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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.TAX_REL_IS_HETEROTYPIC_SYNONYM_OF;
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import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.TAX_REL_IS_HOMOTYPIC_SYNONYM_OF;
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import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.TAX_REL_IS_INCLUDED_IN;
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import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.TAX_REL_IS_MISAPPLIED_NAME_OF;
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import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.TAX_REL_IS_PARTIAL_HETEROTYPIC_SYNONYM_OF;
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import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.TAX_REL_IS_PARTIAL_HOMOTYPIC_SYNONYM_OF;
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import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.TAX_REL_IS_PARTIAL_SYN_OF;
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import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.TAX_REL_IS_PROPARTE_HETEROTYPIC_SYNONYM_OF;
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import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.TAX_REL_IS_PROPARTE_HOMOTYPIC_SYNONYM_OF;
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import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.TAX_REL_IS_PROPARTE_SYN_OF;
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import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.TAX_REL_IS_SYNONYM_OF;
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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 java.util.UUID;
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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.common.ResultWrapper;
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import eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer;
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import eu.etaxonomy.cdm.io.berlinModel.in.validation.BerlinModelTaxonRelationImportValidator;
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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.AnnotatableEntity;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.IdentifiableSource;
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import eu.etaxonomy.cdm.model.reference.ReferenceBase;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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import eu.etaxonomy.cdm.model.taxon.SynonymRelationship;
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import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
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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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import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
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import eu.etaxonomy.cdm.model.taxon.TaxonomicTree;
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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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* @created 20.03.2008
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* @version 1.0
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*/
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@Component
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public class BerlinModelTaxonRelationImport extends BerlinModelImportBase {
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private static final Logger logger = Logger.getLogger(BerlinModelTaxonRelationImport.class);
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public static final String TREE_NAMESPACE = "PTRefFk";
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private static int modCount = 30000;
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private static final String pluralString = "taxon relations";
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private static final String dbTableName = "RelPTaxon";
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public BerlinModelTaxonRelationImport(){
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super();
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}
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/**
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* Creates a taxonomic tree for each PTaxon reference which belongs to a taxon that is included at least in one
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* <i>taxonomically included</i> relationship
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* @param state
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* @return
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* @throws SQLException
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*/
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private boolean makeTaxonomicTrees(BerlinModelImportState state) throws SQLException{
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logger.info("start make taxonomic tree ...");
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Source source = state.getConfig().getSource();
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Set<String> idSet = getTreeReferenceIdSet(source);
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//nom reference map
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String nameSpace = BerlinModelReferenceImport.NOM_REFERENCE_NAMESPACE;
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Class cdmClass = ReferenceBase.class;
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idSet = new HashSet<String>();
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Map<String, ReferenceBase> nomRefMap = (Map<String, ReferenceBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
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//biblio reference map
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nameSpace = BerlinModelReferenceImport.BIBLIO_REFERENCE_NAMESPACE;
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cdmClass = ReferenceBase.class;
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// idSet = new HashSet<String>();
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Map<String, ReferenceBase> biblioRefMap = (Map<String, ReferenceBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
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ResultSet rs = source.getResultSet(getTaxonomicTreeQuery()) ;
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int i = 0;
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//for each reference
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try {
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while (rs.next()){
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if ((i++ % modCount) == 0 && i!= 1 ){ logger.info("RelPTaxa handled: " + (i-1));}
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Object ptRefFkObj = rs.getObject("PTRefFk");
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String ptRefFk= String.valueOf(ptRefFkObj);
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ReferenceBase<?> ref = getReferenceOnlyFromMaps(biblioRefMap, nomRefMap, ptRefFk);
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rs.getString("RefCache");
