app-import/src/main/java/eu/etaxonomy/cdm/io/PalmaeProtologueImport.java -text
app-import/src/main/java/eu/etaxonomy/cdm/io/ProtologueImport.java -text
app-import/src/main/java/eu/etaxonomy/cdm/io/algaterra/AlgaTerraCollectionImport.java -text
+app-import/src/main/java/eu/etaxonomy/cdm/io/algaterra/AlgaTerraEcoFactImport.java -text
+app-import/src/main/java/eu/etaxonomy/cdm/io/algaterra/AlgaTerraFactEcologyImport.java -text
app-import/src/main/java/eu/etaxonomy/cdm/io/algaterra/AlgaTerraImageImportBase.java -text
app-import/src/main/java/eu/etaxonomy/cdm/io/algaterra/AlgaTerraImportConfigurator.java -text
app-import/src/main/java/eu/etaxonomy/cdm/io/algaterra/AlgaTerraImportState.java -text
--- /dev/null
+/**\r
+* Copyright (C) 2007 EDIT\r
+* European Distributed Institute of Taxonomy \r
+* http://www.e-taxonomy.eu\r
+* \r
+* The contents of this file are subject to the Mozilla Public License Version 1.1\r
+* See LICENSE.TXT at the top of this package for the full license terms.\r
+*/\r
+\r
+package eu.etaxonomy.cdm.io.algaterra;\r
+\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
+\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.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.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.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.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.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.DerivedUnitBase;\r
+import eu.etaxonomy.cdm.model.occurrence.FieldObservation;\r
+import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;\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
+\r
+\r
+/**\r
+ * @author a.mueller\r
+ * @created 01.09.2012\r
+ */\r
+@Component\r
+public class AlgaTerraEcoFactImport extends AlgaTerraSpecimenImportBase {\r
+ private static final Logger logger = Logger.getLogger(AlgaTerraEcoFactImport.class);\r
+\r
+ \r
+ private static int modCount = 5000;\r
+ private static final String pluralString = "eco facts";\r
+ private static final String dbTableName = "EcoFact"; //?? \r
+\r
+\r
+ public AlgaTerraEcoFactImport(){\r
+ super(dbTableName, pluralString);\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 EcoFactId " + \r
+ " FROM EcoFact " +\r
+ " ORDER BY EcoFact.DuplicateFk, EcoFact.EcoFactId ";\r
+ return result;\r
+ }\r
+\r
+ /* (non-Javadoc)\r
+ * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getRecordQuery(eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator)\r
+ */\r
+ @Override\r
+ protected String getRecordQuery(BerlinModelImportConfigurator config) {\r
+ String strQuery = \r
+ " SELECT 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
+ " FROM EcoFact " +\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 (EcoFact.EcoFactId IN (" + ID_LIST_TOKEN + ") )" \r
+ + " ORDER BY EcoFact.DuplicateFk, EcoFact.EcoFactId "\r
+ ;\r
+ return strQuery;\r
+ }\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 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<SpecimenOrObservationBase> objectsToSave = new HashSet<SpecimenOrObservationBase>();\r
+ \r
+ //TODO do we still need this map? EcoFacts are not handled separate from Facts.\r
+ //However, they have duplicates on derived unit level. Also check duplicateFk. \r
+ Map<String, FieldObservation> ecoFactFieldObservationMap = (Map<String, FieldObservation>) partitioner.getObjectMap(ECO_FACT_FIELD_OBSERVATION_NAMESPACE);\r
+ \r
+ ResultSet rs = partitioner.getResultSet();\r
+\r
+ try {\r
+ \r
+ int i = 0;\r
+\r
+ //for each reference\r
+ while (rs.next()){\r
+ \r
+ if ((i++ % modCount) == 0 && i!= 1 ){ logger.info(pluralString + " handled: " + (i-1));}\r
+ \r
+ int ecoFactId = rs.getInt("EcoFactId");\r
+ Integer duplicateFk = nullSafeInt(rs, "DuplicateFk");\r
+ \r
