\r
package eu.etaxonomy.cdm.io.algaterra;\r
\r
+import java.net.URI;\r
+import java.sql.Date;\r
import java.sql.ResultSet;\r
import java.sql.SQLException;\r
import java.util.HashMap;\r
import java.util.HashSet;\r
import java.util.Map;\r
import java.util.Set;\r
+import java.util.UUID;\r
\r
import org.apache.commons.lang.StringUtils;\r
import org.apache.log4j.Logger;\r
import org.springframework.stereotype.Component;\r
+import org.springframework.transaction.TransactionStatus;\r
\r
import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;\r
import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade.DerivedUnitType;\r
import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelTaxonImport;\r
import eu.etaxonomy.cdm.io.common.IOValidator;\r
import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;\r
+import eu.etaxonomy.cdm.io.common.Source;\r
+import eu.etaxonomy.cdm.model.agent.Team;\r
import eu.etaxonomy.cdm.model.common.CdmBase;\r
+import eu.etaxonomy.cdm.model.common.DefinedTermBase;\r
+import eu.etaxonomy.cdm.model.common.Language;\r
+import eu.etaxonomy.cdm.model.common.Marker;\r
+import eu.etaxonomy.cdm.model.common.MarkerType;\r
+import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary;\r
+import eu.etaxonomy.cdm.model.common.TimePeriod;\r
+import eu.etaxonomy.cdm.model.description.CategoricalData;\r
+import eu.etaxonomy.cdm.model.description.DescriptionBase;\r
import eu.etaxonomy.cdm.model.description.Feature;\r
import eu.etaxonomy.cdm.model.description.IndividualsAssociation;\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.description.TextData;\r
+import eu.etaxonomy.cdm.model.location.NamedArea;\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.name.BotanicalName;\r
+import eu.etaxonomy.cdm.model.name.Rank;\r
+import eu.etaxonomy.cdm.model.occurrence.FieldObservation;\r
import eu.etaxonomy.cdm.model.reference.Reference;\r
import eu.etaxonomy.cdm.model.taxon.Taxon;\r
import eu.etaxonomy.cdm.model.taxon.TaxonBase;\r
public class AlgaTerraSpecimenImport extends BerlinModelImportBase {\r
private static final Logger logger = Logger.getLogger(AlgaTerraSpecimenImport.class);\r
\r
- public static final String NAMESPACE = "Occurrence";\r
+ public static final String FIELD_OBSERVATION_NAMESPACE = "FieldObservation";\r
+ public static final String TERMS_NAMESPACE = "ALGA_TERRA_TERMS";\r
+ \r
+ //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
+ \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
+ \r
\r
\r
private static int modCount = 5000;\r
super();\r
}\r
\r
+ \r
+ \r
/* (non-Javadoc)\r
* @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getIdQuery()\r
*/\r
@Override\r
protected String getIdQuery(BerlinModelImportState state) {\r
String result = " SELECT factId " + \r
- " FROM " + getTableName() + " INNER JOIN PTaxon ON Fact.PTNameFk = PTaxon.PTNameFk AND Fact.PTRefFk = PTaxon.PTRefFk "\r
+ " FROM Fact " +\r
+ " INNER JOIN EcoFact ON Fact.ExtensionFk = EcoFact.EcoFactId " +\r
+ "INNER JOIN PTaxon ON Fact.PTNameFk = PTaxon.PTNameFk AND Fact.PTRefFk = PTaxon.PTRefFk "\r
+ " WHERE FactCategoryFk = 202 "\r
- + " ORDER BY PTaxon.RIdentifier, Fact.FactId ";\r
+ + " ORDER BY EcoFact.EcoFactId, PTaxon.RIdentifier, Fact.FactId ";\r
return result;\r
}\r
\r
@Override\r
protected String getRecordQuery(BerlinModelImportConfigurator config) {\r
String strQuery = //DISTINCT because otherwise emOccurrenceSource creates multiple records for a single distribution \r
