cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/out/DwcaTypesExport.java

   1 /**
   2 * Copyright (C) 2007 EDIT
   3 * European Distributed Institute of Taxonomy
   4 * http://www.e-taxonomy.eu
   5 *
   6 * The contents of this file are subject to the Mozilla Public License Version 1.1
   7 * See LICENSE.TXT at the top of this package for the full license terms.
   8 */
   9
  10 package eu.etaxonomy.cdm.io.dwca.out;
  11
  12 import java.io.FileNotFoundException;
  13 import java.io.IOException;
  14 import java.io.PrintWriter;
  15 import java.io.UnsupportedEncodingException;
  16 import java.util.List;
  17 import java.util.Set;
  18
  19 import org.apache.log4j.Logger;
  20 import org.springframework.stereotype.Component;
  21 import org.springframework.transaction.TransactionStatus;
  22
  23 import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;
  24 import eu.etaxonomy.cdm.api.facade.DerivedUnitFacadeNotSupportedException;
  25 import eu.etaxonomy.cdm.model.common.CdmBase;
  26 import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
  27 import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
  28 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  29 import eu.etaxonomy.cdm.model.name.NonViralName;
  30 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
  31 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  32 import eu.etaxonomy.cdm.model.name.TypeDesignationBase;
  33 import eu.etaxonomy.cdm.model.name.TypeDesignationStatusBase;
  34 import eu.etaxonomy.cdm.model.occurrence.Collection;
  35 import eu.etaxonomy.cdm.model.occurrence.DerivedUnitBase;
  36 import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;
  37 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
  38 import eu.etaxonomy.cdm.model.taxon.Synonym;
  39 import eu.etaxonomy.cdm.model.taxon.Taxon;
  40 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  41 import eu.etaxonomy.cdm.model.taxon.TaxonNode;
  42
  43 /**
  44  * @author a.mueller
  45  * @created 20.04.2011
  46  */
  47 @Component
  48 public class DwcaTypesExport extends DwcaExportBase {
  49         private static final Logger logger = Logger.getLogger(DwcaTypesExport.class);
  50
  51         private static final String ROW_TYPE = "http://rs.gbif.org/terms/1.0/TypesAndSpecimen";
  52         private static final String fileName = "typesAndSpecimen.txt";
  53
  54         /**
  55          * Constructor
  56          */
  57         public DwcaTypesExport() {
  58                 super();
  59                 this.ioName = this.getClass().getSimpleName();
  60         }
  61
  62         /** Retrieves data from a CDM DB and serializes them CDM to XML.
  63          * Starts with root taxa and traverses the classification to retrieve children taxa, synonyms and relationships.
  64          * Taxa that are not part of the classification are not found.
  65          *
  66          * @param exImpConfig
  67          * @param dbname
  68          * @param filename
  69          */
  70         @Override
  71         protected boolean doInvoke(DwcaTaxExportState state){
  72                 DwcaTaxExportConfigurator config = state.getConfig();
  73                 TransactionStatus txStatus = startTransaction(true);
  74
  75                 PrintWriter writer = null;
  76                 try {
  77
  78                         writer = createPrintWriter(fileName, state);
  79                         DwcaMetaDataRecord metaRecord = new DwcaMetaDataRecord(! IS_CORE, fileName, ROW_TYPE);
  80                         state.addMetaRecord(metaRecord);
  81
  82
  83                         List<TaxonNode> allNodes =  getAllNodes(null);
  84
  85                         for (TaxonNode node : allNodes){
  86                                 Taxon taxon = CdmBase.deproxy(node.getTaxon(), Taxon.class);
  87
  88                                 //TODO use API methods to retrieve all related specimen
  89
  90                                 //individual associations
  91                                 Set<TaxonDescription> descriptions = taxon.getDescriptions();
  92                                 for (TaxonDescription description : descriptions){
  93                                         for (DescriptionElementBase el : description.getElements()){
  94                                                 if (el.isInstanceOf(IndividualsAssociation.class)){
  95                                                         DwcaTypesRecord record = new DwcaTypesRecord(metaRecord, config);
  96                                                         IndividualsAssociation individualAssociation = CdmBase.deproxy(el,IndividualsAssociation.class);
  97                                                         if (! this.recordExistsUuid(individualAssociation) && handleSpecimen(record, individualAssociation, null, taxon, config)){
  98                                                                 record.write(writer);
