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/**
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* Copyright (C) 2017 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.greece;
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import java.text.ParseException;
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import java.util.UUID;
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import org.apache.log4j.Logger;
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import org.springframework.stereotype.Component;
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import org.springframework.transaction.TransactionStatus;
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import eu.etaxonomy.cdm.api.service.ITermService;
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import eu.etaxonomy.cdm.common.URI;
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import eu.etaxonomy.cdm.ext.geo.GeoServiceArea;
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import eu.etaxonomy.cdm.ext.geo.GeoServiceAreaAnnotatedMapping;
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import eu.etaxonomy.cdm.io.common.CdmImportBase;
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import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImportState;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
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import eu.etaxonomy.cdm.model.description.State;
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import eu.etaxonomy.cdm.model.location.NamedArea;
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import eu.etaxonomy.cdm.model.location.NamedAreaType;
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import eu.etaxonomy.cdm.model.term.OrderedTermBase;
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import eu.etaxonomy.cdm.model.term.OrderedTermVocabulary;
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import eu.etaxonomy.cdm.model.term.TermNode;
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import eu.etaxonomy.cdm.model.term.TermTree;
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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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/**
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* @author a.mueller
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* @since 13.05.2017
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*
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*/
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@Component
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public class FloraHellenicaTermImport <CONFIG extends FloraHellenicaImportConfigurator>
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extends CdmImportBase<CONFIG, SimpleExcelTaxonImportState<FloraHellenicaImportConfigurator>>{
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private static final long serialVersionUID = 1347759514044184010L;
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@SuppressWarnings("unused")
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private static final Logger logger = Logger.getLogger(FloraHellenicaTaxonImport.class);
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private NamedArea greece;
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/**
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* {@inheritDoc}
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*/
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@Override
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protected void doInvoke(SimpleExcelTaxonImportState<FloraHellenicaImportConfigurator> state) {
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TransactionStatus tx = this.startTransaction();
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initAreaVocabulary(state);
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initLifeformVocabulary(state);
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initHabitatVocabulary(state);
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initChorologicalVocabulary(state);
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initStatusVocabulary(state);
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makeFeatureTree(state);
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makeMapColors(state);
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this.commitTransaction(tx);
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}
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@SuppressWarnings("unchecked")
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private void initAreaVocabulary(SimpleExcelTaxonImportState<FloraHellenicaImportConfigurator> state) {
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OrderedTermVocabulary<NamedArea> areasVoc = (OrderedTermVocabulary<NamedArea>)this.getVocabularyService().find(FloraHellenicaTransformer.uuidFloraHellenicaAreasVoc);
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if (areasVoc == null){
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createAreasVoc(state);
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}
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}
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/**
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* @param state
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* @return
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*/
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@SuppressWarnings("unchecked")
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private void createAreasVoc(SimpleExcelTaxonImportState<FloraHellenicaImportConfigurator> state) {
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//voc
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URI termSourceUri = null;
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String label = "Checklist of Greece Areas";
