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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.util.HashMap;
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import java.util.HashSet;
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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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import org.apache.log4j.Logger;
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import org.springframework.stereotype.Component;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.io.berlinModel.in.validation.BerlinModelOccurrenceSourceImportValidator;
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import eu.etaxonomy.cdm.io.common.IOValidator;
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import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;
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import eu.etaxonomy.cdm.io.common.Source;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.RelationshipBase.Direction;
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import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
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import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
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import eu.etaxonomy.cdm.model.description.Distribution;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.name.NameRelationshipType;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.reference.OriginalSourceType;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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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.taxon.TaxonNode;
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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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@Component
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public class BerlinModelOccurrenceSourceImport extends BerlinModelImportBase {
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private static final long serialVersionUID = 1139543760239436841L;
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private static final Logger logger = Logger.getLogger(BerlinModelOccurrenceSourceImport.class);
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private static int modCount = 5000;
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private static final String pluralString = "occurrence sources";
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private static final String dbTableName = "emOccurrenceSource"; //??
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private static final String EXACT = "(exact) ";
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private Map<String, Integer> sourceNumberRefIdMap;
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private Map<String, Set<Integer>> nameCache2NameIdMap;
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private Set<String> notFoundReferences = new HashSet<>();
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public BerlinModelOccurrenceSourceImport(){
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super(dbTableName, pluralString);
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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 occurrenceSourceId FROM " + getTableName();
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if (state.getConfig().getOccurrenceSourceFilter() != null){
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result += " WHERE " + state.getConfig().getOccurrenceSourceFilter();
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}
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return result;
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}
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@Override
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protected String getRecordQuery(BerlinModelImportConfigurator config) {
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String strQuery = //DISTINCT because otherwise emOccurrenceSource creates multiple records for a single distribution
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" SELECT occ.*, n.nameCache, n.fullNameCache " +
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" FROM emOccurrenceSource occ LEFT OUTER JOIN Name n ON n.nameId = occ.oldNameFk " +
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" WHERE (OccurrenceSourceId IN (" + ID_LIST_TOKEN + ") )" +
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"";
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return strQuery;
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}
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@Override
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protected void doInvoke(BerlinModelImportState state) {
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notFoundReferences = new HashSet<>();
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try {
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sourceNumberRefIdMap = makeSourceNumberReferenceIdMap(state);
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nameCache2NameIdMap = makeNameCache2NameIdMap(state);
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} catch (SQLException e) {
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e.printStackTrace();
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throw new RuntimeException(e);
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}
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super.doInvoke(state);
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sourceNumberRefIdMap = null;
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nameCache2NameIdMap = null;
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if (notFoundReferences.size()>0){
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String unfound = "'" + CdmUtils.concat("','", notFoundReferences.toArray(new String[]{})) + "'";
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logger.warn("Not found references: " + unfound);
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}
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return;
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}
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@Override
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public boolean doPartition(@SuppressWarnings("rawtypes") ResultSetPartitioner partitioner, BerlinModelImportState state) {
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boolean success = true;
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ResultSet rs = partitioner.getResultSet();
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@SuppressWarnings("unchecked")
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Map<String, Reference> refMap = partitioner.getObjectMap(BerlinModelReferenceImport.REFERENCE_NAMESPACE);
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Set<DescriptionElementBase> objectsToSave = new HashSet<>();
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try {
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int i = 0;
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//for each reference
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while (rs.next()){
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if ((i++ % modCount) == 0 && i!= 1 ){ logger.info("occurrence sources handled: " + (i-1));}
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Integer occurrenceSourceId = rs.getInt("OccurrenceSourceId");
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Integer occurrenceFk =nullSafeInt(rs, "OccurrenceFk");
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String sourceNumber = rs.getString("SourceNumber");
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String oldName = rs.getString("OldName");
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Integer oldNameFk = nullSafeInt(rs, "OldNameFk");
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String oldNameFkCache = rs.getString("nameCache");
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String oldNameFkFullCache = rs.getString("fullNameCache");
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Distribution distribution = (Distribution)state.getRelatedObject(BerlinModelOccurrenceImport.NAMESPACE, String.valueOf(occurrenceFk));
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if (distribution == null){
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//distribution = duplicateMap.get(occurrenceFk);
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}
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if (distribution != null){
