\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 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.api.facade.DerivedUnitFacadeNotSupportedException;\r
import eu.etaxonomy.cdm.io.algaterra.validation.AlgaTerraSpecimenImportValidator;\r
-import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase;\r
import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator;\r
import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportState;\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.common.TermVocabulary;\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.MeasurementUnit;\r
+import eu.etaxonomy.cdm.model.description.Modifier;\r
+import eu.etaxonomy.cdm.model.description.QuantitativeData;\r
import eu.etaxonomy.cdm.model.description.State;\r
+import eu.etaxonomy.cdm.model.description.StatisticalMeasure;\r
+import eu.etaxonomy.cdm.model.description.StatisticalMeasurementValue;\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.Collection;\r
+import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;\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
\r
/**\r
* @author a.mueller\r
- * @created 20.03.2008\r
- * @version 1.0\r
+ * @created 01.09.2012\r
*/\r
@Component\r
-public class AlgaTerraSpecimenImport extends BerlinModelImportBase {\r
+public class AlgaTerraSpecimenImport extends AlgaTerraSpecimenImportBase {\r
private static final Logger logger = Logger.getLogger(AlgaTerraSpecimenImport.class);\r
\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
private static final String pluralString = "specimen and observation";\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
+ String strQuery = \r
+ " SELECT PTaxon.RIdentifier as taxonId, Fact.FactId, Fact.RecordBasis, EcoFact.*, EcoFact.EcoFactId as unitId, " + \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
+ " 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
Set<TaxonBase> taxaToSave = new HashSet<TaxonBase>();\r
\r
Map<String, TaxonBase> taxonMap = (Map<String, TaxonBase>) partitioner.getObjectMap(BerlinModelTaxonImport.NAMESPACE);\r
- Map<String, FieldObservation> fieldObservationMap = (Map<String, FieldObservation>) partitioner.getObjectMap(FIELD_OBSERVATION_NAMESPACE);\r
+ Map<String, DerivedUnit> ecoFactDerivedUnitMap = (Map<String, DerivedUnit>) partitioner.getObjectMap(ECO_FACT_DERIVED_UNIT_NAMESPACE);\r
\r
ResultSet rs = partitioner.getResultSet();\r
\r
Reference<?> sourceRef = state.getTransactionalSourceReference();\r
\r
//facade\r
- FieldObservation fieldObservation = getFieldObservation(ecoFactId, fieldObservationMap);\r
DerivedUnitType type = makeDerivedUnitType(recordBasis);\r
- DerivedUnitFacade facade = DerivedUnitFacade.NewInstance(type, fieldObservation);\r
-\r
+ DerivedUnitFacade facade = getDerivedUnit(state, ecoFactId, ecoFactDerivedUnitMap, type);\r
+ \r
//field observation\r
- handleSingleSpecimen(rs, facade, state);\r
+ handleSingleSpecimen(rs, facade, state, partitioner);\r
+ \r
+ handleEcoFactSpecificSpecimen(rs,facade, state);\r
+ \r
+ state.setCurrentFieldObservationNotNew(false);\r
\r
//description element\r
TaxonDescription taxonDescription = getTaxonDescription(state, newTaxonId, taxonMap, factId, sourceRef);\r
return false;\r
}\r
}\r
+ \r
+ protected String getDerivedUnitNameSpace(){\r
+ return ECO_FACT_DERIVED_UNIT_NAMESPACE;\r
+ }\r
\r
\r
\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
+ private void handleEcoFactSpecificSpecimen(ResultSet rs, DerivedUnitFacade facade, AlgaTerraImportState state) throws SQLException {\r
\r
- if (! state.isSpecimenVocabulariesCreated()){\r
- \r
- TransactionStatus txStatus = this.startTransaction();\r
+ Object alkalinityFlag = rs.getBoolean("AlkalinityFlag");\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
+ //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
