Revision 51688d00
Added by Andreas Müller almost 7 years ago
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/ErmsTaxonRelationImport.java | ||
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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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* European Distributed Institute of Taxonomy |
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* http://www.e-taxonomy.eu |
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*
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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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import eu.etaxonomy.cdm.io.common.mapping.ICheckIgnoreMapper; |
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import eu.etaxonomy.cdm.io.common.mapping.IDbImportMapper; |
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import eu.etaxonomy.cdm.model.common.CdmBase; |
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import eu.etaxonomy.cdm.model.name.TaxonNameBase;
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import eu.etaxonomy.cdm.model.name.TaxonName; |
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import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType; |
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public class ErmsTaxonRelationImport extends ErmsImportBase<TaxonBase<?>> implements ICheckIgnoreMapper{
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@SuppressWarnings("unused")
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private static final Logger logger = Logger.getLogger(ErmsTaxonRelationImport.class); |
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private DbImportMapping<ErmsImportState, ErmsImportConfigurator> mapping; |
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private static final String pluralString = "taxon relations"; |
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private static final String dbTableName = "tu"; |
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private static final Class<?> cdmTargetClass = TaxonBase.class; |
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private ErmsImportState state; //ERMS import will never run in more then one instance |
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public ErmsTaxonRelationImport(){
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super(pluralString, dbTableName, cdmTargetClass); |
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} |
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protected DbImportMapping<ErmsImportState, ErmsImportConfigurator> getMapping() {
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if (mapping == null){
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mapping = new DbImportMapping<ErmsImportState, ErmsImportConfigurator>(); |
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mapping.addMapper(DbImportTaxIncludedInMapper.NewInstance("id", TAXON_NAMESPACE, "parentId", TAXON_NAMESPACE, "accParentId", TAXON_NAMESPACE, null));//there is only one tree
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TaxonRelationshipType taxonRelationshipType = getTaxonRelationshipType(state, ErmsTransformer.uuidTaxRelTypeIsTaxonSynonymOf, "is taxon synonym of", "is synonym of relation used by synonym that are of class Taxon as they can not be handled differently", null, null); |
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mapping.addMapper(DbImportSynonymMapper.NewInstance("id", "tu_acctaxon", TAXON_NAMESPACE, null, taxonRelationshipType));
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mapping.addMapper(DbImportSynonymMapper.NewInstance("id", "tu_acctaxon", TAXON_NAMESPACE, null, taxonRelationshipType));
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mapping.addMapper(DbImportNameTypeDesignationMapper.NewInstance("id", "tu_typetaxon", ErmsTaxonImport.NAME_NAMESPACE, "tu_typedesignationstatus"));
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// mapping.addMapper(DbNotYetImplementedMapper.NewInstance("tu_acctaxon"));
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} |
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return mapping; |
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} |
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/* (non-Javadoc) |
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* @see eu.etaxonomy.cdm.io.erms.ErmsImportBase#getRecordQuery(eu.etaxonomy.cdm.io.erms.ErmsImportConfigurator) |
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*/ |
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protected String getRecordQuery(ErmsImportConfigurator config) {
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@Override |
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protected String getRecordQuery(ErmsImportConfigurator config) {
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//TODO get automatic by second path mappers |
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String selectAttributes = " myTaxon.id, myTaxon.tu_parent, myTaxon.tu_typetaxon, myTaxon.tu_typedesignation, " + |
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" myTaxon.tu_acctaxon, myTaxon.tu_status, parent.tu_status AS parentStatus, parent.id AS parentId, " +
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" accParent.tu_status AS accParentStatus, accParent.id AS accParentId ";
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String strRecordQuery =
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" SELECT " + selectAttributes +
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" myTaxon.tu_acctaxon, myTaxon.tu_status, parent.tu_status AS parentStatus, parent.id AS parentId, " + |
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" accParent.tu_status AS accParentStatus, accParent.id AS accParentId "; |
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String strRecordQuery = |
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" SELECT " + selectAttributes + |
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" FROM tu AS myTaxon LEFT OUTER JOIN " + |
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" tu AS accTaxon ON myTaxon.tu_acctaxon = accTaxon.id LEFT OUTER JOIN " + |
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" tu AS accParent RIGHT OUTER JOIN " +
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" tu AS accParent RIGHT OUTER JOIN " + |
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" tu AS parent ON accParent.id = parent.tu_acctaxon ON myTaxon.tu_parent = parent.id " + |
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" WHERE ( myTaxon.id IN (" + ID_LIST_TOKEN + ") )";
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return strRecordQuery; |
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} |
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@Override |
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protected void doInvoke(ErmsImportState state) {
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Class<?> cdmClass; |
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Set<String> idSet; |
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Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>(); |
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try{
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Set<String> taxonIdSet = new HashSet<String>(); |
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Set<String> nameIdSet = new HashSet<String>(); |
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handleForeignKey(rs, taxonIdSet, "tu_acctaxon"); |
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handleForeignKey(rs, taxonIdSet, "id"); |
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handleForeignKey(rs, nameIdSet, "tu_typetaxon"); |
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handleForeignKey(rs, nameIdSet, "id");
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handleForeignKey(rs, nameIdSet, "id"); |
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} |
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//name map |
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nameSpace = ErmsTaxonImport.NAME_NAMESPACE; |
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cdmClass = TaxonNameBase.class;
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cdmClass = TaxonName.class; |
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idSet = nameIdSet; |
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Map<String, TaxonNameBase<?,?>> nameMap = (Map<String, TaxonNameBase<?,?>>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
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Map<String, TaxonName> nameMap = (Map<String, TaxonName>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
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result.put(nameSpace, nameMap); |
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//taxon map |
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nameSpace = ErmsTaxonImport.TAXON_NAMESPACE; |
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cdmClass = TaxonBase.class; |
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} |
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return result; |
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} |
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/* (non-Javadoc) |
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* @see eu.etaxonomy.cdm.io.erms.ICheckIgnoreMapper#checkIgnoreMapper(eu.etaxonomy.cdm.io.common.mapping.IDbImportMapper, java.sql.ResultSet) |
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*/ |
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public boolean checkIgnoreMapper(IDbImportMapper mapper, ResultSet rs) throws SQLException{
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@Override |
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public boolean checkIgnoreMapper(IDbImportMapper mapper, ResultSet rs) throws SQLException{
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boolean result = false; |
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if (mapper instanceof DbImportTaxIncludedInMapper){
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//old |
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// if (tu_status != 1){
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// result = true; |
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// } |
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int id = rs.getInt("id");
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if (state.getAcceptedTaxaKeys().contains(id)){
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return false; |
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// }else{
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// return false; |
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// }t.tu_acctaxon <> t.id |
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int id = rs.getInt("id");
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Object accTaxonId = rs.getObject("tu_acctaxon");
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if (accTaxonId == null){
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} |
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return result; |
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} |
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@Override |
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protected boolean doCheck(ErmsImportState state){
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// IOValidator<ErmsImportState> validator = new ErmsTaxonImportValidator(); |
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// return validator.validate(state); |
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return true; |
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} |
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@Override |
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protected boolean isIgnore(ErmsImportState state){
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return ! state.getConfig().isDoRelTaxa(); |
Also available in: Unified diff
ref #6368 , ref #6671, ref #6630 adapt pesi to no taxon name model