  99                                                                 this.addExistingRecordUuid(individualAssociation);
 100                                                         }
 101                                                 }
 102                                         }
 103                                 }
 104
 105                                 //type specimen
 106                                 NonViralName<?> nvn = CdmBase.deproxy(taxon.getName(), NonViralName.class);
 107                                 handleTypeName(writer, taxon, nvn, metaRecord, config);
 108                                 for (Synonym synonym : taxon.getSynonyms()){
 109                                         handleTypeName(writer, synonym, nvn, metaRecord, config);
 110                                 }
 111
 112                                 //FIXME
 113                                 //Determinations
 114
 115
 116                                 writer.flush();
 117
 118                         }
 119                 } catch (FileNotFoundException e) {
 120                         e.printStackTrace();
 121                 } catch (UnsupportedEncodingException e) {
 122                         e.printStackTrace();
 123                 } catch (ClassCastException e) {
 124                         e.printStackTrace();
 125                 } catch (IOException e) {
 126                         e.printStackTrace();
 127                 } finally{
 128                         closeWriter(writer, state);
 129                 }
 130                 commitTransaction(txStatus);
 131                 return true;
 132         }
 133
 134         /**
 135          * @param writer
 136          * @param taxon
 137          * @param nvn
 138          * @param config
 139          * @return
 140          */
 141         private Set<TypeDesignationBase<?>> handleTypeName(PrintWriter writer, TaxonBase<?> taxonBase, NonViralName<?> nvn, DwcaMetaDataRecord metaRecord, DwcaTaxExportConfigurator config) {
 142                 Set<TypeDesignationBase<?>> designations = nvn.getTypeDesignations();
 143                 for (TypeDesignationBase<?> designation:designations){
 144                         DwcaTypesRecord record = new DwcaTypesRecord(metaRecord, config);
 145                         if (! this.recordExistsUuid(designation) && handleSpecimen(record, null, designation, taxonBase, config)){
 146                                 record.write(writer);
 147                                 addExistingRecordUuid(designation);
 148                         }
 149                 }
 150                 return designations;
 151         }
 152
 153
 154         private boolean handleSpecimen(DwcaTypesRecord record, IndividualsAssociation individualsAssociation, TypeDesignationBase<?> designation, TaxonBase<?> taxonBase, DwcaTaxExportConfigurator config) {
 155                 TypeDesignationStatusBase<?> status = null;
 156                 DerivedUnitFacade facade = null;
 157                 if (individualsAssociation != null){
 158                         facade = getFacadeFromAssociation(individualsAssociation);
 159                 }else if (designation != null){
 160                         facade = getFacadeFromDesignation(designation);
 161                         status = designation.getTypeStatus();
 162                 }
 163                 if (facade == null){
 164                         return false;
 165                 }
 166
 167                 record.setId(taxonBase.getId());
 168                 record.setUuid(taxonBase.getUuid());
 169                 record.setBibliographicCitation(facade.getTitleCache());
 170                 record.setTypeStatus(status);
 171                 record.setTypeDesignatedBy( (designation == null || designation.getCitation()==null)? null: designation.getCitation().getTitleCache());
 172
 173                 TaxonNameBase<?,?> scientificName = getScientificName(facade);
 174                 if (scientificName != null){
 175                         record.setScientificName(scientificName.getTitleCache());
 176                         record.setTaxonRank(scientificName.getRank());
 177                 }
 178
 179                 record.setOccurrenceId(facade.innerDerivedUnit());
 180                 Collection collection = facade.getCollection();
 181                 if (collection != null){
 182                         record.setCollectionCode(collection.getCode());
 183                         if (collection.getInstitute() != null){
 184                                 record.setInstitutionCode(collection.getInstitute().getCode());
 185                         }
 186                 }
 187                 record.setCatalogNumber(facade.getCatalogNumber());
 188                 record.setLocality(facade.getLocalityText());
 189                 record.setSex(facade.getSex());
 190                 record.setRecordedBy(facade.getCollector());
 191                 //TODO ???
