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/**
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* Copyright (C) 2007 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.io.berlinModel.in;
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import java.sql.ResultSet;
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import java.sql.SQLException;
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import java.sql.Timestamp;
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import java.util.Map;
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import org.apache.log4j.Logger;
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import org.joda.time.DateTime;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer;
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import eu.etaxonomy.cdm.io.common.DbImportBase;
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import eu.etaxonomy.cdm.io.common.ICdmIO;
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import eu.etaxonomy.cdm.io.common.IImportConfigurator.EDITOR;
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import eu.etaxonomy.cdm.io.common.IPartitionedIO;
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import eu.etaxonomy.cdm.io.common.TdwgAreaProvider;
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import eu.etaxonomy.cdm.model.common.AnnotatableEntity;
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import eu.etaxonomy.cdm.model.common.Annotation;
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import eu.etaxonomy.cdm.model.common.AnnotationType;
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import eu.etaxonomy.cdm.model.common.ISourceable;
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import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
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import eu.etaxonomy.cdm.model.common.IdentifiableSource;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.common.MarkerType;
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import eu.etaxonomy.cdm.model.common.User;
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import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
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import eu.etaxonomy.cdm.model.location.Country;
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import eu.etaxonomy.cdm.model.location.NamedArea;
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import eu.etaxonomy.cdm.model.location.NamedAreaType;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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import eu.etaxonomy.cdm.model.term.TermType;
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import eu.etaxonomy.cdm.model.term.TermVocabulary;
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/**
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* @author a.mueller
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* @since 20.03.2008
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*/
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public abstract class BerlinModelImportBase
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extends DbImportBase<BerlinModelImportState, BerlinModelImportConfigurator>
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implements ICdmIO<BerlinModelImportState>, IPartitionedIO<BerlinModelImportState> {
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private static final long serialVersionUID = -4982506434258587864L;
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private static final Logger logger = Logger.getLogger(BerlinModelImportBase.class);
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public BerlinModelImportBase(String tableName, String pluralString ) {
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super(tableName, pluralString);
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}
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/**
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* @return
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*/
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@Override
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protected String getIdQuery(BerlinModelImportState state){
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String result = " SELECT " + getTableName() + "id FROM " + getTableName();
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return result;
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}
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protected boolean doIdCreatedUpdatedNotes(BerlinModelImportState state, DescriptionElementBase descriptionElement, ResultSet rs, String id, String namespace) throws SQLException{
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boolean success = true;
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//id
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success &= doId(state, descriptionElement, id, namespace);
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//createdUpdateNotes
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success &= doCreatedUpdatedNotes(state, descriptionElement, rs);
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return success;
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}
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protected boolean doIdCreatedUpdatedNotes(BerlinModelImportState state, IdentifiableEntity identifiableEntity, ResultSet rs, long id, String namespace, boolean excludeUpdated, boolean excludeNotes)
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throws SQLException{
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boolean success = true;
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//id
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success &= doId(state, identifiableEntity, id, namespace);
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//createdUpdateNotes
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success &= doCreatedUpdatedNotes(state, identifiableEntity, rs, excludeUpdated, excludeNotes);
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return success;
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}
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protected boolean doIdCreatedUpdatedNotes(BerlinModelImportState state, IdentifiableEntity identifiableEntity, ResultSet rs, long id, String namespace)
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throws SQLException{
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boolean excludeUpdated = false;
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return doIdCreatedUpdatedNotes(state, identifiableEntity, rs, id, namespace, excludeUpdated, false);
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}
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protected boolean doCreatedUpdatedNotes(BerlinModelImportState state, AnnotatableEntity annotatableEntity, ResultSet rs)
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throws SQLException{
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boolean excludeUpdated = false;
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return doCreatedUpdatedNotes(state, annotatableEntity, rs, excludeUpdated, false);
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}
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protected boolean doCreatedUpdatedNotes(BerlinModelImportState state, AnnotatableEntity annotatableEntity,
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ResultSet rs, boolean excludeUpdated, boolean excludeNotes)
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throws SQLException{
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BerlinModelImportConfigurator config = state.getConfig();
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Object createdWhen = rs.getObject("Created_When");
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String createdWho = rs.getString("Created_Who");
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createdWho = handleHieraciumPilosella(createdWho);
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Object updatedWhen = null;
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String updatedWho = null;
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if (excludeUpdated == false){
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try {
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updatedWhen = rs.getObject("Updated_When");
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updatedWho = rs.getString("Updated_who");
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} catch (SQLException e) {
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//Table "Name" has no updated when/who
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}
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}
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String notes = rs.getString("notes");
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boolean success = true;
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//Created When, Who, Updated When Who
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if (config.getEditor() == null || config.getEditor().equals(EDITOR.NO_EDITORS)){
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//do nothing
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}else if (config.getEditor().equals(EDITOR.EDITOR_AS_ANNOTATION)){
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String createdAnnotationString = "Berlin Model record was created By: " + String.valueOf(createdWho) + " (" + String.valueOf(createdWhen) + ") ";
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if (updatedWhen != null && updatedWho != null){
