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ede5c502
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Andreas Müller
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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.cuba;
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fb3dec85
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Andreas Müller
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import java.util.ArrayList;
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ede5c502
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Andreas Müller
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import java.util.Arrays;
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import java.util.HashMap;
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c9f78619
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Andreas Müller
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import java.util.HashSet;
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ede5c502
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Andreas Müller
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import java.util.List;
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import java.util.Set;
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import java.util.UUID;
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fb3dec85
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Andreas Müller
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import java.util.regex.Matcher;
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import java.util.regex.Pattern;
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ede5c502
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Andreas Müller
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import org.apache.commons.lang.StringUtils;
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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.common.mapping.UndefinedTransformerMethodException;
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import eu.etaxonomy.cdm.io.excel.common.ExcelImporterBase;
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b9cdcc88
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Andreas Müller
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import eu.etaxonomy.cdm.model.agent.Person;
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fb3dec85
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Andreas Müller
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import eu.etaxonomy.cdm.model.agent.Team;
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import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
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ede5c502
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Andreas Müller
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import eu.etaxonomy.cdm.model.common.Annotation;
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import eu.etaxonomy.cdm.model.common.AnnotationType;
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b9cdcc88
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Andreas Müller
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.IdentifiableSource;
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ede5c502
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Andreas Müller
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import eu.etaxonomy.cdm.model.common.Language;
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c9f78619
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Andreas Müller
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import eu.etaxonomy.cdm.model.common.OriginalSourceType;
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4b9c9c4b
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Andreas Müller
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import eu.etaxonomy.cdm.model.common.Representation;
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b9cdcc88
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Andreas Müller
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import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
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import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
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ede5c502
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Andreas Müller
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import eu.etaxonomy.cdm.model.description.Distribution;
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c9f78619
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Andreas Müller
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import eu.etaxonomy.cdm.model.description.Feature;
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ede5c502
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Andreas Müller
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import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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c9f78619
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Andreas Müller
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import eu.etaxonomy.cdm.model.description.TaxonInteraction;
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import eu.etaxonomy.cdm.model.description.TextData;
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ede5c502
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Andreas Müller
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import eu.etaxonomy.cdm.model.location.NamedArea;
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b9cdcc88
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Andreas Müller
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import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
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7d882578
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Andreas Müller
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import eu.etaxonomy.cdm.model.name.IBotanicalName;
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b9cdcc88
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Andreas Müller
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import eu.etaxonomy.cdm.model.name.NameRelationship;
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fb3dec85
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Andreas Müller
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import eu.etaxonomy.cdm.model.name.NameRelationshipType;
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ede5c502
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Andreas Müller
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
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fb3dec85
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Andreas Müller
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
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ede5c502
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Andreas Müller
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import eu.etaxonomy.cdm.model.name.Rank;
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86536e03
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Andreas Müller
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import eu.etaxonomy.cdm.model.name.TaxonName;
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ded3de15
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Andreas Müller
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import eu.etaxonomy.cdm.model.name.TaxonNameFactory;
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ede5c502
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Andreas Müller
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import eu.etaxonomy.cdm.model.reference.Reference;
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fb3dec85
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Andreas Müller
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import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
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ede5c502
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Andreas Müller
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import eu.etaxonomy.cdm.model.taxon.Classification;
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fb3dec85
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Andreas Müller
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import eu.etaxonomy.cdm.model.taxon.ITaxonTreeNode;
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3ef2e1bd
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Andreas Müller
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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import eu.etaxonomy.cdm.model.taxon.SynonymType;
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ede5c502
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Andreas Müller
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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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c9f78619
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Andreas Müller
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
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6af76d56
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Andreas Müller
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import eu.etaxonomy.cdm.strategy.homotypicgroup.BasionymRelationCreator;
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ede5c502
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Andreas Müller
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import eu.etaxonomy.cdm.strategy.parser.INonViralNameParser;
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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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* @created 05.01.2016
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*/
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@Component
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public class CubaExcelImport extends ExcelImporterBase<CubaImportState> {
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private static final long serialVersionUID = -747486709409732371L;
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private static final Logger logger = Logger.getLogger(CubaExcelImport.class);
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5cdaf78e
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Andreas Müller
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private static final String HOMONYM_MARKER = "\\s+homon.?$";
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fb3dec85
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Andreas Müller
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private static final String DOUBTFUL_MARKER = "^\\?\\s?";
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private static UUID rootUuid = UUID.fromString("206d42e4-ac32-4f20-a093-14826014e667");
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private static UUID plantaeUuid = UUID.fromString("139e7314-dd19-4286-a01d-8cc94ef77a09");
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ede5c502
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Andreas Müller
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private static INonViralNameParser<?> nameParser = NonViralNameParserImpl.NewInstance();
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private static NomenclaturalCode nc = NomenclaturalCode.ICNAFP;
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c9f78619
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Andreas Müller
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private static List<String> expectedKeys= Arrays.asList(new String[]{
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"Fam. default","Fam. FRC","Fam. A&S","Fam. FC",
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"Taxón","(Notas)","Syn.","End","Ind","Ind? D","Nat","Dud P","Adv","Cult C","CuW","PR PR*","Art","Hab(*)","May","Mat","IJ","CuC","VC","Ci","SS","CA","Cam","LT","CuE","Gr","Ho","SC","Gu","Esp","Ja","PR","Men","Bah","Cay","AmN","AmC","AmS","VM"});
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ede5c502
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Andreas Müller
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@Override
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protected void analyzeRecord(HashMap<String, String> record, CubaImportState state) {
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fb3dec85
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Andreas Müller
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//we do everything in firstPass here
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ede5c502
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Andreas Müller
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return;
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}
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/**
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* @param record
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* @param state
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* @param taxon
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*/
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fb3dec85
