cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/tcs/TcsTransformer.java

   1 package eu.etaxonomy.cdm.io.tcs;
   2
   3 import org.apache.log4j.Logger;
   4
   5 import eu.etaxonomy.cdm.model.common.RelationshipBase;
   6 import eu.etaxonomy.cdm.model.common.RelationshipTermBase;
   7 import eu.etaxonomy.cdm.model.location.NamedArea;
   8 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
   9 import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
  10 import eu.etaxonomy.cdm.model.name.Rank;
  11 import eu.etaxonomy.cdm.model.name.TypeDesignationStatus;
  12 import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
  13 import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
  14 import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
  15 import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
  16
  17 public final class TcsTransformer {
  18         private static final Logger logger = Logger.getLogger(TcsTransformer.class);
  19
  20
  21         //TypeDesignation
  22         public static TypeDesignationStatus typeStatusId2TypeStatus (int typeStatusId)  throws UnknownCdmTypeException{
  23                 switch (typeStatusId){
  24                         case 1: return TypeDesignationStatus.HOLOTYPE();
  25                         case 2: return TypeDesignationStatus.LECTOTYPE();
  26                         case 3: return TypeDesignationStatus.NEOTYPE();
  27                         case 4: return TypeDesignationStatus.EPITYPE();
  28                         case 5: return TypeDesignationStatus.ISOLECTOTYPE();
  29                         case 6: return TypeDesignationStatus.ISONEOTYPE();
  30                         case 7: return TypeDesignationStatus.ISOTYPE();
  31                         case 8: return TypeDesignationStatus.PARANEOTYPE();
  32                         case 9: return TypeDesignationStatus.PARATYPE();
  33                         case 10: return TypeDesignationStatus.SECOND_STEP_LECTOTYPE();
  34                         case 11: return TypeDesignationStatus.SECOND_STEP_NEOTYPE();
  35                         case 12: return TypeDesignationStatus.SYNTYPE();
  36                         case 21: return TypeDesignationStatus.ICONOTYPE();
  37                         case 22: return TypeDesignationStatus.PHOTOTYPE();
  38                         default: {
  39                                 throw new UnknownCdmTypeException("Unknown TypeDesignationStatus (id=" + Integer.valueOf(typeStatusId).toString() + ")");
  40                         }
  41                 }
  42         }
  43
  44
  45
  46
  47         /** Creates an cdm-Rank by the tcs rank
  48          */
  49         public static Rank rankString2Rank (String strRank) throws UnknownCdmTypeException{
  50                 String tcsRoot = "http://rs.tdwg.org/ontology/voc/TaxonRank#";
  51                 String tcsGenus = tcsRoot + "Genus";
  52                 String tcsSpecies = tcsRoot + "Species";
  53 //              String tcsGenus = tcsRoot + "Genus";
  54
  55                 if (strRank == null){return null;
  56                 }else if (tcsGenus.equals(strRank)){return Rank.GENUS();
  57                 }else if (tcsSpecies.equals(strRank)){return Rank.SPECIES();
  58                 }
  59                 else {
  60                         throw new UnknownCdmTypeException("Unknown Rank " + strRank);
  61                 }
  62         }
  63
  64         /** Creates an cdm-NomenclaturalCode by the tcs NomenclaturalCode
  65          */
  66         public static NomenclaturalCode nomCodeString2NomCode (String nomCode) throws UnknownCdmTypeException{
  67
  68                 String tcsRoot = "http://rs.tdwg.org/ontology/voc/TaxonName#";
  69                 String tcsICBN = tcsRoot + "ICBN";
  70                 String tcsICZN = tcsRoot + "ICZN";
  71                 String tcsICNCP = tcsRoot + "ICNCP";
  72                 String tcsBacteriological = tcsRoot + "BACTERIOLOGICAL";
  73                 String tcsViral = tcsRoot + "VIRAL";
  74
  75                 if (nomCode == null){ return null;
  76                 }else if (tcsICBN.equals(nomCode)){return NomenclaturalCode.ICBN();
  77                 }else if (tcsICZN.equals(nomCode)){return NomenclaturalCode.ICZN();
  78                 }else if (tcsICNCP.equals(nomCode)){return NomenclaturalCode.ICNCP();
  79                 }else if (tcsBacteriological.equals(nomCode)){return NomenclaturalCode.ICNB();
  80                 }else if (tcsViral.equals(nomCode)){return NomenclaturalCode.ICVCN();
  81                 }
  82                 else {
  83                         throw new UnknownCdmTypeException("Unknown Nomenclatural Code " + nomCode);
  84                 }
  85         }
  86
  87         public static boolean isReverseRelationshipCategory (String tcsRelationshipCategory){
  88                 String str = tcsRelationshipCategory.replace("http://rs.tdwg.org/ontology/voc/TaxonConcept#", "");
  89                 if ("HasSynonym".equalsIgnoreCase(str)
  90                                 || "IsParentTaxonOf".equalsIgnoreCase(str)
  91                                 || "IsIncludedIn".equalsIgnoreCase(str)
  92                                 || "DoesNotInclude".equalsIgnoreCase(str)
  93                                                                         ){