 192                 record.setSource(getSources(facade.innerDerivedUnit(), config));
 193                 record.setEventDate(facade.getGatheringPeriod());
 194                 //TODO missing
 195                 record.setVerbatimLabel(null);
 196                 if (facade.getExactLocation() != null){
 197                         if (facade.getExactLocation().getLongitude() != null){
 198                                 record.setVerbatimLongitude(facade.getExactLocation().getLongitudeSexagesimal().toString());
 199                         }
 200                         if (facade.getExactLocation().getLatitude() != null){
 201                                 record.setVerbatimLatitude(facade.getExactLocation().getLatitudeSexagesimal().toString());
 202                         }
 203                 }
 204                 return true;
 205         }
 206
 207         private TaxonNameBase<?,?> getScientificName(DerivedUnitFacade facade) {
 208                 Set<DeterminationEvent> detEvents = facade.getDeterminations();
 209                 for (DeterminationEvent detEvent : detEvents){
 210                         if (detEvent.getPreferredFlag()== true){
 211                                 return detEvent.getTaxon().getName();
 212                         }
 213                 }
 214                 return null;
 215         }
 216
 217         private DerivedUnitFacade getFacadeFromDesignation(TypeDesignationBase<?> designation) {
 218                 if (designation.isInstanceOf(SpecimenTypeDesignation.class)){
 219                         SpecimenTypeDesignation specDesig = CdmBase.deproxy(designation, SpecimenTypeDesignation.class);
 220                         try {
 221                                 DerivedUnitBase<?> derivedUnit = specDesig.getTypeSpecimen();
 222                                 if (derivedUnit == null){
 223                                         return null;
 224                                 }else{
 225                                         DerivedUnitFacade facade = DerivedUnitFacade.NewInstance(derivedUnit);
 226                                         return facade;
 227                                 }
 228                         } catch (DerivedUnitFacadeNotSupportedException e) {
 229                                 String message = "DerivedUnit is too complex to be handled by facade based darwin core archive export";
 230                                 logger.warn(message);
 231                                 //TODO handle empty records
 232                                 return null;
 233                         }
 234                 }else{
 235                         return null;
 236                 }
 237         }
 238
 239         private DerivedUnitFacade getFacadeFromAssociation(IndividualsAssociation individualsAssociation) {
 240                 SpecimenOrObservationBase<?> specimen = individualsAssociation.getAssociatedSpecimenOrObservation();
 241                 DerivedUnitFacade facade;
 242                 if (! specimen.isInstanceOf(DerivedUnitBase.class)){
 243                         String message = "Non DerivedUnit specimen can not yet be handled by this export";
 244                         logger.warn(message);
 245                         //TODO handle empty records
 246                         return null;
 247                 }else{
 248                         DerivedUnitBase<?> derivedUnit = CdmBase.deproxy(specimen, DerivedUnitBase.class);
 249                         try {
 250                                 facade = DerivedUnitFacade.NewInstance(derivedUnit);
 251                         } catch (DerivedUnitFacadeNotSupportedException e) {
 252                                 String message = "DerivedUnit is too complex to be handled by facade based darwin core archive export";
 253                                 logger.warn(message);
 254                                 //TODO handle empty records
 255                                 return null;
 256                         }
 257
 258                 }
 259                 return facade;
 260         }
 261
 262         @Override
 263         protected boolean doCheck(DwcaTaxExportState state) {
 264                 boolean result = true;
 265                 logger.warn("No check implemented for " + this.ioName);
 266                 return result;
 267         }
 268
 269
 270         @Override
 271         protected boolean isIgnore(DwcaTaxExportState state) {
 272                 return ! state.getConfig().isDoTypesAndSpecimen();
 273         }
 274
 275 }