cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/out/DwcaResourceRelationExport.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.Map;
  18 import java.util.Set;
  19
  20 import org.apache.log4j.Logger;
  21 import org.springframework.stereotype.Component;
  22 import org.springframework.transaction.TransactionStatus;
  23
  24 import eu.etaxonomy.cdm.model.common.CdmBase;
  25 import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
  26 import eu.etaxonomy.cdm.model.common.Language;
  27 import eu.etaxonomy.cdm.model.common.LanguageString;
  28 import eu.etaxonomy.cdm.model.common.RelationshipBase;
  29 import eu.etaxonomy.cdm.model.common.RelationshipTermBase;
  30 import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
  31 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  32 import eu.etaxonomy.cdm.model.description.TaxonInteraction;
  33 import eu.etaxonomy.cdm.model.name.INonViralName;
  34 import eu.etaxonomy.cdm.model.name.NameRelationship;
  35 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  36 import eu.etaxonomy.cdm.model.taxon.Taxon;
  37 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  38 import eu.etaxonomy.cdm.model.taxon.TaxonNode;
  39 import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
  40 import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
  41
  42 /**
  43  * Mapps taxon concept relationships, taxon name relationships and taxon interactions
  44  * @author a.mueller
  45  * @created 20.04.2011
  46  */
  47 @Component
  48 public class DwcaResourceRelationExport extends DwcaExportBase {
  49         private static final Logger logger = Logger.getLogger(DwcaResourceRelationExport.class);
  50
  51         private static final String ROW_TYPE = "http://rs.tdwg.org/dwc/terms/ResourceRelationship";
  52         private static final String fileName = "resourceRelationship.txt";
  53
  54         /**
  55          * Constructor
  56          */
  57         public DwcaResourceRelationExport() {
  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 void 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
  80                         DwcaMetaDataRecord metaRecord = new DwcaMetaDataRecord(! IS_CORE, fileName, ROW_TYPE);
  81                         state.addMetaRecord(metaRecord);
  82
  83                         List<TaxonNode> allNodes =  getAllNodes(null);
  84
  85                         for (TaxonNode node : allNodes){
  86                                 Taxon taxon = CdmBase.deproxy(node.getTaxon(), Taxon.class);
  87
  88                                 //taxon interactions
  89                                 Set<TaxonDescription> descriptions = taxon.getDescriptions();
  90                                 for (TaxonDescription description : descriptions){
  91                                         for (DescriptionElementBase el : description.getElements()){
  92                                                 if (el.isInstanceOf(TaxonInteraction.class)){
  93                                                         DwcaResourceRelationRecord record = new DwcaResourceRelationRecord(metaRecord, config);
  94                                                         TaxonInteraction taxonInteraction = CdmBase.deproxy(el,TaxonInteraction.class);
  95                                                         if (! this.recordExistsUuid(taxonInteraction)){
  96                                                                 handleInteraction(record, taxon, taxonInteraction);
  97                                                                 record.write(writer);
  98                                                                 this.addExistingRecordUuid(taxonInteraction);
  99                                                         }
 100                                                 }
 101                                         }
 102                                 }
 103
 104                                 //concept relationships
 105                                 for (TaxonRelationship rel : taxon.getTaxonRelations()){
 106                                         DwcaResourceRelationRecord record = new DwcaResourceRelationRecord(metaRecord, config);
 107                                         IdentifiableEntity<?> subject = rel.getFromTaxon();
 108                                         IdentifiableEntity<?> object = rel.getToTaxon();
 109
 110                                         if (rel.getType().equals(TaxonRelationshipType.MISAPPLIED_NAME_FOR()) ){
 111                                                 //misapplied names are handled in core (tax)
 112                                                 continue;
 113                                         }
 114                                         if (! this.recordExistsUuid(rel)){
 115                                                 handleRelationship(record, subject, object, rel, false);
 116                                                 record.write(writer);
 117                                                 this.addExistingRecordUuid(rel);
 118                                         }
 119
 120                                 }
 121
 122                                 //Name relationship
 123                                 //TODO
 124                                 INonViralName name = taxon.getName();
 125                                 if (name == null){
 126                                         String message = "There is a taxon node without taxon: " + node.getId();
 127                                         logger.warn(message);
 128                                         continue;
 129                                 }
 130                                 Set<NameRelationship> rels = name.getNameRelations();
 131                                 for (NameRelationship rel : rels){
 132                                         DwcaResourceRelationRecord record = new DwcaResourceRelationRecord(metaRecord, config);
 133                                         IdentifiableEntity<?> subject = CdmBase.deproxy(rel.getFromName(), TaxonNameBase.class);
 134                                         IdentifiableEntity<?> object = CdmBase.deproxy(rel.getToName(), TaxonNameBase.class);
 135                                         boolean isInverse = false;
 136                                         if(subject == name){
 137                                                 subject = taxon;
 138                                         }else if(object == name){
 139                                                 object= subject;
 140                                                 subject = taxon;
 141                                                 isInverse = true;
 142                                         }else{
 143                                                 String message = "Both, subject and object, are not part of the relationship for " + name.getTitleCache();
 144                                                 logger.warn(message);
 145                                         }
 146
 147                                         if (! this.recordExistsUuid(rel)){
 148                                                 //????
