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/**
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* Copyright (C) 2013 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.io.taxonx2013;
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import java.io.BufferedWriter;
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import java.io.File;
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import java.io.FileWriter;
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import java.io.IOException;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import java.util.UUID;
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import java.util.regex.Matcher;
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import java.util.regex.Pattern;
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import javax.xml.transform.TransformerException;
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import javax.xml.transform.TransformerFactoryConfigurationError;
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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.w3c.dom.Node;
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import org.w3c.dom.NodeList;
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import com.ibm.lsid.MalformedLSIDException;
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import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;
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import eu.etaxonomy.cdm.api.service.pager.Pager;
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import eu.etaxonomy.cdm.common.URI;
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import eu.etaxonomy.cdm.model.agent.AgentBase;
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import eu.etaxonomy.cdm.model.agent.Person;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.IdentifiableSource;
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import eu.etaxonomy.cdm.model.common.LSID;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.description.TaxonNameDescription;
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import eu.etaxonomy.cdm.model.description.TextData;
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import eu.etaxonomy.cdm.model.name.INonViralName;
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
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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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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
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import eu.etaxonomy.cdm.model.reference.OriginalSourceType;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
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import eu.etaxonomy.cdm.model.taxon.Classification;
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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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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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import eu.etaxonomy.cdm.model.taxon.TaxonNode;
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import eu.etaxonomy.cdm.model.term.TermNode;
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import eu.etaxonomy.cdm.model.term.TermTree;
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import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;
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import eu.etaxonomy.cdm.persistence.query.MatchMode;
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import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
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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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import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImplRegExBase;
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/**
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* @author pkelbert
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* @since 2 avr. 2013
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*
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*/
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public class TaxonXTreatmentExtractor extends TaxonXExtractor{
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private static final String PUBLICATION_YEAR = "publicationYear";
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private static final Logger logger = Logger.getLogger(TaxonXTreatmentExtractor.class);
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private static final String notMarkedUp = "Not marked-up";
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private static final UUID proIbioTreeUUID = UUID.fromString("2c49f506-c7f7-44de-a8b9-2e695de3769c");
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private static final UUID OtherUUID = UUID.fromString("6465f8aa-2175-446f-807e-7163994b120f");
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private static final UUID NotMarkedUpUUID = UUID.fromString("796fe3a5-2c9c-4a89-b298-7598ca944063");
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private static final boolean skippQuestion = true;
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private final NomenclaturalCode nomenclaturalCode;
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private Classification classification;
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private String treatmentMainName,originalTreatmentName;
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private final HashMap<String,Map<String,String>> namesMap = new HashMap<>();
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private final Pattern keypattern = Pattern.compile("^(\\d+.*|-\\d+.*)");
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private final Pattern keypatternend = Pattern.compile("^.+?\\d$");
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private boolean maxRankRespected =false;
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private Map<String, Feature> featuresMap;
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private MyName currentMyName;
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private Reference sourceUrlRef;
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private String followingText; //text element immediately following a tax:name in tax:nomenclature TODO move do state
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private String usedFollowingTextPrefix; //the part of the following text which has been used during taxon name creation
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private final TaxonXAddSources sourceHandler = new TaxonXAddSources();
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/**
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* @param nomenclaturalCode
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* @param classification
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* @param importer
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* @param configState
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*/
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public TaxonXTreatmentExtractor(NomenclaturalCode nomenclaturalCode, Classification classification, TaxonXImport importer,
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TaxonXImportState configState,Map<String, Feature> featuresMap, Reference urlSource) {
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this.nomenclaturalCode=nomenclaturalCode;
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this.classification = classification;
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this.importer=importer;
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this.state2=configState;
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this.featuresMap=featuresMap;
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this.sourceUrlRef =urlSource;
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prepareCollectors(configState, importer.getAgentService());
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this.sourceHandler.setSourceUrlRef(sourceUrlRef);
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this.sourceHandler.setImporter(importer);
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this.sourceHandler.setConfigState(configState);
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}
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/**
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* extracts all the treament information and save them
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* @param treatmentnode: the XML Node
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* @param tosave: the list of object to save into the CDM
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* @param refMods: the reference extracted from the MODS
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* @param sourceName: the URI of the document
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*/
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@SuppressWarnings({ "rawtypes", "unused" })
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protected void extractTreatment(Node treatmentnode, Reference refMods, URI sourceName) { logger.info("extractTreatment");
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List<TaxonName> namesToSave = new ArrayList<>();
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NodeList children = treatmentnode.getChildNodes();
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Taxon acceptedTaxon =null;
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boolean hasRefgroup=false;
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//needed?
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for (int i=0;i<children.getLength();i++){
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if(children.item(i).getNodeName().equalsIgnoreCase("tax:ref_group")) {
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hasRefgroup=true;
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}
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}
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for (int i=0;i<children.getLength();i++){
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Node child = children.item(i);
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acceptedTaxon = handleSingleNode(refMods, sourceName, namesToSave, child, acceptedTaxon);
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}
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// logger.info("saveUpdateNames");
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if (maxRankRespected){
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importer.getNameService().saveOrUpdate(namesToSave);
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importer.getClassificationService().saveOrUpdate(classification);
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//logger.info("saveUpdateNames-ok");
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}
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buildFeatureTree();
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}
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private Taxon handleSingleNode(Reference refMods, URI sourceName,
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List<TaxonName> namesToSave, Node child, Taxon acceptedTaxon) {
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Taxon defaultTaxon =null;
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String nodeName = child.getNodeName();
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if (nodeName.equalsIgnoreCase("tax:nomenclature")){
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NodeList nomenclatureChildren = child.getChildNodes();
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boolean containsName = false;
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for(int k=0; k<nomenclatureChildren.getLength(); k++){
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if(nomenclatureChildren.item(k).getNodeName().equalsIgnoreCase("tax:name")){
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containsName=true;
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break;
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}
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}
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if (containsName){
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reloadClassification();
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//extract "main" the scientific name
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try{
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acceptedTaxon = extractNomenclature(child, namesToSave, refMods);
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}catch(ClassCastException e){
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//FIXME exception handling
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e.printStackTrace();
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}
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// System.out.println("acceptedTaxon : "+acceptedTaxon);
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}
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}else if (nodeName.equalsIgnoreCase("tax:ref_group") && maxRankRespected){
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reloadClassification();
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//extract the References within the document
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extractReferences(child, namesToSave ,acceptedTaxon,refMods);
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}else if (nodeName.equalsIgnoreCase("tax:div") &&
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child.getAttributes().getNamedItem("type").getNodeValue().equalsIgnoreCase("multiple") && maxRankRespected){
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File file = new File(TaxonXImport.LOG_FOLDER + "multipleTaxonX.txt");
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FileWriter writer;
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try {
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writer = new FileWriter(file ,true);
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writer.write(sourceName+"\n");
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writer.flush();
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writer.close();
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} catch (IOException e1) {
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// TODO Auto-generated catch block
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logger.error(e1.getMessage());
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}
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// String multiple = askMultiple(children.item(i));
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String multiple = "Other";
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if (multiple.equalsIgnoreCase("other")) {
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extractSpecificFeatureNotStructured(child,acceptedTaxon, defaultTaxon,namesToSave, refMods,multiple);
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}else if (multiple.equalsIgnoreCase("synonyms")) {
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try{
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extractSynonyms(child,acceptedTaxon, refMods, null);
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}catch(NullPointerException e){
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logger.warn("the accepted taxon is maybe null");
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}
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}else if(multiple.equalsIgnoreCase("material examined")){
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extractMaterials(child, acceptedTaxon, refMods, namesToSave);
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}else if (multiple.equalsIgnoreCase("distribution")){
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extractDistribution(child, acceptedTaxon, defaultTaxon, namesToSave, refMods);
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}else if (multiple.equalsIgnoreCase("type status")){
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extractDescriptionWithReference(child, acceptedTaxon, defaultTaxon,refMods, "TypeStatus");
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}else if (multiple.equalsIgnoreCase("vernacular name")){
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extractDescriptionWithReference(child, acceptedTaxon, defaultTaxon,refMods, Feature.COMMON_NAME().getTitleCache());
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}else{
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extractSpecificFeature(child,acceptedTaxon,defaultTaxon,namesToSave, refMods,multiple);
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}
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}
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else if(nodeName.equalsIgnoreCase("tax:div") &&
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child.getAttributes().getNamedItem("type").getNodeValue().equalsIgnoreCase("biology_ecology") && maxRankRespected){
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extractFeature(child,acceptedTaxon,defaultTaxon, namesToSave, refMods, Feature.BIOLOGY_ECOLOGY());
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}
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else if(nodeName.equalsIgnoreCase("tax:div") &&
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child.getAttributes().getNamedItem("type").getNodeValue().equalsIgnoreCase("vernacularName") && maxRankRespected){
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extractDescriptionWithReference(child, acceptedTaxon,defaultTaxon,refMods, Feature.COMMON_NAME().getTitleCache());
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}
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else if(nodeName.equalsIgnoreCase("tax:div") &&
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child.getAttributes().getNamedItem("type").getNodeValue().equalsIgnoreCase("description") && maxRankRespected){
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extractFeature(child,acceptedTaxon,defaultTaxon,namesToSave, refMods, Feature.DESCRIPTION());
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}
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else if(nodeName.equalsIgnoreCase("tax:div") &&
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child.getAttributes().getNamedItem("type").getNodeValue().equalsIgnoreCase("diagnosis") && maxRankRespected){
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extractFeature(child,acceptedTaxon,defaultTaxon,namesToSave, refMods,Feature.DIAGNOSIS());
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}
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else if(nodeName.equalsIgnoreCase("tax:div") &&
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child.getAttributes().getNamedItem("type").getNodeValue().equalsIgnoreCase("discussion") && maxRankRespected){
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extractFeature(child,acceptedTaxon,defaultTaxon,namesToSave, refMods, Feature.DISCUSSION());
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}
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else if(nodeName.equalsIgnoreCase("tax:div") &&
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child.getAttributes().getNamedItem("type").getNodeValue().equalsIgnoreCase("note") && maxRankRespected){
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extractFeature(child,acceptedTaxon,defaultTaxon,namesToSave, refMods, Feature.DESCRIPTION());
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}
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else if(nodeName.equalsIgnoreCase("tax:div") &&
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child.getAttributes().getNamedItem("type").getNodeValue().equalsIgnoreCase("distribution") && maxRankRespected){
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extractDistribution(child,acceptedTaxon,defaultTaxon,namesToSave, refMods);
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}
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else if(nodeName.equalsIgnoreCase("tax:div") &&
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child.getAttributes().getNamedItem("type").getNodeValue().equalsIgnoreCase("etymology") && maxRankRespected){
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extractFeature(child,acceptedTaxon,defaultTaxon,namesToSave,refMods,Feature.ETYMOLOGY());
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}
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else if(nodeName.equalsIgnoreCase("tax:div") &&
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child.getAttributes().getNamedItem("type").getNodeValue().equalsIgnoreCase("materials_examined") && maxRankRespected){
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extractMaterials(child,acceptedTaxon, refMods, namesToSave);
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}
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else if(nodeName.equalsIgnoreCase("tax:figure") && maxRankRespected){
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extractSpecificFeature(child,acceptedTaxon,defaultTaxon, namesToSave, refMods, "Figure");
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}
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else if(nodeName.equalsIgnoreCase("tax:div") &&
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child.getAttributes().getNamedItem("type").getNodeValue().equalsIgnoreCase("Other") && maxRankRespected){
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extractSpecificFeature(child, acceptedTaxon,defaultTaxon, namesToSave, refMods, "table");
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}else if(nodeName.equalsIgnoreCase("tax:div") &&
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child.getAttributes().getNamedItem("type").getNodeValue().equalsIgnoreCase("key") && maxRankRespected){
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//TODO IGNORE keys for the moment
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//extractKey(children.item(i),acceptedTaxon, nameToSave,source, refMods);
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extractSpecificFeatureNotStructured(child,acceptedTaxon,defaultTaxon,namesToSave, refMods,"Keys - unparsed");
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}
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else{
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if (! nodeName.equalsIgnoreCase("tax:pb")){
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//logger.info("ANOTHER KIND OF NODES: "+children.item(i).getNodeName()+", "+children.item(i).getAttributes());
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if (child.getAttributes() !=null) {
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logger.info("First Attribute: " + child.getAttributes().item(0));
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}
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extractSpecificFeatureNotStructured(child,acceptedTaxon,defaultTaxon,namesToSave, refMods, notMarkedUp);
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}else{
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//FIXME
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logger.warn("Unhandled");
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}
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}
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return acceptedTaxon;
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}
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protected Map<String,Feature> getFeaturesUsed(){
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return featuresMap;
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}
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/**
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*
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*/
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private void buildFeatureTree() {
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logger.info("buildFeatureTree");
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TermTree proibiospheretree = importer.getFeatureTreeService().find(proIbioTreeUUID);
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if (proibiospheretree == null){
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List<TermTree> trees = importer.getFeatureTreeService().list(TermTree.class, null, null, null, null);
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if (trees.size()==1) {
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TermTree<Feature> ft = trees.get(0);
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if (featuresMap==null) {
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featuresMap=new HashMap<>();
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}
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for (Feature feature: ft.getDistinctTerms()){
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if(feature!=null) {
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featuresMap.put(feature.getTitleCache(), feature);
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}
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}
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}
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proibiospheretree = TermTree.NewFeatureInstance();
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322
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proibiospheretree.setUuid(proIbioTreeUUID);
|
|
323
|
}
|
|
324
|
|
|
325
|
TermNode root2 = proibiospheretree.getRoot();
|
|
326
|
if (root2 != null){
|
|
327
|
int nbChildren = root2.getChildCount()-1;
|
|
328
|
while (nbChildren>-1){
|
|
329
|
try{
|
|
330
|
root2.removeChild(nbChildren);
|
|
331
|
}catch(Exception e){logger.warn("Can't remove child from FeatureTree "+e);}
|
|
332
|
nbChildren --;
|
|
333
|
}
|
|
334
|
|
|
335
|
}
|
|
336
|
|
|
337
|
for (Feature feature:featuresMap.values()) {
|
|
338
|
root2.addChild(feature);
|
|
339
|
}
|
|
340
|
importer.getFeatureTreeService().saveOrUpdate(proibiospheretree);
|
|
341
|
|
|
342
|
}
|
|
343
|
|
|
344
|
|
|
345
|
/**
|
|
346
|
* @param keys
|
|
347
|
* @param acceptedTaxon: the current acceptedTaxon
|
|
348
|
* @param nametosave: the list of objects to save into the CDM
|
|
349
|
* @param refMods: the current reference extracted from the MODS
|
|
350
|
*/
|
|
351
|
/* @SuppressWarnings("rawtypes")
|
|
352
|
private void extractKey(Node keys, Taxon acceptedTaxon,List<TaxonName> nametosave, Reference refMods) {
|
|
353
|
acceptedTaxon = CdmBase.deproxy(acceptedTaxon, Taxon.class);
|
|
354
|
|
|
355
|
NodeList children = keys.getChildNodes();
|
|
356
|
String key="";
|
|
357
|
PolytomousKey poly = PolytomousKey.NewInstance();
|
|
358
|
poly.addSource(OriginalSourceType.Import, null,null,refMods,null);
|
|
359
|
poly.addSource(OriginalSourceType.Import, null,null,sourceUrlRef,null);
|
|
360
|
poly.addTaxonomicScope(acceptedTaxon);
|
|
361
|
poly.setTitleCache("bloup", true);
|
|
362
|
// poly.addCoveredTaxon(acceptedTaxon);
|
|
363
|
PolytomousKeyNode root = poly.getRoot();
|
|
364
|
PolytomousKeyNode previous = null,tmpKey=null;
|
|
365
|
Taxon taxonKey=null;
|
|
366
|
List<PolytomousKeyNode> polyNodes = new ArrayList<PolytomousKeyNode>();
|
|
367
|
|
|
368
|
// String fullContent = keys.getTextContent();
|
|
369
|
for (int i=0;i<children.getLength();i++){
|
|
370
|
if (children.item(i).getNodeName().equalsIgnoreCase("tax:p")){
|
|
371
|
NodeList paragraph = children.item(i).getChildNodes();
|
|
372
|
key="";
|
|
373
|
taxonKey=null;
|
|
374
|
for (int j=0;j<paragraph.getLength();j++){
|
|
375
|
if (paragraph.item(j).getNodeName().equalsIgnoreCase("#text")){
|
|
376
|
if (! paragraph.item(j).getTextContent().trim().isEmpty()){
|
|
377
|
key+=paragraph.item(j).getTextContent().trim();
|
|
378
|
// logger.info("KEY: "+j+"--"+key);
|
|
379
|
}
|
|
380
|
}
|
|
381
|
if(paragraph.item(j).getNodeName().equalsIgnoreCase("tax:name")){
|
|
382
|
taxonKey=getTaxonFromXML(paragraph.item(j),nametosave,refMods);
|
|
383
|
}
|
|
384
|
}
|
|
385
|
// logger.info("keypattern.matcher(key).matches(): "+keypattern.matcher(key).matches());
|
|
386
|
if (keypattern.matcher(key).matches()){
|
|
387
|
tmpKey = PolytomousKeyNode.NewInstance(key);
|
|
388
|
if (taxonKey!=null) {
|
|
389
|
tmpKey.setTaxon(taxonKey);
|
|
390
|
}
|
|
391
|
polyNodes.add(tmpKey);
|
|
392
|
if (previous == null) {
|
|
393
|
root.addChild(tmpKey);
|
|
394
|
} else {
|
|
395
|
previous.addChild(tmpKey);
|
|
396
|
}
|
|
397
|
}else{
|
|
398
|
if (!key.isEmpty()){
|
|
399
|
tmpKey=PolytomousKeyNode.NewInstance(key);
|
|
400
|
if (taxonKey!=null) {
|
|
401
|
tmpKey.setTaxon(taxonKey);
|
|
402
|
}
|
|
403
|
polyNodes.add(tmpKey);
|
|
404
|
if (keypatternend.matcher(key).matches()) {
|
|
405
|
root.addChild(tmpKey);
|
|
406
|
previous=tmpKey;
|
|
407
|
} else{
|
|
408
|
previous.addChild(tmpKey);
|
|
409
|
}
|
|
410
|
|
|
411
|
}
|
|
412
|
}
|
|
413
|
}
|
|
414
|
}
|
|
415
|
importer.getPolytomousKeyNodeService().saveOrUpdate(polyNodes);
|
|
416
|
importer.getPolytomousKeyService().saveOrUpdate(poly);
|
|
417
|
}
|
|
418
|
*/
|
|
419
|
|
|
420
|
|
|
421
|
/**
|
|
422
|
* @param taxons: the XML Nodegroup
|
|
423
|
* @param nametosave: the list of objects to save into the CDM
|
|
424
|
* @param acceptedTaxon: the current accepted Taxon
|
|
425
|
* @param refMods: the current reference extracted from the MODS
|
|
426
|
*
|
|
427
|
* @return Taxon object built
|
|
428
|
*/
|
|
429
|
@SuppressWarnings({ "rawtypes", "unused" })
|
|
430
|
private TaxonName getTaxonNameFromXML(Node taxons, List<TaxonName> nametosave, Reference refMods, boolean isSynonym) {
|
|
431
|
// logger.info("getTaxonFromXML");
|
|
432
|
// logger.info("acceptedTaxon: "+acceptedTaxon);
|
|
433
|
logger.info("getTaxonNameFromXML");
|
|
434
|
TaxonName nameToBeFilled = null;
|
|
435
|
|
|
436
|
currentMyName=new MyName(isSynonym);
|
|
437
|
|
|
438
|
NomenclaturalStatusType statusType = null;
|
|
439
|
try {
|
|
440
|
String followingText = null; //needs to be checked if following text is possible
|
|
441
|
currentMyName = extractScientificName(taxons,refMods, null);
|
|
442
|
} catch (TransformerFactoryConfigurationError e1) {
|
|
443
|
logger.warn(e1);
|
|
444
|
} catch (TransformerException e1) {
|
|
445
|
logger.warn(e1);
|
|
446
|
}
|
|
447
|
/* INonViralNameParser parser = NonViralNameParserImpl.NewInstance();
|
|
448
|
|
|
449
|
nameToBeFilled = parser.parseFullName(currentMyName.getName(), nomenclaturalCode, currentMyName.getRank());
|
|
450
|
if (nameToBeFilled.hasProblem() &&
|
|
451
|
!((nameToBeFilled.getParsingProblems().size()==1) && nameToBeFilled.getParsingProblems().contains(ParserProblem.CheckRank)) ) {
|
|
452
|
// if (nameToBeFilled.hasProblem() && nameToBeFilled.getParsingProblems().contains(ParserProblem.UnparsableNamePart)){
|
|
453
|
addProblemNameToFile(currentMyName.getName(),"",nomenclaturalCode,currentMyName.getRank());
|
|
454
|
nameToBeFilled=solveNameProblem(currentMyName.getOriginalName(), currentMyName.getName(),parser,currentMyName.getAuthor(), currentMyName.getRank());
|
|
455
|
}
|
|
456
|
|
|
457
|
nameToBeFilled = getTaxonName(nameToBeFilled,nametosave,statusType);
|
|
458
|
*/
|
|
459
|
nameToBeFilled = currentMyName.getTaxonName();
|
|
460
|
return nameToBeFilled;
|
|
461
|
|
|
462
|
}
|
|
463
|
|
|
464
|
|
|
465
|
/**
|
|
466
|
*
|
|
467
|
*/
|
|
468
|
private void reloadClassification() {
|
|
469
|
logger.info("reloadClassification");
|
|
470
|
Classification cl = importer.getClassificationService().find(classification.getUuid());
|
|
471
|
if (cl != null){
|
|
472
|
classification = cl;
|
|
473
|
}else{
|
|
474
|
importer.getClassificationService().saveOrUpdate(classification);
|
|
475
|
classification = importer.getClassificationService().find(classification.getUuid());
|
|
476
|
}
|
|
477
|
}
|
|
478
|
|
|
479
|
// /**
|
|
480
|
// * Create a Taxon for the current NameBase, based on the current reference
|
|
481
|
// * @param taxonName
|
|
482
|
// * @param refMods: the current reference extracted from the MODS
|
|
483
|
// * @return Taxon
|
|
484
|
// */
|
|
485
|
// @SuppressWarnings({ "unused", "rawtypes" })
|
|
486
|
// private Taxon getTaxon(TaxonName taxonName, Reference refMods) {
|
|
487
|
// Taxon t = new Taxon(taxonName,null );
|
|
488
|
// if (!configState.getConfig().doKeepOriginalSecundum() || (t.getSec() == null)) {
|
|
489
|
// t.setSec(configState.getConfig().getSecundum());
|
|
490
|
// logger.info("SET SECUNDUM "+configState.getConfig().getSecundum());
|
|
491
|
// }
|
|
492
|
// /*<<<<<<< .courant
|
|
493
|
// boolean sourceExists=false;
|
|
494
|
// Set<IdentifiableSource> sources = t.getSources();
|
|
495
|
// for (IdentifiableSource src : sources){
|
|
496
|
// String micro = src.getCitationMicroReference();
|
|
497
|
// Reference r = src.getCitation();
|
|
498
|
// if (r.equals(refMods) && micro == null) {
|
|
499
|
// sourceExists=true;
|
|
500
|
// }
|
|
501
|
// }
|
|
502
|
// if(!sourceExists) {
|
|
503
|
// t.addSource(null,null,refMods,null);
|
|
504
|
// }
|
|
505
|
//=======*/
|
|
506
|
// t.addSource(OriginalSourceType.Import,null,null,refMods,null);
|
|
507
|
// t.addSource(OriginalSourceType.Import, null,null,sourceUrlRef,null);
|
|
508
|
// return t;
|
|
509
|
// }
|
|
510
|
|
|
511
|
private void extractDescriptionWithReference(Node typestatus, Taxon acceptedTaxon, Taxon defaultTaxon, Reference refMods,
|
|
512
|
String featureName) {
|
|
513
|
// System.out.println("extractDescriptionWithReference !");
|
|
514
|
logger.info("extractDescriptionWithReference");
|
|
515
|
NodeList children = typestatus.getChildNodes();
|
|
516
|
|
|
517
|
Feature currentFeature=getFeatureObjectFromString(featureName);
|
|
518
|
|
|
519
|
String r="";String s="";
|
|
520
|
for (int i=0;i<children.getLength();i++){
|
|
521
|
if (children.item(i).getNodeName().equalsIgnoreCase("tax:p")){
|
|
522
|
s+=children.item(i).getTextContent().trim();
|
|
523
|
}
|
|
524
|
if (children.item(i).getNodeName().equalsIgnoreCase("tax:bibref")){
|
|
525
|
r+= children.item(i).getTextContent().trim();
|
|
526
|
}
|
|
527
|
if (s.indexOf(r)>-1) {
|
|
528
|
s=s.split(r)[0];
|
|
529
|
}
|
|
530
|
}
|
|
531
|
|
|
532
|
Reference currentref = ReferenceFactory.newGeneric();
|
|
533
|
if(!r.isEmpty()) {
|
|
534
|
currentref.setTitleCache(r, true);
|
|
535
|
} else {
|
|
536
|
currentref=refMods;
|
|
537
|
}
|
|
538
|
setParticularDescription(s,acceptedTaxon,defaultTaxon, currentref, refMods,currentFeature);
|
|
539
|
}
|
|
540
|
|
|
541
|
/**
|
|
542
|
* @param nametosave
|
|
543
|
* @param distribution: the XML node group
|
|
544
|
* @param acceptedTaxon: the current accepted Taxon
|
|
545
|
* @param defaultTaxon: the current defaultTaxon, only used if there is no accepted name
|
|
546
|
* @param refMods: the current reference extracted from the MODS
|
|
547
|
*/
|
|
548
|
@SuppressWarnings("rawtypes")
|
|
549
|
private void extractDistribution(Node distribution, Taxon acceptedTaxon, Taxon defaultTaxon, List<TaxonName> nametosave, Reference refMods) {
|
|
550
|
logger.info("extractDistribution");
|
|
551
|
// logger.info("acceptedTaxon: "+acceptedTaxon);
|
|
552
|
NodeList children = distribution.getChildNodes();
|
|
553
|
Map<Integer,List<MySpecimenOrObservation>> specimenOrObservations = new HashMap<>();
|
|
554
|
Map<Integer,String> descriptionsFulltext = new HashMap<>();
|
|
555
|
|
|
556
|
for (int i=0;i<children.getLength();i++){
|
|
557
|
if (children.item(i).getNodeName().equalsIgnoreCase("tax:p")){
|
|
558
|
NodeList paragraph = children.item(i).getChildNodes();
|
|
559
|
for (int j=0;j<paragraph.getLength();j++){
|
|
560
|
if (paragraph.item(j).getNodeName().equalsIgnoreCase("#text")){
|
|
561
|
extractText(descriptionsFulltext, i, paragraph.item(j));
|
|
562
|
}
|
|
563
|
else if (paragraph.item(j).getNodeName().equalsIgnoreCase("tax:name")){
|
|
564
|
extractInLine(nametosave, refMods, descriptionsFulltext, i,paragraph.item(j));
|
|
565
|
}
|
|
566
|
else if (paragraph.item(j).getNodeName().equalsIgnoreCase("tax:collection_event")){
|
|
567
|
MySpecimenOrObservation specimenOrObservation = new MySpecimenOrObservation();
|
|
568
|
DerivedUnit derivedUnitBase = null;
|
|
569
|
specimenOrObservation = extractSpecimenOrObservation(paragraph.item(j), derivedUnitBase, SpecimenOrObservationType.DerivedUnit, null);
|
|
570
|
extractTextFromSpecimenOrObservation(specimenOrObservations, descriptionsFulltext, i, specimenOrObservation);
|
|
571
|
}
|
|
572
|
}
|
|
573
|
}
|
|
574
|
}
|
|
575
|
|
|
576
|
int m=0;
|
|
577
|
for (int k:descriptionsFulltext.keySet()) {
|
|
578
|
if (k>m) {
|
|
579
|
m=k;
|
|
580
|
}
|
|
581
|
}
|
|
582
|
for (int k:specimenOrObservations.keySet()) {
|
|
583
|
if (k>m) {
|
|
584
|
m=k;
|
|
585
|
}
|
|
586
|
}
|
|
587
|
|
|
588
|
|
|
589
|
if(acceptedTaxon!=null){
|
|
590
|
TaxonDescription td =importer.getTaxonDescription(acceptedTaxon, false, true);
|
|
591
|
Feature currentFeature = Feature.DISTRIBUTION();
|
|
592
|
// DerivedUnit derivedUnitBase=null;
|
|
593
|
// String descr="";
|
|
594
|
for (int k=0;k<=m;k++){
|
|
595
|
if(specimenOrObservations.keySet().contains(k)){
|
|
596
|
for (MySpecimenOrObservation soo:specimenOrObservations.get(k) ) {
|
|
597
|
handleAssociation(acceptedTaxon, refMods, td, soo);
|
|
598
|
}
|
|
599
|
}
|
|
600
|
|
|
601
|
if (descriptionsFulltext.keySet().contains(k)){
|
|
602
|
if (!stringIsEmpty(descriptionsFulltext.get(k).trim()) && (descriptionsFulltext.get(k).startsWith("Hab.") || descriptionsFulltext.get(k).startsWith("Habitat"))){
|
|
603
|
setParticularDescription(descriptionsFulltext.get(k),acceptedTaxon,defaultTaxon, refMods, Feature.HABITAT());
|
|
604
|
break;
|
|
605
|
}
|
|
606
|
else{
|
|
607
|
handleTextData(refMods, descriptionsFulltext, td, currentFeature, k);
|
|
608
|
}
|
|
609
|
}
|
|
610
|
|
|
611
|
if (descriptionsFulltext.keySet().contains(k) || specimenOrObservations.keySet().contains(k)){
|
|
612
|
acceptedTaxon.addDescription(td);
|
|
613
|
sourceHandler.addAndSaveSource(refMods, td, null);
|
|
614
|
importer.getTaxonService().saveOrUpdate(acceptedTaxon);
|
|
615
|
}
|
|
616
|
}
|
|
617
|
}
|
|
618
|
}
|
|
619
|
|
|
620
|
/**
|
|
621
|
* @param refMods
|
|
622
|
* @param descriptionsFulltext
|
|
623
|
* @param td
|
|
624
|
* @param currentFeature
|
|
625
|
* @param k
|
|
626
|
*/
|
|
627
|
private void handleTextData(Reference refMods, Map<Integer, String> descriptionsFulltext, TaxonDescription td,
|
|
628
|
Feature currentFeature, int k) {
|
|
629
|
//logger.info("handleTextData");
|
|
630
|
TextData textData = TextData.NewInstance();
|
|
631
|
textData.setFeature(currentFeature);
|
|
632
|
textData.putText(Language.UNKNOWN_LANGUAGE(), descriptionsFulltext.get(k));
|
|
633
|
sourceHandler.addSource(refMods, textData);
|
|
634
|
td.addElement(textData);
|
|
635
|
}
|
|
636
|
|
|
637
|
/**
|
|
638
|
* @param acceptedTaxon
|
|
639
|
* @param refMods
|
|
640
|
* @param td
|
|
641
|
* @param soo
|
|
642
|
*/
|
|
643
|
private void handleAssociation(Taxon acceptedTaxon, Reference refMods, TaxonDescription td, MySpecimenOrObservation soo) {
|
|
644
|
logger.info("handleAssociation");
|
|
645
|
String descr=soo.getDescr();
|
|
646
|
DerivedUnit derivedUnitBase = soo.getDerivedUnitBase();
|
|
647
|
|
|
648
|
sourceHandler.addAndSaveSource(refMods, derivedUnitBase);
|
|
649
|
|
|
650
|
TaxonDescription taxonDescription = importer.getTaxonDescription(acceptedTaxon, false, true);
|
|
651
|
|
|
652
|
Feature feature=null;
|
|
653
|
feature = makeFeature(derivedUnitBase);
|
|
654
|
if(!StringUtils.isEmpty(descr)) {
|
|
655
|
derivedUnitBase.setTitleCache(descr, true);
|
|
656
|
}
|
|
657
|
|
|
658
|
IndividualsAssociation indAssociation = createIndividualAssociation(refMods, derivedUnitBase, feature);
|
|
659
|
|
|
660
|
taxonDescription.addElement(indAssociation);
|
|
661
|
sourceHandler.addAndSaveSource(refMods, taxonDescription,null);
|
|
662
|
importer.getTaxonService().saveOrUpdate(acceptedTaxon);
|
|
663
|
td.setDescribedSpecimenOrObservation(soo.getDerivedUnitBase());
|
|
664
|
}
|
|
665
|
|
|
666
|
/**
|
|
667
|
* create an individualAssociation
|
|
668
|
* @param refMods
|
|
669
|
* @param derivedUnitBase
|
|
670
|
* @param feature
|
|
671
|
* @return
|
|
672
|
*/
|
|
673
|
private IndividualsAssociation createIndividualAssociation(Reference refMods, DerivedUnit derivedUnitBase,
|
|
674
|
Feature feature) {
|
|
675
|
logger.info("createIndividualAssociation");
|
|
676
|
IndividualsAssociation indAssociation = IndividualsAssociation.NewInstance();
|
|
677
|
