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/**
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* Copyright (C) 2013 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.taxonx2013;
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import java.util.Set;
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import org.apache.log4j.Logger;
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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.common.OriginalSourceType;
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import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
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import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.description.TextData;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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/**
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* @author pkelbert
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\* @since 20 déc. 2013
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*
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*/
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public class TaxonXAddSources {
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private Reference sourceUrlRef;
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private TaxonXImport importer;
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private TaxonXImportState configState;
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@SuppressWarnings("unused")
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private static final Logger logger = Logger.getLogger(TaxonXAddSources.class);
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/**
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* @param importer
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*/
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public void setImporter(TaxonXImport importer) {
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this.importer=importer;
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}
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/**
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* @param configState the configState to set
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*/
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public void setConfigState(TaxonXImportState configState) {
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this.configState = configState;
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}
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/**
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* @return the sourceUrlRef
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*/
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public Reference getSourceUrlRef() {
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return sourceUrlRef;
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}
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/**
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* @param sourceUrlRef the sourceUrlRef to set
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*/
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public void setSourceUrlRef(Reference sourceUrlRef) {
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this.sourceUrlRef = sourceUrlRef;
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}
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protected IdentifiableSource getIdentifiableSource(Reference reference, Set<IdentifiableSource> sources, boolean original){
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// logger.info("getIdentifiableSource");
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boolean sourceExists=false;
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IdentifiableSource source=null;
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for (IdentifiableSource src : sources){
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String micro = src.getCitationMicroReference();
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Reference r = src.getCitation();
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if (r.getTitleCache().equals(reference.getTitleCache())) {
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sourceExists=true;
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break;
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}
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}
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if(!sourceExists) {
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if(original) {
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source = IdentifiableSource.NewInstance(OriginalSourceType.PrimaryTaxonomicSource,null,null,reference,null);
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} else {
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source = IdentifiableSource.NewInstance(OriginalSourceType.Import,null,null,reference,null);
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}
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}
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return source;
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}
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protected DescriptionElementSource getDescriptionElementSource(Reference reference, Set<DescriptionElementSource> sources, boolean original){
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//logger.info("getDescriptionElementSource");
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boolean sourceExists=false;
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DescriptionElementSource source=null;
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for (DescriptionElementSource src : sources){
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String micro = src.getCitationMicroReference();
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Reference r = src.getCitation();
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if (r.getTitleCache().equals(reference.getTitleCache())) {
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sourceExists=true;
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break;
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}
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}
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if(!sourceExists) {
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if(original) {
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source = DescriptionElementSource.NewInstance(OriginalSourceType.PrimaryTaxonomicSource,null,null,reference,null);
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} else {
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source = DescriptionElementSource.NewInstance(OriginalSourceType.Import,null,null,reference,null);
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}
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}
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return source;
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}
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/**
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* @param refMods
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* @param synonym
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*/
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protected void addSource(Reference refMods, Synonym synonym) {
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//logger.info("addSource");
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sourceUrlRef=CdmBase.deproxy(sourceUrlRef, Reference.class);
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Reference sec = CdmBase.deproxy(configState.getConfig().getSecundum(), Reference.class);
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IdentifiableSource id = getIdentifiableSource(sourceUrlRef,synonym.getSources(), false);
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IdentifiableSource id2 = getIdentifiableSource(refMods,synonym.getSources(), true);
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IdentifiableSource id3 = getIdentifiableSource(sec,synonym.getSources(), false);
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if( id!=null) {
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synonym.addSource(id);
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}
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if( id2!=null) {
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synonym.addSource(id2);
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}
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if(!configState.getConfig().doKeepOriginalSecundum() && id3!=null) {
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synonym.addSource(id3);
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}
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}
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/**
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* @param refMods
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* @param indAssociation
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*/
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protected IndividualsAssociation addSource(Reference refMods, IndividualsAssociation indAssociation) {
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//logger.info("addSource");
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sourceUrlRef=CdmBase.deproxy(sourceUrlRef, Reference.class);
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Reference sec = CdmBase.deproxy(configState.getConfig().getSecundum(), Reference.class);
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DescriptionElementSource id = getDescriptionElementSource(sourceUrlRef, indAssociation.getSources(), false);
