Revision bb38665e
Added by Andreas Müller over 10 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/io/algaterra/AlgaTerraMorphologyImport.java | ||
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import org.springframework.stereotype.Component; |
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|
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import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade; |
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import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade.DerivedUnitType; |
|
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import eu.etaxonomy.cdm.io.algaterra.validation.AlgaTerraMorphologyImportValidator; |
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import eu.etaxonomy.cdm.io.algaterra.validation.AlgaTerraSpecimenImportValidator; |
|
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import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator; |
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import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportState; |
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import eu.etaxonomy.cdm.io.common.IOValidator; |
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import eu.etaxonomy.cdm.io.common.ResultSetPartitioner; |
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import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException; |
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import eu.etaxonomy.cdm.model.common.CdmBase; |
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import eu.etaxonomy.cdm.model.common.DefinedTerm; |
|
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import eu.etaxonomy.cdm.model.common.DefinedTermBase; |
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import eu.etaxonomy.cdm.model.common.Language; |
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import eu.etaxonomy.cdm.model.common.Marker; |
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import eu.etaxonomy.cdm.model.common.MarkerType; |
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import eu.etaxonomy.cdm.model.common.TermType; |
|
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import eu.etaxonomy.cdm.model.common.TermVocabulary; |
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import eu.etaxonomy.cdm.model.description.CategoricalData; |
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import eu.etaxonomy.cdm.model.description.DescriptionBase; |
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import eu.etaxonomy.cdm.model.description.Feature; |
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import eu.etaxonomy.cdm.model.description.MeasurementUnit; |
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import eu.etaxonomy.cdm.model.description.Modifier; |
|
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import eu.etaxonomy.cdm.model.description.QuantitativeData; |
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import eu.etaxonomy.cdm.model.description.State; |
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import eu.etaxonomy.cdm.model.description.StatisticalMeasure; |
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import eu.etaxonomy.cdm.model.description.StatisticalMeasurementValue; |
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import eu.etaxonomy.cdm.model.description.TextData; |
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import eu.etaxonomy.cdm.model.occurrence.Collection; |
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import eu.etaxonomy.cdm.model.occurrence.DerivedUnitBase;
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import eu.etaxonomy.cdm.model.occurrence.FieldObservation;
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import eu.etaxonomy.cdm.model.occurrence.DerivedUnit; |
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import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
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|
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase; |
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType; |
|
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import eu.etaxonomy.cdm.model.reference.Reference; |
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|
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|
| ... | ... | |
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|
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//TODO do we still need this map? EcoFacts are not handled separate from Facts. |
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//However, they have duplicates on derived unit level. Also check duplicateFk. |
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Map<String, FieldObservation> ecoFactFieldObservationMap = (Map<String, FieldObservation>) partitioner.getObjectMap(ECO_FACT_FIELD_OBSERVATION_NAMESPACE);
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Map<String, FieldUnit> ecoFactFieldObservationMap = (Map<String, FieldUnit>) partitioner.getObjectMap(ECO_FACT_FIELD_OBSERVATION_NAMESPACE);
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ResultSet rs = partitioner.getResultSet(); |
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|
| ... | ... | |
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Reference<?> sourceRef = state.getTransactionalSourceReference(); |
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|
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//facade |
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DerivedUnitType type = makeDerivedUnitType(recordBasis);
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SpecimenOrObservationType type = makeDerivedUnitType(recordBasis);
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|
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DerivedUnitFacade facade; |
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//field observation |
| ... | ... | |
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facade = DerivedUnitFacade.NewInstance(type); |
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handleFieldObservationSpecimen(rs, facade, state, partitioner); |
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handleEcoFactSpecificFieldObservation(rs,facade, state); |
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FieldObservation fieldObservation = facade.getFieldObservation(true);
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FieldUnit fieldObservation = facade.getFieldUnit(true);
