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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.commons.lang.StringUtils;
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import org.apache.log4j.Logger;
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import org.springframework.stereotype.Component;
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import org.springframework.transaction.TransactionStatus;
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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.name.NameRelationshipType;
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
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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.model.reference.ReferenceFactory;
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import eu.etaxonomy.cdm.model.taxon.Classification;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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import eu.etaxonomy.cdm.model.taxon.SynonymType;
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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.TaxonRelationship;
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
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import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
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import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
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import eu.etaxonomy.cdm.strategy.parser.TimePeriodParser;
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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 BerlinModelTaxonRelationImport extends BerlinModelImportBase {
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private static final long serialVersionUID = -7234926279240842557L;
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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 final Integer AUCT_REF_ID = 5959;
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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(dbTableName, pluralString);
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}
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/**
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* Creates a classification for each PTaxon reference which belongs to a taxon that is
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* included at least in one <i>taxonomically included</i> relationship.
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*
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* @param state
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* @throws SQLException
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*/
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private void makeClassifications(BerlinModelImportState state) throws SQLException{
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logger.info("start make classification ...");
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Set<String> idSet = getTreeReferenceIdSet(state);
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//reference map
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String nameSpace = BerlinModelReferenceImport.REFERENCE_NAMESPACE;
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Class<?> cdmClass = Reference.class;
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@SuppressWarnings("unchecked")
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Map<String, Reference> refMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
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String classificationName = "Classification - No Name";
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ResultSet rs = state.getConfig().getSource().getResultSet(getClassificationQuery(state)) ;
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int i = 0;
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//for each reference
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try {
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//TODO handle case useSingleClassification = true && sourceSecId = null, which returns no record
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boolean isFirst = true;
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while (rs.next()){
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try {
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if ((i++ % modCount) == 0 && i!= 1 ){ logger.info("RelPTaxa handled: " + (i-1));}
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Integer ptRefFkInt = nullSafeInt(rs,"PTRefFk");
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String ptRefFk= String.valueOf(ptRefFkInt);
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Reference ref = refMap.get(ptRefFk);
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String refCache = rs.getString("RefCache");
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if (isNotBlank(refCache)){
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classificationName = refCache;
