setIdentifier(getStringValue(elem));
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elem = getDirectChild(origDesc, "datestamp");
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od.setDatestamp(getStringValue(elem));
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elem = getDirectChild(origDesc, "metadataNamespace");
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od.setMetadataNamespace(getStringValue(elem));
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elem = getDirectChild(origDesc, "originDescription");
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if (elem != null) {
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od.setOriginDescription(buildOriginDescription(elem, OriginDescription.newBuilder()));
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}
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return od.build();
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}
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private static String getStringValue(final org.w3c.dom.Element elem, final String defaultValue) {
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return (elem != null && elem.getTextContent() != null) ? elem.getTextContent() : defaultValue;
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}
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private static String getStringValue(final org.w3c.dom.Element elem) {
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return getStringValue(elem, "");
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}
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protected static String getAttributeValue(final NamedNodeMap attributes, final String name) {
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final Node attr = attributes.getNamedItem(name);
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if (attr == null) return "";
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final String value = attr.getNodeValue();
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return value != null ? value : "";
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}
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protected static org.w3c.dom.Element getDirectChild(final org.w3c.dom.Element parent, final String name) {
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for (Node child = parent.getFirstChild(); child != null; child = child.getNextSibling()) {
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if ((child instanceof org.w3c.dom.Element) && name.equals(child.getLocalName())) return (org.w3c.dom.Element) child;
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}
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return null;
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}
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protected static Qualifier.Builder getSimpleQualifier(final String classname, final String schemename) {
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return getQualifier(classname, classname, schemename, schemename);
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}
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protected static Qualifier.Builder getSimpleQualifier(final ProtocolMessageEnum classname, final String schemename) {
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return getQualifier(classname.toString(), classname.toString(), schemename, schemename);
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}
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protected static Qualifier.Builder getQualifier(final String classid, final String classname, final String schemeid, final String schemename) {
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return Qualifier.newBuilder().setClassid(classid).setClassname(classname).setSchemeid(schemeid).setSchemename(schemename);
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}
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230
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protected static Qualifier.Builder setQualifier(final Qualifier.Builder qualifier, final List<String> fields) {
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if ((fields == null) || fields.isEmpty() || fields.get(0).isEmpty()) return null;
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232
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233
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if ((fields != null) && !fields.isEmpty() && (fields.get(0) != null)) {
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qualifier.setClassid(fields.get(0));
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qualifier.setClassname(fields.get(0));
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236
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}
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237
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return qualifier;
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238
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}
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239
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240
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protected static void addStructuredProps(final Builder builder,
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241
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final FieldDescriptor fd,
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242
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final List<String> values,
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243
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final String classid,
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244
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final String schemeid) {
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245
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if (values != null) {
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246
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for (final String s : values) {
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247