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String description = "Areas as used in the Checklist of Greece";
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OrderedTermVocabulary<NamedArea> areasVoc = OrderedTermVocabulary.NewInstance(TermType.NamedArea,
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description, label, null, termSourceUri);
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areasVoc.setUuid(FloraHellenicaTransformer.uuidFloraHellenicaAreasVoc);
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// Representation rep = Representation.NewInstance("Estados Méxicanos", "Estados Méxicanos", null, Language.SPANISH_CASTILIAN());
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// areasVoc.addRepresentation(rep);
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//greece country
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String countryLabel = "Greece";
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greece = NamedArea.NewInstance(countryLabel, countryLabel, "GR");
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greece.setUuid(FloraHellenicaTransformer.uuidAreaGreece);
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greece.setIdInVocabulary("GR");
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greece.setSymbol("GR");
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areasVoc.addTerm(greece);
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//FIXME
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// addMapping(greece, xx "mex_adm0", "iso", "MEX");
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addArea(state, areasVoc, "IoI", "Ionian Islands", 4, FloraHellenicaTransformer.uuidAreaIoI);
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addArea(state, areasVoc, "NPi", "North Pindos", 13, FloraHellenicaTransformer.uuidAreaNPi);
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addArea(state, areasVoc, "SPi", "South Pindos", 11, FloraHellenicaTransformer.uuidAreaSPi);
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addArea(state, areasVoc, "Pe", "Peloponnisos", 1, FloraHellenicaTransformer.uuidAreaPe);
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addArea(state, areasVoc, "StE", "Sterea Ellas", 12, FloraHellenicaTransformer.uuidAreaStE);
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addArea(state, areasVoc, "EC", "East Central Greece", 5, FloraHellenicaTransformer.uuidAreaEC);
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addArea(state, areasVoc, "NC", "North Central Greece", 2, FloraHellenicaTransformer.uuidAreaNC);
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addArea(state, areasVoc, "NE", "North-East Greece", 10, FloraHellenicaTransformer.uuidAreaNE);
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addArea(state, areasVoc, "NAe", "North Aegean islands", 7, FloraHellenicaTransformer.uuidAreaNAe);
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addArea(state, areasVoc, "WAe", "West Aegean islands", 9, FloraHellenicaTransformer.uuidAreaWAe);
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addArea(state, areasVoc, "Kik", "Kiklades", 8, FloraHellenicaTransformer.uuidAreaKik);
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addArea(state, areasVoc, "KK", "Kriti and Karpathos", 6, FloraHellenicaTransformer.uuidAreaKK);
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addArea(state, areasVoc, "EAe", "East Aegean islands", 3, FloraHellenicaTransformer.uuidAreaEAe);
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this.getVocabularyService().save(areasVoc);
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return;
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}
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private void addArea(SimpleExcelTaxonImportState<FloraHellenicaImportConfigurator> state,
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OrderedTermVocabulary<NamedArea> areasVoc,
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String abbrevLabel, String areaLabel,
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Integer id, UUID uuid) {
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addArea(state, areasVoc, abbrevLabel, areaLabel, uuid, String.valueOf(id)); //short cut if label and mapping label are equal
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}
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private void addArea(SimpleExcelTaxonImportState<FloraHellenicaImportConfigurator> state,
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OrderedTermVocabulary<NamedArea> areasVoc,
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String abbrevLabel, String areaLabel,
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UUID uuid, String mappingLabel) {
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addArea(state, areasVoc, abbrevLabel, areaLabel, uuid, mappingLabel, null); //short cut if label and mapping label are equal
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}
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/**
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* @param state
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* @param string
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* @param uuidaguascalientes
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*/
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private void addArea(SimpleExcelTaxonImportState<FloraHellenicaImportConfigurator> state,
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OrderedTermVocabulary<NamedArea> areasVoc,
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String abbrevLabel, String areaLabel,
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UUID uuid, String mappingLabel, Integer id1) {
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NamedArea newArea = NamedArea.NewInstance(
