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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 static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_HAS_SAME_TYPE_AS;
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import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_ALTERNATIVE_NAME_FOR;
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import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_BASIONYM_FOR;
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import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_CONSERVED_TYPE_OF;
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import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_FEMALE_PARENT_OF;
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import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_FIRST_PARENT_OF;
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import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_LATER_HOMONYM_OF;
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import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_LATER_VALIDATION_OF;
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import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_LECTOTYPE_OF;
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import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_MALE_PARENT_OF;
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import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_ORTHOGRAPHIC_VARIANT_OF;
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import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_REJECTED_TYPE_OF;
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import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_REPLACED_SYNONYM_FOR;
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import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_SECOND_PARENT_OF;
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import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_TREATED_AS_LATER_HOMONYM_OF;
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import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_TYPE_OF;
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import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_VALIDATION_OF;
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import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_TYPE_NOT_DESIGNATED;
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import java.lang.reflect.Method;
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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.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.io.berlinModel.BerlinModelTransformer;
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import eu.etaxonomy.cdm.io.berlinModel.in.validation.BerlinModelTaxonNameRelationImportValidator;
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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.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.CdmBase;
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import eu.etaxonomy.cdm.model.name.HybridRelationshipType;
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import eu.etaxonomy.cdm.model.name.IBotanicalName;
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import eu.etaxonomy.cdm.model.name.NameRelationshipType;
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import eu.etaxonomy.cdm.model.name.NameTypeDesignationStatus;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
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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 BerlinModelTaxonNameRelationImport extends BerlinModelImportBase {
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private static final long serialVersionUID = 1197601822023101796L;
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private static final Logger logger = Logger.getLogger(BerlinModelTaxonNameRelationImport.class);
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private static int modCount = 5000;
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private static final String pluralString = "name relations";
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private static final String dbTableName = "RelName";
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public BerlinModelTaxonNameRelationImport(){
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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 nameIdTable = state.getConfig().getNameIdTable();
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String result = super.getIdQuery(state);
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if (isNotBlank(nameIdTable)){
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if (state.getConfig().isEuroMed()){
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result += " WHERE nameFk1 IN (SELECT NameId FROM %s) AND RelNameQualifierFk IN (2, 4, 5, 13, 14, 15, 17, 18, 37, 62) OR ";
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result += " nameFk2 IN (SELECT NameId FROM %s) ";
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//the first part is only to check if there are relations that we have maybe missed.
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//2 is unclear, 17 should be in both, 62 links names to itself
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result = String.format(result, nameIdTable, nameIdTable);
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}else{
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result += " WHERE nameFk1 IN (SELECT NameId FROM %s) OR ";
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result += " nameFk2 IN (SELECT NameId FROM %s) ";
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result = String.format(result, nameIdTable, nameIdTable );
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}
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}else{
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//
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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 =
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" SELECT RelName.*, FromName.nameId as name1Id, ToName.nameId as name2Id, RefDetail.Details " +
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" FROM Name as FromName INNER JOIN " +
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" RelName ON FromName.NameId = RelName.NameFk1 INNER JOIN " +
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" Name AS ToName ON RelName.NameFk2 = ToName.NameId LEFT OUTER JOIN "+
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" RefDetail ON RelName.RefDetailFK = RefDetail.RefDetailId " +
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" WHERE (RelNameId IN ("+ID_LIST_TOKEN +"))";
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return strQuery;
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}
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@Override
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public boolean doPartition(ResultSetPartitioner partitioner, BerlinModelImportState state) {
