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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;
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import java.awt.Dimension;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import java.util.UUID;
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import javax.swing.JOptionPane;
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import javax.swing.JScrollPane;
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import javax.swing.JTextArea;
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import org.apache.commons.lang.StringUtils;
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import org.apache.log4j.Logger;
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import eu.etaxonomy.cdm.api.service.IOccurrenceService;
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import eu.etaxonomy.cdm.api.service.ITermService;
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import eu.etaxonomy.cdm.api.service.IVocabularyService;
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import eu.etaxonomy.cdm.api.service.pager.Pager;
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import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
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import eu.etaxonomy.cdm.io.common.CdmImportBase;
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import eu.etaxonomy.cdm.io.common.ImportConfiguratorBase;
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import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportConfigurator;
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import eu.etaxonomy.cdm.io.specimen.excel.in.SpecimenSynthesysExcelImportConfigurator;
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import eu.etaxonomy.cdm.io.taxonx2013.TaxonXImportConfigurator;
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import eu.etaxonomy.cdm.model.location.Country;
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import eu.etaxonomy.cdm.model.location.NamedArea;
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import eu.etaxonomy.cdm.model.term.DefinedTermBase;
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import eu.etaxonomy.cdm.model.term.OrderedTermVocabulary;
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import eu.etaxonomy.cdm.model.term.TermType;
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import eu.etaxonomy.cdm.model.term.TermVocabulary;
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import eu.etaxonomy.cdm.persistence.query.MatchMode;
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/**
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* @author p.kelbert
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* @since 20.10.2008
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*/
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public class UnitsGatheringArea {
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private static final Logger logger = Logger.getLogger(UnitsGatheringArea.class);
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private static final boolean DEBUG = false;
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private final ArrayList<DefinedTermBase> areas = new ArrayList<DefinedTermBase>();
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private boolean useTDWGarea = false;
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TermVocabulary continentVocabulary = null;
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TermVocabulary countryVocabulary = null;
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TermVocabulary specimenImportVocabulary = null;
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private DefinedTermBase<?> wbc;
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public UnitsGatheringArea(){
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//
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}
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public void setParams(String isoCountry, String country, ImportConfiguratorBase<?, ?> config, ITermService termService,
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IOccurrenceService occurrenceService, IVocabularyService vocService){
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this.setCountry(isoCountry, country, config, termService, occurrenceService, vocService);
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}
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/*
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* Constructor
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* Set a list of NamedAreas
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*/
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public void setAreas(Map<String, String> namedAreaList, ImportConfiguratorBase<?, ?> config, ITermService termService, IVocabularyService vocabularyService){
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this.setAreaNames(namedAreaList, config, termService, vocabularyService);
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}
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/*
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* Return the current list of NamedAreas
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*/
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public ArrayList<DefinedTermBase> getAreas(){
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return this.areas;
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}
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/*
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* Set the list of NamedAreas
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* @param namedAreas
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*/
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@SuppressWarnings("rawtypes")
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public void setAreaNames(Map<String, String> namedAreaList, ImportConfiguratorBase<?, ?> config, ITermService termService, IVocabularyService vocabularyService){
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List<NamedArea> termsList = termService.list(NamedArea.class,0,0,null,null);
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termsList.addAll(termService.list(Country.class, 0, 0, null, null));
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if (DEBUG) {
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logger.info(termService.list(NamedArea.class, 0, 0, null, null));
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}
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HashSet<UUID> areaSet = new HashSet<UUID>();
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HashMap<String, UUID> matchingTermsToUuid = new HashMap<String, UUID>();
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for (java.util.Map.Entry<String, String> entry : namedAreaList.entrySet()){
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String namedAreaStr = entry.getKey();
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String namedAreaClass = entry.getValue();
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UUID areaUUID = null;
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areaUUID = getNamedAreaDecision(namedAreaStr,config);
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//first, check if there is an exact match
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List<DefinedTermBase> exactMatchingTerms = termService.findByTitleWithRestrictions(DefinedTermBase.class, namedAreaStr, MatchMode.EXACT, null, null, null, null, null).getRecords();
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if(!exactMatchingTerms.isEmpty()){
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//check for continents
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List<DefinedTermBase> exactMatchingContinentTerms = new ArrayList<DefinedTermBase>();
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if(namedAreaClass!=null && namedAreaClass.equalsIgnoreCase("continent")){
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if (continentVocabulary == null){
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continentVocabulary = vocabularyService.load(NamedArea.uuidContinentVocabulary);
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}
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Set terms = continentVocabulary.getTerms();
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for (Object object : terms) {
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if(object instanceof DefinedTermBase && exactMatchingTerms.contains(object)){
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exactMatchingContinentTerms.add(HibernateProxyHelper.deproxy(object, DefinedTermBase.class));
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}
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}
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if(exactMatchingContinentTerms.size()==1){
