X-Git-Url: https://dev.e-taxonomy.eu/gitweb/cdmlib.git/blobdiff_plain/8876b54d5cd22238f2eb68224bfc5606b807b606..49e81aee0f9b59a30f61188ed0b0aec9384fdde6:/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/faunaEuropaea/FaunaEuropaeaTransformer.java diff --git a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/faunaEuropaea/FaunaEuropaeaTransformer.java b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/faunaEuropaea/FaunaEuropaeaTransformer.java index ce3f2fede7..fabed907a6 100644 --- a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/faunaEuropaea/FaunaEuropaeaTransformer.java +++ b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/faunaEuropaea/FaunaEuropaeaTransformer.java @@ -13,21 +13,16 @@ import java.sql.ResultSet; import java.sql.SQLException; import java.util.HashMap; import java.util.Map; +import java.util.UUID; import org.apache.log4j.Logger; -import org.springframework.stereotype.Component; -import eu.etaxonomy.cdm.common.ResultWrapper; import eu.etaxonomy.cdm.model.description.AbsenceTerm; -import eu.etaxonomy.cdm.model.description.Feature; import eu.etaxonomy.cdm.model.description.PresenceAbsenceTermBase; import eu.etaxonomy.cdm.model.description.PresenceTerm; import eu.etaxonomy.cdm.model.location.NamedArea; import eu.etaxonomy.cdm.model.location.TdwgArea; -import eu.etaxonomy.cdm.model.name.HybridRelationshipType; import eu.etaxonomy.cdm.model.name.Rank; -import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus; -import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType; import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException; /** @@ -47,12 +42,17 @@ public final class FaunaEuropaeaTransformer { public static final int T_STATUS_NOT_ACCEPTED = 0; // Author - public static final int A_AUCT = 1; + public static final int A_AUCT = 0; // Was A_AUCT = 1 public static final String A_AUCTNAME = "auct."; // Parenthesis public static final int P_PARENTHESIS = 1; + //new AbsencePresenceTermUUIDs + + public static UUID noData; + //public static UUID doubtfull_present; + // Rank public static final int R_KINGDOM = 1; public static final int R_SUBKINGDOM = 2; @@ -80,23 +80,36 @@ public final class FaunaEuropaeaTransformer { private static Map tdwgAreas = null; public static PresenceAbsenceTermBase occStatus2PresenceAbsence(int occStatusId) throws UnknownCdmTypeException{ + + if (Integer.valueOf(occStatusId) == null) { + return PresenceTerm.PRESENT(); + } switch (occStatusId){ - case 0: return AbsenceTerm.ABSENT(); - case 2: return PresenceTerm.INTRODUCED(); - case 1: return PresenceTerm.NATIVE(); - default: { - throw new UnknownCdmTypeException("Unknown presence status (id=" + Integer.valueOf(occStatusId).toString() + ")"); - } + case 0: return PresenceTerm.PRESENT(); + case 2: return AbsenceTerm.ABSENT(); + case 1: return PresenceTerm.PRESENT_DOUBTFULLY(); + + default: { + + return null; + + } + + } + } + public static void setUUIDs(HashMap uuids){ + noData = uuids.get("noData"); + //doubtfull_present = uuids.get("doubtfullPresent"); + } - public static PresenceAbsenceTermBase occStatus2PresenceAbsence_ (int occStatusId) throws UnknownCdmTypeException{ switch (occStatusId){ case 0: return null; - case 110: return PresenceTerm.CULTIVATED_REPORTED_IN_ERROR(); + //case 110: return AbsenceTerm.CULTIVATED_REPORTED_IN_ERROR(); case 120: return PresenceTerm.CULTIVATED(); - case 210: return PresenceTerm.INTRODUCED_REPORTED_IN_ERROR(); + // case 210: return AbsenceTerm.INTRODUCED_REPORTED_IN_ERROR(); case 220: return PresenceTerm.INTRODUCED_PRESENCE_QUESTIONABLE(); case 230: return PresenceTerm.INTRODUCED_FORMERLY_INTRODUCED(); case 240: return PresenceTerm.INTRODUCED_DOUBTFULLY_INTRODUCED(); @@ -104,7 +117,7 @@ public final class FaunaEuropaeaTransformer { case 260: return PresenceTerm.INTRODUCED_UNCERTAIN_DEGREE_OF_NATURALISATION(); case 270: return PresenceTerm.INTRODUCED_ADVENTITIOUS(); case 280: return PresenceTerm.INTRODUCED_NATURALIZED(); - case 310: return PresenceTerm.NATIVE_REPORTED_IN_ERROR(); + //case 310: return