Revision 60ad1ed0
Added by Andreas Müller almost 10 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/io/algaterra/AlgaTerraTypeImport.java | ||
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import java.util.HashSet; |
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import java.util.Map; |
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import java.util.Set; |
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import java.util.UUID; |
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import org.apache.commons.lang.StringUtils; |
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import org.apache.log4j.Logger; |
| ... | ... | |
| 38 | 39 |
import eu.etaxonomy.cdm.model.common.Annotation; |
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import eu.etaxonomy.cdm.model.common.AnnotationType; |
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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.IdentifiableSource; |
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import eu.etaxonomy.cdm.model.common.Language; |
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import eu.etaxonomy.cdm.model.common.User; |
| ... | ... | |
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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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" ts.RefFk as tsRefFk, ts.RefDetailFk as tsRefDetailFk, td.RefFk as tdRefFk, td.RefDetailFk as tdRefDetailFk, " + |
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" SELECT ts.*, ts.TypeSpecimenId as unitId, td.*, gz.ID as GazetteerId, gz.L1Code, gz.L2Code, gz.L3Code, gz.L4Code, gz.ISOCountry, gz.Country, gz.subL4, ts.WaterBody, " +
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" ts.RefFk as tsRefFk, ts.RefDetailFk as tsRefDetailFk, ts.MaterialCategoryFK as tsMaterialCategoryFK, td.RefFk as tdRefFk, td.RefDetailFk as tdRefDetailFk, " +
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" RefDet.Details as tdRefDetails, " + |
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" td.created_When as tdCreated_When, tsd.created_When as tsdCreated_When, td.updated_when as tdUpdated_when, " + |
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" td.created_who as tdCreated_who, tsd.created_who as tsdCreated_who, td.updated_who tdUpdated_who " + |
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" td.created_who as tdCreated_who, tsd.created_who as tsdCreated_who, td.updated_who tdUpdated_who, " + |
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" mc.* " + |
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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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+ " LEFT OUTER JOIN TDWGGazetteer gz ON ts.TDWGGazetteerFk = gz.ID " |
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+ " LEFT OUTER JOIN RefDetail refDet ON td.RefDetailFk = refDet.RefDetailId AND td.RefFk = refDet.RefFk " |
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+ " LEFT OUTER JOIN MaterialCategory mc ON mc.MaterialCategoryId = ts.MaterialCategoryFK " |
|
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+ " WHERE (td.TypeDesignationId IN (" + ID_LIST_TOKEN + ") )"
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+ " ORDER BY NameFk " |
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; |
| ... | ... | |
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Boolean restrictedFlag = nullSafeBoolean(rs, "RestrictedFlag"); |
| 151 | 155 |
|
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String typeSpecimenPhrase = rs.getString("TypeSpecimenPhrase");
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Integer tsMaterialCategoryFK = nullSafeInt(rs, "MaterialCategoryFK"); |
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boolean isIcon = typeSpecimenPhrase != null && typeSpecimenPhrase.toLowerCase().startsWith("\u005bicon");
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|
| ... | ... | |
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type = SpecimenOrObservationType.StillImage; |
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}else if (typeStatusFk != null && typeStatusFk.equals(39)){
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type = SpecimenOrObservationType.LivingSpecimen; |
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}else if (tsMaterialCategoryFK != null && tsMaterialCategoryFK.equals(4)){
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type = SpecimenOrObservationType.Fossil; |
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} |
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if (tsMaterialCategoryFK != null && typeStatusFk != null && |
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( typeStatusFk.equals(39) && !tsMaterialCategoryFK.equals(14) || ! typeStatusFk.equals(39) && tsMaterialCategoryFK.equals(14) )){
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logger.warn("Living Specimen type status should be 39 and materialCategoryFk 14 but one of them wasn't");
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} |
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DerivedUnitFacade facade = getDerivedUnit(state, typeSpecimenId, typeSpecimenMap, type, ecoFactMap, ecoFactId, sourceRef); |
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|
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//field observation |
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handleFieldObservationSpecimen(rs, facade, state, partitioner); |
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// handleTypeSpecimenSpecificFieldObservation(rs,facade, state); |
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//TODO divide like in EcoFact (if necessary) |
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handleTypeSpecimenSpecificSpecimen(rs,facade, state, refMap, typeSpecimenId); |
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|
| ... | ... | |
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|
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DerivedUnit derivedUnit = facade.innerDerivedUnit(); |
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Integer tsMaterialCategoryFK = nullSafeInt(rs, "tsMaterialCategoryFK"); |
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String matCat = rs.getString("MaterialCategory");
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if (tsMaterialCategoryFK != null){
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if (tsMaterialCategoryFK.equals(16)){
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tsMaterialCategoryFK = 9; |
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} |
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UUID uuid = materialCategoryMapping.get(tsMaterialCategoryFK); |
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if (uuid == null){
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logger.warn("Uuid was null. This should not happen.");
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} |
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DefinedTerm kindOfUnit = getKindOfUnit(state, uuid, matCat, null, null, null); //all terms should exist already |
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facade.setKindOfUnit(kindOfUnit); |
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}else{
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logger.warn("Material Category was null. This is not expected");
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} |
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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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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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|
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private SpecimenTypeDesignationStatus getSpecimenTypeDesignationStatusByKey(Integer typeStatusFk) {
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if (typeStatusFk == null){ return null;
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if (typeStatusFk == null){ return SpecimenTypeDesignationStatus.TYPE();
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}else if (typeStatusFk == 1) { return SpecimenTypeDesignationStatus.HOLOTYPE();
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}else if (typeStatusFk == 2) { return SpecimenTypeDesignationStatus.LECTOTYPE();
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}else if (typeStatusFk == 3) { return SpecimenTypeDesignationStatus.NEOTYPE();
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