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/**
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* Copyright (C) 2007 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.io.dwca.out;
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import java.io.FileNotFoundException;
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import java.io.IOException;
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import java.io.PrintWriter;
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import java.io.UnsupportedEncodingException;
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import java.util.Set;
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import org.apache.log4j.Logger;
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import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;
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import eu.etaxonomy.cdm.api.facade.DerivedUnitFacadeNotSupportedException;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
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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.name.INonViralName;
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import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.name.TextualTypeDesignation;
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import eu.etaxonomy.cdm.model.name.TypeDesignationBase;
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import eu.etaxonomy.cdm.model.name.TypeDesignationStatusBase;
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import eu.etaxonomy.cdm.model.occurrence.Collection;
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import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
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import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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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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/**
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* @author a.mueller
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* @since 20.04.2011
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*/
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public class DwcaTypesExport extends DwcaDataExportBase {
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private static final long serialVersionUID = 8879154738843628476L;
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private static final Logger logger = Logger.getLogger(DwcaTypesExport.class);
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private static final String ROW_TYPE = "http://rs.gbif.org/terms/1.0/TypesAndSpecimen";
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protected static final String fileName = "typesAndSpecimen.txt";
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private DwcaMetaDataRecord metaRecord;
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/**
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* Constructor
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*/
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public DwcaTypesExport(DwcaTaxExportState state) {
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super();
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this.ioName = this.getClass().getSimpleName();
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metaRecord = new DwcaMetaDataRecord(! IS_CORE, fileName, ROW_TYPE);
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state.addMetaRecord(metaRecord);
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file = DwcaTaxExportFile.TYPES;
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}
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@Override
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protected void doInvoke(DwcaTaxExportState state){}
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/**
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* @param state
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* @param node
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* @throws IOException
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* @throws FileNotFoundException
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* @throws UnsupportedEncodingException
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*/
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@Override
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protected void handleTaxonNode(DwcaTaxExportState state, TaxonNode node)
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throws IOException, FileNotFoundException, UnsupportedEncodingException {
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try {
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DwcaTaxExportConfigurator config = state.getConfig();
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Taxon taxon = CdmBase.deproxy(node.getTaxon());
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//TODO use API methods to retrieve all related specimen
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//individual associations
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Set<TaxonDescription> descriptions = taxon.getDescriptions();
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for (TaxonDescription description : descriptions){
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for (DescriptionElementBase el : description.getElements()){
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if (el.isInstanceOf(IndividualsAssociation.class)){
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DwcaTypesRecord record = new DwcaTypesRecord(metaRecord, config);
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IndividualsAssociation individualAssociation = CdmBase.deproxy(el, IndividualsAssociation.class);
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if (! state.recordExistsUuid(individualAssociation)
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&& handleSpecimen(state, record, individualAssociation, null, taxon, config)){
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PrintWriter writer = createPrintWriter(state, file);
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record.write(state, writer);
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state.addExistingRecordUuid(individualAssociation);
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}
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}
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}
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}
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//type specimen
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INonViralName nvn = taxon.getName();
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handleTypeName(state, file, taxon, nvn, metaRecord);
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for (Synonym synonym : taxon.getSynonyms()){
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handleTypeName(state, file, synonym, nvn, metaRecord);
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}
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//FIXME
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//Determinations
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} catch (Exception e) {
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String message = "Unexpected exception: " + e.getMessage();
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state.getResult().addException(e, message);
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}finally{
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flushWriter(state, file);
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}
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}
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/**
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* @param state
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* @param writer
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* @param taxon
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* @param nvn
