export all specimenOrObservationBase not only derivedUnits

diff --git a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/cdmLight/CdmLightClassificationExport.java b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/cdmLight/CdmLightClassificationExport.java
index 7dbb1fac58ccc5556c46844f681beb84e65e9656..d751a7f24cfec89b44a025accd86010f4746128c 100755 (executable)
--- a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/cdmLight/CdmLightClassificationExport.java
+++ b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/cdmLight/CdmLightClassificationExport.java
@@ -386,8 +386,8 @@ public class CdmLightClassificationExport
                     if (state.getSpecimenFromStore(indAssociation.getAssociatedSpecimenOrObservation().getId()) == null){
                         SpecimenOrObservationBase<?> specimenBase = HibernateProxyHelper.deproxy(indAssociation.getAssociatedSpecimenOrObservation());
 
-                        if (specimenBase instanceof DerivedUnit){
-                            DerivedUnit derivedUnit = (DerivedUnit)specimenBase;
+                        if (specimenBase instanceof SpecimenOrObservationBase){
+                            SpecimenOrObservationBase derivedUnit = specimenBase;
                             handleSpecimen(state, derivedUnit);
                             csvLine[table.getIndex(CdmLightExportTable.SPECIMEN_FK)] = getId(state, indAssociation.getAssociatedSpecimenOrObservation());
                         }else{
@@ -1420,7 +1420,7 @@ public class CdmLightClassificationExport
      * @param state
      * @param specimen
      */
-    private void handleSpecimen(CdmLightExportState state, DerivedUnit specimen) {
+    private void handleSpecimen(CdmLightExportState state, SpecimenOrObservationBase specimen) {
         try {
             state.addSpecimenToStore(specimen);
             CdmLightExportTable table = CdmLightExportTable.SPECIMEN;
@@ -1430,50 +1430,54 @@ public class CdmLightClassificationExport
             csvLine[table.getIndex(CdmLightExportTable.SPECIMEN_ID)] = specimenId;
             csvLine[table.getIndex(CdmLightExportTable.SPECIMEN_CITATION)] = specimen.getTitleCache();
             csvLine[table.getIndex(CdmLightExportTable.SPECIMEN_IMAGE_URIS)] = extractURIs(state, specimen.getDescriptions(), Feature.IMAGE());
-            if (specimen.getCollection() != null){ csvLine[table.getIndex(CdmLightExportTable.HERBARIUM_ABBREV)] = specimen.getCollection().getCode();}
-            if (specimen instanceof MediaSpecimen){
-                MediaSpecimen mediaSpecimen = (MediaSpecimen) specimen;
-                Iterator<MediaRepresentation> it = mediaSpecimen.getMediaSpecimen().getRepresentations().iterator();
-                String mediaUris = extractMediaUris(it);
-                csvLine[table.getIndex(CdmLightExportTable.MEDIA_SPECIMEN_URL)] = mediaUris;
+            if (specimen instanceof DerivedUnit){
+                    DerivedUnit derivedUnit = (DerivedUnit)specimen;
+                    if (derivedUnit.getCollection() != null){ csvLine[table.getIndex(CdmLightExportTable.HERBARIUM_ABBREV)] = derivedUnit.getCollection().getCode();}
 
-            }
+                if (specimen instanceof MediaSpecimen){
+                    MediaSpecimen mediaSpecimen = (MediaSpecimen) specimen;
+                    Iterator<MediaRepresentation> it = mediaSpecimen.getMediaSpecimen().getRepresentations().iterator();
+                    String mediaUris = extractMediaUris(it);
+                    csvLine[table.getIndex(CdmLightExportTable.MEDIA_SPECIMEN_URL)] = mediaUris;
 