indAssociation.setAssociatedSpecimenOrObservation(derivedUnitBase);
|
|
678
|
indAssociation.setFeature(feature);
|
|
679
|
indAssociation = sourceHandler.addSource(refMods, indAssociation);
|
|
680
|
return indAssociation;
|
|
681
|
}
|
|
682
|
|
|
683
|
/**
|
|
684
|
* @param specimenOrObservations
|
|
685
|
* @param descriptionsFulltext
|
|
686
|
* @param i
|
|
687
|
* @param specimenOrObservation
|
|
688
|
*/
|
|
689
|
private void extractTextFromSpecimenOrObservation(Map<Integer, List<MySpecimenOrObservation>> specimenOrObservations,
|
|
690
|
Map<Integer, String> descriptionsFulltext, int i, MySpecimenOrObservation specimenOrObservation) {
|
|
691
|
logger.info("extractTextFromSpecimenOrObservation");
|
|
692
|
List<MySpecimenOrObservation> speObsList = specimenOrObservations.get(i);
|
|
693
|
if (speObsList == null) {
|
|
694
|
speObsList=new ArrayList<MySpecimenOrObservation>();
|
|
695
|
}
|
|
696
|
speObsList.add(specimenOrObservation);
|
|
697
|
specimenOrObservations.put(i,speObsList);
|
|
698
|
|
|
699
|
String s = specimenOrObservation.getDerivedUnitBase().toString();
|
|
700
|
if (descriptionsFulltext.get(i) !=null){
|
|
701
|
s = descriptionsFulltext.get(i)+" "+s;
|
|
702
|
}
|
|
703
|
descriptionsFulltext.put(i, s);
|
|
704
|
}
|
|
705
|
|
|
706
|
/**
|
|
707
|
* Extract the text with the inline link to a taxon
|
|
708
|
* @param nametosave
|
|
709
|
* @param refMods
|
|
710
|
* @param descriptionsFulltext
|
|
711
|
* @param i
|
|
712
|
* @param paragraph
|
|
713
|
*/
|
|
714
|
@SuppressWarnings("rawtypes")
|
|
715
|
private void extractInLine(List<TaxonName> nametosave, Reference refMods, Map<Integer, String> descriptionsFulltext,
|
|
716
|
int i, Node paragraph) {
|
|
717
|
//logger.info("extractInLine");
|
|
718
|
String inLine=getInlineTextForName(nametosave, refMods, paragraph);
|
|
719
|
if (descriptionsFulltext.get(i) !=null){
|
|
720
|
inLine = descriptionsFulltext.get(i)+inLine;
|
|
721
|
}
|
|
722
|
descriptionsFulltext.put(i, inLine);
|
|
723
|
}
|
|
724
|
|
|
725
|
/**
|
|
726
|
* Extract the raw text from a Node
|
|
727
|
* @param descriptionsFulltext
|
|
728
|
* @param node
|
|
729
|
* @param j
|
|
730
|
*/
|
|
731
|
private void extractText(Map<Integer, String> descriptionsFulltext, int i, Node node) {
|
|
732
|
//logger.info("extractText");
|
|
733
|
if(!node.getTextContent().trim().isEmpty()) {
|
|
734
|
String s =node.getTextContent().trim();
|
|
735
|
if (descriptionsFulltext.get(i) !=null){
|
|
736
|
s = descriptionsFulltext.get(i)+" "+s;
|
|
737
|
}
|
|
738
|
descriptionsFulltext.put(i, s);
|
|
739
|
}
|
|
740
|
}
|
|
741
|
|
|
742
|
|
|
743
|
/**
|
|
744
|
* @param materials: the XML node group
|
|
745
|
* @param acceptedTaxon: the current accepted Taxon
|
|
746
|
* @param refMods: the current reference extracted from the MODS
|
|
747
|
*/
|
|
748
|
@SuppressWarnings("rawtypes")
|
|
749
|
private void extractMaterials(Node materials, Taxon acceptedTaxon, Reference refMods,List<TaxonName> nametosave) {
|
|
750
|
logger.info("EXTRACTMATERIALS");
|
|
751
|
// logger.info("acceptedTaxon: "+acceptedTaxon);
|
|
752
|
NodeList children = materials.getChildNodes();
|
|
753
|
NodeList events = null;
|
|
754
|
// String descr="";
|
|
755
|
|
|
756
|
|
|
757
|
for (int i=0;i<children.getLength();i++){
|
|
758
|
String rawAssociation="";
|
|
759
|
boolean added=false;
|
|
760
|
if (children.item(i).getNodeName().equalsIgnoreCase("tax:p")){
|
|
761
|
events = children.item(i).getChildNodes();
|
|
762
|
for(int k=0;k<events.getLength();k++){
|
|
763
|
if (events.item(k).getNodeName().equalsIgnoreCase("tax:name")){
|
|
764
|
String inLine= getInlineTextForName(nametosave, refMods, events.item(k));
|
|
765
|
if(!inLine.isEmpty()) {
|
|
766
|
rawAssociation+=inLine;
|
|
767
|
}
|
|
768
|
}
|
|
769
|
if (! events.item(k).getNodeName().equalsIgnoreCase("tax:name")
|
|
770
|
&& !events.item(k).getNodeName().equalsIgnoreCase("tax:collection_event")){
|
|
771
|
rawAssociation+= events.item(k).getTextContent().trim();
|
|
772
|
}
|
|
773
|
if(events.item(k).getNodeName().equalsIgnoreCase("tax:collection_event")){
|
|
774
|
if (!containsDistinctLetters(rawAssociation.replaceAll(";",""))) {
|
|
775
|
rawAssociation="no description text";
|
|
776
|
}
|
|
777
|
added=true;
|
|
778
|
handleDerivedUnitFacadeAndBase(acceptedTaxon, refMods, events.item(k), rawAssociation);
|
|
779
|
}
|
|
780
|
if (!rawAssociation.isEmpty() && !added){
|
|
781
|
|
|
782
|
Feature feature = Feature.MATERIALS_EXAMINED();
|
|
783
|
featuresMap.put(feature.getTitleCache(),feature);
|
|
784
|
|
|
785
|
TextData textData = createTextData(rawAssociation, refMods, feature);
|
|
786
|
|
|
787
|
if(! rawAssociation.isEmpty() && (acceptedTaxon!=null)){
|
|
788
|
TaxonDescription td =importer.getTaxonDescription(acceptedTaxon, false, true);
|
|
789
|
td.addElement(textData);
|
|
790
|
acceptedTaxon.addDescription(td);
|
|
791
|
sourceHandler.addAndSaveSource(refMods, td, null);
|
|
792
|
}
|
|
793
|
// DerivedUnitFacade derivedUnitFacade = getFacade(rawAssociation.replaceAll(";",""),SpecimenOrObservationType.DerivedUnit);
|
|
794
|
// derivedUnitBase = derivedUnitFacade.innerDerivedUnit();
|
|
795
|
//
|
|
796
|
// TaxonDescription taxonDescription = importer.getTaxonDescription(acceptedTaxon, false, true);
|
|
797
|
// acceptedTaxon.addDescription(taxonDescription);
|
|
798
|
//
|
|
799
|
// IndividualsAssociation indAssociation = IndividualsAssociation.NewInstance();
|
|
800
|
//
|
|
801
|
// Feature feature = Feature.MATERIALS_EXAMINED();
|
|
802
|
// featuresMap.put(feature.getTitleCache(),feature);
|
|
803
|
// if(!StringUtils.isEmpty(rawAssociation)) {
|
|
804
|
// derivedUnitBase.setTitleCache(rawAssociation, true);
|
|
805
|
// }
|
|
806
|
// indAssociation.setAssociatedSpecimenOrObservation(derivedUnitBase);
|
|
807
|
// indAssociation.setFeature(feature);
|
|
808
|
// indAssociation.addSource(OriginalSourceType.Import, null, null, refMods, null);
|
|
809
|
//
|
|
810
|
// /*boolean sourceExists=false;
|
|
811
|
// Set<DescriptionElementSource> dsources = indAssociation.getSources();
|
|
812
|
// for (DescriptionElementSource src : dsources){
|
|
813
|
// String micro = src.getCitationMicroReference();
|
|
814
|
// Reference r = src.getCitation();
|
|
815
|
// if (r.equals(refMods) && micro == null) {
|
|
816
|
// sourceExists=true;
|
|
817
|
// }
|
|
818
|
// }
|
|
819
|
// if(!sourceExists) {
|
|
820
|
// indAssociation.addSource(null, null, refMods, null);
|
|
821
|
// }*/
|
|
822
|
// taxonDescription.addElement(indAssociation);
|
|
823
|
// taxonDescription.setTaxon(acceptedTaxon);
|
|
824
|
// taxonDescription.addSource(OriginalSourceType.Import, null,null,refMods,null);
|
|
825
|
//
|
|
826
|
// /*sourceExists=false;
|
|
827
|
// Set<IdentifiableSource> sources = taxonDescription.getSources();
|
|
828
|
// for (IdentifiableSource src : sources){
|
|
829
|
// String micro = src.getCitationMicroReference();
|
|
830
|
// Reference r = src.getCitation();
|
|
831
|
// if (r.equals(refMods) && micro == null) {
|
|
832
|
// sourceExists=true;
|
|
833
|
// }
|
|
834
|
// }
|
|
835
|
// if(!sourceExists) {
|
|
836
|
// taxonDescription.addSource(OriginalSourceType.Import,null,null,refMods,null);
|
|
837
|
// }*/
|
|
838
|
//
|
|
839
|
// importer.getDescriptionService().saveOrUpdate(taxonDescription);
|
|
840
|
importer.getTaxonService().saveOrUpdate(acceptedTaxon);
|
|
841
|
|
|
842
|
rawAssociation="";
|
|
843
|
}
|
|
844
|
}
|
|
845
|
}
|
|
846
|
}
|
|
847
|
}
|
|
848
|
|
|
849
|
/**
|
|
850
|
* @param acceptedTaxon
|
|
851
|
* @param refMods
|
|
852
|
* @param events
|
|
853
|
* @param rawAssociation
|
|
854
|
* @param k
|
|
855
|
*/
|
|
856
|
private void handleDerivedUnitFacadeAndBase(Taxon acceptedTaxon, Reference refMods, Node event,
|
|
857
|
String rawAssociation) {
|
|
858
|
logger.info("handleDerivedUnitFacadeAndBase");
|
|
859
|
String descr;
|
|
860
|
DerivedUnit derivedUnitBase;
|
|
861
|
MySpecimenOrObservation myspecimenOrObservation;
|
|
862
|
DerivedUnitFacade derivedUnitFacade = getFacade(rawAssociation.replaceAll(";",""),SpecimenOrObservationType.DerivedUnit);
|
|
863
|
derivedUnitBase = derivedUnitFacade.innerDerivedUnit();
|
|
864
|
|
|
865
|
sourceHandler.addAndSaveSource(refMods, derivedUnitBase);
|
|
866
|
|
|
867
|
//TODO this may not always be correct, ask user
|
|
868
|
TaxonName typifiableName = acceptedTaxon != null ? acceptedTaxon.getName() : null;
|
|
869
|
myspecimenOrObservation = extractSpecimenOrObservation(event,derivedUnitBase,SpecimenOrObservationType.DerivedUnit, typifiableName);
|
|
870
|
derivedUnitBase = myspecimenOrObservation.getDerivedUnitBase();
|
|
871
|
descr=myspecimenOrObservation.getDescr();
|
|
872
|
|
|
873
|
sourceHandler.addAndSaveSource(refMods, derivedUnitBase);
|
|
874
|
|
|
875
|
TaxonDescription taxonDescription = importer.getTaxonDescription(acceptedTaxon, false, true);
|
|
876
|
|
|
877
|
Feature feature = makeFeature(derivedUnitBase);
|
|
878
|
featuresMap.put(feature.getTitleCache(),feature);
|
|
879
|
if(!StringUtils.isEmpty(descr)) {
|
|
880
|
derivedUnitBase.setTitleCache(descr, true);
|
|
881
|
}
|
|
882
|
|
|
883
|
IndividualsAssociation indAssociation = createIndividualAssociation(refMods, derivedUnitBase, feature);
|
|
884
|
|
|
885
|
taxonDescription.addElement(indAssociation);
|
|
886
|
sourceHandler.addAndSaveSource(refMods, taxonDescription,null);
|
|
887
|
importer.getTaxonService().saveOrUpdate(acceptedTaxon);
|
|
888
|
}
|
|
889
|
|
|
890
|
|
|
891
|
|
|
892
|
/**
|
|
893
|
* @param currentName
|
|
894
|
* @param materials: the XML node group
|
|
895
|
* @param acceptedTaxon: the current accepted Taxon
|
|
896
|
* @param refMods: the current reference extracted from the MODS
|
|
897
|
*/
|
|
898
|
private String extractMaterialsDirect(Node materials, Taxon acceptedTaxon, Reference refMods, String event, TaxonName currentName) {
|
|
899
|
logger.info("extractMaterialsDirect");
|
|
900
|
// logger.info("acceptedTaxon: "+acceptedTaxon);
|
|
901
|
String descr="";
|
|
902
|
|
|
903
|
DerivedUnit derivedUnitBase=null;
|
|
904
|
MySpecimenOrObservation myspecimenOrObservation = extractSpecimenOrObservation(materials,derivedUnitBase, SpecimenOrObservationType.DerivedUnit, currentName);
|
|
905
|
derivedUnitBase = myspecimenOrObservation.getDerivedUnitBase();
|
|
906
|
|
|
907
|
sourceHandler.addAndSaveSource(refMods, derivedUnitBase);
|
|
908
|
|
|
909
|
TaxonDescription taxonDescription = importer.getTaxonDescription(acceptedTaxon, false, true);
|
|
910
|
|
|
911
|
Feature feature=null;
|
|
912
|
if (event.equalsIgnoreCase("collection")){
|
|
913
|
feature = makeFeature(derivedUnitBase);
|
|
914
|
}
|
|
915
|
else{
|
|
916
|
feature = Feature.MATERIALS_EXAMINED();
|
|
917
|
}
|
|
918
|
featuresMap.put(feature.getTitleCache(), feature);
|
|
919
|
|
|
920
|
descr=myspecimenOrObservation.getDescr();
|
|
921
|
if(!StringUtils.isEmpty(descr)) {
|
|
922
|
derivedUnitBase.setTitleCache(descr, true);
|
|
923
|
}
|
|
924
|
|
|
925
|
IndividualsAssociation indAssociation = createIndividualAssociation(refMods, derivedUnitBase, feature);
|
|
926
|
|
|
927
|
taxonDescription.addElement(indAssociation);
|
|
928
|
sourceHandler.addAndSaveSource(refMods, taxonDescription,null);
|
|
929
|
importer.getTaxonService().saveOrUpdate(acceptedTaxon);
|
|
930
|
|
|
931
|
return derivedUnitBase.getTitleCache();
|
|
932
|
|
|
933
|
}
|
|
934
|
|
|
935
|
|
|
936
|
/**
|
|
937
|
* @param description: the XML node group
|
|
938
|
* @param acceptedTaxon: the current acceptedTaxon
|
|
939
|
* @param defaultTaxon: the current defaultTaxon, only used if there is no accepted name
|
|
940
|
* @param nametosave: the list of objects to save into the CDM
|
|
941
|
* @param refMods: the current reference extracted from the MODS
|
|
942
|
* @param featureName: the feature name
|
|
943
|
*/
|
|
944
|
@SuppressWarnings({ "rawtypes"})
|
|
945
|
private String extractSpecificFeature(Node description, Taxon acceptedTaxon, Taxon defaultTaxon,
|
|
946
|
List<TaxonName> nametosave, Reference refMods, String featureName ) {
|
|
947
|
logger.info("extractSpecificFeature "+featureName);
|
|
948
|
// System.out.println("GRUUUUuu");
|
|
949
|
NodeList children = description.getChildNodes();
|
|
950
|
NodeList insideNodes ;
|
|
951
|
NodeList trNodes;
|
|
952
|
// String descr ="";
|
|
953
|
String localdescr="";
|
|
954
|
List<String> blabla=null;
|
|
955
|
List<String> text = new ArrayList<String>();
|
|
956
|
|
|
957
|
String table="<table>";
|
|
958
|
String head="";
|
|
959
|
String line="";
|
|
960
|
|
|
961
|
Feature currentFeature=getFeatureObjectFromString(featureName);
|
|
962
|
|
|
963
|
// String fullContent = description.getTextContent();
|
|
964
|
for (int i=0;i<children.getLength();i++){
|
|
965
|
// localdescr="";
|
|
966
|
if (children.item(i).getNodeName().equalsIgnoreCase("#text") && !children.item(i).getTextContent().trim().isEmpty()){
|
|
967
|
text.add(children.item(i).getTextContent().trim());
|
|
968
|
}
|
|
969
|
if (featureName.equalsIgnoreCase("table")){
|
|
970
|
if (children.item(i).getNodeName().equalsIgnoreCase("tax:div") &&
|
|
971
|
children.item(i).getAttributes().getNamedItem("otherType").getNodeValue().equalsIgnoreCase("thead")){
|
|
972
|
head = extractTableHead(children.item(i));
|
|
973
|
table+=head;
|
|
974
|
line = extractTableLine(children.item(i));
|
|
975
|
if (!line.equalsIgnoreCase("<tr></tr>")) {
|
|
976
|
table+=line;
|
|
977
|
}
|
|
978
|
}
|
|
979
|
if (children.item(i).getNodeName().equalsIgnoreCase("tax:div") &&
|
|
980
|
children.item(i).getAttributes().getNamedItem("otherType").getNodeValue().equalsIgnoreCase("tr")){
|
|
981
|
line = extractTableLineWithColumn(children.item(i).getChildNodes());
|
|
982
|
if(!line.equalsIgnoreCase("<tr></tr>")) {
|
|
983
|
table+=line;
|
|
984
|
}
|
|
985
|
}
|
|
986
|
}
|
|
987
|
if (children.item(i).getNodeName().equalsIgnoreCase("tax:p")){
|
|
988
|
insideNodes=children.item(i).getChildNodes();
|
|
989
|
blabla= new ArrayList<String>();
|
|
990
|
for (int j=0;j<insideNodes.getLength();j++){
|
|
991
|
Node insideNode = insideNodes.item(j);
|
|
992
|
if (insideNode.getNodeName().equalsIgnoreCase("tax:name")){
|
|
993
|
String inlinetext = getInlineTextForName(nametosave, refMods, insideNode);
|
|
994
|
if (!inlinetext.isEmpty()) {
|
|
995
|
blabla.add(inlinetext);
|
|
996
|
}
|
|
997
|
}
|
|
998
|
else if (insideNode.getNodeName().equalsIgnoreCase("#text")) {
|
|
999
|
if(!insideNode.getTextContent().trim().isEmpty()){
|
|
1000
|
blabla.add(insideNode.getTextContent().trim());
|
|
1001
|
// localdescr += insideNodes.item(j).getTextContent().trim();
|
|
1002
|
}
|
|
1003
|
}
|
|
1004
|
}
|
|
1005
|
if (!blabla.isEmpty()) {
|
|
1006
|
String blaStr = StringUtils.join(blabla," ").trim();
|
|
1007
|
if(!stringIsEmpty(blaStr)) {
|
|
1008
|
setParticularDescription(blaStr,acceptedTaxon,defaultTaxon, refMods,currentFeature);
|
|
1009
|
text.add(blaStr);
|
|
1010
|
}
|
|
1011
|
}
|
|
1012
|
|
|
1013
|
}
|
|
1014
|
if (children.item(i).getNodeName().equalsIgnoreCase("#text")){
|
|
1015
|
if(!children.item(i).getTextContent().trim().isEmpty()){
|
|
1016
|
localdescr = children.item(i).getTextContent().trim();
|
|
1017
|
if(!stringIsEmpty(localdescr)) {
|
|
1018
|
setParticularDescription(localdescr,acceptedTaxon,defaultTaxon, refMods,currentFeature);
|
|
1019
|
}
|
|
1020
|
}
|
|
1021
|
}
|
|
1022
|
}
|
|
1023
|
|
|
1024
|
table+="</table>";
|
|
1025
|
if (!table.equalsIgnoreCase("<table></table>")){
|
|
1026
|
// System.out.println("TABLE : "+table);
|
|
1027
|
text.add(table);
|
|
1028
|
}
|
|
1029
|
|
|
1030
|
if (text !=null && !text.isEmpty()) {
|
|
1031
|
return StringUtils.join(text," ");
|
|
1032
|
} else {
|
|
1033
|
return "";
|
|
1034
|
}
|
|
1035
|
|
|
1036
|
}
|
|
1037
|
|
|
1038
|
/**
|
|
1039
|
* @param children
|
|
1040
|
* @param i
|
|
1041
|
* @return
|
|
1042
|
*/
|
|
1043
|
private String extractTableLine(Node child) {
|
|
1044
|
//logger.info("extractTableLine");
|
|
1045
|
String line;
|
|
1046
|
line="<tr>";
|
|
1047
|
if (child.getAttributes().getNamedItem("otherType").getNodeValue().equalsIgnoreCase("tr")){
|
|
1048
|
line = extractTableLineWithColumn(child.getChildNodes());
|
|
1049
|
}
|
|
1050
|
line+="</tr>";
|
|
1051
|
return line;
|
|
1052
|
}
|
|
1053
|
|
|
1054
|
/**
|
|
1055
|
* @param children
|
|
1056
|
* @param i
|
|
1057
|
* @return
|
|
1058
|
*/
|
|
1059
|
private String extractTableHead(Node child) {
|
|
1060
|
//logger.info("extractTableHead");
|
|
1061
|
String head;
|
|
1062
|
String line;
|
|
1063
|
head="<th>";
|
|
1064
|
NodeList trNodes = child.getChildNodes();
|
|
1065
|
for (int k=0;k<trNodes.getLength();k++){
|
|
1066
|
if (trNodes.item(k).getNodeName().equalsIgnoreCase("tax:div")
|
|
1067
|
&& trNodes.item(k).getAttributes().getNamedItem("otherType").getNodeValue().equalsIgnoreCase("tr")){
|
|
1068
|
line = extractTableLineWithColumn(trNodes.item(k).getChildNodes());
|
|
1069
|
head+=line;
|
|
1070
|
}
|
|
1071
|
}
|
|
1072
|
head+="</th>";
|
|
1073
|
return head;
|
|
1074
|
}
|
|
1075
|
|
|
1076
|
/**
|
|
1077
|
* build a html table line, with td columns
|
|
1078
|
* @param tdNodes
|
|
1079
|
* @return an html coded line
|
|
1080
|
*/
|
|
1081
|
private String extractTableLineWithColumn(NodeList tdNodes) {
|
|
1082
|
//logger.info("extractTableLineWithColumn");
|
|
1083
|
String line;
|
|
1084
|
line="<tr>";
|
|
1085
|
for (int l=0;l<tdNodes.getLength();l++){
|
|
1086
|
if (tdNodes.item(l).getNodeName().equalsIgnoreCase("tax:p")){
|
|
1087
|
line+="<td>"+tdNodes.item(l).getTextContent()+"</td>";
|
|
1088
|
}
|
|
1089
|
}
|
|
1090
|
line+="</tr>";
|
|
1091
|
return line;
|
|
1092
|
}
|
|
1093
|
|
|
1094
|
/**
|
|
1095
|
* @param description: the XML node group
|
|
1096
|
* @param acceptedTaxon: the current acceptedTaxon
|
|
1097
|
* @param defaultTaxon: the current defaultTaxon, only used if there is no accepted name
|
|
1098
|
* @param nametosave: the list of objects to save into the CDM
|
|
1099
|
* @param refMods: the current reference extracted from the MODS
|
|
1100
|
* @param featureName: the feature name
|
|
1101
|
*/
|
|
1102
|
@SuppressWarnings({ "unused"})
|
|
1103
|
private String extractSpecificFeatureNotStructured(Node description, Taxon acceptedTaxon, Taxon defaultTaxon,
|
|
1104
|
List<TaxonName> nameToSave, Reference refMods, String featureName ) {
|
|
1105
|
logger.info("extractSpecificFeatureNotStructured " + featureName);
|
|
1106
|
NodeList children = description.getChildNodes();
|
|
1107
|
NodeList insideNodes ;
|
|
1108
|
List<String> blabla= new ArrayList<String>();
|
|
1109
|
|
|
1110
|
|
|
1111
|
Feature currentFeature = getFeatureObjectFromString(featureName);
|
|
1112
|
|
|
1113
|
String fullContent = description.getTextContent();
|
|
1114
|
for (int i=0;i<children.getLength();i++){
|
|
1115
|
if (children.item(i).getNodeName().equalsIgnoreCase("tax:p")){
|
|
1116
|
insideNodes=children.item(i).getChildNodes();
|
|
1117
|
for (int j=0;j<insideNodes.getLength();j++){
|
|
1118
|
if (insideNodes.item(j).getNodeName().equalsIgnoreCase("tax:name")){
|
|
1119
|
String inlineText =getInlineTextForName(nameToSave, refMods, insideNodes.item(j));
|
|
1120
|
if(!inlineText.isEmpty()) {
|
|
1121
|
blabla.add(inlineText);
|
|
1122
|
}
|
|
1123
|
}
|
|
1124
|
if (insideNodes.item(j).getNodeName().equalsIgnoreCase("#text")) {
|
|
1125
|
if(!insideNodes.item(j).getTextContent().trim().isEmpty()){
|
|
1126
|
blabla.add(insideNodes.item(j).getTextContent().trim());
|
|
1127
|
}
|
|
1128
|
}
|
|
1129
|
}
|
|
1130
|
}
|
|
1131
|
if (children.item(i).getNodeName().equalsIgnoreCase("#text")){
|
|
1132
|
if(!children.item(i).getTextContent().trim().isEmpty()){
|
|
1133
|
String localdescr = children.item(i).getTextContent().trim();
|
|
1134
|
if(!localdescr.isEmpty())
|
|
1135
|
{
|
|
1136
|
blabla.add(localdescr);
|
|
1137
|
}
|
|
1138
|
}
|
|
1139
|
}
|
|
1140
|
}
|
|
1141
|
|
|
1142
|
if (blabla !=null && !blabla.isEmpty()) {
|
|
1143
|
String blaStr = StringUtils.join(blabla," ").trim();
|
|
1144
|
if (! stringIsEmpty(blaStr)) {
|
|
1145
|
setParticularDescription(blaStr,acceptedTaxon,defaultTaxon, refMods,currentFeature);
|
|
1146
|
return blaStr;
|
|
1147
|
} else {
|
|
1148
|
return "";
|
|
1149
|
}
|
|
1150
|
} else {
|
|
1151
|
return "";
|
|
1152
|
}
|
|
1153
|
|
|
1154
|
}
|
|
1155
|
|
|
1156
|
/**
|
|
1157
|
* @param blaStr
|
|
1158
|
* @return
|
|
1159
|
*/
|
|
1160
|
private boolean stringIsEmpty(String blaStr) {
|
|
1161
|
if (blaStr.matches("(\\.|,|;|\\.-)?")){
|
|
1162
|
return true;
|
|
1163
|
}else{
|
|
1164
|
return false;
|
|
1165
|
}
|
|
1166
|
}
|
|
1167
|
|
|
1168
|
/**
|
|
1169
|
* @param nametosave
|
|
1170
|
* @param refMods
|
|
1171
|
* @param insideNodes
|
|
1172
|
*/
|
|
1173
|
private String getInlineTextForName(List<TaxonName> nametosave, Reference refMods, Node insideNode) {
|
|
1174
|
if (true){
|
|
1175
|
NodeList children = insideNode.getChildNodes();
|
|
1176
|
String result = "";
|
|
1177
|
for (int i=0;i<children.getLength();i++){
|
|
1178
|
Node nameChild = children.item(i);
|
|
1179
|
if(nameChild.getNodeName().equalsIgnoreCase("#text")){
|
|
1180
|
result += nameChild.getTextContent();
|
|
1181
|
}else{
|
|
1182
|
//do nothing
|
|
1183
|
}
|
|
1184
|
}
|
|
1185
|
return result.replace("\n", "").trim();
|
|
1186
|
}else{
|
|
1187
|
TaxonName tnb = getTaxonNameFromXML(insideNode, nametosave,refMods,false);
|
|
1188
|
// Taxon tax = getTaxonFromTxonNameBase(tnb, refMods);
|
|
1189
|
Taxon tax = currentMyName.getTaxon();
|
|
1190
|
if(tnb !=null && tax != null){
|
|
1191
|
String linkedTaxon = tnb.getTitleCache().split("sec")[0];//TODO NOT IMPLEMENTED IN THE CDM YET
|
|
1192
|
return "<cdm:taxon uuid='"+tax.getUuid()+"'>"+linkedTaxon+"</cdm:taxon>";
|
|
1193
|
}else if (tnb != null && tax == null){
|
|
1194
|
//TODO
|
|
1195
|
return "<cdm:taxonName uuid='" + tnb.getUuid() +"'>" + tnb.getTitleCache().split("sec")[0] +"</cdm:taxonName>";
|
|
1196
|
}else{
|
|
1197
|
logger.warn("Inline text has no content yet");
|
|
1198
|
}
|
|
1199
|
return "";
|
|
1200
|
}
|
|
1201
|
}
|
|
1202
|
|
|
1203
|
/**
|
|
1204
|
* @param featureName
|
|
1205
|
* @return
|
|
1206
|
*/
|
|
1207
|
@SuppressWarnings("rawtypes")
|
|
1208
|
private Feature getFeatureObjectFromString(String featureName) {
|
|
1209
|
logger.info("getFeatureObjectFromString");
|
|
1210
|
List<Feature> features = importer.getTermService().list(Feature.class, null,null,null,null);
|
|
1211
|
Feature currentFeature=null;
|
|
1212
|
for (Feature feature: features){
|
|
1213
|
String tmpF = feature.getTitleCache();
|
|
1214
|
if (tmpF.equalsIgnoreCase(featureName)) {
|
|
1215
|
currentFeature=feature;
|
|
1216
|
// System.out.println("currentFeatureFromList "+currentFeature.getUuid());
|
|
1217
|
}
|
|
1218
|
}
|
|
1219
|
if (currentFeature == null) {
|
|
1220
|
currentFeature=Feature.NewInstance(featureName, featureName, featureName);
|
|
1221
|
if(featureName.equalsIgnoreCase("Other")){
|
|
1222
|
currentFeature.setUuid(OtherUUID);
|
|
1223
|
}
|
|
1224
|
if(featureName.equalsIgnoreCase(notMarkedUp)){
|
|
1225
|
currentFeature.setUuid(NotMarkedUpUUID);
|
|
1226
|
}
|
|
1227
|
importer.getTermService().saveOrUpdate(currentFeature);
|
|
1228
|
}
|
|
1229
|
return currentFeature;
|
|
1230
|
}
|
|
1231
|
|
|
1232
|
|
|
1233
|
|
|
1234
|
|
|
1235
|
/**
|
|
1236
|
* @param children: the XML node group
|
|
1237
|
* @param nametosave: the list of objects to save into the CDM
|
|
1238
|
* @param acceptedTaxon: the current acceptedTaxon
|
|
1239
|
* @param refMods: the current reference extracted from the MODS
|
|
1240
|
* @param fullContent :the parsed XML content
|
|
1241
|
* @return a list of description (text)
|
|
1242
|
*/
|
|
1243
|
@SuppressWarnings({ "unused", "rawtypes" })
|
|
1244
|
private List<String> parseParagraph(List<TaxonName> namesToSave, Taxon acceptedTaxon, Reference refMods, Node paragraph, Feature feature){
|
|
1245
|
logger.info("parseParagraph "+feature.toString());
|
|
1246
|
List<String> fullDescription= new ArrayList<String>();
|
|
1247
|
// String localdescr;
|
|
1248
|
String descr="";
|
|
1249
|
NodeList insideNodes ;
|
|
1250
|
boolean collectionEvent = false;
|
|
1251
|
List<Node>collectionEvents = new ArrayList<Node>();
|
|
1252
|
|
|
1253
|
NodeList children = paragraph.getChildNodes();
|
|
1254
|
|
|
1255
|
for (int i=0;i<children.getLength();i++){
|
|
1256
|
// localdescr="";
|
|
1257
|
if (children.item(i).getNodeName().equalsIgnoreCase("#text") && !children.item(i).getTextContent().trim().isEmpty()){
|
|
1258
|
descr += children.item(i).getTextContent().trim();
|
|
1259
|
}
|
|
1260
|
if (children.item(i).getNodeName().equalsIgnoreCase("tax:p")){
|
|
1261
|
insideNodes=children.item(i).getChildNodes();
|
|
1262
|
List<String> blabla= new ArrayList<String>();
|
|
1263
|
for (int j=0;j<insideNodes.getLength();j++){
|
|
1264
|
boolean nodeKnown = false;
|
|
1265
|
// System.out.println("insideNodes.item(j).getNodeName() : "+insideNodes.item(j).getNodeName());
|
|
1266
|
if (insideNodes.item(j).getNodeName().equalsIgnoreCase("tax:name")){
|
|
1267
|
String inlineText = getInlineTextForName(namesToSave, refMods, insideNodes.item(j));
|
|
1268
|
if (!inlineText.isEmpty()) {
|
|
1269
|
blabla.add(inlineText);
|
|
1270
|
}
|
|
1271
|
nodeKnown=true;
|
|
1272
|
}
|
|
1273
|
else if (insideNodes.item(j).getNodeName().equalsIgnoreCase("#text")) {
|
|
1274
|
if(!insideNodes.item(j).getTextContent().trim().isEmpty()){
|
|
1275
|
blabla.add(insideNodes.item(j).getTextContent().trim());
|
|
1276
|
// localdescr += insideNodes.item(j).getTextContent().trim();
|
|
1277
|
}
|
|
1278
|
nodeKnown=true;
|
|
1279
|
}
|
|
1280
|
else if (insideNodes.item(j).getNodeName().equalsIgnoreCase("tax:bibref")) {
|
|
1281
|
String ref = insideNodes.item(j).getTextContent().trim();
|
|
1282
|
if (ref.endsWith(";") && ((ref.length())>1)) {
|
|
1283
|
ref=ref.substring(0, ref.length()-1)+".";
|
|
1284
|
}
|
|
1285
|
Reference reference = ReferenceFactory.newGeneric();
|
|
1286
|
reference.setTitleCache(ref, true);
|
|
1287
|
blabla.add(reference.getTitleCache());
|
|
1288
|
nodeKnown=true;
|
|
1289
|
}
|
|
1290
|
else if (insideNodes.item(j).getNodeName().equalsIgnoreCase("tax:figure")){
|
|
1291
|
String figure = extractSpecificFeature(insideNodes.item(j),acceptedTaxon,acceptedTaxon, namesToSave, refMods, "figure");
|
|
1292
|
blabla.add(figure);
|
|
1293
|
}
|
|
1294
|
else if(insideNodes.item(j).getNodeName().equalsIgnoreCase("tax:div") &&
|
|
1295
|
insideNodes.item(j).getAttributes().getNamedItem("type").getNodeValue().equalsIgnoreCase("Other") &&
|
|
1296
|
insideNodes.item(j).getAttributes().getNamedItem("otherType").getNodeValue().equalsIgnoreCase("table")){
|
|
1297
|
String table = extractSpecificFeature(insideNodes.item(j),acceptedTaxon,acceptedTaxon, namesToSave, refMods, "table");
|
|
1298
|
blabla.add(table);
|
|
1299
|
}
|
|
1300
|
else if (insideNodes.item(j).getNodeName().equalsIgnoreCase("tax:collection_event")) {
|
|
1301
|
// logger.warn("SEEMS TO BE COLLECTION EVENT INSIDE A "+feature.toString());
|
|
1302
|
String titlecache = extractMaterialsDirect(insideNodes.item(j), acceptedTaxon, refMods, "collection", null);
|
|
1303
|
blabla.add(titlecache);
|
|
1304
|
collectionEvent=true;
|
|
1305
|
collectionEvents.add(insideNodes.item(j));
|
|
1306
|
nodeKnown=true;
|
|
1307
|
}else{
|
|
1308
|
logger.warn("node not handled yet: " + insideNodes.item(j).getNodeName());
|
|
1309
|
}
|
|
1310
|
|
|
1311
|
}
|
|
1312
|
if (!StringUtils.isBlank(StringUtils.join(blabla," "))) {
|
|
1313
|
fullDescription.add(StringUtils.join(blabla," "));
|
|
1314
|
}
|
|
1315
|
}
|
|
1316
|
if (children.item(i).getNodeName().equalsIgnoreCase("tax:figure")){
|
|
1317
|
String figure = extractSpecificFeature(children.item(i),acceptedTaxon,acceptedTaxon, namesToSave, refMods, "Figure");
|
|
1318
|
fullDescription.add(figure);
|
|
1319
|
}
|
|
1320
|
if(children.item(i).getNodeName().equalsIgnoreCase("tax:div") &&
|
|
1321
|
children.item(i).getAttributes().getNamedItem("type").getNodeValue().equalsIgnoreCase("Other") &&
|
|
1322
|
children.item(i).getAttributes().getNamedItem("otherType").getNodeValue().equalsIgnoreCase("table")){
|
|
1323
|
String table = extractSpecificFeature(children.item(i),acceptedTaxon,acceptedTaxon, namesToSave, refMods, "table");
|
|
1324
|
fullDescription.add(table);
|
|
1325
|
}
|
|
1326
|
}
|
|
1327
|
|
|
1328
|
if( !stringIsEmpty(descr.trim())){
|
|
1329
|
Feature currentFeature= getNotMarkedUpFeatureObject();
|
|
1330
|
setParticularDescription(descr.trim(),acceptedTaxon,acceptedTaxon, refMods,currentFeature);
|
|
1331
|
}
|
|
1332
|
// if (collectionEvent) {
|
|
1333
|
// logger.warn("SEEMS TO BE COLLECTION EVENT INSIDE A "+feature.toString());
|
|
1334
|
// for (Node coll:collectionEvents){
|
|
1335
|
// = extractMaterialsDirect(coll, acceptedTaxon, refMods, "collection");
|
|
1336
|
// }
|
|
1337
|
// }
|
|
1338
|
return fullDescription;
|
|
1339
|
}
|
|
1340
|
|
|
1341
|
|
|
1342
|
/**
|
|
1343
|
* @param description: the XML node group
|
|
1344
|
* @param acceptedTaxon: the current acceptedTaxon
|
|
1345
|
* @param defaultTaxon: the current defaultTaxon, only used if there is no accepted name
|
|
1346
|
* @param nametosave: the list of objects to save into the CDM
|
|
1347
|
* @param refMods: the current reference extracted from the MODS
|
|
1348
|
* @param feature: the feature to link the data with
|
|
1349
|
*/
|
|
1350
|
@SuppressWarnings("rawtypes")
|
|
1351
|
private void extractFeature(Node description, Taxon acceptedTaxon, Taxon defaultTaxon, List<TaxonName> namesToSave, Reference refMods, Feature feature){
|
|
1352
|
logger.info("EXTRACT FEATURE "+feature.toString());
|
|
1353
|
acceptedTaxon = CdmBase.deproxy(acceptedTaxon, Taxon.class);
|
|
1354
|
List<String> fullDescription= parseParagraph( namesToSave, acceptedTaxon, refMods, description,feature);
|
|
1355
|
|
|
1356
|
// System.out.println("Feature : "+feature.toString()+", "+fullDescription.toString());
|
|
1357
|
if (!fullDescription.isEmpty() &&!stringIsEmpty(StringUtils.join(fullDescription,"\n").trim())) {
|
|
1358
|
setParticularDescription(StringUtils.join(fullDescription,"\n").trim(),acceptedTaxon,defaultTaxon, refMods,feature);
|
|
1359
|
}
|
|
1360
|
|
|
1361
|
}
|
|
1362
|
|
|
1363
|
|
|
1364
|
/**
|
|
1365
|
* @param descr: the XML Nodegroup to parse
|
|
1366
|
* @param acceptedTaxon: the current acceptedTaxon
|
|
1367
|
* @param defaultTaxon: the current defaultTaxon, only used if there is no accepted name
|
|
1368
|
* @param refMods: the current reference extracted from the MODS
|
|
1369
|
* @param currentFeature: the feature name
|
|
1370
|
* @return
|
|
1371
|
*/
|
|
1372
|
private void setParticularDescription(String descr, Taxon acceptedTaxon, Taxon defaultTaxon, Reference refMods, Feature currentFeature) {
|
|
1373
|
logger.info("setParticularDescription " + currentFeature.getTitleCache()+", \n blabla : "+descr);
|
|
1374
|
|
|
1375
|
//remove redundant feature title
|
|
1376
|
String featureStr = currentFeature.getTitleCache();
|
|
1377
|
if (!descr.isEmpty() && descr.toLowerCase().startsWith(featureStr.toLowerCase())){
|
|
1378
|
descr = descr.replaceAll("(?i)" + featureStr + "\\.\\s*", "");
|
|
1379
|
}
|
|
1380
|
|
|
1381
|
|
|
1382
|
acceptedTaxon = CdmBase.deproxy(acceptedTaxon, Taxon.class);
|
|
1383
|
featuresMap.put(currentFeature.getTitleCache(),currentFeature);
|
|
1384
|
|
|
1385
|
TextData textData = createTextData(descr, refMods, currentFeature);
|
|
1386
|
|
|
1387
|
if(acceptedTaxon!=null){
|
|
1388
|
TaxonDescription td =importer.getTaxonDescription(acceptedTaxon, false, true);
|
|
1389
|
td.addElement(textData);
|
|
1390
|
acceptedTaxon.addDescription(td);
|
|
1391
|
|
|
1392
|
sourceHandler.addAndSaveSource(refMods, td, null);
|
|
1393
|
importer.getTaxonService().saveOrUpdate(acceptedTaxon);
|
|
1394
|
}
|
|
1395
|
|
|
1396
|
if(! descr.isEmpty() && (acceptedTaxon == null) && (defaultTaxon != null)){
|
|
1397
|
try{
|
|
1398
|
Taxon tmp =(Taxon) importer.getTaxonService().find(defaultTaxon.getUuid());
|
|
1399
|
if (tmp!=null) {
|
|
1400
|
defaultTaxon=CdmBase.deproxy(tmp,Taxon.class);
|
|
1401
|
}else{
|
|
1402
|
importer.getTaxonService().saveOrUpdate(defaultTaxon);
|
|
1403
|
}
|
|
1404
|
}catch(Exception e){
|
|
1405
|
logger.debug("TAXON EXISTS"+defaultTaxon);
|
|
1406
|
}
|
|
1407
|
|
|
1408
|
TaxonDescription td =importer.getTaxonDescription(defaultTaxon, false, true);
|
|
1409
|
defaultTaxon.addDescription(td);
|
|
1410
|
td.addElement(textData);
|
|
1411
|
sourceHandler.addAndSaveSource(refMods, td, null);
|
|
1412
|
importer.getTaxonService().saveOrUpdate(defaultTaxon);
|
|
1413
|
}
|
|
1414
|
}
|
|
1415
|
|
|
1416
|
/**
|
|
1417
|
* @param descr
|
|
1418
|
* @param refMods
|
|
1419
|
* @param currentFeature
|
|
1420
|
* @return
|
|
1421
|
*/
|
|
1422
|
private TextData createTextData(String descr, Reference refMods, Feature currentFeature) {
|
|
1423
|
//logger.info("createTextData");
|
|
1424
|
TextData textData = TextData.NewInstance();
|
|
1425
|
textData.setFeature(currentFeature);
|
|
1426
|
sourceHandler.addSource(refMods, textData);
|
|
1427
|
|
|
1428
|
textData.putText(Language.UNKNOWN_LANGUAGE(), descr);
|
|
1429
|
return textData;
|
|
1430
|
}
|
|
1431
|
|
|
1432
|
|
|
1433
|
|
|
1434
|
/**
|
|
1435
|
* @param descr: the XML Nodegroup to parse
|
|
1436
|
* @param acceptedTaxon: the current acceptedTaxon
|
|
1437
|
* @param defaultTaxon: the current defaultTaxon, only used if there is no accepted name
|
|
1438
|
* @param refMods: the current reference extracted from the MODS
|
|
1439
|
* @param currentFeature: the feature name
|
|
1440
|
* @return
|
|
1441
|
*/
|
|
1442
|
private void setParticularDescription(String descr, Taxon acceptedTaxon, Taxon defaultTaxon,Reference currentRef, Reference refMods, Feature currentFeature) {
|
|
1443
|
// System.out.println("setParticularDescriptionSPecial "+currentFeature);
|
|
1444
|
// logger.info("acceptedTaxon: "+acceptedTaxon);
|
|
1445
|
logger.info("setParticularDescription");
|
|
1446
|
acceptedTaxon = CdmBase.deproxy(acceptedTaxon, Taxon.class);
|
|
1447
|
|
|
1448
|
featuresMap.put(currentFeature.getTitleCache(),currentFeature);
|
|
1449
|
TextData textData = createTextData(descr, refMods, currentFeature);
|
|
1450
|
|
|
1451
|
if(! descr.isEmpty() && (acceptedTaxon!=null)){
|
|
1452
|
TaxonDescription td =importer.getTaxonDescription(acceptedTaxon, false, true);
|
|
1453
|
td.addElement(textData);
|
|
1454
|
acceptedTaxon.addDescription(td);
|
|
1455
|
|
|
1456
|
sourceHandler.addAndSaveSource(refMods, td, currentRef);
|
|
1457
|
importer.getTaxonService().saveOrUpdate(acceptedTaxon);
|
|
1458
|
}
|
|
1459
|
|
|
1460
|
if(! descr.isEmpty() && (acceptedTaxon == null) && (defaultTaxon != null)){
|
|
1461
|
try{
|
|
1462
|
Taxon tmp =(Taxon) importer.getTaxonService().find(defaultTaxon.getUuid());
|
|
1463
|
if (tmp!=null) {
|
|
1464
|
defaultTaxon=CdmBase.deproxy(tmp,Taxon.class);
|
|
1465
|
}else{
|
|
1466
|
importer.getTaxonService().saveOrUpdate(defaultTaxon);
|
|
1467
|
}
|
|
1468
|
}catch(Exception e){
|
|
1469
|
logger.debug("TAXON EXISTS"+defaultTaxon);
|
|
1470
|
}
|
|
1471
|
|
|
1472
|
TaxonDescription td =importer.getTaxonDescription(defaultTaxon, false, true);
|
|
1473
|
defaultTaxon.addDescription(td);
|
|
1474
|
td.addElement(textData);
|
|
1475
|
sourceHandler.addAndSaveSource(currentRef, td,currentRef);
|
|
1476
|
importer.getTaxonService().saveOrUpdate(defaultTaxon);
|
|
1477
|
}
|
|
1478
|
}
|
|
1479
|
|
|
1480
|
|
|
1481
|
|
|
1482
|
/**
|
|
1483
|
* @param synonyms: the XML Nodegroup to parse
|
|
1484
|
* @param nametosave: the list of objects to save into the CDM
|
|
1485
|
* @param acceptedTaxon: the current acceptedTaxon
|
|
1486
|
* @param refMods: the current reference extracted from the MODS
|
|
1487
|
*/
|
|
1488
|
@SuppressWarnings({ "rawtypes" })
|
|
1489
|
private void extractSynonyms(Node synonymsNode, Taxon acceptedTaxon,Reference refMods, String followingText) {
|
|
1490
|
logger.info("extractSynonyms");
|
|
1491
|
//System.out.println("extractSynonyms for: "+acceptedTaxon);
|
|
1492
|
Taxon ttmp = (Taxon) importer.getTaxonService().find(acceptedTaxon.getUuid());
|
|
1493
|
if (ttmp != null) {
|
|
1494
|
acceptedTaxon = CdmBase.deproxy(ttmp,Taxon.class);
|
|
1495
|
}
|
|
1496
|
else{
|
|
1497
|
acceptedTaxon = CdmBase.deproxy(acceptedTaxon, Taxon.class);
|
|
1498
|
}
|
|
1499
|
NodeList children = synonymsNode.getChildNodes();
|
|
1500
|
List<MyName> names = new ArrayList<MyName>();
|
|
1501
|
|
|
1502
|
if(synonymsNode.getNodeName().equalsIgnoreCase("tax:name")){
|
|
1503
|
try {
|
|
1504
|
MyName myName = extractScientificNameSynonym(synonymsNode, refMods, followingText);
|
|
1505
|
names.add(myName);
|
|
1506
|
} catch (TransformerFactoryConfigurationError e) {
|
|
1507
|
logger.warn(e);
|
|
1508
|
} catch (TransformerException e) {
|
|
1509
|
logger.warn(e);
|
|
1510
|
}
|
|
1511
|
}
|
|
1512
|
|
|
1513
|
|
|
1514
|
for (int i=0;i<children.getLength();i++){
|
|
1515
|
if (children.item(i).getNodeName().equalsIgnoreCase("tax:p")){
|
|
1516
|
NodeList tmp = children.item(i).getChildNodes();
|
|
1517
|
// String fullContent = children.item(i).getTextContent();
|
|
1518
|
for (int j=0; j< tmp.getLength();j++){
|
|
1519
|
if(tmp.item(j).getNodeName().equalsIgnoreCase("tax:name")){
|
|
1520
|
try {
|
|
1521
|
MyName myName = extractScientificNameSynonym(tmp.item(j),refMods, followingText);
|
|
1522
|
names.add(myName);
|
|
1523
|
} catch (TransformerFactoryConfigurationError e) {
|
|
1524
|
logger.warn(e);
|
|
1525
|
} catch (TransformerException e) {
|
|
1526
|
logger.warn(e);
|
|
1527
|
}
|
|
1528
|
}
|
|
1529
|
}
|
|
1530
|
}
|
|
1531
|
if(children.item(i).getNodeName().equalsIgnoreCase("tax:name")){
|
|
1532
|
try {
|
|
1533
|
MyName myName = extractScientificNameSynonym(children.item(i),refMods, followingText);
|
|
1534
|
names.add(myName);
|
|
1535
|
} catch (TransformerFactoryConfigurationError e) {
|
|
1536
|
logger.warn(e);
|
|
1537
|
} catch (TransformerException e) {
|
|
1538
|
logger.warn(e);
|
|
1539
|
}
|
|
1540
|
|
|
1541
|
}
|
|
1542
|
}
|
|
1543
|
|
|
1544
|
for(MyName name:names){
|
|
1545
|
TaxonName nameToBeFilled = name.getTaxonName();
|
|
1546
|
Synonym synonym = name.getSyno();
|
|
1547
|
addFollowingTextToName(nameToBeFilled, followingText);
|
|
1548
|
|
|
1549
|
/* INonViralNameParser parser = NonViralNameParserImpl.NewInstance();
|
|
1550
|
nameToBeFilled = parser.parseFullName(name.getName(), nomenclaturalCode, name.getRank());
|
|
1551
|
if (nameToBeFilled.hasProblem() &&
|
|
1552
|
!((nameToBeFilled.getParsingProblems().size()==1) && nameToBeFilled.getParsingProblems().contains(ParserProblem.CheckRank)) ) {
|
|
1553
|
// if (nameToBeFilled.hasProblem() && nameToBeFilled.getParsingProblems().contains(ParserProblem.UnparsableNamePart)){
|
|
1554
|
addProblemNameToFile(name.getName(),"",nomenclaturalCode,name.getRank());
|
|
1555
|
nameToBeFilled = solveNameProblem(name.getOriginalName(), name.getName(), parser,name.getAuthor(), name.getRank());
|
|
1556
|
}
|
|
1557
|
nameToBeFilled = getTaxonName(nameToBeFilled,nametosave,statusType);
|
|
1558
|
*/
|
|
1559
|
if (!name.getIdentifier().isEmpty() && (name.getIdentifier().length()>2)){
|
|
1560
|
setLSID(name.getIdentifier(), synonym);
|
|
1561
|
}
|
|
1562
|
|
|
1563
|
Set<Synonym> synonymsSet= acceptedTaxon.getSynonyms();
|
|
1564
|
boolean synoExist = false;
|
|
1565
|
for (Synonym syn: synonymsSet){
|
|
1566
|
|
|
1567
|
boolean a =syn.getName().equals(synonym.getName());
|
|
1568
|
boolean b = syn.getSec().equals(synonym.getSec());
|
|
1569
|
if (a && b) {
|
|
1570
|
synoExist=true;
|
|
1571
|
}
|
|
1572
|
}
|
|
1573
|
if (!synonymsSet.contains(synonym) && ! (synoExist)) {
|
|
1574
|
sourceHandler.addSource(refMods, synonym);
|
|
1575
|
acceptedTaxon.addSynonym(synonym, SynonymType.SYNONYM_OF());
|
|
1576
|
}
|
|
1577
|
}
|
|
1578
|
importer.getTaxonService().saveOrUpdate(acceptedTaxon);
|
|
1579
|
}
|
|
1580
|
|
|
1581
|
|
|
1582
|
private boolean addFollowingTextToName(TaxonName nameToBeFilled, String followingText) {
|
|
1583
|
if (nameToBeFilled != null && StringUtils.isNotBlank(followingText)){
|
|
1584
|
if (! followingText.matches("\\d\\.?")){
|
|
1585
|
|
|
1586
|
if (followingText.startsWith(",")){
|
|
1587
|
followingText = followingText.substring(1).trim();
|
|
1588
|
}
|
|
1589
|
nameToBeFilled.setFullTitleCache(nameToBeFilled.getFullTitleCache()+ "," +followingText , true);
|
|
1590
|
}
|
|
1591
|
return true;
|
|
1592
|
}
|
|
1593
|
return false;
|
|
1594
|
|
|
1595
|
}
|
|
1596
|
|
|
1597
|
/**
|
|
1598
|
* @param refgroup: the XML nodes
|
|
1599
|
* @param nametosave: the list of objects to save into the CDM
|
|
1600
|
* @param acceptedTaxon: the current acceptedTaxon
|
|
1601
|
* @param nametosave: the list of objects to save into the CDM
|
|
1602
|
* @param refMods: the current reference extracted from the MODS
|
|
1603
|
* @return the acceptedTaxon (why?)