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DescriptionElementSource id2 = getDescriptionElementSource(refMods, indAssociation.getSources(), true);
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DescriptionElementSource id3 = getDescriptionElementSource(sec, indAssociation.getSources(), false);
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if(id!=null) {
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indAssociation.addSource(id);
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}
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if( id2!=null) {
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indAssociation.addSource(id2);
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}
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if(!configState.getConfig().doKeepOriginalSecundum() && id3!=null) {
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indAssociation.addSource(id3);
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}
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return indAssociation;
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}
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/**
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* @param refMods
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* @param acceptedTaxon
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*/
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protected void addSource(Reference refMods, Taxon acceptedTaxon) {
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//logger.info("addSource");
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sourceUrlRef=CdmBase.deproxy(sourceUrlRef, Reference.class);
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Reference sec = CdmBase.deproxy(configState.getConfig().getSecundum(), Reference.class);
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IdentifiableSource id = getIdentifiableSource(sourceUrlRef, acceptedTaxon.getSources(), false);
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IdentifiableSource id2 = getIdentifiableSource(refMods, acceptedTaxon.getSources(), true);
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IdentifiableSource id3 = getIdentifiableSource(sec, acceptedTaxon.getSources(), false);
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if( id!=null) {
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acceptedTaxon.addSource(id);
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}
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if( id2!=null) {
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acceptedTaxon.addSource(id2);
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}
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if(!configState.getConfig().doKeepOriginalSecundum() && id3!=null) {
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acceptedTaxon.addSource(id3);
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}
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}
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/**
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* @param refMods
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* @param nameToBeFilled
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*/
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protected void addSource(Reference refMods, TaxonName nameToBeFilled) {
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//logger.info("addSource");
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sourceUrlRef=CdmBase.deproxy(sourceUrlRef, Reference.class);
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Reference sec = CdmBase.deproxy(configState.getConfig().getSecundum(), Reference.class);
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IdentifiableSource id = getIdentifiableSource(sourceUrlRef, nameToBeFilled.getSources(), false);
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IdentifiableSource id2 = getIdentifiableSource(refMods, nameToBeFilled.getSources(), true);
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IdentifiableSource id3 = getIdentifiableSource(sec, nameToBeFilled.getSources(), false);
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if( id!=null) {
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nameToBeFilled.addSource(id);
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}
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if( id2!=null) {
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nameToBeFilled.addSource(id2);
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}
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if(!configState.getConfig().doKeepOriginalSecundum() && id3!=null) {
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nameToBeFilled.addSource(id3);
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}
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}
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/**
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* @param refMods
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* @param textData
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*/
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protected void addSource(Reference refMods, TextData textData) {
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//logger.info("addSource");
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sourceUrlRef=CdmBase.deproxy(sourceUrlRef, Reference.class);
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Reference sec = CdmBase.deproxy(configState.getConfig().getSecundum(), Reference.class);
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DescriptionElementSource id = getDescriptionElementSource(sourceUrlRef, textData.getSources(), false);
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DescriptionElementSource id2 = getDescriptionElementSource(refMods, textData.getSources(), true);
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DescriptionElementSource id3 = getDescriptionElementSource(sec, textData.getSources(), false);
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if( id!=null) {
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textData.addSource(id);
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}
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if( id2!=null) {
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textData.addSource(id2);
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}
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if(!configState.getConfig().doKeepOriginalSecundum() && id3!=null) {
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textData.addSource(id3);
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}
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}
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/**
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* @param refMods
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* @param taxonDescription
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* @param currentRef
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*/
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protected void addAndSaveSource(Reference refMods, TaxonDescription taxonDescription, Reference currentRef) {
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//logger.info("addAndSaveSource");
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sourceUrlRef=CdmBase.deproxy(sourceUrlRef, Reference.class);
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Reference sec = CdmBase.deproxy(configState.getConfig().getSecundum(), Reference.class);
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IdentifiableSource id = getIdentifiableSource(sourceUrlRef, taxonDescription.getSources(), false);
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IdentifiableSource id2 = getIdentifiableSource(refMods, taxonDescription.getSources(), true);
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IdentifiableSource id3 = getIdentifiableSource(sec, taxonDescription.getSources(), false);
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if( id!=null) {
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taxonDescription.addSource(id);
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}
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if( id2!=null) {
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taxonDescription.addSource(id2);
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}
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if(!configState.getConfig().doKeepOriginalSecundum() && id3!=null) {
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taxonDescription.addSource(id3);
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}
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importer.getDescriptionService().saveOrUpdate(taxonDescription);
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}
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/**
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* @param refMods
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* @param derivedUnitBase
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*/
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protected void addAndSaveSource(Reference refMods, DerivedUnit derivedUnitBase) {
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//logger.info("addAndSaveSource");
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sourceUrlRef=CdmBase.deproxy(sourceUrlRef, Reference.class);
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Reference sec = CdmBase.deproxy(configState.getConfig().getSecundum(), Reference.class);
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IdentifiableSource id = getIdentifiableSource(sourceUrlRef, derivedUnitBase.getSources(), false);
