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/**
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* Copyright (C) 2016 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.util.Arrays;
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import java.util.HashMap;
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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 org.apache.log4j.Logger;
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import org.springframework.stereotype.Component;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImportState;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary;
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import eu.etaxonomy.cdm.model.description.CategoricalData;
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import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
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import eu.etaxonomy.cdm.model.description.Distribution;
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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.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.location.NamedArea;
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import eu.etaxonomy.cdm.model.name.BotanicalName;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.TaxonNameFactory;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.taxon.Classification;
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import eu.etaxonomy.cdm.model.taxon.ITaxonTreeNode;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonNode;
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import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
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/**
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* @author a.mueller
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* @date 14.12.2016
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*
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*/
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@Component
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public class FloraHellenicaTaxonImport<CONFIG extends FloraHellenicaImportConfigurator>
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extends FloraHellenicaImportBase<CONFIG>{
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private static final long serialVersionUID = -6291948918967763381L;
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private static final Logger logger = Logger.getLogger(FloraHellenicaTaxonImport.class);
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private static final String LIFE_FORM = "Life-form";
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private static final String STATUS = "Status";
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private static final String CHOROLOGICAL_CATEGOGY = "Chorological categogy";
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private static UUID rootUuid = UUID.fromString("aa667b0b-b417-470e-a9b0-ef9409a3431e");
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private static UUID plantaeUuid = UUID.fromString("4f151932-ab97-4d81-b88e-46fe82cd3e88");
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private Map<String, State> lifeformMap = new HashMap<>();
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private Map<String, State> chorologyMap = new HashMap<>();
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private PresenceAbsenceTerm rangeRestricted;
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private PresenceAbsenceTerm doubtfullyRangeRestricted;
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private OrderedTermVocabulary<State> habitatVoc;
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private OrderedTermVocabulary<State> statusVoc;
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private static List<String> expectedKeys= Arrays.asList(new String[]{
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"Unique ID","uuid","Group","Family","Genus","Species","Species Author","Subspecies","Subspecies Author",
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"IoI","NPi","SPi","Pe","StE","EC","NC","NE","NAe","WAe","Kik","KK","EAe",
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STATUS,CHOROLOGICAL_CATEGOGY,LIFE_FORM,"A","C","G","H","M","P","R","W", "Taxon"
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});
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private String lastGenus;
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private String lastSpecies;
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private NonViralNameParserImpl parser = NonViralNameParserImpl.NewInstance();
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@Override
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protected String getWorksheetName() {
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return "valid taxa names";
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}
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/**
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* {@inheritDoc}
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*/
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@Override
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protected void firstPass(SimpleExcelTaxonImportState<CONFIG> state) {
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initLifeFormMap();
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initChorologyMap();
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initOtherTerms(state);
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String line = state.getCurrentLine() + ": ";
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HashMap<String, String> record = state.getOriginalRecord();
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Set<String> keys = record.keySet();
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for (String key: keys) {
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if (! expectedKeys.contains(key)){
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logger.warn(line + "Unexpected Key: " + key);
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}
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}
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String noStr = getValue(record, "Unique ID");
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Taxon taxon = makeTaxon(state, line, record, noStr);
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//Distribution
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TaxonDescription desc = getTaxonDescription(taxon);
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makeDistribution(state, line, noStr, desc);
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makeChorologicalCategory(state, line, noStr, desc);
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//lifeform
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makeLifeform(state, line, noStr, desc);
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//habitat
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makeHabitat(state, line, noStr, desc);
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state.putTaxon(noStr, taxon);
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}
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/**
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* @param state
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*
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*/
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private void initOtherTerms(SimpleExcelTaxonImportState<CONFIG> state) {
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if (state.getConfig().isStatusAsDistribution()){
