cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/tcsrdf/TcsRdfTransformer.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.tcsrdf;
  11
  12 import org.apache.log4j.Logger;
  13 import org.springframework.stereotype.Component;
  14
  15 import eu.etaxonomy.cdm.model.common.RelationshipBase;
  16 import eu.etaxonomy.cdm.model.common.RelationshipTermBase;
  17 import eu.etaxonomy.cdm.model.location.NamedArea;
  18 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
  19 import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
  20 import eu.etaxonomy.cdm.model.name.Rank;
  21 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
  22 /*import eu.etaxonomy.cdm.model.reference.Article;
  23 import eu.etaxonomy.cdm.model.reference.Book;
  24 import eu.etaxonomy.cdm.model.reference.BookSection;
  25 import eu.etaxonomy.cdm.model.reference.Journal;
  26 import eu.etaxonomy.cdm.model.reference.PersonalCommunication;
  27 import eu.etaxonomy.cdm.model.reference.PrintSeries;*/
  28 import eu.etaxonomy.cdm.model.reference.ReferenceBase;
  29 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  30 //import eu.etaxonomy.cdm.model.reference.WebPage;
  31 import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
  32 import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
  33 import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
  34 import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
  35
  36 /**
  37  * @author a.mueller
  38  * @created 29.05.2008
  39  * @version 1.0
  40  */
  41 public final class TcsRdfTransformer {
  42         @SuppressWarnings("unused")
  43         private static final Logger logger = Logger.getLogger(TcsRdfTransformer.class);
  44
  45
  46         //TypeDesignation
  47         public static SpecimenTypeDesignationStatus typeStatusId2TypeStatus (int typeStatusId)  throws UnknownCdmTypeException{
  48                 switch (typeStatusId){
  49                         case 1: return SpecimenTypeDesignationStatus.HOLOTYPE();
  50                         case 2: return SpecimenTypeDesignationStatus.LECTOTYPE();
  51                         case 3: return SpecimenTypeDesignationStatus.NEOTYPE();
  52                         case 4: return SpecimenTypeDesignationStatus.EPITYPE();
  53                         case 5: return SpecimenTypeDesignationStatus.ISOLECTOTYPE();
  54                         case 6: return SpecimenTypeDesignationStatus.ISONEOTYPE();
  55                         case 7: return SpecimenTypeDesignationStatus.ISOTYPE();
  56                         case 8: return SpecimenTypeDesignationStatus.PARANEOTYPE();
  57                         case 9: return SpecimenTypeDesignationStatus.PARATYPE();
  58                         case 10: return SpecimenTypeDesignationStatus.SECOND_STEP_LECTOTYPE();
  59                         case 11: return SpecimenTypeDesignationStatus.SECOND_STEP_NEOTYPE();
  60                         case 12: return SpecimenTypeDesignationStatus.SYNTYPE();
  61                         case 21: return SpecimenTypeDesignationStatus.ICONOTYPE();
  62                         case 22: return SpecimenTypeDesignationStatus.PHOTOTYPE();
  63                         default: {
  64                                 throw new UnknownCdmTypeException("Unknown TypeDesignationStatus (id=" + Integer.valueOf(typeStatusId).toString() + ")");
  65                         }
  66                 }
  67         }
  68
  69
  70
  71
  72         /** Creates an cdm-Rank by the tcs rank
  73          */
  74         public static Rank rankString2Rank (String strRank) throws UnknownCdmTypeException{
  75                 String tcsRoot = "http://rs.tdwg.org/ontology/voc/TaxonRank#";
  76                 String tcsFamily = tcsRoot + "Family";
  77                 String tcsSubFamily = tcsRoot + "Subfamily";
  78                 String tcsTribe = tcsRoot + "Tribe";
  79                 String tcsSubtribe = tcsRoot + "Subtribe";
  80                 String tcsGenus = tcsRoot + "Genus";
  81                 String tcsSpecies = tcsRoot + "Species";
  82                 String tcsSubSpecies = tcsRoot + "Subspecies";
  83                 String tcsVariety = tcsRoot + "Variety";
  84                 String tcsSubVariety = tcsRoot + "Sub-Variety";
  85                 String tcsForm = tcsRoot + "Form";
  86
  87
  88
  89                 if (strRank == null){return null;
  90                 }else if (tcsFamily.equals(strRank)){return Rank.FAMILY();
  91                 }else if (tcsSubFamily.equals(strRank)){return Rank.SUBFAMILY();
  92                 }else if (tcsTribe.equals(strRank)){return Rank.TRIBE();