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Andreas Müller
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private void makeCubanDistribution(HashMap<String, String> record, CubaImportState state) {
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ede5c502
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Andreas Müller
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try {
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4b9c9c4b
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Andreas Müller
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NamedArea cuba = getNamedArea(state, state.getTransformer().getNamedAreaUuid("Cu"), null, null, null, null, null);
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fb3dec85
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Andreas Müller
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TaxonDescription desc = getTaxonDescription(state.getCurrentTaxon(), false, true);
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0a6a64c9
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Andreas Müller
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List<PresenceAbsenceTerm> statuss = makeCubanStatuss(record, state);
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fb3dec85
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Andreas Müller
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for (PresenceAbsenceTerm status : statuss){
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Distribution distribution = Distribution.NewInstance(cuba, status);
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desc.addElement(distribution);
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b9cdcc88
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Andreas Müller
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distribution.addSource(makeDescriptionSource(state));
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fb3dec85
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Andreas Müller
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}
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ede5c502
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Andreas Müller
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} catch (UndefinedTransformerMethodException e) {
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e.printStackTrace();
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}
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}
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/**
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* @param record
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* @param state
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* @return
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* @throws UndefinedTransformerMethodException
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*/
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0a6a64c9
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Andreas Müller
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private List<PresenceAbsenceTerm> makeCubanStatuss(HashMap<String, String> record, CubaImportState state) throws UndefinedTransformerMethodException {
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PresenceAbsenceTerm highestStatus = null;
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ede5c502
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Andreas Müller
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fb3dec85
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Andreas Müller
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String line = state.getCurrentLine() + ": ";
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List<PresenceAbsenceTerm> result = new ArrayList<>();
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ede5c502
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Andreas Müller
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String endemicStr = getValue(record, "End");
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String indigenousStr = getValue(record, "Ind");
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String indigenousDoubtStr = getValue(record, "Ind? D");
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String naturalisedStr = getValue(record, "Nat");
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String dudStr = getValue(record, "Dud P");
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String advStr = getValue(record, "Adv");
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String cultStr = getValue(record, "Cult C");
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b9cdcc88
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Andreas Müller
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state.setEndemic(false);
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ede5c502
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Andreas Müller
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if (endemicStr != null){
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fb3dec85
|
Andreas Müller
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if(endemicStr.equals("+")){
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PresenceAbsenceTerm endemicState = state.getTransformer().getPresenceTermByKey("E");
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result.add(endemicState);
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0a6a64c9
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Andreas Müller
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highestStatus = endemicState;
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b9cdcc88
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Andreas Müller
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state.setEndemic(true);
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fb3dec85
|
Andreas Müller
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}else if(isMinus(endemicStr)){
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UUID endemicUuid = state.getTransformer().getPresenceTermUuid("-E");
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PresenceAbsenceTerm endemicState = getPresenceTerm(state, endemicUuid, null, null, null, false);
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result.add(endemicState);
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0a6a64c9
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Andreas Müller
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checkAbsentHighestState(highestStatus, line, "endemic", false);
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c9f78619
|
Andreas Müller
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}else if(endemicStr.equals("?")){
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UUID endemicDoubtfulUuid = state.getTransformer().getPresenceTermUuid("?E");
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PresenceAbsenceTerm endemicState = getPresenceTerm(state, endemicDoubtfulUuid, null, null, null, false);
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result.add(endemicState);
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checkAbsentHighestState(highestStatus, line, "endemic", false);
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ede5c502
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Andreas Müller
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}else{
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fb3dec85
|
Andreas Müller
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logger.warn(line + "Endemic not recognized: " + endemicStr);
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ede5c502
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Andreas Müller
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}
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| 164 |
fb3dec85
|
Andreas Müller
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}
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if (indigenousStr != null){
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if(indigenousStr.equals("+")){
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b9cdcc88
|
Andreas Müller
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PresenceAbsenceTerm indigenousState = state.getTransformer().getPresenceTermByKey("Ind.");
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// PresenceAbsenceTerm indigenousState = getPresenceTerm(state, indigenousUuid, null, null, null, false);
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| 169 |
fb3dec85
|
Andreas Müller
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result.add(indigenousState);
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| 170 |
0a6a64c9
|
Andreas Müller
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highestStatus = highestStatus != null ? highestStatus : indigenousState;
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| 171 |
fb3dec85
|
Andreas Müller
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}else if(isMinus(indigenousStr)){
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| 172 |
0a6a64c9
|
Andreas Müller
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PresenceAbsenceTerm indigenousState = state.getTransformer().getPresenceTermByKey("-Ind.");
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result.add(indigenousState);
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checkAbsentHighestState(highestStatus, line, "indigenous", false);
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| 175 |
fb3dec85
|
Andreas Müller
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}else if(indigenousStr.equals("?")){
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| 176 |
b9cdcc88
|
Andreas Müller
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PresenceAbsenceTerm indigenousDoubtState = state.getTransformer().getPresenceTermByKey("?Ind.");
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// PresenceAbsenceTerm indigenousDoubtState = getPresenceTerm(state, indigenousDoubtUuid, null, null, null, false);
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fb3dec85
|
Andreas Müller
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result.add(indigenousDoubtState);
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0a6a64c9
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Andreas Müller
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checkAbsentHighestState(highestStatus, line, "indigenous", true);
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ede5c502
|
Andreas Müller
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}else{
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fb3dec85
|
Andreas Müller
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logger.warn(line + "Indigenous not recognized: " + indigenousStr);
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}
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}
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if(indigenousDoubtStr != null){
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| 185 |
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if(indigenousDoubtStr.equals("D")){
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| 186 |
b9cdcc88
|
Andreas Müller
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PresenceAbsenceTerm doubtIndigenousState = state.getTransformer().getPresenceTermByKey("Ind.?");
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// PresenceAbsenceTerm doubtIndigenousState = getPresenceTerm(state, doubtIndigenousUuid, null, null, null, false);
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result.add(doubtIndigenousState);
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highestStatus = highestStatus != null ? highestStatus : doubtIndigenousState;
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| 190 |
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}else if(isMinus(indigenousDoubtStr)){
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| 191 |
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UUID doubtIndigenousErrorUuid = state.getTransformer().getPresenceTermUuid("-Ind.?");
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| 192 |
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PresenceAbsenceTerm doubtIndigenousErrorState = getPresenceTerm(state, doubtIndigenousErrorUuid, null, null, null, false);
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result.add(doubtIndigenousErrorState);
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checkAbsentHighestState(highestStatus, line, "doubtfully indigenous", true);
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| 195 |
fb3dec85
|
Andreas Müller
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}else{
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| 196 |
b9cdcc88
|
Andreas Müller
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logger.warn(line + "doubtfully indigenous not recognized: " + indigenousDoubtStr);
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| 197 |
fb3dec85
|
Andreas Müller
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}
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| 198 |
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}
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| 199 |
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if(naturalisedStr != null){