- " SELECT PTaxon.RIdentifier as taxonId, Fact.FactId, Fact.RecordBasis, EcoFact.* " + \r
+ " SELECT PTaxon.RIdentifier as taxonId, Fact.FactId, Fact.RecordBasis, EcoFact.*, " + \r
+ " tg.ID AS GazetteerId, tg.L2Code, tg.L3Code, tg.L4Code, tg.Country, tg.ISOCountry, " +\r
+ " ec.UUID as climateUuid, eh.UUID as habitatUuid, elf.UUID as lifeFormUuid" +\r
" FROM Fact " + \r
" INNER JOIN EcoFact ON Fact.ExtensionFk = EcoFact.EcoFactId " +\r
" INNER JOIN PTaxon ON dbo.Fact.PTNameFk = dbo.PTaxon.PTNameFk AND dbo.Fact.PTRefFk = dbo.PTaxon.PTRefFk " +\r
- " WHERE Fact.FactCategoryFk = 202 AND (Fact.FactId IN (" + ID_LIST_TOKEN + ") )" \r
- + " ORDER BY PTaxon.RIdentifier, Fact.FactId "\r
+ " LEFT OUTER JOIN TDWGGazetteer tg ON EcoFact.TDWGGazetteerFk = tg.ID " +\r
+ " LEFT OUTER JOIN EcoClimate ec ON EcoFact.ClimateFk = ec.ClimateId " +\r
+ " LEFT OUTER JOIN EcoHabitat eh ON EcoFact.HabitatFk = eh.HabitatId " +\r
+ " LEFT OUTER JOIN EcoLifeForm elf ON EcoFact.LifeFormFk = elf.LifeFormId " +\r
+ " WHERE Fact.FactCategoryFk = 202 AND (Fact.FactId IN (" + ID_LIST_TOKEN + ") )" \r
+ + " ORDER BY EcoFact.EcoFactId, PTaxon.RIdentifier, Fact.FactId "\r
;\r
return strQuery;\r
}\r
/* (non-Javadoc)\r
* @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#doPartition(eu.etaxonomy.cdm.io.berlinModel.in.ResultSetPartitioner, eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportState)\r
*/\r
- public boolean doPartition(ResultSetPartitioner partitioner, BerlinModelImportState state) {\r
+ public boolean doPartition(ResultSetPartitioner partitioner, BerlinModelImportState bmState) {\r
boolean success = true;\r
+ \r
+ AlgaTerraImportState state = (AlgaTerraImportState)bmState;\r
+ try {\r
+ makeVocabulariesAndFeatures(state);\r
+ } catch (SQLException e1) {\r
+ logger.warn("Exception occurred when trying to create Ecofact vocabularies: " + e1.getMessage());\r
+ e1.printStackTrace();\r
+ }\r
Set<TaxonBase> taxaToSave = new HashSet<TaxonBase>();\r
\r
Map<String, TaxonBase> taxonMap = (Map<String, TaxonBase>) partitioner.getObjectMap(BerlinModelTaxonImport.NAMESPACE);\r
- \r
+ Map<String, FieldObservation> fieldObservationMap = (Map<String, FieldObservation>) partitioner.getObjectMap(FIELD_OBSERVATION_NAMESPACE);\r
+ \r
ResultSet rs = partitioner.getResultSet();\r
\r
try {\r
- int oldTaxonId = -1;\r
- TaxonDescription oldDescription = null;\r
+ \r
int i = 0;\r
- int countDescriptions = 0;\r
- int countSpecimen = 0;\r
+\r
//for each reference\r
while (rs.next()){\r
\r
\r
int newTaxonId = rs.getInt("taxonId");\r
int factId = rs.getInt("FactId");\r
+ int ecoFactId = rs.getInt("EcoFactId");\r
+ String recordBasis = rs.getString("RecordBasis");\r
+ \r
try {\r
- \r
- String recordBasis = rs.getString("RecordBasis");\r
\r
+ //source ref\r
Reference<?> sourceRef = state.getTransactionalSourceReference();\r
- //create description(elements)\r
- TaxonDescription taxonDescription = getTaxonDescription(newTaxonId, oldTaxonId, oldDescription, taxonMap, factId, sourceRef);\r
-\r
+ \r
+ //facade\r
+ FieldObservation fieldObservation = getFieldObservation(ecoFactId, fieldObservationMap);\r
DerivedUnitType type = makeDerivedUnitType(recordBasis);\r
- DerivedUnitFacade facade = DerivedUnitFacade.NewInstance(type);\r
- \r
- handleSingleSpecimen(rs, facade);\r
+ DerivedUnitFacade facade = DerivedUnitFacade.NewInstance(type, fieldObservation);\r