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Integer refId = sourceNumberRefIdMap.get(sourceNumber);
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Reference ref = refMap.get(String.valueOf(refId));
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if (ref != null){
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DescriptionElementSource originalSource = DescriptionElementSource.NewInstance(OriginalSourceType.PrimaryTaxonomicSource);
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originalSource.setCitation(ref);
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TaxonName taxonName = getName(state, oldName, oldNameFk, oldNameFkFullCache, oldNameFkCache, occurrenceSourceId, distribution);
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if (taxonName != null){
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if(isNotBlank(oldName) && !oldName.equals(taxonName.getNameCache())){
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originalSource.setOriginalNameString(oldName);
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}
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originalSource.setNameUsedInSource(taxonName);
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}else if(isNotBlank(oldName)){
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originalSource.setOriginalNameString(oldName);
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}
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distribution.addSource(originalSource);
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}else{
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logger.warn("reference for sourceNumber "+sourceNumber+" could not be found. OccurrenceSourceId: " + occurrenceSourceId );
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notFoundReferences.add(sourceNumber);
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}
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}else{
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logger.warn("distribution ("+occurrenceFk+") for occurrence source (" + occurrenceSourceId + ") could not be found." );
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}
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}
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logger.info("Distributions to save: " + objectsToSave.size());
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getDescriptionElementService().save(objectsToSave);
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return success;
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} catch (SQLException e) {
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logger.error("SQLException:" + e);
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return false;
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}
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}
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@Override
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public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, BerlinModelImportState state) {
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String nameSpace;
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Set<String> idSet;
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Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();
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try{
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Set<String> occurrenceIdSet = new HashSet<>();
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Set<String> nameIdSet = new HashSet<>();
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Set<String> sourceNumberSet = new HashSet<>();
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Set<String> oldNamesSet = new HashSet<>();
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while (rs.next()){
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handleForeignKey(rs, occurrenceIdSet, "occurrenceFk");
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handleForeignKey(rs, nameIdSet, "oldNameFk");
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sourceNumberSet.add(CdmUtils.NzTrim(rs.getString("SourceNumber")));
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oldNamesSet.add(CdmUtils.NzTrim(rs.getString("oldName")));
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oldNamesSet.add(CdmUtils.NzTrim(rs.getString("nameCache")));
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oldNamesSet.add(CdmUtils.NzTrim(rs.getString("fullNameCache")));
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}
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sourceNumberSet.remove("");
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Set<String> referenceIdSet = handleSourceNumber(sourceNumberSet);
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oldNamesSet.remove("");
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Set<String> oldNameIdSet = handleRelatedOldNames(oldNamesSet);
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nameIdSet.addAll(oldNameIdSet);
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//occurrence map
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nameSpace = BerlinModelOccurrenceImport.NAMESPACE;
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idSet = occurrenceIdSet;
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Map<String, Distribution> occurrenceMap = getCommonService().getSourcedObjectsByIdInSourceC(Distribution.class, idSet, nameSpace);
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result.put(nameSpace, occurrenceMap);
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//name map
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nameSpace = BerlinModelTaxonNameImport.NAMESPACE;
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idSet =nameIdSet;
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Map<String, TaxonName> nameMap = getCommonService().getSourcedObjectsByIdInSourceC(TaxonName.class, idSet, nameSpace);
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result.put(nameSpace, nameMap);
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//reference map
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nameSpace = BerlinModelReferenceImport.REFERENCE_NAMESPACE;
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Map<String, Reference> referenceMap = getCommonService().getSourcedObjectsByIdInSourceC(Reference.class, idSet, nameSpace);
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result.put(nameSpace, referenceMap);
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} catch (SQLException e) {
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throw new RuntimeException(e);
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}
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return result;
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}
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private Set<String> handleSourceNumber(Set<String> sourceNumberSet) {
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Map<String, Integer> sourceNumberReferenceIdMap = this.sourceNumberRefIdMap;
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Set<String> referenceIdSet = new HashSet<>();
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for(String sourceNumber : sourceNumberSet){
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Integer refId = sourceNumberReferenceIdMap.get(sourceNumber);
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referenceIdSet.add(String.valueOf(refId));
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}
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return referenceIdSet;
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}
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private Set<String> handleRelatedOldNames(Set<String> oldNamesSet) {
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Set<String> oldNameIdSet = new HashSet<>();
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try {
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for(String oldName : oldNamesSet){
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if (isNotBlank(oldName)){
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Set<Integer> nameIds = nameCache2NameIdMap.get(oldName);
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if (nameIds != null){
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for (Integer nameId : nameIds){
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oldNameIdSet.add(String.valueOf(nameId));
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}
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}
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}
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}