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| 200 |
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if(naturalisedStr.equals("N")){
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| 201 |
0a6a64c9
|
Andreas Müller
|
PresenceAbsenceTerm haturalizedState = state.getTransformer().getPresenceTermByKey("Nat.");
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| 202 |
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result.add(haturalizedState);
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| 203 |
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highestStatus = highestStatus != null ? highestStatus : haturalizedState;
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| 204 |
fb3dec85
|
Andreas Müller
|
}else if(isMinus(naturalisedStr)){
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| 205 |
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UUID naturalisedErrorUuid = state.getTransformer().getPresenceTermUuid("-Nat.");
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| 206 |
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PresenceAbsenceTerm naturalisedErrorState = getPresenceTerm(state, naturalisedErrorUuid, null, null, null, false);
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| 207 |
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result.add(naturalisedErrorState);
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| 208 |
0a6a64c9
|
Andreas Müller
|
checkAbsentHighestState(highestStatus, line, "naturalized", false);
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| 209 |
fb3dec85
|
Andreas Müller
|
}else if(naturalisedStr.equals("?")){
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| 210 |
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UUID naturalisedDoubtUuid = state.getTransformer().getPresenceTermUuid("?Nat.");
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| 211 |
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PresenceAbsenceTerm naturalisedDoubtState = getPresenceTerm(state, naturalisedDoubtUuid, null, null, null, false);
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| 212 |
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result.add(naturalisedDoubtState);
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| 213 |
0a6a64c9
|
Andreas Müller
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checkAbsentHighestState(highestStatus, line, "naturalized", true);
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| 214 |
fb3dec85
|
Andreas Müller
|
}else{
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| 215 |
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logger.warn(line + "Naturalized not recognized: " + naturalisedStr);
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| 216 |
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}
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| 217 |
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}
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| 218 |
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if(dudStr != null){
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| 219 |
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if(dudStr.equals("P")){
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| 220 |
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UUID dudUuid = state.getTransformer().getPresenceTermUuid("Dud.");
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| 221 |
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PresenceAbsenceTerm dudState = getPresenceTerm(state, dudUuid, null, null, null, false);
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| 222 |
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result.add(dudState);
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| 223 |
0a6a64c9
|
Andreas Müller
|
highestStatus = highestStatus != null ? highestStatus : dudState;
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| 224 |
fb3dec85
|
Andreas Müller
|
}else if(isMinus(dudStr)){
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| 225 |
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UUID nonNativeErrorUuid = state.getTransformer().getPresenceTermUuid("-Dud.");
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| 226 |
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PresenceAbsenceTerm nonNativeErrorState = getPresenceTerm(state, nonNativeErrorUuid, null, null, null, false);
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| 227 |
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result.add(nonNativeErrorState);
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| 228 |
0a6a64c9
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Andreas Müller
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checkAbsentHighestState(highestStatus, line, "non-native and doubtfully naturalised", false);
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| 229 |
fb3dec85
|
Andreas Müller
|
}else if(dudStr.equals("?")){
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| 230 |
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UUID naturalisedDoubtUuid = state.getTransformer().getPresenceTermUuid("?Dud.");
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| 231 |
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PresenceAbsenceTerm naturalisedDoubtState = getPresenceTerm(state, naturalisedDoubtUuid, null, null, null, false);
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| 232 |
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result.add(naturalisedDoubtState);
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| 233 |
0a6a64c9
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Andreas Müller
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checkAbsentHighestState(highestStatus, line, "non-native and doubtfully naturalised", true);
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| 234 |
fb3dec85
|
Andreas Müller
|
}else{
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| 235 |
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logger.warn(line + "non-native and doubtfully naturalised not recognized: " + dudStr);
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| 236 |
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}
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| 237 |
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}
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| 238 |
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if(advStr != null){
|
| 239 |
|
|
if(advStr.equals("A")){
|
| 240 |
b9cdcc88
|
Andreas Müller
|
PresenceAbsenceTerm advState = state.getTransformer().getPresenceTermByKey("Adv.");
|
| 241 |
|
|
// PresenceAbsenceTerm advState = getPresenceTerm(state, advUuid, null, null, null, false);
|
| 242 |
fb3dec85
|
Andreas Müller
|
result.add(advState);
|
| 243 |
0a6a64c9
|
Andreas Müller
|
highestStatus = highestStatus != null ? highestStatus : advState;
|
| 244 |
fb3dec85
|
Andreas Müller
|
}else if(isMinus(advStr)){
|
| 245 |
|
|
UUID advUuid = state.getTransformer().getPresenceTermUuid("-Adv.");
|
| 246 |
|
|
PresenceAbsenceTerm advState = getPresenceTerm(state, advUuid, null, null, null, false);
|
| 247 |
|
|
result.add(advState);
|
| 248 |
0a6a64c9
|
Andreas Müller
|
checkAbsentHighestState(highestStatus, line, "adventive", false);
|
| 249 |
b9cdcc88
|
Andreas Müller
|
}else if(advStr.equals("(A)")){
|
| 250 |
|
|
UUID rareCasualUuid = state.getTransformer().getPresenceTermUuid("(A)");
|
| 251 |
|
|
PresenceAbsenceTerm rareCasual = getPresenceTerm(state, rareCasualUuid, null, null, null, false);
|
| 252 |
|
|
result.add(rareCasual);
|
| 253 |
fb3dec85
|
Andreas Müller
|
}else{
|
| 254 |
|
|
logger.warn(line + "'adventive (casual) alien' not recognized: " + advStr);
|
| 255 |
|
|
}
|
| 256 |
|
|
}else if(cultStr != null){
|
| 257 |
|
|
if (! (cultStr.matches("(C|\\(C\\)|\\?|–)"))){
|
| 258 |
|
|
logger.warn("'cultivated' not recognized: " + cultStr);
|
| 259 |
|
|
}else if(cultStr.equals("C")){
|
| 260 |
|
|
PresenceAbsenceTerm cultivatedState = state.getTransformer().getPresenceTermByKey("Cult.");
|
| 261 |
|
|
result.add(cultivatedState);
|
| 262 |
0a6a64c9
|
Andreas Müller
|
highestStatus = highestStatus != null ? highestStatus : cultivatedState;
|
| 263 |
fb3dec85
|
Andreas Müller
|
}else if(cultStr.equals("?")){
|
| 264 |
|
|
PresenceAbsenceTerm cultivatedState = state.getTransformer().getPresenceTermByKey("?Cult.");
|
| 265 |
|
|
result.add(cultivatedState);
|
| 266 |
0a6a64c9
|
Andreas Müller
|
checkAbsentHighestState(highestStatus, line, "cultivated", true);
|
| 267 |
fb3dec85
|
Andreas Müller
|
}else if(cultStr.equals("(C)")){
|
| 268 |
|
|
UUID ocassualCultUuid = state.getTransformer().getPresenceTermUuid("(C)");
|
| 269 |
|
|
PresenceAbsenceTerm cultivatedState = getPresenceTerm(state, ocassualCultUuid, null, null, null, false);
|
| 270 |
|
|
result.add(cultivatedState);
|
| 271 |
|
|
}else if(isMinus(cultStr)){
|
| 272 |
|
|
PresenceAbsenceTerm cultivatedState = state.getTransformer().getPresenceTermByKey("-Cult.");
|
| 273 |
|
|
result.add(cultivatedState);
|
| 274 |
0a6a64c9
|
Andreas Müller
|
checkAbsentHighestState(highestStatus, line, "cultivated", false);
|
| 275 |
fb3dec85
|
Andreas Müller
|
}else{
|
| 276 |
|
|
logger.warn(line + "'cultivated' not recognized: " + cultStr);
|
| 277 |
ede5c502
|
Andreas Müller
|
}
|
| 278 |
|
|
}
|
| 279 |
0a6a64c9
|
Andreas Müller
|
state.setHighestStatusForTaxon(highestStatus);
|
| 280 |
fb3dec85
|
Andreas Müller
|
return result;
|
| 281 |
|
|
}
|
| 282 |
|
|
|
| 283 |
|
|
|
| 284 |
0a6a64c9
|
Andreas Müller
|
/**
|
| 285 |
|
|
* @param highestStatus
|
| 286 |
|
|
* @param line
|
| 287 |
|
|
*/
|
| 288 |
|
|
private void checkAbsentHighestState(PresenceAbsenceTerm highestStatus, String line, String stateLabel, boolean doubtful) {
|
| 289 |
b9cdcc88
|
Andreas Müller
|
//can be removed, highest status is not used anymore
|
| 290 |
0a6a64c9
|
Andreas Müller
|
if (highestStatus == null){
|
| 291 |
|
|
String absentStr = doubtful ? "doubtful" : "absent";
|
| 292 |
b9cdcc88
|
Andreas Müller
|
logger.info(line + "Highest cuban state is " + absentStr + " " + stateLabel);
|
| 293 |
0a6a64c9
|
Andreas Müller
|
}
|
| 294 |
|
|
|
| 295 |
|
|
}
|
| 296 |
|
|
|
| 297 |
|
|
|
| 298 |
fb3dec85
|
Andreas Müller
|
/**
|
| 299 |
|
|
* @param indigenousStr
|
| 300 |
|
|
* @return
|
| 301 |
|
|
*/
|
| 302 |
|
|
private boolean isMinus(String str) {
|
| 303 |
b9cdcc88
|
Andreas Müller
|
return str.equals("-") || str.equals("–") || str.equals("‒");
|
| 304 |
ede5c502
|
Andreas Müller
|
}
|
| 305 |
|
|
|
| 306 |
|
|
|
| 307 |
|
|
/**
|
| 308 |
|
|
* @param indigenousStr
|
| 309 |
|
|
* @return
|
| 310 |
|
|
*/
|
| 311 |
fb3dec85
|
Andreas Müller
|
private boolean checkPlusMinusDoubt(String str) {
|
| 312 |
|
|
return str.equals("+") || isMinus(str)|| str.equals("?");
|
| 313 |
ede5c502
|
Andreas Müller
|
}
|
| 314 |
|
|
|
| 315 |
|
|
|
| 316 |
|
|
/**
|
| 317 |
|
|
* @param indigenousStr
|
| 318 |
|
|
* @param indigenousDoubtStr
|
| 319 |
|
|
* @param naturalisedStr
|
| 320 |
|
|
* @param dudStr
|
| 321 |
|
|
* @param advStr
|
| 322 |
|
|
* @param cultStr
|
| 323 |
|
|
*/
|
| 324 |
|
|
private boolean checkAllNull(String ... others) {
|
| 325 |
|
|
for (String other : others){
|
| 326 |
|
|
if (other != null){
|
| 327 |
|
|
return false;
|
| 328 |
|
|
}
|
| 329 |
|
|
}
|
| 330 |
|
|
return true;
|
| 331 |
|
|
}
|
| 332 |
|
|
|
| 333 |
|
|
|
| 334 |
fb3dec85
|
Andreas Müller
|
private static final String acceptedRegExStr = "\\(([^\\[\\]“”]{6,})\\)";
|
| 335 |
|
|
// String heterotypicRegExStr2 = "([^\\(]{5,}" +"(\\(.+\\))?" + "[^\\)\\(]{2,})" +
|
| 336 |
|
|
// + "(\\((.{6,})\\))?";
|
| 337 |
|
|
private static final String heterotypicRegExStr = "([^\\(\\[\\]“”]{5,})"
|
| 338 |
|
|
+"(\\((.{6,})\\))?";
|
| 339 |
|
|
private static final String heterotypicRegExStr_TEST = "([^\\(]{5,}" +"(\\(.+\\))?" + "[^\\)\\(]{2,})"
|
| 340 |
|
|
+"(\\((.{6,})\\))?";
|
| 341 |
b0b606e6
|
Andreas Müller
|
private static final String auctRegExStr = "auct\\."
|
| 342 |
b9cdcc88
|
Andreas Müller
|
+"((\\sFC(\\-S)?(\\s&\\sA&S)?)|(\\sA&S)|\\sSagra|\\sCombs|\\sBritton|\\sGriseb\\.(\\sFC-S|\\sA&S)?|\\sWright"
|
| 343 |
c9f78619
|
Andreas Müller
|
+ "|\\sHammer|\\sEngl\\.||\\sMaza|\\sMiers|\\sRoig|\\sBorhidi|\\sFRC|\\sCoL"
|
| 344 |
|
|
+ "|\\sAckerman|\\sMújica|\\sDíaz|\\sUrb\\.)?(\\s+p\\.\\s*p\\.)?";
|
| 345 |
|
|
|
| 346 |
|
|
|
| 347 |
5cdaf78e
|
Andreas Müller
|
private static final String missapliedRegExStr = "(\\?\\s)?“(.*{5,})”\\s+(" + auctRegExStr + "|sensu\\s+.{2,})";
|
| 348 |
c9f78619
|
Andreas Müller
|
private static final String sphalmRegExStr = "“(.*{5,})”\\s+((FC-S|A&S)\\s)?sphalm\\.(\\s(FC(-S)?|A&S|inval\\.))?";
|
| 349 |
|
|
private static final String nomInvalRegExStr = "“(.*{5,})”\\s+nom\\.\\s+inval\\.(\\s(West|Moldenke|FC|Jacq.))?";
|
| 350 |
fb3dec85
|
Andreas Müller
|
private static final String homonymRegExStr = "\\s*(\\[.*\\])*\\s*";
|
| 351 |
|
|
|
| 352 |
|
|
private static final Pattern acceptedRegEx = Pattern.compile(acceptedRegExStr + homonymRegExStr);
|
| 353 |
|
|
private static final Pattern heterotypicRegEx = Pattern.compile(heterotypicRegExStr + homonymRegExStr);
|
| 354 |
|
|
private static final Pattern missapliedRegEx = Pattern.compile(missapliedRegExStr);
|
| 355 |
|
|
private static final Pattern nomInvalRegEx = Pattern.compile(nomInvalRegExStr);
|
| 356 |
c9f78619
|
