Revision bb38665e
Added by Andreas Müller over 10 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/io/algaterra/AlgaTerraTypeImport.java | ||
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import org.springframework.stereotype.Component; |
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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.api.facade.DerivedUnitFacadeNotSupportedException; |
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import eu.etaxonomy.cdm.io.algaterra.validation.AlgaTerraTypeImportValidator; |
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import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator; |
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import eu.etaxonomy.cdm.io.common.ResultSetPartitioner; |
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import eu.etaxonomy.cdm.model.common.CdmBase; |
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import eu.etaxonomy.cdm.model.common.IdentifiableSource; |
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import eu.etaxonomy.cdm.model.common.OriginalSourceType; |
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import eu.etaxonomy.cdm.model.name.BotanicalName; |
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import eu.etaxonomy.cdm.model.name.Rank; |
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import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation; |
| ... | ... | |
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import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
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import eu.etaxonomy.cdm.model.occurrence.Collection; |
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import eu.etaxonomy.cdm.model.occurrence.DerivedUnit; |
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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.FieldUnit;
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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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//facade |
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//FIXME - depends on material category |
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// DerivedUnitType type = makeDerivedUnitType(recordBasis); |
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DerivedUnitType type = DerivedUnitType.Specimen; |
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if (i<=2){logger.warn("RecordBasis not yet implemented in TypeImport");}
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SpecimenOrObservationType type = SpecimenOrObservationType.PreservedSpecimen; |
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DerivedUnitFacade facade = getDerivedUnit(state, typeSpecimenId, typeSpecimenMap, type, ecoFactMap, ecoFactId); |
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//field observation |
| ... | ... | |
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DerivedUnitBase<?> derivedUnit = facade.innerDerivedUnit();
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DerivedUnit derivedUnit = facade.innerDerivedUnit(); |
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//collection |
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String barcode = rs.getString("Barcode");
|
| ... | ... | |
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if (ref == null){
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logger.warn("TypeSpecimen reference (" + refFk + ")not found in biblioRef. TypeSpecimenId: " + typeSpecimenId);
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}else{
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IdentifiableSource source = IdentifiableSource.NewInstance(ref, null); |
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IdentifiableSource source = IdentifiableSource.NewPrimarySourceInstance(ref, null);
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derivedUnit.addSource(source); |
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} |
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} |
| ... | ... | |
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* @param ecoFactMap |
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* @return |
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*/ |
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private DerivedUnitFacade getDerivedUnit(AlgaTerraImportState state, int typeSpecimenId, Map<String, DerivedUnit> typeSpecimenMap, DerivedUnitType type, Map<String, DerivedUnit> ecoFactMap, Integer ecoFactId2) {
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private DerivedUnitFacade getDerivedUnit(AlgaTerraImportState state, int typeSpecimenId, Map<String, DerivedUnit> typeSpecimenMap, SpecimenOrObservationType type, Map<String, DerivedUnit> ecoFactMap, Integer ecoFactId2) {
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//TODO implement ecoFact map - if not all null anymore |
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String typeKey = String.valueOf(typeSpecimenId); |
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DerivedUnit derivedUnit = typeSpecimenMap.get(typeKey); |
| ... | ... | |
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return facade; |
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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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// 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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private SpecimenTypeDesignationStatus getSpecimenTypeDesignationStatusByKey(Integer typeStatusFk) {
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| ... | ... | |
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//eco fact field observation map |
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nameSpace = AlgaTerraTypeImport.ECO_FACT_FIELD_OBSERVATION_NAMESPACE; |
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cdmClass = FieldObservation.class;
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cdmClass = FieldUnit.class;
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idSet = ecoFieldObservationIdSet; |
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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); |
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//type specimen map |
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nameSpace = AlgaTerraTypeImport.TYPE_SPECIMEN_FIELD_OBSERVATION_NAMESPACE; |
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cdmClass = FieldObservation.class;
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cdmClass = FieldUnit.class;
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idSet = typeSpecimenIdSet; |
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Map<String, FieldObservation> typeSpecimenMap = (Map<String, FieldObservation>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
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Map<String, FieldUnit> typeSpecimenMap = (Map<String, FieldUnit>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
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result.put(nameSpace, typeSpecimenMap); |
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Also available in: Unified diff
reintegrate cdmlib-app-3.3 branch into trunk