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* @param config
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* @return
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* @throws IOException
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* @throws UnsupportedEncodingException
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* @throws FileNotFoundException
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*/
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private Set<TypeDesignationBase<?>> handleTypeName(DwcaTaxExportState state,
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DwcaTaxExportFile file, TaxonBase<?> taxonBase,
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INonViralName nvn, DwcaMetaDataRecord metaRecord)
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throws FileNotFoundException, UnsupportedEncodingException, IOException {
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DwcaTaxExportConfigurator config = state.getConfig();
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Set<TypeDesignationBase<?>> designations = nvn.getTypeDesignations();
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for (TypeDesignationBase<?> designation:designations){
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DwcaTypesRecord record = new DwcaTypesRecord(metaRecord, config);
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if (! state.recordExistsUuid(designation)
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&& handleType(state, record, designation, taxonBase, config)){
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PrintWriter writer = createPrintWriter(state, file);
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record.write(state, writer);
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state.addExistingRecordUuid(designation);
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}
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}
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return designations;
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}
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private boolean handleType(DwcaTaxExportState state, DwcaTypesRecord record,
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TypeDesignationBase<?> designation, TaxonBase<?> taxonBase,
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DwcaTaxExportConfigurator config) {
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designation = CdmBase.deproxy(designation);
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if (designation instanceof TextualTypeDesignation){
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return handleTextualType(state, record, (TextualTypeDesignation)designation, taxonBase, config);
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}else if (designation instanceof TypeDesignationBase){
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return handleSpecimen(state, record, null, designation, taxonBase, config);
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}else{
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throw new RuntimeException ("TypeDesignation type not handled");
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}
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}
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private boolean handleTextualType(DwcaTaxExportState state, DwcaTypesRecord record,
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TextualTypeDesignation designation, TaxonBase<?> taxonBase,
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DwcaTaxExportConfigurator config) {
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if (designation == null){
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return false;
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}
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record.setId(taxonBase.getId());
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record.setUuid(taxonBase.getUuid());
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record.setBibliographicCitation(designation.getPreferredText(Language.DEFAULT()));
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//TODO ???
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// record.setSource(getSources3(facade.innerDerivedUnit(), config));
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// record.setDescriptionSource(source2);
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//TODO missing
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record.setVerbatimLabel(designation.getPreferredText(Language.DEFAULT()));
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return true;
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}
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private boolean handleSpecimen(DwcaTaxExportState state, DwcaTypesRecord record, IndividualsAssociation individualsAssociation,
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TypeDesignationBase<?> designation, TaxonBase<?> taxonBase, DwcaTaxExportConfigurator config) {
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TypeDesignationStatusBase<?> status = null;
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DerivedUnitFacade facade = null;
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if (individualsAssociation != null){
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facade = getFacadeFromAssociation(state, individualsAssociation);
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}else if (designation != null){
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facade = getFacadeFromDesignation(state, designation);
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status = designation.getTypeStatus();
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}
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if (facade == null){
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return false;
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}
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record.setId(taxonBase.getId());
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record.setUuid(taxonBase.getUuid());
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record.setBibliographicCitation(facade.getTitleCache());
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record.setTypeStatus(status);
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record.setTypeDesignatedBy( (designation == null || designation.getCitation()==null)? null: designation.getCitation().getTitleCache());
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TaxonName scientificName = getScientificName(facade);
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if (scientificName != null){
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record.setScientificName(scientificName.getTitleCache());
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record.setTaxonRank(scientificName.getRank());
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}
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record.setOccurrenceId(facade.innerDerivedUnit());
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Collection collection = facade.getCollection();
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if (collection != null){
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record.setCollectionCode(collection.getCode());
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if (collection.getInstitute() != null){
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record.setInstitutionCode(collection.getInstitute().getCode());
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}
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}
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record.setCatalogNumber(facade.getCatalogNumber());
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record.setLocality(facade.getLocalityText());
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record.setSex(facade.getSex());
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record.setRecordedBy(facade.getCollector());
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//TODO ???