Andreas Müller
|
private static final Pattern sphalmRegEx = Pattern.compile(sphalmRegExStr);
|
| 357 |
fb3dec85
|
Andreas Müller
|
|
| 358 |
ede5c502
|
Andreas Müller
|
/**
|
| 359 |
|
|
* @param record
|
| 360 |
|
|
* @param state
|
| 361 |
|
|
* @param taxon
|
| 362 |
|
|
*/
|
| 363 |
b9cdcc88
|
Andreas Müller
|
private void makeSynonyms(HashMap<String, String> record, CubaImportState state, boolean isFirstSynonym) {
|
| 364 |
fb3dec85
|
Andreas Müller
|
// boolean forAccepted = true;
|
| 365 |
|
|
String synonymStr = record.get("Syn.");
|
| 366 |
|
|
String line = state.getCurrentLine() + ": ";
|
| 367 |
|
|
|
| 368 |
b9cdcc88
|
Andreas Müller
|
|
| 369 |
fb3dec85
|
Andreas Müller
|
if (synonymStr == null){
|
| 370 |
|
|
//TODO test that this is not a synonym only line
|
| 371 |
|
|
return;
|
| 372 |
|
|
}
|
| 373 |
b9cdcc88
|
Andreas Müller
|
|
| 374 |
|
|
if (state.getCurrentTaxon() == null){
|
| 375 |
|
|
logger.error(line + "Current taxon is null for synonym");
|
| 376 |
|
|
return;
|
| 377 |
|
|
}
|
| 378 |
|
|
|
| 379 |
|
|
|
| 380 |
fb3dec85
|
Andreas Müller
|
synonymStr = synonymStr.trim();
|
| 381 |
b9cdcc88
|
Andreas Müller
|
synonymStr = synonymStr.replace("[taxon]", "[infraspec.]");
|
| 382 |
fb3dec85
|
Andreas Müller
|
|
| 383 |
|
|
// String heterotypicRegExStr = "([^\\(]{5,}(\\(.+\\))?[^\\)\\(]{2,})(\\((.{6,})\\))?";
|
| 384 |
|
|
// String heterotypicRegExStr = "([^\\(]{5,})(\\((.{6,})\\))?";
|
| 385 |
|
|
|
| 386 |
|
|
// Pattern heterotypicRegEx = Pattern.compile(heterotypicRegExStr + homonymRegExStr);
|
| 387 |
|
|
|
| 388 |
b9cdcc88
|
Andreas Müller
|
|
| 389 |
fb3dec85
|
Andreas Müller
|
Matcher missapliedMatcher = missapliedRegEx.matcher(synonymStr);
|
| 390 |
|
|
Matcher nomInvalMatcher = nomInvalRegEx.matcher(synonymStr);
|
| 391 |
|
|
Matcher acceptedMatcher = acceptedRegEx.matcher(synonymStr);
|
| 392 |
|
|
Matcher heterotypicMatcher = heterotypicRegEx.matcher(synonymStr);
|
| 393 |
c9f78619
|
Andreas Müller
|
Matcher sphalmMatcher = sphalmRegEx.matcher(synonymStr);
|
| 394 |
fb3dec85
|
Andreas Müller
|
|
| 395 |
7d882578
|
Andreas Müller
|
List<IBotanicalName> homonyms = new ArrayList<>();
|
| 396 |
fb3dec85
|
Andreas Müller
|
if (missapliedMatcher.matches()){
|
| 397 |
5cdaf78e
|
Andreas Müller
|
boolean doubtful = missapliedMatcher.group(1) != null;
|
| 398 |
|
|
String firstPart = missapliedMatcher.group(2);
|
| 399 |
86536e03
|
Andreas Müller
|
IBotanicalName name = (IBotanicalName)nameParser.parseSimpleName(firstPart, state.getConfig().getNomenclaturalCode(), Rank.SPECIES());
|
| 400 |
b9cdcc88
|
Andreas Müller
|
name.addSource(makeOriginalSource(state));
|
| 401 |
fb3dec85
|
Andreas Müller
|
|
| 402 |
5cdaf78e
|
Andreas Müller
|
String secondPart = missapliedMatcher.group(3);
|
| 403 |
fb3dec85
|
Andreas Müller
|
Taxon misappliedNameTaxon = Taxon.NewInstance(name, null);
|
| 404 |
b9cdcc88
|
Andreas Müller
|
misappliedNameTaxon.addSource(makeOriginalSource(state));
|
| 405 |
5cdaf78e
|
Andreas Müller
|
misappliedNameTaxon.setDoubtful(doubtful);
|
| 406 |
fb3dec85
|
Andreas Müller
|
if (secondPart.startsWith("sensu")){
|
| 407 |
|
|
secondPart = secondPart.substring(5).trim();
|
| 408 |
|
|
if (secondPart.contains(" ")){
|
| 409 |
5cdaf78e
|
Andreas Müller
|
logger.warn(line + "CHECK: Second part contains more than 1 word. Check if this is correct: " + secondPart);
|
| 410 |
fb3dec85
|
Andreas Müller
|
}
|
| 411 |
8422c0cd
|
Andreas Müller
|
Reference sensu = ReferenceFactory.newGeneric();
|
| 412 |
fb3dec85
|
Andreas Müller
|
Team team = Team.NewTitledInstance(secondPart, null);
|
| 413 |
|
|
sensu.setAuthorship(team);
|
| 414 |
|
|
misappliedNameTaxon.setSec(sensu);
|
| 415 |
b0b606e6
|
Andreas Müller
|
}else if (secondPart.matches(auctRegExStr)){
|
| 416 |
fb3dec85
|
Andreas Müller
|
secondPart = secondPart.replace("p. p.", "p.p.");
|
| 417 |
|
|
misappliedNameTaxon.setAppendedPhrase(secondPart);
|
| 418 |
|
|
}else{
|
| 419 |
|
|
logger.warn(line + "Misapplied second part not recognized: " + secondPart);
|
| 420 |
|
|
}
|
| 421 |
|
|
//TODO
|
| 422 |
8422c0cd
|
Andreas Müller
|
Reference relRef = null;
|
| 423 |
fb3dec85
|
Andreas Müller
|
state.getCurrentTaxon().addMisappliedName(misappliedNameTaxon, relRef, null);
|
| 424 |
|
|
}else if (nomInvalMatcher.matches()){
|
| 425 |
|
|
String firstPart = nomInvalMatcher.group(1);
|
| 426 |
c9f78619
|
Andreas Müller
|
String afterInval = nomInvalMatcher.group(2);
|
| 427 |
|
|
if (StringUtils.isNotBlank(afterInval)){
|
| 428 |
|
|
logger.warn(state.getCurrentLine() + ": After inval to be implemented: " + afterInval);
|
| 429 |
|
|
}
|
| 430 |
86536e03
|
Andreas Müller
|
TaxonName name = (TaxonName)nameParser.parseSimpleName(firstPart, state.getConfig().getNomenclaturalCode(), Rank.SPECIES());
|
| 431 |
b9cdcc88
|
Andreas Müller
|
name.addSource(makeOriginalSource(state));
|
| 432 |
fb3dec85
|
Andreas Müller
|
NomenclaturalStatus status = NomenclaturalStatus.NewInstance( NomenclaturalStatusType.INVALID());
|
| 433 |
|
|
name.addStatus(status);
|
| 434 |
3ef2e1bd
|
Andreas Müller
|
Synonym syn = state.getCurrentTaxon().addSynonymName(name, SynonymType.SYNONYM_OF());
|
| 435 |
|
|
syn.addSource(makeOriginalSource(state));
|
| 436 |
c9f78619
|
Andreas Müller
|
}else if (sphalmMatcher.matches()){
|
| 437 |
|
|
String firstPart = sphalmMatcher.group(1);
|
| 438 |
|
|
String sphalmPart = synonymStr.replace(firstPart, "").replace("“","").replace("”","").trim();
|
| 439 |
86536e03
|
Andreas Müller
|
TaxonName name = (TaxonName)nameParser.parseSimpleName(firstPart, state.getConfig().getNomenclaturalCode(), Rank.SPECIES());
|
| 440 |
c9f78619
|
Andreas Müller
|
// NomenclaturalStatus status = NomenclaturalStatus.NewInstance( NomenclaturalStatusType.INVALID());
|
| 441 |
|
|
// name.addStatus(status);
|
| 442 |
b9cdcc88
|
Andreas Müller
|
name.addSource(makeOriginalSource(state));
|
| 443 |
3ef2e1bd
|
Andreas Müller
|
Synonym syn = state.getCurrentTaxon().addSynonymName(name, SynonymType.SYNONYM_OF());
|
| 444 |
|
|
syn.setAppendedPhrase(sphalmPart);
|
| 445 |
|
|
syn.setSec(null);
|
| 446 |
|
|
syn.addSource(makeOriginalSource(state));
|
| 447 |
fb3dec85
|
Andreas Müller
|
}else if (acceptedMatcher.matches()){
|
| 448 |
|
|
String firstPart = acceptedMatcher.group(1);
|
| 449 |
|
|
String homonymPart = acceptedMatcher.groupCount() < 2 ? null : acceptedMatcher.group(2);
|
| 450 |
7d882578
|
Andreas Müller
|
List<IBotanicalName> list = handleHomotypicGroup(firstPart, state, state.getCurrentTaxon().getName(), false, homonyms, homonymPart, false);
|
| 451 |
b9cdcc88
|
Andreas Müller
|
checkFirstSynonym(state, list, isFirstSynonym, synonymStr, false);
|
| 452 |
fb3dec85
|
Andreas Müller
|
}else if(heterotypicMatcher.matches()){
|
| 453 |
|
|
String firstPart = heterotypicMatcher.group(1).trim();
|
| 454 |
|
|
String secondPart = heterotypicMatcher.groupCount() < 3 ? null : heterotypicMatcher.group(3);
|
| 455 |
|
|
String homonymPart = heterotypicMatcher.groupCount() < 4 ? null : heterotypicMatcher.group(4);
|
| 456 |
|
|
boolean isDoubtful = firstPart.matches("^\\?\\s*.*");
|
| 457 |
c9f78619
|
Andreas Müller
|
firstPart = replaceHomonIlleg(firstPart);
|
| 458 |
|
|
boolean isHomonym = firstPart.matches(".*" + HOMONYM_MARKER);
|
| 459 |
86536e03
|
Andreas Müller
|
TaxonName synName = (TaxonName)makeName(state, firstPart);
|
| 460 |
fb3dec85
|
Andreas Müller
|
if (synName.isProtectedTitleCache()){
|
| 461 |
b9cdcc88
|
Andreas Müller
|
logger.warn(line + "Heterotypic base synonym could not be parsed correctly: " + firstPart);
|
| 462 |
fb3dec85
|
Andreas Müller
|
}
|
| 463 |
|
|
if (isHomonym){
|
| 464 |
|
|
homonyms.add(synName);
|
| 465 |
|
|
}
|
| 466 |
3ef2e1bd
|
Andreas Müller
|
Synonym syn = state.getCurrentTaxon().addHeterotypicSynonymName(synName);
|
| 467 |
|
|
syn.setDoubtful(isDoubtful);
|
| 468 |
|
|
syn.addSource(makeOriginalSource(state));
|
| 469 |
7d882578
|
Andreas Müller
|
List<IBotanicalName> list = handleHomotypicGroup(secondPart, state, synName, true, homonyms, homonymPart, isDoubtful);
|
| 470 |
b9cdcc88
|
Andreas Müller
|
checkFirstSynonym(state, list, isFirstSynonym, synonymStr, true);
|
| 471 |
|
|
|
| 472 |
|
|
}else if (isSpecialHeterotypic(synonymStr)){
|
| 473 |
86536e03
|
Andreas Müller
|
TaxonName synName = (TaxonName)makeName(state, synonymStr);
|
| 474 |
b9cdcc88
|
Andreas Müller
|
if (synName.isProtectedTitleCache()){
|
| 475 |
|
|
logger.warn(line + "Special heterotypic synonym could not be parsed correctly:" + synonymStr);
|
| 476 |
|
|
}
|
| 477 |
3ef2e1bd
|
Andreas Müller
|
Synonym syn = state.getCurrentTaxon().addHeterotypicSynonymName(synName);
|
| 478 |
|
|
syn.addSource(makeOriginalSource(state));
|
| 479 |
fb3dec85
|
Andreas Müller
|
}else{
|
| 480 |
|
|
logger.warn(line + "Synonym entry does not match: " + synonymStr);
|
| 481 |
|
|
}
|
| 482 |
|
|
}
|
| 483 |
|
|
|
| 484 |
b9cdcc88
|
Andreas Müller
|
/**
|
| 485 |
|
|
* @param state
|
| 486 |
|
|
* @param list
|
| 487 |
|
|
* @param isFirstSynonym
|
| 488 |
|
|
* @param synonymStr
|
| 489 |
|
|
* @param b
|
| 490 |
|
|
*/
|
| 491 |
7d882578
|
Andreas Müller
|
private void checkFirstSynonym(CubaImportState state, List<IBotanicalName> list, boolean isFirstSynonym, String synonymStr, boolean isHeterotypicMatcher) {
|
| 492 |
b9cdcc88
|
Andreas Müller
|
if (!isFirstSynonym){
|
| 493 |
|
|
return;
|
| 494 |
|
|
}
|
| 495 |
|
|
String line = state.getCurrentLine() + ": ";
|
| 496 |
7d882578
|
Andreas Müller
|
IBotanicalName currentName = isHeterotypicMatcher? (IBotanicalName)state.getCurrentTaxon().getName(): list.get(0);
|
| 497 |
b9cdcc88
|
Andreas Müller
|
boolean currentHasBasionym = currentName.getBasionymAuthorship() != null;
|
| 498 |
7d882578
|
Andreas Müller
|
IBotanicalName firstSynonym = isHeterotypicMatcher ? list.get(0): list.get(1);
|
| 499 |
b9cdcc88
|
Andreas Müller
|
// if (list.size() <= 1){
|
| 500 |
|
|
// logger.error(line + "homotypic list size is 1 but shouldn't");
|
| 501 |
|
|
// return;
|
| 502 |
|
|
// }
|
| 503 |
|
|
if (isHeterotypicMatcher && currentHasBasionym){
|
| 504 |
|
|
logger.error(line + "Current taxon (" + currentName.getTitleCache() + ") has basionym author but has no homotypic basionym , but : " + synonymStr);
|
| 505 |
|
|
}else if (isHeterotypicMatcher){
|
| 506 |
|
|
//first synonym must not have a basionym author
|
| 507 |
|
|
if (firstSynonym.getBasionymAuthorship() != null){
|
| 508 |
|
|
logger.error(line + "Current taxon (" + currentName.getTitleCache() + ") has no basionym but first synonym requires basionym : " + synonymStr);
|
| 509 |
|
|
}
|
| 510 |
|
|
}else{ //isAcceptedMatcher
|
| 511 |
|
|
if (currentHasBasionym){
|
| 512 |
|
|
if (! matchAuthor(currentName.getBasionymAuthorship(), firstSynonym.getCombinationAuthorship())){
|
| 513 |
|
|
logger.info(line + "Current basionym author and first synonym combination author do not match: " + currentName.getTitleCache() + "<->" + firstSynonym.getTitleCache());
|
| 514 |
|
|
}
|
| 515 |
|
|
}else{
|
| 516 |
|
|
if (! matchAuthor(currentName.getCombinationAuthorship(), firstSynonym.getBasionymAuthorship())){
|
| 517 |
|
|
logger.info(line + "Current combination author and first synonym basionym author do not match: " + currentName.getTitleCache() + "<->" + firstSynonym.getTitleCache());
|
| 518 |
|
|
}
|
| 519 |
|
|
}
|
| 520 |
|
|
}
|
| 521 |
|
|
|
| 522 |
|
|
}
|
| 523 |
|
|
|
| 524 |
|
|
|
| 525 |
|
|
/**
|
| 526 |
|
|
* @param synonymStr
|
| 527 |
|
|
* @return
|
| 528 |
|
|
*/
|
| 529 |
|
|
private boolean isSpecialHeterotypic(String synonymStr) {
|
| 530 |
|
|
if (synonymStr == null){
|
| 531 |
|
|
return false;
|
| 532 |
|
|
}else if (synonymStr.equals("Rhynchospora prenleloupiana (‘prenteloupiana’) Boeckeler")){
|
| 533 |
|
|
return true;
|
| 534 |
|
|
}else if (synonymStr.equals("Psidium longipes var. orbiculare (O.Berg) McVaugh")){
|
| 535 |
|
|
return true;
|
| 536 |
|
|
}
|
| 537 |
|
|
return false;
|
| 538 |
|
|
}
|
| 539 |
|
|
|
| 540 |
|
|
|
| 541 |
|
|
/**
|
| 542 |
|
|
* @param areaKey
|
| 543 |
|
|
* @param record
|
| 544 |
|
|
* @param state
|
| 545 |
|
|
* @param taxon
|
| 546 |
|
|
*/
|
| 547 |
|
|
private void makeSingleProvinceDistribution(String areaKey,
|
| 548 |
|
|
HashMap<String, String> record,
|
| 549 |
|
|
CubaImportState state) {
|
| 550 |
|
|
try {
|
| 551 |
|
|
UUID areaUuid = state.getTransformer().getNamedAreaUuid(areaKey);
|
| 552 |
|
|
if (areaUuid == null){
|
| 553 |
|
|
logger.warn("Area not recognized: " + areaKey);
|
| 554 |
|
|
return;
|
| 555 |
|
|
}
|
| 556 |
|
|
if (record.get(areaKey)==null){
|
| 557 |
|
|
return; //no status defined
|
| 558 |
|
|
}
|
| 559 |
|
|
|
| 560 |
|
|
NamedArea area = getNamedArea(state, areaUuid, null, null, null, null, null);
|
| 561 |
|
|
if (area == null){
|
| 562 |
|
|
logger.warn(state.getCurrentLine() + ": Area not recognized: " + area);
|
| 563 |
|
|
}
|
| 564 |
|
|
TaxonDescription desc = getTaxonDescription(state.getCurrentTaxon(), false, true);
|
| 565 |
|
|
PresenceAbsenceTerm status = makeProvinceStatus(areaKey, record, state);
|
| 566 |
|
|
if (status == null){
|
| 567 |
|
|
logger.warn(state.getCurrentLine() + ": Province distribution status could not be defined: " + record.get(areaKey));
|
| 568 |
|
|
}
|
| 569 |
|
|
Distribution distribution = Distribution.NewInstance(area, status);
|
| 570 |
|
|
desc.addElement(distribution);
|
| 571 |
|
|
distribution.addSource(makeDescriptionSource(state));
|
| 572 |
