import java.sql.Date;\r
import java.sql.ResultSet;\r
import java.sql.SQLException;\r
+import java.util.HashMap;\r
+import java.util.Map;\r
import java.util.Set;\r
import java.util.UUID;\r
\r
import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase;\r
import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;\r
import eu.etaxonomy.cdm.io.common.Source;\r
+import eu.etaxonomy.cdm.io.common.TdwgAreaProvider;\r
import eu.etaxonomy.cdm.model.agent.Team;\r
+import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;\r
+import eu.etaxonomy.cdm.model.common.Annotation;\r
+import eu.etaxonomy.cdm.model.common.AnnotationType;\r
+import eu.etaxonomy.cdm.model.common.DefinedTerm;\r
+import eu.etaxonomy.cdm.model.common.Language;\r
import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary;\r
+import eu.etaxonomy.cdm.model.common.TermType;\r
+import eu.etaxonomy.cdm.model.common.TermVocabulary;\r
import eu.etaxonomy.cdm.model.common.TimePeriod;\r
import eu.etaxonomy.cdm.model.description.DescriptionBase;\r
import eu.etaxonomy.cdm.model.description.Feature;\r
import eu.etaxonomy.cdm.model.description.SpecimenDescription;\r
import eu.etaxonomy.cdm.model.description.State;\r
+import eu.etaxonomy.cdm.model.description.TaxonDescription;\r
+import eu.etaxonomy.cdm.model.location.Country;\r
import eu.etaxonomy.cdm.model.location.NamedArea;\r
+import eu.etaxonomy.cdm.model.location.NamedAreaType;\r
import eu.etaxonomy.cdm.model.location.Point;\r
import eu.etaxonomy.cdm.model.location.ReferenceSystem;\r
-import eu.etaxonomy.cdm.model.location.TdwgArea;\r
-import eu.etaxonomy.cdm.model.location.WaterbodyOrCountry;\r
import eu.etaxonomy.cdm.model.occurrence.Collection;\r
+import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;\r
+import eu.etaxonomy.cdm.model.reference.Reference;\r
+import eu.etaxonomy.cdm.model.taxon.Taxon;\r
\r
/**\r
* @author a.mueller\r
public abstract class AlgaTerraSpecimenImportBase extends BerlinModelImportBase{\r
private static final Logger logger = Logger.getLogger(AlgaTerraSpecimenImportBase.class);\r
\r
- public static final String ECO_FACT_FIELD_OBSERVATION_NAMESPACE = "EcoFact";\r
- public static final String ECO_FACT_DERIVED_UNIT_NAMESPACE = "EcoFact";\r
+ public static final String ECO_FACT_FIELD_OBSERVATION_NAMESPACE = "EcoFact_FieldObservation";\r
+ public static final String ECO_FACT_DERIVED_UNIT_NAMESPACE = "EcoFact_DerivedUnit";\r
public static final String TYPE_SPECIMEN_FIELD_OBSERVATION_NAMESPACE = "TypeSpecimen_FieldObservation";\r
public static final String TYPE_SPECIMEN_DERIVED_UNIT_NAMESPACE = "TypeSpecimen_DerivedUnit";\r
+ public static final String FACT_ECOLOGY_NAMESPACE = "Fact (Ecology)";\r
+ \r
\r
public static final String TERMS_NAMESPACE = "ALGA_TERRA_TERMS";\r
\r
//TODO move to transformrer\r
final static UUID uuidMarkerAlkalinity = UUID.fromString("e52d0ea2-0c1f-4d95-ae6d-e21ab317c594"); \r
final static UUID uuidRefSystemGps = UUID.fromString("c23e4928-c137-4e4a-b6ab-b430da3d0b94"); \r