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addField(builder, fd, getStructuredProperty(s, classid, classid, schemeid, schemeid));
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248
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}
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249
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}
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250
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}
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251
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252
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protected static List<StructuredProperty> parsePids(final NodeList nodelist) {
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253
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254
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final List<StructuredProperty> pids = Lists.newArrayList();
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255
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256
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for (int i = 0; i < nodelist.getLength(); i++) {
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257
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final Node node = nodelist.item(i);
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258
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Node pidType = null;
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259
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if (node.getNodeType() == Node.ELEMENT_NODE) {
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260
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if (node.getLocalName().equalsIgnoreCase("identifier")) {
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261
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pidType = node.getAttributes().getNamedItem("identifierType");
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262
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}
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263
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//this is to handle dataset pids
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264
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if (node.getLocalName().equalsIgnoreCase("alternateIdentifier")) {
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265
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pidType = node.getAttributes().getNamedItem("alternateIdentifierType");
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266
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}
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267
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268
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for (int j = 0; j < node.getChildNodes().getLength(); j++) {
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269
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final Node child = node.getChildNodes().item(j);
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270
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271
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if ((child.getNodeType() == Node.TEXT_NODE) && (pidType != null) && (pidType.getNodeValue() != null) && !pidType.getNodeValue().isEmpty()
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272
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&& !pidType.getNodeValue().equalsIgnoreCase("url")) {
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273
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274
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final String type = pidType.getNodeValue().toLowerCase();
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275
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|
276
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final String value = child.getTextContent();
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277
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278
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pids.add(getStructuredProperty(value, type, type, "dnet:pid_types", "dnet:pid_types"));
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279
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break;
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|
280
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}
|
|
281
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}
|
|
282
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}
|
|
283
|
}
|
|
284
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return pids;
|
|
285
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}
|
|
286
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|
|
287
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@SuppressWarnings("unchecked")
|
|
288
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protected static void addField(final Builder builder, final FieldDescriptor descriptor, Object value) {
|
|
289
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|
|
290
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if (value == null) return;
|
|
291
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|
|
292
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if (value instanceof List<?>) {
|
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293
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for (final Object o : (List<Object>) value) {
|
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294
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addField(builder, descriptor, o);
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|
295
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}
|
|
296
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} else {
|
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297
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Object fieldValue = value;
|
|
298
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switch (descriptor.getType()) {
|
|
299
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case BOOL:
|
|
300
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fieldValue = Boolean.valueOf(value.toString());
