Revision bb38665e
Added by Andreas Müller over 10 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/io/globis/GlobisSpecTaxImport.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.common.CdmUtils; |
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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.model.common.IdentifiableSource; |
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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.OriginalSourceType; |
|
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import eu.etaxonomy.cdm.model.description.Feature; |
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import eu.etaxonomy.cdm.model.location.NamedArea; |
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
| ... | ... | |
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import eu.etaxonomy.cdm.model.name.ZoologicalName; |
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import eu.etaxonomy.cdm.model.occurrence.Collection; |
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import eu.etaxonomy.cdm.model.occurrence.DerivationEvent; |
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import eu.etaxonomy.cdm.model.occurrence.FieldObservation; |
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import eu.etaxonomy.cdm.model.occurrence.Specimen; |
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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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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.Synonym; |
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import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType; |
| ... | ... | |
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name.addExtension(citedTypeLocality, exTypeCitedTypeLoc); |
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} |
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|
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name.addSource(String.valueOf(specTaxId), SPEC_TAX_NAMESPACE, state.getTransactionalSourceReference(), null); |
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name.addSource(OriginalSourceType.Import, String.valueOf(specTaxId), SPEC_TAX_NAMESPACE, state.getTransactionalSourceReference(), null);
|
|
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|
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namesToSave.add(name); |
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|
| ... | ... | |
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return; |
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} |
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|
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FieldObservation fieldObservation = makeTypeFieldObservation(state, rs);
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FieldUnit fieldObservation = makeTypeFieldObservation(state, rs);
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|
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//typeDepository |
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String specTypeDepositoriesStr = rs.getString("SpecTypeDepository");
|
| ... | ... | |
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|
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//TODO several issues |
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if (specTypeDepositories.length == 0){
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Specimen specimen = makeSingleTypeSpecimen(fieldObservation);
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DerivedUnit specimen = makeSingleTypeSpecimen(fieldObservation);
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makeTypeDesignation(name, rs, specimen, specTaxId); |
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makeTypeIdInSource(state, specimen, "null", specTaxId); |
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} |
| ... | ... | |
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specTypeDepositoryStr = specTypeDepositoryStr.trim(); |
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|
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//Specimen |
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Specimen specimen = makeSingleTypeSpecimen(fieldObservation);
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DerivedUnit specimen = makeSingleTypeSpecimen(fieldObservation);
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|
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if (specTypeDepositoryStr.equals("??")){
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//unknown |
| ... | ... | |
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} |
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|
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private void makeTypeIdInSource(GlobisImportState state, Specimen specimen, String collectionCode, Integer specTaxId) {
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private void makeTypeIdInSource(GlobisImportState state, DerivedUnit specimen, String collectionCode, Integer specTaxId) {
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String namespace = TYPE_NAMESPACE; |
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String id = getTypeId(specTaxId, collectionCode); |
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IdentifiableSource source = IdentifiableSource.NewInstance(id, namespace, state.getTransactionalSourceReference(), null); |
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IdentifiableSource source = IdentifiableSource.NewInstance(OriginalSourceType.Import, id, namespace, state.getTransactionalSourceReference(), null);
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specimen.addSource(source); |
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} |
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|
| ... | ... | |
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* @param specimen |
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* @param specTaxId |
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*/ |
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protected Collection makeCollection(GlobisImportState state, String specTypeDepositoryStr, Specimen specimen, Integer specTaxId) {
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protected Collection makeCollection(GlobisImportState state, String specTypeDepositoryStr, DerivedUnit specimen, Integer specTaxId) {
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//Collection |
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specTypeDepositoryStr = specTypeDepositoryStr.replace("Washington, D.C.", "Washington@ D.C.");
|
| ... | ... | |
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* @param specTaxId |
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* @return |
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*/ |
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protected String makeAdditionalSpecimenInformation( String specTypeDepositoryStr, Specimen specimen, Integer specTaxId) {
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protected String makeAdditionalSpecimenInformation( String specTypeDepositoryStr, DerivedUnit specimen, Integer specTaxId) {
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//doubful |
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if (specTypeDepositoryStr.endsWith("?")){
|
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Marker.NewInstance(specimen, true, MarkerType.IS_DOUBTFUL()); |
| ... | ... | |
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* @param fieldObservation |
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* @return |
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*/ |
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protected Specimen makeSingleTypeSpecimen(FieldObservation fieldObservation) {
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protected DerivedUnit makeSingleTypeSpecimen(FieldUnit fieldObservation) {
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DerivationEvent derivEvent = DerivationEvent.NewInstance(); |
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// derivEvent.setType(DerivationEventType.ACCESSIONING()); |
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fieldObservation.addDerivationEvent(derivEvent); |
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Specimen specimen = Specimen.NewInstance();
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DerivedUnit specimen = DerivedUnit.NewPreservedSpecimenInstance();
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specimen.setDerivedFrom(derivEvent); |
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return specimen; |
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} |
| ... | ... | |
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* @return |
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* @throws SQLException |
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*/ |
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protected FieldObservation makeTypeFieldObservation(GlobisImportState state,
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protected FieldUnit makeTypeFieldObservation(GlobisImportState state,
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ResultSet rs) throws SQLException {
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|
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String countryString = rs.getString("SpecTypeCountry");
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DerivedUnitType unitType = DerivedUnitType.Specimen;
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SpecimenOrObservationType unitType = SpecimenOrObservationType.PreservedSpecimen;
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DerivedUnitFacade facade = DerivedUnitFacade.NewInstance(unitType); |
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|
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NamedArea typeCountry = getCountry(state, countryString); |
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facade.setCountry(typeCountry); |
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FieldObservation fieldObservation = facade.innerFieldObservation();
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FieldUnit fieldObservation = facade.innerFieldUnit();
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return fieldObservation; |
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} |
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|
| ... | ... | |
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* @param specTaxId |
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* @throws SQLException |
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*/ |
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protected void makeTypeDesignation(ZoologicalName name, ResultSet rs, Specimen specimen, Integer specTaxId) throws SQLException {
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protected void makeTypeDesignation(ZoologicalName name, ResultSet rs, DerivedUnit specimen, Integer specTaxId) throws SQLException {
|
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//type |
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String specType = rs.getString("SpecType");
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SpecimenTypeDesignationStatus status = getTypeDesigType(specType, specTaxId); |
| ... | ... | |
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Rank rank = null; |
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if (isNotBlank(rankStr)){
|
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try {
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rank = Rank.getRankByNameOrAbbreviation(rankStr, NomenclaturalCode.ICZN, true);
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rank = Rank.getRankByNameOrIdInVoc(rankStr, NomenclaturalCode.ICZN, true);
|
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} catch (UnknownCdmTypeException e) {
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e.printStackTrace(); |
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} |
Also available in: Unified diff
reintegrate cdmlib-app-3.3 branch into trunk