+\r
+ //field observation\r
+ handleSingleSpecimen(rs, facade, state);\r
\r
+ //description element\r
+ TaxonDescription taxonDescription = getTaxonDescription(state, newTaxonId, taxonMap, factId, sourceRef);\r
IndividualsAssociation indAssociation = IndividualsAssociation.NewInstance();\r
Feature feature = makeFeature(type);\r
indAssociation.setAssociatedSpecimenOrObservation(facade.innerDerivedUnit());\r
indAssociation.setFeature(feature);\r
taxonDescription.addElement(indAssociation);\r
\r
- if (taxonDescription != oldDescription){ \r
- taxaToSave.add(taxonDescription.getTaxon()); \r
- oldDescription = taxonDescription; \r
- countDescriptions++; \r
- }\r
+ taxaToSave.add(taxonDescription.getTaxon()); \r
+ \r
+\r
} catch (Exception e) {\r
logger.warn("Exception in ecoFact: FactId " + factId + ". " + e.getMessage());\r
// e.printStackTrace();\r
\r
}\r
\r
- logger.warn("Specimen: " + countSpecimen + ", Descriptions: " + countDescriptions );\r
+// logger.warn("Specimen: " + countSpecimen + ", Descriptions: " + countDescriptions );\r
\r
logger.warn("Taxa to save: " + taxaToSave.size());\r
getTaxonService().save(taxaToSave); \r
}\r
\r
\r
- private void handleSingleSpecimen(ResultSet rs, DerivedUnitFacade facade) throws SQLException {\r
- //TDWGGazetteerFK, CollectionFk, Collector, GeoCodeMethod, Prec, AltitudeMethod, Depth,\r
- //ISOCountrySub, CollectionDate/End, WaterBody, \r
- //CreatedWhen/Who/Updated/who\r
- \r
- //P1-10Value/Unit/Parameter/Method\r
\r
-// int factId = rs.getInt("factId");\r
- String locality = rs.getString("Locality");\r
- Double latitude = rs.getDouble("Latitude");\r
- Double longitude = rs.getDouble("Longitude");\r
- int errorRadius = rs.getInt("Prec");\r
- Integer altitude = rs.getInt("Altitude");\r
- String altitudeUnit = rs.getString("AltitudeUnit");\r
- String collectorsNumber = rs.getString("CollectorsNumber");\r
- \r
- //location\r
- facade.setLocality(locality);\r
- \r
- //exact location\r
- ReferenceSystem referenceSystem = null;\r
- Point exactLocation = Point.NewInstance(longitude, latitude, referenceSystem, errorRadius);\r
- facade.setExactLocation(exactLocation);\r
+\r
+ /**\r
+ * Creates the vocabularies and the features for Climate, Habitat and Lifeform\r
+ * @param state\r
+ * @throws SQLException\r
+ */\r
+ private void makeVocabulariesAndFeatures(AlgaTerraImportState state) throws SQLException {\r
+ String abbrevLabel = null;\r
+ URI uri = null;\r
+ \r
+ if (! state.isSpecimenVocabulariesCreated()){\r
+ \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
+ \r
+ Feature feature = getFeature(state, uuidFeatureAlgaTerraClimate, "Climate","Climate", null, null);\r
+ feature.setSupportsCategoricalData(true);\r
+ \r
+ feature = getFeature(state, uuidFeatureAlgaTerraLifeForm, "LifeForm","LifeForm", null, null);\r
+ feature.setSupportsCategoricalData(true);\r
+ \r
+ feature = Feature.HABITAT();\r
+ feature.setSupportsCategoricalData(true);\r
+ getTermService().saveOrUpdate(feature);\r
+ \r
+ Source source = state.getAlgaTerraConfigurator().getSource();\r
+ \r
+ String climateSql = "SELECT * FROM EcoClimate";\r
+ ResultSet rs = source.getResultSet(climateSql);\r
+ while (rs.next()){\r
+ String climate = rs.getString("Climate");\r
+ String description = rs.getString("Description");\r
+ Integer id = rs.getInt("ClimateId");\r
+ UUID uuid = UUID.fromString(rs.getString("UUID"));\r