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areaLabel, areaLabel, abbrevLabel);
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newArea.setIdInVocabulary(abbrevLabel);
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newArea.setUuid(uuid);
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newArea.setPartOf(greece);
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newArea.setLevel(null);
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newArea.setType(NamedAreaType.NATURAL_AREA());
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areasVoc.addTerm(newArea);
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if (mappingLabel != null){
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addMapping(newArea, "phytogeographical_regions_of_greece", "id", mappingLabel);
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}
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}
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private void addMapping(NamedArea area, String mapping_layer, String mapping_field, String abbrev) {
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GeoServiceAreaAnnotatedMapping mapping = (GeoServiceAreaAnnotatedMapping)this.getBean("geoServiceAreaAnnotatedMapping");
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GeoServiceArea geoServiceArea = new GeoServiceArea();
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geoServiceArea.add(mapping_layer, mapping_field, abbrev);
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mapping.set(area, geoServiceArea);
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}
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/**
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* @param state
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*/
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private void initChorologicalVocabulary(SimpleExcelTaxonImportState<FloraHellenicaImportConfigurator> state) {
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UUID uuid = FloraHellenicaTransformer.uuidFloraHellenicaChorologicalVoc;
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OrderedTermVocabulary<State> chorologicalVoc = (OrderedTermVocabulary<State>)this.getVocabularyService().find(uuid);
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if (chorologicalVoc == null){
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createChorologicalVoc(state, uuid);
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}
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}
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/**
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* @param state
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* @param uuid
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*/
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private void createChorologicalVoc(SimpleExcelTaxonImportState<FloraHellenicaImportConfigurator> state, UUID vocUuid) {
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//voc
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URI termSourceUri = null;
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String label = "Checklist of Greece Chorological Categories";
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String description = "Chorological Categories as used in the Checklist of Greece";
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OrderedTermVocabulary<State> chorologicalVoc = OrderedTermVocabulary.NewInstance(TermType.State,
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description, label, null, termSourceUri);
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chorologicalVoc.setUuid(vocUuid);
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addChorological(state, chorologicalVoc, "*", "Greek endemic", "Greek endemics (incl. single-island and single-mountain endemics)", FloraHellenicaTransformer.uuidChorologicalStar);
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addChorological(state, chorologicalVoc, "Bk", "Balkan", "Taxa restricted to Balkan countries, occasionally extending to adjacent parts of SE Europe", FloraHellenicaTransformer.uuidChorologicalBk);
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addChorological(state, chorologicalVoc, "BI", "Balkan-Italy", "Taxa restricted to Balkan countries and Italy (amphi-Adreatic)", FloraHellenicaTransformer.uuidChorologicalBI);
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addChorological(state, chorologicalVoc, "BA", "Balkan-Anatolia", "Taxa restricted to Balkan countries and to Asia minor (Anatolia), occasionally extending to S Ukraine (Crimea), adjacent Caucasian countries (Georgia, Armenia) or N Iraq", FloraHellenicaTransformer.uuidChorologicalBA);
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addChorological(state, chorologicalVoc, "BC", "Balkan-Central Europe", "Taxa distributed in the Balkans, Carpathians, Alps and adjacent areas (mainly in the mountains)", FloraHellenicaTransformer.uuidChorologicalBC);
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addChorological(state, chorologicalVoc, "EM", "East Mediterranean", "Taxa restricted to the E Mediterranean, occasionally extending to S Italy or adjacent Caucasian countries", FloraHellenicaTransformer.uuidChorologicalEM);
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addChorological(state, chorologicalVoc, "Me", "Mediterranean", "Taxa with a circum-Mediterranean distribution including Portugal, occasionally extending to the Caucasus area and N Iran", FloraHellenicaTransformer.uuidChorologicalMe);
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addChorological(state, chorologicalVoc, "MA", "Mediterranean-Atlantic", "Taxa restricted to maritime W Europe and the Mediterranean", FloraHellenicaTransformer.uuidChorologicalMA);