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String source2 = "";
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if (individualsAssociation!=null) {
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source2 = getSources2(individualsAssociation.getSources(), config);
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}
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record.setSource(getSources3(facade.innerDerivedUnit(), config));
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record.setDescriptionSource(source2);
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record.setEventDate(facade.getGatheringPeriod());
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//TODO missing
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record.setVerbatimLabel(null);
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if (facade.getExactLocation() != null){
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if (facade.getExactLocation().getLongitude() != null){
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// record.setVerbatimLongitude(facade.getExactLocation().getLongitudeSexagesimal().toString());
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record.setVerbatimLongitude(facade.getExactLocation().getLongitude().toString());
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}
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if (facade.getExactLocation().getLatitude() != null){
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// record.setVerbatimLatitude(facade.getExactLocation().getLatitudeSexagesimal().toString());
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record.setVerbatimLatitude(facade.getExactLocation().getLatitude().toString());
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}
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if(facade.getExactLocation().getErrorRadius() != null) {
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record.setCoordinatesPrecisionOrError(facade.getExactLocation().getErrorRadius().toString());
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}
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if(facade.getExactLocation().getReferenceSystem() != null) {
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record.setCoordinatesSystem(facade.getExactLocation().getReferenceSystem().toString());
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}
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}
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return true;
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}
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private TaxonName getScientificName(DerivedUnitFacade facade) {
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Set<DeterminationEvent> detEvents = facade.getDeterminations();
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for (DeterminationEvent detEvent : detEvents){
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if (detEvent.getPreferredFlag()== true || detEvents.size()==1){
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return detEvent.getTaxon() == null ? null : detEvent.getTaxon().getName();
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}
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}
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return null;
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}
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private DerivedUnitFacade getFacadeFromDesignation(DwcaTaxExportState state, TypeDesignationBase<?> designation) {
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if (designation.isInstanceOf(SpecimenTypeDesignation.class)){
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SpecimenTypeDesignation specDesig = CdmBase.deproxy(designation, SpecimenTypeDesignation.class);
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try {
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DerivedUnit derivedUnit = specDesig.getTypeSpecimen();
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if (derivedUnit == null){
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return null;
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}else{
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DerivedUnitFacade facade = DerivedUnitFacade.NewInstance(derivedUnit);
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return facade;
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}
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} catch (DerivedUnitFacadeNotSupportedException e) {
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String message = "DerivedUnit is too complex to be handled by facade based darwin core archive export";
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state.getResult().addError(message, this, "getFacadeFromAssociation()");
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//TODO handle empty records
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return null;
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}
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}else{
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return null;
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}
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}
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private DerivedUnitFacade getFacadeFromAssociation(DwcaTaxExportState state, IndividualsAssociation individualsAssociation) {
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SpecimenOrObservationBase<?> specimen = individualsAssociation.getAssociatedSpecimenOrObservation();
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DerivedUnitFacade facade;
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if (specimen == null){
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String message = "Individuals association " + individualsAssociation.getId() + " has no associated specimen";
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state.getResult().addWarning(message);
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return null;
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}else if (! specimen.isInstanceOf(DerivedUnit.class)){
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String message = "Non DerivedUnit specimen can not yet be handled by this export";
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state.getResult().addWarning(message);
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//TODO handle empty records
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return null;
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}else{
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DerivedUnit derivedUnit = CdmBase.deproxy(specimen, DerivedUnit.class);
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try {
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facade = DerivedUnitFacade.NewInstance(derivedUnit);
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} catch (DerivedUnitFacadeNotSupportedException e) {
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String message = "DerivedUnit is too complex to be handled by facade based darwin core archive export";
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state.getResult().addError(message, e);
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//TODO handle empty records
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return null;
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}
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}
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return facade;
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}
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320
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321
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@Override
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322
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protected boolean doCheck(DwcaTaxExportState state) {
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boolean result = true;
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logger.warn("No check implemented for " + this.ioName);
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return result;
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326
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}
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327
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328
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@Override
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329
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public boolean isIgnore(DwcaTaxExportState state) {
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330
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return ! state.getConfig().isDoTypesAndSpecimen();
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}
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332
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}
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