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ecoFactFieldObservationMap.put(String.valueOf(ecoFactId), fieldObservation); |
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}else{
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FieldObservation fieldObservation = ecoFactFieldObservationMap.get(String.valueOf(duplicateFk));
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FieldUnit fieldObservation = ecoFactFieldObservationMap.get(String.valueOf(duplicateFk));
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facade = DerivedUnitFacade.NewInstance(type, fieldObservation); |
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} |
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|
| ... | ... | |
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handleEcoFactSpecificDerivedUnit(rs,facade, state); |
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|
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DerivedUnitBase<?> objectToSave = facade.innerDerivedUnit();
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DerivedUnit objectToSave = facade.innerDerivedUnit(); |
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objectsToSave.add(objectToSave); |
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|
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|
| ... | ... | |
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MarkerType alkalinityMarkerType = getMarkerType(state, uuidMarkerAlkalinity, "Alkalinity", "Alkalinity", null); |
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boolean alkFlag = Boolean.valueOf(alkalinityFlag.toString()); |
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Marker alkalinityMarker = Marker.NewInstance(alkalinityMarkerType, alkFlag); |
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facade.getFieldObservation(true).addMarker(alkalinityMarker);
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facade.getFieldUnit(true).addMarker(alkalinityMarker);
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} |
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|
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|
| ... | ... | |
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logger.warn("Methods not yet handled: " + method);
|
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} |
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//parameter |
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TermVocabulary<Feature> vocParameter = getVocabulary(uuidVocParameter, "Feature vocabulary for AlgaTerra measurement parameters", "Parameters", null, null, false, Feature.COMMON_NAME()); |
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TermVocabulary<Feature> vocParameter = getVocabulary(TermType.Feature, uuidVocParameter, "Feature vocabulary for AlgaTerra measurement parameters", "Parameters", null, null, false, Feature.COMMON_NAME());
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if (StringUtils.isNotBlank(parameter)){
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UUID featureUuid = getParameterFeatureUuid(state, parameter); |
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Feature feature = getFeature(state, featureUuid, parameter, parameter, null, vocParameter); |
| ... | ... | |
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quantData.setUnit(unit); |
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try {
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Set<Modifier> valueModifier = new HashSet<Modifier>();
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Set<DefinedTerm> valueModifier = new HashSet<DefinedTerm>();
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valueStr = normalizeAndModifyValue(state, valueStr, valueModifier); |
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//value |
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Float valueFlt = Float.valueOf(valueStr); //TODO maybe change model to Double ?? |
| ... | ... | |
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|
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} |
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private String normalizeAndModifyValue(AlgaTerraImportState state, String valueStr, Set<Modifier> valueModifier) {
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private String normalizeAndModifyValue(AlgaTerraImportState state, String valueStr, Set<DefinedTerm> valueModifier) {
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valueStr = valueStr.replace(",", ".");
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if (valueStr.startsWith("<")){
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TermVocabulary<Modifier> measurementValueModifierVocabulary = getVocabulary(uuidMeasurementValueModifier, "Measurement value modifier", "Measurement value modifier", null, null, false, Modifier.NewInstance());
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Modifier modifier = getModifier(state, uuidModifierLowerThan, "Lower", "Lower than the given measurement value", "<", measurementValueModifierVocabulary);
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TermVocabulary<DefinedTerm> measurementValueModifierVocabulary = getVocabulary(TermType.Modifier, uuidMeasurementValueModifier, "Measurement value modifier", "Measurement value modifier", null, null, false, DefinedTerm.NewModifierInstance(null, null, null));
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DefinedTerm modifier = getModifier(state, uuidModifierLowerThan, "Lower", "Lower than the given measurement value", "<", measurementValueModifierVocabulary);
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valueModifier.add(modifier); |
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valueStr = valueStr.replace("<", "");
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} |
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if (valueStr.startsWith(">")){
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TermVocabulary<Modifier> measurementValueModifierVocabulary = getVocabulary(uuidMeasurementValueModifier, "Measurement value modifier", "Measurement value modifier", null, null, false, Modifier.NewInstance());
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Modifier modifier = getModifier(state, uuidModifierGreaterThan, "Lower", "Lower than the given measurement value", "<", measurementValueModifierVocabulary);