+ State stateTerm = getStateTerm(state, uuid, climate, description, null, climateVoc);\r
+ addOriginalSource(stateTerm, id.toString(), "EcoClimate", state.getConfig().getSourceReference());\r
+ getTermService().saveOrUpdate(stateTerm);\r
+ }\r
+ \r
+ String habitatSql = "SELECT * FROM EcoHabitat";\r
+ rs = source.getResultSet(habitatSql);\r
+ while (rs.next()){\r
+ String habitat = rs.getString("Habitat");\r
+ String description = rs.getString("Description");\r
+ Integer id = rs.getInt("HabitatId");\r
+ UUID uuid = UUID.fromString(rs.getString("UUID"));\r
+ State stateTerm = getStateTerm(state, uuid, habitat, description, null, habitatVoc);\r
+ addOriginalSource(stateTerm, id.toString(), "EcoHabitat", state.getConfig().getSourceReference());\r
+ getTermService().saveOrUpdate(stateTerm);\r
+ }\r
+ \r
+ String lifeformSql = "SELECT * FROM EcoLifeForm";\r
+ rs = source.getResultSet(lifeformSql);\r
+ while (rs.next()){\r
+ String lifeform = rs.getString("LifeForm");\r
+ String description = rs.getString("Description");\r
+ Integer id = rs.getInt("LifeFormId");\r
+ UUID uuid = UUID.fromString(rs.getString("UUID"));\r
+ State stateTerm = getStateTerm(state, uuid, lifeform, description, null, lifeformVoc);\r
+ addOriginalSource(stateTerm, id.toString(), "EcoLifeForm", state.getConfig().getSourceReference());\r
+ getTermService().saveOrUpdate(stateTerm);\r
+ }\r
+ \r
+ this.commitTransaction(txStatus);\r
+ \r
+ state.setSpecimenVocabulariesCreated(true);\r
+ }\r
+ \r
+ }\r
+\r
+\r
+\r
+ private void handleSingleSpecimen(ResultSet rs, DerivedUnitFacade facade, AlgaTerraImportState state) throws SQLException {\r
+ //CollectionFk, Collector, AltitudeMethod, \r
+ //ISOCountrySub, CreatedWhen/Who/Updated/who\r
\r
- //altitude\r
- if (StringUtils.isNotBlank(altitudeUnit) && ! altitudeUnit.trim().equalsIgnoreCase("m")){\r
- logger.warn("Altitude unit is not [m] but: " + altitudeUnit);\r
- }\r
- facade.setAbsoluteElevationRange(altitude, altitude); //TODO\r
+ //P1-10Value/Unit/Parameter/Method\r
+ \r
+ try {\r
+ Object alkalinityFlag = rs.getBoolean("AlkalinityFlag");\r
+ \r
+ String locality = rs.getString("Locality");\r
+ Double latitude = nullSafeDouble(rs, "Latitude");\r
+ Double longitude = nullSafeDouble(rs, "Longitude");\r
+ Integer errorRadius = nullSafeInt(rs,"Prec");\r
+ String geoCodeMethod = rs.getString("GeoCodeMethod");\r
+ \r
+ Integer altitude = nullSafeInt(rs, "Altitude");\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
+ \r
+ String collectorsNumber = rs.getString("CollectorsNumber");\r
+ Date collectionDateStart = rs.getDate("CollectionDate");\r
+ Date collectionDateEnd = rs.getDate("CollectionDateEnd");\r
+ \r
+ String climateUuid = rs.getString("climateUuid");\r
+ String habitatUuid = rs.getString("habitatUuid");\r
+ String lifeFormUuid = rs.getString("lifeFormUuid");\r
+ \r
+ String habitat = rs.getString("HabitatExplanation");\r
+ String community = rs.getString("Comunity");\r
+ String additionalData = rs.getString("AdditionalData");\r
+ \r
+ \r
+ \r
+ FieldObservation fieldObservation = facade.innerFieldObservation();\r
+ \r
+ //alkalinity marker\r
+ if (alkalinityFlag != null){\r
+ MarkerType alkalinityMarkerType = getMarkerType(state, uuidMarkerAlkalinity, "Alkalinity", "Alkalinity", null);\r
+ boolean alkFlag = Boolean.valueOf(alkalinityFlag.toString());\r
+ Marker alkalinityMarker = Marker.NewInstance(alkalinityMarkerType, alkFlag);\r