+ //FIXME RecordBasis is in Fact table, which is not part of the query anymore.\r
+ //Some EcoFacts have multiple RecordBasis types in Fact. Henning will check this.\r
+// String recordBasis = rs.getString("RecordBasis");\r
+ String recordBasis = "PreservedSpecimen";\r
+ \r
+ try {\r
+ \r
+ //source ref\r
+ Reference<?> sourceRef = state.getTransactionalSourceReference();\r
+ \r
+ //facade\r
+ DerivedUnitType type = makeDerivedUnitType(recordBasis);\r
+ \r
+ DerivedUnitFacade facade;\r
+ //field observation\r
+ if (duplicateFk == null){\r
+ facade = DerivedUnitFacade.NewInstance(type);\r
+ handleFieldObservationSpecimen(rs, facade, state, partitioner);\r
+ handleEcoFactSpecificFieldObservation(rs,facade, state);\r
+ FieldObservation fieldObservation = facade.getFieldObservation(true);\r
+ ecoFactFieldObservationMap.put(String.valueOf(ecoFactId), fieldObservation);\r
+ }else{\r
+ FieldObservation fieldObservation = ecoFactFieldObservationMap.get(String.valueOf(duplicateFk));\r
+ facade = DerivedUnitFacade.NewInstance(type, fieldObservation);\r
+ }\r
+ \r
+ handleFirstDerivedSpecimen(rs, facade, state, partitioner);\r
+ handleEcoFactSpecificDerivedUnit(rs,facade, state);\r
+\r
+ \r
+ DerivedUnitBase<?> objectToSave = facade.innerDerivedUnit();\r
+ objectsToSave.add(objectToSave); \r
+ \r
+\r
+ } catch (Exception e) {\r
+ logger.warn("Exception in ecoFact: ecoFactId " + ecoFactId + ". " + e.getMessage());\r
+ e.printStackTrace();\r
+ } \r
+ \r
+ }\r
+ \r
+// logger.warn("Specimen: " + countSpecimen + ", Descriptions: " + countDescriptions );\r
+\r
+ logger.warn("Taxa to save: " + objectsToSave.size());\r
+ getOccurrenceService().save(objectsToSave); \r
+ \r
+ return success;\r
+ } catch (SQLException e) {\r
+ logger.error("SQLException:" + e);\r
+ return false;\r
+ }\r
+ }\r
+ \r
+ protected String getDerivedUnitNameSpace(){\r
+ return ECO_FACT_DERIVED_UNIT_NAMESPACE;\r
+ }\r
+ \r
+ protected String getFieldObservationNameSpace(){\r
+ return ECO_FACT_FIELD_OBSERVATION_NAMESPACE;\r
+ }\r
+\r
+\r
+\r
+ private void handleEcoFactSpecificFieldObservation(ResultSet rs, DerivedUnitFacade facade, AlgaTerraImportState state) throws SQLException {\r
+ \r
+ Object alkalinityFlag = rs.getBoolean("AlkalinityFlag");\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
+ facade.getFieldObservation(true).addMarker(alkalinityMarker);\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
+ 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
+ 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
+\r
+ \r
+ //parameters\r
+ makeParameter(state, rs, getFieldObservationDescription(facade));\r
+\r
+ }\r
+ \r
+ private void handleEcoFactSpecificDerivedUnit(ResultSet rs, DerivedUnitFacade facade, AlgaTerraImportState state) throws SQLException {\r
+ //collection\r
+ String voucher = rs.getString("Voucher");\r
+ if (StringUtils.isNotBlank(voucher)){\r
+ facade.setAccessionNumber(voucher);\r
+ }\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
+ Feature feature = getFeature(importState, featureUuid);\r
+ CategoricalData categoricalData = CategoricalData.NewInstance(state, feature);\r
+ description.addElement(categoricalData);\r
+ }\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 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
+\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
+ return uuid;\r
+ }\r
+\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 Feature makeFeature(DerivedUnitType type) {\r
+ if (type.equals(DerivedUnitType.DerivedUnit)){\r
+ return Feature.INDIVIDUALS_ASSOCIATION();\r
+ }else if (type.equals(DerivedUnitType.FieldObservation) || type.equals(DerivedUnitType.Observation) ){\r
+ return Feature.OBSERVATION();\r