- final static UUID uuidFeatureSpecimenCommunity = UUID.fromString("3ff5b1ab-3999-4b5a-b8f7-01fd2f6c12c7");\r
- final static UUID uuidFeatureAdditionalData = UUID.fromString("0ac82ab8-2c2b-4953-98eb-a9f718eb9c57");\r
- final static UUID uuidFeatureHabitatExplanation = UUID.fromString("6fe32295-61a3-44fc-9fcf-a85790ea888f");\r
+ public final static UUID uuidFeatureSpecimenCommunity = UUID.fromString("3ff5b1ab-3999-4b5a-b8f7-01fd2f6c12c7");\r
+ public final static UUID uuidFeatureAdditionalData = UUID.fromString("0ac82ab8-2c2b-4953-98eb-a9f718eb9c57");\r
+ public final static UUID uuidFeatureHabitatExplanation = UUID.fromString("6fe32295-61a3-44fc-9fcf-a85790ea888f");\r
\r
final static UUID uuidVocAlgaTerraClimate = UUID.fromString("b0a677c6-8bb6-43f4-b1b8-fc377a10feb5");\r
final static UUID uuidVocAlgaTerraHabitat = UUID.fromString("06f30114-e19c-4e7d-a8e5-5488c41fcbc5");\r
final static UUID uuidVocAlgaTerraLifeForm = UUID.fromString("3c0b194e-809c-4b42-9498-6ff034066ed7");\r
\r
- final static UUID uuidFeatureAlgaTerraClimate = UUID.fromString("8754674c-9ab9-4f28-95f1-91eeee2314ee");\r
- final static UUID uuidFeatureAlgaTerraHabitat = UUID.fromString("7def3fc2-cdc5-4739-8e13-62edbd053415");\r
- final static UUID uuidFeatureAlgaTerraLifeForm = UUID.fromString("9b657901-1b0d-4a2a-8d21-dd8c1413e2e6");\r
+ public final static UUID uuidFeatureAlgaTerraClimate = UUID.fromString("8754674c-9ab9-4f28-95f1-91eeee2314ee");\r
+ public final static UUID uuidFeatureAlgaTerraHabitat = UUID.fromString("7def3fc2-cdc5-4739-8e13-62edbd053415");\r
+ public final static UUID uuidFeatureAlgaTerraLifeForm = UUID.fromString("9b657901-1b0d-4a2a-8d21-dd8c1413e2e6");\r
\r
final static UUID uuidVocParameter = UUID.fromString("45888b40-5bbb-4293-aa1e-02479796cd7c");\r
final static UUID uuidStatMeasureSingleValue = UUID.fromString("eb4c3d98-4d4b-4c37-8eb4-17315ce79920");\r
TransactionStatus txStatus = this.startTransaction();\r
\r
boolean isOrdered = true;\r
- OrderedTermVocabulary<State> climateVoc = (OrderedTermVocabulary)getVocabulary(uuidVocAlgaTerraClimate, "Climate", "Climate", abbrevLabel, uri, isOrdered, null);\r
- OrderedTermVocabulary<State> habitatVoc = (OrderedTermVocabulary)getVocabulary(uuidVocAlgaTerraHabitat, "Habitat", "Habitat", abbrevLabel, uri, isOrdered, null);\r
- OrderedTermVocabulary<State> lifeformVoc = (OrderedTermVocabulary)getVocabulary(uuidVocAlgaTerraLifeForm, "Lifeform", "Lifeform", abbrevLabel, uri, isOrdered, null);\r
- \r
+ State tmp = State.NewInstance();\r
+ OrderedTermVocabulary<State> climateVoc = (OrderedTermVocabulary<State>)getVocabulary(TermType.State, uuidVocAlgaTerraClimate, "Climate", "Climate", abbrevLabel, uri, isOrdered, tmp);\r
+ OrderedTermVocabulary<State> habitatVoc = (OrderedTermVocabulary<State>)getVocabulary(TermType.State, uuidVocAlgaTerraHabitat, "Habitat", "Habitat", abbrevLabel, uri, isOrdered, tmp);\r
