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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.awt.Dimension;
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import java.io.StringWriter;
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import java.util.ArrayList;
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import java.util.Collections;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Map;
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import java.util.Scanner;
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import java.util.Set;
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import java.util.UUID;
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import javax.swing.JFrame;
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import javax.swing.JOptionPane;
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import javax.swing.JScrollPane;
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import javax.swing.JTextArea;
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import javax.swing.UIManager;
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import javax.xml.transform.OutputKeys;
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import javax.xml.transform.Transformer;
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import javax.xml.transform.TransformerException;
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import javax.xml.transform.TransformerFactory;
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import javax.xml.transform.TransformerFactoryConfigurationError;
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import javax.xml.transform.dom.DOMSource;
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import javax.xml.transform.stream.StreamResult;
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import org.apache.commons.lang.StringUtils;
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import org.apache.logging.log4j.LogManager;import org.apache.logging.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 eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;
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import eu.etaxonomy.cdm.api.service.IAgentService;
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import eu.etaxonomy.cdm.io.specimen.UnitsGatheringArea;
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import eu.etaxonomy.cdm.io.specimen.UnitsGatheringEvent;
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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.Language;
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import eu.etaxonomy.cdm.model.common.TimePeriod;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.description.TextData;
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import eu.etaxonomy.cdm.model.location.NamedArea;
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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.NomenclaturalStatusType;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
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import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
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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.GatheringEvent;
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
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import eu.etaxonomy.cdm.model.reference.IBook;
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import eu.etaxonomy.cdm.model.reference.IBookSection;
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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.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonNode;
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import eu.etaxonomy.cdm.model.term.DefinedTermBase;
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import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;
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import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
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import eu.etaxonomy.cdm.strategy.parser.ParserProblem;
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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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public class TaxonXExtractor {
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protected TaxonXImport importer;
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protected TaxonXImportState state2;
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private final Map<String,String> namesAsked = new HashMap<>();
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private final Map<String,Rank>ranksAsked = new HashMap<>();
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Logger logger = LogManager.getLogger(TaxonXExtractor.class);
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public class ReferenceBuilder{
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private int nbRef=0;
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private boolean foundBibref=false;
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private final TaxonXAddSources sourceHandler;
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public ReferenceBuilder(TaxonXAddSources sourceHandler) {
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this.sourceHandler=sourceHandler;
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}
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public boolean isFoundBibref() {
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return foundBibref;
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}
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public void setFoundBibref(boolean foundBibref) {
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this.foundBibref = foundBibref;
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}
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public void builReference(String mref, String treatmentMainName, NomenclaturalCode nomenclaturalCode,
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Taxon acceptedTaxon, Reference refMods) {
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// System.out.println("builReference "+mref);
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this.setFoundBibref(true);
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String ref= mref;
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if ( (ref.endsWith(";") ||ref.endsWith(",") ) && ((ref.length())>1)) {
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ref=ref.substring(0, ref.length()-1)+".";
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}
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if (ref.startsWith(treatmentMainName) && !ref.endsWith(treatmentMainName)) {
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ref=ref.replace(treatmentMainName, "");
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ref=ref.trim();
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while (ref.startsWith(".") || ref.startsWith(",")) {
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ref=ref.replace(".","").replace(",","").trim();
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}
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}
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// logger.info("Current reference :"+nbRef+", "+ref+", "+treatmentMainName+"--"+ref.indexOf(treatmentMainName));
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Reference reference = ReferenceFactory.newGeneric();
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reference.setTitleCache(ref, true);
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//only add the first one if there is no nomenclatural reference yet
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if (nbRef==0){
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if(acceptedTaxon.getName().getNomenclaturalReference()==null){
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acceptedTaxon.getName().setNomenclaturalReference(reference);
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sourceHandler.addSource(refMods, acceptedTaxon);
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}
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}
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//add all other references as Feature.Citation
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TaxonDescription taxonDescription =importer.getTaxonDescription(acceptedTaxon, false, true);
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acceptedTaxon.addDescription(taxonDescription);
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sourceHandler.addSource(refMods, acceptedTaxon);