+ }else if (type.equals(DerivedUnitType.Fossil) || type.equals(DerivedUnitType.LivingBeing) || type.equals(DerivedUnitType.Specimen )){\r
+ return Feature.SPECIMEN();\r
+ }\r
+ logger.warn("No feature defined for derived unit type: " + type);\r
+ return null;\r
+ }\r
+\r
+\r
+ private DerivedUnitType makeDerivedUnitType(String recordBasis) {\r
+ DerivedUnitType result = null;\r
+ if (StringUtils.isBlank(recordBasis)){\r
+ result = DerivedUnitType.DerivedUnit;\r
+ } else if (recordBasis.equalsIgnoreCase("FossileSpecimen")){\r
+ result = DerivedUnitType.Fossil;\r
+ }else if (recordBasis.equalsIgnoreCase("HumanObservation")){\r
+ result = DerivedUnitType.Observation;\r
+ }else if (recordBasis.equalsIgnoreCase("Literature")){\r
+ logger.warn("Literature record basis not yet supported");\r
+ result = DerivedUnitType.DerivedUnit;\r
+ }else if (recordBasis.equalsIgnoreCase("LivingSpecimen")){\r
+ result = DerivedUnitType.LivingBeing;\r
+ }else if (recordBasis.equalsIgnoreCase("MachineObservation")){\r
+ logger.warn("MachineObservation record basis not yet supported");\r
+ result = DerivedUnitType.Observation;\r
+ }else if (recordBasis.equalsIgnoreCase("PreservedSpecimen")){\r
+ result = DerivedUnitType.Specimen;\r
+ }\r
+ return result;\r
+ }\r
+\r
+ /* (non-Javadoc)\r
+ * @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet)\r
+ */\r
+ public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs) {\r
+ String nameSpace;\r
+ Class cdmClass;\r
+ Set<String> idSet;\r
+ Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();\r
+ \r
+ try{\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, fieldObservationIdSet, "DuplicateFk");\r
+ handleForeignKey(rs, termsIdSet, "ClimateFk");\r
+ handleForeignKey(rs, termsIdSet, "HabitatFk");\r
+ handleForeignKey(rs, termsIdSet, "LifeFormFk");\r
+ handleForeignKey(rs, collectionIdSet, "CollectionFk");\r
+ }\r
+ \r
+ //field observation map for duplicates\r
+ nameSpace = AlgaTerraEcoFactImport.ECO_FACT_FIELD_OBSERVATION_NAMESPACE;\r
+ cdmClass = FieldObservation.class;\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 = AlgaTerraEcoFactImport.TERMS_NAMESPACE;\r
+ cdmClass = FieldObservation.class;\r
+ idSet = termsIdSet;\r
+ Map<String, DefinedTermBase> termMap = (Map<String, DefinedTermBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);\r
+ result.put(nameSpace, termMap);\r
+ \r
+ } catch (SQLException e) {\r
+ throw new RuntimeException(e);\r
+ }\r
+ return result;\r
+ }\r
+\r
+\r
+\r
+ /* (non-Javadoc)\r
+ * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IoStateBase)\r
+ */\r
+ @Override\r
+ protected boolean doCheck(BerlinModelImportState state){\r
+ IOValidator<BerlinModelImportState> validator = new AlgaTerraSpecimenImportValidator();\r
+ return validator.validate(state);\r
+ }\r
+\r
+\r
+ /* (non-Javadoc)\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().isDoEcoFacts();\r
+ }\r
+ \r
+}\r
--- /dev/null
+/**\r
+* Copyright (C) 2007 EDIT\r
+* European Distributed Institute of Taxonomy \r
+* http://www.e-taxonomy.eu\r
+* \r
+* The contents of this file are subject to the Mozilla Public License Version 1.1\r
+* See LICENSE.TXT at the top of this package for the full license terms.\r
+*/\r
+\r
+package eu.etaxonomy.cdm.io.algaterra;\r
+\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
+\r
+import org.apache.commons.lang.StringUtils;\r
+import org.apache.log4j.Logger;\r
+import org.springframework.stereotype.Component;\r
+\r
+import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;\r
+import eu.etaxonomy.cdm.api.facade.DerivedUnitFacadeCacheStrategy;\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.BerlinModelImportConfigurator;\r
+import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportState;\r