  93                 }else if (tcsSubtribe.equals(strRank)){return Rank.SUBTRIBE();
  94                 }else if (tcsGenus.equals(strRank)){return Rank.GENUS();
  95                 }else if (tcsSpecies.equals(strRank)){return Rank.SPECIES();
  96                 }else if (tcsVariety.equals(strRank)){return Rank.VARIETY();
  97                 }else if (tcsSubVariety.equals(strRank)){return Rank.SUBVARIETY();
  98                 }else if (tcsSubSpecies.equals(strRank)){return Rank.SUBSPECIES();
  99                 }else if (tcsForm.equals(strRank)){return Rank.FORM();
 100                 }
 101                 else {
 102                         throw new UnknownCdmTypeException("Unknown Rank " + strRank);
 103                 }
 104         }
 105
 106         /** Creates an cdm-NomenclaturalCode by the tcs NomenclaturalCode
 107          */
 108         public static NomenclaturalCode nomCodeString2NomCode (String nomCode) throws UnknownCdmTypeException{
 109
 110                 String tcsRoot = "http://rs.tdwg.org/ontology/voc/TaxonName#";
 111                 String tcsICBN = tcsRoot + "ICBN";
 112                 String tcsICZN = tcsRoot + "ICZN";
 113                 String tcsICNCP = tcsRoot + "ICNCP";
 114                 String tcsBacteriological = tcsRoot + "BACTERIOLOGICAL";
 115                 String tcsViral = tcsRoot + "VIRAL";
 116
 117                 if (nomCode == null){ return null;
 118                 }else if (tcsICBN.equals(nomCode)){return NomenclaturalCode.ICBN;
 119                 }else if (tcsICZN.equals(nomCode)){return NomenclaturalCode.ICZN;
 120                 }else if (tcsICNCP.equals(nomCode)){return NomenclaturalCode.ICNCP;
 121                 }else if (tcsBacteriological.equals(nomCode)){return NomenclaturalCode.ICNB;
 122                 }else if (tcsViral.equals(nomCode)){return NomenclaturalCode.ICVCN;
 123                 }
 124                 else {
 125                         throw new UnknownCdmTypeException("Unknown Nomenclatural Code " + nomCode);
 126                 }
 127         }
 128
 129         public static boolean isReverseRelationshipCategory (String tcsRelationshipCategory){
 130                 String str = tcsRelationshipCategory.replace("http://rs.tdwg.org/ontology/voc/TaxonConcept#", "");
 131                 if ("HasSynonym".equalsIgnoreCase(str)
 132                                 || "IsParentTaxonOf".equalsIgnoreCase(str)
 133                                 || "IsIncludedIn".equalsIgnoreCase(str)
 134                                 || "DoesNotInclude".equalsIgnoreCase(str)
 135                                                                         ){
 136
 137                         return true;
 138                 }
 139                 return false;
 140         }
 141
 142         /** Creates an cdm-Rank by the tcs rank
 143          */
 144         public static ReferenceBase pubTypeStr2PubType (String strPubType) throws UnknownCdmTypeException{
 145                 String tcsRoot = "http://rs.tdwg.org/ontology/voc/PublicationCitation#";
 146                 String tcsBook = tcsRoot + "Book";
 147                 String tcsJournal = tcsRoot + "Journal";
 148                 String tcsWebPage = tcsRoot + "WebPage";
 149                 String tcsCommunication = tcsRoot + "Communication";
 150                 String tcsBookSeries = tcsRoot + "BookSeries";
 151                 String tcsArticle = tcsRoot + "JournalArticle";
 152                 String tcsBookSection = tcsRoot + "BookSection";
 153
 154
 155 //              Artwork An Artwork type publication.
 156 //              AudiovisualMaterial     A Audiovisual Material type publication.
 157 //              BookSeries      A Book Series type publication.
 158 //              Commentary      A Commentary type publication.
 159 //              Communication   A Communication type publication.
 160 //              ComputerProgram A Computer Program type publication.
 161 //              ConferenceProceedings   A Conference Proceedings type publication.
 162 //              Determination   A Determination type publication.
 163 //              EditedBook      A Edited Book type publication.
 164 //              Generic A generic publication.
 165 //              Journal A Journal type publication.
 166 //              MagazineArticle A Magazine Article type publication.
 167 //              Map     A Map type publication.
 168 //              NewspaperArticle        A Newspaper Article type publication.
 169 //              Patent  A Patent type publication.