AbsenceTerm.NATIVE_REPORTED_IN_ERROR(); case 320: return PresenceTerm.NATIVE_PRESENCE_QUESTIONABLE(); case 330: return PresenceTerm.NATIVE_FORMERLY_NATIVE(); case 340: return PresenceTerm.NATIVE_DOUBTFULLY_NATIVE(); @@ -181,24 +194,24 @@ public final class FaunaEuropaeaTransformer { } - public static NamedArea areaId2TdwgArea (FaunaEuropaeaDistributionTaxon fauEuTaxon) + public static NamedArea areaId2TdwgArea (FaunaEuropaeaDistribution fauEuDistribution) throws UnknownCdmTypeException { NamedArea tdwgArea = null; try { - int areaId = fauEuTaxon.getAreaId(); - String areaName = fauEuTaxon.getAreaName(); - String areaCode = fauEuTaxon.getAreaCode(); - int extraLimital = fauEuTaxon.getExtraLimital(); + int areaId = fauEuDistribution.getAreaId(); + String areaName = fauEuDistribution.getAreaName(); + String areaCode = fauEuDistribution.getAreaCode(); + int extraLimital = fauEuDistribution.getExtraLimital(); //TODO: Verify mappings with comments. Those don't map to TDWG areas. if (areaCode.equals("AD")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("SPA-AN"); - else if (areaCode.equals("AFR")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("24"); // Afro-tropical region - Northeast Tropical Africa + //else if (areaCode.equals("AFR")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("24"); // Afro-tropical region - Northeast Tropical Africa else if (areaCode.equals("AL")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("ALB-OO"); else if (areaCode.equals("AT")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("AUT-AU"); - else if (areaCode.equals("AUS")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("50"); // Australian region - Australia + //else if (areaCode.equals("AUS")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("50"); // Australian region - Australia else if (areaCode.equals("BA")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("YUG-BH"); else if (areaCode.equals("BE")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("BGM-BE"); else if (areaCode.equals("BG")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("BUL-OO"); @@ -210,7 +223,7 @@ public final class FaunaEuropaeaTransformer { else if (areaCode.equals("DK-DEN")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("DEN-OO"); else if (areaCode.equals("DK-FOR")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("FOR-OO"); else if (areaCode.equals("EE")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("BLT-ES"); - else if (areaCode.equals("EPA")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("3"); // Palaearctic - Asia-Temperate + //else if (areaCode.equals("EPA")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("3"); // Palaearctic - Asia-Temperate else if (areaCode.equals("ES-BAL")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("BLT-ES"); else if (areaCode.equals("ES-CNY")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("CNY-OO"); else if (areaCode.equals("ES-SPA")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("SPA-SP"); @@ -221,9 +234,9 @@ public final class FaunaEuropaeaTransformer { else if (areaCode.equals("GB-GI")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("SPA-GI"); else if (areaCode.equals("GB-GRB")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("GRB-OO"); else if (areaCode.equals("GB-NI")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("IRE-NI"); - else if (areaCode.equals("GR-AEG")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("EAI-OO"); // North Aegean Is. - East Aegean Is. - else if (areaCode.equals("GR-CYC")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("GRC-OO"); // Cyclades Is. - Greece - else if (areaCode.equals("GR-DOD")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("EAI-OO"); // Dodecanese Is. - East Aegean Is. + //else if (areaCode.equals("GR-AEG")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("EAI-OO"); // North Aegean Is. - East Aegean Is. + //else if (areaCode.equals("GR-CYC")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("GRC-OO"); // Cyclades Is. - Greece + //else if (areaCode.equals("GR-DOD")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("EAI-OO"); // Dodecanese Is. - East Aegean Is. else if (areaCode.equals("GR-GRC")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("GRC-OO"); else if (areaCode.equals("GR-KRI")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("KRI-OO"); else if (areaCode.equals("HR")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("YUG-CR"); @@ -241,14 +254,14 @@ public final class FaunaEuropaeaTransformer { else if (areaCode.equals("MD")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("UKR-MO"); else if (areaCode.equals("MK")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("YUG-MA"); else if (areaCode.equals("MT")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("SIC-MA"); - else if (areaCode.equals("NAF")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("20"); // North Africa - Northern Africa - else if (areaCode.equals("NEA")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("7"); // Nearctic region - Northern America - else if (areaCode.equals("NEO")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("8"); // Neotropical region - Southern America + //else if (areaCode.equals("NAF")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("20"); // North Africa - Northern Africa + //else if (areaCode.equals("NEA")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("7"); // Nearctic region - Northern America + //else if (areaCode.equals("NEO")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("8"); // Neotropical region - Southern America else if (areaCode.equals("NL")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("NET-OO"); else if (areaCode.equals("NO-NOR")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("NOR-OO"); else if (areaCode.equals("NO-SVA")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("SVA-OO"); - else if (areaCode.equals("NRE")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("34"); // Near East - Western Asia - else if (areaCode.equals("ORR")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("35"); // Oriental region - Arabian Peninsula + //else if (areaCode.equals("NRE")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("34"); // Near East - Western Asia + //else if (areaCode.equals("ORR")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("35"); // Oriental region - Arabian Peninsula else if (areaCode.equals("PL")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("POL-OO"); else if (areaCode.equals("PT-AZO")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("AZO-OO"); else if (areaCode.equals("PT-MDR")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("MDR-OO"); @@ -279,12 +292,31 @@ public final class FaunaEuropaeaTransformer { } } catch (Exception e) { - e.printStackTrace(); - logger.warn("Exception occurred. Area could not be mapped."); + //e.printStackTrace(); + logger.debug("Exception occurred. Area could not be mapped." + fauEuDistribution.getAreaName()); return null; } return tdwgArea; } + public final static HashMap abbrToUUID = new HashMap(); + static + { + abbrToUUID.put("AUS", UUID.fromString("cf979ca8-8cb6-42df-b2ce-1f432ec7c26b")); + abbrToUUID.put("AFR", UUID.fromString("07ac5e75-9fc9-4aa0-938c-1324c9618b97")); + abbrToUUID.put("EPA", UUID.fromString("e83446d7-7379-4beb-be05-295f8da6f5ae")); + abbrToUUID.put("GR-AEG", UUID.fromString("6bd422aa-9911-4b80-8595-0f6d1ecd5eee")); + abbrToUUID.put("GR-CYC", UUID.fromString("8e7d7f1e-3e4d-4f7c-96ec-93ec91e528d6")); + abbrToUUID.put("GR-DOD", UUID.fromString("6d6f6842-924e-440b-9e7e-3df1922bf4a6")); + abbrToUUID.put("NAF", UUID.fromString("d2c54b1e-5f9f-455d-b308-6859cb153c7b")); + abbrToUUID.put("NEA", UUID.fromString("aa87f6b8-110b-44b5-a329-91a08f1a4cc9")); + abbrToUUID.put("NEO", UUID.fromString("0e6e0ce9-c6ab-46bc-80b9-aee4a0620e78")); + abbrToUUID.put("NRE", UUID.fromString("d51876c2-eaf6-4c7f-963e-337dd3e0d729")); + abbrToUUID.put("ORR", UUID.fromString("04cab4f8-b316-4e21-9bcc-236a45e4e83d")); + } + public static UUID getUUIDByAreaAbbr(String abbr){ + return abbrToUUID.get(abbr); + } + }