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TextData textData = TextData.NewInstance(Feature.CITATION());
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Language language = Language.DEFAULT();
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textData.putText(language, ref);
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sourceHandler.addSource(reference, textData,acceptedTaxon.getName(),refMods);
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taxonDescription.addElement(textData);
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sourceHandler.addSource(refMods, taxonDescription);
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importer.getTaxonService().saveOrUpdate(acceptedTaxon);
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// logger.warn("BWAAHHHH: "+nameToBeFilled.getParsingProblems()+", "+ref);
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nbRef++;
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}
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}
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public class MySpecimenOrObservation{
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String descr="";
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DerivedUnit derivedUnitBase=null;
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public String getDescr() {
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return descr;
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}
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public void setDescr(String descr) {
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this.descr = descr;
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}
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public DerivedUnit getDerivedUnitBase() {
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return derivedUnitBase;
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}
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public void setDerivedUnitBase(DerivedUnit derivedUnitBase) {
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this.derivedUnitBase = derivedUnitBase;
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}
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}
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@SuppressWarnings({ "unused", "rawtypes" })
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protected MySpecimenOrObservation extractSpecimenOrObservation(Node specimenObservationNode, DerivedUnit derivedUnitBase,
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SpecimenOrObservationType defaultAssociation, TaxonName typifiableName) {
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String country=null;
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String locality=null;
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String stateprov=null;
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String collector=null;
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String fieldNumber=null;
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Double latitude=null,longitude=null;
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TimePeriod tp =null;
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String day,month,year="";
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String descr="not available";
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String type="";
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boolean asso=false;
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NodeList eventContent =null;
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// create facade
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DerivedUnitFacade derivedUnitFacade = null;
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UnitsGatheringEvent unitsGatheringEvent;
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UnitsGatheringArea unitsGatheringArea;
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DefinedTermBase areaCountry;
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MySpecimenOrObservation specimenOrObservation = new MySpecimenOrObservation();
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NodeList xmldata= specimenObservationNode.getChildNodes();
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for (int n=0;n<xmldata.getLength();n++){
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eventContent=xmldata.item(n).getChildNodes();
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if (xmldata.item(n).getNodeName().equalsIgnoreCase("tax:xmldata")){
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asso=true;
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country=null;
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locality=null;
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stateprov=null;
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collector=null;
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fieldNumber=null;
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latitude=null;
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longitude=null;
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day="";
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month="";
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year="";
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type="";
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for (int j=0;j<eventContent.getLength();j++){
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if(eventContent.item(j).getNodeName().equalsIgnoreCase("dwc:country")){
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country=eventContent.item(j).getTextContent().trim();
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}
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else if(eventContent.item(j).getNodeName().equalsIgnoreCase("dwc:locality")){
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locality=eventContent.item(j).getTextContent().trim();
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}
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else if(eventContent.item(j).getNodeName().equalsIgnoreCase("dwc:stateprovince")){
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stateprov=eventContent.item(j).getTextContent().trim();
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}
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else if(eventContent.item(j).getNodeName().equalsIgnoreCase("dwc:collector")){
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collector=eventContent.item(j).getTextContent().trim();
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}
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else if(eventContent.item(j).getNodeName().equalsIgnoreCase("dwc:yearcollected")){
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year=eventContent.item(j).getTextContent().trim();
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}
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else if(eventContent.item(j).getNodeName().equalsIgnoreCase("dwc:monthcollected")){
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month=eventContent.item(j).getTextContent().trim();
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}
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else if(eventContent.item(j).getNodeName().equalsIgnoreCase("dwc:daycollected")){
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day=eventContent.item(j).getTextContent().trim();
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}
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else if(eventContent.item(j).getNodeName().equalsIgnoreCase("dwc:decimallongitude")){
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String tmp = eventContent.item(j).getTextContent().trim();
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try{longitude=Double.valueOf(tmp);}catch(Exception e){logger.warn("longitude is not a number");}
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}
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else if(eventContent.item(j).getNodeName().equalsIgnoreCase("dwc:decimallatitude")){
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String tmp = eventContent.item(j).getTextContent().trim();
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try{latitude=Double.valueOf(tmp);}catch(Exception e){logger.warn("latitude is not a number");}
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}else if(eventContent.item(j).getNodeName().equalsIgnoreCase("dwc:TypeStatus")){
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type = eventContent.item(j).getTextContent().trim();
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}else if(eventContent.item(j).getNodeName().equalsIgnoreCase("#text") && StringUtils.isBlank(eventContent.item(j).getTextContent())){