|
|
1604
|
* handle cases where the bibref are inside <p> and outside
|
|
1605
|
*/
|
|
1606
|
@SuppressWarnings({ "rawtypes" })
|
|
1607
|
private Taxon extractReferences(Node refgroup, List<TaxonName> nametosave, Taxon acceptedTaxon, Reference refMods) {
|
|
1608
|
logger.info("extractReferences");
|
|
1609
|
acceptedTaxon = CdmBase.deproxy(acceptedTaxon, Taxon.class);
|
|
1610
|
|
|
1611
|
NodeList children = refgroup.getChildNodes();
|
|
1612
|
INonViralName nameToBeFilled = getNonViralNameAccNomenclature();
|
|
1613
|
|
|
1614
|
ReferenceBuilder refBuild = new ReferenceBuilder(sourceHandler);
|
|
1615
|
for (int i=0;i<children.getLength();i++){
|
|
1616
|
if(children.item(i).getNodeName().equalsIgnoreCase("tax:bibref")){
|
|
1617
|
String ref = children.item(i).getTextContent().trim();
|
|
1618
|
refBuild.builReference(ref, treatmentMainName, nomenclaturalCode, acceptedTaxon, refMods);
|
|
1619
|
if (!refBuild.isFoundBibref()){
|
|
1620
|
extractReferenceRawText(children.item(i).getChildNodes(), nameToBeFilled, refMods, acceptedTaxon);
|
|
1621
|
}
|
|
1622
|
}
|
|
1623
|
|
|
1624
|
if(children.item(i).getNodeName().equalsIgnoreCase("tax:p")){
|
|
1625
|
NodeList references = children.item(i).getChildNodes();
|
|
1626
|
String descr="";
|
|
1627
|
for (int j=0;j<references.getLength();j++){
|
|
1628
|
if(references.item(j).getNodeName().equalsIgnoreCase("tax:bibref")){
|
|
1629
|
String ref = references.item(j).getTextContent().trim();
|
|
1630
|
refBuild.builReference(ref, treatmentMainName, nomenclaturalCode, acceptedTaxon, refMods);
|
|
1631
|
}
|
|
1632
|
else
|
|
1633
|
if (references.item(j).getNodeName().equalsIgnoreCase("#text")
|
|
1634
|
&& !references.item(j).getTextContent().trim().isEmpty()){
|
|
1635
|
descr += references.item(j).getTextContent().trim();
|
|
1636
|
}
|
|
1637
|
|
|
1638
|
}
|
|
1639
|
if (!refBuild.isFoundBibref()){
|
|
1640
|
//if it's not tagged, put it as row information.
|
|
1641
|
// extractReferenceRawText(references, nameToBeFilled, nametosave, refMods, acceptedTaxon);
|
|
1642
|
//then put it as a not markup feature if not empty
|
|
1643
|
if (!stringIsEmpty(descr.trim())){
|
|
1644
|
Feature currentFeature= getNotMarkedUpFeatureObject();
|
|
1645
|
setParticularDescription(descr.trim(),acceptedTaxon,acceptedTaxon, refMods,currentFeature);
|
|
1646
|
}
|
|
1647
|
}
|
|
1648
|
}
|
|
1649
|
}
|
|
1650
|
// importer.getClassificationService().saveOrUpdate(classification);
|
|
1651
|
return acceptedTaxon;
|
|
1652
|
|
|
1653
|
}
|
|
1654
|
|
|
1655
|
/**
|
|
1656
|
* get the non viral name according to the current nomenclature
|
|
1657
|
* @return
|
|
1658
|
*/
|
|
1659
|
|
|
1660
|
private INonViralName getNonViralNameAccNomenclature() {
|
|
1661
|
return nomenclaturalCode.getNewTaxonNameInstance(null);
|
|
1662
|
}
|
|
1663
|
|
|
1664
|
/**
|
|
1665
|
* @return the feature object for the category "not marked up"
|
|
1666
|
*/
|
|
1667
|
private Feature getNotMarkedUpFeatureObject() {
|
|
1668
|
// FIXME use getFeature(uuid ....)
|
|
1669
|
logger.info("getNotMarkedUpFeatureObject");
|
|
1670
|
Feature currentFeature = (Feature)importer.getTermService().find(NotMarkedUpUUID);
|
|
1671
|
if (currentFeature == null) {
|
|
1672
|
currentFeature=Feature.NewInstance(notMarkedUp, notMarkedUp, notMarkedUp);
|
|
1673
|
currentFeature.setUuid(NotMarkedUpUUID);
|
|
1674
|
//TODO use userDefined Feature Vocabulary
|
|
1675
|
Feature.DISTRIBUTION().getVocabulary().addTerm(currentFeature);
|
|
1676
|
// importer.getTermService().saveOrUpdate(currentFeature);
|
|
1677
|
importer.getVocabularyService().saveOrUpdate(currentFeature.getVocabulary());
|
|
1678
|
}
|
|
1679
|
return currentFeature;
|
|
1680
|
}
|
|
1681
|
|
|
1682
|
/**
|
|
1683
|
* @param references
|
|
1684
|
* handle cases where the bibref are inside <p> and outside
|
|
1685
|
*/
|
|
1686
|
@SuppressWarnings("rawtypes")
|
|
1687
|
private void extractReferenceRawText(NodeList references, INonViralName nameToBeFilled, Reference refMods,
|
|
1688
|
Taxon acceptedTaxon) {
|
|
1689
|
logger.info("extractReferenceRawText");
|
|
1690
|
String refString="";
|
|
1691
|
currentMyName= new MyName(true);
|
|
1692
|
for (int j=0;j<references.getLength();j++){
|
|
1693
|
acceptedTaxon=CdmBase.deproxy(acceptedTaxon, Taxon.class);
|
|
1694
|
//no bibref tag inside
|
|
1695
|
// System.out.println("references.item(j).getNodeName()"+references.item(j).getNodeName());
|
|
1696
|
if (references.item(j).getNodeName().equalsIgnoreCase("tax:name")){
|
|
1697
|
|
|
1698
|
try {
|
|
1699
|
String followingText = null; //needs to be checked if follText is possible
|
|
1700
|
//TODO create or not create?
|
|
1701
|
currentMyName = extractScientificName(references.item(j), refMods, followingText);
|
|
1702
|
} catch (TransformerFactoryConfigurationError e) {
|
|
1703
|
logger.warn(e);
|
|
1704
|
} catch (TransformerException e) {
|
|
1705
|
logger.warn(e);
|
|
1706
|
}
|
|
1707
|
|
|
1708
|
// name=name.trim();
|
|
1709
|
}
|
|
1710
|
if (references.item(j).getNodeName().equalsIgnoreCase("#text")){
|
|
1711
|
refString = references.item(j).getTextContent().trim();
|
|
1712
|
}
|
|
1713
|
if(references.item(j).getNodeName().equalsIgnoreCase("#text") && !references.item(j).getTextContent().trim().isEmpty()){
|
|
1714
|
//
|
|
1715
|
if (!currentMyName.getStatus().isEmpty()){
|
|
1716
|
String nomNovStatus = this.newNameStatus(currentMyName.getStatus());
|
|
1717
|
if (nomNovStatus != null){
|
|
1718
|
nameToBeFilled.setAppendedPhrase(nomNovStatus);
|
|
1719
|
}else{
|
|
1720
|
try {
|
|
1721
|
NomenclaturalStatusType statusType = nomStatusString2NomStatus(currentMyName.getStatus());
|
|
1722
|
nameToBeFilled.addStatus(NomenclaturalStatus.NewInstance(statusType));
|
|
1723
|
} catch (UnknownCdmTypeException e) {
|
|
1724
|
addProblematicStatusToFile(currentMyName.getStatus());
|
|
1725
|
logger.warn("Problem with status");
|
|
1726
|
}
|
|
1727
|
}
|
|
1728
|
}
|
|
1729
|
|
|
1730
|
String fullLineRefName = references.item(j).getTextContent().trim();
|
|
1731
|
int nameOrRefOrOther=2;
|
|
1732
|
nameOrRefOrOther=askIfNameContained(fullLineRefName);
|
|
1733
|
if (nameOrRefOrOther==0){
|
|
1734
|
TaxonName nameTBF = currentMyName.getTaxonName();
|
|
1735
|
Synonym synonym = Synonym.NewInstance(nameTBF, refMods);
|
|
1736
|
|
|
1737
|
Set<Synonym> synonymsSet= acceptedTaxon.getSynonyms();
|
|
1738
|
// System.out.println(synonym.getName()+" -- "+synonym.getSec());
|
|
1739
|
boolean synoExist = false;
|
|
1740
|
for (Synonym syn: synonymsSet){
|
|
1741
|
// System.out.println(syn.getName()+" -- "+syn.getSec());
|
|
1742
|
boolean a =syn.getName().equals(synonym.getName());
|
|
1743
|
boolean b = syn.getSec().equals(synonym.getSec());
|
|
1744
|
if (a && b) {
|
|
1745
|
synoExist=true;
|
|
1746
|
}
|
|
1747
|
}
|
|
1748
|
if (!synonymsSet.contains(synonym) && ! (synoExist)) {
|
|
1749
|
sourceHandler.addSource(refMods, synonym);
|
|
1750
|
|
|
1751
|
acceptedTaxon.addSynonym(synonym, SynonymType.SYNONYM_OF());
|
|
1752
|
}
|
|
1753
|
}
|
|
1754
|
|
|
1755
|
if (nameOrRefOrOther==1){
|
|
1756
|
Reference re = ReferenceFactory.newGeneric();
|
|
1757
|
re.setTitleCache(fullLineRefName, true);
|
|
1758
|
|
|
1759
|
/* TaxonName nameTBF = parser.parseFullName(currentMyName.getName(), nomenclaturalCode, currentMyName.getRank());
|
|
1760
|
if (nameTBF.hasProblem() &&
|
|
1761
|
!((nameTBF.getParsingProblems().size()==1) && nameTBF.getParsingProblems().contains(ParserProblem.CheckRank)) ) {
|
|
1762
|
addProblemNameToFile(currentMyName.getName(),"",nomenclaturalCode,currentMyName.getRank());
|
|
1763
|
nameTBF=solveNameProblem(currentMyName.getName(), currentMyName.getName(),parser,currentMyName.getAuthor(), currentMyName.getRank());
|
|
1764
|
}
|
|
1765
|
nameTBF = getTaxonName(nameTBF,nametosave,statusType);
|
|
1766
|
*/
|
|
1767
|
TaxonName nameTBF = currentMyName.getTaxonName();
|
|
1768
|
Synonym synonym = Synonym.NewInstance(nameTBF, re);
|
|
1769
|
|
|
1770
|
Set<Synonym> synonymsSet= acceptedTaxon.getSynonyms();
|
|
1771
|
// System.out.println(synonym.getName()+" -- "+synonym.getSec());
|
|
1772
|
boolean synoExist = false;
|
|
1773
|
for (Synonym syn: synonymsSet){
|
|
1774
|
// System.out.println(syn.getName()+" -- "+syn.getSec());
|
|
1775
|
boolean a =syn.getName().equals(synonym.getName());
|
|
1776
|
boolean b = syn.getSec().equals(synonym.getSec());
|
|
1777
|
if (a && b) {
|
|
1778
|
synoExist=true;
|
|
1779
|
}
|
|
1780
|
}
|
|
1781
|
if (!synonymsSet.contains(synonym) && ! (synoExist)) {
|
|
1782
|
sourceHandler.addSource(refMods, synonym);
|
|
1783
|
|
|
1784
|
acceptedTaxon.addSynonym(synonym, SynonymType.SYNONYM_OF());
|
|
1785
|
}
|
|
1786
|
|
|
1787
|
}
|
|
1788
|
|
|
1789
|
|
|
1790
|
if (!currentMyName.getIdentifier().isEmpty() && (currentMyName.getIdentifier().length()>2)){
|
|
1791
|
setLSID(currentMyName.getIdentifier(), acceptedTaxon);
|
|
1792
|
}
|
|
1793
|
}
|
|
1794
|
|
|
1795
|
if(!currentMyName.getName().isEmpty()){
|
|
1796
|
//logger.info("acceptedTaxon and name: *"+acceptedTaxon.getTitleCache()+"*, *"+currentMyName.getName()+"*");
|
|
1797
|
if (acceptedTaxon.getTitleCache().split("sec")[0].trim().equalsIgnoreCase(currentMyName.getName().trim())){
|
|
1798
|
Reference refS = ReferenceFactory.newGeneric();
|
|
1799
|
refS.setTitleCache(refString, true);
|
|
1800
|
// TaxonDescription td =importer.getTaxonDescription(acceptedTaxon, false, true);
|
|
1801
|
// acceptedTaxon.addDescription(td);
|
|
1802
|
// acceptedTaxon.addSource(refSource);
|
|
1803
|
//
|
|
1804
|
// TextData textData = TextData.NewInstance(Feature.CITATION());
|
|
1805
|
//
|
|
1806
|
// textData.addSource(null, null, refS, null);
|
|
1807
|
// td.addElement(textData);
|
|
1808
|
// td.addSource(refSource);
|
|
1809
|
// importer.getDescriptionService().saveOrUpdate(td);
|
|
1810
|
|
|
1811
|
|
|
1812
|
if (!currentMyName.getIdentifier().isEmpty() && (currentMyName.getIdentifier().length()>2)){
|
|
1813
|
setLSID(currentMyName.getIdentifier(), acceptedTaxon);
|
|
1814
|
|
|
1815
|
}
|
|
1816
|
|
|
1817
|
acceptedTaxon.getName().setNomenclaturalReference(refS);
|
|
1818
|
}else{
|
|
1819
|
TaxonName nameTBF = currentMyName.getTaxonName();
|
|
1820
|
Synonym synonym = null;
|
|
1821
|
if (! currentMyName.getStatus().isEmpty()){
|
|
1822
|
String nomNovStatus = this.newNameStatus(currentMyName.getStatus());
|
|
1823
|
if (nomNovStatus != null){
|
|
1824
|
nameToBeFilled.setAppendedPhrase(nomNovStatus);
|
|
1825
|
}else{
|
|
1826
|
try {
|
|
1827
|
NomenclaturalStatusType statusType = nomStatusString2NomStatus(currentMyName.getStatus());
|
|
1828
|
nameToBeFilled.addStatus(NomenclaturalStatus.NewInstance(statusType));
|
|
1829
|
synonym = Synonym.NewInstance(nameTBF, refMods);
|
|
1830
|
} catch (UnknownCdmTypeException e) {
|
|
1831
|
addProblematicStatusToFile(currentMyName.getStatus());
|
|
1832
|
logger.warn("Problem with status");
|
|
1833
|
synonym = Synonym.NewInstance(nameTBF, refMods);
|
|
1834
|
synonym.setAppendedPhrase(currentMyName.getStatus());
|
|
1835
|
}
|
|
1836
|
}
|
|
1837
|
}else{
|
|
1838
|
synonym = Synonym.NewInstance(nameTBF, refMods);
|
|
1839
|
}
|
|
1840
|
|
|
1841
|
|
|
1842
|
if (!currentMyName.getIdentifier().isEmpty() && (currentMyName.getIdentifier().length()>2)){
|
|
1843
|
setLSID(currentMyName.getIdentifier(), synonym);
|
|
1844
|
}
|
|
1845
|
|
|
1846
|
Set<Synonym> synonymsSet= acceptedTaxon.getSynonyms();
|
|
1847
|
// System.out.println(synonym.getName()+" -- "+synonym.getSec());
|
|
1848
|
boolean synoExist = false;
|
|
1849
|
for (Synonym syn: synonymsSet){
|
|
1850
|
// System.out.println(syn.getName()+" -- "+syn.getSec());
|
|
1851
|
boolean a =syn.getName().equals(synonym.getName());
|
|
1852
|
boolean b = syn.getSec().equals(synonym.getSec());
|
|
1853
|
if (a && b) {
|
|
1854
|
synoExist=true;
|
|
1855
|
}
|
|
1856
|
}
|
|
1857
|
if (!synonymsSet.contains(synonym) && ! (synoExist)) {
|
|
1858
|
sourceHandler.addSource(refMods, synonym);
|
|
1859
|
|
|
1860
|
acceptedTaxon.addSynonym(synonym, SynonymType.SYNONYM_OF());
|
|
1861
|
}
|
|
1862
|
}
|
|
1863
|
}
|
|
1864
|
importer.getTaxonService().saveOrUpdate(acceptedTaxon);
|
|
1865
|
}
|
|
1866
|
}
|
|
1867
|
|
|
1868
|
|
|
1869
|
|
|
1870
|
/**
|
|
1871
|
* @param identifier
|
|
1872
|
* @param acceptedTaxon
|
|
1873
|
*/
|
|
1874
|
@SuppressWarnings("rawtypes")
|
|
1875
|
private void setLSID(String identifier, TaxonBase<?> taxon) {
|
|
1876
|
//logger.info("setLSID");
|
|
1877
|
// boolean lsidok=false;
|
|
1878
|
String id = identifier.split("__")[0];
|
|
1879
|
String source = identifier.split("__")[1];
|
|
1880
|
if (id.indexOf("lsid")>-1){
|
|
1881
|
try {
|
|
1882
|
LSID lsid = new LSID(id);
|
|
1883
|
taxon.setLsid(lsid);
|
|
1884
|
// lsidok=true;
|
|
1885
|
} catch (MalformedLSIDException e) {
|
|
1886
|
logger.warn("Malformed LSID");
|
|
1887
|
}
|
|
1888
|
|
|
1889
|
}
|
|
1890
|
|
|
1891
|
//logger.info("search reference for LSID");
|
|
1892
|
// if ((id.indexOf("lsid")<0) || !lsidok){
|
|
1893
|
//ADD ORIGINAL SOURCE ID EVEN IF LSID
|
|
1894
|
Reference re = null;
|
|
1895
|
Pager<Reference> references = importer.getReferenceService().findByTitleWithRestrictions(Reference.class, source, MatchMode.EXACT, null, 1, null, null, null);
|
|
1896
|
if( references !=null && references.getCount()>0){
|
|
1897
|
re=references.getRecords().get(0);
|
|
1898
|
}
|
|
1899
|
//logger.info("search reference for LSID-end");
|
|
1900
|
if(re == null){
|
|
1901
|
re = ReferenceFactory.newGeneric();
|
|
1902
|
re.setTitleCache(source, true);
|
|
1903
|
importer.getReferenceService().saveOrUpdate(re);
|
|
1904
|
}
|
|
1905
|
re=CdmBase.deproxy(re, Reference.class);
|
|
1906
|
|
|
1907
|
//logger.info("search source for LSID");
|
|
1908
|
Set<IdentifiableSource> sources = taxon.getSources();
|
|
1909
|
boolean lsidinsource=false;
|
|
1910
|
boolean urlinsource=false;
|
|
1911
|
for (IdentifiableSource src:sources){
|
|
1912
|
if (id.equalsIgnoreCase(src.getIdInSource()) && re.getTitleCache().equals(src.getCitation().getTitleCache())) {
|
|
1913
|
lsidinsource=true;
|
|
1914
|
}
|
|
1915
|
if (src.getIdInSource() == null && re.getTitleCache().equals(sourceUrlRef.getTitleCache())) {
|
|
1916
|
urlinsource=true;
|
|
1917
|
}
|
|
1918
|
}
|
|
1919
|
if(!lsidinsource) {
|
|
1920
|
taxon.addSource(OriginalSourceType.Import, id,null,re,null);
|
|
1921
|
}
|
|
1922
|
if(!urlinsource)
|
|
1923
|
{
|
|
1924
|
sourceUrlRef=CdmBase.deproxy(sourceUrlRef, Reference.class);
|
|
1925
|
taxon.addSource(OriginalSourceType.Import, null,null,sourceUrlRef,null);
|
|
1926
|
// }
|
|
1927
|
}
|
|
1928
|
|
|
1929
|
}
|
|
1930
|
|
|
1931
|
/**
|
|
1932
|
* try to solve a parsing problem for a scientific name
|
|
1933
|
* @param original : the name from the OCR document
|
|
1934
|
* @param name : the tagged version
|
|
1935
|
* @param parser
|
|
1936
|
* @return the corrected TaxonName
|
|
1937
|
*/
|
|
1938
|
/* @SuppressWarnings({ "unchecked", "rawtypes" })
|
|
1939
|
private TaxonName solveNameProblem(String original, String name, INonViralNameParser parser, String author, Rank rank) {
|
|
1940
|
Map<String,String> ato = namesMap.get(original);
|
|
1941
|
if (ato == null) {
|
|
1942
|
ato = namesMap.get(original+" "+author);
|
|
1943
|
}
|
|
1944
|
|
|
1945
|
|
|
1946
|
if (ato == null && rank.equals(Rank.UNKNOWN_RANK())){
|
|
1947
|
rank=askForRank(original, Rank.UNKNOWN_RANK(), nomenclaturalCode);
|
|
1948
|
}
|
|
1949
|
if (ato != null && rank.equals(Rank.UNKNOWN_RANK())){
|
|
1950
|
rank = getRank(ato);
|
|
1951
|
}
|
|
1952
|
// TaxonName nameTBF = parser.parseFullName(name, nomenclaturalCode, rank);
|
|
1953
|
TaxonName nameTBF = parser.parseSimpleName(name, nomenclaturalCode, rank);
|
|
1954
|
// logger.info("RANK: "+rank);
|
|
1955
|
int retry=0;
|
|
1956
|
List<ParserProblem> problems = nameTBF.getParsingProblems();
|
|
1957
|
for (ParserProblem pb:problems) {
|
|
1958
|
System.out.println(pb.toString());
|
|
1959
|
}
|
|
1960
|
while (nameTBF.hasProblem() && (retry <1) && !((nameTBF.getParsingProblems().size()==1) && nameTBF.getParsingProblems().contains(ParserProblem.CheckRank))){
|
|
1961
|
addProblemNameToFile(name,author,nomenclaturalCode,rank);
|
|
1962
|
String fullname=name;
|
|
1963
|
if(! skippQuestion) {
|
|
1964
|
fullname = getFullReference(name,nameTBF.getParsingProblems());
|
|
1965
|
}
|
|
1966
|
if (nomenclaturalCode.equals(NomenclaturalCode.ICNAFP)){
|
|
1967
|
nameTBF = TaxonNameFactory.NewBotanicalInstance(null);
|
|
1968
|
}
|
|
1969
|
if (nomenclaturalCode.equals(NomenclaturalCode.ICZN)){
|
|
1970
|
nameTBF = TaxonNameFactory.NewZoologicalInstance(null);
|
|
1971
|
}
|
|
1972
|
if (nomenclaturalCode.equals(NomenclaturalCode.ICNP)){
|
|
1973
|
nameTBF= TaxonNameFactory.NewBacterialInstance(null);
|
|
1974
|
}
|
|
1975
|
parser.parseReferencedName(nameTBF, fullname, rank, false);
|
|
1976
|
retry++;
|
|
1977
|
}
|
|
1978
|
if (retry == 1){
|
|
1979
|
if(author != null){
|
|
1980
|
if (name.indexOf(author)>-1) {
|
|
1981
|
nameTBF = parser.parseSimpleName(name.substring(0, name.indexOf(author)), nomenclaturalCode, rank);
|
|
1982
|
} else {
|
|
1983
|
nameTBF = parser.parseSimpleName(name, nomenclaturalCode, rank);
|
|
1984
|
}
|
|
1985
|
if (nameTBF.hasProblem()){
|
|
1986
|
if (name.indexOf(author)>-1) {
|
|
1987
|
addProblemNameToFile(name.substring(0, name.indexOf(author)),author,nomenclaturalCode,rank);
|
|
1988
|
} else {
|
|
1989
|
addProblemNameToFile(name,author,nomenclaturalCode,rank);
|
|
1990
|
}
|
|
1991
|
// System.out.println("TBF still has problems "+nameTBF.hasProblem());
|
|
1992
|
problems = nameTBF.getParsingProblems();
|
|
1993
|
for (ParserProblem pb:problems) {
|
|
1994
|
System.out.println(pb.toString());
|
|
1995
|
}
|
|
1996
|
nameTBF.setFullTitleCache(name, true);
|
|
1997
|
}else{
|
|
1998
|
if (nomenclaturalCode.equals(NomenclaturalCode.ICNAFP)) {
|
|
1999
|
((BotanicalName) nameTBF).setAuthorshipCache(currentMyName.getAuthor());
|
|
2000
|
}
|
|
2001
|
if (nomenclaturalCode.equals(NomenclaturalCode.ICZN)) {
|
|
2002
|
((ZoologicalName) nameTBF).setAuthorshipCache(currentMyName.getAuthor());
|
|
2003
|
}
|
|
2004
|
if (nomenclaturalCode.equals(NomenclaturalCode.ICNP)) {
|
|
2005
|
((BacterialName) nameTBF).setAuthorshipCache(currentMyName.getAuthor());
|
|
2006
|
}
|
|
2007
|
}
|
|
2008
|
// logger.info("FULL TITLE CACHE "+name);
|
|
2009
|
}else{
|
|
2010
|
nameTBF.setFullTitleCache(name, true);
|
|
2011
|
}
|
|
2012
|
}
|
|
2013
|
return nameTBF;
|
|
2014
|
}
|
|
2015
|
|
|
2016
|
*/
|
|
2017
|
|
|
2018
|
/**
|
|
2019
|
* @param nomenclatureNode: the XML nodes
|
|
2020
|
* @param nametosave: the list of objects to save into the CDM
|
|
2021
|
* @param refMods: the current reference extracted from the MODS
|
|
2022
|
* @return
|
|
2023
|
*/
|
|
2024
|
@SuppressWarnings({ "rawtypes" })
|
|
2025
|
private Taxon extractNomenclature(Node nomenclatureNode, List<TaxonName> nametosave, Reference refMods) throws ClassCastException{
|
|
2026
|
refMods=CdmBase.deproxy(refMods, Reference.class);
|
|
2027
|
|
|
2028
|
logger.info("extractNomenclature");
|
|
2029
|
NodeList children = nomenclatureNode.getChildNodes();
|
|
2030
|
String freetext="";
|
|
2031
|
Taxon acceptedTaxon = null;
|
|
2032
|
// INonViralNameParser parser = NonViralNameParserImpl.NewInstance();
|
|
2033
|
|
|
2034
|
// String fullContent = nomenclatureNode.getTextContent();
|
|
2035
|
|
|
2036
|
NomenclaturalStatusType statusType = null;
|
|
2037
|
String newNameStatus = null;
|
|
2038
|
//TODO
|
|
2039
|
for (int i=0;i<children.getLength();i++){
|
|
2040
|
if(children.item(i).getNodeName().equalsIgnoreCase("tax:status")){
|
|
2041
|
String status = children.item(i).getTextContent().trim();
|
|
2042
|
|
|
2043
|
if (!status.isEmpty()){
|
|
2044
|
if (newNameStatus(status) != null){
|
|
2045
|
newNameStatus = newNameStatus(status);
|
|
2046
|
}else{
|
|
2047
|
try {
|
|
2048
|
statusType = nomStatusString2NomStatus(status);
|
|
2049
|
} catch (UnknownCdmTypeException e) {
|
|
2050
|
// nomNovStatus;
|
|
2051
|
addProblematicStatusToFile(status);
|
|
2052
|
logger.warn("Problem with status: " + status);
|
|
2053
|
}
|
|
2054
|
}
|
|
2055
|
}
|
|
2056
|
}
|
|
2057
|
}
|
|
2058
|
|
|
2059
|
boolean containsSynonyms=false;
|
|
2060
|
boolean wasSynonym = false;
|
|
2061
|
usedFollowingTextPrefix = null; //reset
|
|
2062
|
|
|
2063
|
for (int i=0; i<children.getLength(); i++){
|
|
2064
|
Node childNode = children.item(i);
|
|
2065
|
String childName = childNode.getNodeName();
|
|
2066
|
|
|
2067
|
|
|
2068
|
//following text
|
|
2069
|
followingText = null;
|
|
2070
|
if ( i + 1 < children.getLength()){
|
|
2071
|
Node followingTextNode = children.item(i +1);
|
|
2072
|
if (followingTextNode.getNodeName().equals("#text") && !followingTextNode.getTextContent().matches("\\s*") ){
|
|
2073
|
followingText = followingTextNode.getTextContent();
|
|
2074
|
}
|
|
2075
|
}
|
|
2076
|
|
|
2077
|
//traverse nodes
|
|
2078
|
if (childName.equalsIgnoreCase("#text")) {
|
|
2079
|
freetext = childNode.getTextContent().trim();
|
|
2080
|
if (usedFollowingTextPrefix != null && freetext.startsWith(usedFollowingTextPrefix)){
|
|
2081
|
freetext = freetext.substring(usedFollowingTextPrefix.length());
|
|
2082
|
}
|
|
2083
|
usedFollowingTextPrefix = null; //reset
|
|
2084
|
}else if (childName.equalsIgnoreCase("tax:collection_event")) {
|
|
2085
|
// System.out.println("COLLECTION EVENT INSIDE NOMENCLATURE");
|
|
2086
|
extractMaterialsDirect(childNode, acceptedTaxon, refMods, "collection", currentMyName.getTaxonName());
|
|
2087
|
}else if(childName.equalsIgnoreCase("tax:name")){
|
|
2088
|
INonViralName nameToBeFilled;
|
|
2089
|
//System.out.println("HANDLE FIRST NAME OF THE LIST");
|
|
2090
|
if(!containsSynonyms){
|
|
2091
|
wasSynonym = false;
|
|
2092
|
|
|
2093
|
//System.out.println("I : "+i);
|
|
2094
|
currentMyName = new MyName(false);
|
|
2095
|
try {
|
|
2096
|
currentMyName = extractScientificName(childNode, refMods, followingText);
|
|
2097
|
treatmentMainName = currentMyName.getNewName();
|
|
2098
|
originalTreatmentName = currentMyName.getOriginalName();
|
|
2099
|
|
|
2100
|
} catch (TransformerFactoryConfigurationError e1) {
|
|
2101
|
throw new RuntimeException(e1);
|
|
2102
|
} catch (TransformerException e1) {
|
|
2103
|
throw new RuntimeException(e1);
|
|
2104
|
}
|
|
2105
|
|
|
2106
|
if (currentMyName.getRank().equals(Rank.UNKNOWN_RANK()) || currentMyName.getRank().isLower(state2.getConfig().getMaxRank()) || currentMyName.getRank().equals(state2.getConfig().getMaxRank())){
|
|
2107
|
maxRankRespected=true;
|
|
2108
|
|
|
2109
|
nameToBeFilled=currentMyName.getTaxonName();
|
|
2110
|
|
|
2111
|
// acceptedTaxon = importer.getTaxonService().findBestMatchingTaxon(treatmentMainName);
|
|
2112
|
acceptedTaxon=currentMyName.getTaxon();
|
|
2113
|
//System.out.println("TreatmentName "+treatmentMainName+" - "+acceptedTaxon);
|
|
2114
|
|
|
2115
|
|
|
2116
|
boolean statusMatch=false;
|
|
2117
|
if(acceptedTaxon !=null ){
|
|
2118
|
acceptedTaxon = CdmBase.deproxy(acceptedTaxon, Taxon.class);
|
|
2119
|
statusMatch=compareStatus(acceptedTaxon, statusType);
|
|
2120
|