 170 //              Report  A Report type publication.
 171 //              SubReference    A Sub-Reference type publication.
 172 //              Thesis  A Thesis type publication.
 173
 174                 ReferenceFactory refFactory = ReferenceFactory.newInstance();
 175                 if (strPubType == null){return null;
 176                 }else if (tcsBookSection.equals(strPubType)){return refFactory.newBookSection();
 177                 }else if (tcsBook.equals(strPubType)){return refFactory.newBook();
 178                 }else if (tcsArticle.equals(strPubType)){return refFactory.newArticle();
 179                 }else if (tcsJournal.equals(strPubType)){return refFactory.newJournal();
 180                 }else if (tcsWebPage.equals(strPubType)){return refFactory.newWebPage();
 181                 }else if (tcsCommunication.equals(strPubType)){return refFactory.newPersonalCommunication();
 182                 }else if (tcsBookSeries.equals(strPubType)){return refFactory.newPrintSeries();
 183                 }
 184                 else {
 185                         throw new UnknownCdmTypeException("Unknown publication type " + strPubType);
 186                 }
 187         }
 188
 189         /** Creates an cdm-RelationshipTermBase by the tcsRelationshipCategory
 190          */
 191         public static RelationshipTermBase tcsRelationshipCategory2Relationship (String tcsRelationshipCategory) throws UnknownCdmTypeException{
 192                 String tcsRoot = "http://rs.tdwg.org/ontology/voc/TaxonConcept#";
 193                 String doesNotInclude  = tcsRoot + "DoesNotInclude";
 194                 String doesNotOverlap  = tcsRoot + "DoesNotOverlap";
 195                 String excludes  = tcsRoot + "Excludes";
 196                 String hasSynonym  = tcsRoot + "HasSynonym";
 197                 String hasVernacular  = tcsRoot + "HasVernacular";
 198                 String includes  = tcsRoot + "Includes";
 199                 String isAmbiregnalOf  = tcsRoot + "IsAmbiregnalOf";
 200                 String isAnamorphOf  = tcsRoot + "IsAnamorphOf";
 201                 String isChildTaxonOf  = tcsRoot + "IsChildTaxonOf";
 202                 String isCongruentTo  = tcsRoot + "IsCongruentTo";
 203                 String isFemaleParentOf  = tcsRoot + "IsFemaleParentOf";
 204                 String isFirstParentOf  = tcsRoot + "IsFirstParentOf";
 205                 String isHybridChildOf  = tcsRoot + "IsHybridChildOf";
 206                 String isHybridParentOf  = tcsRoot + "IsHybridParentOf";
 207                 String isIncludedIn  = tcsRoot + "IsIncludedIn";
 208                 String isMaleParentOf  = tcsRoot + "IsMaleParentOf";
 209                 String isNotCongruentTo  = tcsRoot + "IsNotCongruentTo";
 210                 String isNotIncludedIn  = tcsRoot + "IsNotIncludedIn";
 211                 String isParentTaxonOf  = tcsRoot + "IsParentTaxonOf";
 212                 String isSecondParentOf  = tcsRoot + "IsSecondParentOf";
 213                 String isSynonymFor  = tcsRoot + "IsSynonymFor";
 214                 String isTeleomorphOf  = tcsRoot + "IsTeleomorphOf";
 215                 String isVernacularFor  = tcsRoot + "IsVernacularFor";
 216                 String overlaps  = tcsRoot + "Overlaps";
 217
 218                 if (tcsRelationshipCategory == null){ return null;
 219
 220                 //Synonym relationships
 221                 }else if (isSynonymFor.equals(tcsRelationshipCategory)){return SynonymRelationshipType.SYNONYM_OF();
 222                 }else if (hasSynonym.equals(tcsRelationshipCategory)){/*isReverse = true; */ return SynonymRelationshipType.SYNONYM_OF();
 223
 224                 //Taxon relationships
 225                 }else if (isChildTaxonOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN();
 226                 }else if (isParentTaxonOf.equals(tcsRelationshipCategory)){/*isReverse = true; */ return TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN();
 227
 228                 //concept relationships
 229                 }else if (doesNotOverlap.equals(tcsRelationshipCategory)){return TaxonRelationshipType.DOES_NOT_OVERLAP();
 230                 }else if (excludes.equals(tcsRelationshipCategory)){return TaxonRelationshipType.EXCLUDES();
 231                 }else if (includes.equals(tcsRelationshipCategory)){return TaxonRelationshipType.INCLUDES();
 232                 }else if (isCongruentTo.equals(tcsRelationshipCategory)){return TaxonRelationshipType.CONGRUENT_TO();
 233                 }else if (isNotCongruentTo.equals(tcsRelationshipCategory)){return TaxonRelationshipType.NOT_CONGRUENT_TO();
 234                 }else if (isNotIncludedIn.equals(tcsRelationshipCategory)){return TaxonRelationshipType.NOT_INCLUDED_IN();
 235                 }else if (overlaps.equals(tcsRelationshipCategory)){return TaxonRelationshipType.OVERLAPS();
 236                 //reverse concept relationships
 237                 }else if (isIncludedIn.equals(tcsRelationshipCategory)){/*isReverse = true; */ return TaxonRelationshipType.INCLUDES();
 238                 }else if (doesNotInclude.equals(tcsRelationshipCategory)){/*isReverse = true; */ return TaxonRelationshipType.NOT_INCLUDED_IN();
 239
 240         //TODO
 241 //              }else if (hasVernacular.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X;
