import org.apache.log4j.Logger;\r
\r
import eu.etaxonomy.cdm.common.ResultWrapper;\r
+import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;\r
import eu.etaxonomy.cdm.model.common.Language;\r
import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary;\r
import eu.etaxonomy.cdm.model.common.RelationshipBase;\r
import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;\r
import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;\r
import eu.etaxonomy.cdm.model.name.Rank;\r
+import eu.etaxonomy.cdm.model.name.RankClass;\r
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;\r
import eu.etaxonomy.cdm.model.reference.ISectionBase;\r
import eu.etaxonomy.cdm.model.reference.Reference;\r
* @created 20.03.2008\r
* @version 1.0\r
*/\r
-public final class BerlinModelTransformer {\r
+public class BerlinModelTransformer {\r
private static final Logger logger = Logger.getLogger(BerlinModelTransformer.class);\r
\r
+ //ranks\r
+ public static UUID uuidRankCollSpecies = UUID.fromString("e14630ee-9446-4bb4-a7b7-4c3881bc5d94");\r
+ public static UUID uuidRankProles = UUID.fromString("8810d1ba-6a34-4ae3-a355-919ccd1cd1a5");\r
+ public static UUID uuidRankRace = UUID.fromString("196dee39-cfd8-4460-8bf0-88b83da27f62");\r
+ public static UUID uuidRankSublusus = UUID.fromString("1fafa596-a8e7-4e62-a378-3cc8cb3627ca");\r
+ \r
//named areas\r
public static UUID euroMedUuid = UUID.fromString("9fe09988-58c0-4c06-8474-f660a0c50014");\r
-\r
\r
+ public static UUID uuidEasternEuropeanRussia = UUID.fromString("3f013375-0e0a-40c3-8a14-84c0535fab40");\r
+ public static UUID uuidSerbiaMontenegro = UUID.fromString("8926dbe6-863e-47a9-98a0-7dc9ed2c57f7");\r
+ public static UUID uuidSerbia = UUID.fromString("4ffed197-3d7e-4cd9-8984-e64b8dee9512");\r
+ public static UUID uuidLebanonSyria = UUID.fromString("0c45f250-99da-4b19-aa89-c3e56cfdf103");\r
+ public static UUID uuidUssr = UUID.fromString("a512e00a-45f3-4be5-82fa-bba8d675696f");\r
+ public static UUID uuidSicilyMalta = UUID.fromString("424d81ee-d272-4ae8-9600-0a334049cd72");\r
+ \r
+ public static UUID uuidDesertas = UUID.fromString("36f5e93e-34e8-45b5-a401-f0e0faad21cf");\r
+ public static UUID uuidMadeira = UUID.fromString("086e27ee-78ff-4236-aca9-9850850cd355");\r
+ public static UUID uuidPortoSanto = UUID.fromString("1f9ab6a0-a402-4dfe-8c5b-b1844eb4d8e5");\r
+ //azores\r
+ public static UUID uuidFlores = UUID.fromString("ef0067c2-8bbb-4e37-8462-97b03f51ba43");\r
+ public static UUID uuidCorvo = UUID.fromString("b1e6117c-2be1-43a3-9233-227dd90bdee9");\r
+ public static UUID uuidFaial = UUID.fromString("14f6dcdb-6524-4700-b80c-66424952ef2b");\r
+ public static UUID uuidGraciosa = UUID.fromString("05f93a7b-d813-4833-864f-eedbba747133");\r
+ public static UUID uuidSaoJorge = UUID.fromString("578e0ecd-b5e3-4c87-8ecc-0fc4c7e217d9");\r
+ public static UUID uuidSaoMiguel = UUID.fromString("0e2f6ad8-7afb-4f01-b134-4f71991e877a");\r
+ public static UUID uuidPico = UUID.fromString("98cc566f-4110-43d5-830f-68436a009f49");\r
+ public static UUID uuidSantaMaria = UUID.fromString("bd5e5d4a-22b7-41aa-8e58-1d1d73a9954d");\r
+ public static UUID uuidTerceira = UUID.fromString("6fc257c0-a131-41f0-b6c3-51ef9c4fa962");\r
+ //Canyry islands\r
