Revision d6ad43ba
Added by Andreas Müller about 11 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/io/algaterra/AlgaTerraTypeImport.java | ||
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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.CdmBase; |
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import eu.etaxonomy.cdm.model.common.IdentifiableSource; |
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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.reference.Reference; |
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|
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protected String getRecordQuery(BerlinModelImportConfigurator config) {
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String strQuery = |
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" SELECT ts.*, ts.TypeSpecimenId as unitId, td.*, gz.ID as GazetteerId, gz.L2Code, gz.L3Code, gz.L4Code, gz.ISOCountry, gz.Country, ts.WaterBody " + |
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" " + |
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" SELECT ts.*, ts.TypeSpecimenId as unitId, td.*, gz.ID as GazetteerId, gz.L2Code, gz.L3Code, gz.L4Code, gz.ISOCountry, gz.Country, ts.WaterBody, " +
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" ts.RefFk as tsRefFk, ts.RefDetailFk as tsRefDetailFk, td.RefFk as tdRefFk, td.RefDetailFk as tdRefDetailFk " +
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" FROM TypeSpecimenDesignation tsd " |
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+ " LEFT OUTER JOIN TypeSpecimen AS ts ON tsd.TypeSpecimenFk = ts.TypeSpecimenId " |
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+ " FULL OUTER JOIN TypeDesignation td ON td.TypeDesignationId = tsd.TypeDesignationFk " |
| ... | ... | |
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Map<String, TaxonNameBase> taxonNameMap = (Map<String, TaxonNameBase>) partitioner.getObjectMap(BerlinModelTaxonNameImport.NAMESPACE); |
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Map<String, DerivedUnit> ecoFactMap = (Map<String, DerivedUnit>) partitioner.getObjectMap(AlgaTerraEcoFactImport.ECO_FACT_FIELD_OBSERVATION_NAMESPACE); |
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Map<String, DerivedUnit> typeSpecimenMap = (Map<String, DerivedUnit>) partitioner.getObjectMap(TYPE_SPECIMEN_FIELD_OBSERVATION_NAMESPACE); |
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Map<String, Reference> biblioReference = (Map<String, Reference>) partitioner.getObjectMap(BerlinModelReferenceImport.BIBLIO_REFERENCE_NAMESPACE); |
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Map<String, Reference> biblioRefMap = (Map<String, Reference>) partitioner.getObjectMap(BerlinModelReferenceImport.BIBLIO_REFERENCE_NAMESPACE); |
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Map<String, Reference> nomRefMap = (Map<String, Reference>) partitioner.getObjectMap(BerlinModelReferenceImport.NOM_REFERENCE_NAMESPACE); |
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ResultSet rs = partitioner.getResultSet(); |
| ... | ... | |
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int typeDesignationId = rs.getInt("TypeDesignationId");
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Integer typeStatusFk = nullSafeInt(rs, "typeStatusFk"); |
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Integer ecoFactId = nullSafeInt(rs, "ecoFactFk"); |
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Integer tdRefFk = nullSafeInt(rs, "tdRefFk"); |
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Integer tdRefDetailFk = nullSafeInt(rs, "tdRefDetailFk"); |
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// String recordBasis = rs.getString("RecordBasis");
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try {
|
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//field observation |
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handleFieldObservationSpecimen(rs, facade, state, partitioner); |
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//TODO devide like in EcoFact (if necessary)
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handleTypeSpecimenSpecificSpecimen(rs,facade, state); |
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//TODO divide like in EcoFact (if necessary)
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handleTypeSpecimenSpecificSpecimen(rs,facade, state, biblioRefMap, nomRefMap, typeSpecimenId);
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handleFirstDerivedSpecimen(rs, facade, state, partitioner); |
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|
| ... | ... | |
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SpecimenTypeDesignationStatus status = getSpecimenTypeDesignationStatusByKey(typeStatusFk); |
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designation.setTypeSpecimen(facade.innerDerivedUnit()); |
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designation.setTypeStatus(status); |
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if (tdRefFk != null){
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Reference<?> typeDesigRef = getReferenceOnlyFromMaps(biblioRefMap, nomRefMap, String.valueOf(tdRefFk)); |
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if (typeDesigRef == null){
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logger.warn("Type designation reference not found in maps: " + tdRefFk);
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}else{
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designation.setCitation(typeDesigRef); |
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} |
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} |
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if (tdRefDetailFk != null){
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logger.warn("TypeDesignation.RefDetailFk not yet implemented: " + typeDesignationId);
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} |
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if (name != null){
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name.addTypeDesignation(designation, true); //TODO check if true is correct |
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}else{
|
| ... | ... | |
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return result; |
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} |
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private void handleTypeSpecimenSpecificSpecimen(ResultSet rs, DerivedUnitFacade facade, AlgaTerraImportState state) throws SQLException {
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private void handleTypeSpecimenSpecificSpecimen(ResultSet rs, DerivedUnitFacade facade, AlgaTerraImportState state, Map<String, Reference> biblioRefMap, Map<String, Reference> nomRefMap, int typeSpecimenId) throws SQLException {
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//TODO |
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DerivedUnitBase<?> derivedUnit = facade.innerDerivedUnit(); |
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//collection |
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String barcode = rs.getString("Barcode");
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if (StringUtils.isNotBlank(barcode)){
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facade.setBarcode(barcode); |
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} |
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//RefFk + RefDetailFk |
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Integer refFk = nullSafeInt(rs, "tsRefFk"); |
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if (refFk != null){
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Reference<?> ref = getReferenceOnlyFromMaps(biblioRefMap, nomRefMap, String.valueOf(refFk)); |
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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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derivedUnit.addSource(source); |
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} |
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} |
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Integer refDetailFk = nullSafeInt(rs, "tsRefDetailFk"); |
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if (refDetailFk != null){
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logger.warn("TypeSpecimen.RefDetailFk should always be NULL but wasn't: " + typeSpecimenId);
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} |
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} |
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|
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/** |
| ... | ... | |
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Set<String> typeSpecimenIdSet = new HashSet<String>(); |
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Set<String> termsIdSet = new HashSet<String>(); |
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Set<String> collectionIdSet = new HashSet<String>(); |
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Set<String> referenceIdSet = new HashSet<String>(); |
|
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|
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while (rs.next()){
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handleForeignKey(rs, nameIdSet, "nameFk"); |
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handleForeignKey(rs, ecoFieldObservationIdSet, "ecoFactFk"); |
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handleForeignKey(rs, typeSpecimenIdSet, "TypeSpecimenId"); |
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handleForeignKey(rs, collectionIdSet, "CollectionFk"); |
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handleForeignKey(rs, referenceIdSet, "tsRefFk"); |
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handleForeignKey(rs, referenceIdSet, "tdRefFk"); |
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} |
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|
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//name map |
| ... | ... | |
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Map<String, Collection> subCollectionMap = (Map<String, Collection>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace); |
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result.put(nameSpace, subCollectionMap); |
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//nom reference map |
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nameSpace = BerlinModelReferenceImport.NOM_REFERENCE_NAMESPACE; |
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cdmClass = Reference.class; |
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idSet = referenceIdSet; |
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Map<String, Reference> nomReferenceMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace); |
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result.put(nameSpace, nomReferenceMap); |
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//biblio reference map |
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nameSpace = BerlinModelReferenceImport.BIBLIO_REFERENCE_NAMESPACE; |
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cdmClass = Reference.class; |
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idSet = referenceIdSet; |
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Map<String, Reference> biblioReferenceMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace); |
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result.put(nameSpace, biblioReferenceMap); |
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// |
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// //terms |
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