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//do nothing
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}
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else {
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logger.info("UNEXTRACTED FIELD FOR SPECIMEN "+eventContent.item(j).getNodeName()+", "+eventContent.item(j).getTextContent()) ;
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}
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}
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if (!day.isEmpty() || !month.isEmpty() || !year.isEmpty()){
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try{
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if (!year.isEmpty()) {
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tp = TimePeriod.NewInstance(Integer.parseInt(year));
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if (!month.isEmpty()) {
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tp.setStartMonth(Integer.parseInt(month));
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if (!day.isEmpty()) {
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tp.setStartDay(Integer.parseInt(day));
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}
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}
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}
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}catch(Exception e){
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logger.warn("Collection date error "+e);
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}
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}
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}
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if(xmldata.item(n).getNodeName().equalsIgnoreCase("#text")){
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descr=xmldata.item(n).getTextContent().replaceAll(";","").trim();
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if (descr.length()>1 && containsDistinctLetters(descr)) {
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specimenOrObservation.setDescr(descr);
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asso=true;
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}
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}
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if(xmldata.item(n).getNodeName().equalsIgnoreCase("tax:p")){
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descr=xmldata.item(n).getTextContent().replaceAll(";","").trim();
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if (descr.length()>1 && containsDistinctLetters(descr)) {
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specimenOrObservation.setDescr(descr);
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asso=true;
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}
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}
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}
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// if(asso && descr.length()>1){
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// logger.info("DESCR: "+descr);
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if (!type.isEmpty()) {
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if (!containsDistinctLetters(type)) {
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type="no description text";
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}
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derivedUnitFacade = getFacade(type.replaceAll(";",""), defaultAssociation);
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SpecimenTypeDesignation designation = SpecimenTypeDesignation.NewInstance();
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if (typifiableName != null){
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typifiableName.addTypeDesignation(designation, true);
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}else{
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logger.warn("No typifiable name available");
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}
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SpecimenTypeDesignationStatus stds= getSpecimenTypeDesignationStatusByKey(type);
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if (stds !=null) {
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stds = (SpecimenTypeDesignationStatus) importer.getTermService().find(stds.getUuid());
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}
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designation.setTypeStatus(stds);
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derivedUnitFacade.innerDerivedUnit().addSpecimenTypeDesignation(designation);
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derivedUnitBase = derivedUnitFacade.innerDerivedUnit();
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// System.out.println("derivedUnitBase: "+derivedUnitBase);
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// designation.setTypeSpecimen(derivedUnitBase);
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// TaxonName name = taxon.getName();
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// name.addTypeDesignation(designation, true);
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} else {
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if (!containsDistinctLetters(descr.replaceAll(";",""))) {
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descr="no description text";
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}
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derivedUnitFacade = getFacade(descr.replaceAll(";",""), defaultAssociation);
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derivedUnitBase = derivedUnitFacade.innerDerivedUnit();
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// System.out.println("derivedUnitBase2: "+derivedUnitBase);
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}
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unitsGatheringEvent = new UnitsGatheringEvent(importer.getTermService(), locality,collector,longitude, latitude,
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state2.getConfig(),importer.getAgentService());
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if(tp!=null) {
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unitsGatheringEvent.setGatheringDate(tp);
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}
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// country
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unitsGatheringArea = new UnitsGatheringArea();
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unitsGatheringArea.setParams(null, country, state2.getConfig(), importer.getTermService(), importer.getVocabularyService());
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//TODO other areas
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if (StringUtils.isNotBlank(stateprov)){
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Map<String, String> namedAreas = new HashMap<>();
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namedAreas.put(stateprov, null);
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unitsGatheringArea.setAreaNames(namedAreas, state2.getConfig(), importer.getTermService(), importer.getVocabularyService());
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}
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339
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areaCountry = unitsGatheringArea.getCountry();
|
|
340
|
|
|
341
|
// // other areas
|
|
342
|
// unitsGatheringArea = new UnitsGatheringArea(namedAreaList,dataHolder.getTermService());
|
|
343
|
// ArrayList<DefinedTermBase> nas = unitsGatheringArea.getAreas();
|
|
344
|
// for (DefinedTermBase namedArea : nas) {
|
|
345
|
// unitsGatheringEvent.addArea(namedArea);
|
|
346
|
// }
|
|
347
|
|
|
348
|
// copy gathering event to facade
|
|
349
|
GatheringEvent gatheringEvent = unitsGatheringEvent.getGatheringEvent();
|
|
350
|
derivedUnitFacade.setGatheringEvent(gatheringEvent);
|
|
351
|
derivedUnitFacade.setLocality(gatheringEvent.getLocality());
|
|
352
|
derivedUnitFacade.setExactLocation(gatheringEvent.getExactLocation());
|
|
353
|
derivedUnitFacade.setCollector(gatheringEvent.getCollector());
|
|
354
|
derivedUnitFacade.setCountry((NamedArea)areaCountry);
|
|
355
|
|
|
356
|
for(DefinedTermBase<?> area:unitsGatheringArea.getAreas()){
|
|
357
|
derivedUnitFacade.addCollectingArea((NamedArea) area);
|
|
358
|
}
|
|
359
|
// derivedUnitFacade.addCollectingAreas(unitsGatheringArea.getAreas());
|
|
360
|
|
|
361
|
// add fieldNumber
|
|
362
|
if (fieldNumber != null) {
|
|
363
|
derivedUnitFacade.setFieldNumber(fieldNumber);
|
|
364
|
}
|
|
365
|
specimenOrObservation.setDerivedUnitBase(derivedUnitBase);