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String treeName = "TaxonTree - No Name";
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String refCache = rs.getString("RefCache");
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if (CdmUtils.isNotEmpty(refCache)){
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treeName = refCache;
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}
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if (ref != null && CdmUtils.isNotEmpty(ref.getTitleCache())){
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treeName = ref.getTitleCache();
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}
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TaxonomicTree tree = TaxonomicTree.NewInstance(treeName);
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tree.setReference(ref);
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if (i == 1 && state.getConfig().getTaxonomicTreeUuid() != null){
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tree.setUuid(state.getConfig().getTaxonomicTreeUuid());
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}
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IdentifiableSource identifiableSource = IdentifiableSource.NewInstance(ptRefFk, TREE_NAMESPACE);
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tree.addSource(identifiableSource);
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getTaxonTreeService().save(tree);
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state.putTaxonomicTreeUuidInt((Integer)ptRefFkObj, tree);
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}
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} catch (SQLException e) {
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logger.error("Error in BerlinModleTaxonRelationImport.makeTaxonomicTrees: " + e.getMessage());
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throw e;
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}
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logger.info("end make taxonomic tree ...");
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return true;
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}
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/**
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* @return
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* @throws SQLException
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*/
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private Set<String> getTreeReferenceIdSet(Source source) throws SQLException {
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Set<String> result = new HashSet<String>();
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ResultSet rs = source.getResultSet(getTaxonomicTreeQuery()) ;
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while (rs.next()){
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Object id = rs.getObject("PTRefFk");
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result.add(String.valueOf(id));
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}
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return result;
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}
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/**
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* @return
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*/
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private String getTaxonomicTreeQuery() {
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String strQuery = "SELECT PTaxon.PTRefFk, Reference.RefCache " +
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" FROM RelPTaxon INNER JOIN " +
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" PTaxon AS PTaxon ON RelPTaxon.PTNameFk2 = PTaxon.PTNameFk AND RelPTaxon.PTRefFk2 = PTaxon.PTRefFk INNER JOIN " +
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" Reference ON PTaxon.PTRefFk = Reference.RefId " +
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" WHERE (RelPTaxon.RelQualifierFk = 1) " +
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" GROUP BY PTaxon.PTRefFk, Reference.RefCache ";
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return strQuery;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getRecordQuery(eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator)
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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 RelPTaxon.*, FromTaxon.RIdentifier as taxon1Id, ToTaxon.RIdentifier as taxon2Id, ToTaxon.PTRefFk as treeRefFk, q.is_concept_relation " +
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" FROM PTaxon as FromTaxon " +
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" INNER JOIN RelPTaxon ON FromTaxon.PTNameFk = RelPTaxon.PTNameFk1 AND FromTaxon.PTRefFk = RelPTaxon.PTRefFk1 " +
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" INNER JOIN PTaxon AS ToTaxon ON RelPTaxon.PTNameFk2 = ToTaxon.PTNameFk AND RelPTaxon.PTRefFk2 = ToTaxon.PTRefFk " +
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" INNER JOIN RelPTQualifier q ON q.RelPTQualifierId = RelPTaxon.RelQualifierFk " +
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" WHERE RelPTaxon.RelPTaxonId IN ("+ID_LIST_TOKEN+") ";
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return strQuery;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#doPartition(eu.etaxonomy.cdm.io.berlinModel.in.ResultSetPartitioner, eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportState)
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*/
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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<TaxonBase> taxaToSave = new HashSet<TaxonBase>();
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Map<String, TaxonBase> taxonMap = (Map<String, TaxonBase>) partitioner.getObjectMap(BerlinModelTaxonImport.NAMESPACE);
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Map<Integer, TaxonomicTree> taxonTreeMap = new HashMap<Integer, TaxonomicTree>();
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Map<String, ReferenceBase> biblioRefMap = (Map<String, ReferenceBase>) partitioner.getObjectMap(BerlinModelReferenceImport.BIBLIO_REFERENCE_NAMESPACE);
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Map<String, ReferenceBase> nomRefMap = (Map<String, ReferenceBase>) partitioner.getObjectMap(BerlinModelReferenceImport.NOM_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 reference
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while (rs.next()){
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if ((i++ % modCount) == 0 && i!= 1 ){ logger.info("RelPTaxa handled: " + (i-1));}
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int relPTaxonId = rs.getInt("RelPTaxonId");
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int taxon1Id = rs.getInt("taxon1Id");
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int taxon2Id = rs.getInt("taxon2Id");
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Object relRefFkObj = rs.getObject("relRefFk");
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int treeRefFk = rs.getInt("treeRefFk");
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int relQualifierFk = rs.getInt("relQualifierFk");