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areaUUID = exactMatchingContinentTerms.iterator().next().getUuid();
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}
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}
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}
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if (areaUUID == null && config.isInteractWithUser()){
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Pager<DefinedTermBase> matchingTerms = termService.findByTitleWithRestrictions(DefinedTermBase.class, namedAreaStr, MatchMode.ANYWHERE, null, null, null, null, null);
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String packagePrefix = "eu.etaxonomy.cdm.model.location.";
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for (DefinedTermBase matchingTerm : matchingTerms.getRecords()) {
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String termLabel = matchingTerm.getTitleCache();
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if(matchingTerm.getClass().toString().contains(packagePrefix)){
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termLabel += " ("+matchingTerm.getClass().toString().split(packagePrefix)[1] + ")";
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}
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matchingTermsToUuid.put(termLabel, matchingTerm.getUuid());
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}
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areaUUID = askForArea(namedAreaStr, matchingTermsToUuid, "area");
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}
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if (DEBUG) {
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logger.info("selected area: "+areaUUID);
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}
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if (areaUUID == null){
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if (namedAreaStr != null){
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createNamedArea(config, termService, vocabularyService, namedAreaStr, namedAreaClass);
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}
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} else {
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areaSet.add(areaUUID);
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addNamedAreaDecision(namedAreaStr,areaUUID, config);
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}
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}
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// for (String areaStr:areaToAdd){
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// if (areaStr != null){
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// NamedArea ar = NamedArea.NewInstance(areaStr, areaStr, areaStr);
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// ar.setTitleCache(areaStr, true);
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//
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// termService.saveOrUpdate(ar);
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// this.areas.add(ar);
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// addNamedAreaDecision(areaStr,ar.getUuid(), config);
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// }
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// }
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if (!areaSet.isEmpty()){
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List<DefinedTermBase> ldtb = termService.find(areaSet);
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if (!ldtb.isEmpty()) {
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this.areas.addAll(ldtb);
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}
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}
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}
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/**
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* @param config
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* @param termService
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* @param vocabularyService
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* @param namedAreaStr
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* @param namedAreaClass
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*/
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private void createNamedArea(ImportConfiguratorBase<?, ?> config, ITermService termService,
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IVocabularyService vocabularyService, String namedAreaStr, String namedAreaClass) {
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if (!StringUtils.isBlank(namedAreaStr)){
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NamedArea ar = NamedArea.NewInstance(namedAreaStr, namedAreaStr, namedAreaStr);
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ar.setTitleCache(namedAreaStr, true);
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if (specimenImportVocabulary == null){
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specimenImportVocabulary = vocabularyService.load(CdmImportBase.uuidUserDefinedNamedAreaVocabulary);
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if (specimenImportVocabulary == null){
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specimenImportVocabulary = OrderedTermVocabulary.NewInstance(TermType.NamedArea, "User defined vocabulary for named areas", "User Defined Named Areas", null, null);
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specimenImportVocabulary.setUuid(CdmImportBase.uuidUserDefinedNamedAreaVocabulary);
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specimenImportVocabulary = vocabularyService.save(specimenImportVocabulary);
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}
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}
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DefinedTermBase term = specimenImportVocabulary.getTermByIdInvocabulary(namedAreaStr);
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if (term == null){
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specimenImportVocabulary.addTerm(ar);
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termService.saveOrUpdate(ar);
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this.areas.add(ar);
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}else{
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this.areas.add(term);
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}
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addNamedAreaDecision(namedAreaStr,ar.getUuid(), config);
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}
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}
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private UUID askForArea(String namedAreaStr, HashMap<String, UUID> matchingTerms, String areaType){
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// matchingTerms.put("Nothing matches, create a new area",null);
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//FIXME names with same label will not make it to the map
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JTextArea textArea = new JTextArea("Several CDM-areas could match the current '"+namedAreaStr+"'");
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JScrollPane scrollPane = new JScrollPane(textArea);
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textArea.setLineWrap(true);
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textArea.setWrapStyleWord(true);
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scrollPane.setPreferredSize( new Dimension( 700, 50 ) );
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String s=null;
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List<String> list = new ArrayList<String>(matchingTerms.keySet());
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list.add("Nothing matches, create a new area");
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if (list.size() <= 1){
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return null;
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}
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while (s == null) {
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s= (String)JOptionPane.showInputDialog(
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null,
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scrollPane,
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"Select the right " + areaType + " from the list",
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JOptionPane.QUESTION_MESSAGE,
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null,
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list.toArray(),
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null);
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}
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return matchingTerms.get(s);
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}
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/*