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} catch (Exception e) {
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e.printStackTrace();
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logger.error("Exception in handleOldNames" + e.getMessage());
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}
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return oldNameIdSet;
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}
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private TaxonName getName(BerlinModelImportState state, String oldNameStr, Integer oldNameFk,
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String oldNameFkFullCache, String oldNameFkCache,
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Integer occSourceId, Distribution distribution) {
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if (oldNameStr == null && oldNameFk == null){
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return null;
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}
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boolean includeMisapplications = state.getConfig().isIncludeMANsForOldNameCheck();
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TaxonName taxonName = (TaxonName)state.getRelatedObject(BerlinModelTaxonNameImport.NAMESPACE, String.valueOf(oldNameFk));
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if (oldNameFk != null && taxonName == null){
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//move down if occ source names are not loaded in name view
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taxonName = handleOldFreetextNameOnly(state, oldNameFkFullCache, occSourceId, distribution);
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if (taxonName == null){
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taxonName = handleOldFreetextNameOnly(state, oldNameFkCache, occSourceId, distribution);
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}
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if (taxonName == null ){
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logger.warn("WARN: OldNameFk "+oldNameFk+" exists but taxonName not found and also search by string not successful for occSource: " + occSourceId +"; Taxon: "+getTaxonStr(distribution));
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oldNameStr = oldNameFkFullCache;
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}
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}else if (taxonName != null){
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taxonName = checkSynonymy(state, oldNameFk, occSourceId, distribution, taxonName, includeMisapplications);
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}
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if (isNotBlank(oldNameStr) && oldNameStr != null){
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if (taxonName == null){
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return handleOldFreetextNameOnly(state, oldNameStr, occSourceId, distribution);
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}else if (!oldNameStr.equals(taxonName.getNameCache())){
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logger.info("INFO: Old name freetext and linked name nameCache are not equal: " + oldNameStr + "/" + taxonName.getNameCache() +"; Taxon: "+getTaxonStr(distribution) + "; occSourceId: " + occSourceId);
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checkSynonymy(state, oldNameFk, occSourceId, distribution, taxonName, includeMisapplications);
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return taxonName;
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}else{
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checkSynonymy(state, oldNameFk, occSourceId, distribution, taxonName, includeMisapplications);
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return taxonName;
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}
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285
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}else{ //taxonName != null
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286
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if (taxonName != null){
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287
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checkSynonymy(state, oldNameFk, occSourceId, distribution, taxonName, includeMisapplications);
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288
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}
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289
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return taxonName;
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290
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}
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291
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}
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292
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293
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/**
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* @param state
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295
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* @param oldName
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296
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* @param occSourceId
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297
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* @param distribution
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* @return
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299
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*/
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300
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protected TaxonName handleOldFreetextNameOnly(BerlinModelImportState state, String oldName, Integer occSourceId,
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Distribution distribution) {
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Set<TaxonName> names = getOldNames(state, oldName);
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303
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if (names.isEmpty()){
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304
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if (getNameIds(oldName).isEmpty()){
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305
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if (state.getConfig().isLogNotMatchingOldNames()){
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306
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logger.warn("No name found for freetext oldName '"+oldName+"'; occSourceId: " + occSourceId);
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}
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308
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}else{
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309
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if (state.getConfig().isLogMatchingNotExportedOldNames()){
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logger.warn("Matching name exists in BM but not in CDM. OldName: " + oldName + "; Taxon: "+getTaxonStr(distribution)+"; occSourceId: " + occSourceId);
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311
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}
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312
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}
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return null;
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314
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}else {
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315
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TaxonName result = names.iterator().next();
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316
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boolean checkOldNameIsSynonym = state.getConfig().isCheckOldNameIsSynonym();
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317
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if (names.size()> 1){
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318
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TaxonName synName = getFirstSynonymName(state, names, distribution, null, occSourceId, true);
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319
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if (synName == null){
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320
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//TODO should we really use a name if not available in synonymy?
