fix #4453 Enhance portal visualization of molecular data

  - used DefinedTerm constants for UUIDS
  - used titleCache for all DerivedUnits
  - move string representations to portal code

diff --git a/cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/OccurrenceServiceImpl.java b/cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/OccurrenceServiceImpl.java
index 466af9e99217314774184c3db7924ea1ea79365b..66b2c33b1b53793be5863f2c0c53bb54b34fcfaf 100644 (file)
--- a/cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/OccurrenceServiceImpl.java
+++ b/cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/OccurrenceServiceImpl.java
@@ -53,6 +53,7 @@ import eu.etaxonomy.cdm.api.service.config.SpecimenDeleteConfigurator;
 import eu.etaxonomy.cdm.api.service.dto.DerivateDTO;
 import eu.etaxonomy.cdm.api.service.dto.DerivateDataDTO;
 import eu.etaxonomy.cdm.api.service.dto.DerivateDataDTO.ContigFile;
+import eu.etaxonomy.cdm.api.service.dto.DerivateDataDTO.Link;
 import eu.etaxonomy.cdm.api.service.dto.DerivateDataDTO.MolecularData;
 import eu.etaxonomy.cdm.api.service.dto.FieldUnitDTO;
 import eu.etaxonomy.cdm.api.service.dto.PreservedSpecimenDTO;
@@ -637,18 +638,22 @@ public class OccurrenceServiceImpl extends IdentifiableServiceBase<SpecimenOrObs
                             logger.error("Could not create BOLD URI", e1);
                         }
                         final DefinedTerm dnaMarker = sequence.getDnaMarker();
-                        MolecularData molecularData = derivateDataDTO.addProviderLink(boldUri != null ? boldUri : null, dnaMarker != null ? dnaMarker.getLabel() : "[no marker]");
+                        Link providerLink = null;
+                        if(boldUri!=null && dnaMarker!=null){
+                               providerLink = new DerivateDataDTO.Link(boldUri, dnaMarker.getLabel());
+                        }
+                        MolecularData molecularData = derivateDataDTO.addProviderLink(providerLink);
 
                         //contig file
                         ContigFile contigFile = null;
                         if (sequence.getContigFile() != null) {
                             MediaRepresentationPart contigMediaRepresentationPart = MediaUtils.getFirstMediaRepresentationPart(sequence.getContigFile());
                             if (contigMediaRepresentationPart != null) {
-                                contigFile = molecularData.addContigFile(contigMediaRepresentationPart.getUri(), "contig");
+                                contigFile = molecularData.addContigFile(new Link(contigMediaRepresentationPart.getUri(), "contig"));
                             }
                         }
-                        if(contigFile==null){
-                            contigFile = molecularData.addContigFile(null, "[no contig]");
+                        else{
+                               contigFile = molecularData.addContigFile(null);
                         }
                         // primer files
                         if (sequence.getSingleReads() != null) {
@@ -670,7 +675,7 @@ public class OccurrenceServiceImpl extends IdentifiableServiceBase<SpecimenOrObs
                 URI mediaUri = getMediaUri(media);
                 if (media.getKindOfUnit() != null) {
                     // specimen scan
-                    if (media.getKindOfUnit().getUuid().equals(UUID.fromString("acda15be-c0e2-4ea8-8783-b9b0c4ad7f03"))) {
+                    if (media.getKindOfUnit().getUuid().equals(DefinedTerm.uuidSpecimenScan)) {
                         derivateDataDTO.addSpecimenScanUuid(media.getMediaSpecimen().getUuid());
                         derivateDTO.setHasSpecimenScan(true);
                         String imageLinkText = "scan";
@@ -680,7 +685,7 @@ public class OccurrenceServiceImpl extends IdentifiableServiceBase<SpecimenOrObs
                         derivateDataDTO.addSpecimenScan(mediaUri, imageLinkText);
                     }
                     // detail image
-                    else if (media.getKindOfUnit().getUuid().equals(UUID.fromString("31eb8d02-bf5d-437c-bcc6-87a626445f34"))) {
+                    else if (media.getKindOfUnit().getUuid().equals(DefinedTerm.uuidDetailImage)) {
                         derivateDataDTO.addDetailImageUuid(media.getMediaSpecimen().getUuid());
                         derivateDTO.setHasDetailImage(true);
                         String motif = "detail image";
@@ -689,7 +694,7 @@ public class OccurrenceServiceImpl extends IdentifiableServiceBase<SpecimenOrObs
                                        motif = media.getMediaSpecimen().getTitleCache();
                                }
                         }
-                        derivateDataDTO.addDetailImage(mediaUri, motif != null ? motif : "[no motif]");
+                        derivateDataDTO.addDetailImage(mediaUri, motif);
                     }
                 }
             }

diff --git a/cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/dto/DerivateDataDTO.java b/cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/dto/DerivateDataDTO.java
index c1c592ed4377b7313fc3fabb0fff71671637b227..d61eda2c9f3cb0c70063795f1d0bc818c5a034e6 100644 (file)
--- a/cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/dto/DerivateDataDTO.java
+++ b/cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/dto/DerivateDataDTO.java
@@ -34,11 +34,11 @@ public class DerivateDataDTO {
         return molecularDataList;
     }
 
-    public MolecularData addProviderLink(URI uri, String linkText) {
+    public MolecularData addProviderLink(Link providerLink) {
         if(this.molecularDataList==null){
             molecularDataList = new ArrayList<MolecularData>();
         }
-        MolecularData molecularData = new MolecularData(new Link(uri, linkText));
+        MolecularData molecularData = new MolecularData(providerLink);
         this.molecularDataList.add(molecularData);
         return molecularData;
     }
@@ -108,11 +108,11 @@ public class DerivateDataDTO {
             this.providerLink = providerLink;
         }
 
-        public ContigFile addContigFile(URI uri, String linkText){
+        public ContigFile addContigFile(Link contigLink){
             if(contigFiles==null){
                 contigFiles = new ArrayList<ContigFile>();
             }
-            ContigFile contigFile = new ContigFile(new Link(uri, linkText));
+            ContigFile contigFile = new ContigFile(contigLink);
             contigFiles.add(contigFile);
             return contigFile;
         }
@@ -152,7 +152,7 @@ public class DerivateDataDTO {
 
     }
 
-    public class Link{
+    public static class Link{
         private String linkText;
         private URI uri;