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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.common;
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import java.lang.reflect.Method;
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import java.util.List;
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import java.util.UUID;
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import org.apache.log4j.Logger;
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import eu.etaxonomy.cdm.api.application.CdmApplicationController;
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import eu.etaxonomy.cdm.database.DataSourceNotFoundException;
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import eu.etaxonomy.cdm.database.DbSchemaValidation;
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import eu.etaxonomy.cdm.database.ICdmDataSource;
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import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;
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import eu.etaxonomy.cdm.io.common.IImportConfigurator.DO_REFERENCES;
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import eu.etaxonomy.cdm.model.agent.Person;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.common.init.TermNotFoundException;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
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import eu.etaxonomy.cdm.model.reference.ReferenceBase;
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/**
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* @author a.mueller
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* @created 20.06.2008
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* @version 1.0
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*/
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public abstract class ImportConfiguratorBase extends IoConfiguratorBase {
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private static final Logger logger = Logger.getLogger(ImportConfiguratorBase.class);
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//check
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private CHECK check = CHECK.CHECK_AND_IMPORT;
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//TODO
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private boolean deleteAll = false;
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// private boolean doAuthors = true;
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// //references
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// private DO_REFERENCES doReferences = DO_REFERENCES.ALL;
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// //names
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// private boolean doTaxonNames = true;
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// private boolean doRelNames = true;
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// private boolean doNameStatus = true;
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// private boolean doTypes = true;
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// private boolean doNameFacts = true;
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//
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// //taxa
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// private boolean doTaxa = true;
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// private boolean doRelTaxa = true;
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// private boolean doFacts = true;
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//
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// //occurrence
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// private boolean doOccurrence = true;
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/* For Jaxb import - is defined in JaxbImportConfigurator */
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// private boolean doTerms = true;
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// private boolean doTermVocabularies = true;
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// private boolean doHomotypicalGroups = true;
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// private boolean doReferencedEntities = true;
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// private boolean doFeatureData = true;
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// private boolean doMedia = true;
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// private boolean doLanguageData = true;
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/* end for Jaxb import */
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//nullValues
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private boolean ignoreNull = false;
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//Nomenclatural Code
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private NomenclaturalCode nomenclaturalCode = null;
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// protected Class<ICdmIO>[] ioClassList;
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private MapWrapper<Feature> featureMap = new MapWrapper<Feature>(null);
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//uuid of concept reference
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private UUID secUuid = UUID.randomUUID();
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private Object sourceSecId = -1;
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private Object source;
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protected ReferenceBase sourceReference;
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private ICdmDataSource destination;
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private Person commentator = Person.NewTitledInstance("automatic BerlinModel2CDM importer");
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private Language factLanguage = Language.ENGLISH();
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private CdmApplicationController cdmApp = null;
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protected Class<ICdmIO>[] ioClassList;
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/* *****************CONSTRUCTOR *****************************/
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public ImportConfiguratorBase(){
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super();
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makeIoClassList();
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}
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abstract protected void makeIoClassList();
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/**
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* @param source the source to set
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*/
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public void setSource(Object source) {
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this.source = source;
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}
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/**
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* @param source the source to get
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*/
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public Object getSource() {
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return source;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.tcs.IImportConfigurator#isValid()
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*/
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public boolean isValid(){
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boolean result = true;
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if (source == null){