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301
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break;
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|
302
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case BYTES:
|
|
303
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fieldValue = value.toString().getBytes(Charset.forName("UTF-8"));
|
|
304
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break;
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305
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case DOUBLE:
|
|
306
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fieldValue = Double.valueOf(value.toString());
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|
307
|
break;
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|
308
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case FLOAT:
|
|
309
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fieldValue = Float.valueOf(value.toString());
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|
310
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break;
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|
311
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case INT32:
|
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312
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case INT64:
|
|
313
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case SINT32:
|
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314
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case SINT64:
|
|
315
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fieldValue = Integer.valueOf(value.toString());
|
|
316
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break;
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|
317
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case MESSAGE:
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|
318
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final Builder q = builder.newBuilderForField(descriptor);
|
|
319
|
|
|
320
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if (value instanceof Builder) {
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321
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value = ((Builder) value).build();
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322
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final byte[] b = ((Message) value).toByteArray();
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|
323
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try {
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324
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q.mergeFrom(b);
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325
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} catch (final InvalidProtocolBufferException e) {
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|
326
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throw new IllegalArgumentException("Unable to merge value: " + value + " with builder: " + q.getDescriptorForType().getName());
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|
327
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}
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|
328
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} else if (Qualifier.getDescriptor().getName().equals(q.getDescriptorForType().getName())) {
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329
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if (value instanceof Qualifier) {
|
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330
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q.mergeFrom((Qualifier) value);
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331
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} else {
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332
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parseMessage(q, Qualifier.getDescriptor(), value.toString(), "@@@");
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|
333
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}
|
|
334
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} else if (StructuredProperty.getDescriptor().getName().equals(q.getDescriptorForType().getName())) {
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|
335
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if (value instanceof StructuredProperty) {
|
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336
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q.mergeFrom((StructuredProperty) value);
|
|
337
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} else {
|
|
338
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parseMessage(q, StructuredProperty.getDescriptor(), value.toString(), "###");
|
|
339
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}
|
|
340
|
} else if (KeyValue.getDescriptor().getName().equals(q.getDescriptorForType().getName())) {
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|
341
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if (value instanceof KeyValue) {
|
|
342
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q.mergeFrom((KeyValue) value);
|
|
343
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} else {
|
|
344
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parseMessage(q, KeyValue.getDescriptor(), value.toString(), "&&&");
|
|
345
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}
|
|
346
|
} else if (StringField.getDescriptor().getName().equals(q.getDescriptorForType().getName())) {
|
|
347
|
if (value instanceof StringField) {
|
|
348
|
q.mergeFrom((StringField) value);
|
|
349
|
} else {
|
|
350
|
q.setField(StringField.getDescriptor().findFieldByName("value"), value);
|
|
351
|
}
|
|
352
|
} else if (BoolField.getDescriptor().getName().equals(q.getDescriptorForType().getName())) {
|
|
353
|
if (value instanceof BoolField) {
|
|
354
|
q.mergeFrom((BoolField) value);
|
|
355
|
} else if (value instanceof String) {
|
|
356
|
q.setField(BoolField.getDescriptor().findFieldByName("value"), Boolean.valueOf((String) value));
|
|
357
|
} else {
|
|
358
|
q.setField(BoolField.getDescriptor().findFieldByName("value"), value);
|
|
359
|
}
|
|
360
|