|
|
366
|
// }
|
|
367
|
return specimenOrObservation;
|
|
368
|
}
|
|
369
|
|
|
370
|
private SpecimenTypeDesignationStatus getSpecimenTypeDesignationStatusByKey(
|
|
371
|
String key) {
|
|
372
|
if (key == null) {
|
|
373
|
return null;
|
|
374
|
} else if (key.matches("(?i)(T|Type)")) {
|
|
375
|
return SpecimenTypeDesignationStatus.TYPE();
|
|
376
|
} else if (key.matches("(?i)(HT|Holotype)")) {
|
|
377
|
return SpecimenTypeDesignationStatus.HOLOTYPE();
|
|
378
|
} else if (key.matches("(?i)(LT|Lectotype)")) {
|
|
379
|
return SpecimenTypeDesignationStatus.LECTOTYPE();
|
|
380
|
} else if (key.matches("(?i)(NT|Neotype)")) {
|
|
381
|
return SpecimenTypeDesignationStatus.NEOTYPE();
|
|
382
|
} else if (key.matches("(?i)(ST|Syntype)")) {
|
|
383
|
return SpecimenTypeDesignationStatus.SYNTYPE();
|
|
384
|
} else if (key.matches("(?i)(ET|Epitype)")) {
|
|
385
|
return SpecimenTypeDesignationStatus.EPITYPE();
|
|
386
|
} else if (key.matches("(?i)(IT|Isotype)")) {
|
|
387
|
return SpecimenTypeDesignationStatus.ISOTYPE();
|
|
388
|
} else if (key.matches("(?i)(ILT|Isolectotype)")) {
|
|
389
|
return SpecimenTypeDesignationStatus.ISOLECTOTYPE();
|
|
390
|
} else if (key.matches("(?i)(INT|Isoneotype)")) {
|
|
391
|
return SpecimenTypeDesignationStatus.ISONEOTYPE();
|
|
392
|
} else if (key.matches("(?i)(IET|Isoepitype)")) {
|
|
393
|
return SpecimenTypeDesignationStatus.ISOEPITYPE();
|
|
394
|
} else if (key.matches("(?i)(PT|Paratype)")) {
|
|
395
|
return SpecimenTypeDesignationStatus.PARATYPE();
|
|
396
|
} else if (key.matches("(?i)(PLT|Paralectotype)")) {
|
|
397
|
return SpecimenTypeDesignationStatus.PARALECTOTYPE();
|
|
398
|
} else if (key.matches("(?i)(PNT|Paraneotype)")) {
|
|
399
|
return SpecimenTypeDesignationStatus.PARANEOTYPE();
|
|
400
|
} else if (key.matches("(?i)(unsp.|Unspecified)")) {
|
|
401
|
return SpecimenTypeDesignationStatus.UNSPECIFIC();
|
|
402
|
} else if (key.matches("(?i)(2LT|Second Step Lectotype)")) {
|
|
403
|
return SpecimenTypeDesignationStatus.SECOND_STEP_LECTOTYPE();
|
|
404
|
} else if (key.matches("(?i)(2NT|Second Step Neotype)")) {
|
|
405
|
return SpecimenTypeDesignationStatus.SECOND_STEP_NEOTYPE();
|
|
406
|
} else if (key.matches("(?i)(OM|Original Material)")) {
|
|
407
|
return SpecimenTypeDesignationStatus.ORIGINAL_MATERIAL();
|
|
408
|
} else if (key.matches("(?i)(IcT|Iconotype)")) {
|
|
409
|
return SpecimenTypeDesignationStatus.ICONOTYPE();
|
|
410
|
} else if (key.matches("(?i)(PT|Phototype)")) {
|
|
411
|
return SpecimenTypeDesignationStatus.PHOTOTYPE();
|
|
412
|
} else if (key.matches("(?i)(IST|Isosyntype)")) {
|
|
413
|
return SpecimenTypeDesignationStatus.ISOSYNTYPE();
|
|
414
|
} else {
|
|
415
|
return null;
|
|
416
|
}
|
|
417
|
}
|
|
418
|
protected DerivedUnitFacade getFacade(String recordBasis, SpecimenOrObservationType defaultAssoc) {
|
|
419
|
// System.out.println("getFacade() for "+recordBasis+", defaultassociation: "+defaultAssoc);
|
|
420
|
SpecimenOrObservationType type = null;
|
|
421
|
|
|
422
|
// create specimen
|
|
423
|
if (recordBasis != null) {
|
|
424
|
String recordBasisL = recordBasis.toLowerCase();
|
|
425
|
if (recordBasisL.startsWith("specimen") || recordBasisL.contains("specimen") || recordBasisL.contains("type")) {// specimen
|
|
426
|
type = SpecimenOrObservationType.PreservedSpecimen;
|
|
427
|
}
|
|
428
|
if (recordBasisL.startsWith("observation")) {
|
|
429
|
type = SpecimenOrObservationType.Observation;
|
|
430
|
}
|
|
431
|
if (recordBasisL.contains("fossil")) {
|
|
432
|
type = SpecimenOrObservationType.Fossil;
|
|
433
|
}
|
|
434
|
|
|
435
|
if (recordBasisL.startsWith("living")) {
|
|
436
|
type = SpecimenOrObservationType.LivingSpecimen;
|
|
437
|
}
|
|
438
|
if (type == null) {
|
|
439
|
logger.info("The basis of record does not seem to be known: *" + recordBasisL+"*");
|
|
440
|
type = defaultAssoc;
|
|
441
|
}
|
|
442
|
// TODO fossils?
|
|
443
|
} else {
|
|
444
|
logger.info("The basis of record is null");
|
|
445
|
type = defaultAssoc;
|
|
446
|
}
|
|
447
|
DerivedUnitFacade derivedUnitFacade = DerivedUnitFacade.NewInstance(type);
|
|
448
|
return derivedUnitFacade;
|
|
449
|
}
|
|
450
|
|
|
451
|
@SuppressWarnings("rawtypes")
|
|
452
|
protected Feature makeFeature(SpecimenOrObservationBase unit) {
|
|
453
|
if (unit == null){
|
|
454
|
return null;
|
|
455
|
}
|
|
456
|
SpecimenOrObservationType type = unit.getRecordBasis();
|
|
457
|
|
|
458
|
if (type.isFeatureObservation()){
|
|
459
|
return Feature.OBSERVATION();
|
|
460
|
}else if (type.isPreservedSpecimen() ||
|
|
461
|
type == SpecimenOrObservationType.LivingSpecimen ||
|
|
462
|
type == SpecimenOrObservationType.OtherSpecimen
|
|
463
|
){
|
|
464
|
return Feature.SPECIMEN();
|
|
465
|
}else if (type == SpecimenOrObservationType.Unknown ||
|
|
466
|
type == SpecimenOrObservationType.DerivedUnit
|
|
467
|
) {
|
|
468
|
return Feature.INDIVIDUALS_ASSOCIATION();
|
|
469
|
}
|
|
470
|
logger.warn("No feature defined for derived unit class: "
|
|
471
|
+ unit.getClass().getSimpleName());
|
|
472
|
return null;
|
|
473
|
}
|
|
474
|
|
|
475
|
protected final static String SPLITTER = ",";
|
|
476
|
|
|
477
|
protected int askQuestion(String question){
|
|
478
|
Scanner scan = new Scanner(System.in);
|
|
479
|
logger.info(question);
|
|
480
|
int index = scan.nextInt();
|
|
481
|
return index;
|
|
482
|
}
|
|
483
|
|
|
484
|
protected Reference getReferenceWithType(int reftype) {
|
|
485
|
Reference ref = null;
|
|
486
|
switch (reftype) {
|
|
487
|
case 1:
|
|
488
|
ref = ReferenceFactory.newGeneric();
|
|
489
|
break;
|
|
490
|
case 2:
|
|
491
|
IBook tmp= ReferenceFactory.newBook();
|
|
492
|
ref = (Reference)tmp;
|
|
493
|
break;
|
|
494
|
case 3:
|
|
495
|
ref = ReferenceFactory.newArticle();
|
|
496
|
break;
|
|
497
|
case 4:
|
|
498
|
IBookSection tmp2 = ReferenceFactory.newBookSection();
|
|
499
|
ref = (Reference)tmp2;
|
|
500
|
break;
|
|
501
|
case 5:
|
|
502
|
ref = ReferenceFactory.newJournal();
|
|
503
|
break;
|
|
504
|
case 6:
|
|
505
|
ref = ReferenceFactory.newPrintSeries();
|
|
506
|
break;
|
|
507
|
case 7:
|
|
508
|
ref = ReferenceFactory.newThesis();
|
|
509
|
break;
|
|
510
|
default:
|
|
511
|
break;
|
|
512
|
}
|
|
513
|
return ref;
|
|
514
|
}
|
|
515
|
|
|
516
|
protected void prepareCollectors(TaxonXImportState state,IAgentService agentService) {
|
|
517
|
// logger.info("PREPARE COLLECTORS");
|
|
518
|
List<String> collectors = new ArrayList<>();
|
|
519
|
String tmp;
|
|
520
|
List<String> collectorsU = new ArrayList<>(new HashSet<>(collectors));
|
|
521
|
Set<UUID> uuids = new HashSet<UUID>();
|
|
522
|
|
|
523
|
//existing persons in DB
|
|
524
|
List<UuidAndTitleCache<Person>> hiberPersons = agentService.getUuidAndTitleCache(Person.class, null, null);
|
|
525
|
Map<String,Person> titleCachePerson = new HashMap<>();
|
|
526
|
uuids = new HashSet<UUID>();
|
|
527
|
for (UuidAndTitleCache<Person> hibernateP:hiberPersons){
|
|
528
|
uuids.add(hibernateP.getUuid());
|
|
529
|
}
|
|
530
|
|
|
531
|
if (!uuids.isEmpty()){
|
|
532
|
List<AgentBase> existingPersons = agentService.find(uuids);
|
|
533
|
for (AgentBase existingP:existingPersons){
|
|
534
|
titleCachePerson.put(existingP.getTitleCache(),CdmBase.deproxy(existingP, Person.class));
|
|
535
|
}
|
|
536
|
}
|
|
537
|
|
|
538
|
Map<String,UUID> personMap = new HashMap<>();
|
|
539
|
for (UuidAndTitleCache<Person> person:hiberPersons){
|
|
540
|
personMap.put(person.getTitleCache(), person.getUuid());
|
|
541
|
}
|
|
542
|
|
|
543
|
java.util.Collection<AgentBase> personToadd = new ArrayList<>();
|
|
544
|
|
|
545
|
for (String collector:collectorsU){
|
|
546
|
Person p = Person.NewInstance();
|
|
547
|
p.setTitleCache(collector,true);
|
|
548
|
if (!personMap.containsKey(p.getTitleCache())){
|
|
549
|
personToadd.add(p);
|
|
550
|
}
|
|
551
|
}
|
|
552
|
|
|
553
|
if(!personToadd.isEmpty()){
|
|
554
|
Map<UUID, AgentBase> uuuidPerson = agentService.save(personToadd);
|
|
555
|
for (UUID u:uuuidPerson.keySet()){
|
|
556
|
titleCachePerson.put(uuuidPerson.get(u).getTitleCache(), CdmBase.deproxy(uuuidPerson.get(u), Person.class));
|
|
557
|
}
|
|
558
|
}
|
|
559
|
|
|
560
|
state.getConfig().setPersons(titleCachePerson);
|
|
561
|
}
|
|
562
|
|
|
563
|
protected String getFullReference(String name, List<ParserProblem> problems) {
|
|
564
|
// logger.info("getFullReference for "+ name);
|
|
565
|
JTextArea textArea = new JTextArea("Complete the reference or the name '"+name+"'.\nThe current problem is "+StringUtils.join(problems,"--"));
|
|
566
|
JScrollPane scrollPane = new JScrollPane(textArea);
|
|
567
|
textArea.setLineWrap(true);
|
|
568
|
textArea.setWrapStyleWord(true);
|
|
569
|
scrollPane.setPreferredSize( new Dimension( 700, 70 ) );
|
|
570
|
|
|
571