+import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelReferenceImport;\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.model.agent.TeamOrPersonBase;\r
+import eu.etaxonomy.cdm.model.common.CdmBase;\r
+import eu.etaxonomy.cdm.model.common.TimePeriod;\r
+import eu.etaxonomy.cdm.model.description.Feature;\r
+import eu.etaxonomy.cdm.model.description.IndividualsAssociation;\r
+import eu.etaxonomy.cdm.model.description.TaxonDescription;\r
+import eu.etaxonomy.cdm.model.name.BotanicalName;\r
+import eu.etaxonomy.cdm.model.name.Rank;\r
+import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;\r
+import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;\r
+import eu.etaxonomy.cdm.model.occurrence.DerivedUnitBase;\r
+import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;\r
+import eu.etaxonomy.cdm.model.occurrence.FieldObservation;\r
+import eu.etaxonomy.cdm.model.occurrence.Fossil;\r
+import eu.etaxonomy.cdm.model.occurrence.LivingBeing;\r
+import eu.etaxonomy.cdm.model.occurrence.Observation;\r
+import eu.etaxonomy.cdm.model.occurrence.Specimen;\r
+import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;\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
+\r
+\r
+/**\r
+ * Alga Terra Import für den Fact mit FactId =202 (Ecology)\r
+ * @author a.mueller\r
+ * @created 01.09.2012\r
+ */\r
+@Component\r
+public class AlgaTerraFactEcologyImport extends AlgaTerraSpecimenImportBase {\r
+ private static final Logger logger = Logger.getLogger(AlgaTerraFactEcologyImport.class);\r
+\r
+ \r
+ private static int modCount = 5000;\r
+ private static final String pluralString = "determinations";\r
+ private static final String dbTableName = "Fact"; \r
+\r
+\r
+ public AlgaTerraFactEcologyImport(){\r
+ super(dbTableName, pluralString);\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 f.factId " + \r
+ " FROM Fact f LEFT JOIN PTaxon pt ON f.PTNameFk = pt.PTNameFk AND f.PTRefFk = pt.PTRefFk " \r
+ + " WHERE f.FactCategoryFk = 202 "\r
+ + " ORDER BY pt.RIdentifier, f.FactId ";\r
+ return result;\r
+ }\r
+\r
+ /* (non-Javadoc)\r
+ * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getRecordQuery(eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator)\r
+ */\r
+ @Override\r
+ protected String getRecordQuery(BerlinModelImportConfigurator config) {\r
+ String strQuery = \r
+ " SELECT pt.RIdentifier as taxonId, f.* " + \r
+ " FROM Fact f " + \r
+ " LEFT JOIN PTaxon pt ON f.PTNameFk =pt.PTNameFk AND f.PTRefFk = pt.PTRefFk " +\r
+ " WHERE f.FactCategoryFk = 202 AND (f.FactId IN (" + ID_LIST_TOKEN + ") )" \r
+ + " ORDER BY pt.RIdentifier, f.FactId "\r
+ ;\r
+ return strQuery;\r
+ }\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 bmState) {\r
+ boolean success = true;\r
+ \r
+ AlgaTerraImportState state = (AlgaTerraImportState)bmState;\r
+ Set<TaxonBase> taxaToSave = new HashSet<TaxonBase>();\r
+ \r
+ Map<String, TaxonBase> taxonMap = (Map<String, TaxonBase>) partitioner.getObjectMap(BerlinModelTaxonImport.NAMESPACE);\r
+ Map<String, DerivedUnitBase> ecoFactDerivedUnitMap = (Map<String, DerivedUnitBase>) partitioner.getObjectMap(ECO_FACT_DERIVED_UNIT_NAMESPACE);\r
+ \r
+ ResultSet rs = partitioner.getResultSet();\r
+\r
+ try {\r
+ \r
+ int i = 0;\r
+\r
+ //for each reference\r
+ while (rs.next()){\r
+ \r
+ if ((i++ % modCount) == 0 && i!= 1 ){ logger.info(pluralString + " handled: " + (i-1));}\r
+ \r
+ Integer taxonId = nullSafeInt(rs, "taxonId");\r
+ int factId = rs.getInt("FactId");\r
+ Integer ecoFactId = nullSafeInt(rs, "ExtensionFk");\r
+ String recordBasis = rs.getString("RecordBasis");\r
+ \r
+ \r
+ try {\r
+ \r
+ //source ref\r
+ Reference<?> sourceRef = state.getTransactionalSourceReference();\r
+ \r
+ DerivedUnitBase<?> ecoFact = ecoFactDerivedUnitMap.get(String.valueOf(ecoFactId));\r
+ \r
+ \r
+ //description element\r