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}
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if (ref != null && StringUtils.isNotBlank(ref.getTitleCache())){
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classificationName = ref.getTitleCache();
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}
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if (isFirst && isNotBlank(state.getConfig().getClassificationName())){
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classificationName = state.getConfig().getClassificationName();
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}
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Classification tree = Classification.NewInstance(classificationName);
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tree.setReference(ref);
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if (i == 1 && state.getConfig().getClassificationUuid() != null){
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tree.setUuid(state.getConfig().getClassificationUuid());
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}
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IdentifiableSource identifiableSource = IdentifiableSource.NewDataImportInstance(ptRefFk, TREE_NAMESPACE);
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tree.addSource(identifiableSource);
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getClassificationService().save(tree);
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state.putClassificationUuidInt(ptRefFkInt, tree);
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isFirst = false;
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} catch (Exception e) {
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logger.error("Error in BerlinModleTaxonRelationImport.makeClassifications: " + e.getMessage());
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e.printStackTrace();
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}
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}
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} catch (SQLException e) {
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logger.error("Error in BerlinModleTaxonRelationImport.makeClassifications: " + e.getMessage());
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throw e;
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}
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logger.info("end make classification ...");
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return;
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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(BerlinModelImportState state) throws SQLException {
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Source source = state.getConfig().getSource();
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Set<String> result = new HashSet<String>();
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ResultSet rs = source.getResultSet(getClassificationQuery(state)) ;
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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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private String getClassificationQuery(BerlinModelImportState state) {
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boolean includeAllClassifications = state.getConfig().isIncludeAllNonMisappliedRelatedClassifications();
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String strQuerySelect = "SELECT PTaxon.PTRefFk, r.RefCache ";
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String strQueryFrom = " FROM RelPTaxon " +
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" INNER JOIN PTaxon AS PTaxon ON RelPTaxon.PTNameFk2 = PTaxon.PTNameFk AND RelPTaxon.PTRefFk2 = PTaxon.PTRefFk " +
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" INNER JOIN Reference r ON PTaxon.PTRefFk = r.RefId ";
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String strQueryWhere = " WHERE (RelPTaxon.RelQualifierFk = 1) ";
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if (includeAllClassifications){
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strQueryWhere = " WHERE (RelPTaxon.RelQualifierFk <> 3) ";
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}else{
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if (state.getConfig().isUseSingleClassification()){
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if (state.getConfig().getSourceSecId()!= null){
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strQueryWhere += " AND PTaxon.PTRefFk = " + state.getConfig().getSourceSecId() + " ";
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}else{
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strQueryWhere += " AND (1=0) ";
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}
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}
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}
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String strQueryGroupBy = " GROUP BY PTaxon.PTRefFk, r.RefCache ";