+ public static UUID uuidGranCanaria = UUID.fromString("a0240c35-0e05-4157-8321-67ba8e31fdb9");\r
+ public static UUID uuidFuerteventura = UUID.fromString("549ce2c1-6d49-4bf3-b75d-cf3f4b5a1398");\r
+ public static UUID uuidGomera = UUID.fromString("895fab09-7478-4210-b42a-423d23c6f85e");\r
+ public static UUID uuidHierro = UUID.fromString("d137b6a5-31bc-418c-9403-f042017dc04b");\r
+ public static UUID uuidLanzaroteWithGraciosa = UUID.fromString("c9b08dc1-f301-4d9d-b447-b8744602c776");\r
+ public static UUID uuidLaPalma = UUID.fromString("fdb3f2b2-f154-4f04-9f31-240a47a0e780");\r
+ public static UUID uuidTenerife = UUID.fromString("73658c7e-a568-465e-bd84-4554fc93ca56");\r
+ //Baleares\r
+ public static UUID uuidIbizaWithFormentera = UUID.fromString("1cda2a33-3469-49d5-8e77-cb5451110519");\r
+ public static UUID uuidMallorca = UUID.fromString("a10cba04-b4b5-4a4b-b69a-fcd4b3916fec");\r
+ public static UUID uuidMenorca = UUID.fromString("9f6ede48-27f8-4270-bf4e-c97eaa86aab7");\r
+ \r
+ //russia\r
+ public static UUID uuidRussiaNorthern = UUID.fromString("c23bc1c9-a775-4426-b883-07d4d7d47eed");\r
+ public static UUID uuidRussiaBaltic = UUID.fromString("579dad44-9439-4b19-8716-ab90d8f27944");\r
+ public static UUID uuidRussiaCentral = UUID.fromString("8bbc8c6a-2ef2-4024-ad51-66fe34c70092");\r
+ public static UUID uuidRussiaSouthWest = UUID.fromString("daa5c207-5567-4690-8742-5e4d153b6a64");\r
+ public static UUID uuidRussiaSouthEast = UUID.fromString("e8516598-b529-489e-9ee8-63bbbd295c1b");\r
+ public static UUID uuidEastAegeanIslands = UUID.fromString("1c429593-c493-46e6-971a-0d70be690da8");\r
+ public static UUID uuidTurkishEastAegeanIslands = UUID.fromString("ba35dba3-ac70-41ae-81c2-2070943f44f2");\r
+ public static UUID uuidBalticStates = UUID.fromString("bf9d64f6-3183-4fa5-8e90-73090e7a2282");\r
+ public static final UUID uuidTurkey = UUID.fromString("d344ee2c-14c8-438d-b03d-11538edb1268");\r
+ public static final UUID uuidCaucasia = UUID.fromString("ebfd3fd1-3859-4e5e-95c7-f66010599d7e");\r
+ \r
+ //language areas\r
+ public static final UUID uuidUkraineAndCrimea = UUID.fromString("99d4d1c2-09f6-416e-86a3-bdde5cae52af");\r
+ public static final UUID uuidAzerbaijanNakhichevan = UUID.fromString("232fbef0-9f4a-4cab-8ac1-e14c717e9de6");\r
+ \r
+ //Marker Types\r
+ public static final UUID uuidMisappliedCommonName = UUID.fromString("25f5cfc3-16ab-4aba-a008-0db0f2cf7f9d");\r
+ \r
+ //Extension Types\r
+ public static final UUID uuidSpeciesExpertName = UUID.fromString("2e8153d2-7412-49e4-87e1-5c38f4c5153a");\r
+ public static final UUID uuidExpertName = UUID.fromString("24becb79-a90c-47d3-be35-efc87bb48fd3");\r
+ \r
+ public static final UUID DETAIL_EXT_UUID = UUID.fromString("c3959b4f-d876-4b7a-a739-9260f4cafd1c");\r
+ public static final UUID ID_IN_SOURCE_EXT_UUID = UUID.fromString("23dac094-e793-40a4-bad9-649fc4fcfd44");\r
+ \r
+ //languages\r
+ public static final UUID uuidLangMajorcan = UUID.fromString("82d696d7-cb4e-49de-ac89-63a0e12ca766");\r
+\r
//REFERENCES\r
public static int REF_ARTICLE = 1;\r
public static int REF_PART_OF_OTHER_TITLE = 2;\r
public static int NAME_REL_IS_REJECTED_IN_FAVOUR_OF = 14;\r
public static int NAME_REL_IS_TREATED_AS_LATER_HOMONYM_OF = 15;\r