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logger.warn("Connection to BerlinModel could not be established");
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result = false;
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}
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if (destination == null){
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logger.warn("Connection to Cdm could not be established");
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result = false;
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}
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return result;
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}
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/* ****************** GETTER/SETTER **************************/
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.tcs.IImportConfigurator#isDeleteAll()
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*/
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public boolean isDeleteAll() {
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return deleteAll;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.tcs.IImportConfigurator#setDeleteAll(boolean)
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*/
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public void setDeleteAll(boolean deleteAll) {
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this.deleteAll = deleteAll;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.tcs.IImportConfigurator#isDoAuthors()
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*/
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// public boolean isDoAuthors() {
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// return doAuthors;
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// }
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// /* (non-Javadoc)
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// * @see eu.etaxonomy.cdm.io.tcs.IImportConfigurator#setDoAuthors(boolean)
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// */
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// public void setDoAuthors(boolean doAuthors) {
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// this.doAuthors = doAuthors;
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// }
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//
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// /* (non-Javadoc)
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// * @see eu.etaxonomy.cdm.io.tcs.IImportConfigurator#getDoReferences()
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// */
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// public DO_REFERENCES getDoReferences() {
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// return doReferences;
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// }
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// /* (non-Javadoc)
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// * @see eu.etaxonomy.cdm.io.tcs.IImportConfigurator#setDoReferences(eu.etaxonomy.cdm.io.tcs.TcsImportConfigurator.DO_REFERENCES)
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// */
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// public void setDoReferences(DO_REFERENCES doReferences) {
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// this.doReferences = doReferences;
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// }
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.tcs.IImportConfigurator#getCheck()
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*/
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public CHECK getCheck() {
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return this.check;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.tcs.IImportConfigurator#setCheck(eu.etaxonomy.cdm.io.tcs.TcsImportConfigurator.CHECK)
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*/
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public void setCheck(CHECK check) {
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this.check = check;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.tcs.IImportConfigurator#isDoTaxonNames()
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*/
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// public boolean isDoTaxonNames() {
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// return doTaxonNames;
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// }
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// /* (non-Javadoc)
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// * @see eu.etaxonomy.cdm.io.tcs.IImportConfigurator#setDoTaxonNames(boolean)
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// */
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// public void setDoTaxonNames(boolean doTaxonNames) {
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// this.doTaxonNames = doTaxonNames;
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// }
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// /* (non-Javadoc)
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// * @see eu.etaxonomy.cdm.io.tcs.IImportConfigurator#isDoRelNames()
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// */
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// public boolean isDoRelNames() {
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// return doRelNames;
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// }
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// /* (non-Javadoc)
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// * @see eu.etaxonomy.cdm.io.tcs.IImportConfigurator#setDoRelNames(boolean)
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// */
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// public void setDoRelNames(boolean doRelNames) {
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// this.doRelNames = doRelNames;
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// }
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// /* (non-Javadoc)
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// * @see eu.etaxonomy.cdm.io.tcs.IImportConfigurator#isDoNameStatus()
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// */
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// public boolean isDoNameStatus() {
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// return doNameStatus;
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// }
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// /* (non-Javadoc)
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// * @see eu.etaxonomy.cdm.io.tcs.IImportConfigurator#setDoNameStatus(boolean)
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// */
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// public void setDoNameStatus(boolean doNameStatus) {
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// this.doNameStatus = doNameStatus;
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// }
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// /* (non-Javadoc)
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// * @see eu.etaxonomy.cdm.io.tcs.IImportConfigurator#isDoNameFacts()
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// */
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// public boolean isDoNameFacts() {
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// return doNameFacts;
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// }
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// /* (non-Javadoc)
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// * @see eu.etaxonomy.cdm.io.tcs.IImportConfigurator#setDoNameFacts(boolean)
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// */