+ OrderedTermVocabulary<State> lifeformVoc = (OrderedTermVocabulary<State>)getVocabulary(TermType.State, uuidVocAlgaTerraLifeForm, "Lifeform", "Lifeform", abbrevLabel, uri, isOrdered, tmp);\r
\r
Feature feature = getFeature(state, uuidFeatureAlgaTerraClimate, "Climate","Climate", null, null);\r
feature.setSupportsCategoricalData(true);\r
addOriginalSource(stateTerm, id.toString(), "EcoLifeForm", state.getTransactionalSourceReference());\r
getTermService().saveOrUpdate(stateTerm);\r
}\r
+ \r
+ //material category\r
+ TermVocabulary<DefinedTerm> materialCategoryVoc = getVocabulary(TermType.KindOfUnit, AlgaTerraImportTransformer.uuidKindOfUnitVoc, "Alga Terra Material Category", "Alga Terra Material Category", abbrevLabel, uri, false, DefinedTerm.NewKindOfUnitInstance(null, null, null));\r
+ getVocabularyService().save(materialCategoryVoc);\r
+ \r
+ String materialSql = "SELECT * FROM MaterialCategory WHERE MaterialCategoryId <> 16 ";\r
+ rs = source.getResultSet(materialSql);\r
+ while (rs.next()){\r
+ Integer id = rs.getInt("MaterialCategoryId");\r
+ String category = rs.getString("MaterialCategory");\r
+ String description = rs.getString("Description");\r
+ UUID uuid = UUID.randomUUID();\r
+ \r
+ DefinedTerm kindOfUnit = DefinedTerm.NewKindOfUnitInstance(description, category, null);\r
+ kindOfUnit.setUuid(uuid);\r
+ addOriginalSource(kindOfUnit, id.toString(), "MaterialCategory", state.getTransactionalSourceReference());\r
+ materialCategoryVoc.addTerm(kindOfUnit);\r
+ getTermService().saveOrUpdate(kindOfUnit);\r
+ materialCategoryMapping.put(id, uuid);\r
+ }\r
+ \r
+ //areas\r
+ OrderedTermVocabulary<NamedArea> informalAreasVoc = (OrderedTermVocabulary<NamedArea>)getVocabulary(TermType.NamedArea, AlgaTerraImportTransformer.uuidNamedAreaVocAlgaTerraInformalAreas, "AlgaTerra Specific Areas", "AlgaTerra Specific Areas", abbrevLabel, uri, true, NamedArea.NewInstance());\r
+ getVocabularyService().save(informalAreasVoc);\r
+ \r
+ String areaSql = "SELECT * FROM TDWGGazetteer WHERE subL4 = 1 ";\r
+ rs = source.getResultSet(areaSql);\r
+ while (rs.next()){\r
+ String l1Code = rs.getString("L1Code");\r
+ String l2Code = rs.getString("L2Code");\r
+ String l3Code = rs.getString("L3Code");\r
+ String l4Code = rs.getString("L4Code");\r
+ String gazetteer = rs.getString("Gazetteer");\r
+ Integer id = rs.getInt("ID");\r
+ String notes = rs.getString("Notes");\r
+ //TODO stable uuids\r
+// UUID uuid = UUID.fromString(rs.getString("UUID"));\r
+ UUID uuid = UUID.randomUUID();\r
+ subL4Mapping.put(id, uuid);\r
+ \r
+ String tdwgCode = (l4Code != null) ? l4Code : (l3Code != null) ? l3Code : (l2Code != null) ? l2Code : l1Code;\r
+ \r
+ NamedArea tdwgArea = TdwgAreaProvider.getAreaByTdwgAbbreviation(tdwgCode);\r
+ NamedArea newArea = getNamedArea(state, uuid ,gazetteer, gazetteer, null, null, null, informalAreasVoc, TermMatchMode.UUID_ONLY, null);\r
+ if (isNotBlank(notes)){\r
+ newArea.addAnnotation(Annotation.NewInstance(notes, AnnotationType.EDITORIAL(), Language.DEFAULT()));\r
