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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.specimen.excel.in;
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import eu.etaxonomy.cdm.common.URI;
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import org.apache.logging.log4j.LogManager;import org.apache.logging.log4j.Logger;
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import eu.etaxonomy.cdm.database.ICdmDataSource;
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import eu.etaxonomy.cdm.io.common.CdmImportBase.TermMatchMode;
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import eu.etaxonomy.cdm.io.common.IImportConfigurator;
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import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer;
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import eu.etaxonomy.cdm.io.excel.common.ExcelImportConfiguratorBase;
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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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/**
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* @author a.mueller
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* @since 05.05.2011
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*/
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public class SpecimenCdmExcelImportConfigurator extends ExcelImportConfiguratorBase implements IImportConfigurator {
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private static final long serialVersionUID = -114046010543496409L;
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private static final Logger logger = LogManager.getLogger(SpecimenCdmExcelImportConfigurator.class);
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private static IInputTransformer defaultTransformer = new SpecimenCdmExcelTransformer();
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//old
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private boolean doParsing = false;
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private boolean reuseMetadata = false;
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private boolean reuseTaxon = false;
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private String taxonReference = null;
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//new
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private boolean doSpecimen = true; //reads the specimen worksheet
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private boolean doAreaLevels = true; //reads the areaLevels worksheet
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private boolean doExtensionTypes = true; //reads the extensionType worksheet
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private boolean useCountry; //if isocountry and country is available, use country instead of isocountry
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//tries to match areas by the abbreviated label
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//TODO still needs to be refined as this may hold only for certain vocabularies, levels, ...
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//there also maybe more strategies like first label, then abbreviated label, ....
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private TermMatchMode areaMatchMode = TermMatchMode.UUID_ONLY;
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private final PersonParserFormatEnum personParserFormat = PersonParserFormatEnum.POSTFIX; //
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//if true, determinations are imported also as individualAssociations
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private boolean makeIndividualAssociations = true;
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private boolean useMaterialsExaminedForIndividualsAssociations = true;
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private boolean firstDeterminationIsStoredUnder = false;
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private boolean determinationsAreDeterminationEvent = true;
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private boolean preferNameCache = true;
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private boolean createTaxonIfNotExists = false;
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// private boolean includeSynonymsForTaxonMatching = false;
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@Override
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@SuppressWarnings("unchecked")
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protected void makeIoClassList(){
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ioClassList = new Class[]{
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NamedAreaLevelExcelImport.class,
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ExtensionTypeExcelImport.class,
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SpecimenCdmExcelImport.class
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};
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}
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public static SpecimenCdmExcelImportConfigurator NewInstance(URI uri, ICdmDataSource destination){
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return new SpecimenCdmExcelImportConfigurator(uri, destination);
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}
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/**
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* @param uri
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* @param object
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* @param b
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* @return
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*/
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public static SpecimenCdmExcelImportConfigurator NewInstance(URI uri, ICdmDataSource destination, boolean interact) {
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return new SpecimenCdmExcelImportConfigurator(uri, destination, interact);
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}
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/**
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* @param berlinModelSource
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* @param sourceReference
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* @param destination
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*/
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private SpecimenCdmExcelImportConfigurator(URI uri, ICdmDataSource destination) {
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super(uri, destination, defaultTransformer);
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}
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/**
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* @param berlinModelSource
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* @param sourceReference
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* @param destination
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*/
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private SpecimenCdmExcelImportConfigurator(URI uri, ICdmDataSource destination, boolean interact) {
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super(uri, destination, defaultTransformer);
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setInteractWithUser(interact);
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}
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@Override
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public SpecimenCdmExcelImportState getNewState() {
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return new SpecimenCdmExcelImportState(this);
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}
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@Override
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public Reference getSourceReference() {
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//TODO
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if (this.sourceReference == null){
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logger.warn("getSource Reference not yet fully implemented");
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sourceReference = ReferenceFactory.newDatabase();
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sourceReference.setTitleCache("Specimen import", true);
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}
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return sourceReference;
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}
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@Override