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boolean success = true ;
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BerlinModelImportConfigurator config = state.getConfig();
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Set<TaxonName> nameToSave = new HashSet<>();
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Map<String, TaxonName> nameMap = partitioner.getObjectMap(BerlinModelTaxonNameImport.NAMESPACE);
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Map<String, Reference> refMap = partitioner.getObjectMap(BerlinModelReferenceImport.REFERENCE_NAMESPACE);
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ResultSet rs = partitioner.getResultSet();
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try {
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int i = 0;
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//for each name relation
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while (rs.next()){
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if ((i++ % modCount) == 0 && i!= 1 ){ logger.info("RelName handled: " + (i-1));}
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int relNameId = rs.getInt("RelNameId");
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int name1Id = rs.getInt("name1Id");
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int name2Id = rs.getInt("name2Id");
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Object relRefFkObj = rs.getObject("refFk");
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String details = rs.getString("details");
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int relQualifierFk = rs.getInt("relNameQualifierFk");
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String notes = rs.getString("notes");
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TaxonName nameFrom = nameMap.get(String.valueOf(name1Id));
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TaxonName nameTo = nameMap.get(String.valueOf(name2Id));
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Reference citation = null;
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if (relRefFkObj != null){
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String relRefFk = String.valueOf(relRefFkObj);
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//get nomRef
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citation = refMap.get(relRefFk);
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}
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//TODO (preliminaryFlag = true testen
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String microcitation = details;
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String rule = null;
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if (nameFrom != null && nameTo != null){
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success = handleNameRelationship(success, config, name1Id, name2Id, relQualifierFk,
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notes, nameFrom, nameTo, citation, microcitation, rule, relNameId);
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if (! nameFrom.isProtectedTitleCache()){
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nameFrom.setTitleCache(null);
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nameFrom.getTitleCache();
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}
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if (! nameTo.isProtectedTitleCache()){
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nameTo.setTitleCache(null);
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nameTo.getTitleCache();
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}
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nameToSave.add(nameFrom);
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//TODO
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//ID
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//etc.
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}else{
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//TODO
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if (nameFrom == null){
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if ( ! (config.isUseEmAreaVocabulary() && relNameId == 28159 )) {
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logger.warn("from TaxonName " + name1Id + " for RelName (" + relNameId + " , type: " + relQualifierFk + " , toName: " + name2Id+ ") does not exist in store. ToName is: " + (nameTo == null ? "" : nameTo.getTitleCache()));
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}
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}
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if (nameTo == null){
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logger.warn("to TaxonName " + name2Id + " for RelName (" + relNameId + " , type: " + relQualifierFk + " , fromName: " + name1Id + ") does not exist in store. FromName is: " + (nameFrom == null ? "" : nameFrom.getTitleCache()));
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}
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success = false;
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}
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}
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partitioner.startDoSave();
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getNameService().save(nameToSave);
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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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/**
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* @param success
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* @param config
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* @param name1Id
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* @param name2Id
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* @param relQualifierFk
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* @param notes
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* @param nameFrom
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* @param nameTo
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* @param citation
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* @param microcitation
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* @param rule
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* @param relNameId
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* @return
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*/
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private boolean handleNameRelationship(boolean success,
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BerlinModelImportConfigurator config, int name1Id, int name2Id,
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int relQualifierFk, String notes, TaxonName nameFrom,
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TaxonName nameTo, Reference citation,
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String microcitation, String rule, int relNameId) {