  94
  95                         return true;
  96                 }
  97                 return false;
  98         }
  99
 100         /** Creates an cdm-RelationshipTermBase by the tcsRelationshipCategory
 101          */
 102         public static RelationshipTermBase tcsRelationshipCategory2Relationship (String tcsRelationshipCategory) throws UnknownCdmTypeException{
 103                 String tcsRoot = "http://rs.tdwg.org/ontology/voc/TaxonConcept#";
 104                 String doesNotInclude  = tcsRoot + "DoesNotInclude";
 105                 String doesNotOverlap  = tcsRoot + "DoesNotOverlap";
 106                 String excludes  = tcsRoot + "Excludes";
 107                 String hasSynonym  = tcsRoot + "HasSynonym";
 108                 String hasVernacular  = tcsRoot + "HasVernacular";
 109                 String includes  = tcsRoot + "Includes";
 110                 String isAmbiregnalOf  = tcsRoot + "IsAmbiregnalOf";
 111                 String isAnamorphOf  = tcsRoot + "IsAnamorphOf";
 112                 String isChildTaxonOf  = tcsRoot + "IsChildTaxonOf";
 113                 String isCongruentTo  = tcsRoot + "IsCongruentTo";
 114                 String isFemaleParentOf  = tcsRoot + "IsFemaleParentOf";
 115                 String isFirstParentOf  = tcsRoot + "IsFirstParentOf";
 116                 String isHybridChildOf  = tcsRoot + "IsHybridChildOf";
 117                 String isHybridParentOf  = tcsRoot + "IsHybridParentOf";
 118                 String isIncludedIn  = tcsRoot + "IsIncludedIn";
 119                 String isMaleParentOf  = tcsRoot + "IsMaleParentOf";
 120                 String isNotCongruentTo  = tcsRoot + "IsNotCongruentTo";
 121                 String isNotIncludedIn  = tcsRoot + "IsNotIncludedIn";
 122                 String isParentTaxonOf  = tcsRoot + "IsParentTaxonOf";
 123                 String isSecondParentOf  = tcsRoot + "IsSecondParentOf";
 124                 String isSynonymFor  = tcsRoot + "IsSynonymFor";
 125                 String isTeleomorphOf  = tcsRoot + "IsTeleomorphOf";
 126                 String isVernacularFor  = tcsRoot + "IsVernacularFor";
 127                 String overlaps  = tcsRoot + "Overlaps";
 128
 129                 if (tcsRelationshipCategory == null){ return null;
 130
 131                 //Synonym relationships
 132                 }else if (isSynonymFor.equals(tcsRelationshipCategory)){return SynonymRelationshipType.SYNONYM_OF();
 133                 }else if (hasSynonym.equals(tcsRelationshipCategory)){/*isReverse = true; */ return SynonymRelationshipType.SYNONYM_OF();
 134
 135                 //Taxon relationships
 136                 }else if (isChildTaxonOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN();
 137                 }else if (isParentTaxonOf.equals(tcsRelationshipCategory)){/*isReverse = true; */ return TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN();
 138
 139                 //concept relationships
 140                 }else if (doesNotOverlap.equals(tcsRelationshipCategory)){return TaxonRelationshipType.DOESNOTOVERLAP();
 141                 }else if (excludes.equals(tcsRelationshipCategory)){return TaxonRelationshipType.EXCLUDES();
 142                 }else if (includes.equals(tcsRelationshipCategory)){return TaxonRelationshipType.INCLUDES();
 143                 }else if (isCongruentTo.equals(tcsRelationshipCategory)){return TaxonRelationshipType.CONGRUENTTO();
 144                 }else if (isNotCongruentTo.equals(tcsRelationshipCategory)){return TaxonRelationshipType.NOTCONGRUENTTO();
 145                 }else if (isNotIncludedIn.equals(tcsRelationshipCategory)){return TaxonRelationshipType.NOTINCLUDEDIN();
 146                 }else if (overlaps.equals(tcsRelationshipCategory)){return TaxonRelationshipType.OVERLAPS();
 147                 //reverse concept relationships
 148                 }else if (isIncludedIn.equals(tcsRelationshipCategory)){/*isReverse = true; */ return TaxonRelationshipType.INCLUDES();
 149                 }else if (doesNotInclude.equals(tcsRelationshipCategory)){/*isReverse = true; */ return TaxonRelationshipType.NOTINCLUDEDIN();
 150
 151         //TODO
 152 //              }else if (hasVernacular.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X;
 153 //              }else if (isAmbiregnalOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X;
 154 //              }else if (isAnamorphOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X;
 155 //              }else if (isFemaleParentOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X;
 156 //              }else if (isFirstParentOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X;
 157 //              }else if (isHybridChildOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X;
 158 //              }else if (isHybridParentOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X;
 159 //              }else if (isMaleParentOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X;
 160 //              }else if (isSecondParentOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X;
 161 //              }else if (isTeleomorphOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X;
 162 //              }else if (isVernacularFor.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X;