//System.out.println("statusMatch: "+statusMatch);
|
|
2121
|
}
|
|
2122
|
if (acceptedTaxon ==null || (acceptedTaxon != null && !statusMatch)){
|
|
2123
|
|
|
2124
|
nameToBeFilled=currentMyName.getTaxonName();
|
|
2125
|
if (nameToBeFilled != null){
|
|
2126
|
if (!originalTreatmentName.isEmpty()) {
|
|
2127
|
TaxonNameDescription td = TaxonNameDescription.NewInstance();
|
|
2128
|
td.setTitleCache(originalTreatmentName, true);
|
|
2129
|
nameToBeFilled.addDescription(td);
|
|
2130
|
}
|
|
2131
|
|
|
2132
|
if(statusType != null) {
|
|
2133
|
nameToBeFilled.addStatus(NomenclaturalStatus.NewInstance(statusType));
|
|
2134
|
}
|
|
2135
|
if(newNameStatus != null){
|
|
2136
|
nameToBeFilled.setAppendedPhrase(newNameStatus);
|
|
2137
|
}
|
|
2138
|
sourceHandler.addSource(refMods, TaxonName.castAndDeproxy(nameToBeFilled));
|
|
2139
|
|
|
2140
|
if (nameToBeFilled.getNomenclaturalReference() == null) {
|
|
2141
|
acceptedTaxon= Taxon.NewInstance(nameToBeFilled,refMods);
|
|
2142
|
//System.out.println("NEW ACCEPTED HERE "+nameToBeFilled);
|
|
2143
|
}
|
|
2144
|
else {
|
|
2145
|
acceptedTaxon= Taxon.NewInstance(nameToBeFilled,nameToBeFilled.getNomenclaturalReference() );//TODO TOFIX reference
|
|
2146
|
//System.out.println("NEW ACCEPTED HERE2 "+nameToBeFilled);
|
|
2147
|
}
|
|
2148
|
|
|
2149
|
sourceHandler.addSource(refMods, acceptedTaxon);
|
|
2150
|
|
|
2151
|
if(!state2.getConfig().doKeepOriginalSecundum()) {
|
|
2152
|
acceptedTaxon.setSec(state2.getConfig().getSecundum());
|
|
2153
|
//logger.info("SET SECUNDUM "+configState.getConfig().getSecundum());
|
|
2154
|
//System.out.println("SET SECUNDUM "+configState.getConfig().getSecundum());
|
|
2155
|
}
|
|
2156
|
|
|
2157
|
if (!currentMyName.getIdentifier().isEmpty() && (currentMyName.getIdentifier().length()>2)){
|
|
2158
|
setLSID(currentMyName.getIdentifier(), acceptedTaxon);
|
|
2159
|
}
|
|
2160
|
|
|
2161
|
|
|
2162
|
importer.getTaxonService().saveOrUpdate(acceptedTaxon);
|
|
2163
|
acceptedTaxon = CdmBase.deproxy(acceptedTaxon, Taxon.class);
|
|
2164
|
}
|
|
2165
|
|
|
2166
|
}else{
|
|
2167
|
acceptedTaxon = CdmBase.deproxy(acceptedTaxon, Taxon.class);
|
|
2168
|
Set<IdentifiableSource> sources = acceptedTaxon.getSources();
|
|
2169
|
boolean sourcelinked=false;
|
|
2170
|
for (IdentifiableSource source:sources){
|
|
2171
|
if (source.getCitation().getTitleCache().equalsIgnoreCase(refMods.getTitleCache())) {
|
|
2172
|
sourcelinked=true;
|
|
2173
|
}
|
|
2174
|
}
|
|
2175
|
if (!state2.getConfig().doKeepOriginalSecundum()) {
|
|
2176
|
acceptedTaxon.setSec(state2.getConfig().getSecundum());
|
|
2177
|
//logger.info("SET SECUNDUM "+configState.getConfig().getSecundum());
|
|
2178
|
//System.out.println("SET SECUNDUM "+configState.getConfig().getSecundum());
|
|
2179
|
}
|
|
2180
|
importer.getTaxonService().saveOrUpdate(acceptedTaxon);
|
|
2181
|
|
|
2182
|
if (!sourcelinked){
|
|
2183
|
sourceHandler.addSource(refMods, acceptedTaxon);
|
|
2184
|
}
|
|
2185
|
if (!sourcelinked || !state2.getConfig().doKeepOriginalSecundum()){
|
|
2186
|
|
|
2187
|
if (!currentMyName.getIdentifier().isEmpty() && (currentMyName.getIdentifier().length()>2)){
|
|
2188
|
//FIXME are these identifiers really related to taxa, not names? Exiting LSIDs come from Zoobank, urn:lsid:biosci.ohio-state.edu:osuc_concepts:134826 (Ants)
|
|
2189
|
setLSID(currentMyName.getIdentifier(), acceptedTaxon);
|
|
2190
|
}
|
|
2191
|
importer.getTaxonService().saveOrUpdate(acceptedTaxon);
|
|
2192
|
}
|
|
2193
|
}
|
|
2194
|
}else{
|
|
2195
|
maxRankRespected=false;
|
|
2196
|
}
|
|
2197
|
containsSynonyms=true; //all folowing names are handled as synonyms
|
|
2198
|
}else{
|
|
2199
|
try{
|
|
2200
|
extractSynonyms(childNode, acceptedTaxon, refMods, followingText);
|
|
2201
|
wasSynonym = true;
|
|
2202
|
|
|
2203
|
}catch(NullPointerException e){
|
|
2204
|
logger.warn("null pointer exception, the accepted taxon might be null");
|
|
2205
|
}
|
|
2206
|
}
|
|
2207
|
containsSynonyms=true;
|
|
2208
|
}else if (childName.equalsIgnoreCase("tax:ref_group") && maxRankRespected){
|
|
2209
|
reloadClassification();
|
|
2210
|
//extract the References within the document
|
|
2211
|
extractReferences(childNode,nametosave,acceptedTaxon,refMods);
|
|
2212
|
}else if (childName.equalsIgnoreCase("tax:bibref")){
|
|
2213
|
logger.warn(childName + " still preliminary");
|
|
2214
|
|
|
2215
|
TaxonName currentName = currentMyName == null ? null : currentMyName.getTaxonName();
|
|
2216
|
boolean handled = addFollowingTextToName (currentName, childNode.getTextContent() );
|
|
2217
|
if (! handled){
|
|
2218
|
setParticularDescription(freetext.trim(), acceptedTaxon,acceptedTaxon, refMods, getNotMarkedUpFeatureObject());
|
|
2219
|
}
|
|
2220
|
}else{
|
|
2221
|
logger.warn(childName + " not yet handled");
|
|
2222
|
}
|
|
2223
|
if(!stringIsEmpty(freetext.trim())) {;
|
|
2224
|
if (! freetext.matches("\\d\\.?")){
|
|
2225
|
TaxonName currentName = currentMyName == null ? null : currentMyName.getTaxonName();
|
|
2226
|
boolean handled = false;
|
|
2227
|
if (currentName != null && !wasSynonym){
|
|
2228
|
handled = addFollowingTextToName (currentName, childNode.getTextContent() );
|
|
2229
|
}
|
|
2230
|
if (! handled){
|
|
2231
|
setParticularDescription(freetext.trim(), acceptedTaxon,acceptedTaxon, refMods, getNotMarkedUpFeatureObject());
|
|
2232
|
}
|
|
2233
|
}
|
|
2234
|
|
|
2235
|
freetext = "";
|
|
2236
|
}
|
|
2237
|
|
|
2238
|
}
|
|
2239
|
//importer.getClassificationService().saveOrUpdate(classification);
|
|
2240
|
return acceptedTaxon;
|
|
2241
|
}
|
|
2242
|
|
|
2243
|
|
|
2244
|
|
|
2245
|
|
|
2246
|
/**
|
|
2247
|
* @return
|
|
2248
|
*/
|
|
2249
|
|
|
2250
|
private boolean compareStatus(TaxonBase<?> t, NomenclaturalStatusType statusType) {
|
|
2251
|
//logger.info("compareStatus");
|
|
2252
|
boolean statusMatch=false;
|
|
2253
|
//found one taxon
|
|
2254
|
Set<NomenclaturalStatus> status = t.getName().getStatus();
|
|
2255
|
if (statusType!=null && status.size()>0){ //the statusType is known for both taxon
|
|
2256
|
for (NomenclaturalStatus st:status){
|
|
2257
|
NomenclaturalStatusType stype = st.getType();
|
|
2258
|
if (stype.toString().equalsIgnoreCase(statusType.toString())) {
|
|
2259
|
statusMatch=true;
|
|
2260
|
}
|
|
2261
|
}
|
|
2262
|
}
|
|
2263
|
else{
|
|
2264
|
if(statusType == null && status.size()==0) {//there is no statusType, we can assume it's the same
|
|
2265
|
statusMatch=true;
|
|
2266
|
}
|
|
2267
|
}
|
|
2268
|
return statusMatch;
|
|
2269
|
}
|
|
2270
|
|
|
2271
|
/**
|
|
2272
|
* @param acceptedTaxon: the current acceptedTaxon
|
|
2273
|
* @param ref: the current reference extracted from the MODS
|
|
2274
|
* @return the parent for the current accepted taxon
|
|
2275
|
*/
|
|
2276
|
/* private Taxon createParent(Taxon acceptedTaxon, Reference ref) {
|
|
2277
|
acceptedTaxon = CdmBase.deproxy(acceptedTaxon, Taxon.class);
|
|
2278
|
|
|
2279
|
List<Rank> rankList = new ArrayList<Rank>();
|
|
2280
|
rankList = importer.getTermService().listByTermClass(Rank.class, null, null, null, null);
|
|
2281
|
|
|
2282
|
List<String> rankListStr = new ArrayList<String>();
|
|
2283
|
for (Rank r:rankList) {
|
|
2284
|
rankListStr.add(r.toString());
|
|
2285
|
}
|
|
2286
|
String r="";
|
|
2287
|
String s = acceptedTaxon.getTitleCache();
|
|
2288
|
Taxon tax = null;
|
|
2289
|
if(!skippQuestion){
|
|
2290
|
int addTaxon = askAddParent(s);
|
|
2291
|
logger.info("ADD TAXON: "+addTaxon);
|
|
2292
|
if (addTaxon == 0 ){
|
|
2293
|
Taxon tmp = askParent(acceptedTaxon, classification);
|
|
2294
|
if (tmp == null){
|
|
2295
|
s = askSetParent(s);
|
|
2296
|
r = askRank(s,rankListStr);
|
|
2297
|
|
|
2298
|
TaxonName nameToBeFilled = null;
|
|
2299
|
if (nomenclaturalCode.equals(NomenclaturalCode.ICNAFP)){
|
|
2300
|
nameToBeFilled = TaxonNameFactory.NewBotanicalInstance(null);
|
|
2301
|
}
|
|
2302
|
if (nomenclaturalCode.equals(NomenclaturalCode.ICZN)){
|
|
2303
|
nameToBeFilled = TaxonNameFactory.NewZoologicalInstance(null);
|
|
2304
|
}
|
|
2305
|
if (nomenclaturalCode.equals(NomenclaturalCode.ICNP)){
|
|
2306
|
nameToBeFilled = TaxonNameFactory.NewBacterialInstance(null);
|
|
2307
|
}
|
|
2308
|
nameToBeFilled.setTitleCache(s, true);
|
|
2309
|
nameToBeFilled.setRank(getRank(r), true);
|
|
2310
|
|
|
2311
|
tax = Taxon.NewInstance(nameToBeFilled, ref);
|
|
2312
|
}
|
|
2313
|
else{
|
|
2314
|
tax=tmp;
|
|
2315
|
}
|
|
2316
|
|
|
2317
|
createParent(tax, ref);
|
|
2318
|
// logger.info("add parent child "+tax.getTitleCache()+", "+acceptedTaxon.getTitleCache());
|
|
2319
|
classification.addParentChild(tax, acceptedTaxon, ref, null);
|
|
2320
|
}
|
|
2321
|
else{
|
|
2322
|
classification.addChildTaxon(acceptedTaxon, ref, null);
|
|
2323
|
tax=acceptedTaxon;
|
|
2324
|
}
|
|
2325
|
} else{
|
|
2326
|
classification.addChildTaxon(acceptedTaxon, ref, null);
|
|
2327
|
tax=acceptedTaxon;
|
|
2328
|
}
|
|
2329
|
// logger.info("RETURN: "+tax );
|
|
2330
|
return tax;
|
|
2331
|
|
|
2332
|
}
|
|
2333
|
|
|
2334
|
*/
|
|
2335
|
|
|
2336
|
|
|
2337
|
private MyName extractScientificNameSynonym(Node name, Reference refMods, String followingText) throws TransformerFactoryConfigurationError, TransformerException {
|
|
2338
|
//System.out.println("extractScientificNameSynonym");
|
|
2339
|
logger.info("extractScientificNameSynonym");
|
|
2340
|
String[] rankListToPrint_tmp ={"dwc:genus","dwc:specificepithet","dwc:species","dwc:subspecies", "dwc:infraspecificepithet","dwc:scientificnameauthorship"};
|
|
2341
|
List<String> rankListToPrint = new ArrayList<String>();
|
|
2342
|
for (String r : rankListToPrint_tmp) {
|
|
2343
|
rankListToPrint.add(r.toLowerCase());
|
|
2344
|
}
|
|
2345
|
|
|
2346
|
Rank rank = Rank.UNKNOWN_RANK();
|
|
2347
|
NodeList children = name.getChildNodes();
|
|
2348
|
String originalName="";
|
|
2349
|
String fullName = "";
|
|
2350
|
String newName="";
|
|
2351
|
String identifier="";
|
|
2352
|
HashMap<String, String> atomisedMap = new HashMap<>();
|
|
2353
|
List<String> atomisedName= new ArrayList<String>();
|
|
2354
|
|
|
2355
|
String rankStr = "";
|
|
2356
|
Rank tmpRank ;
|
|
2357
|
|
|
2358
|
String status= extractStatus(children);
|
|
2359
|
|
|
2360
|
for (int i=0;i<children.getLength();i++){
|
|
2361
|
if(children.item(i).getNodeName().equalsIgnoreCase("tax:xmldata")){
|
|
2362
|
NodeList atom = children.item(i).getChildNodes();
|
|
2363
|
for (int k=0;k<atom.getLength();k++){
|
|
2364
|
identifier = extractIdentifier(identifier, atom.item(k));
|
|
2365
|
tmpRank = null;
|
|
2366
|
rankStr = atom.item(k).getNodeName().toLowerCase();
|
|
2367
|
// logger.info("RANKSTR:*"+rankStr+"*");
|
|
2368
|
if (rankStr.equalsIgnoreCase("dwc:taxonRank")) {
|
|
2369
|
rankStr=atom.item(k).getTextContent().trim();
|
|
2370
|
tmpRank = getRank(rankStr);
|
|
2371
|
}
|
|
2372
|
// if ((tmpRank != null) && (tmpRank.isLower(rank) || rank.equals(Rank.UNKNOWN_RANK()))) {
|
|
2373
|
if (tmpRank != null){
|
|
2374
|
rank=tmpRank;
|
|
2375
|
}
|
|
2376
|
atomisedMap.put(rankStr.toLowerCase(),atom.item(k).getTextContent().trim());
|
|
2377
|
}
|
|
2378
|
addAtomisedNamesToMap(rankListToPrint, rank, atomisedName, atom);
|
|
2379
|
}
|
|
2380
|
if(children.item(i).getNodeName().equalsIgnoreCase("#text") && !StringUtils.isBlank(children.item(i).getTextContent())){
|
|
2381
|
// logger.info("name non atomised: "+children.item(i).getTextContent());
|
|
2382
|
fullName = children.item(i).getTextContent().trim();
|
|
2383
|
// logger.info("fullname: "+fullName);
|
|
2384
|
}
|
|
2385
|
}
|
|
2386
|
originalName=fullName;
|
|
2387
|
fullName = cleanName(fullName, atomisedName);
|
|
2388
|
namesMap.put(fullName,atomisedMap);
|
|
2389
|
|
|
2390
|
String atomisedNameStr = getAtomisedNameStr(atomisedName);
|
|
2391
|
|
|
2392
|
if (fullName != null){
|
|
2393
|
// System.out.println("fullname: "+fullName);
|
|
2394
|
// System.out.println("atomised: "+atomisedNameStr);
|
|
2395
|
if (!fullName.equalsIgnoreCase(atomisedNameStr)) {
|
|
2396
|
if (skippQuestion){
|
|
2397
|
// String defaultN = "";
|
|
2398
|
if (atomisedNameStr.length()>fullName.length()) {
|
|
2399
|
newName=atomisedNameStr;
|
|
2400
|
} else {
|
|
2401
|
if (fullName.length()>atomisedNameStr.length() && (rank.isLower(Rank.SPECIES()) && fullName.length()>2 && !fullName.substring(0, 1).equals("."))) {
|
|
2402
|
newName=askWhichScientificName(fullName,atomisedNameStr,classification.getTitleCache(),name);
|
|
2403
|
} else {
|
|
2404
|
newName=fullName;
|
|
2405
|
}
|
|
2406
|
}
|
|
2407
|
} else {
|
|
2408
|
newName=askWhichScientificName(fullName,atomisedNameStr,classification.getTitleCache(),name);
|
|
2409
|
}
|
|
2410
|
} else {
|
|
2411
|
newName=fullName;
|
|
2412
|
}
|
|
2413
|
}
|
|
2414
|
//not really needed
|
|
2415
|
// rank = askForRank(newName, rank, nomenclaturalCode);
|
|
2416
|
// System.out.println("atomised: "+atomisedMap.toString());
|
|
2417
|
|
|
2418
|
// String[] names = new String[5];
|
|
2419
|
MyName myname = new MyName(true);
|
|
2420
|
|
|
2421
|
//System.out.println("Handle "+newName+ "(rank: "+rank+")");
|
|
2422
|
// System.out.println(atomisedMap.keySet());
|
|
2423
|
fullName = extractAuthorFromNames(rank, fullName, atomisedMap, myname);
|
|
2424
|
myname.setOriginalName(fullName);
|
|
2425
|
myname.setNewName(newName);
|
|
2426
|
myname.setRank(rank);
|
|
2427
|
myname.setIdentifier(identifier);
|
|
2428
|
myname.setStatus(status);
|
|
2429
|
myname.setSource(refMods);
|
|
2430
|
|
|
2431
|
// boolean higherAdded=false;
|
|
2432
|
|
|
2433
|
|
|
2434
|
boolean parseNameManually=false;
|
|
2435
|
INonViralNameParser<?> parser = NonViralNameParserImpl.NewInstance();
|
|
2436
|
TaxonName nameToBeFilledTest ;
|
|
2437
|
|
|
2438
|
//if selected the atomised version
|
|
2439
|
if(newName==atomisedNameStr){
|
|
2440
|
nameToBeFilledTest = parseWithExtension(parser, atomisedNameStr, rank, followingText, atomisedMap);
|
|
2441
|
if (nameToBeFilledTest.hasProblem()){
|
|
2442
|
addProblemNameToFile("ato",atomisedNameStr,nomenclaturalCode,rank, nameToBeFilledTest.getParsingProblems().toString());
|
|
2443
|
nameToBeFilledTest = (TaxonName)parser.parseFullName(fullName, nomenclaturalCode, rank);
|
|
2444
|
if (nameToBeFilledTest.hasProblem()){
|
|
2445
|
addProblemNameToFile("full",fullName,nomenclaturalCode,rank, nameToBeFilledTest.getParsingProblems().toString());
|
|
2446
|
parseNameManually=true;
|
|
2447
|
}
|
|
2448
|
}
|
|
2449
|
}else{
|
|
2450
|
nameToBeFilledTest = parseWithExtension(parser, atomisedNameStr, rank, followingText, atomisedMap);
|
|
2451
|
if (nameToBeFilledTest.hasProblem()){
|
|
2452
|
addProblemNameToFile("fullversion",fullName, nomenclaturalCode,rank, nameToBeFilledTest.getParsingProblems().toString());
|
|
2453
|
nameToBeFilledTest = (TaxonName)parser.parseFullName(fullName, nomenclaturalCode,rank);
|
|
2454
|
parseNameManually=true;
|
|
2455
|
if(!originalName.equalsIgnoreCase(atomisedNameStr)) {
|
|
2456
|
addNameDifferenceToFile(originalName,atomisedNameStr);
|
|
2457
|
}
|
|
2458
|
}
|
|
2459
|
}
|
|
2460
|
|
|
2461
|
if(parseNameManually){
|
|
2462
|
//System.out.println("DO IT MANUALLY");
|
|
2463
|
if (this.state2.getConfig().isUseOldUnparsedSynonymExtraction()){
|
|
2464
|
createUnparsedSynonym(rank, newName, atomisedMap, myname);
|
|
2465
|
}else{
|
|
2466
|
createUnparsedSynonymNew(rank, newName, atomisedMap, myname, refMods);;
|
|
2467
|
}
|
|
2468
|
} else{
|
|
2469
|
//System.out.println("AUTOMATIC!");
|
|
2470
|
// createAtomisedTaxonString(newName, atomisedMap, myname);
|
|
2471
|
myname.setParsedName(nameToBeFilledTest);
|
|
2472
|
myname.buildTaxon();
|
|
2473
|
}
|
|
2474
|
//System.out.println("RETURN SYNONYM "+myname.getSyno().toString());
|
|
2475
|
return myname;
|
|
2476
|
}
|
|
2477
|
|
|
2478
|
|
|
2479
|
/**
|
|
2480
|
* @param name
|
|
2481
|
* @throws TransformerFactoryConfigurationError
|
|
2482
|
* @throws TransformerException
|
|
2483
|
* @return a list of possible names
|
|
2484
|
*/
|
|
2485
|
@SuppressWarnings({"rawtypes" })
|
|
2486
|
private MyName extractScientificName(Node name, Reference refMods, String followingText) throws TransformerFactoryConfigurationError, TransformerException {
|
|
2487
|
logger.info("extractScientificName");
|
|
2488
|
|
|
2489
|
String[] rankListToPrintLowerCase_tmp ={"dwc:genus","dwc:specificepithet","dwc:species","dwc:subspecies", "dwc:infraspecificepithet","dwc:scientificnameauthorship"};
|
|
2490
|
List<String> rankListToPrint = Arrays.asList(rankListToPrintLowerCase_tmp);
|
|
2491
|
|
|
2492
|
Rank rank = Rank.UNKNOWN_RANK();
|
|
2493
|
NodeList children = name.getChildNodes();
|
|
2494
|
String originalName = "";
|
|
2495
|
String fullName = "";
|
|
2496
|
String newName = "";
|
|
2497
|
String identifier = "";
|
|
2498
|
HashMap<String, String> atomisedMap = new HashMap<>();
|
|
2499
|
List<String> atomisedNameList= new ArrayList<>();
|
|
2500
|
|
|
2501
|
String status= extractStatus(children);
|
|
2502
|
|
|
2503
|
for (int i=0;i<children.getLength();i++){
|
|
2504
|
Node nameChild = children.item(i);
|
|
2505
|
if(nameChild.getNodeName().equalsIgnoreCase("tax:xmldata")){
|
|
2506
|
NodeList xmlDataChildren = nameChild.getChildNodes();
|
|
2507
|
for (int k=0;k<xmlDataChildren.getLength();k++){
|
|
2508
|
Node xmlDataChild = xmlDataChildren.item(k);
|
|
2509
|
identifier = extractIdentifier(identifier, xmlDataChild);
|
|
2510
|
String rankStr = xmlDataChild.getNodeName().toLowerCase();
|
|
2511
|
if (rankStr.equalsIgnoreCase("dwc:taxonRank")) {
|
|
2512
|
rankStr=xmlDataChild.getTextContent().trim();
|
|
2513
|
Rank tmpRank = getRank(rankStr);
|
|
2514
|
if (tmpRank != null){
|
|
2515
|
rank=tmpRank;
|
|
2516
|
}
|
|
2517
|
}
|
|
2518
|
// if ((tmpRank != null) && (tmpRank.isLower(rank) || rank.equals(Rank.UNKNOWN_RANK()))) {
|
|
2519
|
|
|
2520
|
atomisedMap.put(rankStr.toLowerCase(),xmlDataChild.getTextContent().trim());
|
|
2521
|
}
|
|
2522
|
addAtomisedNamesToMap(rankListToPrint, rank, atomisedNameList, xmlDataChildren);
|
|
2523
|
}
|
|
2524
|
else if(nameChild.getNodeName().equalsIgnoreCase("#text") && ! nameChild.getTextContent().matches("\\s*")){
|
|
2525
|
// logger.info("name non atomised: "+children.item(i).getTextContent());
|
|
2526
|
fullName = nameChild.getTextContent().trim();
|
|
2527
|
// logger.info("fullname: "+fullName);
|
|
2528
|
}
|
|
2529
|
}
|
|
2530
|
originalName=fullName;
|
|
2531
|
fullName = cleanName(fullName, atomisedNameList);
|
|
2532
|
namesMap.put(fullName,atomisedMap);
|
|
2533
|
|
|
2534
|
String atomisedNameStr = getAtomisedNameStr(atomisedNameList);
|
|
2535
|
|
|
2536
|
if (fullName != null){
|
|
2537
|
if (!fullName.equalsIgnoreCase(atomisedNameStr)) {
|
|
2538
|
if (skippQuestion){
|
|
2539
|
if (atomisedNameStr.length()>fullName.length()) {
|
|
2540
|
newName = atomisedNameStr;
|
|
2541
|
} else {
|
|
2542
|
if (fullName.length()>atomisedNameStr.length() && (rank.isLower(Rank.SPECIES()) && fullName.length()>2 && !fullName.substring(0, 1).equals("."))) {
|
|
2543
|
newName = askWhichScientificName(fullName, atomisedNameStr, classification.getTitleCache(), name);
|
|
2544
|
} else {
|
|
2545
|
newName = fullName;
|
|
2546
|
}
|
|
2547
|
}
|
|
2548
|
} else {
|
|
2549
|
newName=askWhichScientificName(fullName, atomisedNameStr, classification.getTitleCache(), name);
|
|
2550
|
}
|
|
2551
|
} else {
|
|
2552
|
newName=fullName;
|
|
2553
|
}
|
|
2554
|
}
|
|
2555
|
//not really needed
|
|
2556
|
// rank = askForRank(newName, rank, nomenclaturalCode);
|
|
2557
|
// System.out.println("atomised: "+atomisedMap.toString());
|
|
2558
|
|
|
2559
|
// String[] names = new String[5];
|
|
2560
|
MyName myname = new MyName(false);
|
|
2561
|
|
|
2562
|
//System.out.println("\n\nBUILD "+newName+ "(rank: "+rank+")");
|
|
2563
|
// System.out.println(atomisedMap.keySet());
|
|
2564
|
fullName = extractAuthorFromNames(rank, fullName, atomisedMap, myname);
|
|
2565
|
myname.setOriginalName(fullName);
|
|
2566
|
myname.setNewName(newName);
|
|
2567
|
|
|
2568
|
myname.setRank(rank);
|
|
2569
|
myname.setIdentifier(identifier);
|
|
2570
|
myname.setStatus(status);
|
|
2571
|
myname.setSource(refMods);
|
|
2572
|
|
|
2573
|
// boolean higherAdded=false;
|
|
2574
|
|
|
2575
|
|
|
2576
|
boolean parseNameManually=false;
|
|
2577
|
INonViralNameParser parser = NonViralNameParserImpl.NewInstance();
|
|
2578
|
TaxonName nameToBeFilledTest = null;
|
|
2579
|
|
|
2580
|
//if selected the atomised version
|
|
2581
|
if(newName==atomisedNameStr){
|
|
2582
|
nameToBeFilledTest = parseWithExtension(parser, atomisedNameStr, rank, followingText, atomisedMap);
|
|
2583
|
if (nameToBeFilledTest.hasProblem()){
|
|
2584
|
addProblemNameToFile("ato",atomisedNameStr,nomenclaturalCode,rank, nameToBeFilledTest.getParsingProblems().toString());
|
|
2585
|
nameToBeFilledTest = (TaxonName)parser.parseFullName(fullName, nomenclaturalCode,rank);
|
|
2586
|
if (nameToBeFilledTest.hasProblem()){
|
|
2587
|
addProblemNameToFile("full",fullName,nomenclaturalCode,rank, nameToBeFilledTest.getParsingProblems().toString());
|
|
2588
|
parseNameManually=true;
|
|
2589
|
}
|
|
2590
|
}
|
|
2591
|
}else{
|
|
2592
|
nameToBeFilledTest = parseWithExtension(parser, fullName , rank, followingText, atomisedMap);
|
|
2593
|
if (nameToBeFilledTest.hasProblem()){
|
|
2594
|
addProblemNameToFile("fullversion",fullName,nomenclaturalCode,rank, nameToBeFilledTest.getParsingProblems().toString());
|
|
2595
|
nameToBeFilledTest = (TaxonName)parser.parseFullName(fullName, nomenclaturalCode,rank);
|
|
2596
|
parseNameManually=true;
|
|
2597
|
if(!originalName.equalsIgnoreCase(atomisedNameStr)) {
|
|
2598
|
addNameDifferenceToFile(originalName,atomisedNameStr);
|
|
2599
|
}
|
|
2600
|
}
|
|
2601
|
}
|
|
2602
|
|
|
2603
|
//System.out.println("parseNameManually: "+parseNameManually);
|
|
2604
|
if(parseNameManually){
|
|
2605
|
createAtomisedTaxon(rank, newName, atomisedMap, myname);
|
|
2606
|
}
|
|
2607
|
else{
|
|
2608
|
createAtomisedTaxonString(newName, atomisedMap, myname);
|
|
2609
|
myname.setParsedName(nameToBeFilledTest);
|
|
2610
|
//TODO correct handling of createIfNotExists
|
|
2611
|
myname.buildTaxon();
|
|
2612
|
}
|
|
2613
|
return myname;
|
|
2614
|
|
|
2615
|
}
|
|
2616
|
|
|
2617
|
private TaxonName parseWithExtension(INonViralNameParser parser, String atomisedNameStr, Rank rank, String followingText, HashMap<String, String> atomisedMap) {
|
|
2618
|
Object[] nameExtensionResult = getPossibleExtension(followingText, atomisedMap, nomenclaturalCode);
|
|
2619
|
|
|
2620
|
TaxonName name = (TaxonName)parser.parseFullName(atomisedNameStr, nomenclaturalCode, rank);
|
|
2621
|
if (nameExtensionResult != null && nameExtensionResult[0] != null){
|
|
2622
|
String ext = (String)nameExtensionResult[0];
|
|
2623
|
TaxonName extName = (TaxonName)parser.parseFullName(atomisedNameStr + " " + ext, nomenclaturalCode, rank);
|
|
2624
|
if (! extName.hasProblem()){
|
|
2625
|
name = extName;
|
|
2626
|
this.usedFollowingTextPrefix = ext;
|
|
2627
|
//TODO do we need to fill the atomisedMap at all?
|
|
2628
|
if ((Boolean)(nameExtensionResult[1])){
|
|
2629
|
//TODO
|
|
2630
|
}
|
|
2631
|
if ((Boolean)(nameExtensionResult[2])){
|
|
2632
|
//TODO BasionymYear etc.