+ }\r
+ \r
+ addOriginalSource(newArea, id.toString(), "TDWGGazetteer", state.getTransactionalSourceReference());\r
+ getTermService().saveOrUpdate(newArea);\r
+ newArea.setPartOf(tdwgArea);\r
+ informalAreasVoc.addTerm(newArea);\r
+ }\r
\r
this.commitTransaction(txStatus);\r
\r
state.setSpecimenVocabulariesCreated(true);\r
- }\r
- \r
+ } \r
}\r
\r
+ //tmp\r
+ static Map<Integer, UUID> subL4Mapping = new HashMap<Integer, UUID>();\r
+ static Map<Integer, UUID> materialCategoryMapping = new HashMap<Integer, UUID>();\r
+ \r
protected String getLocalityString(){\r
return "Locality";\r
}\r
\r
- protected void handleSingleSpecimen(ResultSet rs, DerivedUnitFacade facade, AlgaTerraImportState state, ResultSetPartitioner partitioner) throws SQLException {\r
+ protected void handleFieldObservationSpecimen(ResultSet rs, DerivedUnitFacade facade, AlgaTerraImportState state, ResultSetPartitioner partitioner) throws SQLException {\r
//FIXME missing fields #3084, #3085, #3080\r
try {\r
\r
String geoCodeMethod = rs.getString("GeoCodeMethod");\r
\r
Integer altitude = nullSafeInt(rs, "Altitude");\r
- Integer lowerAltitude = nullSafeInt(rs,"AltitudeLowerValue");\r
+ Integer lowerAltitude = nullSafeInt(rs, "AltitudeLowerValue");\r
String altitudeUnit = rs.getString("AltitudeUnit");\r
Double depth = nullSafeDouble(rs, "Depth");\r
Double depthLow = nullSafeDouble(rs, "DepthLow");\r
Date collectionDateStart = rs.getDate("CollectionDate");\r
Date collectionDateEnd = rs.getDate("CollectionDateEnd");\r
\r
- Integer collectionFk = nullSafeInt(rs,"CollectionFk");\r
- \r
- \r
//location\r
facade.setLocality(locality);\r
\r
if (lowerAltitude == null){\r
facade.setAbsoluteElevation(altitude);\r
}else{\r
- if (! facade.isEvenDistance(lowerAltitude, altitude)){\r
- //FIXME there is a ticket for this\r
- altitude = altitude + 1;\r
- logger.info("Current implementation of altitude does not allow uneven distances");\r
- }\r
facade.setAbsoluteElevationRange(lowerAltitude,altitude);\r
}\r
}\r
if ( depth != null){\r
- //FIXME needs model change to accept double #3072\r
- Integer intDepth = depth.intValue();\r
if (depthLow == null){\r
- facade.setDistanceToWaterSurface(intDepth);\r
+ facade.setDistanceToWaterSurface(depth);\r
}else{\r
- //FIXME range not yet in model #3074\r
- facade.setDistanceToWaterSurface(intDepth);\r
+ //TODO which direction is correct?\r
+ facade.setDistanceToWaterSurfaceRange(depth, depthLow);\r
}\r
}\r
\r
\r
//areas\r
makeAreas(state, rs, facade);\r
- \r
- //collection\r
- if (collectionFk != null){\r
- Collection subCollection = state.getRelatedObject(AlgaTerraCollectionImport.NAMESPACE_SUBCOLLECTION, String.valueOf(collectionFk), Collection.class);\r
- if (subCollection != null){\r
- facade.setCollection(subCollection);\r
- }else{\r
- Collection collection = state.getRelatedObject(AlgaTerraCollectionImport.NAMESPACE_COLLECTION, String.valueOf(collectionFk), Collection.class);\r