+ fieldObservation.addMarker(alkalinityMarker);\r
+ }\r
+ \r
+ //location\r
+ facade.setLocality(locality);\r
+ \r
+ //exact location\r
+ ReferenceSystem referenceSystem = makeRefrenceSystem(geoCodeMethod, state);\r
+ Point exactLocation = Point.NewInstance(longitude, latitude, referenceSystem, errorRadius);\r
+ facade.setExactLocation(exactLocation);\r
+ \r
+ //altitude, depth\r
+ if (StringUtils.isNotBlank(altitudeUnit) && ! altitudeUnit.trim().equalsIgnoreCase("m")){\r
+ logger.warn("Altitude unit is not [m] but: " + altitudeUnit);\r
+ }\r
+ if ( altitude != null){\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.warn("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
+ }else{\r
+ //FIXME range not yet in model #3074\r
+ facade.setDistanceToWaterSurface(intDepth);\r
+ }\r
+ }\r
+ \r
+ //habitat, ecology, community, etc.\r
+ DescriptionBase<?> fieldDescription = getFieldObservationDescription(facade);\r
+ addCategoricalValue(state, fieldDescription, climateUuid, uuidFeatureAlgaTerraClimate);\r
+ addCategoricalValue(state, fieldDescription, habitatUuid, Feature.HABITAT().getUuid());\r
+ addCategoricalValue(state, fieldDescription, lifeFormUuid, uuidFeatureAlgaTerraLifeForm);\r
+ \r
+ if (isNotBlank(habitat)){\r
+ //FIXME\r
+ facade.setEcology(habitat); //or use an own feature ??\r
+ }\r
+ if (isNotBlank(community)){\r
+ Feature communityFeature = getFeature(state, uuidFeatureSpecimenCommunity, "Community", "The community of a specimen (e.g. other algae in the same sample)", null, null);\r
+ TextData textData = TextData.NewInstance(communityFeature);\r
+ textData.putText(Language.DEFAULT(), community);\r
+ getFieldObservationDescription(facade).addElement(textData);\r
+ }\r
+ if (isNotBlank(additionalData)){ //or handle it as Annotation ??\r
+ Feature additionalDataFeature = getFeature(state, uuidFeatureAdditionalData, "Additional Data", "Additional Data", null, null);\r
+ TextData textData = TextData.NewInstance(additionalDataFeature);\r
+ textData.putText(Language.DEFAULT(), additionalData);\r
+ getFieldObservationDescription(facade).addElement(textData);\r
+ }\r
+ \r
+ //field\r
+ facade.setFieldNumber(collectorsNumber);\r
+ TimePeriod gatheringPeriod = TimePeriod.NewInstance(collectionDateStart, collectionDateEnd);\r
+ facade.setGatheringPeriod(gatheringPeriod);\r
+ handleCollectorTeam(state, facade, rs);\r
+ \r
+ //areas\r
+ makeAreas(state, rs, facade);\r
+ \r
+ //parameters\r
+ //TODO\r
+ \r
+ //notes\r
+ //TODO is this an annotation on field observation or on the derived unit?\r
+ \r
+ //TODO id, created for fact + ecoFact\r
+ // this.doIdCreatedUpdatedNotes(state, descriptionElement, rs, id, namespace);\r
+ \r
+ } catch (IllegalArgumentException e) {\r
+ throw e;\r
+ }\r
\r
- //field\r
- facade.setFieldNumber(collectorsNumber);\r
- \r
+ }\r
+\r
+\r
+ private void addCategoricalValue(AlgaTerraImportState importState, DescriptionBase description, String uuidTerm, UUID featureUuid) {\r
+ if (uuidTerm != null){\r
+ State state = this.getStateTerm(importState, UUID.fromString(uuidTerm));\r
+ Feature feature = getFeature(importState, featureUuid);\r
+ CategoricalData categoricalData = CategoricalData.NewInstance(state, feature);\r
+ description.addElement(categoricalData);\r
+ }\r
+ }\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
+ \r
+ \r
+ \r
+ }\r
+\r