|
|
2633
|
Integer origYear = name.getPublicationYear();
|
|
2634
|
if (origYear != null){
|
|
2635
|
atomisedMap.put(PUBLICATION_YEAR, origYear.toString());
|
|
2636
|
}
|
|
2637
|
}
|
|
2638
|
}
|
|
2639
|
}
|
|
2640
|
return name;
|
|
2641
|
}
|
|
2642
|
|
|
2643
|
private Object[] getPossibleExtension(String followingText, HashMap<String, String> atomisedMap, NomenclaturalCode nomenclaturalCode) {
|
|
2644
|
if (StringUtils.isBlank(followingText)){
|
|
2645
|
return null;
|
|
2646
|
}
|
|
2647
|
|
|
2648
|
boolean includeAuthor = true;
|
|
2649
|
boolean includeYear = false;
|
|
2650
|
if (atomisedMap.containsKey("dwc:scientificnameauthorship")){
|
|
2651
|
includeAuthor = false;
|
|
2652
|
}
|
|
2653
|
if (nomenclaturalCode.equals(NomenclaturalCode.ICZN)){
|
|
2654
|
includeYear = true;
|
|
2655
|
}
|
|
2656
|
String patternStr = "";
|
|
2657
|
if (includeAuthor){
|
|
2658
|
patternStr += NonViralNameParserImplRegExBase.capitalWord;
|
|
2659
|
}
|
|
2660
|
if (includeYear){
|
|
2661
|
patternStr += "\\s*(,|\\s+)\\s*" + "(17|18|19|20)" + "\\d{2}" ;
|
|
2662
|
}
|
|
2663
|
String match = null;
|
|
2664
|
if (! patternStr.isEmpty()){
|
|
2665
|
Pattern pattern = Pattern.compile("^" + patternStr);
|
|
2666
|
Matcher matcher = pattern.matcher(followingText.trim());
|
|
2667
|
if (matcher.find()){
|
|
2668
|
match = matcher.group();
|
|
2669
|
}
|
|
2670
|
}
|
|
2671
|
|
|
2672
|
return new Object[]{match, includeAuthor, includeYear};
|
|
2673
|
}
|
|
2674
|
|
|
2675
|
/**
|
|
2676
|
* @param atomisedName
|
|
2677
|
* @return
|
|
2678
|
*/
|
|
2679
|
private String getAtomisedNameStr(List<String> atomisedName) {
|
|
2680
|
//logger.info("getAtomisedNameStr");
|
|
2681
|
String atomisedNameStr = StringUtils.join(atomisedName," ");
|
|
2682
|
while(atomisedNameStr.contains(" ")) {
|
|
2683
|
atomisedNameStr=atomisedNameStr.replace(" ", " ");
|
|
2684
|
}
|
|
2685
|
atomisedNameStr=atomisedNameStr.trim();
|
|
2686
|
return atomisedNameStr;
|
|
2687
|
}
|
|
2688
|
|
|
2689
|
/**
|
|
2690
|
* @param children
|
|
2691
|
* @param status
|
|
2692
|
* @return
|
|
2693
|
*/
|
|
2694
|
private String extractStatus(NodeList children) {
|
|
2695
|
logger.info("extractStatus");
|
|
2696
|
String status="";
|
|
2697
|
for (int i=0;i<children.getLength();i++){
|
|
2698
|
if(children.item(i).getNodeName().equalsIgnoreCase("tax:status") ||
|
|
2699
|
(children.item(i).getNodeName().equalsIgnoreCase("tax:namePart") &&
|
|
2700
|
children.item(i).getAttributes().getNamedItem("type").getNodeValue().equalsIgnoreCase("status"))){
|
|
2701
|
status = children.item(i).getTextContent().trim();
|
|
2702
|
}
|
|
2703
|
}
|
|
2704
|
return status;
|
|
2705
|
}
|
|
2706
|
|
|
2707
|
/**
|
|
2708
|
* @param identifier
|
|
2709
|
* @param atom
|
|
2710
|
* @param k
|
|
2711
|
* @return
|
|
2712
|
*/
|
|
2713
|
private String extractIdentifier(String identifier, Node atom) {
|
|
2714
|
//logger.info("extractIdentifier");
|
|
2715
|
if (atom.getNodeName().equalsIgnoreCase("tax:xid")){
|
|
2716
|
try{
|
|
2717
|
identifier = atom.getAttributes().getNamedItem("identifier").getNodeValue();
|
|
2718
|
}catch(Exception e){
|
|
2719
|
System.out.println("pb with identifier, maybe empty");
|
|
2720
|
}
|
|
2721
|
try{
|
|
2722
|
identifier+="__"+atom.getAttributes().getNamedItem("source").getNodeValue();
|
|
2723
|
}catch(Exception e){
|
|
2724
|
System.out.println("pb with identifier, maybe empty");
|
|
2725
|
}
|
|
2726
|
}
|
|
2727
|
return identifier;
|
|
2728
|
}
|
|
2729
|
|
|
2730
|
/**
|
|
2731
|
* @param rankListToPrint
|
|
2732
|
* @param rank
|
|
2733
|
* @param atomisedName
|
|
2734
|
* @param atom
|
|
2735
|
*/
|
|
2736
|
private void addAtomisedNamesToMap(List<String> rankListToPrint, Rank rank, List<String> atomisedName, NodeList atom) {
|
|
2737
|
logger.info("addAtomisedNamesToMap");
|
|
2738
|
for (int k=0;k<atom.getLength();k++){
|
|
2739
|
Node node = atom.item(k);
|
|
2740
|
String nodeName = node.getNodeName();
|
|
2741
|
if (! nodeName.equalsIgnoreCase("dwc:taxonRank") ) { //rank has been handled in higher method
|
|
2742
|
if (nodeName.equalsIgnoreCase("dwc:subgenus") || nodeName.equalsIgnoreCase("dwcranks:subgenus")) {
|
|
2743
|
atomisedName.add("("+ node.getTextContent().trim()+")");
|
|
2744
|
} else if(nodeName.equalsIgnoreCase("dwcranks:varietyepithet") || nodeName.equalsIgnoreCase("dwc:Subspecies") || nodeName.equalsIgnoreCase("dwc:infraspecificepithet")) {
|
|
2745
|
if(nodeName.equalsIgnoreCase("dwcranks:varietyepithet")){
|
|
2746
|
atomisedName.add("var. "+node.getTextContent().trim());
|
|
2747
|
}else if(nodeName.equalsIgnoreCase("dwc:Subspecies") || nodeName.equalsIgnoreCase("dwc:infraspecificepithet")) {
|
|
2748
|
atomisedName.add("subsp. "+atom.item(k).getTextContent().trim());
|
|
2749
|
}
|
|
2750
|
} else if(rankListToPrint.contains(nodeName.toLowerCase())) {
|
|
2751
|
atomisedName.add(node.getTextContent().trim());
|
|
2752
|
} else{
|
|
2753
|
if (rank.isHigher(Rank.GENUS()) && (nodeName.indexOf("dwcranks:")>-1 || nodeName.indexOf("dwc:Family")>-1)) {
|
|
2754
|
atomisedName.add(node.getTextContent().trim());
|
|
2755
|
}else if (nodeName.equals("#text")){
|
|
2756
|
String text = node.getTextContent();
|
|
2757
|
if (StringUtils.isNotBlank(text)){
|
|
2758
|
//TODO handle text
|
|
2759
|
logger.warn("name xmldata contains text. This is unhandled");
|
|
2760
|
}
|
|
2761
|
}else if (nodeName.matches("(?i)(dwc:Kingdom|dwc:Class|dwc:Order|dwc:Family)")){
|
|
2762
|
//we currently do not use higher ranks information
|
|
2763
|
}else{
|
|
2764
|
//TODO handle unhandled node
|
|
2765
|
logger.warn("Unhandled node: " + nodeName);
|
|
2766
|
}
|
|
2767
|
}
|
|
2768
|
}
|
|
2769
|
}
|
|
2770
|
}
|
|
2771
|
|
|
2772
|
/**
|
|
2773
|
* @param fullName
|
|
2774
|
* @param atomisedName
|
|
2775
|
* @return
|
|
2776
|
*/
|
|
2777
|
private String cleanName(String name, List<String> atomisedName) {
|
|
2778
|
//logger.info("cleanName");
|
|
2779
|
String fullName =name;
|
|
2780
|
if (fullName != null){
|
|
2781
|
fullName = fullName.replace("( ", "(");
|
|
2782
|
fullName = fullName.replace(" )",")");
|
|
2783
|
|
|
2784
|
if (fullName.trim().isEmpty()){
|
|
2785
|
fullName=StringUtils.join(atomisedName," ");
|
|
2786
|
}
|
|
2787
|
|
|
2788
|
while(fullName.contains(" ")) {
|
|
2789
|
fullName=fullName.replace(" ", " ");
|
|
2790
|
// logger.info("while");
|
|
2791
|
}
|
|
2792
|
fullName=fullName.trim();
|
|
2793
|
}
|
|
2794
|
return fullName;
|
|
2795
|
}
|
|
2796
|
|
|
2797
|
/**
|
|
2798
|
* @param rank
|
|
2799
|
* @param fullName
|
|
2800
|
* @param atomisedMap
|
|
2801
|
* @param myname
|
|
2802
|
* @return
|
|
2803
|
*/
|
|
2804
|
private String extractAuthorFromNames(Rank rank, String name, HashMap<String, String> atomisedMap, MyName myname) {
|
|
2805
|
logger.info("extractAuthorFromNames");
|
|
2806
|
String fullName=name;
|
|
2807
|
if (atomisedMap.get("dwc:scientificnameauthorship") == null && fullName!=null){
|
|
2808
|
// System.out.println("rank : "+rank.toString());
|
|
2809
|
if(rank.isHigher(Rank.SPECIES())){
|
|
2810
|
try{
|
|
2811
|
String author=null;
|
|
2812
|
if(atomisedMap.get("dwcranks:subgenus") != null) {
|
|
2813
|
author = fullName.split(atomisedMap.get("dwcranks:subgenus"))[1].trim();
|
|
2814
|
}
|
|
2815
|
if(atomisedMap.get("dwc:subgenus") != null) {
|
|
2816
|
author = fullName.split(atomisedMap.get("dwc:subgenus"))[1].trim();
|
|
2817
|
}
|
|
2818
|
if(author == null) {
|
|
2819
|
if(atomisedMap.get("dwc:genus") != null) {
|
|
2820
|
author = fullName.split(atomisedMap.get("dwc:genus"))[1].trim();
|
|
2821
|
}
|
|
2822
|
}
|
|
2823
|
if(author != null){
|
|
2824
|
fullName = fullName.substring(0, fullName.indexOf(author));
|
|
2825
|
author=author.replaceAll(",","").trim();
|
|
2826
|
myname.setAuthor(author);
|
|
2827
|
}
|
|
2828
|
}catch(Exception e){
|
|
2829
|
//could not extract the author
|
|
2830
|
}
|
|
2831
|
}
|
|
2832
|
if(rank.equals(Rank.SPECIES())){
|
|
2833
|
try{
|
|
2834
|
String author=null;
|
|
2835
|
if(author == null) {
|
|
2836
|
if(atomisedMap.get("dwc:species") != null) {
|
|
2837
|
String[] t = fullName.split(atomisedMap.get("dwc:species"));
|
|
2838
|
// System.out.println("NB ELEMENTS "+t.length +"fullName "+fullName+", "+atomisedMap.get("dwc:species"));
|
|
2839
|
author = fullName.split(atomisedMap.get("dwc:species"))[1].trim();
|
|
2840
|
// System.out.println("AUTEUR "+author);
|
|
2841
|
}
|
|
2842
|
}
|
|
2843
|
if(author != null){
|
|
2844
|
fullName = fullName.substring(0, fullName.indexOf(author));
|
|
2845
|
author=author.replaceAll(",","").trim();
|
|
2846
|
myname.setAuthor(author);
|
|
2847
|
}
|
|
2848
|
}catch(Exception e){
|
|
2849
|
//could not extract the author
|
|
2850
|
}
|
|
2851
|
}
|
|
2852
|
}else{
|
|
2853
|
myname.setAuthor(atomisedMap.get("dwc:scientificnameauthorship"));
|
|
2854
|
}
|
|
2855
|
return fullName;
|
|
2856
|
}
|
|
2857
|
|
|
2858
|
/**
|
|
2859
|
* @param newName
|
|
2860
|
* @param atomisedMap
|
|
2861
|
* @param myname
|
|
2862
|
*/
|
|
2863
|
private void createAtomisedTaxonString(String newName, HashMap<String, String> atomisedMap, MyName myname) {
|
|
2864
|
logger.info("createAtomisedTaxonString "+atomisedMap);
|
|
2865
|
if(atomisedMap.get("dwc:family") != null && checkRankValidForImport(Rank.FAMILY())){
|
|
2866
|
myname.setFamilyStr(atomisedMap.get("dwc:family"));
|
|
2867
|
}
|
|
2868
|
if(atomisedMap.get("dwcranks:subfamily") != null && checkRankValidForImport(Rank.SUBFAMILY())){
|
|
2869
|
myname.setSubfamilyStr(atomisedMap.get("dwcranks:subfamily"));
|
|
2870
|
}
|
|
2871
|
if(atomisedMap.get("dwcranks:tribe") != null && checkRankValidForImport(Rank.TRIBE())){
|
|
2872
|
myname.setTribeStr(atomisedMap.get("dwcranks:tribe"));
|
|
2873
|
}
|
|
2874
|
if(atomisedMap.get("dwcranks:subtribe") != null && checkRankValidForImport(Rank.SUBTRIBE())){
|
|
2875
|
myname.setSubtribeStr(atomisedMap.get("dwcranks:subtribe"));
|
|
2876
|
}
|
|
2877
|
if(atomisedMap.get("dwc:genus") != null && checkRankValidForImport(Rank.GENUS())){
|
|
2878
|
myname.setGenusStr(atomisedMap.get("dwc:genus"));
|
|
2879
|
}
|
|
2880
|
if(atomisedMap.get("dwcranks:subgenus") != null && checkRankValidForImport(Rank.SUBGENUS())){
|
|
2881
|
myname.setSubgenusStr(atomisedMap.get("dwcranks:subgenus"));
|
|
2882
|
}
|
|
2883
|
if(atomisedMap.get("dwc:subgenus") != null && checkRankValidForImport(Rank.SUBGENUS())){
|
|
2884
|
myname.setSubgenusStr(atomisedMap.get("dwc:subgenus"));
|
|
2885
|
}
|
|
2886
|
if(atomisedMap.get("dwc:species") != null && checkRankValidForImport(Rank.SPECIES())){
|
|
2887
|
String n=newName;
|
|
2888
|
if(atomisedMap.get("dwc:infraspecificepithet") != null) {
|
|
2889
|
n=newName.split(atomisedMap.get("dwc:infraspecificepithet"))[0];
|
|
2890
|
n=n.replace("subsp.","");
|
|
2891
|
}
|
|
2892
|
if(atomisedMap.get("dwc:subspecies") != null) {
|
|
2893
|
n=newName.split(atomisedMap.get("dwc:subspecies"))[0];
|
|
2894
|
n=n.replace("subsp.","");
|
|
2895
|
}
|
|
2896
|
if(atomisedMap.get("dwcranks:varietyepithet") != null) {
|
|
2897
|
n=newName.split(atomisedMap.get("dwcranks:varietyepithet"))[0];
|
|
2898
|
n=n.replace("var.","");
|
|
2899
|
n=n.replace("v.","");
|
|
2900
|
}
|
|
2901
|
if(atomisedMap.get("dwcranks:formepithet") != null) {
|
|
2902
|
//TODO
|
|
2903
|
System.out.println("TODO FORMA");
|
|
2904
|
n=newName.split(atomisedMap.get("dwcranks:formepithet"))[0];
|
|
2905
|
n=n.replace("forma","");
|
|
2906
|
}
|
|
2907
|
n=n.trim();
|
|
2908
|
String author = myname.getAuthor();
|
|
2909
|
if(n.split(" ").length>2){
|
|
2910
|
|
|
2911
|
String n2=n.split(" ")[0]+" "+n.split(" ")[1];
|
|
2912
|
String a= "";
|
|
2913
|
try{
|
|
2914
|
a=n.split(n2)[1].trim();
|
|
2915
|
}catch(Exception e){
|
|
2916
|
logger.info("no author in "+n+"?");}
|
|
2917
|
|
|
2918
|
myname.setAuthor(a);
|
|
2919
|
//System.out.println("FINDCREATESPECIES --"+n2+"--"+n+"**"+a+"##");
|
|
2920
|
n=n2;
|
|
2921
|
|
|
2922
|
}
|
|
2923
|
|
|
2924
|
myname.setSpeciesStr(atomisedMap.get("dwc:species"));
|
|
2925
|
myname.setAuthor(author);
|
|
2926
|
}
|
|
2927
|
if(atomisedMap.get("dwc:subspecies") != null && checkRankValidForImport(Rank.SUBSPECIES())){
|
|
2928
|
myname.setSubspeciesStr(atomisedMap.get("dwc:subspecies"));
|
|
2929
|
}
|
|
2930
|
if(atomisedMap.get("dwc:infraspecificepithet") != null && checkRankValidForImport(Rank.SUBSPECIES())){
|
|
2931
|
myname.setSubspeciesStr(atomisedMap.get("dwc:infraspecificepithet"));
|
|
2932
|
}
|
|
2933
|
if(atomisedMap.get("dwcranks:varietyepithet") != null && checkRankValidForImport(Rank.VARIETY())){
|
|
2934
|
myname.setVarietyStr(atomisedMap.get("dwcranks:varietyepithet"));
|
|
2935
|
}
|
|
2936
|
if(atomisedMap.get("dwcranks:formepithet") != null && checkRankValidForImport(Rank.FORM())){
|
|
2937
|
myname.setFormStr(atomisedMap.get("dwcranks:formepithet"));
|
|
2938
|
}
|
|
2939
|
if (atomisedMap.get(PUBLICATION_YEAR) != null){
|
|
2940
|
myname.setPublicationYear(Integer.valueOf(atomisedMap.get(PUBLICATION_YEAR)));
|
|
2941
|
}
|
|
2942
|
}
|
|
2943
|
|
|
2944
|
/**
|
|
2945
|
* @see #createUnparsedSynonymNew(Rank, String, HashMap, MyName)
|
|
2946
|
* @param rank
|
|
2947
|
* @param newName
|
|
2948
|
* @param atomisedMap
|
|
2949
|
* @param myname
|
|
2950
|
*/
|
|
2951
|
private void createUnparsedSynonym(Rank rank, String newName, HashMap<String, String> atomisedMap, MyName myname) {
|
|
2952
|
logger.info("createSynonym");
|
|
2953
|
//System.out.println("createsynonym");
|
|
2954
|
if(rank.equals(Rank.UNKNOWN_RANK())){
|
|
2955
|
myname.setNotParsableTaxon(newName);
|
|
2956
|
}else{
|
|
2957
|
if(atomisedMap.get("dwc:family") != null && checkRankValidForImport(Rank.FAMILY()) && rank.equals(Rank.FAMILY())){
|
|
2958
|
myname.setFamily(myname.findOrCreateTaxon(atomisedMap.get("dwc:family"),newName, Rank.FAMILY(),rank));
|
|
2959
|
}
|
|
2960
|
if(atomisedMap.get("dwcranks:subfamily") != null && checkRankValidForImport(Rank.SUBFAMILY()) && rank.equals(Rank.SUBFAMILY())){
|
|
2961
|
myname.setSubfamily(myname.findOrCreateTaxon(atomisedMap.get("dwcranks:subfamily"), newName,Rank.SUBFAMILY(),rank));
|
|
2962
|
}
|
|
2963
|
if(atomisedMap.get("dwcranks:tribe") != null && checkRankValidForImport(Rank.TRIBE()) && rank.equals(Rank.TRIBE())){
|
|
2964
|
myname.setTribe(myname.findOrCreateTaxon(atomisedMap.get("dwcranks:tribe"),newName, Rank.TRIBE(),rank));
|
|
2965
|
}
|
|
2966
|
if(atomisedMap.get("dwcranks:subtribe") != null && checkRankValidForImport(Rank.SUBTRIBE()) && rank.equals(Rank.SUBTRIBE())){
|
|
2967
|
myname.setSubtribe(myname.findOrCreateTaxon(atomisedMap.get("dwcranks:subtribe"),newName, Rank.SUBTRIBE(),rank));
|
|
2968
|
}
|
|
2969
|
if(atomisedMap.get("dwc:genus") != null && checkRankValidForImport(Rank.GENUS()) && rank.equals(Rank.GENUS())){
|
|
2970
|
myname.setGenus(myname.findOrCreateTaxon(atomisedMap.get("dwc:genus"),newName, Rank.GENUS(),rank));
|
|
2971
|
}
|
|
2972
|
if(atomisedMap.get("dwcranks:subgenus") != null && checkRankValidForImport(Rank.SUBGENUS()) && rank.equals(Rank.SUBGENUS())){
|
|
2973
|
myname.setSubgenus(myname.findOrCreateTaxon(atomisedMap.get("dwcranks:subgenus"),newName, Rank.SUBGENUS(),rank));
|
|
2974
|
}
|
|
2975
|
if(atomisedMap.get("dwc:subgenus") != null && checkRankValidForImport(Rank.SUBGENUS()) && rank.equals(Rank.SUBGENUS())){
|
|
2976
|
myname.setSubgenus(myname.findOrCreateTaxon(atomisedMap.get("dwc:subgenus"),newName, Rank.SUBGENUS(),rank));
|
|
2977
|
}
|
|
2978
|
if(atomisedMap.get("dwc:species") != null && checkRankValidForImport(Rank.SPECIES()) && rank.equals(Rank.SPECIES())){
|
|
2979
|
String n=newName;
|
|
2980
|
if(atomisedMap.get("dwc:infraspecificepithet") != null) {
|
|
2981
|
n=newName.split(atomisedMap.get("dwc:infraspecificepithet"))[0];
|
|
2982
|
n=n.replace("subsp.","");
|
|
2983
|
}
|
|
2984
|
if(atomisedMap.get("dwc:subspecies") != null) {
|
|
2985
|
n=newName.split(atomisedMap.get("dwc:subspecies"))[0];
|
|
2986
|
n=n.replace("subsp.","");
|
|
2987
|
}
|
|
2988
|
if(atomisedMap.get("dwcranks:varietyepithet") != null) {
|
|
2989
|
n=newName.split(atomisedMap.get("dwcranks:varietyepithet"))[0];
|
|
2990
|
n=n.replace("var.","");
|
|
2991
|
n=n.replace("v.","");
|
|
2992
|
}
|
|
2993
|
if(atomisedMap.get("dwcranks:formepithet") != null) {
|
|
2994
|
//TODO
|
|
2995
|
//System.out.println("TODO FORMA");
|
|
2996
|
n=newName.split(atomisedMap.get("dwcranks:formepithet"))[0];
|
|
2997
|
n=n.replace("forma","");
|
|
2998
|
}
|
|
2999
|
n=n.trim();
|
|
3000
|
String author = myname.getAuthor();
|
|
3001
|
if(n.split(" ").length>2){
|
|
3002
|
|
|
3003
|
String n2=n.split(" ")[0]+" "+n.split(" ")[1];
|
|
3004
|
String a="";
|
|
3005
|
try{
|
|
3006
|
a= n.split(n2)[1].trim();
|
|
3007
|
}catch(Exception e){logger.info("no author in "+n);}
|
|
3008
|
myname.setAuthor(a);
|
|
3009
|
//System.out.println("FINDCREATESPECIES --"+n2+"--"+n+"**"+a+"##");
|
|
3010
|
n=n2;
|
|
3011
|
|
|
3012
|
}
|
|
3013
|
Taxon species = myname.findOrCreateTaxon(atomisedMap.get("dwc:species"),n, Rank.SPECIES(),rank);
|
|
3014
|
myname.setSpecies(species);
|
|
3015
|
myname.setAuthor(author);
|
|
3016
|
}
|
|
3017
|
if(atomisedMap.get("dwc:subspecies") != null && checkRankValidForImport(Rank.SUBSPECIES()) && rank.equals(Rank.SUBSPECIES())){
|
|
3018
|
myname.setSubspecies(myname.findOrCreateTaxon(atomisedMap.get("dwc:subspecies"), newName,Rank.SUBSPECIES(),rank));
|
|
3019
|
}
|
|
3020
|
if(atomisedMap.get("dwc:infraspecificepithet") != null && checkRankValidForImport(Rank.SUBSPECIES()) && rank.equals(Rank.SUBSPECIES())){
|
|
3021
|
myname.setSubspecies(myname.findOrCreateTaxon(atomisedMap.get("dwc:infraspecificepithet"),newName, Rank.SUBSPECIES(),rank));
|
|
3022
|
}
|
|
3023
|
if(atomisedMap.get("dwcranks:varietyepithet") != null && checkRankValidForImport(Rank.VARIETY()) && rank.equals(Rank.VARIETY())){
|
|
3024
|
myname.setVariety(myname.findOrCreateTaxon(atomisedMap.get("dwcranks:varietyepithet"),newName, Rank.VARIETY(),rank));
|
|
3025
|
}
|
|
3026
|
if(atomisedMap.get("dwcranks:formepithet") != null && checkRankValidForImport(Rank.FORM()) && rank.equals(Rank.FORM())){
|
|
3027
|
myname.setForm(myname.findOrCreateTaxon(atomisedMap.get("dwcranks:formepithet"), newName,Rank.FORM(),rank));
|
|
3028
|
}
|
|
3029
|
}
|
|
3030
|
|
|
3031
|
}
|
|
3032
|
|
|
3033
|
|
|
3034
|
/**
|
|
3035
|
* @param refMods
|
|
3036
|
* @see #createUnparsedSynonym(Rank, String, HashMap, MyName)
|
|
3037
|
* the original TaxonXImport extracted Synonyms by creating acc Taxa with partial names
|
|
3038
|
* I (AM) do not understand this but don't want to destroy code which maybe works in some cases) there
|
|
3039
|
* I created this switch for old
|
|
3040
|
* for Spiders the new version is preferred
|
|
3041
|
*/
|
|
3042
|
private void createUnparsedSynonymNew(Rank rank, String newName, HashMap<String, String> atomisedMap, MyName myname, Reference refMods) {
|
|
3043
|
logger.info("createSynonym");
|
|
3044
|
|
|
3045
|
INonViralName nameToBeFilled = this.getNonViralNameAccNomenclature();
|
|
3046
|
//System.out.println("createsynonym");
|
|
3047
|
if(rank.equals(Rank.UNKNOWN_RANK())){
|
|
3048
|
//TODO
|
|
3049
|
myname.setNotParsableTaxon(newName);
|
|
3050
|
|
|
3051
|
nameToBeFilled.setTitleCache(newName, true);
|
|
3052
|
}else{
|
|
3053
|
if(atomisedMap.get("dwc:genus") != null ){
|
|
3054
|
nameToBeFilled.setGenusOrUninomial(atomisedMap.get("dwc:genus"));
|
|
3055
|
}
|
|
3056
|
if (rank.isSupraGeneric()){
|
|
3057
|
if (atomisedMap.get("dwcranks:subtribe") != null ){
|
|
3058
|
nameToBeFilled.setGenusOrUninomial(atomisedMap.get("dwcranks:subtribe"));
|
|
3059
|
}else if (atomisedMap.get("dwcranks:subtribe") != null ){
|
|
3060
|
nameToBeFilled.setGenusOrUninomial(atomisedMap.get("dwcranks:subtribe"));
|
|
3061
|
}else if (atomisedMap.get("dwcranks:tribe") != null ){
|
|
3062
|
nameToBeFilled.setGenusOrUninomial(atomisedMap.get("dwcranks:tribe"));
|
|
3063
|
}else if (atomisedMap.get("dwcranks:subfamily") != null ){
|
|
3064
|
nameToBeFilled.setGenusOrUninomial(atomisedMap.get("dwcranks:subfamily"));
|
|
3065
|
}else if (atomisedMap.get("dwc:family") != null ){
|
|
3066
|
nameToBeFilled.setGenusOrUninomial(atomisedMap.get("dwc:family"));
|
|
3067
|
}else{
|
|
3068
|
logger.warn("Supra generic rank not yet handled or atomisation not available");
|
|
3069
|
}
|
|
3070
|
}
|
|
3071
|
if (atomisedMap.get("dwcranks:subgenus") != null){
|
|
3072
|
nameToBeFilled.setInfraGenericEpithet(atomisedMap.get("dwcranks:subgenus"));
|
|
3073
|
}
|
|
3074
|
if (atomisedMap.get("dwc:subgenus") != null){
|
|
3075
|
nameToBeFilled.setInfraGenericEpithet(atomisedMap.get("dwc:subgenus"));
|
|
3076
|
}
|
|
3077
|
if (atomisedMap.get("dwc:species") != null){
|
|
3078
|
nameToBeFilled.setSpecificEpithet(atomisedMap.get("dwc:species"));
|
|
3079
|
}
|
|
3080
|
if (atomisedMap.get("dwcranks:formepithet") != null){
|
|
3081
|
nameToBeFilled.setInfraSpecificEpithet(atomisedMap.get("dwcranks:formepithet"));
|
|
3082
|
}else if (atomisedMap.get("dwcranks:varietyepithet") != null){
|
|
3083
|
nameToBeFilled.setInfraSpecificEpithet(atomisedMap.get("dwcranks:varietyepithet"));
|
|
3084
|
}else if (atomisedMap.get("dwc:infraspecificepithet") != null){
|
|
3085
|
nameToBeFilled.setInfraSpecificEpithet(atomisedMap.get("dwc:infraspecificepithet"));
|
|
3086
|
}else if (atomisedMap.get("dwc:subspecies") != null){
|
|
3087
|
nameToBeFilled.setInfraSpecificEpithet(atomisedMap.get("dwc:subspecies"));
|
|
3088
|
}
|
|
3089
|
Reference sec = sourceUrlRef;
|
|
3090
|
if(!state2.getConfig().doKeepOriginalSecundum()){
|
|
3091
|
sec = state2.getConfig().getSecundum();
|
|
3092
|
}
|
|
3093
|
Synonym syn = Synonym.NewInstance(nameToBeFilled, sec);
|
|
3094
|
// sourceHandler.addSource(refMods, syn);
|
|
3095
|
myname.setSyno(syn);
|
|
3096
|
myname.setSynonym(true);
|
|
3097
|
}
|
|
3098
|
}
|
|
3099
|
|
|
3100
|
/**
|
|
3101
|
* @param rank
|
|
3102
|
* @param newName
|
|
3103
|
* @param atomisedMap
|
|
3104
|
* @param myname
|
|
3105
|
*/
|
|
3106
|
private void createAtomisedTaxon(Rank rank, String newName, HashMap<String, String> atomisedMap, MyName myname) {
|
|
3107
|
logger.info("createAtomisedTaxon "+atomisedMap);
|
|
3108
|
if(rank.equals(Rank.UNKNOWN_RANK())){
|
|
3109
|
myname.setNotParsableTaxon(newName);
|
|
3110
|
}
|
|
3111
|
else{
|
|
3112
|
if(atomisedMap.get("dwc:family") != null && checkRankValidForImport(Rank.FAMILY())){
|
|
3113
|
myname.setFamily(myname.findOrCreateTaxon(atomisedMap.get("dwc:family"),newName, Rank.FAMILY(),rank));
|
|
3114
|
}
|
|
3115
|
if(atomisedMap.get("dwcranks:subfamily") != null && checkRankValidForImport(Rank.SUBFAMILY())){
|
|
3116
|
myname.setSubfamily(myname.findOrCreateTaxon(atomisedMap.get("dwcranks:subfamily"), newName,Rank.SUBFAMILY(),rank));
|
|
3117
|
}
|
|
3118
|
if(atomisedMap.get("dwcranks:tribe") != null && checkRankValidForImport(Rank.TRIBE())){
|
|
3119
|
myname.setTribe(myname.findOrCreateTaxon(atomisedMap.get("dwcranks:tribe"),newName, Rank.TRIBE(),rank));
|
|
3120
|
}
|
|
3121
|
if(atomisedMap.get("dwcranks:subtribe") != null && checkRankValidForImport(Rank.SUBTRIBE())){
|
|
3122
|
myname.setSubtribe(myname.findOrCreateTaxon(atomisedMap.get("dwcranks:subtribe"),newName, Rank.SUBTRIBE(),rank));
|
|
3123
|
}
|
|
3124
|
if(atomisedMap.get("dwc:genus") != null && checkRankValidForImport(Rank.GENUS())){
|
|
3125
|
myname.setGenus(myname.findOrCreateTaxon(atomisedMap.get("dwc:genus"),newName, Rank.GENUS(),rank));
|
|
3126
|
}
|
|
3127
|
if(atomisedMap.get("dwcranks:subgenus") != null && checkRankValidForImport(Rank.SUBGENUS())){
|
|
3128
|
myname.setSubgenus(myname.findOrCreateTaxon(atomisedMap.get("dwcranks:subgenus"),newName, Rank.SUBGENUS(),rank));
|
|
3129
|
}
|
|
3130
|
if(atomisedMap.get("dwc:subgenus") != null && checkRankValidForImport(Rank.SUBGENUS())){
|
|
3131
|
myname.setSubgenus(myname.findOrCreateTaxon(atomisedMap.get("dwc:subgenus"),newName, Rank.SUBGENUS(),rank));
|
|
3132
|
}
|
|
3133
|
if(atomisedMap.get("dwc:species") != null && checkRankValidForImport(Rank.SPECIES())){
|
|
3134
|
String n=newName;
|
|
3135
|
if(atomisedMap.get("dwc:infraspecificepithet") != null) {
|
|
3136
|
n=newName.split(atomisedMap.get("dwc:infraspecificepithet"))[0];
|
|
3137
|
n=n.replace("subsp.","");
|
|
3138
|
}
|
|
3139
|
if(atomisedMap.get("dwc:subspecies") != null) {
|
|
3140
|
n=newName.split(atomisedMap.get("dwc:subspecies"))[0];
|
|
3141
|
n=n.replace("subsp.","");
|
|
3142
|
}
|
|
3143
|
if(atomisedMap.get("dwcranks:varietyepithet") != null) {
|
|
3144
|
n=newName.split(atomisedMap.get("dwcranks:varietyepithet"))[0];
|
|
3145
|
n=n.replace("var.","");
|
|
3146
|
n=n.replace("v.","");
|
|
3147
|
}
|
|
3148
|
if(atomisedMap.get("dwcranks:formepithet") != null) {
|
|
3149
|
//TODO
|
|
3150
|
//System.out.println("TODO FORMA");
|
|
3151
|
n=newName.split(atomisedMap.get("dwcranks:formepithet"))[0];
|
|
3152
|
n=n.replace("forma","");
|
|
3153
|
}
|
|
3154
|
n=n.trim();
|
|
3155
|
String author = myname.getAuthor();
|
|
3156
|
if(n.split(" ").length>2){
|
|
3157
|
String n2=n.split(" ")[0]+" "+n.split(" ")[1];
|
|
3158
|
String a="";
|
|
3159
|
try{
|
|
3160
|
a= n.split(n2)[1].trim();
|
|
3161
|
}catch(Exception e){logger.info("no author in "+n);}
|
|
3162
|
myname.setAuthor(a);
|
|
3163
|
//System.out.println("FINDCREATESPECIES --"+n2+"--"+n+"**"+a+"##");
|
|
3164
|
n=n2;
|
|
3165
|
|
|
3166
|
}
|
|
3167
|
|
|
3168
|
myname.setSpecies(myname.findOrCreateTaxon(atomisedMap.get("dwc:species"),n, Rank.SPECIES(),rank));
|
|
3169
|
myname.setAuthor(author);
|
|
3170
|
}
|
|
3171
|
if(atomisedMap.get("dwc:subspecies") != null && checkRankValidForImport(Rank.SUBSPECIES())){
|
|
3172
|
myname.setSubspecies(myname.findOrCreateTaxon(atomisedMap.get("dwc:subspecies"), newName,Rank.SUBSPECIES(),rank));
|
|
3173
|
}
|
|
3174
|
if(atomisedMap.get("dwc:infraspecificepithet") != null && checkRankValidForImport(Rank.SUBSPECIES())){
|
|
3175
|
myname.setSubspecies(myname.findOrCreateTaxon(atomisedMap.get("dwc:infraspecificepithet"),newName, Rank.SUBSPECIES(),rank));
|
|
3176
|
}
|
|
3177
|
if(atomisedMap.get("dwcranks:varietyepithet") != null && checkRankValidForImport(Rank.VARIETY())){
|
|
3178
|
myname.setVariety(myname.findOrCreateTaxon(atomisedMap.get("dwcranks:varietyepithet"),newName, Rank.VARIETY(),rank));
|
|
3179
|
}
|
|
3180
|
if(atomisedMap.get("dwcranks:formepithet") != null && checkRankValidForImport(Rank.FORM())){
|
|
3181
|
myname.setForm(myname.findOrCreateTaxon(atomisedMap.get("dwcranks:formepithet"), newName,Rank.FORM(),rank));
|
|
3182
|
}
|
|
3183
|
}
|
|
3184
|
}
|
|
3185
|
|
|
3186
|
/**
|
|
3187
|
* @return
|
|
3188
|
*/
|
|
3189
|
private boolean checkRankValidForImport(Rank currentRank) {
|
|
3190
|
//logger.info("checkRankValidForImport");
|
|
3191
|
return currentRank.isLower(state2.getConfig().getMaxRank()) || currentRank.equals(state2.getConfig().getMaxRank());
|
|
3192
|
}
|
|
3193
|
|
|
3194
|
|
|
3195
|
|
|
3196
|
/**
|
|
3197
|
* @param classification2
|
|
3198
|
*/
|
|
3199
|
public void updateClassification(Classification classification2) {
|
|
3200
|
//logger.info("updateClassification");
|
|
3201
|
classification = classification2;
|
|
3202
|
}
|
|
3203
|
|
|
3204
|
|
|
3205
|
|
|
3206
|
public class MyName {
|
|
3207
|
/**
|
|
3208
|
* @param isSynonym
|
|
3209
|
*/
|
|
3210
|
public MyName(boolean isSynonym) {
|
|
3211
|
super();
|
|
3212
|
this.isSynonym = isSynonym;
|
|
3213
|
}
|
|
3214
|
|
|
3215
|
String originalName="";
|
|
3216
|
String newName="";
|
|
3217
|
Rank rank=Rank.UNKNOWN_RANK();
|
|
3218
|
String identifier="";
|
|
3219
|
String status="";
|
|
3220
|
String author=null;
|
|
3221
|
|
|
3222
|
TaxonName taxonName;
|
|
3223
|
|
|
3224
|
Reference refMods ;
|
|
3225
|
|
|
3226
|
Taxon family,subfamily,tribe,subtribe,genus,subgenus,species,subspecies, variety,form;
|
|
3227
|
INonViralName familyName, subfamilyName, tribeName,subtribeName,genusName,subgenusName,speciesName,subspeciesName;
|
|
3228
|
String familyStr, subfamilyStr, tribeStr,subtribeStr,genusStr,subgenusStr,speciesStr,subspeciesStr,formStr,varietyStr;
|
|
3229
|
Integer publicationYear;
|
|
3230
|
|
|
3231
|
|
|
3232
|
Taxon higherTaxa;
|
|
3233
|
Rank higherRank;
|
|
3234
|
private Taxon taxon;
|
|
3235
|
private Synonym syno;
|
|
3236
|
|
|
3237
|
/**
|
|
3238
|
* @return the syno
|
|
3239
|
*/
|
|
3240
|
public Synonym getSyno() {
|
|
3241
|
return syno;
|
|
3242
|
}
|
|
3243
|
|
|
3244
|
@Override
|
|
3245
|
public String toString(){
|
|
3246
|
List<String> tot=new ArrayList<String>();
|
|
3247
|
String[] n= {familyStr, subfamilyStr, tribeStr,subtribeStr,genusStr,subgenusStr,speciesStr,subspeciesStr,formStr,varietyStr};
|
|
3248
|
for (String elt:n){
|
|
3249
|
if (!StringUtils.isEmpty(elt)) {
|
|
3250
|
tot.add(elt);
|
|
3251
|
} else {
|
|
3252
|
tot.add("*");
|
|
3253
|
}
|
|
3254
|
}
|
|
3255
|
return StringUtils.join(tot," ");
|
|
3256
|
}
|
|
3257
|
/**
|
|
3258
|
* @param syno the syno to set
|
|
3259
|
*/
|
|
3260
|
public void setSyno(Synonym syno) {
|
|
3261
|
this.syno = syno;
|
|
3262
|
}
|
|
3263
|
|
|
3264
|
boolean isSynonym=false;
|
|
3265
|
|
|
3266
|
/**
|
|
3267
|
* @return the isSynonym
|
|
3268
|
*/
|
|
3269
|
public boolean isSynonym() {
|
|
3270
|
return isSynonym;
|
|
3271
|
}
|
|
3272
|
|
|
3273
|
/**
|
|
3274
|
* @param isSynonym the isSynonym to set
|
|
3275
|
*/
|
|
3276
|
public void setSynonym(boolean isSynonym) {
|
|
3277
|
this.isSynonym = isSynonym;
|
|
3278
|
}
|
|
3279
|
|
|
3280
|
public void setSource(Reference re){
|
|
3281
|
refMods=re;
|
|
3282
|
}
|
|
3283
|
|
|
3284
|
/**
|
|
3285
|
* @param string
|
|
3286
|
*/
|
|
3287
|
public void setFormStr(String string) {
|
|
3288
|
this.formStr=string;
|
|
3289
|
|
|
3290
|
}
|
|
3291
|
/**
|
|
3292
|
* @param string
|
|
3293
|
*/
|
|
3294
|
public void setVarietyStr(String string) {
|
|
3295
|
this.varietyStr=string;
|
|
3296
|
|
|
3297
|
}
|
|
3298
|
/**
|
|
3299
|
* @param string
|
|
3300
|
*/
|
|
3301
|
public void setSubspeciesStr(String string) {
|
|