|
|
} catch (UndefinedTransformerMethodException e) {
|
| 573 |
|
|
e.printStackTrace();
|
| 574 |
|
|
}
|
| 575 |
|
|
|
| 576 |
|
|
}
|
| 577 |
fb3dec85
|
Andreas Müller
|
|
| 578 |
|
|
|
| 579 |
|
|
/**
|
| 580 |
|
|
* @param synonymStr
|
| 581 |
|
|
* @param state
|
| 582 |
|
|
* @param homonyms
|
| 583 |
|
|
* @param homonymPart
|
| 584 |
|
|
* @param isDoubtful
|
| 585 |
|
|
* @param taxon
|
| 586 |
|
|
* @param homotypicalGroup
|
| 587 |
|
|
*/
|
| 588 |
7d882578
|
Andreas Müller
|
private List<IBotanicalName> handleHomotypicGroup(String homotypicStrOrig,
|
| 589 |
fb3dec85
|
Andreas Müller
|
CubaImportState state,
|
| 590 |
7d882578
|
Andreas Müller
|
IBotanicalName homotypicName,
|
| 591 |
fb3dec85
|
Andreas Müller
|
boolean isHeterotypic,
|
| 592 |
7d882578
|
Andreas Müller
|
List<IBotanicalName> homonyms,
|
| 593 |
fb3dec85
|
Andreas Müller
|
String homonymPart,
|
| 594 |
|
|
boolean isDoubtful) {
|
| 595 |
|
|
|
| 596 |
7d882578
|
Andreas Müller
|
List<IBotanicalName> homotypicNameList = new ArrayList<>();
|
| 597 |
b9cdcc88
|
Andreas Müller
|
homotypicNameList.add(homotypicName);
|
| 598 |
|
|
|
| 599 |
|
|
String homotypicStr = homotypicStrOrig;
|
| 600 |
fb3dec85
|
Andreas Müller
|
if (homotypicStr == null){
|
| 601 |
b9cdcc88
|
Andreas Müller
|
return homotypicNameList;
|
| 602 |
fb3dec85
|
Andreas Müller
|
}else if (homotypicStr.startsWith("(") && homotypicStr.endsWith("")){
|
| 603 |
|
|
homotypicStr = homotypicStr.substring(1, homotypicStr.length() - 1);
|
| 604 |
|
|
}
|
| 605 |
|
|
|
| 606 |
b9cdcc88
|
Andreas Müller
|
HomotypicalGroup homotypicGroup = homotypicName.getHomotypicalGroup();
|
| 607 |
fb3dec85
|
Andreas Müller
|
String[] splits = homotypicStr.split("\\s*,\\s*");
|
| 608 |
|
|
for (String split : splits){
|
| 609 |
c9f78619
|
Andreas Müller
|
split = replaceHomonIlleg(split);
|
| 610 |
|
|
boolean isHomonym = split.matches(".*" + HOMONYM_MARKER);
|
| 611 |
ea7deae0
|
Andreas Müller
|
TaxonName newName = (TaxonName)makeName(state, split);
|
| 612 |
b9cdcc88
|
Andreas Müller
|
newName.setHomotypicalGroup(homotypicGroup); //not really necessary as this is later set anyway
|
| 613 |
fb3dec85
|
Andreas Müller
|
if (newName.isProtectedTitleCache()){
|
| 614 |
|
|
logger.warn(state.getCurrentLine() + ": homotypic name part could not be parsed: " + split);
|
| 615 |
|
|
}
|
| 616 |
|
|
if (isHomonym){
|
| 617 |
|
|
homonyms.add(newName);
|
| 618 |
|
|
}
|
| 619 |
|
|
if (isHeterotypic){
|
| 620 |
3ef2e1bd
|
Andreas Müller
|
Synonym syn = state.getCurrentTaxon().addHeterotypicSynonymName(newName, null, null, homotypicGroup);
|
| 621 |
|
|
syn.setDoubtful(isDoubtful);
|
| 622 |
|
|
syn.addSource(makeOriginalSource(state));
|
| 623 |
fb3dec85
|
Andreas Müller
|
// newName.addBasionym(homotypicName);
|
| 624 |
|
|
}else{
|
| 625 |
3ef2e1bd
|
Andreas Müller
|
state.getCurrentTaxon().addHomotypicSynonymName(newName);
|
| 626 |
fb3dec85
|
Andreas Müller
|
}
|
| 627 |
b9cdcc88
|
Andreas Müller
|
handleBasionym(state, homotypicNameList, homonyms, newName);
|
| 628 |
|
|
homotypicNameList.add(newName);
|
| 629 |
fb3dec85
|
Andreas Müller
|
}
|
| 630 |
b9cdcc88
|
Andreas Müller
|
makeHomonyms(homonyms, homonymPart, state, homotypicGroup);
|
| 631 |
|
|
return homotypicNameList;
|
| 632 |
c9f78619
|
Andreas Müller
|
}
|
| 633 |
|
|
|
| 634 |
|
|
|
| 635 |
|
|
/**
|
| 636 |
|
|
* @param split
|
| 637 |
|
|
* @return
|
| 638 |
|
|
*/
|
| 639 |
|
|
private String replaceHomonIlleg(String split) {
|
| 640 |
|
|
String result = split.trim().replace("homon. illeg.", "nom. illeg. homon.").trim();
|
| 641 |
|
|
return result;
|
| 642 |
fb3dec85
|
Andreas Müller
|
}
|
| 643 |
|
|
|
| 644 |
|
|
|
| 645 |
|
|
/**
|
| 646 |
|
|
* @param homonyms
|
| 647 |
|
|
* @param homonymPart
|
| 648 |
|
|
* @param state
|
| 649 |
c9f78619
|
Andreas Müller
|
* @param currentBasionym
|
| 650 |
fb3dec85
|
Andreas Müller
|
*/
|
| 651 |
7d882578
|
Andreas Müller
|
private void makeHomonyms(List<IBotanicalName> homonyms, String homonymPartOrig, CubaImportState state,
|
| 652 |
b9cdcc88
|
Andreas Müller
|
HomotypicalGroup homotypicGroup) {
|
| 653 |
fb3dec85
|
Andreas Müller
|
String line = state.getCurrentLine() + ": ";
|
| 654 |
c9f78619
|
Andreas Müller
|
String homonymPart = homonymPartOrig == null ? "" : homonymPartOrig.trim();
|
| 655 |
fb3dec85
|
Andreas Müller
|
if (homonyms.isEmpty() && homonymPart.equals("")){
|
| 656 |
|
|
return;
|
| 657 |
|
|
}else if (homonymPart.equals("")){
|
| 658 |
|
|
logger.warn(line + "SynonymPart has homonyms but homonymPart is empty");
|
| 659 |
|
|
return;
|
| 660 |
|
|
}
|
| 661 |
|
|
homonymPart = homonymPart.substring(1, homonymPart.length() - 1);
|
| 662 |
|
|
String[] splits = homonymPart.split("\\]\\s*\\[");
|
| 663 |
|
|
if (splits.length != homonyms.size()){
|
| 664 |
c9f78619
|
Andreas Müller
|
if(homonyms.size() == 0 && splits.length >= 1){
|
| 665 |
b9cdcc88
|
Andreas Müller
|
handleSimpleBlockingNames(splits, state, homotypicGroup);
|
| 666 |
c9f78619
|
Andreas Müller
|
}else{
|
| 667 |
|
|
logger.warn(line + "Number of homonyms (" + homonyms.size() + ") and homonymParts ("+splits.length+") does not match");
|
| 668 |
|
|
}
|
| 669 |
fb3dec85
|
Andreas Müller
|
return;
|
| 670 |
|
|
}
|
| 671 |
|
|
int i = 0;
|
| 672 |
|
|
for (String split : splits){
|
| 673 |
|
|
split = split.replaceAll("^non\\s+", "");
|
| 674 |
86536e03
|
Andreas Müller
|
TaxonName newName = (TaxonName)makeName(state, split);
|
| 675 |
c9f78619
|
Andreas Müller
|
// BotanicalName newName = (BotanicalName)nameParser.parseReferencedName(split, state.getConfig().getNomenclaturalCode(), Rank.SPECIES());
|
| 676 |
fb3dec85
|
Andreas Müller
|
if (newName.isProtectedTitleCache()){
|
| 677 |
|
|
logger.warn(state.getCurrentLine() + ": homonym name could not be parsed: " + split);
|
| 678 |
|
|
}
|
| 679 |
b9cdcc88
|
Andreas Müller
|
homonyms.get(i).addRelationshipToName(newName, NameRelationshipType.LATER_HOMONYM(), null);
|
| 680 |
fb3dec85
|
Andreas Müller
|
i++;
|
| 681 |
|
|
}
|
| 682 |
|
|
}
|
| 683 |
|
|
|
| 684 |
c9f78619
|
Andreas Müller
|
/**
|
| 685 |
|
|
* @param homonymPart
|
| 686 |
|
|
* @param state
|
| 687 |
b9cdcc88
|
Andreas Müller
|
* @param homotypicGroup
|
| 688 |
c9f78619
|
Andreas Müller
|
*/
|
| 689 |
b9cdcc88
|
Andreas Müller
|
private void handleSimpleBlockingNames(String[] splitsi,
|
| 690 |
|
|
CubaImportState state,
|
| 691 |
|
|
HomotypicalGroup homotypicGroup) {
|
| 692 |
7d882578
|
Andreas Müller
|
List<IBotanicalName> replacementNameCandidates = new ArrayList<>();
|
| 693 |
c9f78619
|
Andreas Müller
|
for (String spliti : splitsi){
|
| 694 |
|
|
|
| 695 |
|
|
String split = spliti.replaceAll("^non\\s+", "");
|
| 696 |
86536e03
|
Andreas Müller
|
IBotanicalName newName = makeName(state, split);
|
| 697 |
c9f78619
|
Andreas Müller
|
if (newName.isProtectedTitleCache()){
|
| 698 |
|
|
logger.warn(state.getCurrentLine() + ": blocking name could not be parsed: " + split);
|
| 699 |
|
|
}
|
| 700 |
7d882578
|
Andreas Müller
|
Set<IBotanicalName> typifiedNames = (Set)homotypicGroup.getTypifiedNames();
|
| 701 |
|
|
Set<IBotanicalName> candidates = new HashSet<>();
|
| 702 |
|
|
for (IBotanicalName name : typifiedNames){
|
| 703 |
c9f78619
|
Andreas Müller
|
if (name.getGenusOrUninomial() != null && name.getGenusOrUninomial().equals(newName.getGenusOrUninomial())){
|
| 704 |
|
|
if (name.getStatus().isEmpty() || ! name.getStatus().iterator().next().getType().equals(NomenclaturalStatusType.ILLEGITIMATE())){
|
| 705 |
|
|
candidates.add(name);
|
| 706 |
|
|
}
|
| 707 |
|
|
}
|
| 708 |
|
|
}
|
| 709 |
|
|
if (candidates.size() == 1){
|
| 710 |
ea7deae0
|
Andreas Müller
|
TaxonName blockedName = (TaxonName)candidates.iterator().next();
|
| 711 |
b9cdcc88
|
Andreas Müller
|
newName.addRelationshipToName(blockedName, NameRelationshipType.BLOCKING_NAME_FOR(), null);
|
| 712 |
|
|
replacementNameCandidates.add(blockedName);
|
| 713 |
c9f78619
|
Andreas Müller
|
}else{
|
| 714 |
|
|
logger.warn(state.getCurrentLine() + ": Blocking name could not be handled. " + candidates.size() + " candidates.");
|
| 715 |
|
|
}
|
| 716 |
|
|
}
|
| 717 |
b9cdcc88
|
Andreas Müller
|
makeReplacedSynonymIfPossible(state, homotypicGroup, replacementNameCandidates);
|
| 718 |
|
|
}
|
| 719 |
|
|
|
| 720 |
|
|
/**
|
| 721 |
|
|
* @param homotypicGroup
|
| 722 |
|
|
* @param replacementNameCandidates
|
| 723 |
|
|
*/
|
| 724 |
|
|
private void makeReplacedSynonymIfPossible(CubaImportState state,
|
| 725 |
|
|
HomotypicalGroup homotypicGroup,
|
| 726 |
7d882578
|
Andreas Müller
|
List<IBotanicalName> replacementNameCandidates) {
|
| 727 |
b9cdcc88
|
Andreas Müller
|
String line = state.getCurrentLine() +": ";
|
| 728 |
86536e03
|
Andreas Müller
|
List<IBotanicalName> replacedCandidates = new ArrayList<>();
|
| 729 |
ea7deae0
|
Andreas Müller
|
for (TaxonName typifiedName : homotypicGroup.getTypifiedNames()){
|
| 730 |
86536e03
|
Andreas Müller
|
IBotanicalName candidate = typifiedName;
|
| 731 |
b9cdcc88
|
Andreas Müller
|
if (candidate.getBasionymAuthorship() == null){
|
| 732 |
|
|
if (candidate.getStatus().isEmpty()){
|
| 733 |
|
|
if (! replacementNameCandidates.contains(candidate)){
|
| 734 |
|
|
replacedCandidates.add(candidate);
|
| 735 |
|
|
}
|
| 736 |
|
|
}
|
| 737 |
|
|
}
|
| 738 |
|
|
}
|
| 739 |
|
|
if (replacedCandidates.size() == 1){
|
| 740 |
ea7deae0
|
Andreas Müller
|
TaxonName replacedSynonym = (TaxonName)replacedCandidates.iterator().next();
|
| 741 |
7d882578
|
Andreas Müller
|
for (IBotanicalName replacementName : replacementNameCandidates){
|
| 742 |
b9cdcc88
|
Andreas Müller
|
replacementName.addReplacedSynonym(replacedSynonym, null, null, null);
|
| 743 |
|
|
}
|
| 744 |
|
|
}else if (replacedCandidates.size() < 1){
|
| 745 |
|
|
logger.warn(line + "No replaced synonym candidate found");
|
| 746 |
|
|
}else{
|
| 747 |
|
|
logger.warn(line + "More than 1 ("+replacedCandidates.size()+") replaced synonym candidates found");
|
| 748 |
|
|
}
|
| 749 |
c9f78619
|
Andreas Müller
|
}
|
| 750 |
|
|
|
| 751 |
|
|
|
| 752 |
fb3dec85
|
Andreas Müller
|
/**
|
| 753 |
b9cdcc88
|
Andreas Müller
|
* @param homotypicGroup
|
| 754 |
fb3dec85
|
Andreas Müller
|
* @param newName
|
| 755 |
b9cdcc88
|
Andreas Müller
|
*/
|
| 756 |
7d882578
|
Andreas Müller
|
private void handleBasionym(CubaImportState state, List<IBotanicalName> homotypicNameList,
|
| 757 |
|
|
List<IBotanicalName> homonyms, IBotanicalName newName) {
|
| 758 |
|
|
for (IBotanicalName existingName : homotypicNameList){
|
| 759 |
b9cdcc88
|
Andreas Müller
|
if (existingName != newName){ //should not happen anymore, as new name is added later
|
| 760 |
|
|
boolean onlyIfNotYetExists = true;
|
| 761 |
|
|
createBasionymRelationIfPossible(state, existingName, newName, homonyms.contains(newName), onlyIfNotYetExists);
|
| 762 |
|
|
}
|
| 763 |
|
|
}
|
| 764 |
|
|
}
|
| 765 |
|
|
|
| 766 |
|
|
/**
|
| 767 |
|
|
* @param state
|
| 768 |
|
|
* @param name1
|
| 769 |
|
|
* @param name2
|
| 770 |
fb3dec85
|
Andreas Müller
|
* @return
|
| 771 |
|
|
*/
|
| 772 |
7d882578
|
Andreas Müller
|
private void createBasionymRelationIfPossible(CubaImportState state, IBotanicalName name1,
|
| 773 |
|
|
IBotanicalName name2,
|
| 774 |
b9cdcc88
|
Andreas Müller
|
boolean name2isHomonym, boolean onlyIfNotYetExists) {
|
| 775 |
ea7deae0
|
Andreas Müller
|
TaxonName basionymName = TaxonName.castAndDeproxy(name1);
|
| 776 |
|
|
TaxonName newCombination = TaxonName.castAndDeproxy(name2);
|
| 777 |
b9cdcc88
|
Andreas Müller
|
//exactly one name must have a basionym author
|
| 778 |
|
|
if (name1.getBasionymAuthorship() == null && name2.getBasionymAuthorship() == null
|
| 779 |
|
|
|| name1.getBasionymAuthorship() != null && name2.getBasionymAuthorship() != null){
|
| 780 |
|
|
return;
|
| 781 |
|
|
}
|
| 782 |
|
|
|
| 783 |
|
|
//switch order if necessary
|
| 784 |
|
|
if (! name2isHomonym && basionymName.getBasionymAuthorship() != null && newCombination.getBasionymAuthorship() == null){
|
| 785 |
86536e03
|
Andreas Müller
|
basionymName = TaxonName.castAndDeproxy(name2);
|
| 786 |
|
|
newCombination = TaxonName.castAndDeproxy(name1);
|
| 787 |
b9cdcc88
|
Andreas Müller
|
}
|
| 788 |
|
|
if (matchAuthor(basionymName.getCombinationAuthorship(), newCombination.getBasionymAuthorship())
|
| 789 |
6af76d56
|
Andreas Müller
|
&& BasionymRelationCreator.matchLastNamePart(basionymName, newCombination)){
|
| 790 |
b9cdcc88
|
Andreas Müller
|
newCombination.addBasionym(basionymName);
|
| 791 |
|
|
}else{
|
| 792 |
|
|
if ( (newCombination.getBasionyms().isEmpty() || ! onlyIfNotYetExists)
|
| 793 |
|
|
&& isLegitimate(basionymName)
|
| 794 |
|
|
&& ! name2isHomonym){
|
| 795 |
|
|
logger.info(state.getCurrentLine() + ": Names are potential basionyms but either author or name part do not match: " + basionymName.getTitleCache() + " <-> " + newCombination.getTitleCache());
|
| 796 |
|
|
}
|
| 797 |
fb3dec85
|
Andreas Müller
|
}
|
| 798 |
b9cdcc88
|
Andreas Müller
|
}
|
| 799 |
|
|
|
| 800 |
|
|
/**
|
| 801 |
|
|
* @param basionymName
|
| 802 |
|
|
* @return
|
| 803 |
|
|
*/
|
| 804 |
7d882578
|
Andreas Müller
|
private boolean isLegitimate(IBotanicalName basionymName) {
|
| 805 |
b9cdcc88
|
Andreas Müller
|
for (NomenclaturalStatus nomStatus : basionymName.getStatus()){
|
| 806 |
|
|
if (nomStatus.getType()!= null && nomStatus.getType().isIllegitimateType()){
|
| 807 |
|
|
return false;
|
| 808 |
|
|
}
|
| 809 |
|
|
}
|