public static int NAME_REL_IS_ORTHOGRAPHIC_VARIANT_OF = 16;\r
+ public static int NAME_REL_IS_ALTERNATIVE_NAME_FOR = 17;\r
public static int NAME_REL_HAS_SAME_TYPE_AS = 18;\r
public static int NAME_REL_IS_LECTOTYPE_OF = 61;\r
public static int NAME_REL_TYPE_NOT_DESIGNATED = 62;\r
public static int FACT_OBSERVATION = 9;\r
public static int FACT_DISTRIBUTION_EM = 10;\r
public static int FACT_DISTRIBUTION_WORLD = 11;\r
+ //E+M\r
+ public static final UUID uuidFeatureMaps = UUID.fromString("8367730e-f3c3-4361-8360-a2057e4295ed");\r
+ public static final UUID uuidFeatureConservationStatus = UUID.fromString("a32f33cd-1966-4a22-986c-94c5e688bbd1");\r
+ public static final UUID uuidFeatureUse = UUID.fromString("199bbbd8-2db6-4335-b454-2e92ae02b699");\r
+ public static final UUID uuidFeatureComments = UUID.fromString("31cc2b92-5cad-44e9-b50f-b8af591a527c");\r
+ public static final UUID uuidFeatureDistrEM = UUID.fromString("a5ba7e7f-ca7f-4f50-afc7-73e76b3231d4");\r
+ public static final UUID uuidFeatureDistrWorld = UUID.fromString("e4e24080-7017-47e6-924e-d2560fa68fb8");\r
+ public static final UUID uuidFeatureEditorBrackets = UUID.fromString("b3b5bc1a-7ba8-4a39-9c0d-63ba599eb5d8");\r
+ public static final UUID uuidFeatureEditorParenthesis = UUID.fromString("6ee10a2e-ff02-4cf4-a520-89630edc5b44");\r
+ public static final UUID uuidFeatureInedited = UUID.fromString("c93e2968-bc52-4165-9755-ce37611faf01");\r
+ public static final UUID uuidFeatureCommentsEditing = UUID.fromString("7a155021-158a-48bb-81d0-9a72b718e2de");\r
\r
- public static UUID uuidRelNameCombIned = UUID.fromString("dde8a2e7-bf9e-42ec-b186-d5bde9c9c128");\r
+ \r
+ \r
+ public static UUID uuidNomStatusCombIned = UUID.fromString("dde8a2e7-bf9e-42ec-b186-d5bde9c9c128");\r
+ public static UUID uuidNomStatusSpNovIned = UUID.fromString("1a359ca1-9364-43bc-93e4-834bdcd52b72");\r
+ public static UUID uuidNomStatusNomOrthCons = UUID.fromString("0f838183-ffa0-4014-928e-0e3a27eb3918");\r
\r
static NomenclaturalStatusType nomStatusCombIned;\r
+ static NomenclaturalStatusType nomStatusSpNovIned;\r
+ static NomenclaturalStatusType nomStatusNomOrthCons;\r
+ \r
public static NomenclaturalStatusType nomStatusTypeAbbrev2NewNomStatusType(String nomStatus){\r
NomenclaturalStatusType result = null;\r
if (nomStatus == null){\r
nomStatusCombIned = new NomenclaturalStatusType();\r
Representation representation = Representation.NewInstance("comb. ined.", "comb. ined.", "comb. ined.", Language.LATIN());\r
nomStatusCombIned.addRepresentation(representation);\r
- nomStatusCombIned.setUuid(uuidRelNameCombIned);\r
+ nomStatusCombIned.setUuid(uuidNomStatusCombIned);\r
NomenclaturalStatusType.ALTERNATIVE().getVocabulary().addTerm(nomStatusCombIned);\r
}\r
result = nomStatusCombIned;\r
+ }else if (nomStatus.equalsIgnoreCase("sp. nov. ined.")){\r
+ if (nomStatusSpNovIned == null){\r
+ nomStatusSpNovIned = new NomenclaturalStatusType();\r
+ Representation representation = Representation.NewInstance("sp. nov. ined.", "sp. nov. ined.", "sp. nov. ined.", Language.LATIN());\r
+ nomStatusSpNovIned.addRepresentation(representation);\r
+ nomStatusSpNovIned.setUuid(uuidNomStatusSpNovIned);\r