- facade.setCollection(collection);\r
- }\r
- }\r
- \r
+\r
//notes\r
- //TODO is this an annotation on field observation or on the derived unit?\r
+ //=> not required according to Henning\r
\r
- //TODO id, created for fact + ecoFact\r
- // this.doIdCreatedUpdatedNotes(state, descriptionElement, rs, id, namespace);\r
+ //id, created, updated, notes\r
if (unitId != null){\r
- this.doIdCreatedUpdatedNotes(state, facade.innerDerivedUnit(), rs, unitId, getDerivedUnitNameSpace());\r
+ this.doIdCreatedUpdatedNotes(state, facade.innerFieldUnit(), rs, unitId, getFieldObservationNameSpace());\r
}else{\r
- logger.warn("Specimen has no unitId: " + facade.innerDerivedUnit() + ": " + getDerivedUnitNameSpace());\r
+ logger.warn("FieldObservation has no unitId: " + facade.innerFieldUnit() + ": " + getFieldObservationNameSpace());\r
}\r
- \r
- \r
} catch (Exception e) {\r
throw new RuntimeException(e);\r
}\r
\r
}\r
\r
+ protected void handleFirstDerivedSpecimen(ResultSet rs, DerivedUnitFacade facade, AlgaTerraImportState state, ResultSetPartitioner partitioner) throws SQLException {\r
+ Integer unitId = nullSafeInt(rs, "unitId");\r
+ Integer collectionFk = nullSafeInt(rs,"CollectionFk");\r
+ String label = rs.getString("Label"); \r
+ \r
+ //collection\r
+ if (collectionFk != null){\r
+ Collection subCollection = state.getRelatedObject(AlgaTerraCollectionImport.NAMESPACE_SUBCOLLECTION, String.valueOf(collectionFk), Collection.class);\r
+ if (subCollection != null){\r
+ facade.setCollection(subCollection);\r
+ }else{\r
+ Collection collection = state.getRelatedObject(AlgaTerraCollectionImport.NAMESPACE_COLLECTION, String.valueOf(collectionFk), Collection.class);\r
+ if (collection == null){\r
+ logger.warn("Collection for collectionFK " + collectionFk + " can not be found.");\r
+ }\r
+ facade.setCollection(collection);\r
+ }\r
+ }\r
+ \r
+ //Label\r
+ if (isNotBlank(label)){\r
+ //TODO implement label #4218, #3090, #3084\r
+ logger.warn("Label not yet implemented for specimen, #4218, #3090, #3084");\r
+ }\r
+ \r
+ //TODO id, created for fact + ecoFact\r
+ // this.doIdCreatedUpdatedNotes(state, descriptionElement, rs, id, namespace);\r
+ if (unitId != null){\r
+ this.doIdCreatedUpdatedNotes(state, facade.innerDerivedUnit(), rs, unitId, getDerivedUnitNameSpace());\r
+ }else{\r
+ logger.warn("Specimen has no unitId: " + facade.innerDerivedUnit() + ": " + getDerivedUnitNameSpace());\r
+ }\r
+ }\r
+ \r
+ \r
+ \r
protected abstract String getDerivedUnitNameSpace();\r
+ \r
+ protected abstract String getFieldObservationNameSpace();\r
+ \r
\r
protected DescriptionBase getFieldObservationDescription(DerivedUnitFacade facade) {\r
- Set<DescriptionBase> descriptions = facade.innerFieldObservation().getDescriptions();\r
+ Set<DescriptionBase> descriptions = facade.innerFieldUnit().getDescriptions();\r
for (DescriptionBase desc : descriptions){\r
if (desc.isImageGallery() == false){\r
return desc;\r