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AnnotatableEntity nameRelationship = null;
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if (relQualifierFk == NAME_REL_IS_BASIONYM_FOR){
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nameRelationship = nameTo.addBasionym(nameFrom, citation, microcitation, rule, null);
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}else if (relQualifierFk == NAME_REL_IS_LATER_HOMONYM_OF){
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nameRelationship = nameFrom.addRelationshipToName(nameTo, NameRelationshipType.LATER_HOMONYM(), citation, microcitation, rule, null) ;
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}else if (relQualifierFk == NAME_REL_IS_TREATED_AS_LATER_HOMONYM_OF){
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nameRelationship = nameFrom.addRelationshipToName(nameTo, NameRelationshipType.LATER_HOMONYM(), citation, microcitation, rule, null) ;
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}else if (relQualifierFk == NAME_REL_IS_REPLACED_SYNONYM_FOR){
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nameRelationship = nameFrom.addRelationshipToName(nameTo, NameRelationshipType.REPLACED_SYNONYM(), citation, microcitation, rule, null) ;
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}else if (relQualifierFk == NAME_REL_HAS_SAME_TYPE_AS){
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nameTo.getHomotypicalGroup().merge(nameFrom.getHomotypicalGroup());
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}else if (relQualifierFk == NAME_REL_IS_VALIDATION_OF){
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nameRelationship = nameTo.addRelationshipToName(nameFrom, NameRelationshipType.VALIDATED_BY_NAME(), citation, microcitation, rule, null) ;
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}else if (relQualifierFk == NAME_REL_IS_LATER_VALIDATION_OF){
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nameRelationship = nameTo.addRelationshipToName(nameFrom, NameRelationshipType.LATER_VALIDATED_BY_NAME(), citation, microcitation, rule, null) ;
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}else if (relQualifierFk == NAME_REL_IS_TYPE_OF || relQualifierFk == NAME_REL_IS_REJECTED_TYPE_OF || relQualifierFk == NAME_REL_IS_CONSERVED_TYPE_OF || relQualifierFk == NAME_REL_IS_LECTOTYPE_OF || relQualifierFk == NAME_REL_TYPE_NOT_DESIGNATED ){
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boolean isRejectedType = (relQualifierFk == NAME_REL_IS_REJECTED_TYPE_OF);
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boolean isConservedType = (relQualifierFk == NAME_REL_IS_CONSERVED_TYPE_OF);
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boolean isLectoType = (relQualifierFk == NAME_REL_IS_LECTOTYPE_OF);
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boolean isNotDesignated = (relQualifierFk == NAME_REL_TYPE_NOT_DESIGNATED);
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NameTypeDesignationStatus status = null;
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String originalNameString = null;
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//TODO addToAllNames true or false?
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boolean addToAllNames = false;
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241
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if (config.getNameTypeDesignationStatusMethod() != null){
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Method method = config.getNameTypeDesignationStatusMethod();
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method.setAccessible(true);
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try {
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status = (NameTypeDesignationStatus)method.invoke(null, notes);
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246
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nameRelationship = nameTo.addNameTypeDesignation(nameFrom, citation, microcitation, originalNameString, status, addToAllNames);
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} catch (Exception e) {
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throw new RuntimeException(e);
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249
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}
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250
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}else{
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251
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if (isLectoType){
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status = NameTypeDesignationStatus.LECTOTYPE();
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253
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}
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254
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if (isNotDesignated && nameTo == nameFrom){
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nameFrom = null; //E+M case
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256
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}
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257
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258
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nameRelationship = nameTo.addNameTypeDesignation(nameFrom, citation, microcitation, originalNameString, status, isRejectedType, isConservedType, isNotDesignated, addToAllNames);
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259
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}
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260
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261
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}else if (relQualifierFk == NAME_REL_IS_ORTHOGRAPHIC_VARIANT_OF){
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nameRelationship = nameFrom.addRelationshipToName(nameTo, NameRelationshipType.ORTHOGRAPHIC_VARIANT(), citation, microcitation, rule, null) ;
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263
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}else if (relQualifierFk == NAME_REL_IS_ALTERNATIVE_NAME_FOR){
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nameRelationship = nameFrom.addRelationshipToName(nameTo, NameRelationshipType.ALTERNATIVE_NAME(), citation, microcitation, rule, null) ;
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265
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}else if (relQualifierFk == NAME_REL_IS_FIRST_PARENT_OF || relQualifierFk == NAME_REL_IS_SECOND_PARENT_OF || relQualifierFk == NAME_REL_IS_FEMALE_PARENT_OF || relQualifierFk == NAME_REL_IS_MALE_PARENT_OF){
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266
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//HybridRelationships
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267
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try {
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HybridRelationshipType hybridRelType = BerlinModelTransformer.relNameId2HybridRel(relQualifierFk);