+ if (taxonId != null){\r
+ Taxon taxon = getTaxon(state, taxonId, taxonMap, factId); \r
+ \r
+ if(taxon != null){\r
+ DerivedUnitBase identifiedSpecimen = makeIdentifiedSpecimen(ecoFact, recordBasis);\r
+ \r
+ makeDetermination(state, rs, taxon, identifiedSpecimen, factId, partitioner);\r
+ \r
+ makeIndividualsAssociation(state, taxon, sourceRef, identifiedSpecimen);\r
+ \r
+ this.doIdCreatedUpdatedNotes(state, identifiedSpecimen, rs, factId, getDerivedUnitNameSpace());\r
+\r
+ identifiedSpecimen.setCacheStrategy(new DerivedUnitFacadeCacheStrategy());\r
+ taxaToSave.add(taxon);\r
+ }\r
+ }else{\r
+ logger.warn("No taxon defined for ecology fact: " + factId);\r
+ }\r
+ \r
+\r
+ } catch (Exception e) {\r
+ logger.warn("Exception in FactEcology: FactId " + factId + ". " + e.getMessage());\r
+ e.printStackTrace();\r
+ } \r
+ \r
+ }\r
+ \r
+// logger.warn("Specimen: " + countSpecimen + ", Descriptions: " + countDescriptions );\r
+\r
+ logger.warn("Taxa to save: " + taxaToSave.size());\r
+ getTaxonService().save(taxaToSave); \r
+ \r
+ return success;\r
+ } catch (SQLException e) {\r
+ logger.error("SQLException:" + e);\r
+ return false;\r
+ }\r
+ }\r
+ \r
+ private void makeIndividualsAssociation(AlgaTerraImportState state, Taxon taxon, Reference<?> sourceRef, DerivedUnitBase<?> identifiedSpecimen){\r
+ TaxonDescription taxonDescription = getTaxonDescription(state, taxon, sourceRef);\r
+ IndividualsAssociation indAssociation = IndividualsAssociation.NewInstance();\r
+ Feature feature = makeFeature(identifiedSpecimen);\r
+ indAssociation.setAssociatedSpecimenOrObservation(identifiedSpecimen);\r
+ indAssociation.setFeature(feature);\r
+ taxonDescription.addElement(indAssociation); \r
+ }\r
+ \r
+ private void makeDetermination(AlgaTerraImportState state, ResultSet rs, Taxon taxon, DerivedUnitBase<?> identifiedSpecimen, int factId, ResultSetPartitioner partitioner) throws SQLException {\r
+ Date identifiedWhen = rs.getDate("IdentifiedWhen");\r
+ Date identifiedWhenEnd = rs.getDate("IdentiedWhenEnd");\r
+ boolean restrictedFlag = rs.getBoolean("RestrictedFlag");\r
+ //Team FK ist immer null\r
+ String identifiedBy = rs.getString("IdentifiedBy");\r
+ String identificationReference = rs.getString("IdentificationReference");\r
+ Integer refFk = nullSafeInt(rs, "IdentifidationRefFk");\r
+ \r
+ \r
+ DeterminationEvent determination = DeterminationEvent.NewInstance(taxon, identifiedSpecimen);\r
+ TimePeriod determinationPeriod = TimePeriod.NewInstance(identifiedWhen, identifiedWhenEnd);\r
+ determination.setTimeperiod(determinationPeriod);\r
+ determination.setPreferredFlag(! restrictedFlag);\r
+ //TODO \r
+ \r
+ TeamOrPersonBase<?> author = getAuthor(identifiedBy);\r
+ determination.setDeterminer(author);\r
+ if (refFk != null){\r
+ Map<String, Reference> biblioRefMap = (Map<String, Reference>) partitioner.getObjectMap(BerlinModelReferenceImport.BIBLIO_REFERENCE_NAMESPACE);\r
+ Map<String, Reference> nomRefMap = (Map<String, Reference>) partitioner.getObjectMap(BerlinModelReferenceImport.NOM_REFERENCE_NAMESPACE);\r
+ \r
+ Reference<?> ref = getReferenceOnlyFromMaps(biblioRefMap, nomRefMap, String.valueOf(refFk));\r
+ determination.addReference(ref);\r
+ }else{\r
+ //IdentificationReference is not to be handled according to Henning\r
+ if (StringUtils.isNotBlank(identificationReference)){\r
+ logger.warn("IdentificationReference exists without IdentificationRefFk. FactId: "+ factId);\r
+ }\r
+ }\r
+ \r
+ \r
+ \r
+ //TODO\r
+// kind of identification, IdentificationUncertainty, IdentificationMethod, \r
+ \r
+ \r
+ }\r
+\r
+\r
+\r
+ private DerivedUnitBase<?> makeIdentifiedSpecimen(DerivedUnitBase<?> ecoFact, String recordBasis) {\r
+ //TODO event type\r
+ DerivationEvent event = DerivationEvent.NewInstance();\r