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createdAnnotationString += " and updated By: " + String.valueOf(updatedWho) + " (" + String.valueOf(updatedWhen) + ")";
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}
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Annotation annotation = Annotation.NewInstance(createdAnnotationString, Language.DEFAULT());
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//TODO make transaction compatible, same as common sec reference
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annotation.setCommentator(config.getCommentator());
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annotation.setAnnotationType(AnnotationType.TECHNICAL());
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annotatableEntity.addAnnotation(annotation);
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}else if (config.getEditor().equals(EDITOR.EDITOR_AS_EDITOR)){
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User creator = getUser(state, createdWho);
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User updator = getUser(state, updatedWho);
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DateTime created = getDateTime(createdWhen);
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DateTime updated = getDateTime(updatedWhen);
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annotatableEntity.setCreatedBy(creator);
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annotatableEntity.setUpdatedBy(updator);
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annotatableEntity.setCreated(created);
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annotatableEntity.setUpdated(updated);
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}else {
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logger.warn("Editor type not yet implemented: " + config.getEditor());
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}
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//notes
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if (! excludeNotes){
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doNotes(annotatableEntity, notes);
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}
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return success;
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}
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/**
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* Special usecase for EDITWP6 import where in the createdWho field the original ID is stored
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* @param createdWho
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* @return
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*/
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private String handleHieraciumPilosella(String createdWho) {
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String result = createdWho;
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if (result == null){
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return null;
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}else if (result.startsWith("Hieracium_Pilosella import from EM")){
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return "Hieracium_Pilosella import from EM";
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}else{
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return result;
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}
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}
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private DateTime getDateTime(Object timeString){
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if (timeString == null){
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return null;
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}
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DateTime dateTime = null;
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if (timeString instanceof Timestamp){
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Timestamp timestamp = (Timestamp)timeString;
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dateTime = new DateTime(timestamp);
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}else{
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logger.warn("time ("+timeString+") is not a timestamp. Datetime set to current date. ");
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dateTime = new DateTime();
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}
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return dateTime;
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}
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/**
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* @param state
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* @param newTaxonId
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* @param taxonMap
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* @param factId
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* @return
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*/
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protected Taxon getTaxon(BerlinModelImportState state, int taxonId, Map<String, TaxonBase> taxonMap, int factId) {
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TaxonBase<?> taxonBase = taxonMap.get(String.valueOf(taxonId));
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//TODO for testing
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// if (taxonBase == null && ! state.getConfig().isDoTaxa()){
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// taxonBase = Taxon.NewInstance(TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES()), null);
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// }
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Taxon taxon;
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if ( taxonBase instanceof Taxon ) {
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taxon = (Taxon) taxonBase;
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} else if (taxonBase != null) {
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logger.warn("TaxonBase (" + taxonId + ") for Fact(Specimen) with factId " + factId + " was not of type Taxon but: " + taxonBase.getClass().getSimpleName());
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return null;
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} else {
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logger.warn("TaxonBase (" + taxonId + ") for Fact(Specimen) with factId " + factId + " is null.");
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return null;
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}
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return taxon;
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}
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/**
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* Searches first in the detail maps then in the ref maps for a reference.
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* Returns the reference as soon as it finds it in one of the map, according
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* to the order of the map.
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* If nomRefDetailFk is <code>null</code> no search on detail maps is performed.
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* If one of the maps is <code>null</code> no search on the according map is
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* performed. <BR>
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* You may define the order of search by the order you pass the maps but
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* make sure to always pass the detail maps first.
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* @param firstDetailMap
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* @param secondDetailMap
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* @param firstRefMap
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* @param secondRefMap
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* @param nomRefDetailFk
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* @param nomRefFk
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* @return
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*/
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protected Reference getReferenceFromMaps(
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Map<String, Reference> detailMap,
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Map<String, Reference> refMap,
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String nomRefDetailFk,
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String nomRefFk) {
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Reference ref = null;
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if (detailMap != null){
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ref = detailMap.get(nomRefDetailFk);
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}
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if (ref == null){
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ref = refMap.get(nomRefFk);
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}
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return ref;
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}
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/**
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* Searches for a reference in the first detail map. If it does not exist it
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* searches in the second detail map. Returns null if it does not exist in any map.