+ private void makeAreas(AlgaTerraImportState state, ResultSet rs, DerivedUnitFacade facade) throws SQLException {\r
+ Object gazetteerId = rs.getObject("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
+ }else{\r
+ String tdwg3 = rs.getString("L3Code");\r
+ if (isNotBlank(tdwg3)){\r
+ tdwgArea = TdwgArea.getAreaByTdwgAbbreviation(tdwg3);\r
+ }else{\r
+ Integer tdwg2 = rs.getInt("L2Code"); \r
+ tdwgArea = TdwgArea.getAreaByTdwgAbbreviation(String.valueOf(tdwg2));\r
+ }\r
+ }\r
+ if (tdwgArea == null){\r
+ logger.warn("TDWG area could not be defined for gazetterId: " + gazetteerId);\r
+ }else{\r
+ facade.addCollectingArea(tdwgArea);\r
+ }\r
+ \r
+ //Countries\r
+ WaterbodyOrCountry country = null;\r
+ String isoCountry = rs.getString("ISOCountry");\r
+ String countryStr = rs.getString("Country");\r
+ if (isNotBlank(isoCountry)){\r
+ country = WaterbodyOrCountry.getWaterbodyOrCountryByIso3166A2(isoCountry);\r
+ }else if (isNotBlank(countryStr)){\r
+ logger.warn("Country exists but no ISO code");\r
+ }\r
+ if (country == null){\r
+ logger.warn("Country does not exist for GazetteerID " + gazetteerId);\r
+ }else{\r
+ facade.setCountry(country);\r
+ }\r
+ \r
+ }\r
+ \r
+ //Waterbody\r
+ WaterbodyOrCountry waterbody = null;\r
+ String waterbodyStr = rs.getString("WaterBody");\r
+ if (isNotBlank(waterbodyStr)){\r
+ if (waterbodyStr.equals("Atlantic Ocean")){\r
+ waterbody = WaterbodyOrCountry.ATLANTICOCEAN();\r
+ }else{\r
+ logger.warn("Waterbody not recognized: " + waterbody);\r
+ }\r
+ if (waterbody != null){\r
+ facade.addCollectingArea(waterbody);\r
+ }\r
+ }\r
+\r
+ \r
+ //countries sub\r
+ //TODO\r
+ }\r
+\r
+ private DescriptionBase getFieldObservationDescription(DerivedUnitFacade facade) {\r
+ Set<DescriptionBase> descriptions = facade.innerFieldObservation().getDescriptions();\r
+ for (DescriptionBase desc : descriptions){\r
+ if (desc.isImageGallery() == false){\r
+ return desc;\r
+ }\r
+ }\r
+ SpecimenDescription specDesc = SpecimenDescription.NewInstance(facade.innerFieldObservation());\r
+ descriptions.add(specDesc);\r
+ return specDesc;\r
+ }\r
+\r
+ private ReferenceSystem makeRefrenceSystem(String geoCodeMethod, AlgaTerraImportState state) {\r
+ if (StringUtils.isBlank(geoCodeMethod)){\r
+ return null;\r
+ }else if(geoCodeMethod.startsWith("GPS")){\r
+ getReferenceSystem(state, uuidRefSystemGps, "GPS", "GPS", "GPS", ReferenceSystem.GOOGLE_EARTH().getVocabulary());\r
+ return ReferenceSystem.WGS84(); \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
+ }else if(geoCodeMethod.startsWith("WikiProjekt Georeferenzierung") || geoCodeMethod.startsWith("http://toolserver.org/~geohack/geohack.php") ){\r
+ return ReferenceSystem.WGS84();\r
+ }else {\r
+ logger.warn("Reference system " + geoCodeMethod + " not yet supported.");\r
+ return null;\r
+ }\r
+ }\r
+\r
+ private FieldObservation getFieldObservation(int ecoFactId, Map<String, FieldObservation> fieldObservationMap) {\r
+ String key = String.valueOf(ecoFactId);\r
+ FieldObservation fieldObservation = fieldObservationMap.get(key);\r
+ if (fieldObservation == null){\r
+ fieldObservation = FieldObservation.NewInstance();\r
+ \r
+ fieldObservationMap.put(key, fieldObservation);\r
+ }\r
+ \r
+ return fieldObservation;\r
}\r
\r
private Feature makeFeature(DerivedUnitType type) {\r
\r
try{\r
Set<String> taxonIdSet = new HashSet<String>();\r
+ Set<String> fieldObservationIdSet = new HashSet<String>();\r