+ NomenclaturalStatusType.ALTERNATIVE().getVocabulary().addTerm(nomStatusSpNovIned);\r
+ }\r
+ result = nomStatusSpNovIned;\r
+ }else if (nomStatus.equalsIgnoreCase("nom. & orth. cons.")){\r
+ if (nomStatusNomOrthCons == null){\r
+ nomStatusNomOrthCons = new NomenclaturalStatusType();\r
+ Representation representation = Representation.NewInstance("nom. & orth. cons.", "nom. & orth. cons.", "nom. & orth. cons.", Language.LATIN());\r
+ nomStatusNomOrthCons.addRepresentation(representation);\r
+ nomStatusNomOrthCons.setUuid(uuidNomStatusNomOrthCons);\r
+ NomenclaturalStatusType.ALTERNATIVE().getVocabulary().addTerm(nomStatusNomOrthCons);\r
+ }\r
+ result = nomStatusNomOrthCons;\r
}\r
return result;\r
}\r
case 23: return TaxonRelationshipType.CONGRUENT_OR_INCLUDES_OR_OVERLAPS();\r
case 24: return TaxonRelationshipType.INCLUDED_OR_INCLUDES_OR_OVERLAPS();\r
\r
- case 26: return TaxonRelationshipType.OVERLAPS();\r
+ case 26: return TaxonRelationshipType.EXCLUDES();\r
+ \r
//TODO other relationshipTypes\r
\r
+ case 40: return TaxonRelationshipType.NOT_CONGRUENT_TO();\r
+ \r
//FIXME doubtful\r
case 43: return TaxonRelationshipType.CONGRUENT_TO();\r
default: {\r
case 120: return PresenceTerm.CULTIVATED();\r
case 210: return AbsenceTerm.INTRODUCED_REPORTED_IN_ERROR();\r
case 220: return PresenceTerm.INTRODUCED_PRESENCE_QUESTIONABLE();\r
- case 230: return PresenceTerm.INTRODUCED_FORMERLY_INTRODUCED();\r
+ case 230: return AbsenceTerm.INTRODUCED_FORMERLY_INTRODUCED();\r
case 240: return PresenceTerm.INTRODUCED_DOUBTFULLY_INTRODUCED();\r
case 250: return PresenceTerm.INTRODUCED();\r
case 260: return PresenceTerm.INTRODUCED_UNCERTAIN_DEGREE_OF_NATURALISATION();\r
case 280: return PresenceTerm.INTRODUCED_NATURALIZED();\r
case 310: return AbsenceTerm.NATIVE_REPORTED_IN_ERROR();\r
case 320: return PresenceTerm.NATIVE_PRESENCE_QUESTIONABLE();\r
- case 330: return PresenceTerm.NATIVE_FORMERLY_NATIVE();\r
+ case 330: return AbsenceTerm.NATIVE_FORMERLY_NATIVE();\r
case 340: return PresenceTerm.NATIVE_DOUBTFULLY_NATIVE();\r
case 350: return PresenceTerm.NATIVE();\r
case 999: {\r
}\r
}\r
\r
+ public static UUID getFeatureUuid(String key) throws UndefinedTransformerMethodException {\r
+ if (key == null){\r
+ return null;\r
+ }else if (key.equalsIgnoreCase("14-Maps")){ return uuidFeatureMaps;\r
+ }else if (key.equalsIgnoreCase("301-Conservation Status")){ return uuidFeatureConservationStatus;\r
+ }else if (key.equalsIgnoreCase("302-Use")){ return uuidFeatureUse;\r
+ }else if (key.equalsIgnoreCase("303-Comments")){ return uuidFeatureComments;\r
+ \r
+ }else if (key.equalsIgnoreCase("10-general distribution (Euro+Med)")){ return uuidFeatureDistrEM;\r
+ }else if (key.equalsIgnoreCase("11-general distribution (world)")){ return uuidFeatureDistrWorld;\r
+ }else if (key.equalsIgnoreCase("250-Editor_Brackets")){ return uuidFeatureEditorBrackets;\r
+ }else if (key.equalsIgnoreCase("251-Editor_Parenthesis")){ return uuidFeatureEditorParenthesis;\r
+ }else if (key.equalsIgnoreCase("252-Inedited")){ return uuidFeatureInedited;\r
+ }else if (key.equalsIgnoreCase("253-Comments on editing process")){ return uuidFeatureCommentsEditing;\r
+ \r
+ }else{\r
+ return null;\r
+ }\r
+ }\r
+ \r
\r