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addChorological(state, chorologicalVoc, "ME", "Mediterranean-European", "Taxa restricted to the Mediterranean and temperate Europe, occasionally extending to NW Africa and the Caucasus area", FloraHellenicaTransformer.uuidChorologicalME);
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addChorological(state, chorologicalVoc, "MS", "Mediterranean-SW Asian", "Taxa distributed in one or more Mediterranean countries and extending to SW and C Asia", FloraHellenicaTransformer.uuidChorologicalMS);
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addChorological(state, chorologicalVoc, "EA", "European-SW Asian", "Eruopean taxa (occasionally reachin N Africa) with a distribution extending to SW Asia, occasionally reaching C Asia", FloraHellenicaTransformer.uuidChorologicalEA);
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addChorological(state, chorologicalVoc, "ES", "Euro-Siberian", "Taxa with main distribution in temperate Eurasia (occasionally reaching the Caucasus area)", FloraHellenicaTransformer.uuidChorologicalES);
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addChorological(state, chorologicalVoc, "Eu", "European", "Taxa with a distribution all over Europe. In S European countries this category in fact represents the C European element", FloraHellenicaTransformer.uuidChorologicalEu);
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addChorological(state, chorologicalVoc, "Pt", "Paleotemperate", "Taxa of extratropical Eurasia including the Himalaya and E Asia, not (or at most marginally) extending to North America", FloraHellenicaTransformer.uuidChorologicalPt);
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addChorological(state, chorologicalVoc, "Ct", "Circumtemperate", "Taxa of both extratropical Eurasia and North America", FloraHellenicaTransformer.uuidChorologicalCt);
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addChorological(state, chorologicalVoc, "IT", "Irano-Turanian", "Taxa with main distribution in arid SW and C Asia, extrazonally extending to the Mediterranean", FloraHellenicaTransformer.uuidChorologicalIT);
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addChorological(state, chorologicalVoc, "SS", "Saharo-Sindian", "Taxa with main distribution in arid N Africa and SQ Asia, extrazonally extending to the Mediterranean", FloraHellenicaTransformer.uuidChorologicalSS);
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addChorological(state, chorologicalVoc, "ST", "Subtropical-tropical", "Taxa widespread in the warmer regions of both hemispheres", FloraHellenicaTransformer.uuidChorologicalST);
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addChorological(state, chorologicalVoc, "Bo", "(Circum-)Boreal", "Taxa with main distribution in N and high-montane Eurasia (occasionally extending to North America)", FloraHellenicaTransformer.uuidChorologicalBo);
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addChorological(state, chorologicalVoc, "AA", "Arctic-Alpine", "Taxa with main distribution beyound the N and aove the high-montane timerlines o fEurasia (occasionally extending to North America)", FloraHellenicaTransformer.uuidChorologicalAA);
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addChorological(state, chorologicalVoc, "Co", "Cosmopolitan", "Taxa distributed in all continents, i.e. beyond the N hemisphere. This category may be given in brackets after the known or supposed native distribution in cases of taxa that have been spread worldwide by humans", FloraHellenicaTransformer.uuidChorologicalCo);
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addChorological(state, chorologicalVoc, "[SS]", "[Saharo-Sindian]", "Taxa with main distribution in arid N Africa and SQ Asia, extrazonally extending to the Mediterranean, not native in Greece", FloraHellenicaTransformer.uuidChorological_SS_);
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addChorological(state, chorologicalVoc, "[?MS]", "[Mediterranean-SW Asian]", "Taxa distributed in one or more Mediterranean countries and extending to SW and C Asia, not native in Greece", FloraHellenicaTransformer.uuidChorological_dMS_);
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addChorological(state, chorologicalVoc, "?EM", "? East Mediterranean", "Taxa restricted to the E Mediterranean, occasionally extending to S Italy or adjacent Caucasian countries", FloraHellenicaTransformer.uuidChorological_dEM);
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addChorological(state, chorologicalVoc, "[trop.]", "[tropical]", "", FloraHellenicaTransformer.uuidChorologicaltrop);
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addChorological(state, chorologicalVoc, "[subtrop.]", "[subtropical]", "", FloraHellenicaTransformer.uuidChorologicalsubtrop);
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addChorological(state, chorologicalVoc, "[paleotrop.]", "[paleotropical]", "", FloraHellenicaTransformer.uuidChorologicalpaleotrop);
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addChorological(state, chorologicalVoc, "[neotrop.]", "[neotropical]", "", FloraHellenicaTransformer.uuidChorologicalneotrop);
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addChorological(state, chorologicalVoc, "[pantrop.]", "[pantropical]", "", FloraHellenicaTransformer.uuidChorologicalpantrop);
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addChorological(state, chorologicalVoc, "[N-Am.]", "[North American]", "", FloraHellenicaTransformer.uuidChorologicalN_Am);
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addChorological(state, chorologicalVoc, "[S-Am.]", "[South American]", "", FloraHellenicaTransformer.uuidChorologicalS_Am);
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addChorological(state, chorologicalVoc, "[E-As.]", "[East Asian]", "", FloraHellenicaTransformer.uuidChorologicalE_As);