 149                                                 handleRelationship(record, subject, object, rel, isInverse);
 150                                                 record.write(writer);
 151                                                 this.addExistingRecordUuid(rel);
 152                                         }
 153
 154                                 }
 155
 156
 157                                 writer.flush();
 158
 159                         }
 160                 } catch (FileNotFoundException e) {
 161                         e.printStackTrace();
 162                 } catch (UnsupportedEncodingException e) {
 163                         e.printStackTrace();
 164                 } catch (ClassCastException e) {
 165                         e.printStackTrace();
 166                 } catch (IOException e) {
 167                         e.printStackTrace();
 168                 } finally{
 169                         closeWriter(writer, state);
 170                 }
 171                 commitTransaction(txStatus);
 172                 return;
 173         }
 174
 175         private void handleRelationship(DwcaResourceRelationRecord record, IdentifiableEntity<?> subject, IdentifiableEntity<?> object,
 176                         RelationshipBase<?,?,?> rel, boolean isInverse) {
 177                 RelationshipTermBase<?> type = rel.getType();
 178
 179                 record.setId(subject.getId());
 180                 record.setUuid(subject.getUuid());
 181
 182
 183                 record.setResourceRelationshipId(rel.getId());
 184                 record.setResourceRelationshipId(rel.getUuid());
 185                 //TODO id / uuid / names ??
 186                 if (object.isInstanceOf(TaxonBase.class)){
 187                         record.setRelatedResourceId(object.getUuid());
 188                 }
 189                 //TODO transform to controlled voc
 190                 String relTypeLabel;
 191                 if (isInverse){
 192                         relTypeLabel = type.getInverseLabel();
 193                 }else{
 194                         relTypeLabel = type.getLabel();
 195                 }
 196                 record.setRelationshipOfResource(relTypeLabel);
 197                 record.setRelationshipAccordingTo(rel.getCitation()== null? null : rel.getCitation().getTitleCache());
 198                 //TODO missing
 199                 record.setRelatioshipEstablishedDate(null);
 200                 record.setRelationshipRemarks(rel.getAnnotations());
 201                 if (object.isInstanceOf(TaxonNameBase.class)){
 202                         record.setScientificName(object.getTitleCache());
 203                 }
 204
 205
 206         }
 207
 208         private void handleInteraction(DwcaResourceRelationRecord record, IdentifiableEntity<?> subject, TaxonInteraction interaction) {
 209                 Taxon object = interaction.getTaxon2();
 210                 Map<Language, LanguageString> description = interaction.getDescription();
 211
 212                 record.setId(subject.getId());
 213                 record.setUuid(subject.getUuid());
 214
 215                 record.setRelatedResourceId(object.getUuid());
 216                 //TODO transform to controlled voc
 217                 if (description != null && description.get(Language.DEFAULT()) != null){
 218                         record.setRelationshipOfResource(description.get(Language.DEFAULT()).getText());
 219                 }else{
 220                         record.setRelationshipOfResource(interaction.getFeature().getLabel());
 221                 }
 222                 //TODO uuid
 223                 record.setResourceRelationshipId(interaction.getId());
 224                 record.setResourceRelationshipId(interaction.getUuid());
 225
 226                 //FIXME multiple sources
 227                 record.setRelationshipAccordingTo(null);
 228                 //TODO missing
 229                 record.setRelatioshipEstablishedDate(null);
 230                 record.setRelationshipRemarks(interaction.getAnnotations());
 231                 //TODO does this need to be filled?
 232                 record.setScientificName(null);
 233
 234         }
 235
 236
 237         @Override
 238         protected boolean doCheck(DwcaTaxExportState state) {
 239                 boolean result = true;
 240                 logger.warn("No check implemented for " + this.ioName);
 241                 return result;
 242         }
 243
 244
 245         @Override
 246         protected boolean isIgnore(DwcaTaxExportState state) {
 247                 return ! state.getConfig().isDoResourceRelation();
 248         }
 249
 250 }