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* A map may be <code>null</code> to avoid search on this map.
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* @param secondDetailMap
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* @param firstDetailMap
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* @param nomRefDetailFk
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* @return
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*/
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private Reference getReferenceDetailFromMaps(Map<String, Reference> firstDetailMap, Map<String, Reference> secondDetailMap, String nomRefDetailFk) {
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Reference result = null;
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if (nomRefDetailFk != null){
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//get ref
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if (firstDetailMap != null){
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result = firstDetailMap.get(nomRefDetailFk);
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}
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if (result == null && secondDetailMap != null){
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result = secondDetailMap.get(nomRefDetailFk);
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}
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}
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return result;
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}
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protected NamedArea getOtherAreas(BerlinModelImportState state, String emCodeString, String tdwgCodeString) {
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String em = CdmUtils.Nz(emCodeString).trim();
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String tdwg = CdmUtils.Nz(tdwgCodeString).trim();
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//Cichorieae + E+M
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if ("EM".equals(em)){
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return getNamedArea(state, BerlinModelTransformer.euroMedUuid, "Euro+Med", "Euro+Med area", "EM", null, null);
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}else if("Rf".equals(em)){
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return Country.RUSSIANFEDERATION();
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}else if("KRY-OO;UKR-UK".equals(tdwg)){
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return Country.UKRAINE();
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}else if("TCS-AZ;TCS-NA".equals(tdwg)){
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return Country.AZERBAIJANREPUBLICOF();
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}else if("TCS-AB;TCS-AD;TCS-GR".equals(tdwg)){
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return Country.GEORGIA();
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}else if("Cc".equals(em)){
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return getNamedArea(state, BerlinModelTransformer.uuidCaucasia, "Caucasia (Ab + Ar + Gg + Rf(CS))", "Euro+Med area 'Caucasia (Ab + Ar + Gg + Rf(CS))'", "Cc", null, null);
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}
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//E+M
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else if("EUR".equals(em)){
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return TdwgAreaProvider.getAreaByTdwgAbbreviation("1");
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}else if("14".equals(em)){
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return TdwgAreaProvider.getAreaByTdwgAbbreviation("14");
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}else if("21".equals(em)){
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return TdwgAreaProvider.getAreaByTdwgAbbreviation("21"); // Macaronesia
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}else if("33".equals(em)){
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return TdwgAreaProvider.getAreaByTdwgAbbreviation("33");
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}else if("SM".equals(em)){
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return getNamedArea(state, BerlinModelTransformer.uuidSerbiaMontenegro, "Serbia & Montenegro", "Euro+Med area 'Serbia & Montenegro'", "SM", NamedAreaType.ADMINISTRATION_AREA(), null);
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}else if("Sr".equals(em)){
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return getNamedArea(state, BerlinModelTransformer.uuidSerbia, "Serbia", "Euro+Med area 'Serbia' (including Kosovo and Vojvodina)", "Sr", NamedAreaType.ADMINISTRATION_AREA(), null);
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//see #2769
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}else if("Rs".equals(em)){
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return getNamedArea(state, BerlinModelTransformer.uuidUssr, "Former USSR", "Euro+Med area 'Former USSR'", "Rs", NamedAreaType.ADMINISTRATION_AREA(), null);
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}else if("Rs(N)".equals(em)){
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return getNamedArea(state, BerlinModelTransformer.uuidRussiaNorthern, "Russia Northern", "Euro+Med area 'Russia Northern'", "Rs(N)", null, null);
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}else if("Rs(B)".equals(em)){
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return getNamedArea(state, BerlinModelTransformer.uuidRussiaBaltic, "Russia Baltic", "Euro+Med area 'Russia Baltic'", "Rs(B)", null, null);
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}else if("Rs(C)".equals(em)){
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return getNamedArea(state, BerlinModelTransformer.uuidRussiaCentral, "Russia Central", "Euro+Med area 'Russia Central'", "Rs(C)", null, null);
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}else if("Rs(W)".equals(em)){
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return getNamedArea(state, BerlinModelTransformer.uuidRussiaSouthWest, "Russia Southwest", "Euro+Med area 'Russia Southwest'", "Rs(W)", null, null);
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}else if("Rs(E)".equals(em)){
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return getNamedArea(state, BerlinModelTransformer.uuidRussiaSouthEast, "Russia Southeast", "Euro+Med area 'Russia Southeast'", "Rs(E)", null, null);
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//see #2770
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}else if("AE".equals(em)){
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return getNamedArea(state, BerlinModelTransformer.uuidEastAegeanIslands, "East Aegean Islands", "Euro+Med area 'East Aegean Islands'", "AE", null, null);
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}else if("AE(T)".equals(em)){
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return getNamedArea(state, BerlinModelTransformer.uuidTurkishEastAegeanIslands, "Turkish East Aegean Islands", "Euro+Med area 'Turkish East Aegean Islands'", "AE(T)", null, null);
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}else if("Tu".equals(em)){
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return getNamedArea(state, BerlinModelTransformer.uuidTurkey, "Turkey", "Euro+Med area 'Turkey' (without AE(T))", "Tu", null, null);
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//TODO Azores, Canary Is.