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String notes = rs.getString("notes");
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boolean isConceptRelationship = rs.getBoolean("is_concept_relation");
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TaxonBase taxon1 = taxonMap.get(String.valueOf(taxon1Id));
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TaxonBase taxon2 = taxonMap.get(String.valueOf(taxon2Id));
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String refFk = String.valueOf(relRefFkObj);
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ReferenceBase citation = getReferenceOnlyFromMaps(biblioRefMap, nomRefMap, refFk);
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String microcitation = null; //does not exist in RelPTaxon
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if (taxon2 != null && taxon1 != null){
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if (!(taxon2 instanceof Taxon)){
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logger.error("TaxonBase (ID = " + taxon2.getId()+ ", RIdentifier = " + taxon2Id + ") can't be casted to Taxon");
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success = false;
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continue;
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}
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AnnotatableEntity taxonRelationship = null;
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Taxon toTaxon = (Taxon)taxon2;
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if (isTaxonRelationship(relQualifierFk)){
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if (!(taxon1 instanceof Taxon)){
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logger.error("TaxonBase (ID = " + taxon1.getId()+ ", RIdentifier = " + taxon1Id + ") can't be casted to Taxon");
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success = false;
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continue;
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}
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Taxon fromTaxon = (Taxon)taxon1;
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if (relQualifierFk == TAX_REL_IS_INCLUDED_IN){
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taxonRelationship = makeTaxonomicallyIncluded(state, taxonTreeMap, treeRefFk, fromTaxon, toTaxon, citation, microcitation);
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}else if (relQualifierFk == TAX_REL_IS_MISAPPLIED_NAME_OF){
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taxonRelationship = toTaxon.addMisappliedName(fromTaxon, citation, microcitation);
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}
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}else if (isSynonymRelationship(relQualifierFk)){
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if (!(taxon1 instanceof Synonym)){
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logger.error("Taxon (ID = " + taxon1.getId()+ ", RIdentifier = " + taxon1Id + ") can't be casted to Synonym");
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success = false;
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continue;
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}
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Synonym synonym = (Synonym)taxon1;
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SynonymRelationship synRel = getSynRel(relQualifierFk, toTaxon, synonym, citation, microcitation);
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taxonRelationship = synRel;
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if (relQualifierFk == TAX_REL_IS_SYNONYM_OF ||
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relQualifierFk == TAX_REL_IS_HOMOTYPIC_SYNONYM_OF ||
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relQualifierFk == TAX_REL_IS_HETEROTYPIC_SYNONYM_OF){
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addProParteAndPartial(synRel, synonym, config);
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}else if (relQualifierFk == TAX_REL_IS_PROPARTE_SYN_OF ||
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relQualifierFk == TAX_REL_IS_PROPARTE_HOMOTYPIC_SYNONYM_OF ||
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relQualifierFk == TAX_REL_IS_PROPARTE_HETEROTYPIC_SYNONYM_OF ){
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synRel.setProParte(true);
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}else if(relQualifierFk == TAX_REL_IS_PARTIAL_SYN_OF ||
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relQualifierFk == TAX_REL_IS_PARTIAL_HOMOTYPIC_SYNONYM_OF ||
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relQualifierFk == TAX_REL_IS_PARTIAL_HETEROTYPIC_SYNONYM_OF ){
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synRel.setPartial(true);
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}else{
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success = false;
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logger.warn("Proparte/Partial not yet implemented for TaxonRelationShipType " + relQualifierFk);
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}
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}else if (isConceptRelationship){
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ResultWrapper<Boolean> isInverse = new ResultWrapper<Boolean>();
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try {
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TaxonRelationshipType relType = BerlinModelTransformer.taxonRelId2TaxonRelType(relQualifierFk, isInverse);
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if (! (taxon1 instanceof Taxon)){
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success = false;
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logger.error("TaxonBase (ID = " + taxon1.getId()+ ", RIdentifier = " + taxon1Id + ") can't be casted to Taxon");
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}else{
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Taxon fromTaxon = (Taxon)taxon1;
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taxonRelationship = fromTaxon.addTaxonRelation(toTaxon, relType, citation, microcitation);
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}
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} catch (UnknownCdmTypeException e) {
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//TODO other relationships
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logger.warn("TaxonRelationShipType " + relQualifierFk + " (conceptRelationship) not yet implemented");
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success = false;
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}
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}else {
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//TODO
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logger.warn("TaxonRelationShipType " + relQualifierFk + " not yet implemented");
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success = false;
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}
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doNotes(taxonRelationship, notes);
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taxaToSave.add(taxon2);
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//TODO
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//etc.