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// public void setDoNameFacts(boolean doNameFacts) {
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// this.doNameFacts = doNameFacts;
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// }
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// /* (non-Javadoc)
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// * @see eu.etaxonomy.cdm.io.tcs.IImportConfigurator#isDoTypes()
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// */
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// public boolean isDoTypes() {
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// return doTypes;
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// }
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// /* (non-Javadoc)
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// * @see eu.etaxonomy.cdm.io.tcs.IImportConfigurator#setDoTypes(boolean)
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// */
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// public void setDoTypes(boolean doTypes) {
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// this.doTypes = doTypes;
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// }
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// /* (non-Javadoc)
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// * @see eu.etaxonomy.cdm.io.tcs.IImportConfigurator#isDoTaxa()
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// */
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// public boolean isDoTaxa() {
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// return doTaxa;
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// }
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// /* (non-Javadoc)
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// * @see eu.etaxonomy.cdm.io.tcs.IImportConfigurator#setDoTaxa(boolean)
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// */
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// public void setDoTaxa(boolean doTaxa) {
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// this.doTaxa = doTaxa;
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// }
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// /* (non-Javadoc)
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// * @see eu.etaxonomy.cdm.io.tcs.IImportConfigurator#isDoRelTaxa()
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// */
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// public boolean isDoRelTaxa() {
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// return doRelTaxa;
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// }
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// /* (non-Javadoc)
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// * @see eu.etaxonomy.cdm.io.tcs.IImportConfigurator#setDoRelTaxa(boolean)
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// */
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// public void setDoRelTaxa(boolean doRelTaxa) {
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// this.doRelTaxa = doRelTaxa;
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// }
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// /* (non-Javadoc)
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// * @see eu.etaxonomy.cdm.io.tcs.IImportConfigurator#isDoFacts()
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// */
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// public boolean isDoFacts() {
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// return doFacts;
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// }
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// /* (non-Javadoc)
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// * @see eu.etaxonomy.cdm.io.tcs.IImportConfigurator#setDoFacts(boolean)
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// */
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// public void setDoFacts(boolean doFacts) {
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// this.doFacts = doFacts;
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// }
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// /* (non-Javadoc)
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// * @see eu.etaxonomy.cdm.io.tcs.IImportConfigurator#isDoOccurrence()
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// */
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// public boolean isDoOccurrence() {
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// return doOccurrence;
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// }
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// /* (non-Javadoc)
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// * @see eu.etaxonomy.cdm.io.tcs.IImportConfigurator#setDoOccurrence(boolean)
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// */
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// public void setDoOccurrence(boolean doOccurrence) {
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// this.doOccurrence = doOccurrence;
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// }
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/*
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* For Jaxb Import
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* TODO: Cleanup
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*/
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// public boolean isDoTerms() {
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// return doTerms;
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// }
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//
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// public void setDoTerms(boolean doTerms) {
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// this.doTerms = doTerms;
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// }
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//
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// public boolean isDoTermVocabularies() {
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// return doTermVocabularies;
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// }
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//
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// public void setDoTermVocabularies(boolean doTermVocabularies) {
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// this.doTermVocabularies = doTermVocabularies;
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// }
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//
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// public boolean isDoHomotypicalGroups() {
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// return doHomotypicalGroups;
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// }
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//
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// public void setDoHomotypicalGroups(boolean doHomotypicalGroups) {
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// this.doHomotypicalGroups = doHomotypicalGroups;
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// }
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//
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// public boolean isDoReferencedEntities() {
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// return doReferencedEntities;
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// }
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//
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// public void setDoReferencedEntities(boolean doReferencedEntities) {
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// this.doReferencedEntities = doReferencedEntities;