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String strQuery = strQuerySelect + " " + strQueryFrom + " " + strQueryWhere + " " + strQueryGroupBy;
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if (includeAllClassifications){
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//add otherdirection
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strQuerySelect = "SELECT PTaxon.PTRefFk, r.RefCache ";
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strQueryFrom = " FROM RelPTaxon rel " +
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" INNER JOIN PTaxon AS PTaxon ON rel.PTNameFk1 = PTaxon.PTNameFk AND rel.PTRefFk1 = PTaxon.PTRefFk " +
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" INNER JOIN Reference r ON PTaxon.PTRefFk = r.RefId ";
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strQueryWhere =" WHERE (rel.RelQualifierFk <> 3) ";
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String strAllQuery = strQuerySelect + " " + strQueryFrom + " " + strQueryWhere + " " + strQueryGroupBy;
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strQuery = strQuery + " UNION " + strAllQuery;
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}
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boolean includeFlatClassifications = state.getConfig().isIncludeFlatClassifications();
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//concepts with
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if (includeFlatClassifications){
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String strFlatQuery =
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" SELECT pt.PTRefFk AS secRefFk, r.RefCache AS secRef " +
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" FROM PTaxon AS pt LEFT OUTER JOIN " +
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" Reference r ON pt.PTRefFk = r.RefId LEFT OUTER JOIN " +
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" RelPTaxon rel1 ON pt.PTNameFk = rel1.PTNameFk2 AND pt.PTRefFk = rel1.PTRefFk2 LEFT OUTER JOIN " +
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" RelPTaxon AS rel2 ON pt.PTNameFk = rel2.PTNameFk1 AND pt.PTRefFk = rel2.PTRefFk1 " +
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" WHERE (rel2.RelQualifierFk IS NULL) AND (rel1.RelQualifierFk IS NULL) " +
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" GROUP BY pt.PTRefFk, r.RefCache "
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;
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strQuery = strQuery + " UNION " + strFlatQuery;
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}
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if (state.getConfig().getClassificationQuery() != null){
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strQuery = state.getConfig().getClassificationQuery();
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}
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return strQuery;
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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, fromTaxon.PTRefFk as fromRefFk, 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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" ORDER BY RelPTaxon.RelPTaxonId ";
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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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Set<TaxonBase> taxaToSave = new HashSet<>();
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Map<String, TaxonBase> taxonMap = partitioner.getObjectMap(BerlinModelTaxonImport.NAMESPACE);
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Map<Integer, Classification> classificationMap = new HashMap<>();
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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 reference
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while (rs.next()){
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260
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if ((i++ % modCount) == 0 && i!= 1 ){ logger.info("RelPTaxa handled: " + (i-1));}
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262
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int relPTaxonId = rs.getInt("RelPTaxonId");
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Integer taxon1Id = nullSafeInt(rs, "taxon1Id");
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Integer taxon2Id = nullSafeInt(rs, "taxon2Id");
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Integer ptRefFk1 = nullSafeInt(rs, "PTRefFk1");
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Integer ptRefFk2 = nullSafeInt(rs, "PTRefFk2");
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268
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int relQualifierFk = -1;
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try {
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Integer relRefFk = nullSafeInt(rs,"relRefFk");
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int treeRefFk = rs.getInt("treeRefFk");
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int fromRefFk = rs.getInt("fromRefFk");