 242 //              }else if (isAmbiregnalOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X;
 243 //              }else if (isAnamorphOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X;
 244 //              }else if (isFemaleParentOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X;
 245 //              }else if (isFirstParentOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X;
 246 //              }else if (isHybridChildOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X;
 247 //              }else if (isHybridParentOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X;
 248 //              }else if (isMaleParentOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X;
 249 //              }else if (isSecondParentOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X;
 250 //              }else if (isTeleomorphOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X;
 251 //              }else if (isVernacularFor.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X;
 252
 253                 }else {
 254                         throw new UnknownCdmTypeException("Unknown RelationshipCategory " + tcsRelationshipCategory);
 255                 }
 256         }
 257
 258
 259         /** Creates an cdm-NomenclaturalCode by the tcs NomenclaturalCode
 260          */
 261         public static NomenclaturalStatusType nomStatusString2NomStatus (String nomStatus) throws UnknownCdmTypeException{
 262
 263                 if (nomStatus == null){ return null;
 264                 }else if ("Valid".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.VALID();
 265
 266                 }else if ("Alternative".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ALTERNATIVE();
 267                 }else if ("nom. altern.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ALTERNATIVE();
 268
 269                 }else if ("Ambiguous".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.AMBIGUOUS();
 270
 271                 }else if ("Doubtful".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.DOUBTFUL();
 272
 273                 }else if ("Confusum".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.CONFUSUM();
 274
 275                 }else if ("Illegitimate".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ILLEGITIMATE();
 276                 }else if ("nom. illeg.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ILLEGITIMATE();
 277
 278                 }else if ("Superfluous".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.SUPERFLUOUS();
 279                 }else if ("nom. superfl.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.SUPERFLUOUS();
 280
 281                 }else if ("Rejected".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.REJECTED();
 282                 }else if ("nom. rej.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.REJECTED();
 283
 284                 }else if ("Utique Rejected".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.UTIQUE_REJECTED();
 285
 286                 }else if ("Conserved Prop".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.CONSERVED_PROP();
 287
 288                 }else if ("Orthography Conserved Prop".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ORTHOGRAPHY_CONSERVED_PROP();
 289
 290                 }else if ("Legitimate".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.LEGITIMATE();
 291
 292                 }else if ("Novum".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.NOVUM();
 293                 }else if ("nom. nov.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.NOVUM();
 294
 295                 }else if ("Utique Rejected Prop".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.UTIQUE_REJECTED_PROP();
 296
 297                 }else if ("Orthography Conserved".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ORTHOGRAPHY_CONSERVED();
 298
 299                 }else if ("Rejected Prop".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.REJECTED_PROP();
 300
 301                 }else if ("Conserved".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.CONSERVED();
 302                 }else if ("nom. cons.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.CONSERVED();
 303
 304                 }else if ("Sanctioned".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.SANCTIONED();
 305
 306                 }else if ("Invalid".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.INVALID();
 307                 }else if ("nom. inval.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.INVALID();
 308
 309                 }else if ("Nudum".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.NUDUM();
 310                 }else if ("nom. nud.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.NUDUM();
 311
 312                 }else if ("Combination Invalid".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.COMBINATION_INVALID();
 313
 314                 }else if ("Provisional".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.PROVISIONAL();
 315                 }else if ("nom. provis.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.PROVISIONAL();
 316                 }
 317                 else {
 318                         throw new UnknownCdmTypeException("Unknown Nomenclatural status type " + nomStatus);
 319                 }
 320         }
 321
 322
 323 }