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if (rangeRestricted == null){
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rangeRestricted = (PresenceAbsenceTerm)getTermService().find(FloraHellenicaTransformer.uuidStatusRangeRestricted);
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}
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if (this.doubtfullyRangeRestricted == null){
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doubtfullyRangeRestricted = (PresenceAbsenceTerm)getTermService().find(FloraHellenicaTransformer.uuidStatusRangeRestrictedDoubtfully);
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}
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}else{
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if (this.statusVoc == null){
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@SuppressWarnings("unchecked")
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OrderedTermVocabulary<State> voc = (OrderedTermVocabulary<State>) getVocabularyService().find(
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FloraHellenicaTransformer.uuidFloraHellenicaStatusVoc);
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statusVoc = voc;
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}
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}
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if (this.habitatVoc == null){
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@SuppressWarnings("unchecked")
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OrderedTermVocabulary<State> voc = (OrderedTermVocabulary<State>) getVocabularyService().find(
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FloraHellenicaTransformer.uuidFloraHellenicaHabitatVoc);
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habitatVoc = voc;
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}
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}
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private void initLifeFormMap() {
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if (lifeformMap.isEmpty()){
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UUID uuid = FloraHellenicaTransformer.uuidFloraHellenicaLifeformVoc;
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@SuppressWarnings("unchecked")
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OrderedTermVocabulary<State> lifeformVoc = (OrderedTermVocabulary<State>)this.getVocabularyService().find(uuid);
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for (State state : lifeformVoc.getTerms()){
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lifeformMap.put(state.getIdInVocabulary(), state);
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}
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}
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}
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private void initChorologyMap() {
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if (chorologyMap.isEmpty()){
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UUID uuid = FloraHellenicaTransformer.uuidFloraHellenicaChorologicalVoc;
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@SuppressWarnings("unchecked")
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OrderedTermVocabulary<State> voc = (OrderedTermVocabulary<State>)this.getVocabularyService().find(uuid);
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for (State state : voc.getTerms()){
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chorologyMap.put(state.getIdInVocabulary(), state);
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}
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}
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}
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/**
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* @param state
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* @param line
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* @param noStr
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* @param desc
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*/
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private void makeChorologicalCategory(SimpleExcelTaxonImportState<CONFIG> state, String line, String noStr,
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TaxonDescription desc) {
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HashMap<String, String> record = state.getOriginalRecord();
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String valueStr = getValue(record, CHOROLOGICAL_CATEGOGY);
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String value = valueStr;
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if (value == null){
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return;
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}
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Feature choroFeature = getFeature(state, FloraHellenicaTransformer.uuidFloraHellenicaChorologyFeature,
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"Chorology", "The Chorological Category", "Choro", null);
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CategoricalData catData = CategoricalData.NewInstance(choroFeature);
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catData.setOrderRelevant(true);
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String[] splits = value.split(" & ");
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replaceDirection(splits, line);
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for (String split: splits){
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String[] splitsA = split.split("/");
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for (String splitA : splitsA){
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String[] splitsB = splitA.split(", ");
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for (String splitB : splitsB){
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splitB = normalizeChorology(splitB);
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State choroTerm = chorologyMap.get(splitB);
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if (choroTerm == null){
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logger.warn(line + "Some chorology could not be recognized in: " + value + "; Term was: " +splitB);
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}else{
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catData.addStateData(choroTerm);
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}
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}
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}
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}
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if (catData.getStateData().size() > 1){
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catData.setOrderRelevant(true);
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}
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desc.addElement(catData);
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}
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/**
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* @param splitB
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* @return
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*/
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private String normalizeChorology(String choroStr) {
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choroStr = choroStr.trim()
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.replace("BK", "Bk")
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.replace("Austral.", "Austr.")