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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(relRefFk);
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Reference citation = refMap.get(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("ToTaxon (ID = " + taxon2.getId()+ ", RIdentifier = " + taxon2Id + ") can't be casted to Taxon. RelPTaxon: " + relPTaxonId );
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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 + ") for TaxonRelation ("+relPTaxonId+") 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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if(state.getConfig().isEuroMed() && CdmUtils.nullSafeEqual(relRefFk, ptRefFk2)){
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citation = null;
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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, classificationMap, treeRefFk, fromTaxon, toTaxon, citation, microcitation);
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}else if (relQualifierFk == TAX_REL_IS_MISAPPLIED_NAME_OF){
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boolean isProParte = "p.p.".equals(notes);
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if (isProParte){
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notes = null;
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}
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boolean isDoubtful = "?".equals(notes);
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312
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if (isDoubtful){
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|
313
|
notes = null;
|
|
314
|
}
|
|
315
|
|
|
316
|
if (notes!= null && notes.startsWith("{non ") && notes.endsWith("}")){
|
|
317
|
notes = notes.substring(1, notes.length() - 1);
|
|
318
|
}
|
|
319
|
//handle auct. author
|
|
320
|
if (fromTaxon.getSec() == null || fromTaxon.getSec().getTitleCache().startsWith("auct.")){
|
|
321
|
String existingSecTitle = fromTaxon.getSec() == null ? null : fromTaxon.getSec().getTitleCache().trim();
|
|
322
|
String existingAppendedPhrase = fromTaxon.getAppendedPhrase();
|
|
323
|
if (fromTaxon.getSec() == null && isBlank(existingAppendedPhrase)){
|
|
324
|
existingAppendedPhrase = "auct.";
|
|
325
|
}
|
|
326
|
fromTaxon.setSec(null);
|
|
327
|
if (isNotBlank(existingAppendedPhrase) && isNotBlank(notes)){
|
|
328
|
logger.warn("Misapplied name has >1 MA relation with a note, RelId: " + relPTaxonId);
|
|
329
|
}
|
|
330
|
|
|
331
|
String newAppendedPhrase = CdmUtils.concat(", ", existingSecTitle, notes);
|
|
332
|
fromTaxon.setAppendedPhrase(CdmUtils.concat("; ", existingAppendedPhrase, newAppendedPhrase));
|
|
333
|
if (isBlank(fromTaxon.getAppendedPhrase())){
|
|
334
|
logger.warn("Appended phrase is empty. This is probably not correct. RelID: " + relPTaxonId);
|
|
335
|
}else if ("auct.".equals(fromTaxon.getAppendedPhrase())){
|
|
336
|
fromTaxon.setAppendedPhrase(null);
|
|
337
|
}
|
|
338
|
notes = null;
|
|
339
|
}else if (notes != null && notes.startsWith("non ")){
|
|
340
|
fromTaxon.setAppendedPhrase(CdmUtils.concat(", ", fromTaxon.getAppendedPhrase(), notes));
|
|
341
|
notes = null;
|
|
342
|
}
|
|
343
|
|
|
344
|
if (isProParte){
|
|
345
|
taxonRelationship = toTaxon.addProParteMisappliedName(fromTaxon, citation, microcitation);
|
|
346
|
}else{
|
|
347
|
taxonRelationship = toTaxon.addMisappliedName(fromTaxon, citation, microcitation);
|
|
348
|
}
|
|
349
|
if (isDoubtful){
|
|
350
|
((TaxonRelationship)taxonRelationship).setDoubtful(true);
|
|
351
|
}
|
|
352
|
}else if (relQualifierFk == TAX_REL_IS_PROPARTE_SYN_OF ||
|
|
353
|
relQualifierFk == TAX_REL_IS_PROPARTE_HOMOTYPIC_SYNONYM_OF ||
|
|
354
|
relQualifierFk == TAX_REL_IS_PROPARTE_HETEROTYPIC_SYNONYM_OF ){
|
|
355
|
if(relQualifierFk == TAX_REL_IS_PROPARTE_HOMOTYPIC_SYNONYM_OF){
|
|
356
|
logger.warn("Homotypic pro parte synonyms not handled in CDM. Please add homotypie manually. RelPTID: " + relPTaxonId);
|
|
357
|
}
|
|
358
|
//heterotypic we expect as the normal relationship, don't store explicitly
|
|
359
|
toTaxon.addProparteSynonym(fromTaxon, citation, microcitation);
|
|
360
|
}else if(relQualifierFk == TAX_REL_IS_PARTIAL_SYN_OF ||
|
|
361
|
relQualifierFk == TAX_REL_IS_PARTIAL_HOMOTYPIC_SYNONYM_OF ||
|
|
362
|
relQualifierFk == TAX_REL_IS_PARTIAL_HETEROTYPIC_SYNONYM_OF ){
|
|
363
|
if (relQualifierFk == TAX_REL_IS_PARTIAL_HOMOTYPIC_SYNONYM_OF ||
|
|
364
|
relQualifierFk == TAX_REL_IS_PARTIAL_HETEROTYPIC_SYNONYM_OF){
|
|
365
|
logger.warn("Homotypie and heterotypie not yet handled for partial synonyms");
|
|
366
|
}
|
|
367
|
toTaxon.addPartialSynonym(fromTaxon, citation, microcitation);
|
|
368
|
}else{
|
|
369
|
handleAllRelatedTaxa(state, fromTaxon, classificationMap, fromRefFk);
|
|
370
|
handleAllRelatedTaxa(state, toTaxon, classificationMap, treeRefFk);
|
|
371
|
logger.warn("Unhandled taxon relationship: RelId:" + relPTaxonId + "; QualifierId: " + relQualifierFk);
|
|
372
|
}
|
|
373
|
}else if (isSynonymRelationship(relQualifierFk)){