+ facade.getFieldObservation(true).addMarker(alkalinityMarker);\r
}\r
\r
- }\r
-\r
+ \r
+ DescriptionBase<?> fieldDescription = getFieldObservationDescription(facade);\r
\r
+ //habitat, ecology, community, etc.\r
+ String habitat = rs.getString("HabitatExplanation");\r
+ \r
+ if (isNotBlank(habitat)){\r
+ Feature habitatExplanation = getFeature(state, uuidFeatureHabitatExplanation, "Habitat Explanation", "HabitatExplanation", null, null);\r
+ TextData textData = TextData.NewInstance(habitatExplanation);\r
+ textData.putText(Language.DEFAULT(), habitat);\r
+ fieldDescription.addElement(textData);\r
+ }\r
+ \r
+ String community = rs.getString("Comunity");\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
+ fieldDescription.addElement(textData);\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
- //P1-10Value/Unit/Parameter/Method\r
+ String additionalData = rs.getString("AdditionalData");\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
+ fieldDescription.addElement(textData);\r
+ }\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
+ String climateUuid = rs.getString("climateUuid");\r
+ String habitatUuid = rs.getString("habitatUuid");\r
+ String lifeFormUuid = rs.getString("lifeFormUuid");\r
+ \r
+ addCategoricalValue(state, fieldDescription, climateUuid, uuidFeatureAlgaTerraClimate);\r
+ addCategoricalValue(state, fieldDescription, habitatUuid, Feature.HABITAT().getUuid());\r
+ addCategoricalValue(state, fieldDescription, lifeFormUuid, uuidFeatureAlgaTerraLifeForm);\r
\r
- } catch (IllegalArgumentException e) {\r
- throw e;\r
+ \r
+ //collection\r
+ String voucher = rs.getString("Voucher");\r
+ if (StringUtils.isNotBlank(voucher)){\r
+ facade.setAccessionNumber(voucher);\r
}\r
- \r
+ \r
+ //parameters\r
+ makeParameter(state, rs, getFieldObservationDescription(facade));\r
+\r
}\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
}\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
+ private void makeParameter(AlgaTerraImportState state, ResultSet rs, DescriptionBase<?> descriptionBase) throws SQLException {\r
+ for (int i = 1; i <= 10; i++){\r
+ String valueStr = rs.getString(String.format("P%dValue", i));\r
+ String unitStr = rs.getString(String.format("P%dUnit", i));\r
+ String parameter = rs.getString(String.format("P%dParameter", i));\r
+ String method = rs.getString(String.format("P%dMethod", i));\r
+ \r
+ //method\r
+ if (StringUtils.isNotBlank(method)){\r
+ logger.warn("Methods not yet handled: " + method);\r
+ }\r
+ //parameter\r
+ TermVocabulary<Feature> vocParameter = getVocabulary(uuidVocParameter, "Feature vocabulary for AlgaTerra measurement parameters", "Parameters", null, null, false, Feature.COMMON_NAME());\r
+ if (StringUtils.isNotBlank(parameter)){\r
+ UUID featureUuid = getParameterFeatureUuid(state, parameter);\r
+ Feature feature = getFeature(state, featureUuid, parameter, parameter, null, vocParameter);\r
+ QuantitativeData quantData = QuantitativeData.NewInstance(feature);\r
+ \r
+ //unit\r
+ MeasurementUnit unit = getMeasurementUnit(state, unitStr);\r
+ quantData.setUnit(unit);\r
+ try {\r
+ \r
+ Set<Modifier> valueModifier = new HashSet<Modifier>();\r
+ valueStr = normalizeAndModifyValue(state, valueStr, valueModifier);\r
+ //value\r
+ Float valueFlt = Float.valueOf(valueStr); //TODO maybe change model to Double ??\r
+ \r
+ StatisticalMeasure measureSingleValue = getStatisticalMeasure(state, uuidStatMeasureSingleValue, "Value", "Single measurement value", null, null);\r
+ StatisticalMeasurementValue value = StatisticalMeasurementValue.NewInstance(measureSingleValue, valueFlt); \r
+ quantData.addStatisticalValue(value);\r
+ descriptionBase.addElement(quantData);\r
+ \r
+ } catch (NumberFormatException e) {\r