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269
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IBotanicalName parent = nameFrom;
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270
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IBotanicalName child = nameTo;
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271
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272
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nameRelationship = parent.addHybridChild(child, hybridRelType, rule);
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273
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274
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} catch (UnknownCdmTypeException e) {
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logger.warn(e);
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276
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success = false;
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277
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}
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278
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}else {
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279
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//TODO
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280
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Method method = config.getNamerelationshipTypeMethod();
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281
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if (method != null){
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282
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try {
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method.invoke(null, relQualifierFk, nameTo, nameFrom);
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284
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} catch (Exception e) {
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logger.error(e.getMessage());
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286
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logger.warn("NameRelationship could not be imported");
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success = false;
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288
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}
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289
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}else{
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290
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logger.warn("NameRelationShipType " + relQualifierFk + " not yet implemented");
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success = false;
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292
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}
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293
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}
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Annotation annotation = doNotes(nameRelationship, notes);
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295
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if (config.isEuroMed() && annotation != null){
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296
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if (relQualifierFk == NAME_REL_IS_BASIONYM_FOR){
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annotation.setAnnotationType(AnnotationType.TECHNICAL());
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}else if ((relQualifierFk == NAME_REL_IS_LECTOTYPE_OF) && !notes.contains("designated")){
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annotation.setAnnotationType(AnnotationType.TECHNICAL());
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300
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}else{
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301
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logger.warn("Annotation type not defined for name relationship " + relNameId);
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302
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}
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303
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}else if (annotation != null){
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logger.warn("Annotation type not defined for name relationship " + relNameId);
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305
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}
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306
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return success;
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307
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}
|
|
308
|
|
|
309
|
@Override
|
|
310
|
public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, BerlinModelImportState state) {
|
|
311
|
|
|
312
|
String nameSpace;
|
|
313
|
Set<String> idSet;
|
|
314
|
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();
|
|
315
|
|
|
316
|
try{
|
|
317
|
Set<String> nameIdSet = new HashSet<>();
|
|
318
|
Set<String> referenceIdSet = new HashSet<>();
|
|
319
|
Set<String> refDetailIdSet = new HashSet<>();
|
|
320
|
while (rs.next()){
|
|
321
|
handleForeignKey(rs, nameIdSet, "name1Id");
|
|
322
|
handleForeignKey(rs, nameIdSet, "name2Id");
|
|
323
|
handleForeignKey(rs, referenceIdSet, "RefFk");
|
|
324
|
handleForeignKey(rs, refDetailIdSet, "RefDetailFk");
|
|
325
|
}
|
|
326
|
|
|
327
|
//name map
|
|
328
|
nameSpace = BerlinModelTaxonNameImport.NAMESPACE;
|
|
329
|
idSet = nameIdSet;
|
|
330
|
Map<String, TaxonName> objectMap = getCommonService().getSourcedObjectsByIdInSourceC(TaxonName.class, idSet, nameSpace);
|
|
331
|
result.put(nameSpace, objectMap);
|
|
332
|
|
|
333
|
//reference map
|
|
334
|
nameSpace = BerlinModelReferenceImport.REFERENCE_NAMESPACE;
|
|
335
|
idSet = referenceIdSet;
|
|
336
|
Map<String, Reference> referenceMap = getCommonService().getSourcedObjectsByIdInSourceC(Reference.class, idSet, nameSpace);
|
|
337
|
result.put(nameSpace, referenceMap);
|
|
338
|
|
|
339
|
//refDetail map
|
|
340
|
nameSpace = BerlinModelRefDetailImport.REFDETAIL_NAMESPACE;
|
|
341
|
idSet = refDetailIdSet;
|
|
342
|
Map<String, Reference> refDetailMap= getCommonService().getSourcedObjectsByIdInSourceC(Reference.class, idSet, nameSpace);
|
|
343
|
result.put(nameSpace, refDetailMap);
|
|
344
|
|
|
345
|
} catch (SQLException e) {
|
|
346
|
throw new RuntimeException(e);
|
|
347
|
}
|
|
348
|
return result;
|
|
349
|
}
|
|
350
|
|
|
351
|
@Override
|
|
352
|
protected boolean doCheck(BerlinModelImportState state){
|
|
353
|
IOValidator<BerlinModelImportState> validator = new BerlinModelTaxonNameRelationImportValidator();
|
|
354
|
return validator.validate(state);
|
|
355
|
}
|
|
356
|
|
|
357
|
@Override
|
|
358
|
protected boolean isIgnore(BerlinModelImportState state){
|
|
359
|
return ! state.getConfig().isDoRelNames();
|
|
360
|
}
|
|
361
|
}
|