}\r
}\r
- SpecimenDescription specDesc = SpecimenDescription.NewInstance(facade.innerFieldObservation());\r
+ SpecimenDescription specDesc = SpecimenDescription.NewInstance(facade.innerFieldUnit());\r
descriptions.add(specDesc);\r
return specDesc;\r
}\r
\r
\r
private void makeAreas(AlgaTerraImportState state, ResultSet rs, DerivedUnitFacade facade) throws SQLException {\r
- Object gazetteerId = rs.getObject("GazetteerId");\r
+ Integer gazetteerId = nullSafeInt(rs, "GazetteerId");\r
if (gazetteerId != null){\r
//TDWG\r
NamedArea tdwgArea;\r
String tdwg4 = rs.getString("L4Code");\r
if (isNotBlank(tdwg4)){\r
- tdwgArea = TdwgArea.getAreaByTdwgAbbreviation(tdwg4);\r
+ tdwgArea = TdwgAreaProvider.getAreaByTdwgAbbreviation(tdwg4);\r
}else{\r
String tdwg3 = rs.getString("L3Code");\r
if (isNotBlank(tdwg3)){\r
- tdwgArea = TdwgArea.getAreaByTdwgAbbreviation(tdwg3);\r
+ tdwgArea = TdwgAreaProvider.getAreaByTdwgAbbreviation(tdwg3);\r
}else{\r
- Integer tdwg2 = rs.getInt("L2Code"); \r
- tdwgArea = TdwgArea.getAreaByTdwgAbbreviation(String.valueOf(tdwg2));\r
+ Number tdwg2D = nullSafeDouble(rs, "L2Code"); \r
+ if (tdwg2D != null){\r
+ Integer tdwg2 = tdwg2D.intValue();\r
+ tdwgArea = TdwgAreaProvider.getAreaByTdwgAbbreviation(String.valueOf(tdwg2));\r
+ }else{\r
+ Number tdwg1D = nullSafeDouble(rs, "L1Code"); \r
+ if (tdwg1D != null){\r
+ Integer tdwg1 = tdwg1D.intValue();\r
+ tdwgArea = TdwgAreaProvider.getAreaByTdwgAbbreviation(String.valueOf(tdwg1));\r
+ }else{\r
+ tdwgArea = null;\r
+ }\r
+ }\r
}\r
}\r
if (tdwgArea == null){\r
}\r
\r
//Countries\r
- WaterbodyOrCountry country = null;\r
+ Country country = null;\r
String isoCountry = rs.getString("ISOCountry");\r
String countryStr = rs.getString("Country");\r
if (isNotBlank(isoCountry)){\r
- country = WaterbodyOrCountry.getWaterbodyOrCountryByIso3166A2(isoCountry);\r
+ country = Country.getCountryByIso3166A2(isoCountry);\r
}else if (isNotBlank(countryStr)){\r
logger.warn("Country exists but no ISO code");\r
+ }else{\r
+ \r
+ }\r
+ \r
+ NamedArea subL4Area = null;\r
+ Boolean subL4 = nullSafeBoolean(rs, "subL4");\r
+ if (subL4 != null && subL4.booleanValue() == true){\r
+ subL4Area = makeSubL4Area(state, gazetteerId);\r
+ if (subL4Area != null){\r
+ facade.addCollectingArea(subL4Area);\r
+ }else{\r
+ logger.warn("SubL4 area not found for gazetteerId: " + gazetteerId);\r
+ }\r
}\r
- if (country == null){\r
- logger.warn("Country does not exist for GazetteerID " + gazetteerId);\r
+ \r
+ if (country == null ){\r
+ if (! gazetteerId.equals(40)){//special handling for Borneo, TDWG area is enough here as it matches exactly\r
+ if (subL4Area == null ){\r
+ logger.warn("Country does not exist and SubL4 could not be found for GazetteerID " + gazetteerId);\r
+ }else { \r
+ logger.info("Country could not be defined but subL4 area was added");\r
+ }\r
+ }\r
}else{\r
facade.setCountry(country);\r
}\r
}\r
\r
//Waterbody\r
- WaterbodyOrCountry waterbody = null;\r