3302
|
this.subspeciesStr=string;
|
|
3303
|
|
|
3304
|
}
|
|
3305
|
/**
|
|
3306
|
* @param string
|
|
3307
|
*/
|
|
3308
|
public void setSpeciesStr(String string) {
|
|
3309
|
this.speciesStr=string;
|
|
3310
|
|
|
3311
|
}
|
|
3312
|
/**
|
|
3313
|
* @param string
|
|
3314
|
*/
|
|
3315
|
public void setSubgenusStr(String string) {
|
|
3316
|
this.subgenusStr=string;
|
|
3317
|
|
|
3318
|
}
|
|
3319
|
/**
|
|
3320
|
* @param string
|
|
3321
|
*/
|
|
3322
|
public void setGenusStr(String string) {
|
|
3323
|
this.genusStr=string;
|
|
3324
|
|
|
3325
|
}
|
|
3326
|
/**
|
|
3327
|
* @param string
|
|
3328
|
*/
|
|
3329
|
public void setSubtribeStr(String string) {
|
|
3330
|
this.subtribeStr=string;
|
|
3331
|
|
|
3332
|
}
|
|
3333
|
/**
|
|
3334
|
* @param string
|
|
3335
|
*/
|
|
3336
|
public void setTribeStr(String string) {
|
|
3337
|
this.tribeStr=string;
|
|
3338
|
|
|
3339
|
}
|
|
3340
|
/**
|
|
3341
|
* @param string
|
|
3342
|
*/
|
|
3343
|
public void setSubfamilyStr(String string) {
|
|
3344
|
this.subfamilyStr=string;
|
|
3345
|
|
|
3346
|
}
|
|
3347
|
/**
|
|
3348
|
* @param string
|
|
3349
|
*/
|
|
3350
|
public void setFamilyStr(String string) {
|
|
3351
|
this.familyStr=string;
|
|
3352
|
|
|
3353
|
}
|
|
3354
|
/**
|
|
3355
|
* @return the familyStr
|
|
3356
|
*/
|
|
3357
|
public String getFamilyStr() {
|
|
3358
|
return familyStr;
|
|
3359
|
}
|
|
3360
|
/**
|
|
3361
|
* @return the subfamilyStr
|
|
3362
|
*/
|
|
3363
|
public String getSubfamilyStr() {
|
|
3364
|
return subfamilyStr;
|
|
3365
|
}
|
|
3366
|
/**
|
|
3367
|
* @return the tribeStr
|
|
3368
|
*/
|
|
3369
|
public String getTribeStr() {
|
|
3370
|
return tribeStr;
|
|
3371
|
}
|
|
3372
|
/**
|
|
3373
|
* @return the subtribeStr
|
|
3374
|
*/
|
|
3375
|
public String getSubtribeStr() {
|
|
3376
|
return subtribeStr;
|
|
3377
|
}
|
|
3378
|
/**
|
|
3379
|
* @return the genusStr
|
|
3380
|
*/
|
|
3381
|
public String getGenusStr() {
|
|
3382
|
return genusStr;
|
|
3383
|
}
|
|
3384
|
/**
|
|
3385
|
* @return the subgenusStr
|
|
3386
|
*/
|
|
3387
|
public String getSubgenusStr() {
|
|
3388
|
return subgenusStr;
|
|
3389
|
}
|
|
3390
|
/**
|
|
3391
|
* @return the speciesStr
|
|
3392
|
*/
|
|
3393
|
public String getSpeciesStr() {
|
|
3394
|
return speciesStr;
|
|
3395
|
}
|
|
3396
|
/**
|
|
3397
|
* @return the subspeciesStr
|
|
3398
|
*/
|
|
3399
|
public String getSubspeciesStr() {
|
|
3400
|
return subspeciesStr;
|
|
3401
|
}
|
|
3402
|
/**
|
|
3403
|
* @return the formStr
|
|
3404
|
*/
|
|
3405
|
public String getFormStr() {
|
|
3406
|
return formStr;
|
|
3407
|
}
|
|
3408
|
/**
|
|
3409
|
* @return the varietyStr
|
|
3410
|
*/
|
|
3411
|
public String getVarietyStr() {
|
|
3412
|
return varietyStr;
|
|
3413
|
}
|
|
3414
|
|
|
3415
|
public Integer getPublicationYear() {
|
|
3416
|
return publicationYear;
|
|
3417
|
}
|
|
3418
|
|
|
3419
|
public void setPublicationYear(Integer publicationYear) {
|
|
3420
|
this.publicationYear = publicationYear;
|
|
3421
|
}
|
|
3422
|
|
|
3423
|
/**
|
|
3424
|
* @param newName2
|
|
3425
|
*/
|
|
3426
|
public void setNotParsableTaxon(String newName2) {
|
|
3427
|
//takes too much time
|
|
3428
|
// List<TaxonBase> tmpList = importer.getTaxonService().list(Taxon.class, 0, 0, null, null);
|
|
3429
|
|
|
3430
|
NomenclaturalStatusType statusType = null;
|
|
3431
|
if (!getStatus().isEmpty()){
|
|
3432
|
try {
|
|
3433
|
statusType = nomStatusString2NomStatus(getStatus());
|
|
3434
|
} catch (UnknownCdmTypeException e) {
|
|
3435
|
addProblematicStatusToFile(getStatus());
|
|
3436
|
logger.warn("Problem with status");
|
|
3437
|
}
|
|
3438
|
}
|
|
3439
|
List<TaxonBase> tmpList = new ArrayList<>();
|
|
3440
|
|
|
3441
|
Pager<TaxonBase> taxontest = importer.getTaxonService().findByTitleWithRestrictions(TaxonBase.class, newName2, MatchMode.BEGINNING, null, null, null, null, null);
|
|
3442
|
tmpList.addAll(taxontest.getRecords());
|
|
3443
|
|
|
3444
|
//logger.info("tmpList returned: "+tmpList.size());
|
|
3445
|
|
|
3446
|
|
|
3447
|
INonViralName identicName = null;
|
|
3448
|
boolean foundIdentic=false;
|
|
3449
|
TaxonBase<?> tmpTaxonBase=null;
|
|
3450
|
// Taxon tmpPartial=null;
|
|
3451
|
for (TaxonBase<?> tmpb:tmpList){
|
|
3452
|
if(tmpb !=null){
|
|
3453
|
TaxonName tnb = tmpb.getName();
|
|
3454
|
Rank crank=null;
|
|
3455
|
if (tnb != null){
|
|
3456
|
if (tnb.getTitleCache().split("sec.")[0].trim().equalsIgnoreCase(newName2) ){
|
|
3457
|
crank =tnb.getRank();
|
|
3458
|
if (crank !=null && rank !=null){
|
|
3459
|
if (crank.equals(rank)){
|
|
3460
|
identicName = tnb;
|
|
3461
|
if (isSynonym && tmpb.isInstanceOf(Synonym.class) || !isSynonym && tmpb.isInstanceOf(Taxon.class)){
|
|
3462
|
foundIdentic=true;
|
|
3463
|
tmpTaxonBase=tmpb;
|
|
3464
|
break;
|
|
3465
|
}
|
|
3466
|
}
|
|
3467
|
}
|
|
3468
|
}
|
|
3469
|
}
|
|
3470
|
}
|
|
3471
|
}
|
|
3472
|
boolean statusMatch=false;
|
|
3473
|
boolean appendedMatch=false;
|
|
3474
|
if(tmpTaxonBase !=null && foundIdentic){
|
|
3475
|
statusMatch=compareStatus(tmpTaxonBase, statusType);
|
|
3476
|
if (!getStatus().isEmpty() && ! (tmpTaxonBase.getAppendedPhrase() == null)) {
|
|
3477
|
appendedMatch=tmpTaxonBase.getAppendedPhrase().equals(getStatus());
|
|
3478
|
}
|
|
3479
|
if (getStatus().isEmpty() && tmpTaxonBase.getAppendedPhrase() == null) {
|
|
3480
|
appendedMatch=true;
|
|
3481
|
}
|
|
3482
|
|
|
3483
|
}
|
|
3484
|
if ((tmpTaxonBase == null || !foundIdentic) || (tmpTaxonBase != null && !statusMatch) || (tmpTaxonBase != null && !appendedMatch && !statusMatch)){
|
|
3485
|
|
|
3486
|
INonViralName tnb;
|
|
3487
|
if (identicName == null){
|
|
3488
|
tnb = getNonViralNameAccNomenclature();
|
|
3489
|
tnb.setRank(rank);
|
|
3490
|
|
|
3491
|
if(statusType != null) {
|
|
3492
|
tnb.addStatus(NomenclaturalStatus.NewInstance(statusType));
|
|
3493
|
}
|
|
3494
|
if(StringUtils.isNotBlank(getStatus())) {
|
|
3495
|
tnb.setAppendedPhrase(getStatus());
|
|
3496
|
}
|
|
3497
|
tnb.setTitleCache(newName2,true);
|
|
3498
|
tmpTaxonBase = findMatchingTaxon(tnb,refMods);
|
|
3499
|
}else{
|
|
3500
|
tnb = identicName;
|
|
3501
|
}
|
|
3502
|
|
|
3503
|
if(tmpTaxonBase==null){
|
|
3504
|
tmpTaxonBase = isSynonym ? Synonym.NewInstance(tnb, refMods) : Taxon.NewInstance(tnb, refMods);
|
|
3505
|
if(!state2.getConfig().doKeepOriginalSecundum()) {
|
|
3506
|
tmpTaxonBase.setSec(state2.getConfig().getSecundum());
|
|
3507
|
}
|
|
3508
|
//tmptaxonbase.setSec(refMods);
|
|
3509
|
if(!isSynonym) {
|
|
3510
|
classification.addChildTaxon((Taxon)tmpTaxonBase, null, null);
|
|
3511
|
sourceHandler.addSource(refMods, (Taxon)tmpTaxonBase);
|
|
3512
|
}
|
|
3513
|
}
|
|
3514
|
}
|
|
3515
|
|
|
3516
|
tmpTaxonBase = CdmBase.deproxy(tmpTaxonBase, TaxonBase.class);
|
|
3517
|
if (author != null) {
|
|
3518
|
if (!getIdentifier().isEmpty() && (getIdentifier().length()>2)){
|
|
3519
|
setLSID(getIdentifier(), tmpTaxonBase);
|
|
3520
|
importer.getTaxonService().saveOrUpdate(tmpTaxonBase);
|
|
3521
|
tmpTaxonBase = CdmBase.deproxy(tmpTaxonBase, TaxonBase.class);
|
|
3522
|
}
|
|
3523
|
}
|
|
3524
|
TaxonName tnb = CdmBase.deproxy(tmpTaxonBase.getName(), TaxonName.class);
|
|
3525
|
|
|
3526
|
if(!isSynonym) {
|
|
3527
|
this.taxon=(Taxon)tmpTaxonBase;
|
|
3528
|
} else {
|
|
3529
|
if (tmpTaxonBase instanceof Taxon){
|
|
3530
|
logger.warn("Incorrect status");
|
|
3531
|
}
|
|
3532
|
this.syno=(Synonym)tmpTaxonBase;
|
|
3533
|
}
|
|
3534
|
|
|
3535
|
taxonName = tnb;
|
|
3536
|
|
|
3537
|
}
|
|
3538
|
|
|
3539
|
/**
|
|
3540
|
*
|
|
3541
|
*/
|
|
3542
|
public void buildTaxon() {
|
|
3543
|
//System.out.println("BUILD TAXON");
|
|
3544
|
logger.info("buildTaxon");
|
|
3545
|
NomenclaturalStatusType statusType = null;
|
|
3546
|
if (!getStatus().isEmpty()){
|
|
3547
|
status = getStatus();
|
|
3548
|
String newNameStatus = newNameStatus(status);
|
|
3549
|
if (newNameStatus != null){
|
|
3550
|
taxonName.setAppendedPhrase(newNameStatus);
|
|
3551
|
}else{
|
|
3552
|
try {
|
|
3553
|
statusType = nomStatusString2NomStatus(getStatus());
|
|
3554
|
taxonName.addStatus(NomenclaturalStatus.NewInstance(statusType));
|
|
3555
|
} catch (UnknownCdmTypeException e) {
|
|
3556
|
addProblematicStatusToFile(getStatus());
|
|
3557
|
logger.warn("Problem with status");
|
|
3558
|
}
|
|
3559
|
}
|
|
3560
|
}
|
|
3561
|
importer.getNameService().save(taxonName);
|
|
3562
|
|
|
3563
|
TaxonBase<?> tmpTaxonBase;
|
|
3564
|
if (!isSynonym) {
|
|
3565
|
tmpTaxonBase =Taxon.NewInstance(taxonName, refMods); //sec set null
|
|
3566
|
}
|
|
3567
|
else {
|
|
3568
|
tmpTaxonBase =Synonym.NewInstance(taxonName, refMods); //sec set null
|
|
3569
|
}
|
|
3570
|
boolean exist = false;
|
|
3571
|
if (!isSynonym){
|
|
3572
|
for (TaxonNode node : classification.getAllNodes()){
|
|
3573
|
try{
|
|
3574
|
Taxon nodeTaxon = node.getTaxon();
|
|
3575
|
boolean titleMatches = nodeTaxon.getTitleCache().equalsIgnoreCase(tmpTaxonBase.getTitleCache());
|
|
3576
|
boolean nomStatusMatches = compareStatus(node.getTaxon(), statusType);
|
|
3577
|
boolean nodeNameReplaceable = checkNodeNameReplaceable(nodeTaxon, tmpTaxonBase);
|
|
3578
|
if(titleMatches && nomStatusMatches) {
|
|
3579
|
if (!isSynonym) {
|
|
3580
|
tmpTaxonBase=CdmBase.deproxy(nodeTaxon, TaxonBase.class);
|
|
3581
|
exist =true;
|
|
3582
|
} else {
|
|
3583
|
logger.info("Found the same name but from another type (taxon/synonym)");
|
|
3584
|
TaxonName existingTnb = getTaxon().getName();
|
|
3585
|
tmpTaxonBase = Synonym.NewInstance(existingTnb, refMods);
|
|
3586
|
importer.getTaxonService().saveOrUpdate(tmpTaxonBase);
|
|
3587
|
exist =true;
|
|
3588
|
}
|
|
3589
|
}else if (nodeNameReplaceable){
|
|
3590
|
nodeTaxon.setName(tmpTaxonBase.getName());
|
|
3591
|
tmpTaxonBase = nodeTaxon;
|
|
3592
|
exist = true;
|
|
3593
|
}
|
|
3594
|
}catch(NullPointerException n){logger.warn(" A taxon is either null or its titlecache is null - ignore it?");}
|
|
3595
|
}
|
|
3596
|
}
|
|
3597
|
if (!exist){
|
|
3598
|
|
|
3599
|
boolean insertAsExisting =false;
|
|
3600
|
List<Taxon> existingTaxons=new ArrayList<Taxon>();
|
|
3601
|
try {
|
|
3602
|
existingTaxons = getMatchingTaxa(taxonName);
|
|
3603
|
} catch (Exception e1) {
|
|
3604
|
e1.printStackTrace();
|
|
3605
|
}
|
|
3606
|
double similarityScore=0.0;
|
|
3607
|
double similarityAuthor=-1;
|
|
3608
|
String author1="";
|
|
3609
|
String author2="";
|
|
3610
|
String t1="";
|
|
3611
|
String t2="";
|
|
3612
|
for (Taxon bestMatchingTaxon : existingTaxons){
|
|
3613
|
//System.out.println("tnbase "+taxonname.getTitleCache());
|
|
3614
|
//System.out.println("bestex "+bestMatchingTaxon.getTitleCache());
|
|
3615
|
if(taxonName.getAuthorshipCache()!=null) {
|
|
3616
|
author1=taxonName.getAuthorshipCache();
|
|
3617
|
}
|
|
3618
|
try {
|
|
3619
|
if(bestMatchingTaxon.getName().getAuthorshipCache()!=null) {
|
|
3620
|
author2=bestMatchingTaxon.getName().getAuthorshipCache();
|
|
3621
|
}
|
|
3622
|
} catch (Exception e) {
|
|
3623
|
// TODO Auto-generated catch block
|
|
3624
|
e.printStackTrace();
|
|
3625
|
}
|
|
3626
|
try {
|
|
3627
|
t1=taxonName.getTitleCache();
|
|
3628
|
if (author1!=null && !StringUtils.isEmpty(author1)) {
|
|
3629
|
t1=t1.split(Pattern.quote(author1))[0];
|
|
3630
|
}
|
|
3631
|
} catch (Exception e) {
|
|
3632
|
// TODO Auto-generated catch block
|
|
3633
|
e.printStackTrace();
|
|
3634
|
}
|
|
3635
|
try {
|
|
3636
|
t2=bestMatchingTaxon.getTitleCache().split("sec.")[0].trim();
|
|
3637
|
if (author2!=null && !StringUtils.isEmpty(author2)) {
|
|
3638
|
t2=t2.split(Pattern.quote(author2))[0];
|
|
3639
|
}
|
|
3640
|
} catch (Exception e) {
|
|
3641
|
// TODO Auto-generated catch block
|
|
3642
|
e.printStackTrace();
|
|
3643
|
}
|
|
3644
|
|
|
3645
|
similarityScore=similarity(t1.trim(), t2.trim());
|
|
3646
|
//System.out.println("taxonscore "+similarityScore);
|
|
3647
|
similarityAuthor=similarity(author1.trim(), author2.trim());
|
|
3648
|
//System.out.println("authorscore "+similarityAuthor);
|
|
3649
|
insertAsExisting = compareAndCheckTaxon(taxonName, refMods, similarityScore, bestMatchingTaxon, similarityAuthor);
|
|
3650
|
if(insertAsExisting) {
|
|
3651
|
tmpTaxonBase=bestMatchingTaxon;
|
|
3652
|
break;
|
|
3653
|
}
|
|
3654
|
}
|
|
3655
|
if ( !insertAsExisting ){
|
|
3656
|
if(!state2.getConfig().doKeepOriginalSecundum()) {
|
|
3657
|
tmpTaxonBase.setSec(state2.getConfig().getSecundum());
|
|
3658
|
}
|
|
3659
|
|
|
3660
|
// tmptaxonbase.setSec(refMods);
|
|
3661
|
if (taxonName.getRank().equals(state2.getConfig().getMaxRank())) {
|
|
3662
|
//System.out.println("****************************"+tmptaxonbase);
|
|
3663
|
if (!isSynonym) {
|
|
3664
|
classification.addChildTaxon((Taxon)tmpTaxonBase, refMods, null);
|
|
3665
|
}
|
|
3666
|
} else{
|
|
3667
|
hierarchy = new HashMap<>();
|
|
3668
|
//System.out.println("LOOK FOR PARENT "+taxonname.toString()+", "+tmptaxonbase.toString());
|
|
3669
|
if (!isSynonym){
|
|
3670
|
lookForParentNode(taxonName,(Taxon)tmpTaxonBase, refMods,this);
|
|
3671
|
//System.out.println("HIERARCHY "+hierarchy);
|
|
3672
|
Taxon parent = buildHierarchy();
|
|
3673
|
if(!taxonExistsInClassification(parent,(Taxon)tmpTaxonBase)){
|
|
3674
|
if(parent !=null) {
|
|
3675
|
classification.addParentChild(parent, (Taxon)tmpTaxonBase, refMods, null);
|
|
3676
|
} else {
|
|
3677
|
classification.addChildTaxon((Taxon)tmpTaxonBase, refMods, null);
|
|
3678
|
}
|
|
3679
|
importer.getClassificationService().saveOrUpdate(classification);
|
|
3680
|
}
|
|
3681
|
}
|
|
3682
|
// Set<TaxonNode> nodeList = classification.getAllNodes();
|
|
3683
|
// for(TaxonNode tn:nodeList) {
|
|
3684
|
// System.out.println(tn.getTaxon());
|
|
3685
|
// }
|
|
3686
|
}
|
|
3687
|
}
|
|
3688
|
importer.getClassificationService().saveOrUpdate(classification);
|
|
3689
|
if(isSynonym) {
|
|
3690
|
try{
|
|
3691
|
Synonym castTest=CdmBase.deproxy(tmpTaxonBase, Synonym.class);
|
|
3692
|
}catch(Exception e){
|
|
3693
|
TaxonName existingTnb = tmpTaxonBase.getName();
|
|
3694
|
Synonym castTest = Synonym.NewInstance(existingTnb, refMods);
|
|
3695
|
importer.getTaxonService().saveOrUpdate(castTest);
|
|
3696
|
tmpTaxonBase=CdmBase.deproxy(castTest, Synonym.class);
|
|
3697
|
}
|
|
3698
|
}
|
|
3699
|
}
|
|
3700
|
if(!isSynonym) {
|
|
3701
|
taxon=CdmBase.deproxy(tmpTaxonBase, Taxon.class);
|
|
3702
|
} else {
|
|
3703
|
syno=CdmBase.deproxy(tmpTaxonBase, Synonym.class);
|
|
3704
|
}
|
|
3705
|
|
|
3706
|
}
|
|
3707
|
|
|
3708
|
private boolean checkNodeNameReplaceable(Taxon nodeTaxon, TaxonBase<?> newTaxon) {
|
|
3709
|
//TODO preliminary check
|
|
3710
|
if (newTaxon.isInstanceOf(Synonym.class)){
|
|
3711
|
return false;
|
|
3712
|
}
|
|
3713
|
INonViralName nodeName = nodeTaxon.getName();
|
|
3714
|
INonViralName newName = newTaxon.getName();
|
|
3715
|
if (nodeTaxon.getName() == null || newName == null){
|
|
3716
|
return false;
|
|
3717
|
}
|
|
3718
|
if (nodeTaxon.getDescriptions().size() > 0 || nodeName.getDescriptions().size() > 0 || nodeName.getTypeDesignations().size() > 0 ){
|
|
3719
|
return false;
|
|
3720
|
}
|
|
3721
|
boolean compare = true;
|
|
3722
|
for (NomenclaturalStatus status : newName.getStatus() ){
|
|
3723
|
compare &= compareStatus(nodeTaxon, status.getType());
|
|
3724
|
}
|
|
3725
|
if (! compare){
|
|
3726
|
return false;
|
|
3727
|
}
|
|
3728
|
|
|
3729
|
if (nodeName.getNameCache() != null && nodeName.getNameCache().equals(newName.getNameCache())){
|
|
3730
|
if (nodeName.getNameCache().equals(nodeName.getTitleCache())){
|
|
3731
|
if (newName.getNameCache().length() < newName.getTitleCache().length()){
|
|
3732
|
logger.warn("We still need to check, if node was automatically created via hierarchy creation: " + nodeName.getNameCache());
|
|
3733
|
return true;
|
|
3734
|
}
|
|
3735
|
}
|
|
3736
|
}
|
|
3737
|
|
|
3738
|
return false;
|
|
3739
|
}
|
|
3740
|
|
|
3741
|
/**
|
|
3742
|
*
|
|
3743
|
*/
|
|
3744
|
private Taxon buildHierarchy() {
|
|
3745
|
logger.info("buildHierarchy");
|
|
3746
|
Taxon higherTaxon = null;
|
|
3747
|
//add the maxRank as a root
|
|
3748
|
if(hierarchy.containsKey(state2.getConfig().getMaxRank())){
|
|
3749
|
Taxon ct=hierarchy.get(state2.getConfig().getMaxRank());
|
|
3750
|
if(!taxonExistsInClassification(higherTaxon, ct)) {
|
|
3751
|
classification.addChildTaxon(ct, refMods, null);
|
|
3752
|
}
|
|
3753
|
higherTaxon = hierarchy.get(state2.getConfig().getMaxRank());
|
|
3754
|
// return higherTaxon;
|
|
3755
|
}
|
|
3756
|
//add the relation to the highertaxon, except if the current rank to add IS the maxRank
|
|
3757
|
|
|
3758
|
//TODO higher Ranks
|
|
3759
|
|
|
3760
|
if(hierarchy.containsKey(Rank.FAMILY()) && !state2.getConfig().getMaxRank().equals(Rank.FAMILY())){
|
|
3761
|
higherTaxon=saveAndGetHigherTaxon(Rank.FAMILY(),higherTaxon);
|
|
3762
|
}
|
|
3763
|
if(hierarchy.containsKey(Rank.SUBFAMILY()) && !state2.getConfig().getMaxRank().equals(Rank.SUBFAMILY())){
|
|
3764
|
higherTaxon=saveAndGetHigherTaxon(Rank.SUBFAMILY(),higherTaxon);
|
|
3765
|
}
|
|
3766
|
if(hierarchy.containsKey(Rank.TRIBE())&& !state2.getConfig().getMaxRank().equals(Rank.TRIBE())){
|
|
3767
|
higherTaxon=saveAndGetHigherTaxon(Rank.TRIBE(),higherTaxon);
|
|
3768
|
}
|
|
3769
|
if(hierarchy.containsKey(Rank.SUBTRIBE())&& !state2.getConfig().getMaxRank().equals(Rank.SUBTRIBE())){
|
|
3770
|
higherTaxon=saveAndGetHigherTaxon(Rank.SUBTRIBE(),higherTaxon);
|
|
3771
|
}
|
|
3772
|
if(hierarchy.containsKey(Rank.GENUS())&& !state2.getConfig().getMaxRank().equals(Rank.SUBGENUS())){
|
|
3773
|
higherTaxon=saveAndGetHigherTaxon(Rank.GENUS(),higherTaxon);
|
|
3774
|
}
|
|
3775
|
if(hierarchy.containsKey(Rank.SUBGENUS())&& !state2.getConfig().getMaxRank().equals(Rank.SUBGENUS())){
|
|
3776
|
higherTaxon=saveAndGetHigherTaxon(Rank.SUBGENUS(),higherTaxon);
|
|
3777
|
}
|
|
3778
|
importer.getClassificationService().saveOrUpdate(classification);
|
|
3779
|
return higherTaxon;
|
|
3780
|
}
|
|
3781
|
|
|
3782
|
private Taxon saveAndGetHigherTaxon(Rank r, Taxon higherTaxon){
|
|
3783
|
Taxon ct=hierarchy.get(r);
|
|
3784
|
if(!taxonExistsInClassification(higherTaxon,ct )) {
|
|
3785
|
if(higherTaxon != null && ct!=null) {
|
|
3786
|
classification.addParentChild(higherTaxon, ct, refMods, null);
|
|
3787
|
} else
|
|
3788
|
if(higherTaxon == null && ct !=null) {
|
|
3789
|
classification.addChildTaxon(ct, refMods, null);
|
|
3790
|
}
|
|
3791
|
}
|
|
3792
|
return ct;
|
|
3793
|
}
|
|
3794
|
|
|
3795
|
private boolean taxonExistsInClassification(Taxon parent, Taxon child){
|
|
3796
|
logger.info("taxonExistsInClassification");
|
|
3797
|
// System.out.println("LOOK IF TAXA EXIST "+parent+", "+child);
|
|
3798
|
boolean found=false;
|
|
3799
|
if(parent !=null){
|
|
3800
|
for (TaxonNode p : classification.getAllNodes()){
|
|
3801
|
if(p.getTaxon().getTitleCache().equalsIgnoreCase(parent.getTitleCache())) {
|
|
3802
|
for (TaxonNode c : p.getChildNodes()) {
|
|
3803
|
if (c.getTaxon().getTitleCache().equalsIgnoreCase(child.getTitleCache())) {
|
|
3804
|
found=true;
|
|
3805
|
break;
|
|
3806
|
}
|
|
3807
|
}
|
|
3808
|
}
|
|
3809
|
}
|
|
3810
|
}
|
|
3811
|
else{
|
|
3812
|
for (TaxonNode p : classification.getAllNodes()){
|
|
3813
|
if(p.getTaxon().getTitleCache().equalsIgnoreCase(child.getTitleCache())) {
|
|
3814
|
found=true;
|
|
3815
|
break;
|
|
3816
|
}
|
|
3817
|
}
|
|
3818
|
}
|
|
3819
|
// System.out.println("LOOK IF TAXA EXIST? "+found);
|
|
3820
|
return found;
|
|
3821
|
}
|
|
3822
|
/**
|
|
3823
|
* @param nameToBeFilledTest
|
|
3824
|
*/
|
|
3825
|
public void setParsedName(TaxonName nameToBeFilledTest) {
|
|
3826
|
this.taxonName = TaxonName.castAndDeproxy(nameToBeFilledTest);
|
|
3827
|
|
|
3828
|
}
|
|
3829
|
//variety dwcranks:varietyEpithet
|
|
3830
|
/**
|
|
3831
|
* @return the author
|
|
3832
|
*/
|
|
3833
|
public String getAuthor() {
|
|
3834
|
return author;
|
|
3835
|
}
|
|
3836
|
/**
|
|
3837
|
* @return
|
|
3838
|
*/
|
|
3839
|
public Taxon getTaxon() {
|
|
3840
|
return taxon;
|
|
3841
|
}
|
|
3842
|
/**
|
|
3843
|
* @return
|
|
3844
|
*/
|
|
3845
|
public TaxonName getTaxonName() {
|
|
3846
|
return taxonName;
|
|
3847
|
}
|
|
3848
|
|
|
3849
|
/**
|
|
3850
|
* @param findOrCreateTaxon
|
|
3851
|
*/
|
|
3852
|
public void setForm(Taxon form) {
|
|
3853
|
this.form=form;
|
|
3854
|
|
|
3855
|
}
|
|
3856
|
/**
|
|
3857
|
* @param findOrCreateTaxon
|
|
3858
|
*/
|
|
3859
|
public void setVariety(Taxon variety) {
|
|
3860
|
this.variety=variety;
|
|
3861
|
|
|
3862
|
}
|
|
3863
|
/**
|
|
3864
|
* @param string
|
|
3865
|
* @return
|
|
3866
|
*/
|
|
3867
|
@SuppressWarnings("rawtypes")
|
|
3868
|
public Taxon findOrCreateTaxon(String partialname,String fullname, Rank rank, Rank globalrank) {
|
|
3869
|
logger.info("findOrCreateTaxon");
|
|
3870
|
sourceUrlRef=CdmBase.deproxy(sourceUrlRef, Reference.class);
|
|
3871
|
//takes too much time
|
|
3872
|
// List<TaxonBase> tmpList = importer.getTaxonService().list(Taxon.class, 0, 0, null, null);
|
|
3873
|
// logger.info("tmpList returned: "+tmpList.size());
|
|
3874
|
|
|
3875
|
NomenclaturalStatusType statusType = null;
|
|
3876
|
if (!getStatus().isEmpty()){
|
|
3877
|
try {
|
|
3878
|
statusType = nomStatusString2NomStatus(getStatus());
|
|
3879
|
} catch (UnknownCdmTypeException e) {
|
|
3880
|
addProblematicStatusToFile(getStatus());
|
|
3881
|
logger.warn("Problem with status");
|
|
3882
|
}
|
|
3883
|
}
|
|
3884
|
|
|
3885
|
List<TaxonBase> tmpListFiltered = new ArrayList<TaxonBase>();
|
|
3886
|
|
|
3887
|
Pager<TaxonBase> taxontest = importer.getTaxonService().findByTitleWithRestrictions(TaxonBase.class, fullname, MatchMode.BEGINNING, null, null, null, null, null);
|
|
3888
|
|
|
3889
|
tmpListFiltered.addAll(taxontest.getRecords());
|
|
3890
|
taxontest = importer.getTaxonService().findByTitleWithRestrictions(TaxonBase.class, partialname, MatchMode.BEGINNING, null, null, null, null, null);
|
|
3891
|
tmpListFiltered.addAll(taxontest.getRecords());
|
|
3892
|
|
|
3893
|
//logger.info("tmpListFiltered returned: "+tmpListFiltered.size());
|
|
3894
|
|
|
3895
|
boolean nameCorrected=false;
|
|
3896
|
if (fullname.indexOf(partialname)<0) {
|
|
3897
|
nameCorrected=true;
|
|
3898
|
}
|
|
3899
|
|
|
3900
|
boolean foundIdentic=false;
|
|
3901
|
Taxon tmp=null;
|
|
3902
|
for (TaxonBase tmpb:tmpListFiltered){
|
|
3903
|
if(tmpb !=null){
|
|
3904
|
TaxonName tnb = tmpb.getName();
|
|
3905
|
Rank crank=null;
|
|
3906
|
if (tnb != null){
|
|
3907
|
if(globalrank.equals(rank) || (globalrank.isLower(Rank.SPECIES()) && rank.equals(Rank.SPECIES()))){
|
|
3908
|
if (tnb.getTitleCache().split("sec.")[0].trim().equalsIgnoreCase(fullname) ){
|
|
3909
|
crank =tnb.getRank();
|
|
3910
|
if (crank !=null && rank !=null){
|
|
3911
|
if (crank.equals(rank)){
|
|
3912
|
foundIdentic=true;
|
|
3913
|
try{
|
|
3914
|
tmp=(Taxon)tmpb;
|
|
3915
|
break;
|
|
3916
|
}catch(Exception e){
|
|
3917
|
e.printStackTrace();
|
|
3918
|
}
|
|
3919
|
}
|
|
3920
|
}
|
|
3921
|
}
|
|
3922
|
if(nameCorrected){ //for corrected names such as Anochetus -- A. blf-pat
|
|
3923
|
if (tnb.getTitleCache().split("sec.")[0].trim().equalsIgnoreCase(partialname) ){
|
|
3924
|
crank =tnb.getRank();
|
|
3925
|
if (crank !=null && rank !=null){
|
|
3926
|
if (crank.equals(rank)){
|
|
3927
|
foundIdentic=true;
|
|
3928
|
try{
|
|
3929
|
tmp=(Taxon)tmpb;
|
|
3930
|
break;
|
|
3931
|
}catch(Exception e){
|
|
3932
|
e.printStackTrace();
|
|
3933
|
}
|
|
3934
|
}
|
|
3935
|
}
|
|
3936
|
}
|
|
3937
|
}
|
|
3938
|
}
|
|
3939
|
else{
|
|
3940
|
if (tnb.getTitleCache().split("sec.")[0].trim().equalsIgnoreCase(partialname) ){
|
|
3941
|
crank =tnb.getRank();
|
|
3942
|
if (crank !=null && rank !=null){
|
|
3943
|
if (crank.equals(rank)){
|
|
3944
|
foundIdentic=true;
|
|
3945
|
try{
|
|
3946
|
tmp=(Taxon)tmpb;
|
|
3947
|
break;
|
|
3948
|
}catch(Exception e){
|
|
3949
|
e.printStackTrace();
|
|
3950
|
}
|
|
3951
|
}
|
|
3952
|
}
|
|
3953
|
}
|
|
3954
|
}
|
|
3955
|
}
|
|
3956
|
}
|
|
3957
|
}
|
|
3958
|
boolean statusMatch=false;
|
|
3959
|
boolean appendedMatch=false;
|
|
3960
|
if(tmp !=null && foundIdentic){
|
|
3961
|
statusMatch=compareStatus(tmp, statusType);
|
|
3962
|
if (!getStatus().isEmpty() && ! (tmp.getAppendedPhrase() == null)) {
|
|
3963
|
appendedMatch=tmp.getAppendedPhrase().equals(getStatus());
|
|
3964
|
}
|
|
3965
|
if (getStatus().isEmpty() && tmp.getAppendedPhrase() == null) {
|
|
3966
|
appendedMatch=true;
|
|
3967
|
}
|
|
3968
|
|
|
3969
|
}
|
|
3970
|
if ((tmp == null || !foundIdentic) || (tmp != null && !statusMatch) || (tmp != null && !appendedMatch && !statusMatch)){
|
|
3971
|
|
|
3972
|
INonViralName tnb = getNonViralNameAccNomenclature();
|
|
3973
|
tnb.setRank(rank);
|
|
3974
|
|
|
3975
|
if(statusType != null) {
|
|
3976
|
tnb.addStatus(NomenclaturalStatus.NewInstance(statusType));
|
|
3977
|
}
|
|
3978
|
if(StringUtils.isNotBlank(getStatus())) {
|
|
3979
|
tnb.setAppendedPhrase(getStatus());
|
|
3980
|
}
|
|
3981
|
|
|
3982
|
if(rank.equals(Rank.UNKNOWN_RANK())){
|
|
3983
|
tnb.setTitleCache(fullname, true);
|
|
3984
|
// tnb.setGenusOrUninomial(fullname);
|
|
3985
|
}
|
|
3986
|
if(rank.isHigher(Rank.GENUS())) {
|
|
3987
|
tnb.setGenusOrUninomial(partialname);
|
|
3988
|
}
|
|
3989
|
|
|
3990
|
if(rank.isHigher(Rank.SPECIES())) {
|
|
3991
|
tnb.setTitleCache(partialname, true);
|
|
3992
|
}
|
|
3993
|
|
|
3994
|
if (rank.equals(globalrank) && author != null) {
|
|
3995
|
|
|
3996
|
tnb.setCombinationAuthorship(findOrCreateAuthor(author));
|
|
3997
|
if (getIdentifier() !=null && !getIdentifier().isEmpty()){
|
|
3998
|
Taxon taxonLSID = getTaxonByLSID(getIdentifier());
|
|
3999
|
if (taxonLSID !=null) {
|
|
4000
|
tmp=taxonLSID;
|
|
4001
|
}
|
|
4002
|
}
|
|
4003
|
}
|
|
4004
|
|
|
4005
|
if(tmp == null){
|
|
4006
|
if (rank.equals(Rank.FAMILY())) {
|
|
4007
|
tmp = buildFamily(tnb);
|
|
4008
|
}
|
|
4009
|
if (rank.equals(Rank.SUBFAMILY())) {
|
|
4010
|
tmp = buildSubfamily(tnb);
|
|
4011
|
}
|
|
4012
|
if (rank.equals(Rank.TRIBE())) {
|
|
4013
|
tmp = buildTribe(tnb);
|
|
4014
|
}
|
|
4015
|
if (rank.equals(Rank.SUBTRIBE())) {
|
|
4016
|
tmp = buildSubtribe(tnb);
|
|
4017
|
}
|
|
4018
|
if (rank.equals(Rank.GENUS())) {
|
|
4019
|
tmp = buildGenus(partialname, tnb);
|
|
4020
|
}
|
|
4021
|
|
|
4022
|
if (rank.equals(Rank.SUBGENUS())) {
|
|
4023
|
tmp = buildSubgenus(partialname, tnb);
|
|
4024
|
}
|
|
4025
|
if (rank.equals(Rank.SPECIES())) {
|
|
4026
|
tmp = buildSpecies(partialname, tnb);
|
|
4027
|
}
|
|
4028
|
|
|
4029
|
if (rank.equals(Rank.SUBSPECIES())) {
|
|
4030
|
tmp = buildSubspecies(partialname, tnb);
|
|
4031
|
}
|
|
4032
|
|
|
4033
|
if (rank.equals(Rank.VARIETY())) {
|
|
4034
|
tmp = buildVariety(fullname, partialname, tnb);
|
|
4035
|
}
|
|
4036
|
|
|
4037
|
if (rank.equals(Rank.FORM())) {
|
|
4038
|
tmp = buildForm(fullname, partialname, tnb);
|
|
4039
|
}
|
|
4040
|
if (tmp != null){
|
|
4041
|
TaxonXTreatmentExtractor.this.sourceHandler.addSource(refMods, tmp);
|
|
4042
|
}
|
|
4043
|
|
|
4044
|
importer.getClassificationService().saveOrUpdate(classification);
|
|
4045
|
}
|
|
4046
|
|
|
4047
|
}
|
|
4048
|
|
|
4049
|
tmp = CdmBase.deproxy(tmp, Taxon.class);
|
|
4050
|
if (rank.equals(globalrank) && author != null) {
|
|
4051
|
if (!getIdentifier().isEmpty() && (getIdentifier().length()>2)){
|
|
4052
|
setLSID(getIdentifier(), tmp);
|
|
4053
|
importer.getTaxonService().saveOrUpdate(tmp);
|
|
4054
|
tmp = CdmBase.deproxy(tmp, Taxon.class);
|
|
4055
|
}
|
|
4056
|
}
|
|
4057
|
|
|
4058
|
this.taxon=tmp;
|
|
4059
|
|
|
4060
|
return tmp;
|
|
4061
|
}
|
|
4062
|
|
|
4063
|
/**
|
|
4064
|
* @param tnb
|
|
4065
|
* @return
|
|
4066
|
*/
|
|
4067
|
private Taxon buildSubfamily(INonViralName tnb) {
|
|
4068
|
Taxon tmp;
|
|
4069
|
// tnb.generateTitle();
|
|
4070
|
tmp = findMatchingTaxon(tnb,refMods);
|
|
4071
|
if(tmp ==null){
|
|
4072
|
tmp = Taxon.NewInstance(tnb, sourceUrlRef);
|
|
4073
|
if(!state2.getConfig().doKeepOriginalSecundum()) {
|
|
4074
|
tmp.setSec(state2.getConfig().getSecundum());
|
|
4075
|
}
|
|
4076
|
// tmp.setSec(refMods);
|
|
4077
|
// sourceHandler.addSource(refMods, tmp);
|
|
4078
|
if(family != null) {
|
|
4079
|
classification.addParentChild(family, tmp, null, null);
|
|
4080
|
higherRank=Rank.FAMILY();
|
|
4081
|
higherTaxa=family;
|
|
4082
|
} else {
|
|
4083
|
//System.out.println("ADDCHILDTAXON SUBFAMILY "+tmp);
|
|
4084
|
classification.addChildTaxon(tmp, null, null);
|
|
4085
|
}
|
|
4086
|
}
|
|
4087
|
return tmp;
|
|
4088
|
}
|
|
4089
|
/**
|
|
4090
|
* @param tnb
|
|
4091
|
* @return
|
|
4092
|
*/
|
|
4093
|
private Taxon buildFamily(INonViralName tnb) {
|
|
4094
|
Taxon tmp;
|
|
4095
|
// tnb.generateTitle();
|
|
4096
|
tmp = findMatchingTaxon(tnb,refMods);
|
|
4097
|
if(tmp ==null){
|
|
4098
|
tmp = Taxon.NewInstance(tnb, sourceUrlRef);
|
|
4099
|
if(!state2.getConfig().doKeepOriginalSecundum()) {
|
|
4100
|
tmp.setSec(state2.getConfig().getSecundum());
|
|
4101
|
}
|
|
4102
|
// tmp.setSec(refMods);
|
|
4103
|
//sourceHandler.addSource(refMods, tmp);
|
|
4104
|
//System.out.println("ADDCHILDTAXON FAMILY "+tmp);
|
|
4105
|
classification.addChildTaxon(tmp, null, null);
|
|
4106
|
}
|
|
4107
|
return tmp;
|
|
4108
|
}
|
|
4109
|
/**
|
|
4110
|
* @param fullname
|
|
4111
|
* @param tnb
|
|
4112
|
* @return
|
|
4113
|
*/
|
|
4114
|
private Taxon buildForm(String fullname, String partialname, INonViralName tnb) {
|
|
4115
|
if (genusName !=null) {
|
|
4116
|
tnb.setGenusOrUninomial(genusName.getGenusOrUninomial());
|
|
4117
|
}
|
|
4118
|
if (subgenusName !=null) {
|
|
4119
|
tnb.setInfraGenericEpithet(subgenusName.getInfraGenericEpithet());
|
|
4120
|
}
|
|
4121
|
if(speciesName !=null) {
|
|
4122
|
tnb.setSpecificEpithet(speciesName.getSpecificEpithet());
|
|
4123
|
}
|
|
4124
|
if(subspeciesName != null) {
|
|
4125
|
tnb.setInfraSpecificEpithet(subspeciesName.getInfraSpecificEpithet());
|
|
4126
|
}
|
|
4127
|
if(partialname!= null) {
|
|
4128
|
tnb.setInfraSpecificEpithet(partialname);
|
|
4129
|
}
|
|
4130
|
//TODO how to save form??
