Revision bb38665e
Added by Andreas Müller over 10 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/io/algaterra/AlgaTerraFactEcologyImport.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.DerivedUnitFacadeCacheStrategy; |
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import eu.etaxonomy.cdm.api.facade.DerivedUnitFacadeNotSupportedException; |
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import eu.etaxonomy.cdm.common.CdmUtils; |
| ... | ... | |
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import eu.etaxonomy.cdm.model.description.TaxonDescription; |
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import eu.etaxonomy.cdm.model.occurrence.DerivationEvent; |
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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.DeterminationEvent; |
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import eu.etaxonomy.cdm.model.occurrence.FieldObservation; |
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import eu.etaxonomy.cdm.model.occurrence.Fossil; |
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import eu.etaxonomy.cdm.model.occurrence.LivingBeing; |
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import eu.etaxonomy.cdm.model.occurrence.Observation; |
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import eu.etaxonomy.cdm.model.occurrence.Specimen; |
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import eu.etaxonomy.cdm.model.occurrence.FieldUnit; |
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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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import eu.etaxonomy.cdm.model.taxon.Taxon; |
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import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
| ... | ... | |
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Set<TaxonBase> taxaToSave = new HashSet<TaxonBase>(); |
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Map<String, TaxonBase> taxonMap = (Map<String, TaxonBase>) partitioner.getObjectMap(BerlinModelTaxonImport.NAMESPACE); |
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Map<String, DerivedUnitBase> ecoFactDerivedUnitMap = (Map<String, DerivedUnitBase>) partitioner.getObjectMap(ECO_FACT_DERIVED_UNIT_NAMESPACE);
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Map<String, DerivedUnit> ecoFactDerivedUnitMap = (Map<String, DerivedUnit>) partitioner.getObjectMap(ECO_FACT_DERIVED_UNIT_NAMESPACE);
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ResultSet rs = partitioner.getResultSet(); |
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|
| ... | ... | |
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//source ref |
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Reference<?> sourceRef = state.getTransactionalSourceReference(); |
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DerivedUnitBase<?> ecoFact = ecoFactDerivedUnitMap.get(String.valueOf(ecoFactId));
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DerivedUnit ecoFact = ecoFactDerivedUnitMap.get(String.valueOf(ecoFactId)); |
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if (ecoFact == null){
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logger.warn("EcoFact is null for EcoFact: " + CdmUtils.Nz(ecoFactId) + ", taxonId: " + CdmUtils.Nz(taxonId));
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} |
| ... | ... | |
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Taxon taxon = getTaxon(state, taxonId, taxonMap, factId); |
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if(taxon != null){
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DerivedUnitBase identifiedSpecimen = makeIdentifiedSpecimen(ecoFact, recordBasis);
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DerivedUnit identifiedSpecimen = makeIdentifiedSpecimen(ecoFact, recordBasis); |
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makeDetermination(state, rs, taxon, identifiedSpecimen, factId, partitioner); |
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|
| ... | ... | |
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} |
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} |
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private void makeIndividualsAssociation(AlgaTerraImportState state, Taxon taxon, Reference<?> sourceRef, DerivedUnitBase<?> identifiedSpecimen){
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private void makeIndividualsAssociation(AlgaTerraImportState state, Taxon taxon, Reference<?> sourceRef, DerivedUnit identifiedSpecimen){
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TaxonDescription taxonDescription = getTaxonDescription(state, taxon, sourceRef); |
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IndividualsAssociation indAssociation = IndividualsAssociation.NewInstance(); |
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Feature feature = makeFeature(identifiedSpecimen); |
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Feature feature = makeFeature(identifiedSpecimen.getRecordBasis());
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indAssociation.setAssociatedSpecimenOrObservation(identifiedSpecimen); |
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indAssociation.setFeature(feature); |
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taxonDescription.addElement(indAssociation); |
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} |
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private void makeDetermination(AlgaTerraImportState state, ResultSet rs, Taxon taxon, DerivedUnitBase<?> identifiedSpecimen, int factId, ResultSetPartitioner partitioner) throws SQLException {
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private void makeDetermination(AlgaTerraImportState state, ResultSet rs, Taxon taxon, DerivedUnit identifiedSpecimen, int factId, ResultSetPartitioner partitioner) throws SQLException {
