cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/taxonx2013/TaxonXAddSources.java

   1 // $Id$
   2 /**
   3  * Copyright (C) 2013 EDIT
   4  * European Distributed Institute of Taxonomy
   5  * http://www.e-taxonomy.eu
   6  *
   7  * The contents of this file are subject to the Mozilla Public License Version 1.1
   8  * See LICENSE.TXT at the top of this package for the full license terms.
   9  */
  10 package eu.etaxonomy.cdm.io.taxonx2013;
  11
  12 import java.util.Set;
  13
  14 import org.apache.log4j.Logger;
  15
  16 import eu.etaxonomy.cdm.model.common.CdmBase;
  17 import eu.etaxonomy.cdm.model.common.IdentifiableSource;
  18 import eu.etaxonomy.cdm.model.common.OriginalSourceType;
  19 import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
  20 import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
  21 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  22 import eu.etaxonomy.cdm.model.description.TextData;
  23 import eu.etaxonomy.cdm.model.name.NonViralName;
  24 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  25 import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
  26 import eu.etaxonomy.cdm.model.reference.Reference;
  27 import eu.etaxonomy.cdm.model.taxon.Synonym;
  28 import eu.etaxonomy.cdm.model.taxon.Taxon;
  29
  30 /**
  31  * @author pkelbert
  32  * @date 20 déc. 2013
  33  *
  34  */
  35 public class TaxonXAddSources {
  36
  37     private Reference sourceUrlRef;
  38     private TaxonXImport importer;
  39     private TaxonXImportState configState;
  40     @SuppressWarnings("unused")
  41         private static final Logger logger = Logger.getLogger(TaxonXAddSources.class);
  42
  43     /**
  44      * @param importer
  45      */
  46     public void setImporter(TaxonXImport importer) {
  47         this.importer=importer;
  48     }
  49
  50
  51     /**
  52      * @param configState the configState to set
  53      */
  54     public void setConfigState(TaxonXImportState configState) {
  55         this.configState = configState;
  56     }
  57
  58
  59     /**
  60      * @return the sourceUrlRef
  61      */
  62     public Reference getSourceUrlRef() {
  63         return sourceUrlRef;
  64     }
  65
  66     /**
  67      * @param sourceUrlRef the sourceUrlRef to set
  68      */
  69     public void setSourceUrlRef(Reference sourceUrlRef) {
  70         this.sourceUrlRef = sourceUrlRef;
  71     }
  72
  73
  74     protected IdentifiableSource getIdentifiableSource(Reference reference, Set<IdentifiableSource> sources, boolean original){
  75 //        logger.info("getIdentifiableSource");
  76         boolean sourceExists=false;
  77         IdentifiableSource source=null;
  78         for (IdentifiableSource src : sources){
  79             String micro = src.getCitationMicroReference();
  80             Reference r = src.getCitation();
  81             if (r.getTitleCache().equals(reference.getTitleCache())) {
  82                 sourceExists=true;
  83                 break;
  84             }
  85         }
  86         if(!sourceExists) {
  87             if(original) {
  88                 source = IdentifiableSource.NewInstance(OriginalSourceType.PrimaryTaxonomicSource,null,null,reference,null);
  89             } else {
  90                 source = IdentifiableSource.NewInstance(OriginalSourceType.Import,null,null,reference,null);
  91             }
  92         }
  93         return source;
  94     }
  95
  96     protected DescriptionElementSource getDescriptionElementSource(Reference reference, Set<DescriptionElementSource> sources, boolean original){
  97         //logger.info("getDescriptionElementSource");
  98         boolean sourceExists=false;
  99         DescriptionElementSource source=null;
 100         for (DescriptionElementSource src : sources){
 101             String micro = src.getCitationMicroReference();
 102             Reference r = src.getCitation();
 103             if (r.getTitleCache().equals(reference.getTitleCache())) {