|
|
4131
|
tnb.setTitleCache(fullname, true);
|
|
4132
|
Taxon tmp = findMatchingTaxon(tnb,refMods);
|
|
4133
|
if(tmp ==null){
|
|
4134
|
tmp = Taxon.NewInstance(tnb, sourceUrlRef);
|
|
4135
|
if(!state2.getConfig().doKeepOriginalSecundum()) {
|
|
4136
|
tmp.setSec(state2.getConfig().getSecundum());
|
|
4137
|
}
|
|
4138
|
// tmp.setSec(refMods);
|
|
4139
|
//sourceHandler.addSource(refMods, tmp);
|
|
4140
|
if (subspecies !=null) {
|
|
4141
|
classification.addParentChild(subspecies, tmp, null, null);
|
|
4142
|
higherRank=Rank.SUBSPECIES();
|
|
4143
|
higherTaxa=subspecies;
|
|
4144
|
} else {
|
|
4145
|
if (species !=null) {
|
|
4146
|
classification.addParentChild(species, tmp, null, null);
|
|
4147
|
higherRank=Rank.SPECIES();
|
|
4148
|
higherTaxa=species;
|
|
4149
|
}
|
|
4150
|
else{
|
|
4151
|
// System.out.println("ADDCHILDTAXON FORM "+tmp);
|
|
4152
|
classification.addChildTaxon(tmp, null, null);
|
|
4153
|
}
|
|
4154
|
}
|
|
4155
|
}
|
|
4156
|
return tmp;
|
|
4157
|
}
|
|
4158
|
/**
|
|
4159
|
* @param fullname
|
|
4160
|
* @param tnb
|
|
4161
|
* @return
|
|
4162
|
*/
|
|
4163
|
private Taxon buildVariety(String fullname, String partialname, INonViralName tnb) {
|
|
4164
|
Taxon tmp;
|
|
4165
|
if (genusName !=null) {
|
|
4166
|
tnb.setGenusOrUninomial(genusName.getGenusOrUninomial());
|
|
4167
|
}
|
|
4168
|
if (subgenusName !=null) {
|
|
4169
|
tnb.setInfraGenericEpithet(subgenusName.getInfraGenericEpithet());
|
|
4170
|
}
|
|
4171
|
if(speciesName !=null) {
|
|
4172
|
tnb.setSpecificEpithet(speciesName.getSpecificEpithet());
|
|
4173
|
}
|
|
4174
|
if(subspeciesName != null) {
|
|
4175
|
tnb.setInfraSpecificEpithet(subspeciesName.getSpecificEpithet());
|
|
4176
|
}
|
|
4177
|
if(partialname != null) {
|
|
4178
|
tnb.setInfraSpecificEpithet(partialname);
|
|
4179
|
}
|
|
4180
|
//TODO how to save variety?
|
|
4181
|
tnb.setTitleCache(fullname, true);
|
|
4182
|
tmp = findMatchingTaxon(tnb,refMods);
|
|
4183
|
if(tmp ==null){
|
|
4184
|
tmp = Taxon.NewInstance(tnb, sourceUrlRef);
|
|
4185
|
if(!state2.getConfig().doKeepOriginalSecundum()) {
|
|
4186
|
tmp.setSec(state2.getConfig().getSecundum());
|
|
4187
|
}
|
|
4188
|
// tmp.setSec(refMods);
|
|
4189
|
//sourceHandler.addSource(refMods, tmp);
|
|
4190
|
if (subspecies !=null) {
|
|
4191
|
classification.addParentChild(subspecies, tmp, null, null);
|
|
4192
|
higherRank=Rank.SUBSPECIES();
|
|
4193
|
higherTaxa=subspecies;
|
|
4194
|
} else {
|
|
4195
|
if(species !=null) {
|
|
4196
|
classification.addParentChild(species, tmp, null, null);
|
|
4197
|
higherRank=Rank.SPECIES();
|
|
4198
|
higherTaxa=species;
|
|
4199
|
}
|
|
4200
|
else{
|
|
4201
|
//System.out.println("ADDCHILDTAXON VARIETY "+tmp);
|
|
4202
|
classification.addChildTaxon(tmp, null, null);
|
|
4203
|
}
|
|
4204
|
}
|
|
4205
|
}
|
|
4206
|
return tmp;
|
|
4207
|
}
|
|
4208
|
/**
|
|
4209
|
* @param partialname
|
|
4210
|
* @param tnb
|
|
4211
|
* @return
|
|
4212
|
*/
|
|
4213
|
private Taxon buildSubspecies(String partialname, INonViralName tnb) {
|
|
4214
|
if (genusName !=null) {
|
|
4215
|
tnb.setGenusOrUninomial(genusName.getGenusOrUninomial());
|
|
4216
|
}
|
|
4217
|
if (subgenusName !=null) {
|
|
4218
|
// System.out.println("SUB:"+subgenusName.getInfraGenericEpithet());
|
|
4219
|
tnb.setInfraGenericEpithet(subgenusName.getInfraGenericEpithet());
|
|
4220
|
}
|
|
4221
|
if(speciesName !=null) {
|
|
4222
|
// System.out.println("SPE:"+speciesName.getSpecificEpithet());
|
|
4223
|
tnb.setSpecificEpithet(speciesName.getSpecificEpithet());
|
|
4224
|
}
|
|
4225
|
tnb.setInfraSpecificEpithet(partialname);
|
|
4226
|
Taxon tmp = findMatchingTaxon(tnb,refMods);
|
|
4227
|
if(tmp ==null){
|
|
4228
|
tmp = Taxon.NewInstance(tnb, sourceUrlRef);
|
|
4229
|
if(!state2.getConfig().doKeepOriginalSecundum())
|
|
4230
|
{
|
|
4231
|
tmp.setSec(state2.getConfig().getSecundum());
|
|
4232
|
// tmp.setSec(refMods);
|
|
4233
|
//sourceHandler.addSource(refMods, tmp);
|
|
4234
|
}
|
|
4235
|
|
|
4236
|
if(species != null) {
|
|
4237
|
classification.addParentChild(species, tmp, null, null);
|
|
4238
|
higherRank=Rank.SPECIES();
|
|
4239
|
higherTaxa=species;
|
|
4240
|
}
|
|
4241
|
else{
|
|
4242
|
//System.out.println("ADDCHILDTAXON SUBSPECIES "+tmp);
|
|
4243
|
classification.addChildTaxon(tmp, null, null);
|
|
4244
|
}
|
|
4245
|
}
|
|
4246
|
return tmp;
|
|
4247
|
}
|
|
4248
|
/**
|
|
4249
|
* @param partialname
|
|
4250
|
* @param tnb
|
|
4251
|
* @return
|
|
4252
|
*/
|
|
4253
|
private Taxon buildSpecies(String partialname, INonViralName tnb) {
|
|
4254
|
if (genusName !=null) {
|
|
4255
|
tnb.setGenusOrUninomial(genusName.getGenusOrUninomial());
|
|
4256
|
}
|
|
4257
|
if (subgenusName !=null) {
|
|
4258
|
tnb.setInfraGenericEpithet(subgenusName.getInfraGenericEpithet());
|
|
4259
|
}
|
|
4260
|
tnb.setSpecificEpithet(partialname.toLowerCase());
|
|
4261
|
Taxon tmp = findMatchingTaxon(tnb,refMods);
|
|
4262
|
if(tmp ==null){
|
|
4263
|
tmp = Taxon.NewInstance(tnb, sourceUrlRef);
|
|
4264
|
if(!state2.getConfig().doKeepOriginalSecundum()) {
|
|
4265
|
tmp.setSec(state2.getConfig().getSecundum());
|
|
4266
|
}
|
|
4267
|
// tmp.setSec(refMods);
|
|
4268
|
//sourceHandler.addSource(refMods, tmp);
|
|
4269
|
if (subgenus !=null) {
|
|
4270
|
classification.addParentChild(subgenus, tmp, null, null);
|
|
4271
|
higherRank=Rank.SUBGENUS();
|
|
4272
|
higherTaxa=subgenus;
|
|
4273
|
} else {
|
|
4274
|
if (genus !=null) {
|
|
4275
|
classification.addParentChild(genus, tmp, null, null);
|
|
4276
|
higherRank=Rank.GENUS();
|
|
4277
|
higherTaxa=genus;
|
|
4278
|
}
|
|
4279
|
else{
|
|
4280
|
//System.out.println("ADDCHILDTAXON SPECIES "+tmp);
|
|
4281
|
classification.addChildTaxon(tmp, null, null);
|
|
4282
|
}
|
|
4283
|
}
|
|
4284
|
}
|
|
4285
|
return tmp;
|
|
4286
|
}
|
|
4287
|
/**
|
|
4288
|
* @param partialname
|
|
4289
|
* @param tnb
|
|
4290
|
* @return
|
|
4291
|
*/
|
|
4292
|
private Taxon buildSubgenus(String partialname, INonViralName tnb) {
|
|
4293
|
tnb.setInfraGenericEpithet(partialname);
|
|
4294
|
if (genusName !=null) {
|
|
4295
|
tnb.setGenusOrUninomial(genusName.getGenusOrUninomial());
|
|
4296
|
}
|
|
4297
|
Taxon tmp = findMatchingTaxon(tnb,refMods);
|
|
4298
|
if(tmp ==null){
|
|
4299
|
tmp = Taxon.NewInstance(tnb, sourceUrlRef);
|
|
4300
|
if(!state2.getConfig().doKeepOriginalSecundum()) {
|
|
4301
|
tmp.setSec(state2.getConfig().getSecundum());
|
|
4302
|
}
|
|
4303
|
// tmp.setSec(refMods);
|
|
4304
|
//sourceHandler.addSource(refMods, tmp);
|
|
4305
|
if(genus != null) {
|
|
4306
|
classification.addParentChild(genus, tmp, null, null);
|
|
4307
|
higherRank=Rank.GENUS();
|
|
4308
|
higherTaxa=genus;
|
|
4309
|
} else{
|
|
4310
|
//System.out.println("ADDCHILDTAXON SUBGENUS "+tmp);
|
|
4311
|
classification.addChildTaxon(tmp, null, null);
|
|
4312
|
}
|
|
4313
|
}
|
|
4314
|
return tmp;
|
|
4315
|
}
|
|
4316
|
/**
|
|
4317
|
* @param partialname
|
|
4318
|
* @param tnb
|
|
4319
|
* @return
|
|
4320
|
*/
|
|
4321
|
private Taxon buildGenus(String partialname, INonViralName tnb) {
|
|
4322
|
Taxon tmp;
|
|
4323
|
tnb.setGenusOrUninomial(partialname);
|
|
4324
|
|
|
4325
|
|
|
4326
|
tmp = findMatchingTaxon(tnb,refMods);
|
|
4327
|
if(tmp ==null){
|
|
4328
|
tmp = Taxon.NewInstance(tnb, sourceUrlRef);
|
|
4329
|
if(!state2.getConfig().doKeepOriginalSecundum())
|
|
4330
|
{
|
|
4331
|
tmp.setSec(state2.getConfig().getSecundum());
|
|
4332
|
// tmp.setSec(refMods);
|
|
4333
|
//sourceHandler.addSource(refMods, tmp);
|
|
4334
|
}
|
|
4335
|
|
|
4336
|
if(subtribe != null) {
|
|
4337
|
classification.addParentChild(subtribe, tmp, null, null);
|
|
4338
|
higherRank=Rank.SUBTRIBE();
|
|
4339
|
higherTaxa=subtribe;
|
|
4340
|
} else{
|
|
4341
|
if(tribe !=null) {
|
|
4342
|
classification.addParentChild(tribe, tmp, null, null);
|
|
4343
|
higherRank=Rank.TRIBE();
|
|
4344
|
higherTaxa=tribe;
|
|
4345
|
} else{
|
|
4346
|
if(subfamily !=null) {
|
|
4347
|
classification.addParentChild(subfamily, tmp, null, null);
|
|
4348
|
higherRank=Rank.SUBFAMILY();
|
|
4349
|
higherTaxa=subfamily;
|
|
4350
|
} else
|
|
4351
|
if(family !=null) {
|
|
4352
|
classification.addParentChild(family, tmp, null, null);
|
|
4353
|
higherRank=Rank.FAMILY();
|
|
4354
|
higherTaxa=family;
|
|
4355
|
}
|
|
4356
|
else{
|
|
4357
|
//System.out.println("ADDCHILDTAXON GENUS "+tmp);
|
|
4358
|
classification.addChildTaxon(tmp, null, null);
|
|
4359
|
}
|
|
4360
|
}
|
|
4361
|
}
|
|
4362
|
}
|
|
4363
|
return tmp;
|
|
4364
|
}
|
|
4365
|
|
|
4366
|
/**
|
|
4367
|
* @param tnb
|
|
4368
|
* @return
|
|
4369
|
*/
|
|
4370
|
private Taxon buildSubtribe(INonViralName tnb) {
|
|
4371
|
Taxon tmp = findMatchingTaxon(tnb,refMods);
|
|
4372
|
if(tmp==null){
|
|
4373
|
tmp = Taxon.NewInstance(tnb, sourceUrlRef);
|
|
4374
|
if(!state2.getConfig().doKeepOriginalSecundum()) {
|
|
4375
|
tmp.setSec(state2.getConfig().getSecundum());
|
|
4376
|
}
|
|
4377
|
// tmp.setSec(refMods);
|
|
4378
|
//sourceHandler.addSource(refMods, tmp);
|
|
4379
|
if(tribe != null) {
|
|
4380
|
classification.addParentChild(tribe, tmp, null, null);
|
|
4381
|
higherRank=Rank.TRIBE();
|
|
4382
|
higherTaxa=tribe;
|
|
4383
|
} else{
|
|
4384
|
//System.out.println("ADDCHILDTAXON SUBTRIBE "+tmp);
|
|
4385
|
classification.addChildTaxon(tmp, null, null);
|
|
4386
|
}
|
|
4387
|
}
|
|
4388
|
return tmp;
|
|
4389
|
}
|
|
4390
|
/**
|
|
4391
|
* @param tnb
|
|
4392
|
* @return
|
|
4393
|
*/
|
|
4394
|
private Taxon buildTribe(INonViralName tnb) {
|
|
4395
|
Taxon tmp = findMatchingTaxon(tnb,refMods);
|
|
4396
|
if(tmp==null){
|
|
4397
|
tmp = Taxon.NewInstance(tnb, sourceUrlRef);
|
|
4398
|
if(!state2.getConfig().doKeepOriginalSecundum()) {
|
|
4399
|
tmp.setSec(state2.getConfig().getSecundum());
|
|
4400
|
}
|
|
4401
|
// tmp.setSec(refMods);
|
|
4402
|
//sourceHandler.addSource(refMods, tmp);
|
|
4403
|
if (subfamily !=null) {
|
|
4404
|
classification.addParentChild(subfamily, tmp, null, null);
|
|
4405
|
higherRank=Rank.SUBFAMILY();
|
|
4406
|
higherTaxa=subfamily;
|
|
4407
|
} else {
|
|
4408
|
if(family != null) {
|
|
4409
|
classification.addParentChild(family, tmp, null, null);
|
|
4410
|
higherRank=Rank.FAMILY();
|
|
4411
|
higherTaxa=family;
|
|
4412
|
}
|
|
4413
|
else{
|
|
4414
|
//System.out.println("ADDCHILDTAXON TRIBE "+tmp);
|
|
4415
|
classification.addChildTaxon(tmp, null, null);
|
|
4416
|
}
|
|
4417
|
}
|
|
4418
|
}
|
|
4419
|
return tmp;
|
|
4420
|
}
|
|
4421
|
|
|
4422
|
/**
|
|
4423
|
* @param identifier2
|
|
4424
|
* @return
|
|
4425
|
*/
|
|
4426
|
@SuppressWarnings("rawtypes")
|
|
4427
|
private Taxon getTaxonByLSID(String identifier) {
|
|
4428
|
//logger.info("getTaxonByLSID");
|
|
4429
|
// boolean lsidok=false;
|
|
4430
|
String id = identifier.split("__")[0];
|
|
4431
|
// String source = identifier.split("__")[1];
|
|
4432
|
LSID lsid = null;
|
|
4433
|
if (id.indexOf("lsid")>-1){
|
|
4434
|
try {
|
|
4435
|
lsid = new LSID(id);
|
|
4436
|
// lsidok=true;
|
|
4437
|
} catch (MalformedLSIDException e) {
|
|
4438
|
logger.warn("Malformed LSID");
|
|
4439
|
}
|
|
4440
|
}
|
|
4441
|
if (lsid !=null){
|
|
4442
|
List<Taxon> taxa = importer.getTaxonService().list(Taxon.class, 0, 0, null, null);
|
|
4443
|
LSID currentlsid=null;
|
|
4444
|
for (Taxon t:taxa){
|
|
4445
|
currentlsid = t.getLsid();
|
|
4446
|
if (currentlsid !=null){
|
|
4447
|
if (currentlsid.getLsid().equals(lsid.getLsid())){
|
|
4448
|
try{
|
|
4449
|
return t;
|
|
4450
|
}
|
|
4451
|
catch(Exception e){logger.warn("Exception occurred while comparing LSIDs "+e );}
|
|
4452
|
}
|
|
4453
|
}
|
|
4454
|
}
|
|
4455
|
}
|
|
4456
|
return null;
|
|
4457
|
}
|
|
4458
|
/**
|
|
4459
|
* @param author2
|
|
4460
|
* @return
|
|
4461
|
*/
|
|
4462
|
@SuppressWarnings("rawtypes")
|
|
4463
|
private Person findOrCreateAuthor(String author2) {
|
|
4464
|
//logger.info("findOrCreateAuthor");
|
|
4465
|
List<UuidAndTitleCache<Person>> hiberPersons = importer.getAgentService().getPersonUuidAndTitleCache();
|
|
4466
|
for (UuidAndTitleCache<Person> hibernateP:hiberPersons){
|
|
4467
|
if(hibernateP.getTitleCache().equals(author2)) {
|
|
4468
|
AgentBase existing = importer.getAgentService().find(hibernateP.getUuid());
|
|
4469
|
return CdmBase.deproxy(existing, Person.class);
|
|
4470
|
}
|
|
4471
|
}
|
|
4472
|
Person p = Person.NewInstance();
|
|
4473
|
p.setTitleCache(author2,true);
|
|
4474
|
importer.getAgentService().saveOrUpdate(p);
|
|
4475
|
return CdmBase.deproxy(p, Person.class);
|
|
4476
|
}
|
|
4477
|
/**
|
|
4478
|
* @param author the author to set
|
|
4479
|
*/
|
|
4480
|
public void setAuthor(String author) {
|
|
4481
|
this.author = author;
|
|
4482
|
}
|
|
4483
|
|
|
4484
|
/**
|
|
4485
|
* @return the higherTaxa
|
|
4486
|
*/
|
|
4487
|
public Taxon getHigherTaxa() {
|
|
4488
|
return higherTaxa;
|
|
4489
|
}
|
|
4490
|
/**
|
|
4491
|
* @param higherTaxa the higherTaxa to set
|
|
4492
|
*/
|
|
4493
|
public void setHigherTaxa(Taxon higherTaxa) {
|
|
4494
|
this.higherTaxa = higherTaxa;
|
|
4495
|
}
|
|
4496
|
/**
|
|
4497
|
* @return the higherRank
|
|
4498
|
*/
|
|
4499
|
public Rank getHigherRank() {
|
|
4500
|
return higherRank;
|
|
4501
|
}
|
|
4502
|
/**
|
|
4503
|
* @param higherRank the higherRank to set
|
|
4504
|
*/
|
|
4505
|
public void setHigherRank(Rank higherRank) {
|
|
4506
|
this.higherRank = higherRank;
|
|
4507
|
}
|
|
4508
|
public String getName(){
|
|
4509
|
if (newName.isEmpty()) {
|
|
4510
|
return originalName;
|
|
4511
|
} else {
|
|
4512
|
return newName;
|
|
4513
|
}
|
|
4514
|
|
|
4515
|
}
|
|
4516
|
/**
|
|
4517
|
* @return the fullName
|
|
4518
|
*/
|
|
4519
|
public String getOriginalName() {
|
|
4520
|
return originalName;
|
|
4521
|
}
|
|
4522
|
/**
|
|
4523
|
* @param fullName the fullName to set
|
|
4524
|
*/
|
|
4525
|
public void setOriginalName(String fullName) {
|
|
4526
|
this.originalName = fullName;
|
|
4527
|
}
|
|
4528
|
/**
|
|
4529
|
* @return the newName
|
|
4530
|
*/
|
|
4531
|
public String getNewName() {
|
|
4532
|
return newName;
|
|
4533
|
}
|
|
4534
|
/**
|
|
4535
|
* @param newName the newName to set
|
|
4536
|
*/
|
|
4537
|
public void setNewName(String newName) {
|
|
4538
|
this.newName = newName;
|
|
4539
|
}
|
|
4540
|
/**
|
|
4541
|
* @return the rank
|
|
4542
|
*/
|
|
4543
|
public Rank getRank() {
|
|
4544
|
return rank;
|
|
4545
|
}
|
|
4546
|
/**
|
|
4547
|
* @param rank the rank to set
|
|
4548
|
*/
|
|
4549
|
public void setRank(Rank rank) {
|
|
4550
|
this.rank = rank;
|
|
4551
|
}
|
|
4552
|
/**
|
|
4553
|
* @return the idenfitiger
|
|
4554
|
*/
|
|
4555
|
public String getIdentifier() {
|
|
4556
|
return identifier;
|
|
4557
|
}
|
|
4558
|
/**
|
|
4559
|
* @param idenfitiger the idenfitiger to set
|
|
4560
|
*/
|
|
4561
|
public void setIdentifier(String identifier) {
|
|
4562
|
this.identifier = identifier;
|
|
4563
|
}
|
|
4564
|
/**
|
|
4565
|
* @return the status
|
|
4566
|
*/
|
|
4567
|
public String getStatus() {
|
|
4568
|
if (status == null) {
|
|
4569
|
return "";
|
|
4570
|
}
|
|
4571
|
return status;
|
|
4572
|
}
|
|
4573
|
/**
|
|
4574
|
* @param status the status to set
|
|
4575
|
*/
|
|
4576
|
public void setStatus(String status) {
|
|
4577
|
this.status = status;
|
|
4578
|
}
|
|
4579
|
/**
|
|
4580
|
* @return the family
|
|
4581
|
*/
|
|
4582
|
public Taxon getFamily() {
|
|
4583
|
return family;
|
|
4584
|
}
|
|
4585
|
/**
|
|
4586
|
* @param family the family to set
|
|
4587
|
*/
|
|
4588
|
@SuppressWarnings("rawtypes")
|
|
4589
|
public void setFamily(Taxon family) {
|
|
4590
|
this.family = family;
|
|
4591
|
familyName = CdmBase.deproxy(family.getName());
|
|
4592
|
}
|
|
4593
|
/**
|
|
4594
|
* @return the subfamily
|
|
4595
|
*/
|
|
4596
|
public Taxon getSubfamily() {
|
|
4597
|
return subfamily;
|
|
4598
|
}
|
|
4599
|
/**
|
|
4600
|
* @param subfamily the subfamily to set
|
|
4601
|
*/
|
|
4602
|
@SuppressWarnings("rawtypes")
|
|
4603
|
public void setSubfamily(Taxon subfamily) {
|
|
4604
|
this.subfamily = subfamily;
|
|
4605
|
subfamilyName = CdmBase.deproxy(subfamily.getName());
|
|
4606
|
}
|
|
4607
|
/**
|
|
4608
|
* @return the tribe
|
|
4609
|
*/
|
|
4610
|
public Taxon getTribe() {
|
|
4611
|
return tribe;
|
|
4612
|
}
|
|
4613
|
/**
|
|
4614
|
* @param tribe the tribe to set
|
|
4615
|
*/
|
|
4616
|
@SuppressWarnings("rawtypes")
|
|
4617
|
public void setTribe(Taxon tribe) {
|
|
4618
|
this.tribe = tribe;
|
|
4619
|
tribeName = CdmBase.deproxy(tribe.getName());
|
|
4620
|
}
|
|
4621
|
/**
|
|
4622
|
* @return the subtribe
|
|
4623
|
*/
|
|
4624
|
public Taxon getSubtribe() {
|
|
4625
|
return subtribe;
|
|
4626
|
}
|
|
4627
|
/**
|
|
4628
|
* @param subtribe the subtribe to set
|
|
4629
|
*/
|
|
4630
|
@SuppressWarnings("rawtypes")
|
|
4631
|
public void setSubtribe(Taxon subtribe) {
|
|
4632
|
this.subtribe = subtribe;
|
|
4633
|
subtribeName =CdmBase.deproxy(subtribe.getName());
|
|
4634
|
}
|
|
4635
|
/**
|
|
4636
|
* @return the genus
|
|
4637
|
*/
|
|
4638
|
public Taxon getGenus() {
|
|
4639
|
return genus;
|
|
4640
|
}
|
|
4641
|
/**
|
|
4642
|
* @param genus the genus to set
|
|
4643
|
*/
|
|
4644
|
@SuppressWarnings("rawtypes")
|
|
4645
|
public void setGenus(Taxon genus) {
|
|
4646
|
if (genus != null){
|
|
4647
|
this.genus = genus;
|
|
4648
|
genusName = CdmBase.deproxy(genus.getName());
|
|
4649
|
}
|
|
4650
|
}
|
|
4651
|
/**
|
|
4652
|
* @return the subgenus
|
|
4653
|
*/
|
|
4654
|
public Taxon getSubgenus() {
|
|
4655
|
return subgenus;
|
|
4656
|
}
|
|
4657
|
/**
|
|
4658
|
* @param subgenus the subgenus to set
|
|
4659
|
*/
|
|
4660
|
@SuppressWarnings("rawtypes")
|
|
4661
|
public void setSubgenus(Taxon subgenus) {
|
|
4662
|
this.subgenus = subgenus;
|
|
4663
|
subgenusName = CdmBase.deproxy(subgenus.getName());
|
|
4664
|
}
|
|
4665
|
/**
|
|
4666
|
* @return the species
|
|
4667
|
*/
|
|
4668
|
public Taxon getSpecies() {
|
|
4669
|
return species;
|
|
4670
|
}
|
|
4671
|
/**
|
|
4672
|
* @param species the species to set
|
|
4673
|
*/
|
|
4674
|
public void setSpecies(Taxon species) {
|
|
4675
|
if (species != null){
|
|
4676
|
this.species = species;
|
|
4677
|
speciesName = CdmBase.deproxy(species.getName());
|
|
4678
|
}
|
|
4679
|
}
|
|
4680
|
/**
|
|
4681
|
* @return the subspecies
|
|
4682
|
*/
|
|
4683
|
public Taxon getSubspecies() {
|
|
4684
|
return subspecies;
|
|
4685
|
}
|
|
4686
|
/**
|
|
4687
|
* @param subspecies the subspecies to set
|
|
4688
|
*/
|
|
4689
|
@SuppressWarnings("rawtypes")
|
|
4690
|
public void setSubspecies(Taxon subspecies) {
|
|
4691
|
this.subspecies = subspecies;
|
|
4692
|
subspeciesName = CdmBase.deproxy(subspecies.getName());
|
|
4693
|
|
|
4694
|
}
|
|
4695
|
|
|
4696
|
|
|
4697
|
|
|
4698
|
}
|
|
4699
|
|
|
4700
|
|
|
4701
|
/**
|
|
4702
|
* @param status
|
|
4703
|
*/
|
|
4704
|
private void addProblematicStatusToFile(String status) {
|
|
4705
|
try{
|
|
4706
|
FileWriter fstream = new FileWriter(TaxonXImport.LOG_FOLDER + "StatusUnknown_"+classification.getTitleCache()+".txt",true);
|
|
4707
|
BufferedWriter out = new BufferedWriter(fstream);
|
|
4708
|
out.write(status+"\n");
|
|
4709
|
//Close the output stream
|
|
4710
|
out.close();
|
|
4711
|
}catch (Exception e){//Catch exception if any
|
|
4712
|
System.err.println("Error: " + e.getMessage());
|
|
4713
|
}
|
|
4714
|
|
|
4715
|
}
|
|
4716
|
|
|
4717
|
|
|
4718
|
|
|
4719
|
/**
|
|
4720
|
* @param tnb
|
|
4721
|
* @return
|
|
4722
|
*/
|
|
4723
|
private Taxon findMatchingTaxon(INonViralName tnb, Reference refMods) {
|
|
4724
|
logger.info("findMatchingTaxon");
|
|
4725
|
Taxon tmp=null;
|
|
4726
|
|
|
4727
|
refMods=CdmBase.deproxy(refMods, Reference.class);
|
|
4728
|
boolean insertAsExisting =false;
|
|
4729
|
List<Taxon> existingTaxa = new ArrayList<Taxon>();
|
|
4730
|
try {
|
|
4731
|
existingTaxa = getMatchingTaxa(TaxonName.castAndDeproxy(tnb));
|
|
4732
|
} catch (Exception e1) {
|
|
4733
|
// TODO Auto-generated catch block
|
|
4734
|
e1.printStackTrace();
|
|
4735
|
}
|
|
4736
|
double similarityScore=0.0;
|
|
4737
|
double similarityAuthor=-1;
|
|
4738
|
String author1="";
|
|
4739
|
String author2="";
|
|
4740
|
String t1="";
|
|
4741
|
String t2="";
|
|
4742
|
for (Taxon bestMatchingTaxon : existingTaxa){
|
|
4743
|
if (!existingTaxa.isEmpty() && state2.getConfig().isInteractWithUser() && !insertAsExisting) {
|
|
4744
|
// System.out.println("tnb "+tnb.getTitleCache());
|
|
4745
|
// System.out.println("ext "+bestMatchingTaxon.getTitleCache());
|
|
4746
|
try {
|
|
4747
|
if(tnb.getAuthorshipCache()!=null) {
|
|
4748
|
author1=tnb.getAuthorshipCache();
|
|
4749
|
}
|
|
4750
|
} catch (Exception e) {
|
|
4751
|
// TODO Auto-generated catch block
|
|
4752
|
e.printStackTrace();
|
|
4753
|
}
|
|
4754
|
try {
|
|
4755
|
if(bestMatchingTaxon.getName().getAuthorshipCache()!=null) {
|
|
4756
|
author2=bestMatchingTaxon.getName().getAuthorshipCache();
|
|
4757
|
}
|
|
4758
|
} catch (Exception e) {
|
|
4759
|
// TODO Auto-generated catch block
|
|
4760
|
e.printStackTrace();
|
|
4761
|
}
|
|
4762
|
try {
|
|
4763
|
t1=tnb.getTitleCache().split("sec.")[0].trim();
|
|
4764
|
if (author1!=null && !StringUtils.isEmpty(author1)) {
|
|
4765
|
t1=t1.split(Pattern.quote(author1))[0];
|
|
4766
|
}
|
|
4767
|
} catch (Exception e) {
|
|
4768
|
// TODO Auto-generated catch block
|
|
4769
|
e.printStackTrace();
|
|
4770
|
}
|
|
4771
|
try {
|
|
4772
|
t2=bestMatchingTaxon.getTitleCache().split("sec.")[0].trim();
|
|
4773
|
if (author2!=null && !StringUtils.isEmpty(author2)) {
|
|
4774
|
t2=t2.split(Pattern.quote(author2))[0];
|
|
4775
|
}
|
|
4776
|
} catch (Exception e) {
|
|
4777
|
// TODO Auto-generated catch block
|
|
4778
|
e.printStackTrace();
|
|
4779
|
}
|
|
4780
|
similarityScore=similarity(t1.trim(), t2.trim());
|
|
4781
|
// System.out.println("taxascore: "+similarityScore);
|
|
4782
|
similarityAuthor=similarity(author1.trim(), author2.trim());
|
|
4783
|
// System.out.println("authorscore: "+similarityAuthor);
|
|
4784
|
insertAsExisting = compareAndCheckTaxon(tnb, refMods, similarityScore, bestMatchingTaxon,similarityAuthor);
|
|
4785
|
}
|
|
4786
|
if(insertAsExisting) {
|
|
4787
|
//System.out.println("KEEP "+bestMatchingTaxon.toString());
|
|
4788
|
tmp=bestMatchingTaxon;
|
|
4789
|
sourceHandler.addSource(refMods, tmp);
|
|
4790
|
return tmp;
|
|
4791
|
}
|
|
4792
|
}
|
|
4793
|
return tmp;
|
|
4794
|
}
|
|
4795
|
|
|
4796
|
|
|
4797
|
/**
|
|
4798
|
* @param tnb
|
|
4799
|
* @param refMods
|
|
4800
|
* @param similarityScore
|
|
4801
|
* @param bestMatchingTaxon
|
|
4802
|
* @param similarityAuthor
|
|
4803
|
* @return
|
|
4804
|
*/
|
|
4805
|
private boolean compareAndCheckTaxon(INonViralName tnb, Reference refMods, double similarityScore,
|
|
4806
|
Taxon bestMatchingTaxon, double similarityAuthor) {
|
|
4807
|
//logger.info("compareAndCheckTaxon");
|
|
4808
|
boolean insertAsExisting;
|
|
4809
|
// if (tnb.getTitleCache().split("sec.")[0].equalsIgnoreCase("Chenopodium") && bestMatchingTaxon.getTitleCache().split("sec.")[0].indexOf("Chenopodium album")>-1) {
|
|
4810
|
// insertAsExisting=false;
|
|
4811
|
// } else{
|
|
4812
|
//a small hack/automatisation for Chenopodium only
|
|
4813
|
if (tnb.getTitleCache().split("sec.")[0].trim().equalsIgnoreCase("Chenopodium") &&
|
|
4814
|
bestMatchingTaxon.getTitleCache().split("sec.")[0].indexOf("Chenopodium L.")>-1) {
|
|
4815
|
insertAsExisting=true;
|
|
4816
|
} else {
|
|
4817
|
insertAsExisting=askIfReuseBestMatchingTaxon(tnb, bestMatchingTaxon, refMods, similarityScore,similarityAuthor);
|
|
4818
|
}
|
|
4819
|
// }
|
|
4820
|
|
|
4821
|
logDecision(tnb, bestMatchingTaxon, insertAsExisting, refMods);
|
|
4822
|
return insertAsExisting;
|
|
4823
|
}
|
|
4824
|
|
|
4825
|
/**
|
|
4826
|
* @return
|
|
4827
|
*/
|
|
4828
|
@SuppressWarnings("rawtypes")
|
|
4829
|
private List<Taxon> getMatchingTaxa(TaxonName tnb) {
|
|
4830
|
//logger.info("getMatchingTaxon");
|
|
4831
|
if (tnb.getTitleCache() == null){
|
|
4832
|
tnb.setTitleCache(tnb.toString(), tnb.isProtectedTitleCache());
|
|
4833
|
}
|
|
4834
|
|
|
4835
|
Pager<TaxonBase> pager=importer.getTaxonService().findByTitleWithRestrictions(TaxonBase.class, tnb.getTitleCache().split("sec.")[0].trim(), MatchMode.BEGINNING, null, null, null, null, null);
|
|
4836
|
List<TaxonBase>records = pager.getRecords();
|
|
4837
|
|
|
4838
|
List<Taxon> existingTaxons = new ArrayList<Taxon>();
|
|
4839
|
for (TaxonBase r:records){
|
|
4840
|
try{
|
|
4841
|
Taxon bestMatchingTaxon = (Taxon)r;
|
|
4842
|
// System.out.println("best: "+bestMatchingTaxon.getTitleCache());
|
|
4843
|
if(compareTaxonNameLength(bestMatchingTaxon.getTitleCache().split(".sec")[0],tnb.getTitleCache().split(".sec")[0])) {
|
|
4844
|
existingTaxons.add(bestMatchingTaxon);
|
|
4845
|
}
|
|
4846
|
}catch(ClassCastException e){logger.warn("classcast exception, might be a synonym, ignore it");}
|
|
4847
|
}
|
|
4848
|
Taxon bmt = importer.getTaxonService().findBestMatchingTaxon(tnb.getTitleCache());
|
|
4849
|
if (!existingTaxons.contains(bmt) && bmt!=null) {
|
|
4850
|
if(compareTaxonNameLength(bmt.getTitleCache().split(".sec")[0],tnb.getTitleCache().split(".sec")[0])) {
|
|
4851
|
existingTaxons.add(bmt);
|
|
4852
|
}