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.replace("trop.As.", "trop. As.");
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if (choroStr.startsWith("[") && !choroStr.endsWith("]")){
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choroStr += "]";
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}else if (!choroStr.startsWith("[") && choroStr.endsWith("]")){
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choroStr = "[" + choroStr;
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}
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return choroStr;
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}
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/**
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* @param splits
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* @param line
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*/
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private void replaceDirection(String[] splits, String line) {
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if (splits.length > 1){
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String[] divs = splits[1].split("-");
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if (divs.length == 2){
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splits[0] = splits[0] + "-" + divs[1];
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}else{
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logger.warn(line + "Splits[1] has not expected format: " + splits[1]);
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}
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}
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}
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/**
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* @param state
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* @param line
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* @param noStr
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* @param desc
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*/
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private void makeLifeform(SimpleExcelTaxonImportState<CONFIG> state, String line, String noStr,
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TaxonDescription desc) {
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HashMap<String, String> record = state.getOriginalRecord();
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String value = getValue(record, LIFE_FORM);
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String[] splits = value.split("\\s+");
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if (splits.length > 2){
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logger.warn("Unexpected length of lifeform: " + value + " line: " + line );
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}
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CategoricalData catData = CategoricalData.NewInstance(Feature.LIFEFORM());
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for (String split : splits){
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State lifeform = lifeformMap.get(split);
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if (lifeform == null){
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logger.warn(line + "Unexpected lifeform: " + value);
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}else{
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catData.addStateData(lifeform);
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}
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}
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desc.addElement(catData);
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}
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/**
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* @param state
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* @param line
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* @param noStr
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* @param desc
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*/
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private void makeHabitat(SimpleExcelTaxonImportState<CONFIG> state, String line, String noStr,
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TaxonDescription desc) {
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CategoricalData catData = CategoricalData.NewInstance(Feature.HABITAT());
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handleHabitat(state, catData, "A", FloraHellenicaTransformer.uuidHabitatA, line, noStr);
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handleHabitat(state, catData, "C", FloraHellenicaTransformer.uuidHabitatC, line, noStr);
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handleHabitat(state, catData, "G", FloraHellenicaTransformer.uuidHabitatG, line, noStr);
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handleHabitat(state, catData, "H", FloraHellenicaTransformer.uuidHabitatH, line, noStr);
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handleHabitat(state, catData, "M", FloraHellenicaTransformer.uuidHabitatM, line, noStr);