|
|
374
|
if (!(taxon1 instanceof Synonym)){
|
|
375
|
logger.warn("Validated: Taxon (ID = " + taxon1.getId()+ ", RIdentifier = " + taxon1Id + ") can't be casted to Synonym");
|
|
376
|
success = false;
|
|
377
|
continue;
|
|
378
|
}
|
|
379
|
handleAllRelatedTaxa(state, toTaxon, classificationMap, treeRefFk);
|
|
380
|
Synonym synonym = (Synonym)taxon1;
|
|
381
|
if (synonym.getAcceptedTaxon()!= null){
|
|
382
|
logger.warn("RelID: " + relPTaxonId + ". Synonym ("+taxon1Id +") already has an accepted taxon. Create clone.");
|
|
383
|
synonym = (Synonym)synonym.clone();
|
|
384
|
}
|
|
385
|
makeSynRel(state, relQualifierFk, toTaxon, synonym, citation, microcitation);
|
|
386
|
|
|
387
|
if (relQualifierFk == TAX_REL_IS_SYNONYM_OF ||
|
|
388
|
relQualifierFk == TAX_REL_IS_HOMOTYPIC_SYNONYM_OF ||
|
|
389
|
relQualifierFk == TAX_REL_IS_HETEROTYPIC_SYNONYM_OF){
|
|
390
|
}else{
|
|
391
|
success = false;
|
|
392
|
logger.warn("Synonym relationship type not yet implemented: " + relQualifierFk);
|
|
393
|
}
|
|
394
|
//
|
|
395
|
notes = handleSynonymNotes(state, toTaxon, synonym, notes, relPTaxonId);
|
|
396
|
}else if (isConceptRelationship){
|
|
397
|
ResultWrapper<Boolean> isInverse = ResultWrapper.NewInstance(false);
|
|
398
|
ResultWrapper<Boolean> isDoubtful = ResultWrapper.NewInstance(false);
|
|
399
|
try {
|
|
400
|
TaxonRelationshipType relType = BerlinModelTransformer.taxonRelId2TaxonRelType(relQualifierFk, isInverse, isDoubtful);
|
|
401
|
|
|
402
|
if (! (taxon1 instanceof Taxon)){
|
|
403
|
success = false;
|
|
404
|
logger.error("TaxonBase (ID = " + taxon1.getId()+ ", RIdentifier = " + taxon1Id + ") can't be casted to Taxon");
|
|
405
|
}else{
|
|
406
|
Taxon fromTaxon = (Taxon)taxon1;
|
|
407
|
if (isInverse.getValue() == true){
|
|
408
|
Taxon tmp = fromTaxon;
|
|
409
|
fromTaxon = toTaxon;
|
|
410
|
toTaxon = tmp;
|
|
411
|
}
|
|
412
|
taxonRelationship = fromTaxon.addTaxonRelation(toTaxon, relType, citation, microcitation);
|
|
413
|
handleAllRelatedTaxa(state, toTaxon, classificationMap, treeRefFk);
|
|
414
|
handleAllRelatedTaxa(state, fromTaxon, classificationMap, fromRefFk);
|
|
415
|
if (isDoubtful.getValue() == true){
|
|
416
|
((TaxonRelationship)taxonRelationship).setDoubtful(true);
|
|
417
|
}
|
|
418
|
}
|
|
419
|
} catch (UnknownCdmTypeException e) {
|
|
420
|
logger.warn("TaxonRelationShipType " + relQualifierFk + " (conceptRelationship) not yet implemented");
|
|
421
|
success = false;
|
|
422
|
}
|
|
423
|
}else {
|
|
424
|
logger.warn("TaxonRelationShipType " + relQualifierFk + " not yet implemented: RelPTaxonId = " + relPTaxonId );
|
|
425
|
success = false;
|
|
426
|
}
|
|
427
|
|
|
428
|
if (taxonRelationship != null && isNotBlank(notes)){
|
|
429
|
doNotes(taxonRelationship, notes);
|
|
430
|
}
|
|
431
|
if (isNotBlank(notes)){
|
|
432
|
logger.warn("Notes in RelPTaxon should all be handled explicitly and should not exist as notes anymore. RelID: " + relPTaxonId + ". Note: " + notes);
|
|
433
|
}
|
|
434
|
taxaToSave.add(taxon2);
|
|
435
|
|
|
436
|
//TODO
|
|
437
|
//etc.
|
|
438
|
}else{
|
|
439
|
if (taxon2 != null && taxon1 == null){
|
|
440
|
logger.warn("First taxon ("+taxon1Id+") for RelPTaxon " + relPTaxonId + " does not exist in store. RelType: " + relQualifierFk);
|
|
441
|
}else if (taxon2 == null && taxon1 != null){
|
|
442
|
logger.warn("Second taxon ("+taxon2Id +") for RelPTaxon " + relPTaxonId + " does not exist in store. RelType: " + relQualifierFk);
|
|
443
|
}else{
|
|
444
|
logger.warn("Both taxa ("+taxon1Id+","+taxon2Id +") for RelPTaxon " + relPTaxonId + " do not exist in store. RelType: " + relQualifierFk);
|
|
445
|
}
|
|
446
|
|
|
447
|
success = false;
|
|
448
|
}
|
|
449
|
} catch (Exception e) {
|
|
450
|
logger.error("Exception occurred when trying to handle taxon relationship " + relPTaxonId + " relQualifierFK " + relQualifierFk + " (" + taxon1Id + ","+ taxon2Id + "): " + e.getMessage());
|
|
451
|
e.printStackTrace();
|
|
452
|
}
|
|
453
|
}
|
|
454
|
}catch(SQLException e){
|
|
455
|
throw new RuntimeException(e);
|
|
456
|
}
|
|
457
|
logger.info("Taxa to save: " + taxaToSave.size());
|
|
458
|
partitioner.startDoSave();
|
|
459
|
getTaxonService().saveOrUpdate(taxaToSave);
|
|
460
|
classificationMap = null;
|
|
461
|
taxaToSave = null;
|
|
462
|
|
|
463
|
return success;
|
|
464
|
}
|
|
465
|
|
|
466
|
|
|
467
|
/**
|
|
468
|
* @param toTaxon
|
|
469
|
* @param synonym
|
|
470
|
* @param notes
|
|
471
|
* @return
|
|
472
|
*/
|
|
473
|
private String handleSynonymNotes(BerlinModelImportState state, Taxon toTaxon, Synonym synonym, String notes, int relId) {
|
|
474
|
if (state.getConfig().isEuroMed() && isNotBlank(notes)){
|
|
475
|
notes = notes.trim();
|
|
476
|
if (notes.startsWith("[non ") && notes.endsWith("]")){
|
|
477
|
notes = notes.substring(5, notes.length()-1).trim();
|
|
478
|
String[] splits = notes.split(", nec ");
|
|
479
|
for (String split : splits){
|
|
480
|
String nameStr = split.replace("<i>", "").replace("</i>", "");
|
|
481
|
NonViralNameParserImpl parser = NonViralNameParserImpl.NewInstance();