|
|
4853
|
}
|
|
4854
|
return existingTaxons;
|
|
4855
|
}
|
|
4856
|
|
|
4857
|
/**
|
|
4858
|
* Check if the found Taxon can reasonnably be the same
|
|
4859
|
* example: with and without author should match, but the subspecies should not be suggested for a genus
|
|
4860
|
* */
|
|
4861
|
private boolean compareTaxonNameLength(String f, String o){
|
|
4862
|
//logger.info("compareTaxonNameLength");
|
|
4863
|
boolean lengthOk=false;
|
|
4864
|
int sizeF = f.length();
|
|
4865
|
int sizeO = o.length();
|
|
4866
|
if (sizeO>=sizeF) {
|
|
4867
|
lengthOk=true;
|
|
4868
|
}
|
|
4869
|
if(sizeF>sizeO) {
|
|
4870
|
if (sizeF-sizeO>10) {
|
|
4871
|
lengthOk=false;
|
|
4872
|
} else {
|
|
4873
|
lengthOk=true;
|
|
4874
|
}
|
|
4875
|
}
|
|
4876
|
|
|
4877
|
// System.out.println(lengthOk+": compare "+f+" ("+f.length()+") and "+o+" ("+o.length()+")");
|
|
4878
|
return lengthOk;
|
|
4879
|
}
|
|
4880
|
|
|
4881
|
private double similarity(String s1, String s2) {
|
|
4882
|
//logger.info("similarity");
|
|
4883
|
//System.out.println("similarity *"+s1+"* vs. *"+s2+"*");
|
|
4884
|
if(!StringUtils.isEmpty(s1) && !StringUtils.isEmpty(s2)){
|
|
4885
|
String l1=s1.toLowerCase().trim();
|
|
4886
|
String l2=s2.toLowerCase().trim();
|
|
4887
|
if (l1.length() < l2.length()) { // s1 should always be bigger
|
|
4888
|
String swap = l1; l1 = l2; l2 = swap;
|
|
4889
|
}
|
|
4890
|
int bigLen = l1.length();
|
|
4891
|
if (bigLen == 0) { return 1.0; /* both strings are zero length */ }
|
|
4892
|
return (bigLen - computeEditDistance(l1, l2)) / (double) bigLen;
|
|
4893
|
}
|
|
4894
|
else{
|
|
4895
|
if(s1!=null && s2!=null){
|
|
4896
|
if (s1.equalsIgnoreCase(s2)) {
|
|
4897
|
return 1;
|
|
4898
|
}
|
|
4899
|
}
|
|
4900
|
return -1;
|
|
4901
|
}
|
|
4902
|
}
|
|
4903
|
|
|
4904
|
private int computeEditDistance(String s1, String s2) {
|
|
4905
|
//logger.info("computeEditDistance");
|
|
4906
|
int[] costs = new int[s2.length() + 1];
|
|
4907
|
for (int i = 0; i <= s1.length(); i++) {
|
|
4908
|
int lastValue = i;
|
|
4909
|
for (int j = 0; j <= s2.length(); j++) {
|
|
4910
|
if (i == 0) {
|
|
4911
|
costs[j] = j;
|
|
4912
|
} else {
|
|
4913
|
if (j > 0) {
|
|
4914
|
int newValue = costs[j - 1];
|
|
4915
|
if (s1.charAt(i - 1) != s2.charAt(j - 1)) {
|
|
4916
|
newValue = Math.min(Math.min(newValue, lastValue),
|
|
4917
|
costs[j]) + 1;
|
|
4918
|
}
|
|
4919
|
costs[j - 1] = lastValue;
|
|
4920
|
lastValue = newValue;
|
|
4921
|
}
|
|
4922
|
}
|
|
4923
|
}
|
|
4924
|
if (i > 0) {
|
|
4925
|
costs[s2.length()] = lastValue;
|
|
4926
|
}
|
|
4927
|
}
|
|
4928
|
return costs[s2.length()];
|
|
4929
|
}
|
|
4930
|
|
|
4931
|
Map<Rank, Taxon> hierarchy = new HashMap<>();
|
|
4932
|
/**
|
|
4933
|
* @param taxonName
|
|
4934
|
*/
|
|
4935
|
@SuppressWarnings("rawtypes")
|
|
4936
|
public void lookForParentNode(INonViralName taxonName, Taxon tax, Reference ref, MyName myName) {
|
|
4937
|
logger.info("lookForParentNode "+taxonName.getTitleCache()+" for "+myName.toString());
|
|
4938
|
//System.out.println("LOOK FOR PARENT NODE "+taxonname.toString()+"; "+tax.toString()+"; "+taxonname.getRank());
|
|
4939
|
INonViralNameParser parser = NonViralNameParserImpl.NewInstance();
|
|
4940
|
if (taxonName.getRank().equals(Rank.FORM())){
|
|
4941
|
handleFormHierarchy(ref, myName, parser);
|
|
4942
|
}
|
|
4943
|
else if (taxonName.getRank().equals(Rank.VARIETY())){
|
|
4944
|
handleVarietyHierarchy(ref, myName, parser);
|
|
4945
|
}
|
|
4946
|
else if (taxonName.getRank().equals(Rank.SUBSPECIES())){
|
|
4947
|
handleSubSpeciesHierarchy(ref, myName, parser);
|
|
4948
|
}
|
|
4949
|
else if (taxonName.getRank().equals(Rank.SPECIES())){
|
|
4950
|
handleSpeciesHierarchy(ref, myName, parser);
|
|
4951
|
}
|
|
4952
|
else if (taxonName.getRank().equals(Rank.SUBGENUS())){
|
|
4953
|
handleSubgenusHierarchy(ref, myName, parser);
|
|
4954
|
}
|
|
4955
|
|
|
4956
|
if (taxonName.getRank().equals(Rank.GENUS())){
|
|
4957
|
handleGenusHierarchy(ref, myName, parser);
|
|
4958
|
}
|
|
4959
|
if (taxonName.getRank().equals(Rank.SUBTRIBE())){
|
|
4960
|
handleSubtribeHierarchy(ref, myName, parser);
|
|
4961
|
}
|
|
4962
|
if (taxonName.getRank().equals(Rank.TRIBE())){
|
|
4963
|
handleTribeHierarchy(ref, myName, parser);
|
|
4964
|
}
|
|
4965
|
|
|
4966
|
if (taxonName.getRank().equals(Rank.SUBFAMILY())){
|
|
4967
|
handleSubfamilyHierarchy(ref, myName, parser);
|
|
4968
|
}
|
|
4969
|
}
|
|
4970
|
|
|
4971
|
/**
|
|
4972
|
* @param ref
|
|
4973
|
* @param myName
|
|
4974
|
* @param parser
|
|
4975
|
*/
|
|
4976
|
private void handleSubfamilyHierarchy(Reference ref, MyName myName, INonViralNameParser<?> parser) {
|
|
4977
|
System.out.println("handleSubfamilyHierarchy");
|
|
4978
|
String parentStr = myName.getFamilyStr();
|
|
4979
|
Rank r = Rank.FAMILY();
|
|
4980
|
if(parentStr!=null){
|
|
4981
|
|
|
4982
|
Taxon parent = null;
|
|
4983
|
Pager<TaxonBase> taxontest = importer.getTaxonService().findByTitleWithRestrictions(TaxonBase.class, parentStr, MatchMode.BEGINNING, null, null, null, null, null);
|
|
4984
|
for(TaxonBase tb:taxontest.getRecords()){
|
|
4985
|
try {
|
|
4986
|
if (tb.getName().getRank().equals(r)) {
|
|
4987
|
parent=CdmBase.deproxy(tb, Taxon.class);
|
|
4988
|
}
|
|
4989
|
break;
|
|
4990
|
} catch (Exception e) {
|
|
4991
|
// TODO Auto-generated catch block
|
|
4992
|
e.printStackTrace();
|
|
4993
|
}
|
|
4994
|
}
|
|
4995
|
if(parent == null) {
|
|
4996
|
INonViralName parentNameName = parser.parseFullName(parentStr, nomenclaturalCode, r);
|
|
4997
|
Taxon tmp = findMatchingTaxon(parentNameName,ref);
|
|
4998
|
if(tmp ==null)
|
|
4999
|
{
|
|
5000
|
parent=Taxon.NewInstance(parentNameName, ref);
|
|
5001
|
importer.getTaxonService().save(parent);
|
|
5002
|
parent = CdmBase.deproxy(parent, Taxon.class);
|
|
5003
|
} else {
|
|
5004
|
parent=tmp;
|
|
5005
|
}
|
|
5006
|
lookForParentNode(parentNameName, parent, ref,myName);
|
|
5007
|
|
|
5008
|
}
|
|
5009
|
hierarchy.put(r,parent);
|
|
5010
|
}
|
|
5011
|
}
|
|
5012
|
|
|
5013
|
/**
|
|
5014
|
* @param ref
|
|
5015
|
* @param myName
|
|
5016
|
* @param parser
|
|
5017
|
*/
|
|
5018
|
private void handleTribeHierarchy(Reference ref, MyName myName, INonViralNameParser<?> parser) {
|
|
5019
|
String parentStr = myName.getSubfamilyStr();
|
|
5020
|
Rank r = Rank.SUBFAMILY();
|
|
5021
|
if (parentStr == null){
|
|
5022
|
parentStr = myName.getFamilyStr();
|
|
5023
|
r = Rank.FAMILY();
|
|
5024
|
}
|
|
5025
|
if(parentStr!=null){
|
|
5026
|
INonViralName parentNameName = parser.parseFullName(parentStr, nomenclaturalCode, r);
|
|
5027
|
Taxon parent = Taxon.NewInstance(parentNameName, ref); //sec set null
|
|
5028
|
// importer.getTaxonService().save(parent);
|
|
5029
|
// parent = CdmBase.deproxy(parent, Taxon.class);
|
|
5030
|
|
|
5031
|
boolean parentDoesNotExists = true;
|
|
5032
|
for (TaxonNode p : classification.getAllNodes()){
|
|
5033
|
if(p.getTaxon().getTitleCache().equalsIgnoreCase(parent.getTitleCache())) {
|
|
5034
|
parentDoesNotExists = false;
|
|
5035
|
parent=CdmBase.deproxy(p.getTaxon(), Taxon.class);
|
|
5036
|
break;
|
|
5037
|
}
|
|
5038
|
}
|
|
5039
|
// if(parentDoesNotExists) {
|
|
5040
|
// importer.getTaxonService().save(parent);
|
|
5041
|
// parent = CdmBase.deproxy(parent, Taxon.class);
|
|
5042
|
// lookForParentNode(parentNameName, parent, ref,myName);
|
|
5043
|
// }
|
|
5044
|
if(parentDoesNotExists) {
|
|
5045
|
Taxon tmp = findMatchingTaxon(parentNameName,ref);
|
|
5046
|
if(tmp ==null)
|
|
5047
|
{
|
|
5048
|
parent=Taxon.NewInstance(parentNameName, ref);
|
|
5049
|
importer.getTaxonService().save(parent);
|
|
5050
|
parent = CdmBase.deproxy(parent, Taxon.class);
|
|
5051
|
} else {
|
|
5052
|
parent=tmp;
|
|
5053
|
}
|
|
5054
|
lookForParentNode(parentNameName, parent, ref,myName);
|
|
5055
|
|
|
5056
|
}
|
|
5057
|
hierarchy.put(r,parent);
|
|
5058
|
}
|
|
5059
|
}
|
|
5060
|
|
|
5061
|
/**
|
|
5062
|
* @param ref
|
|
5063
|
* @param myName
|
|
5064
|
* @param parser
|
|
5065
|
*/
|
|
5066
|
private void handleSubtribeHierarchy(Reference ref, MyName myName, INonViralNameParser<?> parser) {
|
|
5067
|
String parentStr = myName.getTribeStr();
|
|
5068
|
Rank r = Rank.TRIBE();
|
|
5069
|
if (parentStr == null){
|
|
5070
|
parentStr = myName.getSubfamilyStr();
|
|
5071
|
r = Rank.SUBFAMILY();
|
|
5072
|
}
|
|
5073
|
if (parentStr == null){
|
|
5074
|
parentStr = myName.getFamilyStr();
|
|
5075
|
r = Rank.FAMILY();
|
|
5076
|
}
|
|
5077
|
if(parentStr!=null){
|
|
5078
|
INonViralName parentNameName = parser.parseFullName(parentStr, nomenclaturalCode, r);
|
|
5079
|
Taxon parent = Taxon.NewInstance(parentNameName, ref); //sec set null
|
|
5080
|
// importer.getTaxonService().save(parent);
|
|
5081
|
// parent = CdmBase.deproxy(parent, Taxon.class);
|
|
5082
|
|
|
5083
|
boolean parentDoesNotExists = true;
|
|
5084
|
for (TaxonNode p : classification.getAllNodes()){
|
|
5085
|
if(p.getTaxon().getTitleCache().equalsIgnoreCase(parent.getTitleCache())) {
|
|
5086
|
parentDoesNotExists = false;
|
|
5087
|
parent=CdmBase.deproxy(p.getTaxon(), Taxon.class);
|
|
5088
|
|
|
5089
|
break;
|
|
5090
|
}
|
|
5091
|
}
|
|
5092
|
// if(parentDoesNotExists) {
|
|
5093
|
// importer.getTaxonService().save(parent);
|
|
5094
|
// parent = CdmBase.deproxy(parent, Taxon.class);
|
|
5095
|
// lookForParentNode(parentNameName, parent, ref,myName);
|
|
5096
|
// }
|
|
5097
|
if(parentDoesNotExists) {
|
|
5098
|
Taxon tmp = findMatchingTaxon(parentNameName,ref);
|
|
5099
|
if(tmp ==null)
|
|
5100
|
{
|
|
5101
|
parent=Taxon.NewInstance(parentNameName, ref);
|
|
5102
|
importer.getTaxonService().save(parent);
|
|
5103
|
parent = CdmBase.deproxy(parent, Taxon.class);
|
|
5104
|
} else {
|
|
5105
|
parent=tmp;
|
|
5106
|
}
|
|
5107
|
lookForParentNode(parentNameName, parent, ref,myName);
|
|
5108
|
|
|
5109
|
}
|
|
5110
|
hierarchy.put(r,parent);
|
|
5111
|
}
|
|
5112
|
}
|
|
5113
|
|
|
5114
|
/**
|
|
5115
|
* @param ref
|
|
5116
|
* @param myName
|
|
5117
|
* @param parser
|
|
5118
|
*/
|
|
5119
|
private void handleGenusHierarchy(Reference ref, MyName myName, INonViralNameParser<?> parser) {
|
|
5120
|
String parentStr = myName.getSubtribeStr();
|
|
5121
|
Rank r = Rank.SUBTRIBE();
|
|
5122
|
if (parentStr == null){
|
|
5123
|
parentStr = myName.getTribeStr();
|
|
5124
|
r = Rank.TRIBE();
|
|
5125
|
}
|
|
5126
|
if (parentStr == null){
|
|
5127
|
parentStr = myName.getSubfamilyStr();
|
|
5128
|
r = Rank.SUBFAMILY();
|
|
5129
|
}
|
|
5130
|
if (parentStr == null){
|
|
5131
|
parentStr = myName.getFamilyStr();
|
|
5132
|
r = Rank.FAMILY();
|
|
5133
|
}
|
|
5134
|
if(parentStr!=null){
|
|
5135
|
INonViralName parentNameName = parser.parseFullName(parentStr, nomenclaturalCode, r);
|
|
5136
|
Taxon parent = Taxon.NewInstance(parentNameName, ref); //sec set null
|
|
5137
|
// importer.getTaxonService().save(parent);
|
|
5138
|
// parent = CdmBase.deproxy(parent, Taxon.class);
|
|
5139
|
|
|
5140
|
boolean parentDoesNotExist = true;
|
|
5141
|
for (TaxonNode p : classification.getAllNodes()){
|
|
5142
|
if(p.getTaxon().getTitleCache().equalsIgnoreCase(parent.getTitleCache())) {
|
|
5143
|
// System.out.println(p.getTaxon().getUuid());
|
|
5144
|
// System.out.println(parent.getUuid());
|
|
5145
|
parentDoesNotExist = false;
|
|
5146
|
parent=CdmBase.deproxy(p.getTaxon(), Taxon.class);
|
|
5147
|
break;
|
|
5148
|
}
|
|
5149
|
}
|
|
5150
|
// if(parentDoesNotExists) {
|
|
5151
|
// importer.getTaxonService().save(parent);
|
|
5152
|
// parent = CdmBase.deproxy(parent, Taxon.class);
|
|
5153
|
// lookForParentNode(parentNameName, parent, ref,myName);
|
|
5154
|
// }
|
|
5155
|
if(parentDoesNotExist) {
|
|
5156
|
Taxon tmp = findMatchingTaxon(parentNameName,ref);
|
|
5157
|
if(tmp ==null){
|
|
5158
|
|
|
5159
|
parent=Taxon.NewInstance(parentNameName, ref);
|
|
5160
|
importer.getTaxonService().save(parent);
|
|
5161
|
parent = CdmBase.deproxy(parent, Taxon.class);
|
|
5162
|
} else {
|
|
5163
|
parent=tmp;
|
|
5164
|
}
|
|
5165
|
lookForParentNode(parentNameName, parent, ref,myName);
|
|
5166
|
|
|
5167
|
}
|
|
5168
|
hierarchy.put(r,parent);
|
|
5169
|
}
|
|
5170
|
}
|
|
5171
|
|
|
5172
|
/**
|
|
5173
|
* @param ref
|
|
5174
|
* @param myName
|
|
5175
|
* @param parser
|
|
5176
|
*/
|
|
5177
|
private void handleSubgenusHierarchy(Reference ref, MyName myName, INonViralNameParser<?> parser) {
|
|
5178
|
String parentStr = myName.getGenusStr();
|
|
5179
|
Rank r = Rank.GENUS();
|
|
5180
|
|
|
5181
|
if(parentStr==null){
|
|
5182
|
parentStr = myName.getSubtribeStr();
|
|
5183
|
r = Rank.SUBTRIBE();
|
|
5184
|
}
|
|
5185
|
if (parentStr == null){
|
|
5186
|
parentStr = myName.getTribeStr();
|
|
5187
|
r = Rank.TRIBE();
|
|
5188
|
}
|
|
5189
|
if (parentStr == null){
|
|
5190
|
parentStr = myName.getSubfamilyStr();
|
|
5191
|
r = Rank.SUBFAMILY();
|
|
5192
|
}
|
|
5193
|
if (parentStr == null){
|
|
5194
|
parentStr = myName.getFamilyStr();
|
|
5195
|
r = Rank.FAMILY();
|
|
5196
|
}
|
|
5197
|
if(parentStr!=null){
|
|
5198
|
INonViralName parentNameName = parser.parseFullName(parentStr, nomenclaturalCode, r);
|
|
5199
|
Taxon parent = Taxon.NewInstance(parentNameName, ref); //sec set null
|
|
5200
|
// importer.getTaxonService().save(parent);
|
|
5201
|
// parent = CdmBase.deproxy(parent, Taxon.class);
|
|
5202
|
|
|
5203
|
boolean parentDoesNotExists = true;
|
|
5204
|
for (TaxonNode p : classification.getAllNodes()){
|
|
5205
|
if(p.getTaxon().getTitleCache().equalsIgnoreCase(parent.getTitleCache())) {
|
|
5206
|
// System.out.println(p.getTaxon().getUuid());
|
|
5207
|
// System.out.println(parent.getUuid());
|
|
5208
|
parentDoesNotExists = false;
|
|
5209
|
parent=CdmBase.deproxy(p.getTaxon(), Taxon.class);
|
|
5210
|
break;
|
|
5211
|
}
|
|
5212
|
}
|
|
5213
|
// if(parentDoesNotExists) {
|
|
5214
|
// importer.getTaxonService().save(parent);
|
|
5215
|
// parent = CdmBase.deproxy(parent, Taxon.class);
|
|
5216
|
// lookForParentNode(parentNameName, parent, ref,myName);
|
|
5217
|
// }
|
|
5218
|
if(parentDoesNotExists) {
|
|
5219
|
Taxon tmp = findMatchingTaxon(parentNameName,ref);
|
|
5220
|
if(tmp ==null)
|
|
5221
|
{
|
|
5222
|
parent=Taxon.NewInstance(parentNameName, ref);
|
|
5223
|
importer.getTaxonService().save(parent);
|
|
5224
|
parent = CdmBase.deproxy(parent, Taxon.class);
|
|
5225
|
} else {
|
|
5226
|
parent=tmp;
|
|
5227
|
}
|
|
5228
|
lookForParentNode(parentNameName, parent, ref,myName);
|
|
5229
|
|
|
5230
|
}
|
|
5231
|
hierarchy.put(r,parent);
|
|
5232
|
}
|
|
5233
|
}
|
|
5234
|
|
|
5235
|
/**
|
|
5236
|
* @param ref
|
|
5237
|
* @param myName
|
|
5238
|
* @param parser
|
|
5239
|
*/
|
|
5240
|
private void handleSpeciesHierarchy(Reference ref, MyName myName, INonViralNameParser<?> parser) {
|
|
5241
|
String parentStr = myName.getSubgenusStr();
|
|
5242
|
Rank r = Rank.SUBGENUS();
|
|
5243
|
|
|
5244
|
if(parentStr==null){
|
|
5245
|
parentStr = myName.getGenusStr();
|
|
5246
|
r = Rank.GENUS();
|
|
5247
|
}
|
|
5248
|
|
|
5249
|
if(parentStr==null){
|
|
5250
|
parentStr = myName.getSubtribeStr();
|
|
5251
|
r = Rank.SUBTRIBE();
|
|
5252
|
}
|
|
5253
|
if (parentStr == null){
|
|
5254
|
parentStr = myName.getTribeStr();
|
|
5255
|
r = Rank.TRIBE();
|
|
5256
|
}
|
|
5257
|
if (parentStr == null){
|
|
5258
|
parentStr = myName.getSubfamilyStr();
|
|
5259
|
r = Rank.SUBFAMILY();
|
|
5260
|
}
|
|
5261
|
if (parentStr == null){
|
|
5262
|
parentStr = myName.getFamilyStr();
|
|
5263
|
r = Rank.FAMILY();
|
|
5264
|
}
|
|
5265
|
if(parentStr!=null){
|
|
5266
|
Taxon parent = handleParentName(ref, myName, parser, parentStr, r);
|
|
5267
|
//System.out.println("PUT IN HIERARCHY "+r+", "+parent);
|
|
5268
|
hierarchy.put(r,parent);
|
|
5269
|
}
|
|
5270
|
}
|
|
5271
|
|
|
5272
|
/**
|
|
5273
|
* @param ref
|
|
5274
|
* @param myName
|
|
5275
|
* @param parser
|
|
5276
|
*/
|
|
5277
|
private void handleSubSpeciesHierarchy(Reference ref, MyName myName, INonViralNameParser<?> parser) {
|
|
5278
|
String parentStr = myName.getSpeciesStr();
|
|
5279
|
Rank r = Rank.SPECIES();
|
|
5280
|
|
|
5281
|
|
|
5282
|
if(parentStr==null){
|
|
5283
|
parentStr = myName.getSubgenusStr();
|
|
5284
|
r = Rank.SUBGENUS();
|
|
5285
|
}
|
|
5286
|
|
|
5287
|
if(parentStr==null){
|
|
5288
|
parentStr = myName.getGenusStr();
|
|
5289
|
r = Rank.GENUS();
|
|
5290
|
}
|
|
5291
|
|
|
5292
|
if(parentStr==null){
|
|
5293
|
parentStr = myName.getSubtribeStr();
|
|
5294
|
r = Rank.SUBTRIBE();
|
|
5295
|
}
|
|
5296
|
if (parentStr == null){
|
|
5297
|
parentStr = myName.getTribeStr();
|
|
5298
|
r = Rank.TRIBE();
|
|
5299
|
}
|
|
5300
|
if (parentStr == null){
|
|
5301
|
parentStr = myName.getSubfamilyStr();
|
|
5302
|
r = Rank.SUBFAMILY();
|
|
5303
|
}
|
|
5304
|
if (parentStr == null){
|
|
5305
|
parentStr = myName.getFamilyStr();
|
|
5306
|
r = Rank.FAMILY();
|
|
5307
|
}
|
|
5308
|
if(parentStr!=null){
|
|
5309
|
Taxon parent = handleParentName(ref, myName, parser, parentStr, r);
|
|
5310
|
//System.out.println("PUT IN HIERARCHY "+r+", "+parent);
|
|
5311
|
hierarchy.put(r,parent);
|
|
5312
|
}
|
|
5313
|
}
|
|
5314
|
|
|
5315
|
|
|
5316
|
/**
|
|
5317
|
* @param ref
|
|
5318
|
* @param myName
|
|
5319
|
* @param parser
|
|
5320
|
*/
|
|
5321
|
private void handleFormHierarchy(Reference ref, MyName myName, INonViralNameParser<?> parser) {
|
|
5322
|
String parentStr = myName.getSubspeciesStr();
|
|
5323
|
Rank r = Rank.SUBSPECIES();
|
|
5324
|
|
|
5325
|
|
|
5326
|
if(parentStr==null){
|
|
5327
|
parentStr = myName.getSpeciesStr();
|
|
5328
|
r = Rank.SPECIES();
|
|
5329
|
}
|
|
5330
|
|
|
5331
|
if(parentStr==null){
|
|
5332
|
parentStr = myName.getSubgenusStr();
|
|
5333
|
r = Rank.SUBGENUS();
|
|
5334
|
}
|
|
5335
|
|
|
5336
|
if(parentStr==null){
|
|
5337
|
parentStr = myName.getGenusStr();
|
|
5338
|
r = Rank.GENUS();
|
|
5339
|
}
|
|
5340
|
|
|
5341
|
if(parentStr==null){
|
|
5342
|
parentStr = myName.getSubtribeStr();
|
|
5343
|
r = Rank.SUBTRIBE();
|
|
5344
|
}
|
|
5345
|
if (parentStr == null){
|
|
5346
|
parentStr = myName.getTribeStr();
|
|
5347
|
r = Rank.TRIBE();
|
|
5348
|
}
|
|
5349
|
if (parentStr == null){
|
|
5350
|
parentStr = myName.getSubfamilyStr();
|
|
5351
|
r = Rank.SUBFAMILY();
|
|
5352
|
}
|
|
5353
|
if (parentStr == null){
|
|
5354
|
parentStr = myName.getFamilyStr();
|
|
5355
|
r = Rank.FAMILY();
|
|
5356
|
}
|
|
5357
|
if(parentStr!=null){
|
|
5358
|
Taxon parent = handleParentName(ref, myName, parser, parentStr, r);
|
|
5359
|
//System.out.println("PUT IN HIERARCHY "+r+", "+parent);
|
|
5360
|
hierarchy.put(r,parent);
|
|
5361
|
}
|
|
5362
|
}
|
|
5363
|
|
|
5364
|
/**
|
|
5365
|
* @param ref
|
|
5366
|
* @param myName
|
|
5367
|
* @param parser
|
|
5368
|
*/
|
|
5369
|
private void handleVarietyHierarchy(Reference ref, MyName myName, INonViralNameParser<?> parser) {
|
|
5370
|
String parentStr = myName.getSubspeciesStr();
|
|
5371
|
Rank r = Rank.SUBSPECIES();
|
|
5372
|
|
|
5373
|
if(parentStr==null){
|
|
5374
|
parentStr = myName.getSpeciesStr();
|
|
5375
|
r = Rank.SPECIES();
|
|
5376
|
}
|
|
5377
|
|
|
5378
|
if(parentStr==null){
|
|
5379
|
parentStr = myName.getSubgenusStr();
|
|
5380
|
r = Rank.SUBGENUS();
|
|
5381
|
}
|
|
5382
|
|
|
5383
|
if(parentStr==null){
|
|
5384
|
parentStr = myName.getGenusStr();
|
|
5385
|
r = Rank.GENUS();
|
|
5386
|
}
|
|
5387
|
|
|
5388
|
if(parentStr==null){
|
|
5389
|
parentStr = myName.getSubtribeStr();
|
|
5390
|
r = Rank.SUBTRIBE();
|
|
5391
|
}
|
|
5392
|
if (parentStr == null){
|
|
5393
|
parentStr = myName.getTribeStr();
|
|
5394
|
r = Rank.TRIBE();
|
|
5395
|
}
|
|
5396
|
if (parentStr == null){
|
|
5397
|
parentStr = myName.getSubfamilyStr();
|
|
5398
|
r = Rank.SUBFAMILY();
|
|
5399
|
}
|
|
5400
|
if (parentStr == null){
|
|
5401
|
parentStr = myName.getFamilyStr();
|
|
5402
|
r = Rank.FAMILY();
|
|
5403
|
}
|
|
5404
|
if(parentStr!=null){
|
|
5405
|
Taxon parent = handleParentName(ref, myName, parser, parentStr, r);
|
|
5406
|
//System.out.println("PUT IN HIERARCHY "+r+", "+parent);
|
|
5407
|
hierarchy.put(r,parent);
|
|
5408
|
}
|
|
5409
|
}
|
|
5410
|
|
|
5411
|
/**
|
|
5412
|
* @param ref
|
|
5413
|
* @param myName
|
|
5414
|
* @param parser
|
|
5415
|
* @param parentStr
|
|
5416
|
* @param r
|
|
5417
|
* @return
|
|
5418
|
*/
|
|
5419
|
private Taxon handleParentName(Reference ref, MyName myName, INonViralNameParser<?> parser, String parentStr, Rank r) {
|
|
5420
|
INonViralName parentNameName = parser.parseFullName(parentStr, nomenclaturalCode, r);
|
|
5421
|
Taxon parent = Taxon.NewInstance(parentNameName, ref); //sec set null
|
|
5422
|
// importer.getTaxonService().save(parent);
|
|
5423
|
// parent = CdmBase.deproxy(parent, Taxon.class);
|
|
5424
|
|
|
5425
|
boolean parentDoesNotExists = true;
|
|
5426
|
for (TaxonNode p : classification.getAllNodes()){
|
|
5427
|
if(p.getTaxon().getTitleCache().split("sec.")[0].trim().equalsIgnoreCase(parent.getTitleCache().split("sec.")[0].trim())) {
|
|
5428
|
// System.out.println(p.getTaxon().getUuid());
|
|
5429
|
// System.out.println(parent.getUuid());
|
|
5430
|
parentDoesNotExists = false;
|
|
5431
|
parent=CdmBase.deproxy(p.getTaxon(), Taxon.class);
|
|
5432
|
break;
|
|
5433
|
}
|
|
5434
|
}
|
|
5435
|
if(parentDoesNotExists) {
|
|
5436
|
Taxon tmp = findMatchingTaxon(parentNameName,ref);
|
|
5437
|
// System.out.println("FOUND PARENT "+tmp.toString()+" for "+parentNameName.toString());
|
|
5438
|
if(tmp ==null){
|
|
5439
|
|
|
5440
|
parent=Taxon.NewInstance(parentNameName, ref);
|
|
5441
|
importer.getTaxonService().save(parent);
|
|
5442
|
|
|
5443
|
} else {
|
|
5444
|
parent=tmp;
|
|
5445
|
}
|
|
5446
|
lookForParentNode(parentNameName, parent, ref,myName);
|
|
5447
|
|
|
5448
|
}
|
|
5449
|
return parent;
|
|
5450
|
}
|
|
5451
|
|
|
5452
|
private void addNameDifferenceToFile(String originalname, String atomisedname){
|
|
5453
|
try{
|
|
5454
|
FileWriter fstream = new FileWriter(TaxonXImport.LOG_FOLDER + "NamesDifferent_"+classification.getTitleCache()+".txt",true);
|
|
5455
|
BufferedWriter out = new BufferedWriter(fstream);
|
|
5456
|
out.write(originalname+" (original) versus "+replaceNull(atomisedname)+" (atomised) \n");
|
|
5457
|
//Close the output stream
|
|
5458
|
out.close();
|
|
5459
|
}catch (Exception e){//Catch exception if any
|
|
5460
|
System.err.println("Error: " + e.getMessage());
|
|
5461
|
}
|
|
5462
|
}
|
|
5463
|
/**
|
|
5464
|
* @param name
|
|
5465
|
* @param author
|
|
5466
|
* @param nomenclaturalCode2
|
|
5467
|
* @param rank
|
|
5468
|
*/
|
|
5469
|
private void addProblemNameToFile(String name, String author, NomenclaturalCode nomenclaturalCode2, Rank rank) {
|
|
5470
|
try{
|
|
5471
|
FileWriter fstream = new FileWriter(TaxonXImport.LOG_FOLDER + "NameNotParsed.txt",true);
|
|
5472
|
BufferedWriter out = new BufferedWriter(fstream);
|
|
5473
|
out.write(name+"\t"+replaceNull(author)+"\t"+replaceNull(nomenclaturalCode2)+"\t"+replaceNull(rank)+"\n");
|
|
5474
|
//Close the output stream
|
|
5475
|
out.close();
|
|
5476
|
}catch (Exception e){//Catch exception if any
|
|
5477
|
System.err.println("Error: " + e.getMessage());
|
|
5478
|
}
|
|
5479
|
}
|
|
5480
|
|
|
5481
|
|
|
5482
|
/**
|
|
5483
|
* @param tnb
|
|
5484
|
* @param bestMatchingTaxon
|
|
5485
|
* @param insertAsExisting
|
|
5486
|
* @param refMods
|
|
5487
|
*/
|
|
5488
|
private void logDecision(INonViralName tnb, Taxon bestMatchingTaxon, boolean insertAsExisting, Reference refMods) {
|
|
5489
|
try{
|
|
5490
|
FileWriter fstream = new FileWriter(TaxonXImport.LOG_FOLDER + "Decisions_"+classification.toString()+".txt", true);
|
|
5491
|
BufferedWriter out = new BufferedWriter(fstream);
|
|
5492
|
out.write(tnb.getTitleCache() + " sec. " + refMods + "\t" + bestMatchingTaxon.getTitleCache() + "\t" + insertAsExisting + "\n");
|
|
5493
|
//Close the output stream
|
|
5494
|
out.close();
|
|
5495
|
}catch (Exception e){//Catch exception if any
|
|
5496
|
System.err.println("Error: " + e.getMessage());
|
|
5497
|
}
|
|
5498
|
}
|
|
5499
|
|
|
5500
|
|
|
5501
|
@SuppressWarnings("unused")
|
|
5502
|
private String replaceNull(Object in){
|
|
5503
|
if (in == null) {
|
|
5504
|
return "";
|
|
5505
|
}
|
|
5506
|
if (in.getClass().equals(NomenclaturalCode.class)) {
|
|
5507
|
return ((NomenclaturalCode)in).getTitleCache();
|
|
5508
|
}
|
|
5509
|
return in.toString();
|
|
5510
|
}
|
|
5511
|
|
|
5512
|
/**
|
|
5513
|
* @param fullName
|
|
5514
|
* @param nomenclaturalCode2
|
|
5515
|
* @param rank
|
|
5516
|
*/
|
|
5517
|
private void addProblemNameToFile(String type, String name, NomenclaturalCode nomenclaturalCode2, Rank rank, String problems) {
|
|
5518
|
try{
|
|
5519
|
FileWriter fstream = new FileWriter(TaxonXImport.LOG_FOLDER + "NameNotParsed_"+classification.getTitleCache()+".txt",true);
|
|
5520
|
BufferedWriter out = new BufferedWriter(fstream);
|
|
5521
|
out.write(type+"\t"+name+"\t"+replaceNull(nomenclaturalCode2)+"\t"+replaceNull(rank)+"\t"+problems+"\n");
|
|
5522
|
//Close the output stream
|
|
5523
|
out.close();
|
|
5524
|
}catch (Exception e){//Catch exception if any
|
|
5525
|
System.err.println("Error: " + e.getMessage());
|
|
5526
|
}
|
|
5527
|
|
|
5528
|
}
|
|
5529
|
|
|
5530
|
}
|
|
5531
|
|
|
5532
|
|
|
5533
|
|