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Revision d9dd1907

Added by Katja Luther about 6 years ago

ID d9dd1907fa661f9a68e47b809721fe0e28a942bc
Parent 5a339c11
Child 0ce60f9b

smaller changes in ABCD import

     import eu.etaxonomy.cdm.model.agent.Person;
     import eu.etaxonomy.cdm.model.agent.Team;
     import eu.etaxonomy.cdm.model.common.CdmBase;
     import eu.etaxonomy.cdm.model.common.DefinedTerm;
     import eu.etaxonomy.cdm.model.common.ISourceable;
     import eu.etaxonomy.cdm.model.common.IdentifiableSource;
     import eu.etaxonomy.cdm.model.common.LanguageString;
-...
     	private static final String COLON = ":";
     	protected Map<String, DefinedTerm> kindOfUnitsMap;
     	@Override
         protected abstract void doInvoke(STATE state);
-...
     	            String preferred = identification.getPreferred();
     	            preferredFlag = false;
     	            if (preferred != null){
     	            if (preferred != null || state.getDataHolder().getIdentificationList().size()==1){
         	            if (preferred.equals("1") || preferred.toLowerCase().indexOf("true") != -1 || state.getDataHolder().getIdentificationList().size()==1) {
         	                preferredFlag = true;
+        	            }

     import eu.etaxonomy.cdm.model.common.LanguageString;
     import eu.etaxonomy.cdm.model.common.OriginalSourceBase;
     import eu.etaxonomy.cdm.model.common.OriginalSourceType;
     import eu.etaxonomy.cdm.model.common.TermType;
     import eu.etaxonomy.cdm.model.common.TermVocabulary;
     import eu.etaxonomy.cdm.model.location.NamedArea;
     import eu.etaxonomy.cdm.model.media.Media;
     import eu.etaxonomy.cdm.model.molecular.DnaSample;
-...
     /**
      * @author p.kelbert
      * @author p.plitzner
      * @author k.luther
      * @since 20.10.2008
      */
     @Component
-...
             MapWrapper<TeamOrPersonBase<?>> authorStore = (MapWrapper<TeamOrPersonBase<?>>)stores.get(ICdmIO.TEAM_STORE);
             state.setPersonStore(authorStore);
             MapWrapper<Reference> referenceStore = (MapWrapper<Reference>)stores.get(ICdmIO.REFERENCE_STORE);
             createKindOfUnitsMap(state);
             URI sourceUri = config.getSourceUri();
             try{
                 state.setTx(startTransaction());
-...
+        }
         /**
+         *
          */
         private void createKindOfUnitsMap(Abcd206ImportState state) {
             ICdmRepository cdmRepository = state.getConfig().getCdmAppController();
             if (cdmRepository == null){
                 cdmRepository = this;
+            }
             List<DefinedTerm> terms = cdmRepository.getTermService().listByTermType(TermType.KindOfUnit, null, 0, null, null);
             kindOfUnitsMap = new HashMap<>();
             for (DefinedTerm kindOfUnit:terms) {
                 kindOfUnitsMap.put(kindOfUnit.getLabel().toLowerCase(), kindOfUnit);
+            }
+        }
         /**
          * @param state
          * @param item
          */
         private void getSiblings(Abcd206ImportState state, Object item, DerivedUnitFacade facade) {
             String unitId = facade.getCatalogNumber();
             if (unitId == null){
                 unitId = facade.getAccessionNumber();
+            }
             UnitAssociationParser unitParser = new UnitAssociationParser(state.getPrefix(), state.getReport(), state.getCdmRepository());
             UnitAssociationWrapper unitAssociationWrapper = null;
             for (URI accessPoint: state.getActualAccesPoint()){
                 unitAssociationWrapper = unitParser.parseSiblings(unitId, accessPoint);
                 if (unitAssociationWrapper.getAssociatedUnits() != null){
                 if (unitAssociationWrapper != null &&  unitAssociationWrapper.getAssociatedUnits() != null){
                     break;
+                }
+            }
-...
+            }
             if (NB((state.getDataHolder()).getKindOfUnit()) != null) {
                 if (state.getDataHolder().getKindOfUnit().toLowerCase().indexOf("clone")>-1) {
                     kindOfUnit = getKindOfUnit(state, null, "clone culture", "clone culture", "cc", null);
+                }
                 else if (state.getDataHolder().getKindOfUnit().toLowerCase().startsWith("live"))  {
                     kindOfUnit = getKindOfUnit(state, null, "live sample", "live sample", "ls", null);
+                }
                 kindOfUnit =  getKindOfUnit(state, null, state.getDataHolder().getKindOfUnit().toLowerCase(), null, null, null);
                 if (kindOfUnit == null){
                     if (state.getDataHolder().getKindOfUnit().toLowerCase().indexOf("clone")>-1) {
                         kindOfUnit = getKindOfUnit(state, null, "clone culture", "clone culture", "cc", null);
+                    }
                     else if (state.getDataHolder().getKindOfUnit().toLowerCase().startsWith("live"))  {
                         kindOfUnit = getKindOfUnit(state, null, "live sample", "live sample", "ls", null);
+                    }
                     else if (state.getDataHolder().getKindOfUnit().toLowerCase().startsWith("microscopic slide"))  {
                         kindOfUnit = getKindOfUnit(state, null, "microscopic slide", "microscopic slide", "ms", null);
+                    }
                 if (kindOfUnit == null) {
                     logger.info("The kind of unit does not seem to be known: " + state.getDataHolder().getKindOfUnit());
                     if (kindOfUnit == null) {
                         logger.info("The kind of unit does not seem to be known: " + state.getDataHolder().getKindOfUnit());
+                    }
+                }
             } else {
                 logger.info("The kind of unit is null");
-...
             return false;
+        }
         @Override
         protected DefinedTerm getKindOfUnit(Abcd206ImportState state, UUID uuid, String label, String description, String labelAbbrev, TermVocabulary<DefinedTerm> voc){
             DefinedTerm unit = null;
             if (uuid == null){
                 unit = this.kindOfUnitsMap.get(label.toLowerCase());
             }else{
                 unit = state.getKindOfUnit(uuid);
+            }
             if (unit == null){
                 unit = (DefinedTerm)getTermService().find(uuid);
                 if (unit == null){
                     if (uuid == null){
                         uuid = UUID.randomUUID();
+                    }
                     unit = DefinedTerm.NewKindOfUnitInstance(description, label, labelAbbrev);
                     unit.setUuid(uuid);
                     if (voc == null){
                         boolean isOrdered = false;
                         voc = getVocabulary(TermType.KindOfUnit, uuidUserDefinedKindOfUnitVocabulary, "User defined vocabulary for kind-of-units", "User Defined Measurement kind-of-units", null, null, isOrdered, unit);
+                    }
                     voc.addTerm(unit);
                     getTermService().save(unit);
+                }
                 state.putKindOfUnit(unit);
                 kindOfUnitsMap.put(unit.getLabel().toLowerCase(), unit);
+            }
             return unit;
+        }
+    }

           result.append(":");
           result.append(this.isOverwriteExistingSpecimens());
           result.append(";");
           result.append("nomenclaturalCode");
           result.append(":");
           result.append(this.getNomenclaturalCode().getKey());
           result.append(";");
         return result.toString();

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Revision d9dd1907

Added by Katja Luther about 6 years ago