 163
 164                 }else {
 165                         throw new UnknownCdmTypeException("Unknown RelationshipCategory " + tcsRelationshipCategory);
 166                 }
 167         }
 168
 169
 170         /** Creates an cdm-NomenclaturalCode by the tcs NomenclaturalCode
 171          */
 172         public static NomenclaturalStatusType nomStatusString2NomStatus (String nomStatus) throws UnknownCdmTypeException{
 173
 174                 if (nomStatus == null){ return null;
 175                 }else if ("Valid".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.VALID();
 176
 177                 }else if ("Alternative".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ALTERNATIVE();
 178                 }else if ("nom. altern.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ALTERNATIVE();
 179
 180                 }else if ("Ambiguous".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.AMBIGUOUS();
 181
 182                 }else if ("Doubtful".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.DOUBTFUL();
 183
 184                 }else if ("Confusum".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.CONFUSUM();
 185
 186                 }else if ("Illegitimate".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ILLEGITIMATE();
 187                 }else if ("nom. illeg.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ILLEGITIMATE();
 188
 189                 }else if ("Superfluous".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.SUPERFLUOUS();
 190                 }else if ("nom. superfl.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.SUPERFLUOUS();
 191
 192                 }else if ("Rejected".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.REJECTED();
 193                 }else if ("nom. rej.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.REJECTED();
 194
 195                 }else if ("Utique Rejected".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.UTIQUE_REJECTED();
 196
 197                 }else if ("Conserved Prop".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.CONSERVED_PROP();
 198
 199                 }else if ("Orthography Conserved Prop".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ORTHOGRAPHY_CONSERVED_PROP();
 200
 201                 }else if ("Legitimate".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.LEGITIMATE();
 202
 203                 }else if ("Novum".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.NOVUM();
 204                 }else if ("nom. nov.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.NOVUM();
 205
 206                 }else if ("Utique Rejected Prop".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.UTIQUE_REJECTED_PROP();
 207
 208                 }else if ("Orthography Conserved".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ORTHOGRAPHY_CONSERVED();
 209
 210                 }else if ("Rejected Prop".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.REJECTED_PROP();
 211
 212                 }else if ("Conserved".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.CONSERVED();
 213                 }else if ("nom. cons.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.CONSERVED();
 214
 215                 }else if ("Sanctioned".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.SANCTIONED();
 216
 217                 }else if ("Invalid".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.INVALID();
 218                 }else if ("nom. inval.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.INVALID();
 219
 220                 }else if ("Nudum".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.NUDUM();
 221                 }else if ("nom. nud.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.NUDUM();
 222
 223                 }else if ("Combination Invalid".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.COMBINATION_INVALID();
 224
 225                 }else if ("Provisional".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.PROVISIONAL();
 226                 }else if ("nom. provis.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.PROVISIONAL();
 227                 }
 228                 else {
 229                         throw new UnknownCdmTypeException("Unknown Nomenclatural status type " + nomStatus);
 230                 }
 231         }
 232
 233 //
 234 //      /** Creates an NameArea by a TDWG Label
 235 //       */
 236 //      public static NamedArea strTdwgArea2NamedArea (String tdwgArea) throws UnknownCdmTypeException{
 237 //
 238 //              if (tdwgArea == null){ return null;
 239 //              }else if ("Valid".equalsIgnoreCase(tdwgArea)){return NamedArea.VALID();
 240 //
 241 //              }else if ("Alternative".equalsIgnoreCase(tdwgArea)){return NamedArea.ALTERNATIVE();
 242 //              }else if ("nom. altern.".equalsIgnoreCase(tdwgArea)){return NamedArea.ALTERNATIVE();
 243 //
 244 //              }else if ("Provisional".equalsIgnoreCase(tdwgArea)){return NamedArea.PROVISIONAL();
 245 //              }else if ("nom. provis.".equalsIgnoreCase(tdwgArea)){return NamedArea.PROVISIONAL();
 246 //              }
 247 //              else {
 248 //                      throw new UnknownCdmTypeException("Unknown Nomenclatural status type " + nomStatus);
 249 //              }
 250 //      }
 251
 252 }