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IdentifiableSource id2 = getIdentifiableSource(refMods, derivedUnitBase.getSources(), true);
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IdentifiableSource id3 = getIdentifiableSource(sec, derivedUnitBase.getSources(), false);
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if( id!=null) {
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derivedUnitBase.addSource(id);
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}
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if( id2!=null) {
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derivedUnitBase.addSource(id2);
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}
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if(!configState.getConfig().doKeepOriginalSecundum() && id3!=null) {
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derivedUnitBase.addSource(id3);
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}
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importer.getOccurrenceService().saveOrUpdate(derivedUnitBase);
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derivedUnitBase= CdmBase.deproxy(derivedUnitBase, DerivedUnit.class);
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}
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/**
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* @param refMods
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* @param taxonDescription
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*/
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public void addSource(Reference refMods, TaxonDescription taxonDescription) {
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//logger.info("addSource");
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sourceUrlRef=CdmBase.deproxy(sourceUrlRef, Reference.class);
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Reference sec = CdmBase.deproxy(configState.getConfig().getSecundum(), Reference.class);
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IdentifiableSource id = getIdentifiableSource(sourceUrlRef, taxonDescription.getSources(), false);
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IdentifiableSource id2 = getIdentifiableSource(refMods, taxonDescription.getSources(), true);
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IdentifiableSource id3 = getIdentifiableSource(sec, taxonDescription.getSources(), false);
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if( id!=null) {
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taxonDescription.addSource(id);
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}
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if( id2!=null) {
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taxonDescription.addSource(id2);
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}
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if(!configState.getConfig().doKeepOriginalSecundum() && id3!=null) {
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taxonDescription.addSource(id3);
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}
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importer.getDescriptionService().saveOrUpdate(taxonDescription);
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}
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312
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/**
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* @param reference
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314
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* @param textData
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315
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* @param name
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316
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* @param ref
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*/
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public void addSource(Reference reference, TextData textData, TaxonName name, Reference refMods) {
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//logger.info("addSource");
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sourceUrlRef=CdmBase.deproxy(sourceUrlRef, Reference.class);
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Reference sec = CdmBase.deproxy(configState.getConfig().getSecundum(), Reference.class);
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DescriptionElementSource id1 = getDescriptionElementSource(refMods, textData.getSources(),name, true);
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DescriptionElementSource id2 = getDescriptionElementSource(reference, textData.getSources(),name, false);
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if( id1!=null) {
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textData.addSource(id1);
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}
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327
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328
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if( id2!=null) {
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textData.addSource(id2);
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}
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331
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332
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}
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333
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334
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335
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@SuppressWarnings({ "unused", "rawtypes" })
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336
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private DescriptionElementSource getDescriptionElementSource(Reference reference, Set<DescriptionElementSource> sources,
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337
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TaxonName originalname, boolean original){
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338
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//logger.info("getDescriptionElementSource");
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339
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boolean sourceExists=false;
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340
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DescriptionElementSource source=null;
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341
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for (DescriptionElementSource src : sources){
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342
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String micro = src.getCitationMicroReference();
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Reference r = src.getCitation();
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TaxonName oname = src.getNameUsedInSource();
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345
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try {
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346
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if (r.getTitleCache().equals(reference.getTitleCache())) {
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347
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if (oname.getTitleCache().equalsIgnoreCase(originalname.getTitleCache())) {
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sourceExists=true;
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349
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break;
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350
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}
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351
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}
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352
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} catch (Exception e) {
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353
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// TODO Auto-generated catch block
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354
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e.printStackTrace();
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355
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}
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356
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}
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357
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if(!sourceExists) {
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358
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if(original) {
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359
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source = DescriptionElementSource.NewInstance(OriginalSourceType.PrimaryTaxonomicSource, null,null, reference, null, originalname, null);
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360
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} else {
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361
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source = DescriptionElementSource.NewInstance(OriginalSourceType.Import, null,null, reference, null, originalname, null);
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362
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}
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363
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}
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364
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return source;
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365
|
}
|
|
366
|
|
|
367
|
|
|
368
|
|
|
369
|
}
|