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String message = "INFO: There is more than one matching oldName for '"+oldName+"' but none of them is a synonym of the accepted taxon '"+getTaxonStr(distribution)+"'.";
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message += (checkOldNameIsSynonym ? "":"Take arbitrary one. ") + "OccSourceId: " + occSourceId;
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logger.info(message);
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return checkOldNameIsSynonym ? null : result;
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}else{
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return synName;
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}
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328
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}else{
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329
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//names.size() = 1
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330
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if (checkOldNameIsSynonym){
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TaxonName synName = getFirstSynonymName(state, names, distribution, null, occSourceId, true);
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332
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if (synName == null){
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333
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if (state.getConfig().isCheckOldNameIsSynonym()){
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334
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logger.warn("There is a matching oldName for '"+oldName+"' but it is not a synonym/misapplication of the accepted taxon '"+getTaxonStr(distribution)+"'. OccSourceId: " + occSourceId);
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335
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return null;
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336
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}else{
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337
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return result;
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338
|
}
|
|
339
|
}else if (!synName.equals(result)){
|
|
340
|
//TODO strange, how can this happen if it is the only matching?
|
|
341
|
logger.warn("There is a matching oldName for '"+oldName+"'("+result.getUuid()+") but another matching name "+synName.getUuid()+"exists in the synonymy of the accepted taxon '"+getTaxonStr(distribution)+"'. OccSourceId: " + occSourceId);
|
|
342
|
return synName;
|
|
343
|
}else{
|
|
344
|
return result;
|
|
345
|
}
|
|
346
|
}else{
|
|
347
|
return result;
|
|
348
|
}
|
|
349
|
}
|
|
350
|
}
|
|
351
|
}
|
|
352
|
|
|
353
|
protected TaxonName checkSynonymy(BerlinModelImportState state, Integer oldNameFk, Integer occSourceId,
|
|
354
|
Distribution distribution, TaxonName taxonName, boolean includeMisapplications) {
|
|
355
|
|
|
356
|
if (!state.getConfig().isCheckOldNameIsSynonym()){
|
|
357
|
return taxonName;
|
|
358
|
}else{
|
|
359
|
Set<TaxonName> names = new HashSet<>();
|
|
360
|
names.add(taxonName);
|
|
361
|
TaxonName synName = getFirstSynonymName(state, names, distribution, null, occSourceId, includeMisapplications);
|
|
362
|
if (synName != null){
|
|
363
|
return synName; //same as taxonName?
|
|
364
|
}else{
|
|
365
|
boolean hasTaxon = !taxonName.getTaxonBases().isEmpty();
|
|
366
|
String orphaned = hasTaxon ? "" : "Orphaned name: ";
|
|
367
|
Set<TaxonName> existingNames = getOldNames(state, taxonName.getNameCache());
|
|
368
|
existingNames.remove(taxonName);
|
|
369
|
if (existingNames.isEmpty()){
|
|
370