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addChorological(state, chorologicalVoc, "[SE-As.", "[South East Asian]", "", FloraHellenicaTransformer.uuidChorologicalSE_As);
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addChorological(state, chorologicalVoc, "[S-Afr.]", "[South African]", "", FloraHellenicaTransformer.uuidChorologicalS_Afr);
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addChorological(state, chorologicalVoc, "[Arab.]", "[Arabian]", "", FloraHellenicaTransformer.uuidChorologicalArab);
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addChorological(state, chorologicalVoc, "[Arab. NE-Afr.]", "[Arabian and North East African]", "", FloraHellenicaTransformer.uuidChorologicalArab_NE_Afr);
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addChorological(state, chorologicalVoc, "[Caucas.]", "[Caucasian]", "", FloraHellenicaTransformer.uuidChorologicalCaucas);
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addChorological(state, chorologicalVoc, "[Pontic]", "[Pontic]", "", FloraHellenicaTransformer.uuidChorologicalPontic);
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addChorological(state, chorologicalVoc, "[Europ.]", "[European]", "", FloraHellenicaTransformer.uuidChorologicalEurop);
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addChorological(state, chorologicalVoc, "[Austr.]", "[Australian]", "", FloraHellenicaTransformer.uuidChorologicalAustral);
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addChorological(state, chorologicalVoc, "[W-Med.]", "[West Mediterranean]", "", FloraHellenicaTransformer.uuidChorologicalW_Med);
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addChorological(state, chorologicalVoc, "[C-Med.]", "[Central Mediterranean]", "", FloraHellenicaTransformer.uuidChorologicalC_Med);
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addChorological(state, chorologicalVoc, "[W-Eur.]", "[West European]", "", FloraHellenicaTransformer.uuidChorologicalW_Eur);
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addChorological(state, chorologicalVoc, "[S-Eur.]", "[South European]", "", FloraHellenicaTransformer.uuidChorologicalS_Eur);
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addChorological(state, chorologicalVoc, "[C-Am.]", "[Central American]", "", FloraHellenicaTransformer.uuidChorologicalC_Am);
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addChorological(state, chorologicalVoc, "[C-As.]", "[Central Asian]", "", FloraHellenicaTransformer.uuidChorologicalC_As);
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addChorological(state, chorologicalVoc, "[SW-As.]", "[South West Asian]", "", FloraHellenicaTransformer.uuidChorologicalSW_As);
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addChorological(state, chorologicalVoc, "[unknown]", "[unknown]", "", FloraHellenicaTransformer.uuidChorologicalUnknown);
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addChorological(state, chorologicalVoc, "[N-Afr.]", "[North African]", "", FloraHellenicaTransformer.uuidChorologicalN_Afr);
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addChorological(state, chorologicalVoc, "[Am.]", "[American]", "", FloraHellenicaTransformer.uuidChorologicalAm);
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addChorological(state, chorologicalVoc, "[paleosubtrop.]", "[paleosubtropical]", "", FloraHellenicaTransformer.uuidChorologicalPaleosubtrop);
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addChorological(state, chorologicalVoc, "[SW-Eur.]", "[South West European]", "", FloraHellenicaTransformer.uuidChorologicalSW_Eur);
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addChorological(state, chorologicalVoc, "[S-As.]", "[South Asian]", "", FloraHellenicaTransformer.uuidChorologicalS_As);
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addChorological(state, chorologicalVoc, "[NE-Afr.]", "[North East African]", "", FloraHellenicaTransformer.uuidChorologicalNE_Afr);
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addChorological(state, chorologicalVoc, "[NW-Afr.]", "[North West African]", "", FloraHellenicaTransformer.uuidChorologicalNW_Afr);
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addChorological(state, chorologicalVoc, "[trop. Afr.]", "[tropical African]", "", FloraHellenicaTransformer.uuidChorologicalTrop_Afr);
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addChorological(state, chorologicalVoc, "[Afr.]", "[Arican]", "", FloraHellenicaTransformer.uuidChorologicalAfr);
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addChorological(state, chorologicalVoc, "[As.]", "[Asian]", "", FloraHellenicaTransformer.uuidChorologicalAs);
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addChorological(state, chorologicalVoc, "[W-As.]", "[West Asian]", "", FloraHellenicaTransformer.uuidChorologicalW_As);
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addChorological(state, chorologicalVoc, "[C-Eur.]", "[Central European]", "", FloraHellenicaTransformer.uuidChorologicalC_Eur);
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addChorological(state, chorologicalVoc, "[E-Afr.]", "[East African]", "", FloraHellenicaTransformer.uuidChorologicalE_Afr);
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addChorological(state, chorologicalVoc, "[W-Austr.]", "[West Australian]", "", FloraHellenicaTransformer.uuidChorologicalW_Austr);
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addChorological(state, chorologicalVoc, "[trop. As.]", "[tropical Asian]", "", FloraHellenicaTransformer.uuidChorologicaltrop_As);
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addChorological(state, chorologicalVoc, "[Co]", "[Cosmopolitan]", "Taxa distributed in all continents, i.e. beyond the N hemisphere. This category may be given in brackets after the known or supposed native distribution in cases of taxa that have been spread worldwide by humans", FloraHellenicaTransformer.uuidChorological__Co_);