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}else{
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//TODO
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logger.warn("Taxa for RelPTaxon " + relPTaxonId + " do not exist in store");
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success = false;
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}
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}
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}catch(SQLException e){
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throw new RuntimeException(e);
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}
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logger.info("Taxa to save: " + taxaToSave.size());
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partitioner.startDoSave();
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307
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getTaxonService().save(taxaToSave);
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308
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taxonTreeMap = null;
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309
|
taxaToSave = null;
|
|
310
|
|
|
311
|
return success;
|
|
312
|
}
|
|
313
|
|
|
314
|
|
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315
|
/* (non-Javadoc)
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316
|
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#doInvoke(eu.etaxonomy.cdm.io.common.IImportConfigurator, eu.etaxonomy.cdm.api.application.CdmApplicationController, java.util.Map)
|
|
317
|
*/
|
|
318
|
@Override
|
|
319
|
protected boolean doInvoke(BerlinModelImportState state){
|
|
320
|
try {
|
|
321
|
boolean success = true;
|
|
322
|
success &= makeTaxonomicTrees(state);
|
|
323
|
success &= super.doInvoke(state);
|
|
324
|
return success;
|
|
325
|
} catch (SQLException e) {
|
|
326
|
throw new RuntimeException(e);
|
|
327
|
}
|
|
328
|
|
|
329
|
}
|
|
330
|
|
|
331
|
|
|
332
|
/* (non-Javadoc)
|
|
333
|
* @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet)
|
|
334
|
*/
|
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335
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public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition( ResultSet rs) {
|
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336
|
String nameSpace;
|
|
337
|
Class cdmClass;
|
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338
|
Set<String> idSet;
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339
|
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
|
|
340
|
|
|
341
|
try{
|
|
342
|
Set<String> taxonIdSet = new HashSet<String>();
|
|
343
|
Set<String> referenceIdSet = new HashSet<String>();
|
|
344
|
// Set<String> taxonTreeIdSet = new HashSet<String>();
|
|
345
|
while (rs.next()){
|
|
346
|
handleForeignKey(rs, taxonIdSet, "taxon1Id");
|
|
347
|
handleForeignKey(rs, taxonIdSet, "taxon2Id");
|
|
348
|
// handleForeignKey(rs, taxonTreeIdSet, "treeRefFk");
|
|
349
|
handleForeignKey(rs, referenceIdSet, "RelRefFk");
|
|
350
|
}
|
|
351
|
|
|
352
|
//taxon map
|
|
353
|
nameSpace = BerlinModelTaxonImport.NAMESPACE;