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TermVocabulary<DefinedTerm> measurementValueModifierVocabulary = getVocabulary(TermType.Modifier, uuidMeasurementValueModifier, "Measurement value modifier", "Measurement value modifier", null, null, false, DefinedTerm.NewModifierInstance(null, null, null));
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DefinedTerm modifier = getModifier(state, uuidModifierGreaterThan, "Lower", "Lower than the given measurement value", "<", measurementValueModifierVocabulary);
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valueModifier.add(modifier); |
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valueStr = valueStr.replace(">", "");
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} |
| ... | ... | |
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} |
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} |
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private Feature makeFeature(DerivedUnitType type) {
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if (type.equals(DerivedUnitType.DerivedUnit)){
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return Feature.INDIVIDUALS_ASSOCIATION(); |
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}else if (type.equals(DerivedUnitType.FieldObservation) || type.equals(DerivedUnitType.Observation) ){
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return Feature.OBSERVATION(); |
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}else if (type.equals(DerivedUnitType.Fossil) || type.equals(DerivedUnitType.LivingBeing) || type.equals(DerivedUnitType.Specimen )){
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return Feature.SPECIMEN(); |
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} |
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logger.warn("No feature defined for derived unit type: " + type);
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return null; |
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} |
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private DerivedUnitType makeDerivedUnitType(String recordBasis) {
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DerivedUnitType result = null; |
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if (StringUtils.isBlank(recordBasis)){
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result = DerivedUnitType.DerivedUnit; |
|
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} else if (recordBasis.equalsIgnoreCase("FossileSpecimen")){
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result = DerivedUnitType.Fossil; |
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}else if (recordBasis.equalsIgnoreCase("HumanObservation")){
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result = DerivedUnitType.Observation; |
|
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}else if (recordBasis.equalsIgnoreCase("Literature")){
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logger.warn("Literature record basis not yet supported");
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result = DerivedUnitType.DerivedUnit; |
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}else if (recordBasis.equalsIgnoreCase("LivingSpecimen")){
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result = DerivedUnitType.LivingBeing; |
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}else if (recordBasis.equalsIgnoreCase("MachineObservation")){
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logger.warn("MachineObservation record basis not yet supported");
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result = DerivedUnitType.Observation; |
|
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}else if (recordBasis.equalsIgnoreCase("PreservedSpecimen")){
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result = DerivedUnitType.Specimen; |
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} |
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return result; |
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} |
|
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|
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/* (non-Javadoc) |
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* @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet) |
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*/ |
|
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@Override |
|
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public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs) {
|
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String nameSpace; |
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Class cdmClass; |
| ... | ... | |
| 430 | 394 |
|
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//field observation map for duplicates |
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nameSpace = AlgaTerraMorphologyImport.ECO_FACT_FIELD_OBSERVATION_NAMESPACE; |
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cdmClass = FieldObservation.class;
|
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cdmClass = FieldUnit.class;
|
|
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idSet = fieldObservationIdSet; |
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Map<String, FieldObservation> fieldObservationMap = (Map<String, FieldObservation>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
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Map<String, FieldUnit> fieldObservationMap = (Map<String, FieldUnit>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
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result.put(nameSpace, fieldObservationMap); |
| 437 | 401 |
|
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//collections |
| ... | ... | |
| 451 | 415 |
|
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//terms |
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nameSpace = AlgaTerraMorphologyImport.TERMS_NAMESPACE; |
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cdmClass = FieldObservation.class;
|
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cdmClass = FieldUnit.class;
|
|
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idSet = termsIdSet; |
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Map<String, DefinedTermBase> termMap = (Map<String, DefinedTermBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace); |
| 457 | 421 |
result.put(nameSpace, termMap); |
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reintegrate cdmlib-app-3.3 branch into trunk