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this.getVocabularyService().save(chorologicalVoc);
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return;
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}
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/**
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* @param state
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* @param chorologicalVoc
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* @param string
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* @param string2
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* @param string3
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* @param uuidchorologicalstar
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*/
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private void addChorological(SimpleExcelTaxonImportState<FloraHellenicaImportConfigurator> state,
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OrderedTermVocabulary<State> chorologicalVoc, String abbrevLabel, String label,
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String desc, UUID uuidChorological) {
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desc = isBlank(desc)? label : desc;
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State chorologyTerm = addState(state, abbrevLabel, label, desc, uuidChorological, chorologicalVoc);
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}
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// ***************************** LIFEFORM ********************************/
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@SuppressWarnings("unchecked")
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private void initLifeformVocabulary(SimpleExcelTaxonImportState<FloraHellenicaImportConfigurator> state) {
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UUID uuid = FloraHellenicaTransformer.uuidFloraHellenicaLifeformVoc;
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OrderedTermVocabulary<State> lifeformVoc = (OrderedTermVocabulary<State>)this.getVocabularyService().find(uuid);
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if (lifeformVoc == null){
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createLifeformVoc(state, uuid);
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}
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}
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/**
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* @param state
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* @param vocUuid
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300
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*/
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private void createLifeformVoc(SimpleExcelTaxonImportState<FloraHellenicaImportConfigurator> state,
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302
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UUID vocUuid) {
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//voc
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URI termSourceUri = null;
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305
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String label = "Checklist of Greece Lifeforms";
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String description = "Lifeforms as used in the Checklist of Greece";
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OrderedTermVocabulary<State> lifeformVoc = OrderedTermVocabulary.NewInstance(TermType.State,
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description, label, null, termSourceUri);
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lifeformVoc.setUuid(vocUuid);
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addLifeform(state, lifeformVoc, "A", "Aquatic", FloraHellenicaTransformer.uuidLifeformA);
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addLifeform(state, lifeformVoc, "C", "Chamaephyte", FloraHellenicaTransformer.uuidLifeformC);
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addLifeform(state, lifeformVoc, "G", "Geophyte (Cryptophyte)", FloraHellenicaTransformer.uuidLifeformG);
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addLifeform(state, lifeformVoc, "H", "Hemicryptophyte", FloraHellenicaTransformer.uuidLifeformH);
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addLifeform(state, lifeformVoc, "P", "Phanerophyte", FloraHellenicaTransformer.uuidLifeformP);
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addLifeform(state, lifeformVoc, "T", "Therophyte", FloraHellenicaTransformer.uuidLifeformT);
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this.getVocabularyService().save(lifeformVoc);
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return;
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}
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/**
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* @param state
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* @param lifeformVoc
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* @param string
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* @param uuidlifeformt
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*/
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private void addLifeform(SimpleExcelTaxonImportState<FloraHellenicaImportConfigurator> state,
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OrderedTermVocabulary<State> lifeformVoc, String abbrevLabel, String label, UUID uuidlifeform) {
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addState(state, abbrevLabel, label, label, uuidlifeform, lifeformVoc);
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}
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332
|
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333
