Merge branch 'hotfix/3.12.4' into develop

[taxeditor.git] / eu.etaxonomy.taxeditor.store / src / main / java / eu / etaxonomy / taxeditor / view / derivateSearch / DerivateLabelProvider.java

diff --git a/eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/view/derivateSearch/DerivateLabelProvider.java b/eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/view/derivateSearch/DerivateLabelProvider.java
index 9db13819c0184568e6234eee5f31ce7fe2aa8154..14265f1d5f179233886d219201d6128b78435e42 100644 (file)
--- a/eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/view/derivateSearch/DerivateLabelProvider.java
+++ b/eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/view/derivateSearch/DerivateLabelProvider.java
@@ -9,7 +9,13 @@
 */
 package eu.etaxonomy.taxeditor.view.derivateSearch;
 
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
 import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
 import java.util.Set;
 import java.util.UUID;
 
@@ -19,6 +25,10 @@ import org.eclipse.swt.graphics.Image;
 import org.hibernate.LazyInitializationException;
 
 import eu.etaxonomy.cdm.api.conversation.ConversationHolder;
+import eu.etaxonomy.cdm.api.service.IOccurrenceService;
+import eu.etaxonomy.cdm.api.service.molecular.ISequenceService;
+import eu.etaxonomy.cdm.format.CdmFormatter;
+import eu.etaxonomy.cdm.format.ICdmFormatter.FormatKey;
 import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
 import eu.etaxonomy.cdm.model.common.CdmBase;
 import eu.etaxonomy.cdm.model.common.DefinedTerm;
@@ -26,6 +36,7 @@ import eu.etaxonomy.cdm.model.common.Identifier;
 import eu.etaxonomy.cdm.model.molecular.DnaSample;
 import eu.etaxonomy.cdm.model.molecular.Sequence;
 import eu.etaxonomy.cdm.model.molecular.SingleRead;
+import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
 import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
 import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
 import eu.etaxonomy.cdm.model.occurrence.GatheringEvent;
@@ -48,7 +59,9 @@ public class DerivateLabelProvider extends ColumnLabelProvider {
 
     private static final String NO_SAMPLE_DESIGNATION = "[no sample designation]";
 
-    private Set<SingleRead> multiLinkSingleReads;
+    private static Set<SingleRead> multiLinkSingleReads;
+
+    private static Map<DerivedUnit, Collection<SpecimenTypeDesignation>> typeDesignations;
 
     private ConversationHolder conversation;
 
@@ -119,7 +132,26 @@ public class DerivateLabelProvider extends ColumnLabelProvider {
     /** {@inheritDoc} */
     @Override
     public String getText(Object element) {
-        return getDerivateText(element);
+        if(element instanceof TreeNode){
+            element = ((TreeNode) element).getValue();
+        }
+        CdmFormatter formatter = new CdmFormatter(
+                FormatKey.GATHERING_COUNTRY, FormatKey.SPACE,
+                FormatKey.GATHERING_LOCALITY_TEXT, FormatKey.SPACE,
+                FormatKey.GATHERING_DATE, FormatKey.SPACE,
+                FormatKey.GATHERING_COLLECTOR, FormatKey.SPACE,
+                FormatKey.FIELD_NUMBER, FormatKey.SPACE,
+                FormatKey.COLLECTION_CODE, FormatKey.SPACE,
+                FormatKey.MOST_SIGNIFICANT_IDENTIFIER, FormatKey.SPACE,
+                FormatKey.KIND_OF_UNIT, FormatKey.SPACE,
+                FormatKey.SAMPLE_DESIGNATION, FormatKey.SPACE,
+                FormatKey.SINGLE_READ_PRIMER, FormatKey.SPACE,
+                FormatKey.SEQUENCE_DNA_MARKER, FormatKey.SPACE,
+                FormatKey.AMPLIFICATION_LABEL, FormatKey.SPACE,
+                FormatKey.MEDIA_TITLE, FormatKey.SPACE,
+                FormatKey.MEDIA_ARTIST, FormatKey.SPACE
+                );
+        return formatter.format(element);
     }
 