+ DerivedUnitType derivedUnitType = makeDerivedUnitType(recordBasis);\r
+ if (derivedUnitType == null){\r
+ logger.warn("NULL");\r
+ }\r
+ \r
+ DerivedUnitBase<?> result = derivedUnitType.getNewDerivedUnitInstance();\r
+ result.setDerivedFrom(event);\r
+ ecoFact.addDerivationEvent(event);\r
+ \r
+ return result;\r
+ }\r
+\r
+\r
+\r
+ protected String getDerivedUnitNameSpace(){\r
+ return FACT_ECOLOGY_NAMESPACE;\r
+ }\r
+ \r
+ protected String getFieldObservationNameSpace(){\r
+ return null;\r
+ }\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
+ 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 facade;\r
+ }\r
+ \r
+ private Feature makeFeature(SpecimenOrObservationBase unit) {\r
+ if (unit.isInstanceOf(DerivedUnit.class)){\r
+ return Feature.INDIVIDUALS_ASSOCIATION();\r
+ }else if (unit.isInstanceOf(FieldObservation.class) || unit.isInstanceOf(Observation.class) ){\r
+ return Feature.OBSERVATION();\r
+ }else if (unit.isInstanceOf(Fossil.class) || unit.isInstanceOf(LivingBeing.class) || unit.isInstanceOf(Specimen.class )){\r
+ return Feature.SPECIMEN();\r
+ }\r
+ logger.warn("No feature defined for derived unit class: " + unit.getClass().getSimpleName());\r
+ return null;\r
+ }\r
+\r
+\r
+ private DerivedUnitType makeDerivedUnitType(String recordBasis) {\r
+ DerivedUnitType result = null;\r
+ if (StringUtils.isBlank(recordBasis)){\r
+ result = DerivedUnitType.DerivedUnit;\r
+ } else if (recordBasis.equalsIgnoreCase("FossileSpecimen")){\r
+ result = DerivedUnitType.Fossil;\r
+ }else if (recordBasis.equalsIgnoreCase("Observation")){\r
+ result = DerivedUnitType.Observation;\r
+ }else if (recordBasis.equalsIgnoreCase("HumanObservation")){\r
+ result = DerivedUnitType.Observation;\r
+ }else if (recordBasis.equalsIgnoreCase("Literature")){\r
+ logger.warn("Literature record basis not yet supported");\r
+ result = DerivedUnitType.DerivedUnit;\r
+ }else if (recordBasis.equalsIgnoreCase("LivingSpecimen")){\r
+ result = DerivedUnitType.LivingBeing;\r
+ }else if (recordBasis.equalsIgnoreCase("LivingCulture")){\r
+ logger.warn("LivingCulture record basis not yet supported");\r
+ result = DerivedUnitType.DerivedUnit;\r
+ }else if (recordBasis.equalsIgnoreCase("MachineObservation")){\r
+ logger.warn("MachineObservation record basis not yet supported");\r
+ result = DerivedUnitType.Observation;\r
+ }else if (recordBasis.equalsIgnoreCase("PreservedSpecimen")){\r
+ result = DerivedUnitType.Specimen;\r
+ }\r
+ return result;\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * @param state\r
+ * @param newTaxonId\r
+ * @param taxonMap\r
+ * @param factId\r
+ * @return\r
+ */\r
+ private Taxon getTaxon(AlgaTerraImportState state, int taxonId, Map<String, TaxonBase> taxonMap, int factId) {\r
+ TaxonBase<?> taxonBase = taxonMap.get(String.valueOf(taxonId));\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 (" + taxonId + ") for Fact(Specimen) with factId " + factId + " was not of type Taxon but: " + taxonBase.getClass().getSimpleName());\r
+ return null;\r
+ } else {\r
+ logger.warn("TaxonBase (" + taxonId + ") for Fact(Specimen) with factId " + factId + " is null.");\r
+ return null;\r
+ }\r
+ return taxon;\r
+ }\r
+ \r
+ /* (non-Javadoc)\r
+ * @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet)\r
+ */\r
+ public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs) {\r
+ String nameSpace;\r
+ Class cdmClass;\r
+ Set<String> idSet;\r
+ Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();\r
+ \r
+ try{\r
+ Set<String> taxonIdSet = new HashSet<String>();\r
+ Set<String> extensionFkSet = new HashSet<String>();\r
+ Set<String> referenceIdSet = new HashSet<String>();\r
+ \r
+ while (rs.next()){\r
+ handleForeignKey(rs, taxonIdSet, "taxonId");\r