+ NamedArea waterbody = null;\r
String waterbodyStr = rs.getString("WaterBody");\r
if (isNotBlank(waterbodyStr)){\r
if (waterbodyStr.equals("Atlantic Ocean")){\r
- waterbody = WaterbodyOrCountry.ATLANTICOCEAN();\r
+ waterbody = NamedArea.ATLANTICOCEAN();\r
+ }else if (waterbodyStr.equals("Pacific Ocean")){\r
+ waterbody = NamedArea.PACIFICOCEAN();\r
+ }else if (waterbodyStr.equals("Indian Ocean")){\r
+ waterbody = NamedArea.INDIANOCEAN();\r
+ }else if (waterbodyStr.equals("Arctic Ocean")){\r
+ waterbody = NamedArea.ARCTICOCEAN();\r
}else{\r
logger.warn("Waterbody not recognized: " + waterbody);\r
}\r
}\r
\r
\r
- \r
+ private NamedArea makeSubL4Area(AlgaTerraImportState state, Integer gazetteerId) {\r
+ UUID uuid = subL4Mapping.get(gazetteerId);\r
+ NamedArea area = (NamedArea)getTermService().find(uuid);\r
+ if (area == null){\r
+ logger.warn("SubL4 area could not be found in repository");\r
+ }\r
+ return area;\r
+ }\r
\r
+ private boolean handleMissingCountry(AlgaTerraImportState state, DerivedUnitFacade facade, Integer gazetteerId) {\r
+ NamedArea area = null;\r
+ if (gazetteerId != null){\r
+ if (gazetteerId.equals(42)){\r
+ area = getNamedArea(state, AlgaTerraImportTransformer.uuidNamedAreaBorneo, null, null, null, null, null);\r
+ }else if (gazetteerId.equals(1684)){\r
+ area = getNamedArea(state, AlgaTerraImportTransformer.uuidNamedAreaPatagonia, null, null, null, null, null);\r
+ }else if (gazetteerId.equals(2167)){\r
+ area = getNamedArea(state, AlgaTerraImportTransformer.uuidNamedAreaTierraDelFuego, null, null, null, null, null);\r
+ }\r
+ }\r
+ if (area != null){\r
+ facade.addCollectingArea(area);\r
+ return true;\r
+ }\r
+ return false;\r
+ \r
+ }\r
+\r
+ protected SpecimenOrObservationType makeDerivedUnitType(String recordBasis) {\r
+ SpecimenOrObservationType result = null;\r
+ if (StringUtils.isBlank(recordBasis)){\r
+ result = SpecimenOrObservationType.DerivedUnit;\r
+ } else if (recordBasis.equalsIgnoreCase("FossileSpecimen")){\r
+ result = SpecimenOrObservationType.Fossil;\r
+ }else if (recordBasis.equalsIgnoreCase("HumanObservation")){\r
+ result = SpecimenOrObservationType.HumanObservation;\r
+ }else if (recordBasis.equalsIgnoreCase("Literature")){\r
+ //FIXME\r
+ logger.warn("Literature record basis not yet supported");\r
+ result = SpecimenOrObservationType.DerivedUnit;\r
+ }else if (recordBasis.equalsIgnoreCase("LivingSpecimen")){\r
+ result = SpecimenOrObservationType.LivingSpecimen;\r
+ }else if (recordBasis.equalsIgnoreCase("MachineObservation")){\r
+ result = SpecimenOrObservationType.MachineObservation;\r
+ }else if (recordBasis.equalsIgnoreCase("Observation")){\r
+ result = SpecimenOrObservationType.Observation;\r
+ }else if (recordBasis.equalsIgnoreCase("LivingCulture")){\r
+ //FIXME\r
+ logger.warn("LivingCulture record basis not yet supported");\r
+ result = SpecimenOrObservationType.DerivedUnit;\r
+ }else if (recordBasis.equalsIgnoreCase("PreservedSpecimen")){\r