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public String getSourceNameString() {
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if (this.getSource() == null){
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return null;
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}else{
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return this.getSource().toString();
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}
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}
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// **************************** OLD ******************************************
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public void setTaxonReference(String taxonReference) {
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this.taxonReference = taxonReference;
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}
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public Reference getTaxonReference() {
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//TODO
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if (this.taxonReference == null){
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logger.info("getTaxonReference not yet fully implemented");
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}
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return sourceReference;
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}
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public void setDoAutomaticParsing(boolean doParsing){
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this.doParsing=doParsing;
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}
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public boolean getDoAutomaticParsing(){
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return this.doParsing;
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}
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public void setReUseExistingMetadata(boolean reuseMetadata){
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this.reuseMetadata = reuseMetadata;
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}
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public boolean getReUseExistingMetadata(){
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return this.reuseMetadata;
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}
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public void setReUseTaxon(boolean reuseTaxon){
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this.reuseTaxon = reuseTaxon;
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}
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public boolean getDoReUseTaxon(){
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return this.reuseTaxon;
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}
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public void setDoSpecimen(boolean doSpecimen) {
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this.doSpecimen = doSpecimen;
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}
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public boolean isDoSpecimen() {
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return doSpecimen;
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}
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public void setDoAreaLevels(boolean doAreaLevels) {
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this.doAreaLevels = doAreaLevels;
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}
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public boolean isDoAreaLevels() {
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return doAreaLevels;
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}
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public void setMakeIndividualAssociations(boolean makeIndividualAssociations) {
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this.makeIndividualAssociations = makeIndividualAssociations;
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}
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public boolean isMakeIndividualAssociations() {
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return makeIndividualAssociations;
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}
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public boolean isFirstDeterminationIsStoredUnder() {
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return firstDeterminationIsStoredUnder ;
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}
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/**
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* @param firstDeterminationIsStoredUnder the firstDeterminationIsStoredUnder to set
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*/
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public void setFirstDeterminationIsStoredUnder(boolean firstDeterminationIsStoredUnder) {
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this.firstDeterminationIsStoredUnder = firstDeterminationIsStoredUnder;
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}
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public boolean isDeterminationsAreDeterminationEvent() {
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return determinationsAreDeterminationEvent ;
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}
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/**
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* @param determinationsAreDeterminationEvent the determinationsAreDeterminationEvent to set
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*/
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public void setDeterminationsAreDeterminationEvent( boolean determinationsAreDeterminationEvent) {
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this.determinationsAreDeterminationEvent = determinationsAreDeterminationEvent;
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}
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public void setPreferNameCache(boolean preferNameCache) {
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this.preferNameCache = preferNameCache;
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}
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public boolean isPreferNameCache() {
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return preferNameCache;
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}
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public void setDoExtensionTypes(boolean doExtensionTypes) {
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this.doExtensionTypes = doExtensionTypes;
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}
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public boolean isDoExtensionTypes() {
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return doExtensionTypes;
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}
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public void setCreateTaxonIfNotExists(boolean createTaxonIfNotExists) {
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this.createTaxonIfNotExists = createTaxonIfNotExists;
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}
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public boolean isCreateTaxonIfNotExists() {
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return createTaxonIfNotExists;
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}
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public void setUseMaterialsExaminedForIndividualsAssociations(
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boolean useMaterialsExaminedForIndividualsAssociations) {
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this.useMaterialsExaminedForIndividualsAssociations = useMaterialsExaminedForIndividualsAssociations;
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}
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public boolean isUseMaterialsExaminedForIndividualsAssociations() {
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return useMaterialsExaminedForIndividualsAssociations;
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}
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public void setAreaMatchMode(TermMatchMode areaMatchMode) {
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this.areaMatchMode = areaMatchMode;
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}
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public TermMatchMode getAreaMatchMode() {
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return areaMatchMode;
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}
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}
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