|
// JFrame frame = new JFrame("I have a question");
|
|
572
|
// frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
|
|
573
|
String s = (String)JOptionPane.showInputDialog(
|
|
574
|
null,
|
|
575
|
scrollPane,
|
|
576
|
"Get full reference or name",
|
|
577
|
JOptionPane.PLAIN_MESSAGE,
|
|
578
|
null,
|
|
579
|
null,
|
|
580
|
name);
|
|
581
|
return s;
|
|
582
|
}
|
|
583
|
|
|
584
|
|
|
585
|
|
|
586
|
/**
|
|
587
|
* @param name
|
|
588
|
* @return
|
|
589
|
* @throws TransformerException
|
|
590
|
* @throws TransformerFactoryConfigurationError
|
|
591
|
*/
|
|
592
|
protected String askWhichScientificName(String fullname,String atomised,String classificationName, Node fullParagraph) throws TransformerFactoryConfigurationError, TransformerException {
|
|
593
|
// logger.info("getScientificName for "+ fullname);
|
|
594
|
// JFrame frame = new JFrame("I have a question");
|
|
595
|
// frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
|
|
596
|
String k = fullname+"_"+atomised;
|
|
597
|
|
|
598
|
String defaultN = "";
|
|
599
|
if (atomised.length()>fullname.length()) {
|
|
600
|
defaultN=atomised;
|
|
601
|
} else {
|
|
602
|
defaultN=fullname;
|
|
603
|
}
|
|
604
|
|
|
605
|
if (namesAsked.containsKey(k)){
|
|
606
|
return namesAsked.get(k);
|
|
607
|
}
|
|
608
|
else{
|
|
609
|
//activate it for ants because a lot of markup is incomplete
|
|
610
|
if (classificationName.indexOf("Ants")>-1) {
|
|
611
|
return defaultN;
|
|
612
|
}
|
|
613
|
|
|
614
|
JTextArea textArea = new JTextArea("The names in the free text and in the xml tags do not match : "+fullname+
|
|
615
|
", or "+atomised+"\n"+formatNode(fullParagraph));
|
|
616
|
JScrollPane scrollPane = new JScrollPane(textArea);
|
|
617
|
textArea.setLineWrap(true);
|
|
618
|
textArea.setWrapStyleWord(true);
|
|
619
|
scrollPane.setPreferredSize( new Dimension( 700, 200 ) );
|
|
620
|
String s = (String)JOptionPane.showInputDialog(
|
|
621
|
null,
|
|
622
|
scrollPane,
|
|
623
|
"Which name do I have to use? The current classification is "+classificationName,
|
|
624
|
JOptionPane.PLAIN_MESSAGE,
|
|
625
|
null,
|
|
626
|
null,
|
|
627
|
defaultN);
|
|
628
|
namesAsked.put(k, s);
|
|
629
|
return s;
|
|
630
|
}
|
|
631
|
}
|
|
632
|
|
|
633
|
|
|
634
|
protected int askAddParent(String s){
|
|
635
|
// boolean hack=true;
|
|
636
|
// if (hack) {
|
|
637
|
// return 1;
|
|
638
|
// }
|
|
639
|
JTextArea textArea = new JTextArea("If you want to add a parent taxa for "+s+", click \"Yes\"." +
|
|
640
|
" If it is a root for this classification, click \"No\" or \"Cancel\".");
|
|
641
|
JScrollPane scrollPane = new JScrollPane(textArea);
|
|
642
|
textArea.setLineWrap(true);
|
|
643
|
textArea.setWrapStyleWord(true);
|
|
644
|
scrollPane.setPreferredSize( new Dimension( 600, 70 ) );
|
|
645
|
|
|
646
|
Object[] options = { UIManager.getString("OptionPane.yesButtonText"),
|
|
647
|
UIManager.getString("OptionPane.noButtonText")};
|
|
648
|
|
|
649
|
|
|
650
|
int addTaxon = JOptionPane.showOptionDialog(null,
|
|
651
|
scrollPane,
|
|
652
|
"",
|
|
653
|
JOptionPane.YES_NO_OPTION,
|
|
654
|
0,
|
|
655
|
null,
|
|
656
|
options,
|
|
657
|
options[1]);
|
|
658
|
return addTaxon;
|
|
659
|
}
|
|
660
|
|
|
661
|
protected String askSetParent(String s){
|
|
662
|
JTextArea textArea = new JTextArea("What is the first taxon parent for "+s+"?\n"+
|
|
663
|
"The rank will be asked later. ");
|
|
664
|
JScrollPane scrollPane = new JScrollPane(textArea);
|
|
665
|
textArea.setLineWrap(true);
|
|
666
|
textArea.setWrapStyleWord(true);
|
|
667
|
scrollPane.setPreferredSize( new Dimension( 700, 200 ) );
|
|
668
|
|
|
669
|
String s2 = (String)JOptionPane.showInputDialog(
|
|
670
|
null,
|
|
671
|
scrollPane,
|
|
672
|
"",
|
|
673
|
JOptionPane.PLAIN_MESSAGE,
|
|
674
|
null,
|
|
675
|
null,
|
|
676
|
s);
|
|
677
|
return s2;
|
|
678
|
}
|
|
679
|
|
|
680
|
protected String askRank(String s, List<String> rankListStr){
|
|
681
|
JTextArea textArea = new JTextArea("What is the rank for "+s+"?");
|
|
682
|
JScrollPane scrollPane = new JScrollPane(textArea);
|
|
683
|
textArea.setLineWrap(true);
|
|
684
|
textArea.setWrapStyleWord(true);
|
|
685
|
scrollPane.setPreferredSize( new Dimension( 700, 200 ) );
|
|
686
|
|
|
687
|
String r = (String)JOptionPane.showInputDialog(
|
|
688
|
null,
|
|
689
|
scrollPane,
|
|
690
|
"",
|
|
691
|
JOptionPane.PLAIN_MESSAGE,
|
|
692
|
null,
|
|
693
|
rankListStr.toArray(),
|
|
694
|
null);
|
|
695
|
return r;
|
|
696
|
}
|
|
697
|
|
|
698
|
/**
|
|
699
|
* @param name
|
|
700
|
* @return
|
|
701
|
* @throws TransformerException
|
|
702
|
* @throws TransformerFactoryConfigurationError
|
|
703
|
*/
|
|
704
|
protected String askFeatureName(String paragraph){
|
|
705
|
// logger.info("getScientificName for "+ fullname);
|
|
706
|
// JFrame frame = new JFrame("I have a question");
|
|
707
|
// frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
|
|
708
|
JTextArea textArea = new JTextArea("How should the feature be named? \n"+paragraph);
|
|
709
|
JScrollPane scrollPane = new JScrollPane(textArea);
|
|
710
|
textArea.setLineWrap(true);
|
|
711
|
textArea.setWrapStyleWord(true);
|
|
712
|
scrollPane.setPreferredSize( new Dimension( 700, 200 ) );
|
|
713
|
String s = (String)JOptionPane.showInputDialog(
|
|
714
|
null,
|
|
715
|
scrollPane,
|
|
716
|
"",
|
|
717
|
JOptionPane.PLAIN_MESSAGE,
|
|
718
|
null,
|
|
719
|
null,
|
|
720
|
"Other");
|
|
721
|
return s;
|
|
722
|
}
|
|
723
|
|
|
724
|
/**
|
|
725
|
* @param taxonname2
|
|
726
|
* @param bestMatchingTaxon
|
|
727
|
* @param refMods
|
|
728
|
* @param similarityAuthor
|
|
729
|
* @return
|
|
730
|
*/
|
|
731
|
protected boolean askIfReuseBestMatchingTaxon(INonViralName taxonname2, Taxon bestMatchingTaxon, Reference refMods, double similarityScore, double similarityAuthor) {
|
|
732
|
Object[] options = { UIManager.getString("OptionPane.yesButtonText"),
|
|
733
|
UIManager.getString("OptionPane.noButtonText")};
|
|
734
|
|
|
735
|
if (similarityScore<0.66 && similarityAuthor<0.5) {
|
|
736
|
return false;
|
|
737
|
// System.out.println("should say NO");
|
|
738
|
}
|
|
739
|
|
|
740
|
boolean sameSource=false;
|
|
741
|
boolean noRef=false;
|
|
742
|
|
|
743
|
String sec = refMods.getTitleCache();
|
|
744
|
String secBest = "";
|
|
745
|
try{
|
|
746
|
secBest=bestMatchingTaxon.getSec().getTitleCache();
|
|
747
|
}
|
|
748
|
catch(NullPointerException e){
|
|
749
|
logger.warn("no sec - ignore");
|
|
750
|
}
|
|
751
|
|
|
752
|
if (secBest.isEmpty()) {
|
|
753
|
noRef=true;
|
|
754
|
}
|
|
755
|
|
|
756
|
Object defaultOption=options[1];
|
|
757
|
if(sec.equalsIgnoreCase(secBest)
|
|
758
|
// || taxonname2.getTitleCache().split("sec.")[0].trim().equalsIgnoreCase(bestMatchingTaxon.getTitleCache().split("sec.")[0].trim())
|
|
759
|
) {
|
|
760
|
//System.out.println(sec+" and "+secBest);
|
|
761
|
sameSource=true;
|
|
762
|
//-1 <=> no author
|
|
763
|
if (similarityScore>0.65 && (similarityAuthor==-1 || similarityAuthor>0.8)) {
|
|
764
|
defaultOption=options[0];
|
|
765
|
} else {
|
|
766
|
defaultOption=options[1];
|
|
767
|
}
|
|
768
|
} else {
|
|
769
|
if (similarityScore>0.65 && similarityAuthor>0.8) {
|
|
770
|
if(similarityScore==1 ) {
|
|
771
|
return true;
|
|
772
|
}
|
|
773
|
defaultOption=options[0];
|
|
774
|
} else {
|
|
775
|
defaultOption=options[1];
|
|
776
|
}
|
|
777
|
}
|
|
778
|
|
|
779
|
String sourcesStr="";
|
|
780
|
|
|
781
|
Set<IdentifiableSource> sources = bestMatchingTaxon.getSources();
|
|
782
|
for (IdentifiableSource src:sources){
|
|
783
|
try{
|
|
784
|
String srcSec=src.getCitation().getTitleCache();
|
|
785
|
if(!srcSec.isEmpty()){
|
|
786
|
sourcesStr+="\n "+srcSec;
|
|
787
|
if (srcSec.equalsIgnoreCase(sec)){
|
|
788
|
sameSource=true;
|
|
789
|
if (similarityScore>0.65 && similarityAuthor>0.8) {
|
|
790
|
defaultOption=options[0];
|
|
791
|
} else {
|
|
792
|
defaultOption=options[1];
|
|
793
|
}
|
|
794
|
}
|
|
795
|
}
|
|
796
|
}catch(Exception e){
|
|
797
|
logger.warn("the source reference is maybe null, just ignore it.");
|
|
798
|
}
|
|
799
|
}
|
|
800
|
|
|
801
|
if (sameSource && similarityScore>0.9999 && (similarityAuthor==-1 || similarityAuthor>0.8)) {
|
|
802
|
return true;
|
|
803
|
}
|
|
804
|
if(similarityScore<0.66) {
|
|
805
|
defaultOption=options[1];
|
|
806
|
}
|
|
807
|
|
|
808
|
// //only activate it if you know the data you are importing (ok for Chenopodium)
|
|
809
|
if(defaultOption==options[1]) {
|
|
810
|
return false;
|
|
811
|
}
|
|
812
|
|
|
813
|
JTextArea textArea =null;
|
|
814
|
if (!sourcesStr.isEmpty()) {
|
|
815
|
textArea = new JTextArea("Does "+taxonname2.toString()+" correspond to "
|
|
816
|
+ bestMatchingTaxon.toString()+" ?\n Click \"Yes\". if it does, click \"No\" if it does not."