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Date identifiedWhen = rs.getDate("IdentifiedWhen");
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Date identifiedWhenEnd = rs.getDate("IdentiedWhenEnd");
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boolean restrictedFlag = rs.getBoolean("RestrictedFlag");
|
| ... | ... | |
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private DerivedUnitBase<?> makeIdentifiedSpecimen(DerivedUnitBase<?> ecoFact, String recordBasis) {
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private DerivedUnit makeIdentifiedSpecimen(DerivedUnit ecoFact, String recordBasis) {
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//TODO event type |
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DerivationEvent event = DerivationEvent.NewInstance(); |
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DerivedUnitType derivedUnitType = makeDerivedUnitType(recordBasis);
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SpecimenOrObservationType derivedUnitType = makeDerivedUnitType(recordBasis);
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if (derivedUnitType == null){
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logger.warn("NULL");
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logger.warn("derivedUnitType is NULL");
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} |
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DerivedUnitBase<?> result = derivedUnitType.getNewDerivedUnitInstance();
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DerivedUnit result = DerivedUnit.NewInstance(derivedUnitType);
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result.setDerivedFrom(event); |
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ecoFact.addDerivationEvent(event); |
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|
| ... | ... | |
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* @param type |
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* @return |
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*/ |
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private DerivedUnitFacade getDerivedUnit(AlgaTerraImportState state, int ecoFactId, Map<String, DerivedUnit> derivedUnitMap, DerivedUnitType type) {
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private DerivedUnitFacade getDerivedUnit(AlgaTerraImportState state, int ecoFactId, Map<String, DerivedUnit> derivedUnitMap, SpecimenOrObservationType type) {
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String key = String.valueOf(ecoFactId); |
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DerivedUnit derivedUnit = derivedUnitMap.get(key); |
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DerivedUnitFacade facade; |
| ... | ... | |
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return facade; |
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} |
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private Feature makeFeature(SpecimenOrObservationBase unit) {
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if (unit.isInstanceOf(DerivedUnit.class)){
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return Feature.INDIVIDUALS_ASSOCIATION(); |
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}else if (unit.isInstanceOf(FieldObservation.class) || unit.isInstanceOf(Observation.class) ){
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return Feature.OBSERVATION(); |
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}else if (unit.isInstanceOf(Fossil.class) || unit.isInstanceOf(LivingBeing.class) || unit.isInstanceOf(Specimen.class )){
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return Feature.SPECIMEN(); |
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} |
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logger.warn("No feature defined for derived unit class: " + unit.getClass().getSimpleName());
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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("Observation")){
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result = DerivedUnitType.Observation; |
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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("LivingCulture")){
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logger.warn("LivingCulture record basis not yet supported");
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result = DerivedUnitType.DerivedUnit; |
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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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/* (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; |
| ... | ... | |
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|
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//derived unit map |
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nameSpace = AlgaTerraFactEcologyImport.ECO_FACT_DERIVED_UNIT_NAMESPACE; |
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cdmClass = DerivedUnitBase.class;
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cdmClass = DerivedUnit.class; |
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idSet = extensionFkSet; |
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Map<String, DerivedUnitBase> derivedUnitMap = (Map<String, DerivedUnitBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
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Map<String, DerivedUnit> derivedUnitMap = (Map<String, DerivedUnit>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
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result.put(nameSpace, derivedUnitMap); |
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|
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//nom reference map |
Also available in: Unified diff
reintegrate cdmlib-app-3.3 branch into trunk