+ logger.warn(String.format("Value '%s' can't be converted to double. Parameter %s not imported.", valueStr, parameter));\r
+ }\r
+ }else if (isNotBlank(valueStr) || isNotBlank(unitStr) ){\r
+ logger.warn("There is value or unit without parameter: " + i);\r
+ }\r
+ \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
+ private String normalizeAndModifyValue(AlgaTerraImportState state, String valueStr, Set<Modifier> valueModifier) {\r
+ valueStr = valueStr.replace(",", ".");\r
+ if (valueStr.startsWith("<")){\r
+ TermVocabulary<Modifier> measurementValueModifierVocabulary = getVocabulary(uuidMeasurementValueModifier, "Measurement value modifier", "Measurement value modifier", null, null, false, Modifier.NewInstance());\r
+ Modifier modifier = getModifier(state, uuidModifierLowerThan, "Lower", "Lower than the given measurement value", "<", measurementValueModifierVocabulary);\r
+ valueModifier.add(modifier);\r
+ valueStr = valueStr.replace("<", "");\r
+ }\r
+ if (valueStr.startsWith(">")){\r
+ TermVocabulary<Modifier> measurementValueModifierVocabulary = getVocabulary(uuidMeasurementValueModifier, "Measurement value modifier", "Measurement value modifier", null, null, false, Modifier.NewInstance());\r
+ Modifier modifier = getModifier(state, uuidModifierGreaterThan, "Lower", "Lower than the given measurement value", "<", measurementValueModifierVocabulary);\r
+ valueModifier.add(modifier);\r
+ valueStr = valueStr.replace(">", "");\r
+ }\r
+ return valueStr;\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
+\r
+ private UUID getParameterFeatureUuid(AlgaTerraImportState state, String key) {\r
+ //TODO define some UUIDs in Transformer\r
+ UUID uuid = state.getParameterFeatureUuid(key);\r
+ if (uuid == null){\r
+ uuid = UUID.randomUUID();\r
+ state.putParameterFeatureUuid(key, uuid);\r
}\r
- SpecimenDescription specDesc = SpecimenDescription.NewInstance(facade.innerFieldObservation());\r
- descriptions.add(specDesc);\r
- return specDesc;\r
+ return uuid;\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
+\r
+\r
+ /**\r
+ * TODO move to InputTransformerBase\r
+ * @param state\r
+ * @param unitStr\r
+ * @return\r
+ */\r
+ private MeasurementUnit getMeasurementUnit(AlgaTerraImportState state, String unitStr) {\r
+ if (StringUtils.isNotBlank(unitStr)){\r
+ UUID uuidMeasurementUnitMgL = UUID.fromString("7ac302c5-3cbd-4334-964a-bf5d11eb9ead");\r
+ UUID uuidMeasurementUnitMolMol = UUID.fromString("96b78d78-3e49-448f-8100-e7779b71dd53");\r
+ UUID uuidMeasurementUnitMicroMolSiL = UUID.fromString("2cb8bc85-a4af-42f1-b80b-34c36c9f75d4");\r
+ UUID uuidMeasurementUnitMicroMolL = UUID.fromString("a631f62e-377e-405c-bd1a-76885b13a72b");\r
+ UUID uuidMeasurementUnitDegreeC = UUID.fromString("55222aec-d5be-413e-8db7-d9a48c316c6c");\r
+ UUID uuidMeasurementUnitPercent = UUID.fromString("3ea3110e-f048-4bed-8bfe-33c60f63626f");\r
+ UUID uuidMeasurementUnitCm = UUID.fromString("3ea3110e-f048-4bed-8bfe-33c60f63626f");\r
+ UUID uuidMeasurementUnitMicroSiCm = UUID.fromString("3ea3110e-f048-4bed-8bfe-33c60f63626f");\r
+ \r
+ \r
+ if (unitStr.equalsIgnoreCase("mg/L")){\r
+ return getMeasurementUnit(state, uuidMeasurementUnitMgL, unitStr, unitStr, unitStr, null);\r
+ }else if (unitStr.equalsIgnoreCase("mol/mol")){\r
+ return getMeasurementUnit(state, uuidMeasurementUnitMolMol, unitStr, unitStr, unitStr, null);\r
+ }else if (unitStr.equalsIgnoreCase("\u00B5mol Si/L")){ //µmol Si/L\r
+ return getMeasurementUnit(state, uuidMeasurementUnitMicroMolSiL, unitStr, unitStr, unitStr, null);\r
+ }else if (unitStr.equalsIgnoreCase("\u00B5mol/L")){ //µmol/L\r
+ return getMeasurementUnit(state, uuidMeasurementUnitMicroMolL, unitStr, unitStr, unitStr, null);\r
+ }else if (unitStr.equalsIgnoreCase("\u00B0C")){ //°C\r
+ return getMeasurementUnit(state, uuidMeasurementUnitDegreeC, unitStr, unitStr, unitStr, null);\r