| 810 |
|
|
for (NameRelationship nameRel : basionymName.getNameRelations()){
|
| 811 |
|
|
if (nameRel.getType()!= null && nameRel.getType().isIllegitimateType()){
|
| 812 |
|
|
return false;
|
| 813 |
|
|
}
|
| 814 |
fb3dec85
|
Andreas Müller
|
}
|
| 815 |
b9cdcc88
|
Andreas Müller
|
return true;
|
| 816 |
|
|
}
|
| 817 |
|
|
|
| 818 |
|
|
|
| 819 |
fb3dec85
|
Andreas Müller
|
/**
|
| 820 |
|
|
* @param combinationAuthorship
|
| 821 |
|
|
* @param basi
|
| 822 |
|
|
* @return
|
| 823 |
|
|
*/
|
| 824 |
|
|
private boolean matchAuthor(TeamOrPersonBase<?> author1, TeamOrPersonBase<?> author2) {
|
| 825 |
|
|
if (author1 == null || author2 == null){
|
| 826 |
|
|
return false;
|
| 827 |
|
|
}else {
|
| 828 |
|
|
return author1.getNomenclaturalTitle().equals(author2.getNomenclaturalTitle());
|
| 829 |
|
|
}
|
| 830 |
ede5c502
|
Andreas Müller
|
}
|
| 831 |
|
|
|
| 832 |
|
|
|
| 833 |
|
|
/**
|
| 834 |
|
|
* @param record
|
| 835 |
|
|
* @param state
|
| 836 |
|
|
* @param taxon
|
| 837 |
|
|
*/
|
| 838 |
fb3dec85
|
Andreas Müller
|
private void makeNotes(HashMap<String, String> record, CubaImportState state) {
|
| 839 |
ede5c502
|
Andreas Müller
|
String notesStr = getValue(record, "(Notas)");
|
| 840 |
|
|
if (notesStr == null){
|
| 841 |
|
|
return;
|
| 842 |
|
|
}else{
|
| 843 |
|
|
Annotation annotation = Annotation.NewDefaultLanguageInstance(notesStr);
|
| 844 |
|
|
//TODO
|
| 845 |
0a6a64c9
|
Andreas Müller
|
annotation.setAnnotationType(AnnotationType.TECHNICAL());
|
| 846 |
fb3dec85
|
Andreas Müller
|
state.getCurrentTaxon().addAnnotation(annotation);
|
| 847 |
ede5c502
|
Andreas Müller
|
}
|
| 848 |
|
|
}
|
| 849 |
|
|
|
| 850 |
|
|
|
| 851 |
|
|
/**
|
| 852 |
|
|
* @param record
|
| 853 |
|
|
* @param state
|
| 854 |
|
|
* @param familyTaxon
|
| 855 |
|
|
* @return
|
| 856 |
|
|
*/
|
| 857 |
fb3dec85
|
Andreas Müller
|
private Taxon makeTaxon(HashMap<String, String> record, CubaImportState state, TaxonNode familyNode, boolean isSynonym) {
|
| 858 |
4b9c9c4b
|
Andreas Müller
|
String taxonStrOrig = getValue(record, "Taxón");
|
| 859 |
|
|
if (taxonStrOrig == null){
|
| 860 |
fb3dec85
|
Andreas Müller
|
return isSynonym ? state.getCurrentTaxon() : null;
|
| 861 |
ede5c502
|
Andreas Müller
|
}
|
| 862 |
b9cdcc88
|
Andreas Müller
|
|
| 863 |
ede5c502
|
Andreas Müller
|
boolean isAbsent = false;
|
| 864 |
4b9c9c4b
|
Andreas Müller
|
String taxonStr = taxonStrOrig;
|
| 865 |
|
|
if (taxonStrOrig.startsWith("[") && taxonStrOrig.endsWith("]")){
|
| 866 |
ede5c502
|
Andreas Müller
|
taxonStr = taxonStr.substring(1, taxonStr.length() - 1);
|
| 867 |
|
|
isAbsent = true;
|
| 868 |
|
|
}
|
| 869 |
|
|
|
| 870 |
b9cdcc88
|
Andreas Müller
|
boolean isAuct = false;
|
| 871 |
|
|
if (taxonStr.endsWith("auct.")){
|
| 872 |
|
|
isAuct = true;
|
| 873 |
|
|
taxonStr.replace("auct.", "").trim();
|
| 874 |
|
|
}
|
| 875 |
|
|
state.setTaxonIsAbsent(isAbsent);
|
| 876 |
86536e03
|
Andreas Müller
|
IBotanicalName botanicalName = makeName(state, taxonStr);
|
| 877 |
8422c0cd
|
Andreas Müller
|
Reference sec = getSecReference(state);
|
| 878 |
fb3dec85
|
Andreas Müller
|
Taxon taxon = Taxon.NewInstance(botanicalName, sec);
|
| 879 |
b9cdcc88
|
Andreas Müller
|
if (isAuct){
|
| 880 |
|
|
taxon.setAppendedPhrase("auct.");
|
| 881 |
|
|
}
|
| 882 |
|
|
|
| 883 |
fb3dec85
|
Andreas Müller
|
TaxonNode higherNode;
|
| 884 |
ede5c502
|
Andreas Müller
|
if (botanicalName.isProtectedTitleCache()){
|
| 885 |
4b9c9c4b
|
Andreas Müller
|
logger.warn(state.getCurrentLine() + ": Taxon could not be parsed: " + taxonStrOrig);
|
| 886 |
fb3dec85
|
Andreas Müller
|
higherNode = familyNode;
|
| 887 |
|
|
}else{
|
| 888 |
|
|
String genusStr = botanicalName.getGenusOrUninomial();
|
| 889 |
|
|
Taxon genus = state.getHigherTaxon(genusStr);
|
| 890 |
|
|
if (genus != null){
|
| 891 |
|
|
higherNode = genus.getTaxonNodes().iterator().next();
|
| 892 |
|
|
}else{
|
| 893 |
86536e03
|
Andreas Müller
|
IBotanicalName name = TaxonNameFactory.NewBotanicalInstance(Rank.GENUS());
|
| 894 |
b9cdcc88
|
Andreas Müller
|
name.addSource(makeOriginalSource(state));
|
| 895 |
fb3dec85
|
Andreas Müller
|
name.setGenusOrUninomial(genusStr);
|
| 896 |
|
|
genus = Taxon.NewInstance(name, sec);
|
| 897 |
b9cdcc88
|
Andreas Müller
|
genus.addSource(makeOriginalSource(state));
|
| 898 |
fb3dec85
|
Andreas Müller
|
higherNode = familyNode.addChildTaxon(genus, null, null);
|
| 899 |
|
|
state.putHigherTaxon(genusStr, genus);
|
| 900 |
|
|
}
|
| 901 |
ede5c502
|
Andreas Müller
|
}
|
| 902 |
f4682883
|
Andreas Müller
|
taxon.addSource(makeOriginalSource(state));
|
| 903 |
|
|
|
| 904 |
|
|
TaxonNode newNode = higherNode.addChildTaxon(taxon, null, null);
|
| 905 |
4b9c9c4b
|
Andreas Müller
|
if(isAbsent){
|
| 906 |
|
|
botanicalName.setTitleCache(taxonStrOrig, true);
|
| 907 |
f4682883
|
Andreas Müller
|
newNode.setExcluded(true);
|
| 908 |
4b9c9c4b
|
Andreas Müller
|
}
|
| 909 |
fb3dec85
|
Andreas Müller
|
|
| 910 |
ede5c502
|
Andreas Müller
|
return taxon;
|
| 911 |
|
|
}
|
| 912 |
|
|
|
| 913 |
c9f78619
|
Andreas Müller
|
private final String orthVarRegExStr = "[A-Z][a-z]+\\s[a-z]+\\s(\\(‘([a-z]){3,}’\\))\\s(\\([A-Z][a-z]+\\.?\\)\\s)?[A-Z][a-zó]+\\.?";
|
| 914 |
|
|
private final Pattern orthVarRegEx = Pattern.compile(orthVarRegExStr);
|
| 915 |
|
|
/**
|
| 916 |
|
|
* @param taxonStr
|
| 917 |
|
|
* @return
|
| 918 |
|
|
*/
|
| 919 |
86536e03
|
Andreas Müller
|
private IBotanicalName makeName(CubaImportState state, String nameStrOrig) {
|
| 920 |
c9f78619
|
Andreas Müller
|
//normalize
|
| 921 |
|
|
String nameStr = normalizeStatus(nameStrOrig);
|
| 922 |
|
|
//orthVar
|
| 923 |
|
|
Matcher orthVarMatcher = orthVarRegEx.matcher(nameStr);
|
| 924 |
|
|
String orthVar = null;
|
| 925 |
|
|
if (orthVarMatcher.matches()) {
|
| 926 |
|
|
orthVar = orthVarMatcher.group(1);
|
| 927 |
|
|
nameStr = nameStr.replace(" " + orthVar, "").trim().replaceAll("\\s{2,}", " ");
|
| 928 |
|
|
orthVar = orthVar.substring(2, orthVar.length() - 2);
|
| 929 |
b9cdcc88
|
Andreas Müller
|
}
|
| 930 |
c9f78619
|
Andreas Müller
|
|
| 931 |
b9cdcc88
|
Andreas Müller
|
boolean isNomInval = false;
|
| 932 |
|
|
if (nameStr.endsWith("nom. inval.")){
|
| 933 |
|
|
isNomInval = true;
|
| 934 |
|
|
nameStr = nameStr.replace("nom. inval.", "").trim();
|
| 935 |
c9f78619
|
Andreas Müller
|
}
|
| 936 |
b9cdcc88
|
Andreas Müller
|
|
| 937 |
86536e03
|
Andreas Müller
|
TaxonName result = (TaxonName)nameParser.parseReferencedName(nameStr, nc, Rank.SPECIES());
|
| 938 |
b9cdcc88
|
Andreas Müller
|
result.addSource(makeOriginalSource(state));
|
| 939 |
|
|
if (isNomInval){
|
| 940 |
|
|
result.addStatus(NomenclaturalStatus.NewInstance(NomenclaturalStatusType.INVALID()));
|
| 941 |
|
|
}
|
| 942 |
c9f78619
|
Andreas Müller
|
if (orthVar != null){
|
| 943 |
86536e03
|
Andreas Müller
|
TaxonName orthVarName = (TaxonName)result.clone();
|
| 944 |
b9cdcc88
|
Andreas Müller
|
orthVarName.addSource(makeOriginalSource(state));
|
| 945 |
c9f78619
|
Andreas Müller
|
//TODO
|
| 946 |
8422c0cd
|
Andreas Müller
|
Reference citation = null;
|
| 947 |
c9f78619
|
Andreas Müller
|
orthVarName.addRelationshipToName(result, NameRelationshipType.ORTHOGRAPHIC_VARIANT(), citation, null, null);
|
| 948 |
|
|
orthVarName.setSpecificEpithet(orthVar);
|
| 949 |
|
|
}
|
| 950 |
b9cdcc88
|
Andreas Müller
|
normalizeAuthors(result);
|
| 951 |
c9f78619
|
Andreas Müller
|
return result;
|
| 952 |
|
|
|
| 953 |
|
|
}
|
| 954 |
|
|
|
| 955 |
b9cdcc88
|
Andreas Müller
|
/**
|
| 956 |
|
|
* @param result
|
| 957 |
|
|
*/
|
| 958 |
7d882578
|
Andreas Müller
|
private void normalizeAuthors(IBotanicalName result) {
|
| 959 |
b9cdcc88
|
Andreas Müller
|
result.setCombinationAuthorship(normalizeAuthor(result.getCombinationAuthorship()));
|
| 960 |
|
|
result.setExCombinationAuthorship(normalizeAuthor(result.getExCombinationAuthorship()));
|
| 961 |
|
|
result.setExBasionymAuthorship(normalizeAuthor(result.getExBasionymAuthorship()));
|
| 962 |
|
|
result.setBasionymAuthorship(normalizeAuthor(result.getBasionymAuthorship()));
|
| 963 |
|
|
|
| 964 |
|
|
}
|
| 965 |
|
|
|
| 966 |
|
|
|
| 967 |
|
|
/**
|
| 968 |
|
|
* @param combinationAuthorship
|
| 969 |
|
|
* @return
|
| 970 |
|
|
*/
|
| 971 |
|
|
private TeamOrPersonBase<?> normalizeAuthor(TeamOrPersonBase<?> author) {
|
| 972 |
|
|
if (author == null){
|
| 973 |
|
|
return null;
|
| 974 |
|
|
}
|
| 975 |
|
|
TeamOrPersonBase<?> result;
|
| 976 |
|
|
if (author.isInstanceOf(Person.class)){
|
| 977 |
|
|
result = normalizePerson(CdmBase.deproxy(author, Person.class));
|
| 978 |
|
|
}else{
|
| 979 |
|
|
Team team = CdmBase.deproxy(author, Team.class);
|
| 980 |
|
|
List<Person> list = team.getTeamMembers();
|
| 981 |
|
|
for(int i = 0; i < list.size(); i++){
|
| 982 |
|
|
Person person = list.get(i);
|
| 983 |
|
|
Person tmpMember = normalizePerson(person);
|
| 984 |
|
|
list.set(i, tmpMember);
|
| 985 |
|
|
}
|
| 986 |
|
|
return team;
|
| 987 |
|
|
}
|
| 988 |
|
|
return result;
|
| 989 |
|
|
}
|
| 990 |
|
|
|
| 991 |
|
|
|
| 992 |
|
|
/**
|
| 993 |
|
|
* @param deproxy
|
| 994 |
|
|
* @return
|
| 995 |
|
|
*/
|
| 996 |
|
|
private Person normalizePerson(Person person) {
|
| 997 |
|
|
String title = person.getNomenclaturalTitle();
|
| 998 |
|
|
title = title.replaceAll("(?<=[a-zA-Z])\\.(?=[a-zA-Z])", ". ");
|
| 999 |
|
|
person.setNomenclaturalTitle(title);
|
| 1000 |
|
|
boolean isFilius = title.endsWith(" f.");
|
| 1001 |
|
|
if (isFilius){
|
| 1002 |
|
|
title.replace(" f.", "");
|
| 1003 |
|
|
}
|
| 1004 |
|
|
|
| 1005 |
|
|
String[] splits = title.split("\\s+");
|
| 1006 |
|
|
int nNotFirstName = isFilius ? 2 : 1;
|
| 1007 |
|
|
person.setLastname(splits[splits.length - nNotFirstName] + (isFilius? " f." : ""));
|
| 1008 |
|
|
person.setFirstname(CdmUtils.concat(" ", Arrays.copyOfRange(splits, 0, splits.length-nNotFirstName)));
|
| 1009 |
|
|
return person;
|
| 1010 |
|
|
}
|
| 1011 |
|
|
|
| 1012 |
|
|
|
| 1013 |
fb3dec85
|
Andreas Müller
|
/**
|
| 1014 |
|
|
* @param state
|
| 1015 |
|
|
* @return
|
| 1016 |
|
|
*/
|
| 1017 |
8422c0cd
|
Andreas Müller
|
private Reference getSecReference(CubaImportState state) {
|
| 1018 |
|
|
Reference result = state.getSecReference();
|
| 1019 |
fb3dec85
|
Andreas Müller
|
if (result == null){
|
| 1020 |
|
|
result = ReferenceFactory.newDatabase();
|
| 1021 |
|
|
result.setTitle("Flora of Cuba");
|
| 1022 |
|
|
state.setSecReference(result);
|
| 1023 |
|
|
}
|
| 1024 |
|
|
return result;
|
| 1025 |
|
|
}
|
| 1026 |
|
|
|
| 1027 |
|
|
|
| 1028 |
|
|
private static final String[] nomStatusStrings = new String[]{"nom. cons.", "ined.", "nom. illeg.",
|
| 1029 |
c9f78619
|
Andreas Müller
|
"nom. rej.","nom. cons. prop.","nom. altern.","nom. confus.","nom. dub.", "nom. nud."};
|
| 1030 |
fb3dec85
|
Andreas Müller
|
/**
|
| 1031 |
|
|
* @param taxonStr
|
| 1032 |
|
|
* @return
|
| 1033 |
|
|
*/
|
| 1034 |
c9f78619
|
Andreas Müller
|
private String normalizeStatus(String nameStr) {
|
| 1035 |
|
|
if (nameStr == null){
|
| 1036 |
fb3dec85
|
Andreas Müller
|
return null;
|
| 1037 |
|
|
}
|
| 1038 |
c9f78619
|
Andreas Müller
|
String result = nameStr.replaceAll(HOMONYM_MARKER, "").trim();
|
| 1039 |
fb3dec85
|
Andreas Müller
|
for (String nomStatusStr : nomStatusStrings){
|
| 1040 |
|
|
nomStatusStr = " " + nomStatusStr;
|
| 1041 |
c9f78619
|
Andreas Müller
|
if (result.endsWith(nomStatusStr)){
|
| 1042 |
|
|
result = result.replace(nomStatusStr, "," + nomStatusStr);
|
| 1043 |
fb3dec85
|
Andreas Müller
|
}
|
| 1044 |
|
|
}
|
| 1045 |
c9f78619
|
Andreas Müller
|
result = result.replaceAll(DOUBTFUL_MARKER, "").trim();
|
| 1046 |
|
|
result = result.replace("[taxon]", "[infraspec.]");
|
| 1047 |
|
|
return result;
|
| 1048 |
fb3dec85
|
Andreas Müller
|
|
| 1049 |
|
|
|
| 1050 |
|
|
}
|
| 1051 |
|
|
|
| 1052 |
ede5c502
|
Andreas Müller
|
|
| 1053 |
|
|
/**
|
| 1054 |
|
|
* @param record
|
| 1055 |
|
|
* @param state
|
| 1056 |
|
|
* @return
|
| 1057 |
|
|
*/
|
| 1058 |
|
|
private TaxonNode getFamilyTaxon(HashMap<String, String> record, CubaImportState state) {
|
| 1059 |
c9f78619
|
Andreas Müller
|
String familyStr = getValue(record, "Fam. default");
|
| 1060 |
ede5c502
|
Andreas Müller
|
if (familyStr == null){
|
| 1061 |
|
|
return null;
|
| 1062 |
|
|
}
|
| 1063 |
b9cdcc88
|
Andreas Müller
|
familyStr = familyStr.trim();
|
| 1064 |
|
|
String alternativeFamilyStr = null;
|
| 1065 |
|
|
if (familyStr.contains("/")){
|
| 1066 |
|
|
String[] splits = familyStr.split("/");
|
| 1067 |
|
|
if (splits.length > 2){
|
| 1068 |
|
|
logger.warn(state.getCurrentLine() +": " + "More than 1 alternative name:" + familyStr);
|
| 1069 |
|
|
}
|
| 1070 |
|
|
familyStr = splits[0].trim();
|
| 1071 |
|
|
alternativeFamilyStr = splits[1].trim();
|
| 1072 |
|
|
}
|
| 1073 |
|
|
|
| 1074 |
ede5c502
|
Andreas Müller
|
Taxon family = state.getHigherTaxon(familyStr);
|
| 1075 |
|
|
TaxonNode familyNode;
|
| 1076 |
|
|
if (family != null){
|
| 1077 |
|
|
familyNode = family.getTaxonNodes().iterator().next();
|
| 1078 |
|
|
}else{
|
| 1079 |
86536e03
|
Andreas Müller
|
TaxonName name = (TaxonName)makeFamilyName(state, familyStr);
|
| 1080 |
8422c0cd
|
Andreas Müller
|
Reference sec = getSecReference(state);
|
| 1081 |
b9cdcc88
|
Andreas Müller
|
family = Taxon.NewInstance(name, sec);
|
| 1082 |
fb3dec85
|
Andreas Müller
|
ITaxonTreeNode rootNode = getClassification(state);
|
| 1083 |
b9cdcc88
|
Andreas Müller
|