|
logger.info("INFO:" + orphaned + "NameInSource (" + oldNameFk + " - " +taxonName.getTitleCache() + ") could not be found in synonymy. Similar name does not exist. Use the not in synonymy name. "+getTaxonStr(distribution)+". OccSourceId: " + occSourceId);
|
|
371
|
return taxonName;
|
|
372
|
}else{
|
|
373
|
TaxonName existingSynonym = getFirstSynonymName(state, existingNames, distribution, null, occSourceId, false);
|
|
374
|
if (existingSynonym != null){
|
|
375
|
boolean isExact = CdmUtils.nullSafeEqual(existingSynonym.getTitleCache(),taxonName.getTitleCache());
|
|
376
|
String exact = isExact ? EXACT : "";
|
|
377
|
logger.info("INFO: " + exact + orphaned + "A similar name ("+existingSynonym.getUuid()+") was found in synonymy but is not the nameInSource. Use synonymie name (" + oldNameFk + " - " +taxonName.getTitleCache() + "); Taxon: "+getTaxonStr(distribution)+". OccSourceId: " + occSourceId);
|
|
378
|
return existingSynonym;
|
|
379
|
}else{
|
|
380
|
TaxonName existingMisapplication = getFirstMisapplication(state, existingNames, distribution, occSourceId);
|
|
381
|
if (existingMisapplication != null){
|
|
382
|
boolean isExact = CdmUtils.nullSafeEqual(existingMisapplication.getTitleCache(),taxonName.getTitleCache());
|
|
383
|
String exact = isExact ? EXACT : "";
|
|
384
|
logger.info("INFO: " + exact + orphaned + "A similar misapplied name ("+existingMisapplication.getUuid()+") can be found in misapplications but is not the nameInSource. Use synonymie name (" + oldNameFk + " - " +taxonName.getTitleCache() + "); Taxon: "+getTaxonStr(distribution)+". OccSourceId: " + occSourceId);
|
|
385
|
return existingMisapplication;
|
|
386
|
}else{
|
|
387
|
logger.info("INFO: NameInSource not found in synonymy. Similar names exist but also not in synonymy. Use name in source (" + oldNameFk + " - " +taxonName.getTitleCache() + "); Taxon: "+getTaxonStr(distribution)+". OccSourceId: " + occSourceId);
|
|
388
|
return taxonName;
|
|
389
|
}
|
|
390
|
}
|
|
391
|
}
|
|
392
|
}
|
|
393
|
}
|
|
394
|
}
|
|
395
|
|
|
396
|
private TaxonName getFirstSynonymName(BerlinModelImportState state, Set<TaxonName> names, Distribution distribution,
|
|
397
|
Taxon taxon, Integer occSourceId, boolean includeMisapplications) {
|
|
398
|
TaxonName result = null;
|
|
399
|
taxon = (taxon == null) ? getTaxon(distribution): taxon;
|
|
400
|
Set<Synonym> synonyms = taxon.getSynonyms();
|
|
401
|
Set<TaxonName> synonymNames = new HashSet<>();
|
|
402
|
|
|
403
|
//taxon, orthvars, synonyms and their orthvars
|
|
404
|
synonymNames.add(taxon.getName());
|
|
405
|
synonymNames.addAll(getOrthographicVariants(taxon));
|
|
406
|
|
|
407
|
for (Synonym synonym : synonyms){
|
|
408
|
synonymNames.add(synonym.getName());
|
|
409
|
synonymNames.addAll(getOrthographicVariants(synonym));
|
|
410
|
}
|
|
411
|
for (TaxonName name : names){
|
|
412
|
if (synonymNames.contains(name)){
|
|
413
|
if (result != null){
|
|
414
|
logger.warn("There is more than 1 matching synonym/taxon for " + name.getNameCache() + "; occSourceId: " + occSourceId);
|
|
415
|
}
|
|
416
|
result = name;
|
|
417
|
}
|
|
418
|
}
|
|
419
|
|
|
420
|
//parent
|
|
421
|
if (result == null){
|
|
422
|
if (taxon.getName().isInfraSpecific()){
|
|
423
|
if (!taxon.getTaxonNodes().isEmpty()){
|
|
424
|
TaxonNode parent = taxon.getTaxonNodes().iterator().next().getParent();
|
|
425
|
if (parent != null && parent.getTaxon() != null){
|
|
426
|
Set<TaxonName> parentNames = new HashSet<>();
|
|
427
|
TaxonName parentName = parent.getTaxon().getName();
|
|
428
|
parentNames.add(parentName);
|
|
429
|
parentNames.addAll(getOrthographicVariants(parent.getTaxon()));
|
|
430
|
|
|
431
|
for (TaxonName name : names){
|
|
432
|
if (parentNames.contains(name)){