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handleHabitat(state, catData, "P", FloraHellenicaTransformer.uuidHabitatP, line, noStr);
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handleHabitat(state, catData, "R", FloraHellenicaTransformer.uuidHabitatR, line, noStr);
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handleHabitat(state, catData, "W", FloraHellenicaTransformer.uuidHabitatW, line, noStr);
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desc.addElement(catData);
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}
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/**
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* @param state
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* @param catData
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* @param string
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* @param uuidhabitata
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* @param line
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* @param noStr
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*/
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private void handleHabitat(SimpleExcelTaxonImportState<CONFIG> state, CategoricalData catData, String label,
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UUID uuidHabitat, String line, String noStr) {
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HashMap<String, String> record = state.getOriginalRecord();
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String value = getValue(record, "" + label);
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if (value == null){
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//do nothing
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}else if (value.matches("[ACGHMPRW]")){
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State habitatState = this.getStateTerm(state, uuidHabitat, null, null, null, habitatVoc);
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catData.addStateData(habitatState);
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}else{
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logger.warn(line + "Unrecognized habitat state '" + value + "' for " + label);
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}
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}
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/**
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* @param state
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* @param line
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* @param noStr
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* @param desc
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*/
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private void makeDistribution(SimpleExcelTaxonImportState<CONFIG> state, String line, String noStr,
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TaxonDescription desc) {
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//TODO status Greece
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handleStatus(state, desc, STATUS, FloraHellenicaTransformer.uuidAreaGreece, line, noStr);
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handleDistribution(state, desc, "IoI", FloraHellenicaTransformer.uuidAreaIoI, line, noStr);
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handleDistribution(state, desc, "NPi", FloraHellenicaTransformer.uuidAreaNPi, line, noStr);
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handleDistribution(state, desc, "SPi", FloraHellenicaTransformer.uuidAreaSPi, line, noStr);
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handleDistribution(state, desc, "Pe", FloraHellenicaTransformer.uuidAreaPe, line, noStr);
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handleDistribution(state, desc, "StE", FloraHellenicaTransformer.uuidAreaStE, line, noStr);
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handleDistribution(state, desc, "EC", FloraHellenicaTransformer.uuidAreaEC, line, noStr);
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handleDistribution(state, desc, "NC", FloraHellenicaTransformer.uuidAreaNC, line, noStr);
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handleDistribution(state, desc, "NE", FloraHellenicaTransformer.uuidAreaNE, line, noStr);
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handleDistribution(state, desc, "NAe", FloraHellenicaTransformer.uuidAreaNAe, line, noStr);
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handleDistribution(state, desc, "WAe", FloraHellenicaTransformer.uuidAreaWAe, line, noStr);
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handleDistribution(state, desc, "Kik", FloraHellenicaTransformer.uuidAreaKik, line, noStr);
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handleDistribution(state, desc, "KK", FloraHellenicaTransformer.uuidAreaKK, line, noStr);
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handleDistribution(state, desc, "EAe", FloraHellenicaTransformer.uuidAreaEAe, line, noStr);
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}
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/**