familyNode = rootNode.addChildTaxon(family, sec, null);
|
| 1084 |
|
|
state.putHigherTaxon(familyStr, family);
|
| 1085 |
|
|
|
| 1086 |
|
|
}
|
| 1087 |
|
|
|
| 1088 |
|
|
if (isNotBlank(alternativeFamilyStr)){
|
| 1089 |
|
|
NameRelationshipType type = NameRelationshipType.ALTERNATIVE_NAME();
|
| 1090 |
86536e03
|
Andreas Müller
|
TaxonName alternativeName = (TaxonName)makeFamilyName(state, alternativeFamilyStr);
|
| 1091 |
|
|
IBotanicalName familyName = family.getName();
|
| 1092 |
b9cdcc88
|
Andreas Müller
|
boolean hasRelation = false;
|
| 1093 |
|
|
for (NameRelationship nameRel : familyName.getRelationsToThisName()){
|
| 1094 |
|
|
if (nameRel.getType().equals(type)){
|
| 1095 |
|
|
if (nameRel.getFromName().equals(alternativeName)){
|
| 1096 |
|
|
hasRelation = true;
|
| 1097 |
|
|
}
|
| 1098 |
|
|
}
|
| 1099 |
|
|
}
|
| 1100 |
|
|
if (!hasRelation){
|
| 1101 |
|
|
familyName.addRelationshipFromName(alternativeName, type, null);
|
| 1102 |
|
|
}
|
| 1103 |
|
|
|
| 1104 |
ede5c502
|
Andreas Müller
|
}
|
| 1105 |
|
|
|
| 1106 |
|
|
return familyNode;
|
| 1107 |
|
|
}
|
| 1108 |
|
|
|
| 1109 |
b9cdcc88
|
Andreas Müller
|
|
| 1110 |
|
|
/**
|
| 1111 |
|
|
* @param state
|
| 1112 |
|
|
* @param taxon
|
| 1113 |
|
|
*/
|
| 1114 |
|
|
private void validateTaxonIsAbsent(CubaImportState state, Taxon taxon) {
|
| 1115 |
|
|
if (!state.isTaxonIsAbsent()){
|
| 1116 |
|
|
return;
|
| 1117 |
|
|
}
|
| 1118 |
|
|
|
| 1119 |
|
|
for (DescriptionElementBase el : taxon.getDescriptions().iterator().next().getElements()){
|
| 1120 |
|
|
if (el instanceof Distribution){
|
| 1121 |
|
|
Distribution dist = (Distribution)el;
|
| 1122 |
|
|
NamedArea area = dist.getArea();
|
| 1123 |
|
|
if (isCubanArea(area)){
|
| 1124 |
|
|
PresenceAbsenceTerm status = dist.getStatus();
|
| 1125 |
|
|
if (status != null && !status.isAbsenceTerm()){
|
| 1126 |
|
|
if (!isDoubtfulTerm(status)){
|
| 1127 |
|
|
String name = taxon.getName().getTitleCache();
|
| 1128 |
|
|
logger.error(state.getCurrentLine() +": Taxon ("+name+")is absent'[]' but has presence distribution: " + status.getTitleCache());
|
| 1129 |
|
|
return;
|
| 1130 |
|
|
}
|
| 1131 |
|
|
}
|
| 1132 |
|
|
}
|
| 1133 |
|
|
}
|
| 1134 |
|
|
}
|
| 1135 |
|
|
}
|
| 1136 |
|
|
|
| 1137 |
|
|
/**
|
| 1138 |
|
|
* @param state
|
| 1139 |
|
|
* @param taxon
|
| 1140 |
|
|
*/
|
| 1141 |
|
|
private void validateEndemic(CubaImportState state, Taxon taxon) {
|
| 1142 |
|
|
|
| 1143 |
|
|
boolean hasExternalPresence = false;
|
| 1144 |
|
|
for (DescriptionElementBase el : taxon.getDescriptions().iterator().next().getElements()){
|
| 1145 |
|
|
if (el instanceof Distribution){
|
| 1146 |
|
|
Distribution dist = (Distribution)el;
|
| 1147 |
|
|
NamedArea area = dist.getArea();
|
| 1148 |
|
|
if (!isCubanArea(area)){
|
| 1149 |
|
|
PresenceAbsenceTerm status = dist.getStatus();
|
| 1150 |
|
|
if (status != null && !status.isAbsenceTerm()){
|
| 1151 |
|
|
if (!isDoubtfulTerm(status)){
|
| 1152 |
|
|
hasExternalPresence = true;
|
| 1153 |
|
|
if (state.isEndemic()){
|
| 1154 |
|
|
String name = taxon.getName().getTitleCache();
|
| 1155 |
|
|
logger.error(state.getCurrentLine() +": Taxon ("+name+")is endemic but has non-cuban distribution: " + area.getIdInVocabulary() + "-" + status.getIdInVocabulary());
|
| 1156 |
|
|
return;
|
| 1157 |
|
|
}
|
| 1158 |
|
|
}
|
| 1159 |
|
|
}
|
| 1160 |
|
|
}
|
| 1161 |
|
|
}
|
| 1162 |
|
|
}
|
| 1163 |
|
|
if (!state.isEndemic() && ! hasExternalPresence){
|
| 1164 |
|
|
String name = taxon.getName().getTitleCache();
|
| 1165 |
|
|
logger.error(state.getCurrentLine() +": Taxon ("+name+")is not endemic but has no non-cuban distribution" );
|
| 1166 |
|
|
}
|
| 1167 |
|
|
}
|
| 1168 |
|
|
|
| 1169 |
|
|
|
| 1170 |
c9f78619
|
Andreas Müller
|
/**
|
| 1171 |
|
|
* @param state
|
| 1172 |
|
|
* @param taxon
|
| 1173 |
|
|
* @param famStr
|
| 1174 |
|
|
* @param famRef
|
| 1175 |
|
|
* @return
|
| 1176 |
|
|
*/
|
| 1177 |
8422c0cd
|
Andreas Müller
|
private Taxon makeAlternativeFamilyTaxon(CubaImportState state, String famStr, Reference famRef) {
|
| 1178 |
c9f78619
|
Andreas Müller
|
String key = famRef.getTitle() + ":"+ famStr;
|
| 1179 |
|
|
Taxon family = state.getHigherTaxon(key);
|
| 1180 |
|
|
if (family == null){
|
| 1181 |
86536e03
|
Andreas Müller
|
IBotanicalName name = makeFamilyName(state, famStr);
|
| 1182 |
c9f78619
|
Andreas Müller
|
family = Taxon.NewInstance(name, famRef);
|
| 1183 |
|
|
state.putHigherTaxon(key, family);
|
| 1184 |
|
|
}
|
| 1185 |
|
|
|
| 1186 |
|
|
return family;
|
| 1187 |
|
|
}
|
| 1188 |
|
|
|
| 1189 |
ede5c502
|
Andreas Müller
|
|
| 1190 |
b9cdcc88
|
Andreas Müller
|
/**
|
| 1191 |
|
|
* @param state
|
| 1192 |
|
|
* @param famStr
|
| 1193 |
|
|
* @return
|
| 1194 |
|
|
*/
|
| 1195 |
86536e03
|
Andreas Müller
|
private IBotanicalName makeFamilyName(CubaImportState state, String famStr) {
|
| 1196 |
|
|
IBotanicalName name = state.getFamilyName(famStr);
|
| 1197 |
b9cdcc88
|
Andreas Müller
|
if (name == null){
|
| 1198 |
ded3de15
|
Andreas Müller
|
name = TaxonNameFactory.NewBotanicalInstance(Rank.FAMILY());
|
| 1199 |
b9cdcc88
|
Andreas Müller
|
name.setGenusOrUninomial(famStr);
|
| 1200 |
|
|
state.putFamilyName(famStr, name);
|
| 1201 |
|
|
name.addSource(makeOriginalSource(state));
|
| 1202 |
|
|
}
|
| 1203 |
|
|
return name;
|
| 1204 |
|
|
}
|
| 1205 |
|
|
|
| 1206 |
|
|
|
| 1207 |
ede5c502
|
Andreas Müller
|
/**
|
| 1208 |
|
|
* @param state
|
| 1209 |
|
|
* @return
|
| 1210 |
|
|
*/
|
| 1211 |
fb3dec85
|
Andreas Müller
|
private TaxonNode getClassification(CubaImportState state) {
|
| 1212 |
ede5c502
|
Andreas Müller
|
Classification classification = state.getClassification();
|
| 1213 |
|
|
if (classification == null){
|
| 1214 |
fb3dec85
|
Andreas Müller
|
classification = getClassificationService().find(state.getConfig().getClassificationUuid());
|
| 1215 |
|
|
}
|
| 1216 |
|
|
TaxonNode rootNode = state.getRootNode();
|
| 1217 |
|
|
if (rootNode == null){
|
| 1218 |
|
|
rootNode = getTaxonNodeService().find(plantaeUuid);
|
| 1219 |
|
|
}
|
| 1220 |
|
|
if (rootNode == null){
|
| 1221 |
8422c0cd
|
Andreas Müller
|
Reference sec = getSecReference(state);
|
| 1222 |
fb3dec85
|
Andreas Müller
|
if (classification == null){
|
| 1223 |
|
|
String classificationName = state.getConfig().getClassificationName();
|
| 1224 |
|
|
//TODO
|
| 1225 |
|
|
Language language = Language.DEFAULT();
|
| 1226 |
|
|
classification = Classification.NewInstance(classificationName, sec, language);
|
| 1227 |
|
|
state.setClassification(classification);
|
| 1228 |
|
|
classification.setUuid(state.getConfig().getClassificationUuid());
|
| 1229 |
|
|
classification.getRootNode().setUuid(rootUuid);
|
| 1230 |
|
|
}
|
| 1231 |
|
|
|
| 1232 |
86536e03
|
Andreas Müller
|
IBotanicalName plantaeName = TaxonNameFactory.NewBotanicalInstance(Rank.KINGDOM());
|
| 1233 |
fb3dec85
|
Andreas Müller
|
plantaeName.setGenusOrUninomial("Plantae");
|
| 1234 |
|
|
Taxon plantae = Taxon.NewInstance(plantaeName, sec);
|
| 1235 |
|
|
TaxonNode plantaeNode = classification.addChildTaxon(plantae, null, null);
|
| 1236 |
|
|
plantaeNode.setUuid(plantaeUuid);
|
| 1237 |
|
|
state.setRootNode(plantaeNode);
|
| 1238 |
ede5c502
|
Andreas Müller
|
getClassificationService().save(classification);
|
| 1239 |
fb3dec85
|
Andreas Müller
|
|
| 1240 |
|
|
rootNode = plantaeNode;
|
| 1241 |
ede5c502
|
Andreas Müller
|
}
|
| 1242 |
fb3dec85
|
Andreas Müller
|
return rootNode;
|
| 1243 |
ede5c502
|
Andreas Müller
|
}
|
| 1244 |
|
|
|
| 1245 |
|
|
|
| 1246 |
|
|
/**
|
| 1247 |
|
|
* @param record
|
| 1248 |
|
|
* @param originalKey
|
| 1249 |
|
|
* @return
|
| 1250 |
|
|
*/
|
| 1251 |
|
|
private String getValue(HashMap<String, String> record, String originalKey) {
|
| 1252 |
|
|
String value = record.get(originalKey);
|
| 1253 |
|
|
if (! StringUtils.isBlank(value)) {
|
| 1254 |
|
|
if (logger.isDebugEnabled()) { logger.debug(originalKey + ": " + value); }
|
| 1255 |
|
|
value = CdmUtils.removeDuplicateWhitespace(value.trim()).toString();
|
| 1256 |
|
|
return value;
|
| 1257 |
|
|
}else{
|
| 1258 |
|
|
return null;
|
| 1259 |
|
|
}
|
| 1260 |
|
|
}
|
| 1261 |
|
|
|
| 1262 |
|
|
|
| 1263 |
|
|
|
| 1264 |
|
|
/**
|
| 1265 |
|
|
* Stores taxa records in DB
|
| 1266 |
|
|
*/
|
| 1267 |
|
|
@Override
|
| 1268 |
|
|
protected void firstPass(CubaImportState state) {
|
| 1269 |
b9cdcc88
|
Andreas Müller
|
boolean isSynonymOnly = false;
|
| 1270 |
ede5c502
|
Andreas Müller
|
|
| 1271 |
f5c05984
|
Andreas Müller
|
String line = state.getCurrentLine() + ": ";
|
| 1272 |
fb3dec85
|
Andreas Müller
|
HashMap<String, String> record = state.getOriginalRecord();
|
| 1273 |
ede5c502
|
Andreas Müller
|
|
| 1274 |
fb3dec85
|
Andreas Müller
|
Set<String> keys = record.keySet();
|
| 1275 |
|
|
for (String key: keys) {
|
| 1276 |
|
|
if (! expectedKeys.contains(key)){
|
| 1277 |
f5c05984
|
Andreas Müller
|
logger.warn(line + "Unexpected Key: " + key);
|
| 1278 |
fb3dec85
|
Andreas Müller
|
}
|
| 1279 |
|
|
}
|
| 1280 |
ede5c502
|
Andreas Müller
|
|
| 1281 |
c9f78619
|
Andreas Müller
|
if (record.get("Fam. default") == null && keys.size() == 2 && record.get("Syn.") == null && record.get("Nat") != null && record.get("Adv") != null){
|
| 1282 |
fb3dec85
|
Andreas Müller
|
//second header line, don't handle
|
| 1283 |
|
|
return;
|
| 1284 |
|
|
}
|
| 1285 |
ede5c502
|
Andreas Müller
|
|
| 1286 |
fb3dec85
|
Andreas Müller
|
//Fam.
|
| 1287 |
|
|
TaxonNode familyTaxon = getFamilyTaxon(record, state);
|
| 1288 |
|
|
if (familyTaxon == null){
|
| 1289 |
|
|
if (record.get("Taxón") != null){
|
| 1290 |
f5c05984
|
Andreas Müller
|
logger.warn(line + "Family not recognized but taxon exists: " + record.get("Taxón"));
|
| 1291 |
fb3dec85
|
Andreas Müller
|
return;
|
| 1292 |
|
|
}else if (record.get("Syn.") == null){
|
| 1293 |
f5c05984
|
Andreas Müller
|
logger.warn(line + "Family not recognized but also no synonym exists");
|
| 1294 |
fb3dec85
|
Andreas Müller
|
return;
|
| 1295 |
|
|
}else{
|
| 1296 |
b9cdcc88
|
Andreas Müller
|
isSynonymOnly = true;
|
| 1297 |
fb3dec85
|
Andreas Müller
|
}
|
| 1298 |
|
|
}
|
| 1299 |
ede5c502
|
Andreas Müller
|
|
| 1300 |
b9cdcc88
|
Andreas Müller
|
//Taxón
|
| 1301 |
|
|
Taxon taxon = makeTaxon(record, state, familyTaxon, isSynonymOnly);
|
| 1302 |
|
|
if (taxon == null && ! isSynonymOnly){
|
| 1303 |
f5c05984
|
Andreas Müller
|
logger.warn(line + "taxon could not be created and is null");
|
| 1304 |
fb3dec85
|
Andreas Müller
|
return;
|
| 1305 |
|
|
}
|
| 1306 |
|
|
state.setCurrentTaxon(taxon);
|
| 1307 |
ede5c502
|
Andreas Müller
|
|
| 1308 |
c9f78619
|
Andreas Müller
|
//Fam. ALT
|
| 1309 |
4b9c9c4b
|
Andreas Müller
|
if (!isSynonymOnly){
|
| 1310 |
|
|
makeAlternativeFamilies(record, state, familyTaxon, taxon);
|
| 1311 |
|
|
}
|
| 1312 |
c9f78619
|
Andreas Müller
|
|
| 1313 |
fb3dec85
|
Andreas Müller
|
//(Notas)
|
| 1314 |
|
|
makeNotes(record, state);
|
| 1315 |
ede5c502
|
Andreas Müller
|
|
| 1316 |
fb3dec85
|
Andreas Müller
|
//Syn.
|
| 1317 |
b9cdcc88
|
Andreas Müller
|
makeSynonyms(record, state, !isSynonymOnly);
|
| 1318 |
ede5c502
|
Andreas Müller
|
|
| 1319 |
fb3dec85
|
Andreas Müller
|
//End, Ind, Ind? D, Nat N, Dud P, Adv A, Cult C
|
| 1320 |
|
|
makeCubanDistribution(record, state);
|
| 1321 |
ede5c502
|
Andreas Müller
|
|
| 1322 |
|
|
|
| 1323 |
0a6a64c9
|
Andreas Müller
|
// "CuW","PR PR*","Art","Hab(*)","May","Mat","IJ",
|
| 1324 |
fb3dec85
|
Andreas Müller
|
// "CuC","VC","Ci","SS","CA","Cam","LT",
|
| 1325 |
|
|
// "CuE","Gr","Ho","SC","Gu",
|
| 1326 |
|
|
makeProvincesDistribution(record, state);
|
| 1327 |
ede5c502
|
Andreas Müller
|
|
| 1328 |
c9f78619
|
Andreas Müller
|
// "Esp","Ja","PR","Men","Bah","Cay",
|
| 1329 |
|
|
// "AmN","AmC","AmS","VM"});
|
| 1330 |
|
|
makeOtherAreasDistribution(record, state);
|
| 1331 |
0a6a64c9
|
Andreas Müller
|
|
| 1332 |
b9cdcc88
|
Andreas Müller
|
validateTaxonIsAbsent(state, taxon);
|
| 1333 |
|
|
if (!isSynonymOnly){
|
| 1334 |
|
|
validateEndemic(state, taxon);
|
| 1335 |
|
|
}
|
| 1336 |
0a6a64c9
|
Andreas Müller
|
|
| 1337 |
|
|
state.setHighestStatusForTaxon(null);
|
| 1338 |
|
|
|
| 1339 |
fb3dec85
|
Andreas Müller
|
return;
|
| 1340 |
|
|
}
|
| 1341 |
ede5c502
|
Andreas Müller
|
|
| 1342 |
|
|
|
| 1343 |
b9cdcc88
|
Andreas Müller
|
/**
|
| 1344 |
|
|
* @param state
|
| 1345 |
|
|
* @return
|
| 1346 |
|
|
*/
|
| 1347 |
|
|
private IdentifiableSource makeOriginalSource(CubaImportState state) {
|
| 1348 |
|
|
return IdentifiableSource.NewDataImportInstance("line: " + state.getCurrentLine(), null, state.getConfig().getSourceReference());
|
| 1349 |
|
|
}
|
| 1350 |
|
|
/**
|
| 1351 |
|
|
* @param state
|
| 1352 |
|
|
* @return
|
| 1353 |
|
|
*/
|
| 1354 |
|
|
private DescriptionElementSource makeDescriptionSource(CubaImportState state) {
|
| 1355 |
|
|
return DescriptionElementSource.NewDataImportInstance("line: " + state.getCurrentLine(), null, state.getConfig().getSourceReference());
|
| 1356 |
|
|
}
|
| 1357 |
|
|
|
| 1358 |
|
|
private static Set<UUID> doubtfulStatus = new HashSet<>();
|
| 1359 |
ede5c502
|
Andreas Müller
|
|
| 1360 |
b9cdcc88
|
Andreas Müller
|
/**
|
| 1361 |
|
|
* @param status
|
| 1362 |
|
|
* @return
|
| 1363 |
|
|
*/
|
| 1364 |
|
|
private boolean isDoubtfulTerm(PresenceAbsenceTerm status) {
|
| 1365 |
|
|
if (doubtfulStatus.isEmpty()){
|
| 1366 |
|
|
doubtfulStatus.add(CubaTransformer.nonNativeDoubtfullyNaturalisedUuid);
|
| 1367 |
|