+ handleForeignKey(rs, extensionFkSet, "extensionFk");\r
+ handleForeignKey(rs, referenceIdSet, "IdentifidationRefFk");\r
+ }\r
+ \r
+ //taxon map\r
+ nameSpace = BerlinModelTaxonImport.NAMESPACE;\r
+ cdmClass = TaxonBase.class;\r
+ idSet = taxonIdSet;\r
+ Map<String, TaxonBase> objectMap = (Map<String, TaxonBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);\r
+ result.put(nameSpace, objectMap);\r
+\r
+ //derived unit map\r
+ nameSpace = AlgaTerraFactEcologyImport.ECO_FACT_DERIVED_UNIT_NAMESPACE;\r
+ cdmClass = DerivedUnitBase.class;\r
+ idSet = extensionFkSet;\r
+ Map<String, DerivedUnitBase> derivedUnitMap = (Map<String, DerivedUnitBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);\r
+ result.put(nameSpace, derivedUnitMap);\r
+\r
+ //nom reference map\r
+ nameSpace = BerlinModelReferenceImport.NOM_REFERENCE_NAMESPACE;\r
+ cdmClass = Reference.class;\r
+ idSet = referenceIdSet;\r
+ Map<String, Reference> nomReferenceMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);\r
+ result.put(nameSpace, nomReferenceMap);\r
+\r
+ //biblio reference map\r
+ nameSpace = BerlinModelReferenceImport.BIBLIO_REFERENCE_NAMESPACE;\r
+ cdmClass = Reference.class;\r
+ idSet = referenceIdSet;\r
+ Map<String, Reference> biblioReferenceMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);\r
+ result.put(nameSpace, biblioReferenceMap);\r
+\r
+ \r
+ } catch (SQLException e) {\r
+ throw new RuntimeException(e);\r
+ }\r
+ return result;\r
+ }\r
+\r
+ /* (non-Javadoc)\r
+ * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IoStateBase)\r
+ */\r
+ @Override\r
+ protected boolean doCheck(BerlinModelImportState state){\r
+ IOValidator<BerlinModelImportState> validator = new AlgaTerraSpecimenImportValidator();\r
+ return validator.validate(state);\r
+ }\r
+\r
+\r
+ /* (non-Javadoc)\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().isDoEcoFacts();\r
+ }\r
+ \r
+}\r
import eu.etaxonomy.cdm.database.ICdmDataSource;\r
import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelAuthorImport;\r
import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelAuthorTeamImport;\r
-import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelCommonNamesImport;\r
import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelFactsImport;\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.BerlinModelNameFactsImport;\r
import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelNameStatusImport;\r
-import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelOccurrenceImport;\r
-import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelOccurrenceSourceImport;\r
import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelRefDetailImport;\r
import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelReferenceImport;\r
import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelTaxonImport;\r
import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelTaxonNameImport;\r
import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelTaxonNameRelationImport;\r
import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelTaxonRelationImport;\r
-import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelTypesImport;\r
import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelUserImport;\r
import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelWebMarkerCategoryImport;\r
import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelWebMarkerImport;\r
import eu.etaxonomy.cdm.io.berlinModel.in.validation.BerlinModelGeneralImportValidator;\r
-import eu.etaxonomy.cdm.io.common.DbImportStateBase;\r
-import eu.etaxonomy.cdm.io.common.ImportStateBase;\r
import eu.etaxonomy.cdm.io.common.Source;\r
-import eu.etaxonomy.cdm.model.name.NomenclaturalCode;\r
\r
/**\r
* @author pesiimport\r