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// }
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//
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// public boolean isDoFeatureData() {
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// return doFeatureData;
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// }
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//
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// public void setDoFeatureData(boolean doFeatureData) {
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// this.doFeatureData = doFeatureData;
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// }
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//
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// public boolean isDoMedia() {
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// return doMedia;
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// }
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//
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// public void setDoMedia(boolean doMedia) {
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// this.doMedia = doMedia;
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// }
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//
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// public boolean isDoLanguageData() {
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// return doLanguageData;
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// }
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//
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// public void setDoLanguageData(boolean doLanguageData) {
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// this.doLanguageData = doLanguageData;
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// }
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/*
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* end for Jaxb import
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*/
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/**
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* If true, no errors occurs if objects are not found that should exist. This may
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* be needed e.g. when only subsets of the data are imported.
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370
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* Default value is <cod>false</code>.
|
|
371
|
* @return the ignoreNull
|
|
372
|
*/
|
|
373
|
public boolean isIgnoreNull() {
|
|
374
|
return ignoreNull;
|
|
375
|
}
|
|
376
|
|
|
377
|
/**
|
|
378
|
* @param ignoreNull the ignoreNull to set
|
|
379
|
*/
|
|
380
|
public void setIgnoreNull(boolean ignoreNull) {
|
|
381
|
this.ignoreNull = ignoreNull;
|
|
382
|
}
|
|
383
|
|
|
384
|
/* (non-Javadoc)
|
|
385
|
* @see eu.etaxonomy.cdm.io.tcs.IImportConfigurator#getDestination()
|
|
386
|
*/
|
|
387
|
public ICdmDataSource getDestination() {
|
|
388
|
return destination;
|
|
389
|
}
|
|
390
|
/* (non-Javadoc)
|
|
391
|
* @see eu.etaxonomy.cdm.io.tcs.IImportConfigurator#setDestination(eu.etaxonomy.cdm.database.ICdmDataSource)
|
|
392
|
*/
|
|
393
|
public void setDestination(ICdmDataSource destination) {
|
|
394
|
this.destination = destination;
|
|
395
|
}
|
|
396
|
|
|
397
|
/* (non-Javadoc)
|
|
398
|
* @see eu.etaxonomy.cdm.io.tcs.IImportConfigurator#getDbSchemaValidation()
|
|
399
|
*/
|
|
400
|
// public DbSchemaValidation getDbSchemaValidation() {
|
|
401
|
// return dbSchemaValidation;
|
|
402
|
// }
|
|
403
|
/* (non-Javadoc)
|
|
404
|
* @see eu.etaxonomy.cdm.io.tcs.IImportConfigurator#setDbSchemaValidation(eu.etaxonomy.cdm.database.DbSchemaValidation)
|
|
405
|
*/
|
|
406
|
// public void setDbSchemaValidation(DbSchemaValidation dbSchemaValidation) {
|
|
407
|
// this.dbSchemaValidation = dbSchemaValidation;
|
|
408
|
// }
|
|
409
|
|
|
410
|
/* (non-Javadoc)
|
|
411
|
* @see eu.etaxonomy.cdm.io.tcs.IImportConfigurator#getSourceReference()
|
|
412
|
*/
|
|
413
|
public abstract ReferenceBase getSourceReference();
|
|
414
|
/* (non-Javadoc)
|
|
415
|
* @see eu.etaxonomy.cdm.io.tcs.IImportConfigurator#setSourceReference(eu.etaxonomy.cdm.model.reference.ReferenceBase)
|
|
416
|
*/
|
|
417
|
public void setSourceReference(ReferenceBase sourceReference) {
|
|
418
|
this.sourceReference = sourceReference;
|
|
419
|
}
|
|
420
|
/* (non-Javadoc)
|
|
421
|
* @see eu.etaxonomy.cdm.io.tcs.IImportConfigurator#getSourceReferenceTitle()
|
|
422
|
*/
|
|
423
|
public String getSourceReferenceTitle() {
|
|
424
|
return getSourceReference().getTitleCache();
|
|
425
|
}
|
|
426
|
/* (non-Javadoc)
|
|
427
|
* @see eu.etaxonomy.cdm.io.tcs.IImportConfigurator#setSourceReferenceTitle(java.lang.String)
|
|
428
|
*/
|
|
429
|
public void setSourceReferenceTitle(String sourceReferenceTitle) {
|
|
430
|
getSourceReference().setTitleCache(sourceReferenceTitle);
|
|
431
|
}
|
|
432
|
|
|
433
|
|
|
434
|
/* (non-Javadoc)
|
|
435
|
* @see eu.etaxonomy.cdm.io.tcs.IImportConfigurator#getCommentator()
|
|
436
|
*/
|
|
437
|
public Person getCommentator() {
|
|
438
|
return commentator;
|
|
439
|
}
|
|
440
|
|
|
441
|
/* (non-Javadoc)
|
|
442
|
* @see eu.etaxonomy.cdm.io.tcs.IImportConfigurator#setCommentator(eu.etaxonomy.cdm.model.agent.Person)
|
|
443
|
*/
|
|
444
|
public void setCommentator(Person commentator) {
|
|
445
|
this.commentator = commentator;
|
|
446
|
}
|
|
447
|
|
|
448
|
|
|
449
|
/* (non-Javadoc)
|
|
450
|
* @see eu.etaxonomy.cdm.io.tcs.IImportConfigurator#getFactLanguage()
|
|
451
|
*/
|
|
452
|
public Language getFactLanguage() {
|
|
453
|
return factLanguage;
|
|
454
|
}
|
|
455
|
|
|
456
|
|
|
457
|
/* (non-Javadoc)
|
|
458
|
* @see eu.etaxonomy.cdm.io.tcs.IImportConfigurator#setFactLanguage(eu.etaxonomy.cdm.model.common.Language)
|
|
459
|
*/
|
|
460
|
public void setFactLanguage(Language factLanguage) {
|
|
461
|
this.factLanguage = factLanguage;
|
|
462
|
}
|
|
463
|
|
|
464
|
|
|
465
|
/**
|
|
466
|
* @return the nomenclaturalCode
|
|
467
|
*/
|
|
468
|
public NomenclaturalCode getNomenclaturalCode() {
|
|
469
|
return nomenclaturalCode;
|
|
470
|
}
|
|
471
|
|
|
472
|
|
|
473
|
/**
|
|
474
|
* @param nomenclaturalCode the nomenclaturalCode to set
|
|
475
|
*/
|
|
476
|
public void setNomenclaturalCode(NomenclaturalCode nomenclaturalCode) {
|
|
477
|
this.nomenclaturalCode = nomenclaturalCode;
|
|
478
|
}
|
|
479
|
|
|
480
|
|
|
481
|
/**
|
|
482
|
* @return the secUuid
|
|
483
|
*/
|
|
484
|
public UUID getSecUuid() {
|
|
485
|
return secUuid;
|
|
486
|
}
|
|
487
|
|
|
488
|
|
|
489
|
/**
|
|
490
|
* @param secUuid the secUuid to set
|
|
491
|
*/
|
|
492
|
public void setSecUuid(UUID secUuid) {
|
|
493
|
this.secUuid = secUuid;
|
|
494
|
}
|
|
495
|
|
|
496
|
/**
|
|
497
|
* @return the sourceSecId
|
|
498
|
*/
|
|
499
|
public Object getSourceSecId() {
|
|
500
|
return sourceSecId;
|
|
501
|
}
|
|
502
|
|
|
503
|
/**
|
|
504
|
* @param sourceSecId the sourceSecId to set
|
|
505
|
*/
|
|
506
|
public void setSourceSecId(Object sourceSecId) {
|
|
507
|
this.sourceSecId = sourceSecId;
|
|
508
|
}
|
|
509
|
|
|
510
|
public Class<ICdmIO>[] getIoClassList(){
|
|
511
|
return ioClassList;
|
|
512
|
}
|
|
513
|
|
|
514
|
|
|
515
|
/**
|
|
516
|
* @return the featureMap
|
|
517
|
*/
|
|
518
|
public MapWrapper<Feature> getFeatureMap() {
|
|
519
|
return featureMap;
|
|
520
|
}
|
|
521
|
|
|
522
|
/**
|
|
523
|
* @param featureMap the featureMap to set
|
|
524
|
*/
|
|
525
|
public void setFeatureMap(MapWrapper<Feature> featureMap) {
|
|
526
|
this.featureMap = featureMap;
|
|
527
|
}
|
|
528
|
|
|
529
|
|
|
530
|
/**
|
|
531
|
* Returns a <code>CdmApplicationController</code> created by the values of this configuration.