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* Set the current Country
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* Search in the DB if the isoCode is known
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* If not, search if the country name is in the DB
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* If not, create a new Label with the Level Country
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* @param iso: the country iso code
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* @param fullName: the country's full name
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* @param app: the CDM application controller
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*/
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public void setCountry(String iso, String fullName, ImportConfiguratorBase<?, ?> config, ITermService termService,
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IOccurrenceService occurrenceService, IVocabularyService vocService){
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if (!StringUtils.isEmpty(iso)){
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wbc = occurrenceService.getCountryByIso(iso);
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}
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if (wbc == null){
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if (!StringUtils.isEmpty(fullName)){
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// logger.info("matchingterms: "+matchingTerms.keySet().toString());
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UUID areaUUID = null;
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//TODO Critical, should be a country decision
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areaUUID = getNamedAreaDecision(fullName,config);
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if (areaUUID == null){
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List<UUID> countryUuids = new ArrayList<UUID>();
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HashMap<String, UUID> matchingTerms = new HashMap<String, UUID>();
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Pager<Country> countryList = termService.findByRepresentationText(fullName, Country.class, 100, 0);
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for (NamedArea na:countryList.getRecords()){
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if (na.getTitleCache().equalsIgnoreCase(fullName)) {
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countryUuids.add(na.getUuid());
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}
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if (na.getTitleCache().toLowerCase().indexOf(fullName.toLowerCase()) != -1) {
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matchingTerms.put(na.getTitleCache()+" ("+na.getTermType().getMessage() + ")",na.getUuid());
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}
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}
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if (countryUuids.isEmpty()){
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List<NamedArea> namedAreaList = termService.list(NamedArea.class,0,0,null,null);
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for (NamedArea na:namedAreaList){
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if (! na.getClass().isAssignableFrom(Country.class) && na.getTitleCache().toLowerCase().indexOf(fullName.toLowerCase()) != -1) {
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matchingTerms.put(na.getTitleCache()+" ("+na.getType().getLabel() + ")",na.getUuid());
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}
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}
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}
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if (countryUuids.size() == 1){
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areaUUID = countryUuids.get(0);
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}else{
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if ((matchingTerms.keySet().size()>0) && config.isInteractWithUser()){
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areaUUID = askForArea(fullName, matchingTerms, "country");
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logger.info("selected area: "+areaUUID);
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}else{
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logger.warn("Non interaction not yet implemented correctly");
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}
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}
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}
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if (areaUUID == null){
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createNamedArea(config, termService, vocService, fullName, "country");
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NamedArea ar = NamedArea.NewInstance(fullName, fullName, null);
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//FIXME add vocabulary
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logger.warn("Vocabulary not yet set for new country");
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ar.setTitleCache(fullName, true);
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termService.saveOrUpdate(ar);
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wbc = ar;
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} else {
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wbc = termService.find(areaUUID);
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}
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addNamedAreaDecision(fullName,wbc.getUuid(),config);
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}
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}
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}
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/**
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* @param fullName
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* @param uuid
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*/
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private void addNamedAreaDecision(String fullName, UUID uuid,ImportConfiguratorBase<?, ?> config) {
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if (config.getClass().equals(SpecimenSynthesysExcelImportConfigurator.class)) {
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((SpecimenSynthesysExcelImportConfigurator) config).putNamedAreaDecision(fullName, uuid);
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}
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if (config.getClass().equals(Abcd206ImportConfigurator.class)) {
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((Abcd206ImportConfigurator) config).putNamedAreaDecision(fullName, uuid);
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}
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if (config.getClass().equals(TaxonXImportConfigurator.class)) {
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((TaxonXImportConfigurator) config).putNamedAreaDecision(fullName, uuid);
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}
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}
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/**
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* @param fullName
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* @return
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*/
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private UUID getNamedAreaDecision(String fullName, ImportConfiguratorBase<?, ?> config) {
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UUID areaUUID = null;
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if (config.getClass().equals(SpecimenSynthesysExcelImportConfigurator.class)) {
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areaUUID = ((SpecimenSynthesysExcelImportConfigurator) config).getNamedAreaDecision(fullName);
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}
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if (config.getClass().equals(Abcd206ImportConfigurator.class)) {
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areaUUID = ((Abcd206ImportConfigurator) config).getNamedAreaDecision(fullName);
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}
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if (config.getClass().equals(TaxonXImportConfigurator.class)) {
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345
|
areaUUID = ((TaxonXImportConfigurator) config).getNamedAreaDecision(fullName);
|
|
346
|
}
|
|
347
|
return areaUUID;
|
|
348
|
}
|
|
349
|
|
|
350
|
/**
|
|
351
|
* @param useTDWGarea2
|
|
352
|
*/
|
|
353
|
public void useTDWGareas(boolean useTDWGarea) {
|
|
354
|
this.useTDWGarea=useTDWGarea;
|
|
355
|
|
|
356
|
}
|
|
357
|
|
|
358
|
/**
|
|
359
|
* @return
|
|
360
|
*/
|
|
361
|
public DefinedTermBase<?> getCountry() {
|
|
362
|
return wbc;
|
|
363
|
}
|
|
364
|
|
|
365
|
|
|
366
|
|
|
367
|
}
|