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|
335
|
}else if("Md(D)".equals(em)){
|
|
336
|
return getNamedArea(state, BerlinModelTransformer.uuidDesertas, "Desertas", "Euro+Med area 'Desertas'", "Md(D)", null, null);
|
|
337
|
}else if("Md(M)".equals(em)){
|
|
338
|
return getNamedArea(state, BerlinModelTransformer.uuidMadeira, "Madeira", "Euro+Med area 'Madeira'", "Md(M)", null, null);
|
|
339
|
}else if("Md(P)".equals(em)){
|
|
340
|
return getNamedArea(state, BerlinModelTransformer.uuidPortoSanto, "Porto Santo", "Euro+Med area 'Porto Santo'", "Md(P)", null, null);
|
|
341
|
//Azores
|
|
342
|
}else if("Az(L)".equals(em)){
|
|
343
|
return getNamedArea(state, BerlinModelTransformer.uuidFlores, "Flores", "Euro+Med area 'Flores'", "Az(L)", null, null);
|
|
344
|
}else if("Az(C)".equals(em)){
|
|
345
|
return getNamedArea(state, BerlinModelTransformer.uuidCorvo, "Corvo", "Euro+Med area 'Corvo'", "Az(C)", null, null);
|
|
346
|
}else if("Az(F)".equals(em)){
|
|
347
|
return getNamedArea(state, BerlinModelTransformer.uuidFaial, "Faial", "Euro+Med area 'Faial'", "Az(F)", null, null);
|
|
348
|
}else if("Az(G)".equals(em)){
|
|
349
|
return getNamedArea(state, BerlinModelTransformer.uuidGraciosa, "Graciosa", "Euro+Med area 'Graciosa'", "Az(G)", null, null);
|
|
350
|
}else if("Az(J)".equals(em)){
|
|
351
|
return getNamedArea(state, BerlinModelTransformer.uuidSaoJorge, "S\u00E3o Jorge", "Euro+Med area 'S\u00E3o Jorge'", "Az(J)", null, null);
|
|
352
|
}else if("Az(M)".equals(em)){
|
|
353
|
return getNamedArea(state, BerlinModelTransformer.uuidSaoMiguel, "S\u00E3o Miguel", "Euro+Med area 'S\u00E3o Miguel'", "Az(M)", null, null);
|
|
354
|
}else if("Az(P)".equals(em)){
|
|
355
|
return getNamedArea(state, BerlinModelTransformer.uuidPico, "Pico", "Euro+Med area 'Pico'", "Az(P)", null, null);
|
|
356
|
}else if("Az(S)".equals(em)){
|
|
357
|
return getNamedArea(state, BerlinModelTransformer.uuidSantaMaria, "Santa Maria", "Euro+Med area 'Santa Maria'", "Az(S)", null, null);
|
|
358
|
}else if("Az(T)".equals(em)){
|
|
359
|
return getNamedArea(state, BerlinModelTransformer.uuidTerceira, "Terceira", "Euro+Med area 'Terceira'", "Az(T)", null, null);
|
|
360
|
//Canary Islands
|
|
361
|
}else if("Ca(C)".equals(em)){
|
|
362
|
return getNamedArea(state, BerlinModelTransformer.uuidGranCanaria, "Gran Canaria", "Euro+Med area 'Gran Canaria'", "Ca(C)", null, null);
|
|
363
|
}else if("Ca(F)".equals(em)){
|
|
364
|
return getNamedArea(state, BerlinModelTransformer.uuidFuerteventura, "Fuerteventura with Lobos", "Euro+Med area 'Fuerteventura with Lobos'", "Ca(F)", null, null);
|
|
365
|
}else if("Ca(G)".equals(em)){
|
|
366
|
return getNamedArea(state, BerlinModelTransformer.uuidGomera, "Gomera", "Euro+Med area 'Gomera'", "Ca(G)", null, null);
|
|
367
|
}else if("Ca(H)".equals(em)){
|
|
368
|