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* @param state
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* @param line
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* @param record
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* @param noStr
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* @return
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*/
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private Taxon makeTaxon(SimpleExcelTaxonImportState<CONFIG> state, String line, HashMap<String, String> record,
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String noStr) {
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TaxonNode familyTaxon = getFamilyTaxon(record, state);
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if (familyTaxon == null){
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logger.warn(line + "Family not created: " + record.get("Family"));
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}
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String genusStr = getValue(record, "Genus");
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String speciesStr = getValue(record, "Species");
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String speciesAuthorStr = getValue(record, "Species Author");
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String subSpeciesStr = getValue(record, "Subspecies");
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String subSpeciesAuthorStr = getValue(record, "Subspecies Author");
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String uuidStr = getValue(record, "uuid");
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UUID uuid = UUID.fromString(uuidStr);
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boolean isSubSpecies = isNotBlank(subSpeciesStr);
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boolean isAutonym = isSubSpecies && speciesStr.equals(subSpeciesStr);
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if (isSubSpecies && ! isAutonym && isBlank(subSpeciesAuthorStr)){
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logger.warn(line + "Non-Autonym subspecies has no auhtor");
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}else if (isSubSpecies && isAutonym && isNotBlank(subSpeciesAuthorStr)){
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logger.warn(line + "Autonym subspecies has subspecies auhtor");
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}
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String[] nameParts;
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if (!isSubSpecies){
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nameParts = new String[]{genusStr, speciesStr, speciesAuthorStr};
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}else if (!isAutonym){
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nameParts = new String[]{genusStr, speciesStr, "subsp. " + subSpeciesStr, subSpeciesAuthorStr};
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}else{
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nameParts = new String[]{genusStr, speciesStr, speciesAuthorStr, "subsp. " + subSpeciesStr};
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}
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String nameStr = CdmUtils.concat(" ", nameParts);
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boolean isSensuStrictu = false;
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|
if (nameStr.endsWith("s.str.")){
|
392
|
isSensuStrictu = true;
|
393
|
nameStr = nameStr.substring(0, nameStr.length() - "s.str.".length() ).trim();
|
394
|
}
|
395
|
Rank rank = isSubSpecies ? Rank.SUBSPECIES() : Rank.SPECIES();
|
396
|
BotanicalName name = (BotanicalName)parser.parseFullName(nameStr, state.getConfig().getNomenclaturalCode(), rank);
|
397
|
if (name.isProtectedTitleCache()){
|
398
|
logger.warn(line + "Name could not be parsed: " + nameStr);
|
399
|
}
|
400
|
name = replaceNameAuthorsAndReferences(state, name);
|
401
|
|
402
|
Taxon taxon = Taxon.NewInstance(name, getSecReference(state));
|
403
|
taxon.addImportSource(noStr, getWorksheetName(), getSourceCitation(state), null);
|
404
|
if (isSensuStrictu){
|
405
|
taxon.setAppendedPhrase("s.str.");
|
406
|
}
|
407
|
String parentStr = isSubSpecies ?
|
408
|
makeSpeciesKey(genusStr, speciesStr, speciesAuthorStr) : genusStr;
|
409
|
taxon.setUuid(uuid);
|
410
|
boolean genusAsBefore = genusStr.equals(lastGenus);
|
411
|
boolean speciesAsBefore = speciesStr.equals(lastSpecies);
|
412
|
TaxonNode parent = getParent(state, parentStr);
|
413
|
if (parent != null){
|
414
|
if (!isSubSpecies && genusAsBefore || isSubSpecies && speciesAsBefore){
|
415
|
// if (genusAsBefore ){
|
416
|
//everything as expected
|
417
|
TaxonNode newNode = parent.addChildTaxon(taxon, getSecReference(state), null);
|
418
|
getTaxonNodeService().saveOrUpdate(newNode);
|
419
|
}else{
|
420
|
logger.warn(line + "Unexpected non-missing parent");
|
421
|
}
|
422
|
}else{
|
423
|
if (isSubSpecies){
|
424
|
logger.warn(line + "Subspecies should always have an existing parent");
|
425
|
}else if (genusAsBefore){
|
426
|