|
|
482
|
TaxonName name;
|
|
483
|
NomenclaturalStatusType status = null;
|
|
484
|
if (nameStr.endsWith(", nom. rej.") || nameStr.endsWith(", nom. cons.")||nameStr.endsWith(", nom. illeg.")){
|
|
485
|
String statusStr = nameStr.endsWith(", nom. rej.")? ", nom. rej.":
|
|
486
|
nameStr.endsWith(", nom. cons.")? ", nom. cons.":
|
|
487
|
", nom. illeg.";
|
|
488
|
nameStr = nameStr.replace(statusStr, "");
|
|
489
|
statusStr = statusStr.replace(", ", "");
|
|
490
|
try {
|
|
491
|
status = NomenclaturalStatusType.getNomenclaturalStatusTypeByAbbreviation(statusStr, null);
|
|
492
|
} catch (UnknownCdmTypeException e) {
|
|
493
|
logger.warn("NomStatusType not recognized: "+ statusStr + ", RelId: " + relId);
|
|
494
|
}
|
|
495
|
}
|
|
496
|
|
|
497
|
if (nameStr.contains(",") || nameStr.contains(" in ") ){
|
|
498
|
name = parser.parseReferencedName(nameStr, state.getConfig().getNomenclaturalCode(), null);
|
|
499
|
}else if (nameStr.matches(".*\\s\\d{4}")){
|
|
500
|
String nameStr2 = nameStr.substring(0, nameStr.length() - 5).trim();
|
|
501
|
String yearStr = nameStr.substring(nameStr.length()-4);
|
|
502
|
name = (TaxonName)parser.parseFullName(nameStr2, state.getConfig().getNomenclaturalCode(), null);
|
|
503
|
Reference nomRef = name.getNomenclaturalReference();
|
|
504
|
if (nomRef == null){
|
|
505
|
nomRef = ReferenceFactory.newGeneric();
|
|
506
|
name.setNomenclaturalReference(nomRef);
|
|
507
|
}
|
|
508
|
nomRef.setDatePublished(TimePeriodParser.parseStringVerbatim(yearStr));
|
|
509
|
}else if (nameStr.endsWith(" 1831-1832")){
|
|
510
|
String nameStr2 = nameStr.substring(0, nameStr.length() - 10).trim();
|
|
511
|
name = (TaxonName)parser.parseFullName(nameStr2, state.getConfig().getNomenclaturalCode(), null);
|
|
512
|
Reference nomRef = name.getNomenclaturalReference();
|
|
513
|
if (nomRef == null){
|
|
514
|
nomRef = ReferenceFactory.newGeneric();
|
|
515
|
name.setNomenclaturalReference(nomRef);
|
|
516
|
}
|
|
517
|
nomRef.setDatePublished(TimePeriodParser.parseStringVerbatim("1831-1832"));
|
|
518
|
}else{
|
|
519
|
name = parser.parseReferencedName(nameStr, state.getConfig().getNomenclaturalCode(), null);
|
|
520
|
}
|
|
521
|
if (name.isProtectedTitleCache() || name.isProtectedNameCache()
|
|
522
|
|| name.getNomenclaturalReference() != null && (name.getNomenclaturalReference().isProtectedAbbrevTitleCache()|| name.getNomenclaturalReference().isProtectedTitleCache() )){
|
|
523
|
logger.warn("Blocking name for synonym relation could not be parsed: " + nameStr + ", RelId: "+ relId);
|
|
524
|
}
|
|
525
|
if (status != null){
|
|
526
|
name.addStatus(NomenclaturalStatus.NewInstance(status));
|
|
527
|
}
|
|
528
|
synonym.getName().addRelationshipFromName(name, NameRelationshipType.BLOCKING_NAME_FOR(), null, null, null);
|
|
529
|
|
|
530
|
getNameService().saveOrUpdate(name);
|
|
531
|
}
|
|
532
|
return null;
|
|
533
|
}else{
|
|
534
|
return notes;
|
|
535
|
}
|
|
536
|
}else{
|
|
537
|
return notes;
|
|
538
|
}
|
|
539
|
}
|
|
540
|
|
|
541
|
private void handleAllRelatedTaxa(BerlinModelImportState state, Taxon taxon,
|
|
542
|
Map<Integer, Classification> classificationMap, Integer secRefFk) {
|
|
543
|
if (taxon.getTaxonNodes().size() > 0){
|
|
544
|
return;
|
|
545
|
}else{
|
|
546
|
Classification classification = getClassificationTree(state, classificationMap, secRefFk);
|
|
547
|
classification.addChildTaxon(taxon, null, null);
|
|
548
|
}
|
|
549
|
}
|
|
550
|
|
|
551
|
@Override
|
|
552
|
protected void doInvoke(BerlinModelImportState state){
|
|
553
|
try {
|
|
554
|
makeClassifications(state);
|
|
555
|
super.doInvoke(state);
|
|
556
|
makeFlatClassificationTaxa(state);
|
|
557
|
return;
|
|
558
|
} catch (SQLException e) {
|
|
559
|
throw new RuntimeException(e);
|
|
560
|
}
|
|
561
|
|
|
562
|
}
|
|
563
|
|
|
564
|
|
|
565
|
private void makeFlatClassificationTaxa(BerlinModelImportState state) {
|
|
566
|
//Note: this part still does not use partitions
|
|
567
|
logger.info("Flat classifications start");
|
|
568
|
TransactionStatus txStatus = startTransaction();
|
|
569
|
if (! state.getConfig().isIncludeFlatClassifications()){
|
|
570
|
return;
|
|
571
|
}
|
|
572
|
String sql = " SELECT pt.PTRefFk AS secRefFk, pt.RIdentifier " +
|
|
573
|
" FROM PTaxon AS pt " +
|
|
574
|
" LEFT OUTER JOIN RelPTaxon ON pt.PTNameFk = RelPTaxon.PTNameFk2 AND pt.PTRefFk = RelPTaxon.PTRefFk2 " +
|
|
575
|
" LEFT OUTER JOIN RelPTaxon AS RelPTaxon_1 ON pt.PTNameFk = RelPTaxon_1.PTNameFk1 AND pt.PTRefFk = RelPTaxon_1.PTRefFk1 " +
|
|
576
|
" WHERE (RelPTaxon_1.RelQualifierFk IS NULL) AND (dbo.RelPTaxon.RelQualifierFk IS NULL) " +
|
|
577
|
" ORDER BY pt.PTRefFk " ;
|
|
578
|
ResultSet rs = state.getConfig().getSource().getResultSet(sql);
|
|
579
|
Map<Object, Map<String, ? extends CdmBase>> maps = getRelatedObjectsForFlatPartition(rs);
|
|
580
|
|
|
581
|
Map<String, TaxonBase> taxonMap = (Map<String, TaxonBase>) maps.get(BerlinModelTaxonImport.NAMESPACE);
|
|
582
|
Map<Integer, Classification> classificationMap = new HashMap<>();