return getNamedArea(state, BerlinModelTransformer.uuidHierro, "Hierro", "Euro+Med area 'Hierro'", "Ca(H)", null, null);
|
|
369
|
}else if("Ca(L)".equals(em)){
|
|
370
|
return getNamedArea(state, BerlinModelTransformer.uuidLanzaroteWithGraciosa, "Lanzarote with Graciosa", "Euro+Med area 'Lanzarote with Graciosa'", "Ca(L)", null, null);
|
|
371
|
}else if("Ca(P)".equals(em)){
|
|
372
|
return getNamedArea(state, BerlinModelTransformer.uuidLaPalma, "La Palma", "Euro+Med area 'La Palma'", "Ca(P)", null, null);
|
|
373
|
}else if("Ca(T)".equals(em)){
|
|
374
|
return getNamedArea(state, BerlinModelTransformer.uuidTenerife, "Tenerife", "Euro+Med area 'Tenerife'", "Ca(T)", null, null);
|
|
375
|
//Baleares
|
|
376
|
}else if("Bl(I)".equals(em)){
|
|
377
|
return getNamedArea(state, BerlinModelTransformer.uuidIbizaWithFormentera, "Ibiza with Formentera", "Euro+Med area 'Ibiza with Formentera'", "Bl(I)", null, null);
|
|
378
|
}else if("Bl(M)".equals(em)){
|
|
379
|
return getNamedArea(state, BerlinModelTransformer.uuidTerceira, "Mallorca", "Euro+Med area 'Mallorca'", "Bl(M)", null, null);
|
|
380
|
}else if("Bl(N)".equals(em)){
|
|
381
|
return getNamedArea(state, BerlinModelTransformer.uuidTerceira, "Menorca", "Euro+Med area 'Menorca'", "Bl(N)", null, null);
|
|
382
|
}
|
|
383
|
|
|
384
|
logger.warn("Area(em: '" + em + "', tdwg: '" + tdwg +"') could not be found");
|
|
385
|
|
|
386
|
return null;
|
|
387
|
}
|
|
388
|
|
|
389
|
/**
|
|
390
|
* @return
|
|
391
|
*/
|
|
392
|
protected TermVocabulary<MarkerType> getEuroMedMarkerTypeVoc() {
|
|
393
|
TermVocabulary<MarkerType> markerTypeVoc = getVocabulary(TermType.MarkerType, BerlinModelTransformer.uuidVocEMMarkerType,
|
|
394
|
"Euro+Med marker type vocabulary", "E+M marker types", null, null, false, MarkerType.COMPLETE());
|
|
395
|
return markerTypeVoc;
|
|
396
|
}
|
|
397
|
|
|
398
|
|
|
399
|
/**
|
|
400
|
* @param sourceReference
|
|
401
|
* @return
|
|
402
|
*/
|
|
403
|
protected Reference getSourceReference(Reference sourceReference) {
|
|
404
|
Reference persistentSourceReference = getReferenceService().find(sourceReference.getUuid()); //just to be sure
|
|
405
|
if (persistentSourceReference != null){
|
|
406
|
sourceReference = persistentSourceReference;
|
|
407
|
}
|
|
408
|
return sourceReference;
|
|
409
|
}
|
|
410
|
|
|
411
|
protected static <T extends IdentifiableSource> boolean importSourceExists(ISourceable<T> sourceable, String idInSource,
|
|
412
|
String namespace, Reference ref) {
|
|
413
|
for (T source : sourceable.getSources()){
|
|
414
|
if (CdmUtils.nullSafeEqual(namespace, source.getIdNamespace()) &&
|
|
415
|
CdmUtils.nullSafeEqual(idInSource, source.getIdInSource()) &&
|
|
416
|
CdmUtils.nullSafeEqual(ref, source.getCitation())){
|
|
417
|
return true;
|
|
418
|
}
|
|
419
|
}
|
|
420
|
return false;
|
|
421
|
}
|
|
422
|
|
|
423
|
}
|