|
|
433
|
if (result != null){
|
|
434
|
logger.warn("There is more than 1 matching parent for " + name.getNameCache() + "; occSourceId: " + occSourceId);
|
|
435
|
}
|
|
436
|
result = name;
|
|
437
|
}
|
|
438
|
}
|
|
439
|
if (result == null){
|
|
440
|
TaxonName parentSyn = getFirstSynonymName(state, names, distribution, parent.getTaxon(), occSourceId, includeMisapplications);
|
|
441
|
if (parentSyn != null){
|
|
442
|
result = parentSyn;
|
|
443
|
}
|
|
444
|
}
|
|
445
|
}
|
|
446
|
}
|
|
447
|
}
|
|
448
|
}
|
|
449
|
|
|
450
|
//child
|
|
451
|
if (result == null){
|
|
452
|
if (taxon.getName().isSpecies() || taxon.getName().isSupraSpecific()){
|
|
453
|
if (!taxon.getTaxonNodes().isEmpty()){
|
|
454
|
List<TaxonNode> children = taxon.getTaxonNodes().iterator().next().getChildNodes();
|
|
455
|
Set<TaxonName> childNames = new HashSet<>();
|
|
456
|
for (TaxonNode child : children){
|
|
457
|
childNames.add(child.getTaxon().getName());
|
|
458
|
childNames.addAll(getOrthographicVariants(child.getTaxon()));
|
|
459
|
}
|
|
460
|
for (TaxonName name : names){
|
|
461
|
if (childNames.contains(name)){
|
|
462
|
if (result != null){
|
|
463
|
logger.warn("There is more than 1 matching child for " + name.getNameCache() + "; occSourceId: " + occSourceId);
|
|
464
|
}
|
|
465
|
result = name;
|
|
466
|
}
|
|
467
|
}
|
|
468
|
}
|
|
469
|
}
|
|
470
|
}
|
|
471
|
|
|
472
|
if (result == null && includeMisapplications){
|
|
473
|
result = getFirstMisapplication(state, names, distribution, occSourceId);
|
|
474
|
}
|
|
475
|
|
|
476
|
return result;
|
|
477
|
}
|
|
478
|
|
|
479
|
private TaxonName getFirstMisapplication(BerlinModelImportState state, Set<TaxonName> names, Distribution distribution, Integer occSourceId) {
|
|
480
|
TaxonName result = null;
|
|
481
|
Taxon taxon = getTaxon(distribution);
|
|
482
|
|
|
483
|
//MAN
|
|
484
|
Set<Taxon> misappliedTaxa = taxon.getMisappliedNames(true);
|
|
485
|
Set<TaxonName> misappliedNames = new HashSet<>();
|
|
486
|
for (Taxon misTaxon : misappliedTaxa){
|
|
487
|
misappliedNames.add(misTaxon.getName());
|
|
488
|
misappliedNames.addAll(getOrthographicVariants(misTaxon));
|
|
489
|
}
|
|
490
|
|
|
491
|
for (TaxonName name : names){
|
|
492
|
if (misappliedNames.contains(name)){
|
|
493
|
if (result != null){
|
|
494
|
logger.info("INFO: There is more than 1 matching misapplied name or invalid designation for " + name.getNameCache() + ". Take arbitrary one.; occSourceId: " + occSourceId);
|
|
495
|
}
|
|
496
|
result = name;
|
|
497
|
}
|
|
498
|
}
|
|
499
|
return result;
|
|
500
|
}
|
|
501
|
|
|
502
|
protected Set<TaxonName> getOrthographicVariants(TaxonBase<?> taxonBase) {
|
|
503
|
Set<TaxonName> result = taxonBase.getName().getRelatedNames(Direction.relatedTo, NameRelationshipType.ORTHOGRAPHIC_VARIANT());
|
|
504
|
result.addAll(taxonBase.getName().getRelatedNames(Direction.relatedTo, NameRelationshipType.MISSPELLING()));
|
|
505
|
result.add(taxonBase.getName().getOriginalSpelling());
|
|
506
|
return result;
|
|
507
|
}
|
|
508
|
|
|
509
|
protected String getTaxonStr(Distribution distribution) {
|
|
510
|
Taxon taxon = CdmBase.deproxy(distribution.getInDescription(), TaxonDescription.class).getTaxon();
|
|
511
|
String areaStr = distribution.getArea().getIdInVocabulary();
|
|
512
|
return areaStr + ": " + taxon.getName().getTitleCache();
|
|
513
|
}
|
|
514
|
|
|
515
|
protected Taxon getTaxon(Distribution distribution) {
|
|
516
|
Taxon taxon = CdmBase.deproxy(distribution.getInDescription(), TaxonDescription.class).getTaxon();
|
|
517
|
return taxon;
|
|
518
|
}
|
|
519
|
|
|
520
|
/**
|
|
521
|
* returns all names in DB matching the given name string.
|
|
522
|
* The name needs to be loaded via related objects previously.