+ result = SpecimenOrObservationType.PreservedSpecimen;\r
+ }\r
+ return result;\r
+ }\r
+\r
+\r
+ protected Feature makeFeature(SpecimenOrObservationType type, AlgaTerraImportState state) {\r
+ if (type.equals(SpecimenOrObservationType.DerivedUnit)){\r
+ return Feature.INDIVIDUALS_ASSOCIATION();\r
+ }else if (type.isFeatureObservation()){\r
+ return Feature.OBSERVATION();\r
+ }else if (type.isPreservedSpecimen()){\r
+ return Feature.SPECIMEN();\r
+ }else if (type.equals(SpecimenOrObservationType.LivingSpecimen)){\r
+ UUID uuid = AlgaTerraImportTransformer.uuidFeatureLivingSpecimen;\r
+ Feature feature = getFeature(state, uuid, "Living Specimen", "Living Specimen", null, Feature.SPECIMEN().getVocabulary());\r
+ if (feature == null){\r
+ logger.warn("Living Specimen Feature could not be created");\r
+ }\r
+ return feature;\r
+ }\r
+ logger.warn("No feature defined for derived unit type: " + type);\r
+ return null;\r
+ }\r
+ \r
private ReferenceSystem makeRefrenceSystem(String geoCodeMethod, AlgaTerraImportState state) {\r
if (StringUtils.isBlank(geoCodeMethod)){\r
return null;\r
}else if(geoCodeMethod.startsWith("Google")){\r
return ReferenceSystem.GOOGLE_EARTH();\r
}else if(geoCodeMethod.startsWith("Map")){\r
- logger.warn("Reference system " + geoCodeMethod + " not yet supported.");\r
- return null;\r
+ return ReferenceSystem.MAP();\r
}else if(geoCodeMethod.startsWith("WikiProjekt Georeferenzierung") || geoCodeMethod.startsWith("http://toolserver.org/~geohack/geohack.php") ){\r
return ReferenceSystem.WGS84();\r
}else {\r
\r
\r
private void handleCollectorTeam(AlgaTerraImportState state, DerivedUnitFacade facade, ResultSet rs) throws SQLException {\r
- // FIXME parsen\r
String collector = rs.getString("Collector");\r
- Team team = Team.NewTitledInstance(collector, collector);\r
- facade.setCollector(team);\r
+ TeamOrPersonBase<?> author = getAuthor(collector);\r
+ facade.setCollector(author);\r
+ }\r
+\r
+ /**\r
+ * @param facade\r
+ * @param collector\r
+ */\r
+ protected TeamOrPersonBase<?> getAuthor(String author) {\r
+ // FIXME TODO parsen und deduplizieren\r
+ Team team = Team.NewTitledInstance(author, author);\r
+ return team;\r
+ }\r
+ \r
+\r
+ /**\r
+ * Use same TaxonDescription if two records belong to the same taxon \r
+ * @param state \r
+ * @param newTaxonId\r
+ * @param oldTaxonId\r
+ * @param oldDescription\r
+ * @param taxonMap\r
+ * @return\r
+ */\r
+ protected TaxonDescription getTaxonDescription(AlgaTerraImportState state, Taxon taxon, Reference<?> sourceSec){\r
+ TaxonDescription result = null;\r
+ Set<TaxonDescription> descriptionSet= taxon.getDescriptions();\r
+ if (descriptionSet.size() > 0) {\r
+ result = descriptionSet.iterator().next(); \r
+ }else{\r
+ result = TaxonDescription.NewInstance();\r
+ result.setTitleCache(sourceSec.getTitleCache(), true);\r
+ taxon.addDescription(result);\r
+ }\r
+ return result;\r
}\r
\r
\r
BGBM BDI Projects / cdmlib-apps.git / blobdiff