 104                 sourceExists=true;
 105                 break;
 106             }
 107         }
 108         if(!sourceExists) {
 109             if(original) {
 110                 source = DescriptionElementSource.NewInstance(OriginalSourceType.PrimaryTaxonomicSource,null,null,reference,null);
 111             } else {
 112                 source = DescriptionElementSource.NewInstance(OriginalSourceType.Import,null,null,reference,null);
 113             }
 114         }
 115         return source;
 116
 117     }
 118
 119     /**
 120      * @param refMods
 121      * @param synonym
 122      */
 123     protected void addSource(Reference refMods, Synonym synonym) {
 124         //logger.info("addSource");
 125         sourceUrlRef=CdmBase.deproxy(sourceUrlRef, Reference.class);
 126         Reference sec = CdmBase.deproxy(configState.getConfig().getSecundum(), Reference.class);
 127         IdentifiableSource id = getIdentifiableSource(sourceUrlRef,synonym.getSources(), false);
 128         IdentifiableSource id2 = getIdentifiableSource(refMods,synonym.getSources(), true);
 129         IdentifiableSource id3 = getIdentifiableSource(sec,synonym.getSources(), false);
 130         if( id!=null) {
 131             synonym.addSource(id);
 132         }
 133         if( id2!=null) {
 134             synonym.addSource(id2);
 135         }
 136         if(!configState.getConfig().doKeepOriginalSecundum() && id3!=null) {
 137             synonym.addSource(id3);
 138         }
 139     }
 140
 141
 142     /**
 143      * @param refMods
 144      * @param indAssociation
 145      */
 146     protected IndividualsAssociation addSource(Reference refMods, IndividualsAssociation indAssociation) {
 147         //logger.info("addSource");
 148         sourceUrlRef=CdmBase.deproxy(sourceUrlRef, Reference.class);
 149         Reference sec = CdmBase.deproxy(configState.getConfig().getSecundum(), Reference.class);
 150         DescriptionElementSource id = getDescriptionElementSource(sourceUrlRef, indAssociation.getSources(), false);
 151         DescriptionElementSource id2 = getDescriptionElementSource(refMods, indAssociation.getSources(), true);
 152         DescriptionElementSource id3 = getDescriptionElementSource(sec, indAssociation.getSources(), false);
 153
 154         if(id!=null) {
 155             indAssociation.addSource(id);
 156         }
 157         if( id2!=null) {
 158             indAssociation.addSource(id2);
 159         }
 160         if(!configState.getConfig().doKeepOriginalSecundum() && id3!=null) {
 161             indAssociation.addSource(id3);
 162         }
 163         return indAssociation;
 164     }
 165
 166     /**
 167      * @param refMods
 168      * @param acceptedTaxon
 169      */
 170     protected void addSource(Reference refMods, Taxon acceptedTaxon) {
 171         //logger.info("addSource");
 172         sourceUrlRef=CdmBase.deproxy(sourceUrlRef, Reference.class);
 173         Reference sec = CdmBase.deproxy(configState.getConfig().getSecundum(), Reference.class);
 174         IdentifiableSource id = getIdentifiableSource(sourceUrlRef, acceptedTaxon.getSources(), false);
 175         IdentifiableSource id2 = getIdentifiableSource(refMods, acceptedTaxon.getSources(), true);
 176         IdentifiableSource id3 = getIdentifiableSource(sec, acceptedTaxon.getSources(), false);
 177         if( id!=null) {
 178             acceptedTaxon.addSource(id);
 179         }
 180         if( id2!=null) {
 181             acceptedTaxon.addSource(id2);
 182         }
 183         if(!configState.getConfig().doKeepOriginalSecundum() && id3!=null) {
 184             acceptedTaxon.addSource(id3);
 185         }
 186     }
 187
 188     /**
 189      * @param refMods
 190      * @param nameToBeFilled
 191      */
 192     protected void addSource(Reference refMods, NonViralName<?> nameToBeFilled) {
 193         //logger.info("addSource");
 194         sourceUrlRef=CdmBase.deproxy(sourceUrlRef, Reference.class);