|
doubtfulStatus.add(CubaTransformer.doubtfulIndigenousDoubtfulUuid);
|
| 1368 |
|
|
doubtfulStatus.add(CubaTransformer.endemicDoubtfullyPresentUuid);
|
| 1369 |
|
|
doubtfulStatus.add(CubaTransformer.naturalisedDoubtfullyPresentUuid);
|
| 1370 |
|
|
doubtfulStatus.add(CubaTransformer.nonNativeDoubtfullyPresentUuid);
|
| 1371 |
|
|
doubtfulStatus.add(CubaTransformer.occasionallyCultivatedUuid);
|
| 1372 |
|
|
doubtfulStatus.add(CubaTransformer.rareCasualUuid);
|
| 1373 |
|
|
doubtfulStatus.add(PresenceAbsenceTerm.NATIVE_PRESENCE_QUESTIONABLE().getUuid());
|
| 1374 |
|
|
doubtfulStatus.add(PresenceAbsenceTerm.CULTIVATED_PRESENCE_QUESTIONABLE().getUuid());
|
| 1375 |
|
|
}
|
| 1376 |
|
|
boolean isDoubtful = doubtfulStatus.contains(status.getUuid());
|
| 1377 |
|
|
return isDoubtful;
|
| 1378 |
|
|
}
|
| 1379 |
|
|
|
| 1380 |
|
|
|
| 1381 |
|
|
/**
|
| 1382 |
|
|
* @param area
|
| 1383 |
|
|
* @return
|
| 1384 |
|
|
*/
|
| 1385 |
|
|
private boolean isCubanArea(NamedArea area) {
|
| 1386 |
|
|
if (area.getUuid().equals(CubaTransformer.uuidCuba)){
|
| 1387 |
|
|
return true;
|
| 1388 |
|
|
}else if (area.getPartOf()!= null){
|
| 1389 |
|
|
return isCubanArea(area.getPartOf());
|
| 1390 |
|
|
}else{
|
| 1391 |
|
|
return false;
|
| 1392 |
|
|
}
|
| 1393 |
|
|
}
|
| 1394 |
|
|
|
| 1395 |
|
|
|
| 1396 |
|
|
/**
|
| 1397 |
fb3dec85
|
Andreas Müller
|
* @param record
|
| 1398 |
|
|
* @param state
|
| 1399 |
c9f78619
|
Andreas Müller
|
* @param familyTaxon
|
| 1400 |
|
|
* @param taxon
|
| 1401 |
|
|
*/
|
| 1402 |
|
|
private void makeAlternativeFamilies(HashMap<String, String> record,
|
| 1403 |
|
|
CubaImportState state,
|
| 1404 |
|
|
TaxonNode familyTaxon,
|
| 1405 |
|
|
Taxon taxon) {
|
| 1406 |
|
|
|
| 1407 |
|
|
String famFRC = record.get("Fam. FRC");
|
| 1408 |
|
|
String famAS = record.get("Fam. A&S");
|
| 1409 |
|
|
String famFC = record.get("Fam. FC");
|
| 1410 |
|
|
|
| 1411 |
8422c0cd
|
Andreas Müller
|
Reference refFRC = makeReference(state, CubaTransformer.uuidRefFRC);
|
| 1412 |
|
|
Reference refAS = makeReference(state, CubaTransformer.uuidRefAS);
|
| 1413 |
|
|
Reference refFC = makeReference(state, CubaTransformer.uuidRefFC);
|
| 1414 |
c9f78619
|
Andreas Müller
|
|
| 1415 |
|
|
makeSingleAlternativeFamily(state, taxon, famFRC, refFRC);
|
| 1416 |
|
|
makeSingleAlternativeFamily(state, taxon, famAS, refAS);
|
| 1417 |
|
|
makeSingleAlternativeFamily(state, taxon, famFC, refFC);
|
| 1418 |
|
|
}
|
| 1419 |
|
|
|
| 1420 |
|
|
|
| 1421 |
|
|
/**
|
| 1422 |
|
|
* @param state
|
| 1423 |
|
|
* @param uuidreffrc
|
| 1424 |
|
|
* @return
|
| 1425 |
|
|
*/
|
| 1426 |
8422c0cd
|
Andreas Müller
|
private Reference makeReference(CubaImportState state, UUID uuidRef) {
|
| 1427 |
|
|
Reference ref = state.getReference(uuidRef);
|
| 1428 |
c9f78619
|
Andreas Müller
|
if (ref == null){
|
| 1429 |
|
|
ref = getReferenceService().find(uuidRef);
|
| 1430 |
|
|
state.putReference(uuidRef, ref);
|
| 1431 |
|
|
}
|
| 1432 |
|
|
return ref;
|
| 1433 |
|
|
}
|
| 1434 |
|
|
|
| 1435 |
|
|
|
| 1436 |
|
|
/**
|
| 1437 |
|
|
* @param state
|
| 1438 |
|
|
* @param taxon
|
| 1439 |
|
|
* @param famString
|
| 1440 |
|
|
* @param famRef
|
| 1441 |
|
|
*/
|
| 1442 |
8422c0cd
|
Andreas Müller
|
private void makeSingleAlternativeFamily(CubaImportState state, Taxon taxon, String famStr, Reference famRef) {
|
| 1443 |
c9f78619
|
Andreas Müller
|
if (isBlank(famStr)){
|
| 1444 |
4b9c9c4b
|
Andreas Müller
|
famStr = "-";
|
| 1445 |
|
|
// return;
|
| 1446 |
c9f78619
|
Andreas Müller
|
}
|
| 1447 |
|
|
|
| 1448 |
|
|
TaxonDescription desc = getTaxonDescription(taxon, false, true);
|
| 1449 |
|
|
|
| 1450 |
|
|
UUID altFamUuid1;
|
| 1451 |
|
|
UUID altFamUuid2;
|
| 1452 |
|
|
try {
|
| 1453 |
|
|
altFamUuid1 = state.getTransformer().getFeatureUuid("Alt.Fam.");
|
| 1454 |
|
|
altFamUuid2 = state.getTransformer().getFeatureUuid("Alt.Fam.2");
|
| 1455 |
|
|
} catch (UndefinedTransformerMethodException e) {
|
| 1456 |
|
|
throw new RuntimeException(e);
|
| 1457 |
|
|
}
|
| 1458 |
|
|
|
| 1459 |
|
|
|
| 1460 |
|
|
Taxon famTaxon = makeAlternativeFamilyTaxon(state, famStr, famRef);
|
| 1461 |
|
|
|
| 1462 |
|
|
|
| 1463 |
|
|
//TextData
|
| 1464 |
4b9c9c4b
|
Andreas Müller
|
Feature feature1 = getFeature(state, altFamUuid1, "Families in other Floras (Text)", "Families in other Floras (Text)", "Other floras", null);
|
| 1465 |
|
|
feature1.addRepresentation(Representation.NewInstance("Familias en otras Floras", "Familias en otras Floras", null, Language.SPANISH_CASTILIAN()));
|
| 1466 |
c9f78619
|
Andreas Müller
|
// TextData textData = TextData.NewInstance(feature1, famStr, Language.DEFAULT(), null);
|
| 1467 |
|
|
TextData textData = TextData.NewInstance(feature1, null, Language.DEFAULT(), null);
|
| 1468 |
|
|
textData.addSource(OriginalSourceType.PrimaryTaxonomicSource, null,null, famRef, null, famTaxon.getName(),null);
|
| 1469 |
|
|
desc.addElement(textData);
|
| 1470 |
|
|
|
| 1471 |
|
|
|
| 1472 |
|
|
|
| 1473 |
|
|
//TaxonInteraction
|
| 1474 |
4b9c9c4b
|
Andreas Müller
|
Feature feature2 = getFeature(state, altFamUuid2, "Families in other Floras", "Families in other Floras", "Other floras(2)", null);
|
| 1475 |
c9f78619
|
Andreas Müller
|
feature2.setSupportsTaxonInteraction(true);
|
| 1476 |
4b9c9c4b
|
Andreas Müller
|
feature2.addRepresentation(Representation.NewInstance("Familias en otras Floras", "Familias en otras Floras", null, Language.SPANISH_CASTILIAN()));
|
| 1477 |
c9f78619
|
Andreas Müller
|
TaxonInteraction taxInteract = TaxonInteraction.NewInstance(feature2);
|
| 1478 |
4b9c9c4b
|
Andreas Müller
|
textData.putText(Language.SPANISH_CASTILIAN(), "Familias en otras Floras");
|
| 1479 |
c9f78619
|
Andreas Müller
|
taxInteract.setTaxon2(famTaxon);
|
| 1480 |
|
|
taxInteract.addSource(OriginalSourceType.PrimaryTaxonomicSource, null,null, famRef, null);
|
| 1481 |
|
|
desc.addElement(taxInteract);
|
| 1482 |
|
|
|
| 1483 |
|
|
//Concept Relation
|
| 1484 |
|
|
famTaxon.addTaxonRelation(taxon, TaxonRelationshipType.INCLUDES(), taxon.getSec(), null);
|
| 1485 |
|
|
|
| 1486 |
|
|
}
|
| 1487 |
|
|
|
| 1488 |
|
|
|
| 1489 |
|
|
|
| 1490 |
|
|
|
| 1491 |
|
|
|
| 1492 |
|
|
/**
|
| 1493 |
|
|
* @param record
|
| 1494 |
|
|
* @param state
|
| 1495 |
fb3dec85
|
Andreas Müller
|
* @param taxon
|
| 1496 |
|
|
*/
|
| 1497 |
|
|
// "CuW","PR PR*","Art","Hab(*)","May","Mat","IJ",
|
| 1498 |
|
|
// "CuC","VC","Ci","SS","CA","Cam","LT",
|
| 1499 |
|
|
// "CuE","Gr","Ho","SC","Gu",
|
| 1500 |
|
|
private void makeProvincesDistribution(HashMap<String, String> record, CubaImportState state) {
|
| 1501 |
|
|
List<String> areaKeys = Arrays.asList(new String[]{
|
| 1502 |
|
|
"CuW","PR PR*","Art","Hab(*)","May","Mat","IJ",
|
| 1503 |
|
|
"CuC","VC","Ci","SS","CA","Cam","LT",
|
| 1504 |
|
|
"CuE","Gr","Ho","SC","Gu",
|
| 1505 |
0a6a64c9
|
Andreas Müller
|
});
|
| 1506 |
|
|
for (String areaKey : areaKeys){
|
| 1507 |
|
|
state.setCubanProvince(true);
|
| 1508 |
|
|
makeSingleProvinceDistribution(areaKey, record, state);
|
| 1509 |
|
|
}
|
| 1510 |
|
|
}
|
| 1511 |
|
|
|
| 1512 |
|
|
private void makeOtherAreasDistribution(HashMap<String, String> record, CubaImportState state) {
|
| 1513 |
|
|
List<String> areaKeys = Arrays.asList(new String[]{
|
| 1514 |
fb3dec85
|
Andreas Müller
|
"Esp","Ja","PR","Men","Bah","Cay",
|
| 1515 |
|
|
"AmN","AmC","AmS","VM"});
|
| 1516 |
|
|
for (String areaKey : areaKeys){
|
| 1517 |
0a6a64c9
|
Andreas Müller
|
state.setCubanProvince(false);
|
| 1518 |
fb3dec85
|
Andreas Müller
|
makeSingleProvinceDistribution(areaKey, record, state);
|
| 1519 |
|
|
}
|
| 1520 |
|
|
}
|
| 1521 |
ede5c502
|
Andreas Müller
|
|
| 1522 |
fb3dec85
|
Andreas Müller
|
|
| 1523 |
ede5c502
|
Andreas Müller
|
|
| 1524 |
|
|
|
| 1525 |
fb3dec85
|
Andreas Müller
|
/**
|
| 1526 |
|
|
* @param areaKey
|
| 1527 |
|
|
* @param record
|
| 1528 |
|
|
* @param state
|
| 1529 |
0a6a64c9
|
Andreas Müller
|
* @param highestStatus
|
| 1530 |
fb3dec85
|
Andreas Müller
|
* @return
|
| 1531 |
|
|
* @throws UndefinedTransformerMethodException
|
| 1532 |
|
|
*/
|
| 1533 |
0a6a64c9
|
Andreas Müller
|
private PresenceAbsenceTerm makeProvinceStatus(String areaKey,
|
| 1534 |
|
|
HashMap<String, String> record,
|
| 1535 |
|
|
CubaImportState state) throws UndefinedTransformerMethodException {
|
| 1536 |
|
|
|
| 1537 |
fb3dec85
|
Andreas Müller
|
String statusStr = record.get(areaKey);
|
| 1538 |
|
|
if (statusStr == null){
|
| 1539 |
|
|
return null;
|
| 1540 |
b9cdcc88
|
Andreas Müller
|
}else{
|
| 1541 |
|
|
statusStr = statusStr.trim();
|
| 1542 |
fb3dec85
|
Andreas Müller
|
}
|
| 1543 |
|
|
PresenceAbsenceTerm status = state.getTransformer().getPresenceTermByKey(statusStr);
|
| 1544 |
|
|
if (status == null){
|
| 1545 |
b9cdcc88
|
Andreas Müller
|
// PresenceAbsenceTerm highestStatus = state.getHighestStatusForTaxon();
|
| 1546 |
0a6a64c9
|
Andreas Müller
|
if (state.isCubanProvince() && isMinus(statusStr)){
|
| 1547 |
b9cdcc88
|
Andreas Müller
|
// getAbsenceTermForStatus(state, highestStatus);
|
| 1548 |
|
|
//we now handle cuban provinces same as external regions
|
| 1549 |
|
|
status = state.getTransformer().getPresenceTermByKey("--");
|
| 1550 |
0a6a64c9
|
Andreas Müller
|
}else if (! state.isCubanProvince() && isMinus(statusStr)){
|
| 1551 |
c9f78619
|
Andreas Müller
|
status = state.getTransformer().getPresenceTermByKey("--");
|
| 1552 |
0a6a64c9
|
Andreas Müller
|
}else{
|
| 1553 |
b9cdcc88
|
Andreas Müller
|
// logger.warn("Unhandled status str for provinces / external regions: " + statusStr);
|
| 1554 |
0a6a64c9
|
Andreas Müller
|
UUID statusUuid = state.getTransformer().getPresenceTermUuid(statusStr);
|
| 1555 |
b9cdcc88
|
Andreas Müller
|
if (statusUuid == null){
|
| 1556 |
|
|
logger.error(state.getCurrentLine() + ": Undefined status str for provinces / external regions. No UUID given: '" + statusStr + "'");
|
| 1557 |
|
|
}else{
|
| 1558 |
|
|
status = getPresenceTerm(state, statusUuid, statusStr, statusStr, statusStr, false);
|
| 1559 |
|
|
}
|
| 1560 |
0a6a64c9
|
Andreas Müller
|
}
|
| 1561 |
|
|
}
|
| 1562 |
|
|
|
| 1563 |
|
|
return status;
|
| 1564 |
|
|
}
|
| 1565 |
|
|
|
| 1566 |
|
|
|
| 1567 |
|
|
/**
|
| 1568 |
|
|
* @param highestStatus
|
| 1569 |
|
|
* @throws UndefinedTransformerMethodException
|
| 1570 |
|
|
*/
|
| 1571 |
|
|
private PresenceAbsenceTerm getAbsenceTermForStatus(CubaImportState state, PresenceAbsenceTerm highestStatus) throws UndefinedTransformerMethodException {
|
| 1572 |
|
|
if (highestStatus == null){
|
| 1573 |
|
|
logger.warn(state.getCurrentLine() + ": Highest status not defined");
|
| 1574 |
|
|
return null;
|
| 1575 |
|
|
}
|
| 1576 |
|
|
PresenceAbsenceTerm result = null;
|
| 1577 |
|
|
if (highestStatus.equals(getStatus(state, "E"))){
|
| 1578 |
|
|
result = getStatus(state, "-E");
|
| 1579 |
|
|
}else if (highestStatus.getUuid().equals(state.getTransformer().getPresenceTermUuid("Ind.")) || highestStatus.equals(PresenceAbsenceTerm.NATIVE())){
|
| 1580 |
|
|
result = getStatus(state, "-Ind.");
|
| 1581 |
|
|
}else if (highestStatus.equals(getStatus(state, "Ind.?"))){
|
| 1582 |
|
|
result = getStatus(state, "-Ind.?"); //TODO
|
| 1583 |
|
|
}else if (highestStatus.equals(getStatus(state, "N"))){
|
| 1584 |
|
|
result = getStatus(state, "-N");
|
| 1585 |
|
|
}else if (highestStatus.equals(getStatus(state, "P"))){
|
| 1586 |
|
|
result = getStatus(state, "-P");
|
| 1587 |
|
|
}else if (highestStatus.equals(getStatus(state, "A"))){
|
| 1588 |
|
|
result = getStatus(state, "-A");
|
| 1589 |
|
|
}else if (highestStatus.equals(getStatus(state, "C"))){
|
| 1590 |
|
|
result = getStatus(state, "-C");
|
| 1591 |
|
|
}
|
| 1592 |
|
|
logger.warn(state.getCurrentLine() + ": Absent province status could not be defined for highest status " + highestStatus.getTitleCache());
|
| 1593 |
|
|
return result;
|
| 1594 |
|
|
}
|
| 1595 |
|
|
|
| 1596 |
|
|
|
| 1597 |
|
|
/**
|
| 1598 |
|
|
* @param string
|
| 1599 |
|
|
* @return
|
| 1600 |
|
|
* @throws UndefinedTransformerMethodException
|
| 1601 |
|
|
*/
|
| 1602 |
|
|
private PresenceAbsenceTerm getStatus(CubaImportState state, String key) throws UndefinedTransformerMethodException {
|
| 1603 |
|
|
PresenceAbsenceTerm status = state.getTransformer().getPresenceTermByKey(key);
|
| 1604 |
|
|
if (status == null){
|
| 1605 |
|
|
UUID statusUuid = state.getTransformer().getPresenceTermUuid(key);
|
| 1606 |
fb3dec85
|
Andreas Müller
|
status = getPresenceTerm(state, statusUuid, null, null, null, false);
|
| 1607 |
|
|
}
|
| 1608 |
|
|
return status;
|
| 1609 |
|
|
}
|
| 1610 |
ede5c502
|
Andreas Müller
|
|
| 1611 |
|
|
|
| 1612 |
fb3dec85
|
Andreas Müller
|
/**
|
| 1613 |
ede5c502
|
Andreas Müller
|
* Stores parent-child, synonym and common name relationships
|
| 1614 |
|
|
*/
|
| 1615 |
|
|
@Override
|
| 1616 |
|
|
protected void secondPass(CubaImportState state) {
|
| 1617 |
|
|
// CyprusRow cyprusRow = state.getCyprusRow();
|
| 1618 |
|
|
return;
|
| 1619 |
|
|
}
|
| 1620 |
|
|
|
| 1621 |
|
|
|
| 1622 |
|
|
@Override
|
| 1623 |
|
|
protected boolean isIgnore(CubaImportState state) {
|
| 1624 |
|
|
return ! state.getConfig().isDoTaxa();
|
| 1625 |
|
|
}
|
| 1626 |
|
|
|
| 1627 |
|
|
@Override
|
| 1628 |
|
|
protected boolean doCheck(CubaImportState state) {
|
| 1629 |
|
|
logger.warn("DoCheck not yet implemented for CubaExcelImport");
|
| 1630 |
|
|
return true;
|
| 1631 |
|
|
}
|
| 1632 |
|
|
|
| 1633 |
|
|
}
|