|
|
583
|
|
|
584
|
rs = state.getConfig().getSource().getResultSet(sql);
|
|
585
|
try {
|
|
586
|
while (rs.next()){
|
|
587
|
Integer treeRefFk = rs.getInt("secRefFk");
|
|
588
|
String taxonId = rs.getString("RIdentifier");
|
|
589
|
Classification classification = getClassificationTree(state, classificationMap, treeRefFk);
|
|
590
|
TaxonBase<?> taxon = taxonMap.get(taxonId);
|
|
591
|
if (taxon == null){
|
|
592
|
String message = "TaxonBase for taxon id (%s) not found in taxonMap";
|
|
593
|
logger.warn(String.format(message, taxonId, taxonId));
|
|
594
|
}else if (taxon.isInstanceOf(Taxon.class)){
|
|
595
|
classification.addChildTaxon(CdmBase.deproxy(taxon, Taxon.class), null, null);
|
|
596
|
}else{
|
|
597
|
String message = "TaxonBase for taxon is not of class Taxon but %s (RIdentifier %s)";
|
|
598
|
logger.warn(String.format(message, taxon.getClass(), taxonId));
|
|
599
|
}
|
|
600
|
}
|
|
601
|
} catch (SQLException e) {
|
|
602
|
e.printStackTrace();
|
|
603
|
}
|
|
604
|
commitTransaction(txStatus);
|
|
605
|
logger.info("Flat classifications end");
|
|
606
|
|
|
607
|
}
|
|
608
|
|
|
609
|
@Override
|
|
610
|
protected String getIdQuery(BerlinModelImportState state) {
|
|
611
|
if (state.getConfig().getRelTaxaIdQuery() != null){
|
|
612
|
return state.getConfig().getRelTaxaIdQuery();
|
|
613
|
}else{
|
|
614
|
return super.getIdQuery(state);
|
|
615
|
}
|
|
616
|
}
|
|
617
|
|
|
618
|
@Override
|
|
619
|
public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, BerlinModelImportState state) {
|
|
620
|
String nameSpace;
|
|
621
|
Class<?> cdmClass;
|
|
622
|
Set<String> idSet;
|
|
623
|
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();
|
|
624
|
|
|
625
|
try{
|
|
626
|
Set<String> taxonIdSet = new HashSet<>();
|
|
627
|
Set<String> referenceIdSet = new HashSet<>();
|
|
628
|
// Set<String> classificationIdSet = new HashSet<>();
|
|
629
|
while (rs.next()){
|
|
630
|
handleForeignKey(rs, taxonIdSet, "taxon1Id");
|
|
631
|
handleForeignKey(rs, taxonIdSet, "taxon2Id");
|
|
632
|
// handleForeignKey(rs, classificationIdSet, "treeRefFk");
|
|
633
|
handleForeignKey(rs, referenceIdSet, "RelRefFk");
|
|
634
|
}
|
|
635
|
|
|
636
|
//taxon map
|
|
637
|
nameSpace = BerlinModelTaxonImport.NAMESPACE;
|
|
638
|
cdmClass = TaxonBase.class;
|
|
639
|
idSet = taxonIdSet;
|
|
640
|
Map<String, TaxonBase> taxonMap = (Map<String, TaxonBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
641
|
result.put(nameSpace, taxonMap);
|
|
642
|
|
|
643
|
// //tree map
|
|
644
|
// nameSpace = "Classification";
|
|
645
|
// cdmClass = Classification.class;
|
|
646
|
// idSet = classificationIdSet;
|
|
647
|
// Map<String, Classification> treeMap = (Map<String, Classification>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
648
|
// result.put(cdmClass, treeMap);
|
|
649
|
// Set<UUID> treeUuidSet = state
|
|
650
|
// getClassificationService().find(uuidSet);
|
|
651
|
//
|
|
652
|
//reference map
|
|
653
|
nameSpace = BerlinModelReferenceImport.REFERENCE_NAMESPACE;
|
|
654
|
cdmClass = Reference.class;
|
|
655
|
idSet = referenceIdSet;
|
|
656
|
Map<String, Reference> referenceMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
657
|
result.put(nameSpace, referenceMap);
|
|
658
|
|
|
659
|
} catch (SQLException e) {
|
|
660
|
throw new RuntimeException(e);
|
|
661
|
}
|
|
662
|
return result;
|
|
663
|
}
|
|
664
|
|
|
665
|
|
|
666
|
private Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForFlatPartition( ResultSet rs) {
|
|
667
|
String nameSpace;
|
|
668
|
Class cdmClass;
|
|
669
|
Set<String> idSet;
|
|
670
|
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();
|
|
671
|
|
|
672
|
try{
|
|
673
|
Set<String> taxonIdSet = new HashSet<>();
|
|
674
|
Set<String> referenceIdSet = new HashSet<>();
|
|
675
|
// Set<String> classificationIdSet = new HashSet<>();
|
|
676
|
while (rs.next()){
|
|
677
|
handleForeignKey(rs, taxonIdSet, "RIdentifier");
|
|
678
|
// handleForeignKey(rs, classificationIdSet, "treeRefFk");
|
|
679
|
}
|
|
680
|
|
|
681
|
//taxon map
|
|
682
|
nameSpace = BerlinModelTaxonImport.NAMESPACE;
|
|
683
|
cdmClass = TaxonBase.class;
|
|
684
|
idSet = taxonIdSet;
|
|
685
|
Map<String, TaxonBase> taxonMap = (Map<String, TaxonBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
686
|
result.put(nameSpace, taxonMap);
|
|
687
|
|
|
688
|
// //tree map
|
|
689
|
// nameSpace = "Classification";
|
|
690
|
// cdmClass = Classification.class;
|
|
691
|
// idSet = classificationIdSet;
|
|
692
|
// Map<String, Classification> treeMap = (Map<String, Classification>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
693
|
// result.put(cdmClass, treeMap);
|
|
694
|
// Set<UUID> treeUuidSet = state
|
|
695
|
// getClassificationService().find(uuidSet);
|
|
696
|
//
|
|
697
|
|
|
698
|
} catch (SQLException e) {
|
|
699
|
throw new RuntimeException(e);
|
|
700
|
}
|
|
701
|
return result;
|
|
702
|
}
|
|
703
|
|
|
704
|
|
|
705
|
private void makeSynRel (BerlinModelImportState state, int relQualifierFk, Taxon toTaxon, Synonym synonym, Reference citation, String microcitation){