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// ***************************** HABITAT ********************************/
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private void initHabitatVocabulary(SimpleExcelTaxonImportState<FloraHellenicaImportConfigurator> state) {
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336
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UUID uuid = FloraHellenicaTransformer.uuidFloraHellenicaHabitatVoc;
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337
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OrderedTermVocabulary<State> habitatVoc = (OrderedTermVocabulary<State>)this.getVocabularyService().find(uuid);
|
338
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if (habitatVoc == null){
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339
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createHabitatVoc(state, uuid);
|
340
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}
|
341
|
}
|
342
|
|
343
|
/**
|
344
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* @param state
|
345
|
*/
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346
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private void createHabitatVoc(SimpleExcelTaxonImportState<FloraHellenicaImportConfigurator> state, UUID vocUuid) {
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347
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//voc
|
348
|
URI termSourceUri = null;
|
349
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String label = "Checklist of Greece Habitats";
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350
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String description = "Habitats as used in the Checklist of Greece";
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351
|
OrderedTermVocabulary<State> habitatVoc = OrderedTermVocabulary.NewInstance(TermType.State,
|
352
|
description, label, null, termSourceUri);
|
353
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habitatVoc.setUuid(vocUuid);
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354
|
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355
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addHabitat(state, habitatVoc, "A", "Freshwater habitats", "Freshwater habitats (Aquatic habitats, springs and fens, reedbeds and damp tall herb vegetation, seasonally flooded depressions, damp and seepage meadows, streambanks, river and lake shores)", FloraHellenicaTransformer.uuidHabitatA);
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356
|
addHabitat(state, habitatVoc, "C", "Cliffs, rocks, walls, ravines, boulders", "Cliffs, rocks, walls, ravines, boulders", FloraHellenicaTransformer.uuidHabitatC);
|
357
|
addHabitat(state, habitatVoc, "G", "Temperate and submediterranean Grasslands", "Temperate and submediterranean Grasslands (lowland to montane dry and mesic meadows and pastures, rock outcrops and stony ground, grassy non-ruderal verges and forest edges)", FloraHellenicaTransformer.uuidHabitatG);
|
358
|
addHabitat(state, habitatVoc, "H", "High mountain vegetation", "High mountain vegetation (subalpine and alpine grasslands, screes and rocks, scrub above the treeline)", FloraHellenicaTransformer.uuidHabitatH);
|
359
|
addHabitat(state, habitatVoc, "M", "Coastal habitats", "Coastal habitats (Marine waters and mudflats, salt marshes, sand dunes, littoral rocks, halo-nitrophilous scrub)", FloraHellenicaTransformer.uuidHabitatM);
|
360
|
addHabitat(state, habitatVoc, "P", "Xeric Mediterranean Phrygana and grasslands", "Xeric Mediterranean Phrygana and grasslands (Mediterranean dwarf shrub formations, annual-rich pastures and lowland screes)", FloraHellenicaTransformer.uuidHabitatP);
|
361
|
addHabitat(state, habitatVoc, "R", "Agricultural and Ruderal habitats", "Agricultural and Ruderal habitats (fields, gardens and plantations, roadsides and trampled sites, frequently disturbed and pioneer habitats)", FloraHellenicaTransformer.uuidHabitatR);
|
362
|
addHabitat(state, habitatVoc, "W", "Woodlands and scrub", "Woodlands and scrub (broadleaved and coniferous forest, riparian and mountain forest and scrub, hedges, shady woodland margins)", FloraHellenicaTransformer.uuidHabitatW);
|
363
|
|
364
|
this.getVocabularyService().save(habitatVoc);
|
365
|
return;
|
366
|
}
|
367
|
|
368
|
/**
|
369
|
* @param state
|
370
|
* @param habitatVoc
|
371
|
* @param string
|
372
|
* @param uuidlifeformt
|
373
|
*/
|
374
|
private void addHabitat(SimpleExcelTaxonImportState<FloraHellenicaImportConfigurator> state,
|
375
|
OrderedTermVocabulary<State> habitatVoc, String abbrev, String label, String desc, UUID uuidHabitat) {
|
376
|
addState(state, abbrev, label, desc, uuidHabitat, habitatVoc);
|
377
|
}
|
378
|
|
379
|
// ***************************** STATUS ********************************/
|
380
|
|
381
|
private void initStatusVocabulary(SimpleExcelTaxonImportState<FloraHellenicaImportConfigurator> state) {
|
382
|
UUID uuid = FloraHellenicaTransformer.uuidFloraHellenicaStatusVoc;
|
383
|
OrderedTermVocabulary<?> statusVoc = (OrderedTermVocabulary<?>)this.getVocabularyService().find(uuid);
|
384
|
if (statusVoc == null){
|
385
|
createStatusVoc(state, uuid);
|
386
|
}
|
387
|
}
|
388
|
|
389
|
/**
|
390
|
* @param state
|
391
|
*/
|
392
|
private void createStatusVoc(SimpleExcelTaxonImportState<FloraHellenicaImportConfigurator> state, UUID vocUuid) {
|
393
|
//voc
|
394
|
URI termSourceUri = null;
|
395
|
String label = "Checklist of Greece Status";
|
396
|
String description = "Status as used in the Checklist of Greece";
|
397
|
|
398
|
OrderedTermVocabulary<?> statusVoc;
|
399
|
if (state.getConfig().isStatusAsDistribution()){
|
400
|
statusVoc = OrderedTermVocabulary.NewInstance(TermType.PresenceAbsenceTerm,
|
401
|
description, label, null, termSourceUri);
|
402
|
}else{
|
403
|
statusVoc = OrderedTermVocabulary.NewInstance(TermType.State,