|
|
817
|
+ "\n The current sources are:"+ sourcesStr);
|
|
818
|
} else {
|
|
819
|
textArea = new JTextArea("Does "+taxonname2.toString()+" correspond to "
|
|
820
|
+ bestMatchingTaxon.toString()+" ?\n Click \"Yes\". if it does, click \"No\" if it does not.");
|
|
821
|
}
|
|
822
|
JScrollPane scrollPane = new JScrollPane(textArea);
|
|
823
|
textArea.setLineWrap(true);
|
|
824
|
textArea.setWrapStyleWord(true);
|
|
825
|
scrollPane.setPreferredSize( new Dimension( 600, 70 ) );
|
|
826
|
|
|
827
|
int addTaxon = JOptionPane.showOptionDialog(null,
|
|
828
|
scrollPane,
|
|
829
|
refMods.toString(),
|
|
830
|
JOptionPane.YES_NO_OPTION,
|
|
831
|
0,
|
|
832
|
null,
|
|
833
|
options,
|
|
834
|
defaultOption);
|
|
835
|
if(addTaxon==1) {
|
|
836
|
return false;
|
|
837
|
} else {
|
|
838
|
return true;
|
|
839
|
}
|
|
840
|
}
|
|
841
|
|
|
842
|
/**
|
|
843
|
* @param fullLineRefName
|
|
844
|
* @return
|
|
845
|
*/
|
|
846
|
protected int askIfNameContained(String fullLineRefName) {
|
|
847
|
|
|
848
|
JTextArea textArea = new JTextArea("Is a scientific name contained in this sentence ? Type 0 if contains a name, 1 if it's only a reference. Press 2 if it's to be ignored \n"+fullLineRefName);
|
|
849
|
JScrollPane scrollPane = new JScrollPane(textArea);
|
|
850
|
textArea.setLineWrap(true);
|
|
851
|
textArea.setWrapStyleWord(true);
|
|
852
|
scrollPane.setPreferredSize( new Dimension( 600, 400 ) );
|
|
853
|
|
|
854
|
String s = (String)JOptionPane.showInputDialog(
|
|
855
|
null,
|
|
856
|
scrollPane,
|
|
857
|
"",
|
|
858
|
JOptionPane.PLAIN_MESSAGE,
|
|
859
|
null,
|
|
860
|
null,
|
|
861
|
"0");
|
|
862
|
return Integer.valueOf(s);
|
|
863
|
}
|
|
864
|
|
|
865
|
|
|
866
|
/**
|
|
867
|
* @param name
|
|
868
|
* @return
|
|
869
|
*/
|
|
870
|
protected Rank askForRank(String fullname,Rank rank, NomenclaturalCode nomenclaturalCode) {
|
|
871
|
// logger.info("askForRank for "+ fullname+ ", "+rank);
|
|
872
|
// JFrame frame = new JFrame("I have a question");
|
|
873
|
// frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
|
|
874
|
|
|
875
|
if (ranksAsked.containsKey(fullname)){
|
|
876
|
return ranksAsked.get(fullname);
|
|
877
|
}
|
|
878
|
else{
|
|
879
|
boolean np=false;
|
|
880
|
int npi=0;
|
|
881
|
Rank cR = null;
|
|
882
|
|
|
883
|
while (!np && npi<2)
|
|
884
|
{
|
|
885
|
|
|
886
|
|
|
887
|
JTextArea textArea = new JTextArea("What is the correct rank for "+fullname+"?");
|
|
888
|
JScrollPane scrollPane = new JScrollPane(textArea);
|
|
889
|
textArea.setLineWrap(true);
|
|
890
|
textArea.setWrapStyleWord(true);
|
|
891
|
scrollPane.setPreferredSize( new Dimension( 600, 50 ) );
|
|
892
|
|
|
893
|
List<Rank> rankList = new ArrayList<Rank>();
|
|
894
|
rankList = importer.getTermService().list(Rank.class, null, null, null, null);
|
|
895
|
|
|
896
|
List<String> rankListStr = new ArrayList<String>();
|
|
897
|
for (Rank r:rankList) {
|
|
898
|
rankListStr.add(r.toString());
|
|
899
|
}
|
|
900
|
String s = (String)JOptionPane.showInputDialog(
|
|
901
|
null,
|
|
902
|
scrollPane,
|
|
903
|
"The rank extracted from the TaxonX file is "+rank.toString(),
|
|
904
|
JOptionPane.PLAIN_MESSAGE,
|
|
905
|
null,
|
|
906
|
rankListStr.toArray(),
|
|
907
|
rank.toString());
|
|
908
|
|
|
909
|
|
|
910
|
try {
|
|
911
|
npi++;
|
|
912
|
cR = Rank.getRankByEnglishName(s,nomenclaturalCode,true);
|
|
913
|
np=true;
|
|
914
|
} catch (UnknownCdmTypeException e) {
|
|
915
|
logger.warn("Unknown rank ?!"+s);
|
|
916
|
logger.warn(e);
|
|
917
|
}
|
|
918
|
}
|
|
919
|
ranksAsked.put(fullname,cR);
|
|
920
|
return cR;
|
|
921
|
|
|
922
|
}
|
|
923
|
}
|
|
924
|
|
|
925
|
/**
|
|
926
|
* ask user to specify what kind of paragraph the current "multiple" section is
|
|
927
|
* default possibilities are "synonyms","material examined","distribution","image caption","other"
|
|
928
|
* could make sense to replace this list with the CDM-Feature list
|
|
929
|
* if "other" is selected, a second pop-up will be prompted to ask user to specify a new Feature name.
|
|
930
|
* @param fullParagraph : the current Node
|
|
931
|
* @return the section name
|
|
932
|
* */
|
|
933
|
protected String askMultiple(Node fullParagraph){
|
|
934
|
String fp = "";
|
|
935
|
try {
|
|
936
|
fp = formatNode(fullParagraph);
|
|
937
|
} catch (TransformerFactoryConfigurationError e1) {
|
|
938
|
// TODO Auto-generated catch block
|
|
939
|
e1.printStackTrace();
|
|
940
|
} catch (TransformerException e1) {
|
|
941
|
// TODO Auto-generated catch block
|
|
942
|
e1.printStackTrace();
|
|
943
|
}
|
|
944
|
JTextArea textArea = new JTextArea("What category is it for this paragraph \n"+fp);
|
|
945
|
JScrollPane scrollPane = new JScrollPane(textArea);
|
|
946
|
textArea.setLineWrap(true);
|
|
947
|
textArea.setWrapStyleWord(true);
|
|
948
|
scrollPane.setPreferredSize( new Dimension( 600, 400 ) );
|
|
949
|
|
|
950
|
String[] possiblities = {"synonyms","material examined","distribution","image caption","Other","vernacular name","type status","new category"};
|
|
951
|
|
|
952
|
|
|
953
|
String s = (String)JOptionPane.showInputDialog(
|
|
954
|
null,
|
|
955
|
scrollPane,
|
|
956
|
"",
|
|
957
|
JOptionPane.PLAIN_MESSAGE,
|
|
958
|
null,
|
|
959
|
possiblities,
|
|
960
|
"Other");
|
|
961
|
|
|
962
|
if (s.equalsIgnoreCase("new category")) {
|
|
963
|
try {
|
|
964
|
s=askFeatureName(formatNode(fullParagraph));
|
|
965
|
} catch (TransformerFactoryConfigurationError e) {
|
|
966
|
logger.warn(e);
|
|
967
|
} catch (TransformerException e) {
|
|
968
|
logger.warn(e);
|
|
969
|
}
|
|
970
|
}
|
|
971
|
return s;
|
|
972
|
|
|
973
|
}
|
|
974
|
|
|
975
|
|
|
976
|
|
|
977
|
/**
|
|
978
|
* asks for the hierarchical parent, based on the current classification
|
|
979
|
* @param taxon
|
|
980
|
* @param classification
|
|
981
|
* @return Taxon, the parent Taxon
|
|
982
|
*/
|
|
983
|
protected Taxon askParent(Taxon taxon,Classification classification ) {
|
|
984
|
// System.out.println("ASK PARENT "+classification);
|
|
985
|
// logger.info("ask Parent "+taxon.getTitleCache());
|
|
986
|
Set<TaxonNode> allNodes = classification.getAllNodes();
|
|
987
|