|
|
354
|
cdmClass = TaxonBase.class;
|
|
355
|
idSet = taxonIdSet;
|
|
356
|
Map<String, TaxonBase> taxonMap = (Map<String, TaxonBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
357
|
result.put(nameSpace, taxonMap);
|
|
358
|
|
|
359
|
// //tree map
|
|
360
|
// nameSpace = "TaxonomicTree";
|
|
361
|
// cdmClass = TaxonomicTree.class;
|
|
362
|
// idSet = taxonTreeIdSet;
|
|
363
|
// Map<String, TaxonomicTree> treeMap = (Map<String, TaxonomicTree>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
364
|
// result.put(cdmClass, treeMap);
|
|
365
|
// Set<UUID> treeUuidSet = state
|
|
366
|
// getTaxonTreeService().find(uuidSet);
|
|
367
|
//
|
|
368
|
|
|
369
|
//nom reference map
|
|
370
|
nameSpace = BerlinModelReferenceImport.NOM_REFERENCE_NAMESPACE;
|
|
371
|
cdmClass = ReferenceBase.class;
|
|
372
|
idSet = referenceIdSet;
|
|
373
|
Map<String, ReferenceBase> nomReferenceMap = (Map<String, ReferenceBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
374
|
result.put(nameSpace, nomReferenceMap);
|
|
375
|
|
|
376
|
//biblio reference map
|
|
377
|
nameSpace = BerlinModelReferenceImport.BIBLIO_REFERENCE_NAMESPACE;
|
|
378
|
cdmClass = ReferenceBase.class;
|
|
379
|
idSet = referenceIdSet;
|
|
380
|
Map<String, ReferenceBase> biblioReferenceMap = (Map<String, ReferenceBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
381
|
result.put(nameSpace, biblioReferenceMap);
|
|
382
|
|
|
383
|
} catch (SQLException e) {
|
|
384
|
throw new RuntimeException(e);
|
|
385
|
}
|
|
386
|
return result;
|
|
387
|
}
|
|
388
|
|
|
389
|
private SynonymRelationship getSynRel (int relQualifierFk, Taxon toTaxon, Synonym synonym, ReferenceBase citation, String microcitation){
|
|
390
|
SynonymRelationship result;
|
|
391
|
if (relQualifierFk == TAX_REL_IS_HOMOTYPIC_SYNONYM_OF ||
|
|
392
|
relQualifierFk == TAX_REL_IS_PROPARTE_HOMOTYPIC_SYNONYM_OF ||
|
|
393
|
relQualifierFk == TAX_REL_IS_PARTIAL_HOMOTYPIC_SYNONYM_OF){
|
|
394
|
result = toTaxon.addHomotypicSynonym(synonym, citation, microcitation);
|
|
395
|
}else if (relQualifierFk == TAX_REL_IS_HETEROTYPIC_SYNONYM_OF ||
|
|
396
|
relQualifierFk == TAX_REL_IS_PROPARTE_HETEROTYPIC_SYNONYM_OF ||
|
|
397
|
relQualifierFk == TAX_REL_IS_PARTIAL_HETEROTYPIC_SYNONYM_OF){
|
|
398
|
result = toTaxon.addSynonym(synonym, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF(), citation, microcitation);
|
|
399
|
}else if (relQualifierFk == TAX_REL_IS_SYNONYM_OF ||
|
|
400
|
relQualifierFk == TAX_REL_IS_PROPARTE_SYN_OF ||
|
|
401
|
relQualifierFk == TAX_REL_IS_PARTIAL_SYN_OF){
|
|
402
|
result = toTaxon.addSynonym(synonym, SynonymRelationshipType.SYNONYM_OF(), citation, microcitation);
|
|
403
|
}else{
|
|
404
|
logger.warn("SynonymyRelationShipType could not be defined for relQualifierFk " + relQualifierFk + ". 'Unknown'-Type taken instead.");
|
|
405
|
result = toTaxon.addSynonym(synonym, SynonymRelationshipType.SYNONYM_OF(), citation, microcitation);
|
|
406
|
}
|
|
407
|
return result;
|
|
408
|
|
|
409
|
}
|
|
410
|
|
|
411
|
private boolean isSynonymRelationship(int relQualifierFk){
|
|
412
|
if (relQualifierFk == TAX_REL_IS_SYNONYM_OF ||
|
|