-            if (specimen.getDerivedFrom() != null){
-                for (SpecimenOrObservationBase<?> original: specimen.getDerivedFrom().getOriginals()){
-                    //TODO: What to do if there are more then one FieldUnit??
-                    if (original instanceof FieldUnit){
-                        FieldUnit fieldUnit = (FieldUnit)original;
-                        csvLine[table.getIndex(CdmLightExportTable.COLLECTOR_NUMBER)] = fieldUnit.getFieldNumber();
-
-                        GatheringEvent gathering = fieldUnit.getGatheringEvent();
-                        if (gathering != null){
-                            if (gathering.getLocality() != null){ csvLine[table.getIndex(CdmLightExportTable.LOCALITY)] = gathering.getLocality().getText();}
-                            if (gathering.getCountry() != null){csvLine[table.getIndex(CdmLightExportTable.COUNTRY)] = gathering.getCountry().getLabel();}
-                            csvLine[table.getIndex(CdmLightExportTable.COLLECTOR_STRING)] = createCollectorString(state, gathering, fieldUnit);
-                            addCollectingAreas(state, gathering);
-                            if (gathering.getGatheringDate() != null){csvLine[table.getIndex(CdmLightExportTable.COLLECTION_DATE)] = gathering.getGatheringDate().toString();}
-                            if (!gathering.getCollectingAreas().isEmpty()){
-                                int index = 0;
-                                csvLine[table.getIndex(CdmLightExportTable.FURTHER_AREAS)] = "0";
-                                for (NamedArea area: gathering.getCollectingAreas()){
-                                    if (index == 0){
-                                        csvLine[table.getIndex(CdmLightExportTable.AREA_CATEGORY1)] = area.getTermType().getKey();
-                                        csvLine[table.getIndex(CdmLightExportTable.AREA_NAME1)] = area.getLabel();
-                                    }
-                                    if (index == 1){
-                                        csvLine[table.getIndex(CdmLightExportTable.AREA_CATEGORY2)] = area.getTermType().getKey();
-                                        csvLine[table.getIndex(CdmLightExportTable.AREA_NAME2)] = area.getLabel();
-                                    }
-                                    if (index == 2){
-                                        csvLine[table.getIndex(CdmLightExportTable.AREA_CATEGORY3)] = area.getTermType().getKey();
-                                        csvLine[table.getIndex(CdmLightExportTable.AREA_NAME3)] = area.getLabel();
-                                    }
-                                    if (index == 3){
-                                        csvLine[table.getIndex(CdmLightExportTable.FURTHER_AREAS)] = "1";
-                                        break;
+                }
+
+                if (derivedUnit.getDerivedFrom() != null){
+                    for (SpecimenOrObservationBase<?> original: derivedUnit.getDerivedFrom().getOriginals()){
+                        //TODO: What to do if there are more then one FieldUnit??
+                        if (original instanceof FieldUnit){
+                            FieldUnit fieldUnit = (FieldUnit)original;
+                            csvLine[table.getIndex(CdmLightExportTable.COLLECTOR_NUMBER)] = fieldUnit.getFieldNumber();
+
+                            GatheringEvent gathering = fieldUnit.getGatheringEvent();
+                            if (gathering != null){
+                                if (gathering.getLocality() != null){ csvLine[table.getIndex(CdmLightExportTable.LOCALITY)] = gathering.getLocality().getText();}
+                                if (gathering.getCountry() != null){csvLine[table.getIndex(CdmLightExportTable.COUNTRY)] = gathering.getCountry().getLabel();}
+                                csvLine[table.getIndex(CdmLightExportTable.COLLECTOR_STRING)] = createCollectorString(state, gathering, fieldUnit);
+                                addCollectingAreas(state, gathering);
+                                if (gathering.getGatheringDate() != null){csvLine[table.getIndex(CdmLightExportTable.COLLECTION_DATE)] = gathering.getGatheringDate().toString();}
+                                if (!gathering.getCollectingAreas().isEmpty()){
+                                    int index = 0;
+                                    csvLine[table.getIndex(CdmLightExportTable.FURTHER_AREAS)] = "0";
+                                    for (NamedArea area: gathering.getCollectingAreas()){
+                                        if (index == 0){
+                                            csvLine[table.getIndex(CdmLightExportTable.AREA_CATEGORY1)] = area.getTermType().getKey();
+                                            csvLine[table.getIndex(CdmLightExportTable.AREA_NAME1)] = area.getLabel();
+                                        }
+                                        if (index == 1){
+                                            csvLine[table.getIndex(CdmLightExportTable.AREA_CATEGORY2)] = area.getTermType().getKey();
+                                            csvLine[table.getIndex(CdmLightExportTable.AREA_NAME2)] = area.getLabel();
+                                        }
+                                        if (index == 2){
+                                            csvLine[table.getIndex(CdmLightExportTable.AREA_CATEGORY3)] = area.getTermType().getKey();
+                                            csvLine[table.getIndex(CdmLightExportTable.AREA_NAME3)] = area.getLabel();
+                                        }
+                                        if (index == 3){
+                                            csvLine[table.getIndex(CdmLightExportTable.FURTHER_AREAS)] = "1";
+                                            break;
+                                        }
+                                        index++;
                                     }
-                                    index++;
                                 }
                             }
                         }

diff --git a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/cdmLight/CdmLightExportState.java b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/cdmLight/CdmLightExportState.java
index 082e08098c96f3dab7122b980bf805846f77cab3..a5baf63eb46a0e157984090bf71f7556ebf9e7ce 100755 (executable)
--- a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/cdmLight/CdmLightExportState.java
+++ b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/cdmLight/CdmLightExportState.java
@@ -18,7 +18,7 @@ import eu.etaxonomy.cdm.io.common.ExportStateBase;
 import eu.etaxonomy.cdm.io.common.mapping.out.IExportTransformer;
 import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
 import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
-import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
+import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
 import eu.etaxonomy.cdm.model.reference.Reference;
 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
 
@@ -38,7 +38,7 @@ public class CdmLightExportState
 
     private Map<Integer, HomotypicalGroup> homotypicalGroupStore = new HashMap<>();
     private Map<Integer, TeamOrPersonBase<?>> authorStore = new HashMap<>();
-    private Map<Integer, DerivedUnit> specimenStore = new HashMap<>();
+    private Map<Integer, SpecimenOrObservationBase> specimenStore = new HashMap<>();
     private Map<Integer, Reference> referenceStore = new HashMap<>();
 
     /**
@@ -124,13 +124,13 @@ public class CdmLightExportState
     }
 
 
-    public void addSpecimenToStore(DerivedUnit specimen) {
+    public void addSpecimenToStore(SpecimenOrObservationBase specimen) {
         this.specimenStore.put(specimen.getId(), specimen);
 
     }
 
 
-    public DerivedUnit getSpecimenFromStore(Integer id){
+    public SpecimenOrObservationBase getSpecimenFromStore(Integer id){
         return specimenStore.get(id);
     }