public class AlgaTerraImportConfigurator extends BerlinModelImportConfigurator {\r
\r
private boolean doEcoFacts = true;\r
+ private boolean doFactEcology = true;\r
\r
private boolean doImages = true;\r
\r
, BerlinModelWebMarkerImport.class\r
\r
, AlgaTerraCollectionImport.class\r
- , AlgaTerraSpecimenImport.class\r
+ , AlgaTerraEcoFactImport.class\r
+ , AlgaTerraFactEcologyImport.class\r
, AlgaTerraTypeImport.class\r
, AlgaTerraTypeImagesImport.class\r
, AlgaTerraVoucherImagesImport.class\r
, AlgaTerraSiteImagesImport.class\r
+ , AlgaTerraPictureImport.class\r
\r
}; \r
\r
this.doImages = doImages;\r
}\r
\r
+ public boolean isDoFactEcology() {\r
+ return doFactEcology;\r
+ }\r
+\r
+ public void setDoFactEcology(boolean doFactEcology) {\r
+ this.doFactEcology = doFactEcology;\r
+ }\r
+\r
\r
}\r
import org.apache.log4j.Logger;\r
\r
import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportState;\r
-import eu.etaxonomy.cdm.model.description.StatisticalMeasure;\r
\r
/**\r
* @author a.mueller\r
private static final Logger logger = Logger.getLogger(AlgaTerraImportState.class);\r
\r
private boolean specimenVocabulariesCreated = false;\r
- private boolean currentFieldObservationNotNew = false;\r
private Map<String, UUID> parameterFeatureUuidMap = new HashMap<String, UUID>(); \r
\r
public AlgaTerraImportState(AlgaTerraImportConfigurator config) {\r
this.specimenVocabulariesCreated = specimenVocabulariesCreated;\r
}\r
\r
- public boolean isCurrentFieldObservationNotNew() {\r
- return currentFieldObservationNotNew;\r
- }\r
-\r
- public void setCurrentFieldObservationNotNew(\r
- boolean currentFieldObservationNotNew) {\r
- this.currentFieldObservationNotNew = currentFieldObservationNotNew;\r
- }\r
-\r
public UUID getParameterFeatureUuid(String key) {\r
return parameterFeatureUuidMap.get(key);\r
}\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.agent.TeamOrPersonBase;\r
import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary;\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.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.occurrence.Collection;\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
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
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
\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
\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.innerFieldObservation(), rs, unitId, getFieldObservationNameSpace());\r
}else{\r
- logger.warn("Specimen has no unitId: " + facade.innerDerivedUnit() + ": " + getDerivedUnitNameSpace());\r
+ logger.warn("FieldObservation has no unitId: " + facade.innerFieldObservation() + ": " + 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
+ \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
+ //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
\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
DerivedUnitFacade facade = getDerivedUnit(state, typeSpecimenId, typeSpecimenMap, type, ecoFactMap, ecoFactId);\r
\r
//field observation\r
- handleSingleSpecimen(rs, facade, state, partitioner);\r
+ handleFieldObservationSpecimen(rs, facade, state, partitioner);\r
\r
+ //TODO devide like in EcoFact (if necessary)\r
handleTypeSpecimenSpecificSpecimen(rs,facade, state);\r
\r
+ handleFirstDerivedSpecimen(rs, facade, state, partitioner);\r
+ \r
+ \r
//Designation\r
TaxonNameBase<?,?> name = getTaxonName(state, taxonNameMap, nameId);\r
SpecimenTypeDesignation designation = SpecimenTypeDesignation.NewInstance();\r
protected String getDerivedUnitNameSpace(){\r
return TYPE_SPECIMEN_DERIVED_UNIT_NAMESPACE;\r
}\r
+ \r
+ protected String getFieldObservationNameSpace(){\r
+ return TYPE_SPECIMEN_FIELD_OBSERVATION_NAMESPACE;\r
+ }\r
\r
/**\r
* @param state \r
BGBM BDI Projects / cdmlib-apps.git / commitdiff