 195         Reference sec = CdmBase.deproxy(configState.getConfig().getSecundum(), Reference.class);
 196         IdentifiableSource id = getIdentifiableSource(sourceUrlRef, nameToBeFilled.getSources(), false);
 197         IdentifiableSource id2 = getIdentifiableSource(refMods, nameToBeFilled.getSources(), true);
 198         IdentifiableSource id3 = getIdentifiableSource(sec, nameToBeFilled.getSources(), false);
 199
 200         if( id!=null) {
 201             nameToBeFilled.addSource(id);
 202         }
 203         if( id2!=null) {
 204             nameToBeFilled.addSource(id2);
 205         }
 206         if(!configState.getConfig().doKeepOriginalSecundum() && id3!=null) {
 207             nameToBeFilled.addSource(id3);
 208         }
 209
 210     }
 211
 212     /**
 213      * @param refMods
 214      * @param textData
 215      */
 216     protected void addSource(Reference refMods, TextData textData) {
 217         //logger.info("addSource");
 218         sourceUrlRef=CdmBase.deproxy(sourceUrlRef, Reference.class);
 219         Reference sec = CdmBase.deproxy(configState.getConfig().getSecundum(), Reference.class);
 220         DescriptionElementSource id = getDescriptionElementSource(sourceUrlRef, textData.getSources(), false);
 221         DescriptionElementSource id2 = getDescriptionElementSource(refMods, textData.getSources(), true);
 222         DescriptionElementSource id3 = getDescriptionElementSource(sec, textData.getSources(), false);
 223
 224         if( id!=null) {
 225             textData.addSource(id);
 226         }
 227         if( id2!=null) {
 228             textData.addSource(id2);
 229         }
 230         if(!configState.getConfig().doKeepOriginalSecundum() && id3!=null) {
 231             textData.addSource(id3);
 232         }
 233
 234     }
 235
 236     /**
 237      * @param refMods
 238      * @param taxonDescription
 239      * @param currentRef
 240      */
 241     protected void addAndSaveSource(Reference refMods, TaxonDescription taxonDescription, Reference currentRef) {
 242         //logger.info("addAndSaveSource");
 243         sourceUrlRef=CdmBase.deproxy(sourceUrlRef, Reference.class);
 244         Reference sec = CdmBase.deproxy(configState.getConfig().getSecundum(), Reference.class);
 245         IdentifiableSource id = getIdentifiableSource(sourceUrlRef, taxonDescription.getSources(), false);
 246         IdentifiableSource id2 = getIdentifiableSource(refMods, taxonDescription.getSources(), true);
 247         IdentifiableSource id3 = getIdentifiableSource(sec, taxonDescription.getSources(), false);
 248
 249         if( id!=null) {
 250             taxonDescription.addSource(id);
 251         }
 252         if( id2!=null) {
 253             taxonDescription.addSource(id2);
 254         }
 255         if(!configState.getConfig().doKeepOriginalSecundum() && id3!=null) {
 256             taxonDescription.addSource(id3);
 257         }
 258
 259         importer.getDescriptionService().saveOrUpdate(taxonDescription);
 260     }
 261
 262     /**
 263      * @param refMods
 264      * @param derivedUnitBase
 265      */
 266     protected void addAndSaveSource(Reference refMods, DerivedUnit derivedUnitBase) {
 267         //logger.info("addAndSaveSource");
 268         sourceUrlRef=CdmBase.deproxy(sourceUrlRef, Reference.class);
 269         Reference sec = CdmBase.deproxy(configState.getConfig().getSecundum(), Reference.class);
 270         IdentifiableSource id = getIdentifiableSource(sourceUrlRef, derivedUnitBase.getSources(), false);
 271         IdentifiableSource id2 = getIdentifiableSource(refMods, derivedUnitBase.getSources(), true);
 272         IdentifiableSource id3 = getIdentifiableSource(sec, derivedUnitBase.getSources(), false);
 273
 274         if( id!=null) {
 275             derivedUnitBase.addSource(id);
 276         }
 277         if( id2!=null) {
 278             derivedUnitBase.addSource(id2);
 279         }