|
404
|
description, label, null, termSourceUri);
|
405
|
}
|
406
|
|
407
|
statusVoc.setUuid(vocUuid);
|
408
|
|
409
|
if (!state.getConfig().isStatusAsDistribution()){
|
410
|
addStatus(state, "N", "Native", "", FloraHellenicaTransformer.uuidStatusNative, statusVoc);
|
411
|
addStatus(state, "X", "Xenophyte", "", FloraHellenicaTransformer.uuidStatusXenophyte, statusVoc);
|
412
|
addStatus(state, "?X", "?Xenophyte", "", FloraHellenicaTransformer.uuidStatusXenophyteDoubtfully, statusVoc);
|
413
|
}
|
414
|
addStatus(state, "RR", "Range-restricted", "", FloraHellenicaTransformer.uuidStatusRangeRestricted, statusVoc);
|
415
|
addStatus(state, "?RR", "?Range-restricted", "", FloraHellenicaTransformer.uuidStatusRangeRestrictedDoubtfully, statusVoc);
|
416
|
|
417
|
|
418
|
|
419
|
this.getVocabularyService().save(statusVoc);
|
420
|
return;
|
421
|
}
|
422
|
|
423
|
// ************************** FEATURE TREE ************************************/
|
424
|
|
425
|
boolean hasFeatureTree = false;
|
426
|
|
427
|
/**
|
428
|
* @param state
|
429
|
*/
|
430
|
private void makeFeatureTree(SimpleExcelTaxonImportState<FloraHellenicaImportConfigurator> state) {
|
431
|
if (hasFeatureTree ){
|
432
|
return;
|
433
|
}
|
434
|
if (getTermTreeService().find(state.getConfig().getUuidFeatureTree()) != null){
|
435
|
hasFeatureTree = true;
|
436
|
return;
|
437
|
}
|
438
|
TermTree<Feature> result = TermTree.NewFeatureInstance(state.getConfig().getUuidFeatureTree());
|
439
|
result.setTitleCache(state.getConfig().getFeatureTreeTitle(), true);
|
440
|
TermNode<Feature> root = result.getRoot();
|
441
|
ITermService service = getTermService();
|
442
|
|
443
|
UUID uuid = FloraHellenicaTransformer.uuidFloraHellenicaTaxonInfoFeature;
|
444
|
Feature newFeature = getFeature(state, uuid, "Taxon info", "Taxon info", null, null);
|
445
|
root.addChild(newFeature);
|
446
|
|
447
|
newFeature = (Feature)service.find(Feature.DISTRIBUTION().getUuid());
|
448
|
root.addChild(newFeature);
|
449
|
|
450
|
newFeature = (Feature)service.find(Feature.STATUS().getUuid());
|
451
|
root.addChild(newFeature);
|
452
|
newFeature.setSupportsCategoricalData(true);
|
453
|
TermVocabulary<State> voc = this.getVocabularyService().find(FloraHellenicaTransformer.uuidFloraHellenicaStatusVoc);
|
454
|
newFeature.addSupportedCategoricalEnumeration(voc);
|
455
|
|
456
|
|
457
|
uuid = FloraHellenicaTransformer.uuidFloraHellenicaChorologyFeature;
|
458
|
newFeature = getFeature(state, uuid, "Chorology", "Chorology", null, null);
|
459
|
newFeature.setSupportsCategoricalData(true);
|
460
|
voc = this.getVocabularyService().find(FloraHellenicaTransformer.uuidFloraHellenicaChorologicalVoc);
|
461
|
newFeature.addSupportedCategoricalEnumeration(voc);
|
462
|
root.addChild(newFeature);
|
463
|
|
464
|
newFeature = (Feature)service.find(Feature.LIFEFORM().getUuid());
|
465
|
root.addChild(newFeature);
|
466
|
newFeature.setSupportsCategoricalData(true);
|
467
|
voc = this.getVocabularyService().find(FloraHellenicaTransformer.uuidFloraHellenicaLifeformVoc);
|
468
|
newFeature.addSupportedCategoricalEnumeration(voc);
|
469
|
|
470
|
newFeature = (Feature)service.find(Feature.HABITAT().getUuid());
|
471
|
root.addChild(newFeature);
|
472
|
newFeature.setSupportsCategoricalData(true);
|
473
|
voc = this.getVocabularyService().find(FloraHellenicaTransformer.uuidFloraHellenicaHabitatVoc);
|
474
|
newFeature.addSupportedCategoricalEnumeration(voc);
|
475
|
|
476
|
|
477
|
newFeature = (Feature)service.find(Feature.NOTES().getUuid());
|
478
|
root.addChild(newFeature);
|
479
|
|
480
|
getTermTreeService().saveOrUpdate(result);
|
481
|
hasFeatureTree = true;
|
482
|
}
|
483
|
|
484
|
private State addState(SimpleExcelTaxonImportState<FloraHellenicaImportConfigurator> state,
|
485
|
String abbrev, String stateLabel, String description, UUID uuid, OrderedTermVocabulary<State> voc) {
|
486
|
State newState = State.NewInstance(
|
487
|
description, stateLabel, abbrev);
|
488
|
newState.setUuid(uuid);
|
489
|
newState.setIdInVocabulary(abbrev);
|
490
|
voc.addTerm(newState);
|
491
|
return newState;
|
492
|
}
|
493
|
|
494
|
private OrderedTermBase addStatus(SimpleExcelTaxonImportState<FloraHellenicaImportConfigurator> state,
|
495
|
String abbrev, String stateLabel, String description, UUID uuid,
|
496
|
OrderedTermVocabulary voc) {
|
497
|
FloraHellenicaImportConfigurator config = state.getConfig();
|
498
|
OrderedTermBase<?> newStatus;
|
499
|
if (config.isStatusAsDistribution()){
|
500
|
newStatus = PresenceAbsenceTerm.NewPresenceInstance( description, stateLabel, abbrev);
|
501
|
}else{
|
502
|
newStatus = State.NewInstance(description, stateLabel, abbrev);
|
503
|
}
|
504
|
|
505
|
newStatus.setUuid(uuid);
|
506
|
newStatus.setIdInVocabulary(abbrev);
|
507
|
newStatus.setSymbol(abbrev);
|
508
|
voc.addTerm(newStatus);
|
509
|
return newStatus;
|
510
|
}
|
511
|
|
512
|
|
513
|
/**
|
514
|
* @param state
|
515
|
*/
|
516
|
private void makeMapColors(SimpleExcelTaxonImportState<FloraHellenicaImportConfigurator> state) {
|
517
|
PresenceAbsenceTerm presentTerm = (PresenceAbsenceTerm)getTermService().find(PresenceAbsenceTerm.uuidPresent);
|
518
|
try {
|
519
|
presentTerm.setDefaultColor("ff0000");
|
520
|
getTermService().saveOrUpdate(presentTerm);
|
521
|
} catch (ParseException e) {
|
522
|
// TODO Auto-generated catch block
|
523
|
e.printStackTrace();
|
524
|
}
|
525
|
|
526
|
}
|
527
|
|
528
|
|
529
|
/**
|
530
|
* {@inheritDoc}
|
531
|
*/
|
532
|
@Override
|
533
|
protected boolean doCheck(SimpleExcelTaxonImportState<FloraHellenicaImportConfigurator> state) {
|
534
|
return false;
|
535
|
}
|
536
|
|
537
|
|
538
|
/**
|
539
|
* {@inheritDoc}
|
540
|
*/
|
541
|
@Override
|
542
|
protected boolean isIgnore(SimpleExcelTaxonImportState<FloraHellenicaImportConfigurator> state) {
|
543
|
return false;
|
544
|
}
|
545
|
}
|