+ }else if (unitStr.equalsIgnoreCase("%")){\r
+ return getMeasurementUnit(state, uuidMeasurementUnitPercent, unitStr, unitStr, unitStr, null);\r
+ }else if (unitStr.equalsIgnoreCase("cm")){\r
+ return getMeasurementUnit(state, uuidMeasurementUnitCm, unitStr, unitStr, unitStr, null);\r
+ }else if (unitStr.equalsIgnoreCase("\u00B5S/cm")){ //µS/cm\r
+ return getMeasurementUnit(state, uuidMeasurementUnitMicroSiCm, unitStr, unitStr, unitStr, null);\r
+ }else{\r
+ logger.warn("MeasurementUnit was not recognized");\r
+ return null;\r
+ }\r
+ }else{\r
return null;\r
}\r
}\r
\r
- private FieldObservation getFieldObservation(int ecoFactId, Map<String, FieldObservation> fieldObservationMap) {\r
+\r
+\r
+\r
+\r
+ /**\r
+ * @param state\r
+ * @param ecoFactId\r
+ * @param derivedUnitMap\r
+ * @param type \r
+ * @return\r
+ */\r
+ private DerivedUnitFacade getDerivedUnit(AlgaTerraImportState state, int ecoFactId, Map<String, DerivedUnit> derivedUnitMap, DerivedUnitType type) {\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
+ DerivedUnit derivedUnit = derivedUnitMap.get(key);\r
+ DerivedUnitFacade facade;\r
+ if (derivedUnit == null){\r
+ facade = DerivedUnitFacade.NewInstance(type);\r
+ derivedUnitMap.put(key, derivedUnit);\r
+ }else{\r
+ try {\r
+ facade = DerivedUnitFacade.NewInstance(derivedUnit);\r
+ } catch (DerivedUnitFacadeNotSupportedException e) {\r
+ logger.error(e.getMessage());\r
+ facade = DerivedUnitFacade.NewInstance(type);\r
+ }\r
}\r
\r
- return fieldObservation;\r
+ return facade;\r
}\r
\r
private Feature makeFeature(DerivedUnitType type) {\r
Set<String> taxonIdSet = new HashSet<String>();\r
Set<String> fieldObservationIdSet = new HashSet<String>();\r
Set<String> termsIdSet = new HashSet<String>();\r
+ Set<String> collectionIdSet = new HashSet<String>();\r
\r
while (rs.next()){\r
handleForeignKey(rs, taxonIdSet, "taxonId");\r
handleForeignKey(rs, termsIdSet, "ClimateFk");\r
handleForeignKey(rs, termsIdSet, "HabitatFk");\r
handleForeignKey(rs, termsIdSet, "LifeFormFk");\r
+ handleForeignKey(rs, collectionIdSet, "CollectionFk");\r
}\r
\r
//taxon map\r
result.put(nameSpace, objectMap);\r
\r
//field observation map map\r
- nameSpace = AlgaTerraSpecimenImport.FIELD_OBSERVATION_NAMESPACE;\r
+ nameSpace = AlgaTerraSpecimenImport.ECO_FACT_FIELD_OBSERVATION_NAMESPACE;\r
cdmClass = FieldObservation.class;\r
- idSet = taxonIdSet;\r
+ idSet = fieldObservationIdSet;\r
Map<String, FieldObservation> fieldObservationMap = (Map<String, FieldObservation>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);\r
result.put(nameSpace, fieldObservationMap);\r
\r
+ //collections\r
+ nameSpace = AlgaTerraCollectionImport.NAMESPACE_COLLECTION;\r
+ cdmClass = Collection.class;\r
+ idSet = collectionIdSet;\r
+ Map<String, Collection> collectionMap = (Map<String, Collection>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);\r
+ result.put(nameSpace, collectionMap);\r
+\r
+ //sub-collections\r
+ nameSpace = AlgaTerraCollectionImport.NAMESPACE_SUBCOLLECTION;\r
+ cdmClass = Collection.class;\r
+ idSet = collectionIdSet;\r
+ Map<String, Collection> subCollectionMap = (Map<String, Collection>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);\r
+ result.put(nameSpace, subCollectionMap);\r
+\r
//terms\r
nameSpace = AlgaTerraSpecimenImport.TERMS_NAMESPACE;\r
cdmClass = FieldObservation.class;\r
- idSet = taxonIdSet;\r
+ idSet = termsIdSet;\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
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)\r
*/\r
protected boolean isIgnore(BerlinModelImportState state){\r
- return ! ((AlgaTerraImportState)state).getAlgaTerraConfigurator().isDoSpecimen();\r
+ return ! ((AlgaTerraImportState)state).getAlgaTerraConfigurator().isDoEcoFacts();\r
}\r
\r
}\r
BGBM BDI Projects / cdmlib-apps.git / blobdiff