 280         if(!configState.getConfig().doKeepOriginalSecundum() &&  id3!=null) {
 281             derivedUnitBase.addSource(id3);
 282         }
 283         importer.getOccurrenceService().saveOrUpdate(derivedUnitBase);
 284         derivedUnitBase= CdmBase.deproxy(derivedUnitBase, DerivedUnit.class);
 285     }
 286
 287
 288     /**
 289      * @param refMods
 290      * @param taxonDescription
 291      */
 292     public void addSource(Reference refMods, TaxonDescription taxonDescription) {
 293         //logger.info("addSource");
 294         sourceUrlRef=CdmBase.deproxy(sourceUrlRef, Reference.class);
 295         Reference sec = CdmBase.deproxy(configState.getConfig().getSecundum(), Reference.class);
 296         IdentifiableSource id = getIdentifiableSource(sourceUrlRef, taxonDescription.getSources(), false);
 297         IdentifiableSource id2 = getIdentifiableSource(refMods, taxonDescription.getSources(), true);
 298         IdentifiableSource id3 = getIdentifiableSource(sec, taxonDescription.getSources(), false);
 299
 300         if( id!=null) {
 301             taxonDescription.addSource(id);
 302         }
 303         if( id2!=null) {
 304             taxonDescription.addSource(id2);
 305         }
 306         if(!configState.getConfig().doKeepOriginalSecundum() &&  id3!=null) {
 307             taxonDescription.addSource(id3);
 308         }
 309         importer.getDescriptionService().saveOrUpdate(taxonDescription);
 310
 311     }
 312
 313
 314     /**
 315      * @param reference
 316      * @param textData
 317      * @param name
 318      * @param ref
 319      */
 320     public void addSource(Reference reference, TextData textData, TaxonNameBase name, Reference refMods) {
 321         //logger.info("addSource");
 322         sourceUrlRef=CdmBase.deproxy(sourceUrlRef, Reference.class);
 323         Reference sec = CdmBase.deproxy(configState.getConfig().getSecundum(), Reference.class);
 324         DescriptionElementSource id1 = getDescriptionElementSource(refMods, textData.getSources(),name, true);
 325         DescriptionElementSource id2 = getDescriptionElementSource(reference, textData.getSources(),name, false);
 326         if( id1!=null) {
 327             textData.addSource(id1);
 328         }
 329
 330         if( id2!=null) {
 331             textData.addSource(id2);
 332         }
 333
 334     }
 335
 336
 337     @SuppressWarnings({ "unused", "rawtypes" })
 338     private DescriptionElementSource getDescriptionElementSource(Reference reference, Set<DescriptionElementSource> sources,
 339             TaxonNameBase originalname, boolean original){
 340         //logger.info("getDescriptionElementSource");
 341         boolean sourceExists=false;
 342         DescriptionElementSource source=null;
 343         for (DescriptionElementSource src : sources){
 344             String micro = src.getCitationMicroReference();
 345             Reference r = src.getCitation();
 346             TaxonNameBase oname = src.getNameUsedInSource();
 347             try {
 348                 if (r.getTitleCache().equals(reference.getTitleCache())) {
 349                     if (oname.getTitleCache().equalsIgnoreCase(originalname.getTitleCache())) {
 350                             sourceExists=true;
 351                             break;
 352                     }
 353                 }
 354             } catch (Exception e) {
 355                 // TODO Auto-generated catch block
 356                 e.printStackTrace();
 357             }
 358         }
 359         if(!sourceExists) {
 360             if(original) {
 361                 source = DescriptionElementSource.NewInstance(OriginalSourceType.PrimaryTaxonomicSource, null,null, reference, null, originalname, null);
 362             } else {
 363                 source = DescriptionElementSource.NewInstance(OriginalSourceType.Import, null,null, reference, null, originalname, null);
 364             }
 365         }
 366         return source;
 367     }
 368
 369
 370
 371 }