logger.warn(line + "Unexpected missing genus parent");
|
427
|
}else{
|
428
|
parent = makeGenusNode(state, record, genusStr);
|
429
|
TaxonNode newNode = parent.addChildTaxon(taxon, getSecReference(state), null);
|
430
|
getTaxonNodeService().save(newNode);
|
431
|
}
|
432
|
}
|
433
|
if (!isSubSpecies){
|
434
|
state.putHigherTaxon(makeSpeciesKey(genusStr, speciesStr, speciesAuthorStr), taxon);
|
435
|
}
|
436
|
|
437
|
// this.lastFamily = familyStr
|
438
|
this.lastGenus = genusStr;
|
439
|
this.lastSpecies = speciesStr;
|
440
|
return taxon;
|
441
|
}
|
442
|
|
443
|
/**
|
444
|
* @param genusStr
|
445
|
* @param speciesStr
|
446
|
* @param speciesAuthorStr
|
447
|
* @return
|
448
|
*/
|
449
|
private String makeSpeciesKey(String genusStr, String speciesStr, String speciesAuthorStr) {
|
450
|
return CdmUtils.concat(" ", new String[]{genusStr, speciesStr, speciesAuthorStr});
|
451
|
}
|
452
|
|
453
|
/**
|
454
|
* @param state
|
455
|
* @param record
|
456
|
* @param genusStr
|
457
|
* @return
|
458
|
*/
|
459
|
private TaxonNode makeGenusNode(SimpleExcelTaxonImportState<CONFIG> state,
|
460
|
HashMap<String, String> record, String genusStr) {
|
461
|
BotanicalName name = TaxonNameFactory.NewBotanicalInstance(Rank.GENUS());
|
462
|
name.setGenusOrUninomial(genusStr);
|
463
|
name = replaceNameAuthorsAndReferences(state, name);
|
464
|
Taxon genus = Taxon.NewInstance(name, getSecReference(state));
|
465
|
TaxonNode family = getFamilyTaxon(record, state);
|
466
|
TaxonNode genusNode = family.addChildTaxon(genus, getSecReference(state), null);
|
467
|
state.putHigherTaxon(genusStr, genus);
|
468
|
genus.addSource(makeOriginalSource(state));
|
469
|
getTaxonNodeService().save(genusNode);
|
470
|
return genusNode;
|
471
|
}
|
472
|
|
473
|
/**
|
474
|
* @param state
|
475
|
* @param parentStr
|
476
|
* @return
|
477
|
*/
|
478
|
private TaxonNode getParent(SimpleExcelTaxonImportState<CONFIG> state, String parentStr) {
|
479
|
Taxon taxon = state.getHigherTaxon(parentStr);
|
480
|
|
481
|
return taxon == null ? null : taxon.getTaxonNodes().iterator().next();
|
482
|
}
|
483
|
|
484
|
/**
|
485
|
* @param record
|
486
|
* @param state
|
487
|
* @return
|
488
|
*/
|
489
|
private TaxonNode getFamilyTaxon(HashMap<String, String> record, SimpleExcelTaxonImportState<CONFIG> state) {
|
490
|
String familyStr = getValue(record, "Family");
|
491
|
if (familyStr == null){
|
492
|
return null;
|
493
|
}
|
494
|
familyStr = familyStr.trim();
|
495
|
|
496
|
Taxon family = state.getHigherTaxon(familyStr);
|
497
|
TaxonNode familyNode;
|
498
|
if (family != null){
|
499
|
familyNode = family.getTaxonNodes().iterator().next();
|
500
|
}else{
|
501
|
BotanicalName name = makeFamilyName(state, familyStr);
|
502
|
name = replaceNameAuthorsAndReferences(state, name);
|
503
|
|
504
|
Reference sec = getSecReference(state);
|
505
|
family = Taxon.NewInstance(name, sec);
|
506
|
|
507
|
ITaxonTreeNode groupNode = getGroupTaxon(record, state);
|
508
|
familyNode = groupNode.addChildTaxon(family, sec, null);
|
509
|
state.putHigherTaxon(familyStr, family);
|
510
|
getTaxonNodeService().save(familyNode);
|
511
|
}
|
512
|
|
513
|
return familyNode;
|
514
|
}
|
515
|
|
516
|
/**
|
517
|
* @param record
|
518
|
* @param state
|
519
|
* @return
|
520
|
*/
|
521
|
private TaxonNode getGroupTaxon(HashMap<String, String> record, SimpleExcelTaxonImportState<CONFIG> state) {
|
522
|
String groupStr = getValue(record, "Group");
|
523
|
if (groupStr == null){
|
524
|
return null;
|
525
|
}
|
526
|
groupStr = groupStr.trim();
|
527
|
|
528
|
Taxon group = state.getHigherTaxon(groupStr);
|
529
|
TaxonNode groupNode;
|
530
|
if (group != null){
|
531
|
groupNode = group.getTaxonNodes().iterator().next();
|
532
|
}else{
|
533
|
BotanicalName name = makeFamilyName(state, groupStr);
|
534
|
name = replaceNameAuthorsAndReferences(state, name);
|
535
|
|
536
|
Reference sec = getSecReference(state);
|
537
|
group = Taxon.NewInstance(name, sec);
|
538
|
ITaxonTreeNode rootNode = getClassification(state);
|
539
|
groupNode = rootNode.addChildTaxon(group, sec, null);
|
540
|
state.putHigherTaxon(groupStr, group);
|
541
|
getTaxonNodeService().save(groupNode);
|
542
|
}
|
543
|
|
544
|
return groupNode;
|
545
|
}
|
546
|
|
547
|
private TaxonNode rootNode;
|
548
|
private TaxonNode getClassification(SimpleExcelTaxonImportState<CONFIG> state) {
|
549
|
if (rootNode == null){
|
550
|
Reference sec = getSecReference(state);
|
551
|
String classificationName = state.getConfig().getClassificationName();
|
552
|
Language language = Language.DEFAULT();
|
553
|
Classification classification = Classification.NewInstance(classificationName, sec, language);
|
554
|
classification.setUuid(state.getConfig().getClassificationUuid());
|
555
|
classification.getRootNode().setUuid(rootUuid);
|
556
|
|
557
|
BotanicalName plantaeName = TaxonNameFactory.NewBotanicalInstance(Rank.KINGDOM());
|
558
|
plantaeName.setGenusOrUninomial("Plantae");
|
559
|
plantaeName = replaceNameAuthorsAndReferences(state, plantaeName);
|
560
|
|
561
|
Taxon plantae = Taxon.NewInstance(plantaeName, sec);
|
562
|
TaxonNode plantaeNode = classification.addChildTaxon(plantae, null, null);