413
|
relQualifierFk == TAX_REL_IS_HOMOTYPIC_SYNONYM_OF ||
|
|
414
|
relQualifierFk == TAX_REL_IS_HETEROTYPIC_SYNONYM_OF ||
|
|
415
|
relQualifierFk == TAX_REL_IS_PROPARTE_SYN_OF ||
|
|
416
|
relQualifierFk == TAX_REL_IS_PARTIAL_SYN_OF ||
|
|
417
|
relQualifierFk == TAX_REL_IS_PROPARTE_HOMOTYPIC_SYNONYM_OF ||
|
|
418
|
relQualifierFk == TAX_REL_IS_PROPARTE_HETEROTYPIC_SYNONYM_OF ||
|
|
419
|
relQualifierFk == TAX_REL_IS_PARTIAL_HOMOTYPIC_SYNONYM_OF ||
|
|
420
|
relQualifierFk == TAX_REL_IS_PARTIAL_HETEROTYPIC_SYNONYM_OF
|
|
421
|
){
|
|
422
|
return true;
|
|
423
|
}else{
|
|
424
|
return false;
|
|
425
|
}
|
|
426
|
}
|
|
427
|
|
|
428
|
private boolean isTaxonRelationship(int relQualifierFk){
|
|
429
|
if (relQualifierFk == TAX_REL_IS_INCLUDED_IN ||
|
|
430
|
relQualifierFk == TAX_REL_IS_MISAPPLIED_NAME_OF){
|
|
431
|
return true;
|
|
432
|
}else{
|
|
433
|
return false;
|
|
434
|
}
|
|
435
|
}
|
|
436
|
|
|
437
|
private void addProParteAndPartial(SynonymRelationship synRel, Synonym synonym, BerlinModelImportConfigurator bmiConfig){
|
|
438
|
if (bmiConfig.isPartialSynonym(synonym)){
|
|
439
|
synRel.setPartial(true);
|
|
440
|
}
|
|
441
|
if (bmiConfig.isProParteSynonym(synonym)){
|
|
442
|
synRel.setProParte(true);
|
|
443
|
}
|
|
444
|
}
|
|
445
|
|
|
446
|
private TaxonNode makeTaxonomicallyIncluded(BerlinModelImportState state, Map<Integer, TaxonomicTree> taxonTreeMap, int treeRefFk, Taxon child, Taxon parent, ReferenceBase citation, String microCitation){
|
|
447
|
TaxonomicTree tree = taxonTreeMap.get(treeRefFk);
|
|
448
|
if (tree == null){
|
|
449
|
UUID treeUuid = state.getTreeUuidByIntTreeKey(treeRefFk);
|
|
450
|
tree = getTaxonTreeService().getTaxonomicTreeByUuid(treeUuid);
|
|
451
|
taxonTreeMap.put(treeRefFk, tree);
|
|
452
|
}
|
|
453
|
if (tree == null){
|
|
454
|
throw new IllegalStateException("Tree for ToTaxon reference does not exist.");
|
|
455
|
}
|
|
456
|
return tree.addParentChild(parent, child, citation, microCitation);
|
|
457
|
}
|
|
458
|
|
|
459
|
|
|
460
|
/* (non-Javadoc)
|
|
461
|
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IoStateBase)
|
|
462
|
*/
|
|
463
|
@Override
|
|
464
|
protected boolean doCheck(BerlinModelImportState state){
|
|
465
|
IOValidator<BerlinModelImportState> validator = new BerlinModelTaxonRelationImportValidator();
|
|
466
|
return validator.validate(state);
|
|
467
|
}
|
|
468
|
|
|
469
|
|
|
470
|
/* (non-Javadoc)
|
|
471
|
* @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getTableName()
|
|
472
|
*/
|
|
473
|
@Override
|
|
474
|
protected String getTableName() {
|
|
475
|
return dbTableName;
|
|
476
|
}
|
|
477
|
|
|
478
|
/* (non-Javadoc)
|
|
479
|
* @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getPluralString()
|
|
480
|
*/
|
|
481
|
@Override
|
|
482
|
public String getPluralString() {
|
|
483
|
return pluralString;
|
|
484
|
}
|
|
485
|
|
|
486
|
/* (non-Javadoc)
|
|
487
|
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
|
|
488
|
*/
|
|
489
|
protected boolean isIgnore(BerlinModelImportState state){
|
|
490
|
return ! state.getConfig().isDoRelTaxa();
|
|
491
|
}
|
|
492
|
|
|
493
|
|
|
494
|
}
|