|
|
532
|
* If a controller was already created before the last created controller is returned.
|
|
533
|
* @return
|
|
534
|
*/
|
|
535
|
public CdmApplicationController getCdmAppController(){
|
|
536
|
return getCdmAppController(false);
|
|
537
|
}
|
|
538
|
|
|
539
|
/**
|
|
540
|
* Returns a new instance of <code>CdmApplicationController</code> created by the values of this configuration.
|
|
541
|
* @return
|
|
542
|
*/
|
|
543
|
public CdmApplicationController getNewCdmAppController(){
|
|
544
|
return getCdmAppController(true);
|
|
545
|
}
|
|
546
|
|
|
547
|
/**
|
|
548
|
* Returns a <code>CdmApplicationController</code> created by the values of this configuration.
|
|
549
|
* If create new is true always a new controller is returned, else the last created controller is returned. If no controller has
|
|
550
|
* been created before a new controller is returned.
|
|
551
|
* @return
|
|
552
|
*/
|
|
553
|
public CdmApplicationController getCdmAppController(boolean createNew){
|
|
554
|
if (cdmApp == null || createNew == true){
|
|
555
|
try {
|
|
556
|
cdmApp = CdmApplicationController.NewInstance(this.getDestination(), this.getDbSchemaValidation());
|
|
557
|
} catch (DataSourceNotFoundException e) {
|
|
558
|
logger.error("could not connect to destination database");
|
|
559
|
return null;
|
|
560
|
}catch (TermNotFoundException e) {
|
|
561
|
logger.error("could not find needed term in destination datasource");
|
|
562
|
return null;
|
|
563
|
}
|
|
564
|
}
|
|
565
|
return cdmApp;
|
|
566
|
}
|
|
567
|
|
|
568
|
|
|
569
|
/**
|
|
570
|
* Returns a <code>CdmApplicationController</code> created by the values of this configuration.
|
|
571
|
* If create new is true always a new controller is returned, else the last created controller is returned. If no controller has
|
|
572
|
* been created before a new controller is returned.
|
|
573
|
* @return
|
|
574
|
*/
|
|
575
|
public CdmApplicationController getCdmAppController(boolean createNew, boolean omitTermLoading){
|
|
576
|
if (cdmApp == null || createNew == true){
|
|
577
|
try {
|
|
578
|
cdmApp = CdmApplicationController.NewInstance(this.getDestination(), this.getDbSchemaValidation(), omitTermLoading);
|
|
579
|
} catch (DataSourceNotFoundException e) {
|
|
580
|
logger.error("could not connect to destination database");
|
|
581
|
return null;
|
|
582
|
}catch (TermNotFoundException e) {
|
|
583
|
logger.error("could not find needed term in destination datasource");
|
|
584
|
return null;
|
|
585
|
}
|
|
586
|
}
|
|
587
|
return cdmApp;
|
|
588
|
}
|
|
589
|
|
|
590
|
|
|
591
|
protected static Method getDefaultFunction(Class<?> clazz, String methodName){
|
|
592
|
try {
|
|
593
|
return clazz.getMethod(methodName, List.class) ;
|
|
594
|
} catch (SecurityException e) {
|
|
595
|
logger.error(e.getMessage());
|
|
596
|
e.printStackTrace();
|
|
597
|
} catch (NoSuchMethodException e) {
|
|
598
|
logger.error(e.getMessage());
|
|
599
|
e.printStackTrace();
|
|
600
|
}
|
|
601
|
return null;
|
|
602
|
}
|
|
603
|
|
|
604
|
|
|
605
|
}
|