+ Set<String> termsIdSet = new HashSet<String>();\r
+ \r
while (rs.next()){\r
handleForeignKey(rs, taxonIdSet, "taxonId");\r
+ handleForeignKey(rs, fieldObservationIdSet, "ecoFactId");\r
+ handleForeignKey(rs, termsIdSet, "ClimateFk");\r
+ handleForeignKey(rs, termsIdSet, "HabitatFk");\r
+ handleForeignKey(rs, termsIdSet, "LifeFormFk");\r
}\r
\r
//taxon map\r
Map<String, TaxonBase> objectMap = (Map<String, TaxonBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);\r
result.put(nameSpace, objectMap);\r
\r
+ //field observation map map\r
+ nameSpace = AlgaTerraSpecimenImport.FIELD_OBSERVATION_NAMESPACE;\r
+ cdmClass = FieldObservation.class;\r
+ idSet = taxonIdSet;\r
+ Map<String, FieldObservation> fieldObservationMap = (Map<String, FieldObservation>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);\r
+ result.put(nameSpace, fieldObservationMap);\r
+\r
+ //terms\r
+ nameSpace = AlgaTerraSpecimenImport.TERMS_NAMESPACE;\r
+ cdmClass = FieldObservation.class;\r
+ idSet = taxonIdSet;\r
+ Map<String, DefinedTermBase> termMap = (Map<String, DefinedTermBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);\r
+ result.put(nameSpace, termMap);\r
+\r
+ \r
+ \r
+ \r
} catch (SQLException e) {\r
throw new RuntimeException(e);\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
- private TaxonDescription getTaxonDescription(int newTaxonId, int oldTaxonId, TaxonDescription oldDescription, Map<String, TaxonBase> taxonMap, int factId, Reference<?> sourceSec){\r
+ private TaxonDescription getTaxonDescription(AlgaTerraImportState state, int newTaxonId, Map<String, TaxonBase> taxonMap, int factId, Reference<?> sourceSec){\r
TaxonDescription result = null;\r
- if (oldDescription == null || newTaxonId != oldTaxonId){\r
- TaxonBase<?> taxonBase = taxonMap.get(String.valueOf(newTaxonId));\r
- //TODO for testing\r
- //TaxonBase taxonBase = Taxon.NewInstance(BotanicalName.NewInstance(Rank.SPECIES()), null);\r
- Taxon taxon;\r
- if ( taxonBase instanceof Taxon ) {\r
- taxon = (Taxon) taxonBase;\r
- } else if (taxonBase != null) {\r
- logger.warn("TaxonBase for Fact(Specimen) with factId" + factId + " was not of type Taxon but: " + taxonBase.getClass().getSimpleName());\r
- return null;\r
- } else {\r
- logger.warn("TaxonBase for Fact(Specimen) " + factId + " is null.");\r
- return null;\r
- } \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
+ TaxonBase<?> taxonBase = taxonMap.get(String.valueOf(newTaxonId));\r
+ \r
+ //TODO for testing\r
+ if (taxonBase == null && ! state.getConfig().isDoTaxa()){\r
+ taxonBase = Taxon.NewInstance(BotanicalName.NewInstance(Rank.SPECIES()), null);\r
+ }\r
+ \r
+ Taxon taxon;\r
+ if ( taxonBase instanceof Taxon ) {\r
+ taxon = (Taxon) taxonBase;\r
+ } else if (taxonBase != null) {\r
+ logger.warn("TaxonBase for Fact(Specimen) with factId" + factId + " was not of type Taxon but: " + taxonBase.getClass().getSimpleName());\r
+ return null;\r
+ } else {\r
+ logger.warn("TaxonBase for Fact(Specimen) " + factId + " is null.");\r
+ return null;\r
+ } \r
+ Set<TaxonDescription> descriptionSet= taxon.getDescriptions();\r
+ if (descriptionSet.size() > 0) {\r
+ result = descriptionSet.iterator().next(); \r
}else{\r
- result = oldDescription;\r
+ result = TaxonDescription.NewInstance();\r
+ result.setTitleCache(sourceSec.getTitleCache(), true);\r
+ taxon.addDescription(result);\r
}\r
return result;\r
}\r
BGBM BDI Projects / cdmlib-apps.git / commitdiff