|
|
523
|
*/
|
|
524
|
private Set<TaxonName> getOldNames(BerlinModelImportState state, String nameStr) {
|
|
525
|
Set<TaxonName> names = new HashSet<>();
|
|
526
|
Set<Integer> nameIds = getNameIds(nameStr);
|
|
527
|
for (Integer id : nameIds){
|
|
528
|
TaxonName name = (TaxonName)state.getRelatedObject(BerlinModelTaxonNameImport.NAMESPACE, String.valueOf(id));
|
|
529
|
if (name != null){
|
|
530
|
names.add(name);
|
|
531
|
}else{
|
|
532
|
// logger.warn("Name for existing id "+id+" not found in related objects: " + nameStr);
|
|
533
|
}
|
|
534
|
}
|
|
535
|
return names;
|
|
536
|
}
|
|
537
|
|
|
538
|
private Set<Integer> getNameIds(String oldName) {
|
|
539
|
Set<Integer> result = nameCache2NameIdMap.get(oldName);
|
|
540
|
return result == null ? new HashSet<>(): result;
|
|
541
|
}
|
|
542
|
|
|
543
|
/**
|
|
544
|
* Creates a map which maps source numbers on references
|
|
545
|
*/
|
|
546
|
private Map<String, Integer> makeSourceNumberReferenceIdMap(BerlinModelImportState state) throws SQLException {
|
|
547
|
Map<String, Integer> result = new HashMap<>();
|
|
548
|
|
|
549
|
Source source = state.getConfig().getSource();
|
|
550
|
String strQuery = " SELECT RefId, IdInSource " +
|
|
551
|
" FROM Reference " +
|
|
552
|
" WHERE (IdInSource IS NOT NULL) AND (IdInSource NOT LIKE '') ";
|
|
553
|
|
|
554
|
ResultSet rs = source.getResultSet(strQuery) ;
|
|
555
|
while (rs.next()){
|
|
556
|
int refId = rs.getInt("RefId");
|
|
557
|
String idInSource = rs.getString("IdInSource");
|
|
558
|
if (idInSource != null){
|
|
559
|
String[] singleSources = idInSource.split("\\|");
|
|
560
|
for (String singleSource : singleSources){
|
|
561
|
singleSource = singleSource.trim();
|
|
562
|
result.put(singleSource, refId);
|
|
563
|
}
|
|
564
|
}
|
|
565
|
}
|
|
566
|
return result;
|
|
567
|
}
|
|
568
|
|
|
569
|
/**
|
|
570
|
* Creates a map which maps nameCaches to nameIDs numbers on references
|
|
571
|
* @param state
|
|
572
|
* @return
|
|
573
|
* @throws SQLException
|
|
574
|
*/
|
|
575
|
private Map<String, Set<Integer>> makeNameCache2NameIdMap(BerlinModelImportState state) throws SQLException {
|
|
576
|
Map<String, Set<Integer>> result = new HashMap<>();
|
|
577
|
try {
|
|
578
|
|
|
579
|
Source source = state.getConfig().getSource();
|
|
580
|
String strQuery = " SELECT NameId, nameCache " +
|
|
581
|
" FROM Name " +
|
|
582
|
" WHERE (nameCache IS NOT NULL) AND (nameCache NOT LIKE '') ";
|
|
583
|
|
|
584
|
ResultSet rs = source.getResultSet(strQuery) ;
|
|
585
|
while (rs.next()){
|
|
586
|
int nameId = rs.getInt("NameId");
|
|
587
|
String nameCache = rs.getString("nameCache");
|
|
588
|
if (isNotBlank(nameCache)){
|
|
589
|
nameCache = nameCache.trim();
|
|
590
|
Set<Integer> set = result.get(nameCache);
|
|
591
|
if (set == null){
|
|
592
|
set = new HashSet<>();
|
|
593
|
result.put(nameCache, set);
|
|
594
|
}
|
|
595
|
set.add(nameId);
|
|
596
|
}
|
|
597
|
}
|
|
598
|
} catch (Exception e) {
|
|
599
|
e.printStackTrace();
|
|
600
|
logger.error("Exception in makeNameCache2NameIdMap" + e.getMessage());
|
|
601
|
}
|
|
602
|
return result;
|
|
603
|
}
|
|
604
|
|
|
605
|
@Override
|
|
606
|
protected boolean doCheck(BerlinModelImportState state){
|
|
607
|
IOValidator<BerlinModelImportState> validator = new BerlinModelOccurrenceSourceImportValidator();
|
|
608
|
return validator.validate(state);
|
|
609
|
}
|
|
610
|
|
|
611
|
@Override
|
|
612
|
protected boolean isIgnore(BerlinModelImportState state){
|
|
613
|
if (! state.getConfig().isDoOccurrenceSources()){
|
|
614
|
return true;
|
|
615
|
}else{
|
|
616
|
if (!this.checkSqlServerColumnExists(state.getConfig().getSource(), "emOccurrenceSource", "OccurrenceSourceId")){
|
|
617
|
logger.error("emOccurrenceSource table or emOccurrenceSourceId does not exist. Must ignore occurrence import");
|
|
618
|
return true;
|
|
619
|
}else{
|
|
620
|
return false;
|
|
621
|
}
|
|
622
|
}
|
|
623
|
}
|
|
624
|
}
|