} else if (IntField.getDescriptor().getName().equals(q.getDescriptorForType().getName())) {
|
|
361
|
if (value instanceof IntField) {
|
|
362
|
q.mergeFrom((IntField) value);
|
|
363
|
} else if (value instanceof String) {
|
|
364
|
q.setField(IntField.getDescriptor().findFieldByName("value"), NumberUtils.toInt((String) value));
|
|
365
|
} else {
|
|
366
|
q.setField(IntField.getDescriptor().findFieldByName("value"), value);
|
|
367
|
}
|
|
368
|
}
|
|
369
|
|
|
370
|
fieldValue = q.buildPartial();
|
|
371
|
break;
|
|
372
|
default:
|
|
373
|
break;
|
|
374
|
}
|
|
375
|
|
|
376
|
doAddField(builder, descriptor, fieldValue);
|
|
377
|
}
|
|
378
|
|
|
379
|
}
|
|
380
|
|
|
381
|
protected static void doAddField(final Builder builder, final FieldDescriptor fd, final Object value) {
|
|
382
|
if (value != null) {
|
|
383
|
if (fd.isRepeated()) {
|
|
384
|
builder.addRepeatedField(fd, value);
|
|
385
|
} else if (fd.isOptional() || fd.isRequired()) {
|
|
386
|
builder.setField(fd, value);
|
|
387
|
}
|
|
388
|
}
|
|
389
|
}
|
|
390
|
|
|
391
|
protected static void parseMessage(final Builder builder, final Descriptor descriptor, final String value, final String split) {
|
|
392
|
|
|
393
|
Iterable<Pair> iterablePair = () -> {
|
|
394
|
|
|
395
|
final Iterator<FieldDescriptor> fields = descriptor.getFields().iterator();
|
|
396
|
final Iterator<String> values = Lists.newArrayList(Splitter.on(split).trimResults().split(value)).iterator();
|
|
397
|
|
|
398
|
return new Iterator<Pair>() {
|
|
399
|
@Override
|
|
400
|
public boolean hasNext() {
|
|
401
|
return fields.hasNext() && values.hasNext();
|
|
402
|
}
|
|
403
|
|
|
404
|
@Override
|
|
405
|
public Pair next() {
|
|
406
|
final FieldDescriptor field = fields.next();
|
|
407
|
final String value1 = values.next();
|
|
408
|
return new Pair(field, value1);
|
|
409
|
}
|
|
410
|
|
|
411
|
@Override
|
|
412
|
public void remove() {
|
|
413
|
throw new UnsupportedOperationException("cannot remove");
|
|
414
|
}
|
|
415
|
};
|
|
416
|
};
|
|
417
|
|
|
418
|
// final IterablePair<FieldDescriptor, String> iterablePair =
|
|
419
|
// new IterablePair<FieldDescriptor, String>(descriptor.getFields(), Lists.newArrayList(Splitter
|
|
420
|
// .on(split).trimResults().split(value)));
|
|
421
|
|
|
422
|
for (final Pair<FieldDescriptor, String> p : iterablePair) {
|
|
423
|
addField(builder, p.getKey(), p.getValue());
|
|
424
|
}
|
|
425
|
}
|
|
426
|
|
|
427
|
protected static String base64(final byte[] data) {
|
|
428
|
final byte[] bytes = Base64.encodeBase64(data);
|
|
429
|
return new String(bytes);
|
|
430
|
}
|
|
431
|
|
|
432
|
public static String replace(final String s, final String regex, final String replacement) {
|
|
433
|
return s.replaceAll(regex, replacement);
|
|
434
|
}
|
|
435
|
|
|
436
|
public static String trim(final String s) {
|
|
437
|
return s.trim();
|
|
438
|
}
|
|
439
|
|
|
440
|
protected static String removePrefix(final Type type, final String s) {
|
|
441
|
return removePrefix(type.toString(), s);
|
|
442
|
}
|
|
443
|
|
|
444
|
private static String removePrefix(final String prefix, final String s) {
|
|
445
|
return StringUtils.removeStart("" + s, prefix + "|");
|
|
446
|
}
|
|
447
|
|
|
448
|
protected static Qualifier.Builder getDefaultQualifier(final String scheme) {
|
|
449
|
final Qualifier.Builder qualifier = Qualifier.newBuilder().setSchemeid(scheme).setSchemename(scheme);
|
|
450
|
return qualifier;
|
|
451
|
}
|
|
452
|
|
|
453
|
protected static StructuredProperty getStructuredProperty(final String value,
|
|
454
|
final String classid,
|
|
455
|
final String classname,
|
|
456
|
final String schemeid,
|
|
457
|
final String schemename) {
|
|
458
|
if ((value == null) || value.isEmpty()) return null;
|
|
459
|
return StructuredProperty.newBuilder().setValue(value).setQualifier(getQualifier(classid, classname, schemeid, schemename)).build();
|
|
460
|
}
|
|
461
|
|
|
462
|
protected static StringField.Builder sf(final String s) {
|
|
463
|
return StringField.newBuilder().setValue(s);
|
|
464
|
}
|
|
465
|
|
|
466
|
public static String generateNsPrefix(final String prefix, final String externalId) {
|
|
467
|
return StringUtils.substring(prefix + StringUtils.leftPad(externalId, MAX_NSPREFIX_LEN - prefix.length(), "_"), 0, MAX_NSPREFIX_LEN);
|
|
468
|
}
|
|
469
|
|
|
470
|
public static String md5(final String s) {
|
|
471
|
try {
|
|
472
|
final MessageDigest md = MessageDigest.getInstance("MD5");
|
|
473
|
md.update(s.getBytes("UTF-8"));
|
|
474
|
return new String(Hex.encodeHex(md.digest()));
|
|
475
|
} catch (final Exception e) {
|
|
476
|
System.err.println("Error creating id");
|
|
477
|
return null;
|
|
478
|
}
|
|
479
|
}
|
|
480
|
|
|
481
|
public static String oafId(final String entityType, final String prefix, final String id) {
|
|
482
|
if (id.isEmpty() || prefix.isEmpty()) return "";
|
|
483
|
return oafSimpleId(entityType, prefix + "::" + md5(id));
|
|
484
|
}
|
|
485
|
|
|
486
|
public static String oafSimpleId(final String entityType, final String id) {
|
|
487
|
return (Type.valueOf(entityType).getNumber() + "|" + id).replaceAll("\\s|\\n", "");
|
|
488
|
}
|
|
489
|
|
|
490
|
public static String oafSplitId(final String entityType, final String fullId) {
|
|
491
|
return oafId(entityType, StringUtils.substringBefore(fullId, "::"), StringUtils.substringAfter(fullId, "::"));
|
|
492
|
}
|
|
493
|
|
|
494
|
/**
|
|
495
|
* Utility method, allows to perform param based map lookups in xsl
|
|
496
|
*
|
|
497
|
* @param map
|
|
498
|
* @param key
|
|
499
|
* @return value associated to the key.
|
|
500
|
*/
|
|
501
|
public static Object lookupValue(final Map<String, Object> map, final String key) {
|
|
502
|
return map.get(key);
|
|
503
|
}
|
|
504
|
|
|
505
|
/**
|
|
506
|
* Utility method, allows to perform param based map lookups in xsl
|
|
507
|
*
|
|
508
|
* @param map
|
|
509
|
* @param key
|
|
510
|
* @return value associated to the key.
|
|
511
|
*/
|
|
512
|
public static int mustMerge(final Map<String, Object> map, final String key) {
|
|
513
|
final Object val = lookupValue(map, key);
|
|
514
|
return (val != null) && (val instanceof String) && val.equals("true") ? 1 : 0;
|
|
515
|
}
|
|
516
|
|
|
517
|
}
|