Map<String,Taxon> nodesMap = new HashMap<String, Taxon>();
|
|
988
|
|
|
989
|
for (TaxonNode tn:allNodes){
|
|
990
|
Taxon t = tn.getTaxon();
|
|
991
|
nodesMap.put(t.getTitleCache(), t);
|
|
992
|
}
|
|
993
|
List<String> nodeList = new ArrayList<String>();
|
|
994
|
for (String nl : nodesMap.keySet()) {
|
|
995
|
nodeList.add(nl+" - "+nodesMap.get(nl).getName().getRank());
|
|
996
|
}
|
|
997
|
Collections.sort(nodeList);
|
|
998
|
nodeList.add(0, "Not here!");
|
|
999
|
|
|
1000
|
JFrame frame = new JFrame("I have a question");
|
|
1001
|
frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
|
|
1002
|
String s = (String)JOptionPane.showInputDialog(
|
|
1003
|
frame,
|
|
1004
|
"What is the taxon parent for "+taxon.getTitleCache()+"?",
|
|
1005
|
"The current classification is "+classification.getTitleCache(),
|
|
1006
|
JOptionPane.PLAIN_MESSAGE,
|
|
1007
|
null,
|
|
1008
|
nodeList.toArray(),
|
|
1009
|
"Not here!");
|
|
1010
|
|
|
1011
|
Taxon returnTaxon = nodesMap.get(s.split(" - ")[0]);
|
|
1012
|
// logger.info("ask Parent returns "+s);
|
|
1013
|
return returnTaxon;
|
|
1014
|
}
|
|
1015
|
|
|
1016
|
|
|
1017
|
/**
|
|
1018
|
*
|
|
1019
|
* @param r: the rank as string (with dwc tags)
|
|
1020
|
* @return Rank : the Rank object corresponding to the current string
|
|
1021
|
*
|
|
1022
|
*/
|
|
1023
|
protected Rank getRank(String r){
|
|
1024
|
if (r==null) {
|
|
1025
|
r=Rank.UNKNOWN_RANK().toString();
|
|
1026
|
}
|
|
1027
|
r=r.replace("dwcranks:", "");
|
|
1028
|
r =r.replace("dwc:","");
|
|
1029
|
|
|
1030
|
Rank rank = Rank.UNKNOWN_RANK();
|
|
1031
|
if (r.equalsIgnoreCase("Superfamily")) {
|
|
1032
|
rank=Rank.SUPERFAMILY();
|
|
1033
|
}
|
|
1034
|
else if (r.equalsIgnoreCase("Family")) {
|
|
1035
|
rank=Rank.FAMILY();
|
|
1036
|
}
|
|
1037
|
else if (r.equalsIgnoreCase("Subfamily")) {
|
|
1038
|
rank=Rank.SUBFAMILY();
|
|
1039
|
}
|
|
1040
|
else if (r.equalsIgnoreCase("Tribe")) {
|
|
1041
|
rank=Rank.TRIBE();
|
|
1042
|
}
|
|
1043
|
else if (r.equalsIgnoreCase("Subtribe")) {
|
|
1044
|
rank=Rank.SUBTRIBE();
|
|
1045
|
}
|
|
1046
|
else if (r.equalsIgnoreCase("Genus")) {
|
|
1047
|
rank=Rank.GENUS();
|
|
1048
|
}
|
|
1049
|
else if (r.equalsIgnoreCase("Subgenus")) {
|
|
1050
|
rank=Rank.SUBGENUS();
|
|
1051
|
}
|
|
1052
|
else if (r.equalsIgnoreCase("Section")) {
|
|
1053
|
rank=Rank.SECTION_BOTANY();
|
|
1054
|
}
|
|
1055
|
else if (r.equalsIgnoreCase("Subsection")) {
|
|
1056
|
rank=Rank.SUBSECTION_BOTANY();
|
|
1057
|
}
|
|
1058
|
else if (r.equalsIgnoreCase("Series")) {
|
|
1059
|
rank=Rank.SERIES();
|
|
1060
|
}
|
|
1061
|
else if (r.equalsIgnoreCase("Subseries")) {
|
|
1062
|
rank=Rank.SUBSERIES();
|
|
1063
|
}
|
|
1064
|
else if (r.equalsIgnoreCase("Species")) {
|
|
1065
|
rank=Rank.SPECIES();
|
|
1066
|
}
|
|
1067
|
else if (r.equalsIgnoreCase("Subspecies")) {
|
|
1068
|
rank=Rank.SUBSPECIES();
|
|
1069
|
}
|
|
1070
|
else if (r.equalsIgnoreCase("Variety") || r.equalsIgnoreCase("varietyEpithet")) {
|
|
1071
|
rank=Rank.VARIETY();
|
|
1072
|
}
|
|
1073
|
else if (r.equalsIgnoreCase("Subvariety")) {
|
|
1074
|
rank=Rank.SUBVARIETY();
|
|
1075
|
}
|
|
1076
|
else if (r.equalsIgnoreCase("Form")) {
|
|
1077
|
rank=Rank.FORM();
|
|
1078
|
}
|
|
1079
|
else if (r.equalsIgnoreCase("Subform")) {
|
|
1080
|
rank=Rank.SUBFORM();
|
|
1081
|
}else if (r.equalsIgnoreCase("higher")) {
|
|
1082
|
// rank=Rank.SUPRAGENERICTAXON();
|
|
1083
|
logger.warn("handling of 'higher' rank still unclear");
|
|
1084
|
}
|
|
1085
|
|
|
1086
|
return rank;
|
|
1087
|
}
|
|
1088
|
|
|
1089
|
|
|
1090
|
/**
|
|
1091
|
* @param ato: atomised taxon name data
|
|
1092
|
* @return rank present in the xmldata fields
|
|
1093
|
*/
|
|
1094
|
protected Rank getRank(Map<String, String> ato) {
|
|
1095
|
Rank rank=Rank.UNKNOWN_RANK();
|
|
1096
|
|
|
1097
|
if (ato == null) {
|
|
1098
|
return rank;
|
|
1099
|
}
|
|
1100
|
if (ato.containsKey("dwc:family")){
|
|
1101
|
rank=Rank.FAMILY();
|
|
1102
|
}
|
|
1103
|
if (ato.containsKey("dwc:tribe") || ato.containsKey("dwcranks:tribe")){
|
|
1104
|
rank=Rank.TRIBE();
|
|
1105
|
}
|
|
1106
|
if (ato.containsKey("dwc:genus")) {
|
|
1107
|
rank= Rank.GENUS();
|
|
1108
|
}
|
|
1109
|
if (ato.containsKey("dwc:subgenus")) {
|
|
1110
|
rank= Rank.SUBGENUS();
|
|
1111
|
}
|
|
1112
|
if (ato.containsKey("dwc:specificepithet") || ato.containsKey("dwc:species")) {
|
|
1113
|
rank= Rank.SPECIES();
|
|
1114
|
}
|
|
1115
|
if (ato.containsKey("dwc:infraspecificepithet")) {
|
|
1116
|
rank= Rank.INFRASPECIES();
|
|
1117
|
}
|
|
1118
|
if (ato.containsKey("dwcranks:varietyepithet")) {
|
|
1119
|
rank=Rank.VARIETY();
|
|
1120
|
}
|
|
1121
|
//popUp(rank.getTitleCache());
|
|
1122
|
return rank;
|
|
1123
|
}
|
|
1124
|
|
|
1125
|
/**
|
|
1126
|
* Format a XML node for a clean (screen) output with tags
|
|
1127
|
* @param Node : the node to format
|
|
1128
|
* @return String : the XML section formated for a screen output
|
|
1129
|
* */
|
|
1130
|
|
|
1131
|
protected String formatNode(Node node) throws TransformerFactoryConfigurationError, TransformerException{
|
|
1132
|
Transformer transformer = TransformerFactory.newInstance().newTransformer();
|
|
1133
|
transformer.setOutputProperty(OutputKeys.INDENT, "yes");
|
|
1134
|
//initialize StreamResult with File object to save to file
|
|
1135
|
StreamResult result = new StreamResult(new StringWriter());
|
|
1136
|
DOMSource source = new DOMSource(node);
|
|
1137
|
transformer.transform(source, result);
|
|
1138
|
String xmlString = result.getWriter().toString();
|
|
1139
|
return xmlString;
|
|
1140
|
}
|
|
1141
|
|
|
1142
|
protected boolean containsDistinctLetters(String word){
|
|
1143
|
Set<Character> dl = new HashSet<>();
|
|
1144
|
for (char a: word.toCharArray()) {
|
|
1145
|
dl.add(a);
|
|
1146
|
}
|
|
1147
|
if(dl.size()>1 && word.indexOf("no description text")==-1) {
|
|
1148
|
return true;
|
|
1149
|
} else {
|
|
1150
|
return false;
|
|
1151
|
}
|
|
1152
|
}
|
|
1153
|
|
|
1154
|
/**
|
|
1155
|
* Tries to match the status string against any new name status
|
|
1156
|
* and returns the status if it matches. Returns <code>null</code> otherwise.