|
563
|
plantaeNode.setUuid(plantaeUuid);
|
564
|
getClassificationService().save(classification);
|
565
|
|
566
|
rootNode = plantaeNode;
|
567
|
}
|
568
|
return rootNode;
|
569
|
}
|
570
|
|
571
|
/**
|
572
|
* @param desc
|
573
|
* @param string
|
574
|
* @param uuidUserDefinedAnnotationTypeVocabulary
|
575
|
*/
|
576
|
private void handleDistribution(SimpleExcelTaxonImportState<CONFIG> state,
|
577
|
TaxonDescription desc, String key, UUID uuid, String line, String id) {
|
578
|
HashMap<String, String> record = state.getOriginalRecord();
|
579
|
String value = getValue(record, key);
|
580
|
if (value == null || value.matches("[x\\.\\?]")){
|
581
|
NamedArea area = getNamedArea(state, uuid, null, null, null, null, null);
|
582
|
Distribution dist;
|
583
|
if (".".equals(value)){
|
584
|
logger.warn(line + "'.' Should not exist anmore as a distribution status: '" + value + "' for " + key);
|
585
|
dist = Distribution.NewInstance(area, PresenceAbsenceTerm.ABSENT());
|
586
|
}else if (value == null){
|
587
|
//TODO is absent wanted
|
588
|
dist = Distribution.NewInstance(area, PresenceAbsenceTerm.ABSENT());
|
589
|
}else if ("x".equals(value)){
|
590
|
dist = Distribution.NewInstance(area, PresenceAbsenceTerm.PRESENT());
|
591
|
}else if ("?".equals(value)){
|
592
|
dist = Distribution.NewInstance(area, PresenceAbsenceTerm.PRESENT_DOUBTFULLY());
|
593
|
}else {
|
594
|
logger.warn(line + "Not matching status. THis should not happpen '" + value + "' for " + key);
|
595
|
return;
|
596
|
}
|
597
|
desc.addElement(dist);
|
598
|
dist.addImportSource(id, getWorksheetName(), getSourceCitation(state), line);
|
599
|
}else {
|
600
|
logger.warn(line + "Unrecognized distribution status '" + value + "' for " + key);
|
601
|
}
|
602
|
}
|
603
|
|
604
|
private void handleStatus(SimpleExcelTaxonImportState<CONFIG> state,
|
605
|
TaxonDescription desc, String key, UUID uuid, String line, String id) {
|
606
|
HashMap<String, String> record = state.getOriginalRecord();
|
607
|
String value = getValue(record, key);
|
608
|
DescriptionElementBase descEl;
|
609
|
if (state.getConfig().isStatusAsDistribution()){
|
610
|
NamedArea area = getNamedArea(state, uuid, null, null, null, null, null);
|
611
|
if (value == null || ".".equals(value) ){
|
612
|
descEl = Distribution.NewInstance(area, PresenceAbsenceTerm.NATIVE());
|
613
|
if (".".equals(value)){
|
614
|
logger.warn(line + "'.' Should not exist anymore as a distribution status: '" + value + "' for " + key);
|
615
|
}
|
616
|
}else if ("Range-restricted".equals(value)){
|
617
|
descEl = Distribution.NewInstance(area, rangeRestricted);
|
618
|
}else if ("?Range-restricted".equals(value)){
|
619
|
descEl = Distribution.NewInstance(area, doubtfullyRangeRestricted);
|
620
|
}else if ("Xenophyte".equals(value)){
|
621
|
descEl = Distribution.NewInstance(area, PresenceAbsenceTerm.INTRODUCED());
|
622
|
}else if ("?Xenophyte".equals(value)){
|
623
|
descEl = Distribution.NewInstance(area, PresenceAbsenceTerm.INTRODUCED_DOUBTFULLY_INTRODUCED());
|
624
|
}else {
|
625
|
logger.warn(line + "Not matching status. This should not happpen '" + value + "' for " + key);
|
626
|
return;
|
627
|
}
|
628
|
}else{
|
629
|
CategoricalData catData = CategoricalData.NewInstance(Feature.STATUS());
|
630
|
descEl = catData;
|
631
|
if (value == null || ".".equals(value) ){
|
632
|
handleSingleStatus(state, catData, FloraHellenicaTransformer.uuidStatusNative, line);
|
633
|
if (".".equals(value)){
|
634
|
logger.warn(line + "'.' Should not exist anymore as a status: '" + value + "' for " + key);
|
635
|
}
|
636
|
}else if ("Range-restricted".equals(value)){
|
637
|
handleSingleStatus(state, catData, FloraHellenicaTransformer.uuidStatusRangeRestricted, line);
|
638
|
}else if ("?Range-restricted".equals(value)){
|
639
|
handleSingleStatus(state, catData, FloraHellenicaTransformer.uuidStatusRangeRestrictedDoubtfully, line);
|
640
|
}else if ("Xenophyte".equals(value)){
|
641
|
handleSingleStatus(state, catData, FloraHellenicaTransformer.uuidStatusXenophyte, line);
|
642
|
}else if ("?Xenophyte".equals(value)){
|
643
|
handleSingleStatus(state, catData, FloraHellenicaTransformer.uuidStatusXenophyteDoubtfully, line);
|
644
|
}else {
|
645
|
logger.warn(line + "Not matching status. This should not happpen '" + value + "' for " + key);
|
646
|
return;
|
647
|
}
|
648
|
}
|
649
|
|
650
|
desc.addElement(descEl);
|
651
|
descEl.addImportSource(id, getWorksheetName(), getSourceCitation(state), line);
|
652
|
}
|
653
|
|
654
|
private void handleSingleStatus(SimpleExcelTaxonImportState<CONFIG> state, CategoricalData catData,
|
655
|
UUID uuidStatus, String line) {
|
656
|
|
657
|
HashMap<String, String> record = state.getOriginalRecord();
|
658
|
String value = getValue(record, "Status");
|
659
|
if (value == null || value.matches("(\\??Range-restricted|\\??Xenophyte)")){
|
660
|
State statusState = this.getStateTerm(state, uuidStatus, null, null, null, statusVoc);
|
661
|
catData.addStateData(statusState);
|
662
|
}else{
|
663
|
logger.warn(line + "Unrecognized status '" + value + "' for column 'Status'");
|
664
|
}
|
665
|
}
|
666
|
|
667
|
|
668
|
}
|