     /** {@inheritDoc} */
@@ -217,6 +249,12 @@ public class DerivateLabelProvider extends ColumnLabelProvider {
         else if(derivate instanceof DerivedUnit){
             DerivedUnit derivedUnit = (DerivedUnit)derivate;
             if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.PreservedSpecimen){
+                //check for type designation
+                if(typeDesignations.get(derivedUnit)==null){
+                    for (SpecimenTypeDesignation specimenTypeDesignation : CdmStore.getService(IOccurrenceService.class).listTypeDesignations(derivedUnit, null, null, null, null)) {
+                        addTypeDesignation(derivedUnit, specimenTypeDesignation);
+                    }
+                }
                 //java.util.Collection<FieldUnit> fieldUnits = CdmStore.getService(IOccurrenceService.class).getFieldUnits(derivedUnit.getUuid());
                 //TODO : This is not generic anymore for performance reasons
                 Set<SpecimenOrObservationBase> originals = derivedUnit.getOriginals();
@@ -294,9 +332,6 @@ public class DerivateLabelProvider extends ColumnLabelProvider {
         return label;
     }
 
-    /* (non-Javadoc)
-     * @see org.eclipse.jface.viewers.ColumnLabelProvider#getImage(java.lang.Object)
-     */
     @Override
     public Image getImage(Object element) {
         if(element instanceof TreeNode){
@@ -316,6 +351,7 @@ public class DerivateLabelProvider extends ColumnLabelProvider {
             }
             else if(cdmBase.isInstanceOf(DerivedUnit.class)){
                 DerivedUnit derivedUnit = HibernateProxyHelper.deproxy(element, DerivedUnit.class);
+
                 if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.FieldUnit){
                     return hasCharacterData?ImageResources.getImage(ImageResources.FIELD_UNIT_CHARACTER_DATA):ImageResources.getImage(ImageResources.FIELD_UNIT);
                 }
@@ -326,6 +362,9 @@ public class DerivateLabelProvider extends ColumnLabelProvider {
                     return hasCharacterData?ImageResources.getImage(ImageResources.TISSUE_SAMPLE_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.TISSUE_SAMPLE_DERIVATE);
                 }
                 else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.PreservedSpecimen){
+                    if(typeDesignations.get(derivedUnit)!=null && !typeDesignations.get(derivedUnit).isEmpty()){
+                        return ImageResources.getImage(ImageResources.SPECIMEN_DERIVATE_TYPE);
+                    }
                     return hasCharacterData?ImageResources.getImage(ImageResources.SPECIMEN_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.SPECIMEN_DERIVATE);
                 }
                 else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.Media){
@@ -380,11 +419,37 @@ public class DerivateLabelProvider extends ColumnLabelProvider {
         return null;
     }
 
-    /**
-     * @param multiLinkSingleReads2
-     */
-    public void setMultiLinkSingleReads(Set<SingleRead> multiLinkSingleReads) {
-        this.multiLinkSingleReads = multiLinkSingleReads;
+    private static void addTypeDesignation(DerivedUnit derivedUnit, SpecimenTypeDesignation typeDesignation){
+        Collection<SpecimenTypeDesignation> list = typeDesignations.get(derivedUnit);
+        if(list==null){
+            list = new ArrayList<SpecimenTypeDesignation>();
+        }
+        list.add(typeDesignation);
+        typeDesignations.put(derivedUnit, list);
+    }
+
+    public static Set<SingleRead> getMultiLinkSingleReads() {
+        return multiLinkSingleReads;
+    }
+
+    public void updateLabelCache(Collection<SpecimenOrObservationBase<?>> rootElements) {
+        DerivateLabelProvider.multiLinkSingleReads = new HashSet<SingleRead>();
+        DerivateLabelProvider.typeDesignations = new HashMap<DerivedUnit, Collection<SpecimenTypeDesignation>>();
+        for(Entry<SingleRead, Collection<Sequence>> entry:CdmStore.getService(ISequenceService.class).getSingleReadSequencesMap().entrySet()){
+            if(entry.getValue().size()>1){
+                multiLinkSingleReads.add(entry.getKey());
+            }
+        }
+        if(rootElements!=null){
+            Collection<DerivedUnit> derivedUnits = new ArrayList<DerivedUnit>();
+            for (SpecimenOrObservationBase specimenOrObservationBase : rootElements) {
+                derivedUnits.addAll(CdmStore.getService(IOccurrenceService.class).getAllChildDerivatives(specimenOrObservationBase.getUuid()));
+                if(specimenOrObservationBase.isInstanceOf(DerivedUnit.class)){
+                    derivedUnits.add(HibernateProxyHelper.deproxy(specimenOrObservationBase, DerivedUnit.class));
+                }
+            }
+            typeDesignations = CdmStore.getService(IOccurrenceService.class).listTypeDesignations(derivedUnits, null, null, null, null);
+        }
     }
 
 }