|
|
1157
|
* @param status
|
|
1158
|
* @return
|
|
1159
|
*/
|
|
1160
|
protected String newNameStatus(String status){
|
|
1161
|
String pattern = "(" + "((sp|spec|gen|comb|)\\.\\s*nov.)" +
|
|
1162
|
"|(new\\s*(species|combination))" +
|
|
1163
|
"|(n\\.\\s*sp\\.)" +
|
|
1164
|
"|(sp\\.\\s*n\\.)" +
|
|
1165
|
")";
|
|
1166
|
if (status.trim().matches(pattern)){
|
|
1167
|
//FIXME
|
|
1168
|
return null;
|
|
1169
|
// return status;
|
|
1170
|
}else{
|
|
1171
|
return null;
|
|
1172
|
}
|
|
1173
|
}
|
|
1174
|
|
|
1175
|
/** Creates an cdm-NomenclaturalCode by the tcs NomenclaturalCode
|
|
1176
|
*/
|
|
1177
|
protected NomenclaturalStatusType nomStatusString2NomStatus (String nomStatus) throws UnknownCdmTypeException{
|
|
1178
|
|
|
1179
|
if (nomStatus == null){ return null;
|
|
1180
|
}else if ("Valid".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.VALID();
|
|
1181
|
|
|
1182
|
}else if ("Alternative".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ALTERNATIVE();
|
|
1183
|
}else if ("nom. altern.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ALTERNATIVE();
|
|
1184
|
|
|
1185
|
}else if ("Ambiguous".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.AMBIGUOUS();
|
|
1186
|
|
|
1187
|
}else if ("Doubtful".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.DOUBTFUL();
|
|
1188
|
|
|
1189
|
}else if ("Confusum".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.CONFUSUM();
|
|
1190
|
|
|
1191
|
}else if ("Illegitimate".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ILLEGITIMATE();
|
|
1192
|
}else if ("nom. illeg.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ILLEGITIMATE();
|
|
1193
|
|
|
1194
|
}else if ("Superfluous".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.SUPERFLUOUS();
|
|
1195
|
}else if ("nom. superfl.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.SUPERFLUOUS();
|
|
1196
|
|
|
1197
|
}else if ("Rejected".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.REJECTED();
|
|
1198
|
}else if ("nom. rej.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.REJECTED();
|
|
1199
|
|
|
1200
|
}else if ("Utique Rejected".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.UTIQUE_REJECTED();
|
|
1201
|
|
|
1202
|
}else if ("Conserved Prop".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.CONSERVED_PROP();
|
|
1203
|
|
|
1204
|
}else if ("Orthography Conserved Prop".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ORTHOGRAPHY_CONSERVED_PROP();
|
|
1205
|
|
|
1206
|
}else if ("Legitimate".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.LEGITIMATE();
|
|
1207
|
|
|
1208
|
}else if ("Novum".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.NOVUM();
|
|
1209
|
}else if ("nom. nov.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.NOVUM();
|
|
1210
|
|
|
1211
|
}else if ("Utique Rejected Prop".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.UTIQUE_REJECTED_PROP();
|
|
1212
|
|
|
1213
|
}else if ("Orthography Conserved".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ORTHOGRAPHY_CONSERVED();
|
|
1214
|
|
|
1215
|
}else if ("Rejected Prop".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.REJECTED_PROP();
|
|
1216
|
|
|
1217
|
}else if ("Conserved".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.CONSERVED();
|
|
1218
|
}else if ("nom. cons.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.CONSERVED();
|
|
1219
|
|
|
1220
|
}else if ("Sanctioned".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.SANCTIONED();
|
|
1221
|
|
|
1222
|
}else if ("Invalid".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.INVALID();
|
|
1223
|
}else if ("nom. inval.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.INVALID();
|
|
1224
|
|
|
1225
|
}else if ("Nudum".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.NUDUM();
|
|
1226
|
}else if ("nom. nud.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.NUDUM();
|
|
1227
|
|
|
1228
|
}else if ("Combination Invalid".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.COMBINATION_INVALID();
|
|
1229
|
|
|
1230
|
}else if ("Provisional".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.PROVISIONAL();
|
|
1231
|
}else if ("nom. provis.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.PROVISIONAL();
|
|
1232
|
}
|
|
1233
|
else {
|
|
1234
|
throw new UnknownCdmTypeException("Unknown Nomenclatural status type " + nomStatus);
|
|
1235
|
}
|
|
1236
|
}
|
|
1237
|
|
|
1238
|
//TypeDesignation
|
|
1239
|
protected SpecimenTypeDesignationStatus typeStatusId2TypeStatus (int typeStatusId) throws UnknownCdmTypeException{
|
|
1240
|
switch (typeStatusId){
|
|
1241
|
case 0: return null;
|
|
1242
|
case 1: return SpecimenTypeDesignationStatus.HOLOTYPE();
|
|
1243
|
case 2: return SpecimenTypeDesignationStatus.LECTOTYPE();
|
|
1244
|
case 3: return SpecimenTypeDesignationStatus.NEOTYPE();
|
|
1245
|
case 4: return SpecimenTypeDesignationStatus.EPITYPE();
|
|
1246
|
case 5: return SpecimenTypeDesignationStatus.ISOLECTOTYPE();
|
|
1247
|
case 6: return SpecimenTypeDesignationStatus.ISONEOTYPE();
|
|
1248
|
case 7: return SpecimenTypeDesignationStatus.ISOTYPE();
|
|
1249
|
case 8: return SpecimenTypeDesignationStatus.PARANEOTYPE();
|
|
1250
|
case 9: return SpecimenTypeDesignationStatus.PARATYPE();
|
|
1251
|
case 10: return SpecimenTypeDesignationStatus.SECOND_STEP_LECTOTYPE();
|
|
1252
|
case 11: return SpecimenTypeDesignationStatus.SECOND_STEP_NEOTYPE();
|
|
1253
|
case 12: return SpecimenTypeDesignationStatus.SYNTYPE();
|
|
1254
|
case 21: return SpecimenTypeDesignationStatus.ICONOTYPE();
|
|
1255
|
case 22: return SpecimenTypeDesignationStatus.PHOTOTYPE();
|
|
1256
|
default: {
|
|
1257
|
throw new UnknownCdmTypeException("Unknown TypeDesignationStatus (id=" + Integer.valueOf(typeStatusId).toString() + ")");
|
|
1258
|
}
|
|
1259
|
}
|
|
1260
|
}
|
|
1261
|
}
|