- public static UUID uuidRankCollSpecies = UUID.fromString("e14630ee-9446-4bb4-a7b7-4c3881bc5d94");\r
static Rank collSpeciesRank;\r
/**\r
* @param i\r
* @return\r
*/\r
- private static Rank rankId2NewRank(Integer rankId) {\r
+ private static Rank rankId2NewRank(Integer rankId, boolean switchRank) {\r
Rank result = null;\r
if (rankId == null){\r
return null;\r
}else if (rankId == 57){\r
+ \r
if (collSpeciesRank == null){\r
- collSpeciesRank = new Rank();\r
- Representation representation = Representation.NewInstance("Collective species", "Coll. species", "coll.", Language.ENGLISH());\r
- collSpeciesRank.addRepresentation(representation);\r
+ collSpeciesRank = Rank.NewInstance(RankClass.SpeciesGroup, "Collective species", "Coll. species", "coll.");\r
collSpeciesRank.setUuid(uuidRankCollSpecies);\r
OrderedTermVocabulary<Rank> voc = (OrderedTermVocabulary<Rank>)Rank.SPECIES().getVocabulary();\r
voc.addTermBelow(collSpeciesRank, Rank.SPECIESGROUP());\r
}\r
return result;\r
}\r
+\r
\r
- public static Rank rankId2Rank (ResultSet rs, boolean useUnknown) throws UnknownCdmTypeException{\r
+ public static Rank rankId2Rank (ResultSet rs, boolean useUnknown, boolean switchSpeciesGroup) throws UnknownCdmTypeException{\r
Rank result;\r
try {\r
int rankId = rs.getInt("rankFk");\r
if (logger.isDebugEnabled()){logger.debug(abbrev);}\r
if (logger.isDebugEnabled()){logger.debug(rankName);}\r
\r
+ if (switchSpeciesGroup){\r
+ if (rankId == 59){\r
+ rankId = 57;\r
+ }else if (rankId == 57){\r
+ rankId = 59;\r
+ }\r
+ }\r
try {\r
result = Rank.getRankByNameOrAbbreviation(abbrev);\r
} catch (UnknownCdmTypeException e) {\r
case 60: return Rank.SPECIES();\r
case 61: return Rank.GREX();\r
case 65: return Rank.SUBSPECIES();\r
+ case 66: {System.out.println("Rank 66 not yet implemented"); throw new UnknownCdmTypeException("Unknown Rank id" + Integer.valueOf(rankId).toString());}\r
+ case 67: {System.out.println("Rank 67 not yet implemented"); throw new UnknownCdmTypeException("Unknown Rank id" + Integer.valueOf(rankId).toString());}\r
case 68: return Rank.CONVAR();\r
case 70: return Rank.VARIETY();\r
case 73: return Rank.SUBVARIETY();\r
case 830: return Rank.SUPERFAMILY();\r
\r
default: {\r
- Rank rank = rankId2NewRank(57);\r
+ Rank rank = rankId2NewRank(57, switchSpeciesGroup);\r
if (rank != null){\r
return rank;\r
}\r
return Rank.UNKNOWN_RANK();\r
} \r
}\r
- \r
+\r
+\r
public static Integer rank2RankId (Rank rank){\r
if (rank == null){\r
return null;\r
\r
}\r
\r
+ public static UUID getWebMarkerUuid (int markerCategoryId){\r
+ if (markerCategoryId == 1){\r
+ return UUID.fromString("d8554418-d1ae-471d-a1bd-a0cbc7ab860c"); //any as not to find in cichorieae\r
+ }else if (markerCategoryId == 2){\r
+ return UUID.fromString("7f189c48-8632-4870-9ec8-e4d2489f324e");\r
+ }else if (markerCategoryId == 3){\r
+ return UUID.fromString("9a115e6b-8210-4dd3-825a-6fed11016c63");\r
+ }else if (markerCategoryId == 4){\r
+ return UUID.fromString("1d287011-2054-41c5-a919-17ac1d0a9270");\r
+ }else if (markerCategoryId == 9){\r
+ return UUID.fromString("cc5eca5c-1ae5-4feb-9a95-507fc167b0c9");\r
+ }else{\r
+ logger.warn("Unknown webMarker category: " + markerCategoryId);\r
+ return null;\r
+ }\r
+ \r
+ }\r
\r
}\r
BGBM BDI Projects / cdmlib.git / blobdiff