|
|
706
|
if (state.getConfig().isWarnForDifferingSynonymReference() && citation != null && !citation.equals(synonym.getSec())){
|
|
707
|
logger.warn("A synonym relationship citation is given and differs from synonym secundum. This can not be handled in CDM");
|
|
708
|
}
|
|
709
|
if (isNotBlank(microcitation) && !microcitation.equals(synonym.getSecMicroReference())){
|
|
710
|
logger.warn("A synonym relationship microcitation is given and differs from synonym secundum micro reference. This can not be handled in CDM");
|
|
711
|
}
|
|
712
|
if (relQualifierFk == TAX_REL_IS_HOMOTYPIC_SYNONYM_OF ||
|
|
713
|
relQualifierFk == TAX_REL_IS_PROPARTE_HOMOTYPIC_SYNONYM_OF ||
|
|
714
|
relQualifierFk == TAX_REL_IS_PARTIAL_HOMOTYPIC_SYNONYM_OF){
|
|
715
|
toTaxon.addHomotypicSynonym(synonym);
|
|
716
|
}else if (relQualifierFk == TAX_REL_IS_HETEROTYPIC_SYNONYM_OF ||
|
|
717
|
relQualifierFk == TAX_REL_IS_PROPARTE_HETEROTYPIC_SYNONYM_OF ||
|
|
718
|
relQualifierFk == TAX_REL_IS_PARTIAL_HETEROTYPIC_SYNONYM_OF){
|
|
719
|
toTaxon.addSynonym(synonym, SynonymType.HETEROTYPIC_SYNONYM_OF());
|
|
720
|
}else if (relQualifierFk == TAX_REL_IS_SYNONYM_OF ||
|
|
721
|
relQualifierFk == TAX_REL_IS_PROPARTE_SYN_OF ||
|
|
722
|
relQualifierFk == TAX_REL_IS_PARTIAL_SYN_OF){
|
|
723
|
toTaxon.addSynonym(synonym, SynonymType.SYNONYM_OF());
|
|
724
|
}else{
|
|
725
|
logger.warn("SynonymyRelationShipType could not be defined for relQualifierFk " + relQualifierFk + ". 'Unknown'-Type taken instead.");
|
|
726
|
toTaxon.addSynonym(synonym, SynonymType.SYNONYM_OF());
|
|
727
|
}
|
|
728
|
return;
|
|
729
|
|
|
730
|
}
|
|
731
|
|
|
732
|
private boolean isSynonymRelationship(int relQualifierFk){
|
|
733
|
if (relQualifierFk == TAX_REL_IS_SYNONYM_OF ||
|
|
734
|
relQualifierFk == TAX_REL_IS_HOMOTYPIC_SYNONYM_OF ||
|
|
735
|
relQualifierFk == TAX_REL_IS_HETEROTYPIC_SYNONYM_OF ||
|
|
736
|
relQualifierFk == TAX_REL_IS_PROPARTE_SYN_OF ||
|
|
737
|
relQualifierFk == TAX_REL_IS_PARTIAL_SYN_OF ||
|
|
738
|
relQualifierFk == TAX_REL_IS_PROPARTE_HOMOTYPIC_SYNONYM_OF ||
|
|
739
|
relQualifierFk == TAX_REL_IS_PROPARTE_HETEROTYPIC_SYNONYM_OF ||
|
|
740
|
relQualifierFk == TAX_REL_IS_PARTIAL_HOMOTYPIC_SYNONYM_OF ||
|
|
741
|
relQualifierFk == TAX_REL_IS_PARTIAL_HETEROTYPIC_SYNONYM_OF
|
|
742
|
){
|
|
743
|
return true;
|
|
744
|
}else{
|
|
745
|
return false;
|
|
746
|
}
|
|
747
|
}
|
|
748
|
|
|
749
|
private boolean isTaxonRelationship(int relQualifierFk){
|
|
750
|
if (relQualifierFk == TAX_REL_IS_INCLUDED_IN ||
|
|
751
|
relQualifierFk == TAX_REL_IS_MISAPPLIED_NAME_OF){
|
|
752
|
return true;
|
|
753
|
}else if (relQualifierFk == TAX_REL_IS_PROPARTE_SYN_OF ||
|
|
754
|
relQualifierFk == TAX_REL_IS_PARTIAL_SYN_OF ||
|
|
755
|
relQualifierFk == TAX_REL_IS_PROPARTE_HOMOTYPIC_SYNONYM_OF ||
|
|
756
|
relQualifierFk == TAX_REL_IS_PROPARTE_HETEROTYPIC_SYNONYM_OF ||
|
|
757
|
relQualifierFk == TAX_REL_IS_PARTIAL_HOMOTYPIC_SYNONYM_OF ||
|
|
758
|
relQualifierFk == TAX_REL_IS_PARTIAL_HETEROTYPIC_SYNONYM_OF
|
|
759
|
){
|
|
760
|
return true;
|
|
761
|
|
|
762
|
}else{
|
|
763
|
return false;
|
|
764
|
}
|
|
765
|
}
|
|
766
|
|
|
767
|
private TaxonNode makeTaxonomicallyIncluded(BerlinModelImportState state, Map<Integer, Classification> classificationMap,
|
|
768
|
int treeRefFk, Taxon child, Taxon parent, Reference citation, String microCitation){
|
|
769
|
Classification tree = getClassificationTree(state, classificationMap, treeRefFk);
|
|
770
|
return tree.addParentChild(parent, child, citation, microCitation);
|
|
771
|
}
|
|
772
|
|
|
773
|
private Classification getClassificationTree(BerlinModelImportState state, Map<Integer, Classification> classificationMap, int treeRefFk) {
|
|
774
|
if (state.getConfig().isUseSingleClassification()){
|
|
775
|
if (state.getConfig().getSourceSecId() != null){
|
|
776
|
treeRefFk = (Integer)state.getConfig().getSourceSecId();
|
|
777
|
}else{
|
|
778
|
treeRefFk = 1;
|
|
779
|
}
|
|
780
|
|
|
781
|
}
|
|
782
|
Classification tree = classificationMap.get(treeRefFk);
|
|
783
|
if (tree == null){
|
|
784
|
UUID treeUuid = state.getTreeUuidByIntTreeKey(treeRefFk);
|
|
785
|
if (treeUuid == null){
|
|
786
|
throw new IllegalStateException("treeUUID does not exist in state for " + treeRefFk );
|
|
787
|
}
|
|
788
|
tree = getClassificationService().find(treeUuid);
|
|
789
|
classificationMap.put(treeRefFk, tree);
|
|
790
|
}
|
|
791
|
if (tree == null){
|
|
792
|
throw new IllegalStateException("Tree for ToTaxon reference " + treeRefFk + " does not exist.");
|
|
793
|
}
|
|
794
|
return tree;
|
|
795
|
}
|
|
796
|
|
|
797
|
@Override
|
|
798
|
protected boolean doCheck(BerlinModelImportState state){
|
|
799
|
IOValidator<BerlinModelImportState> validator = new BerlinModelTaxonRelationImportValidator();
|
|
800
|
return validator.validate(state);
|
|
801
|
}
|
|
802
|
|
|
803
|
@Override
|
|
804
|
protected boolean isIgnore(BerlinModelImportState state){
|
|
805
|
return ! state.getConfig().isDoRelTaxa();
|
|
806
|
}
|
|
807
|
|
|
808
|
|
|
809
|
}
|