Changeset 2103

Timestamp:

Oct 25, 2013, 8:36:36 AM (9 years ago)

Author:

Nicklas Nordborg

Message:

References #471: Add library preparation information to the 'Case summary' feature

Fixes issue with items having no bioplate location. Eg. *.dil items never have a location.

File:

• extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/CaseSummaryServlet.java (modified) (6 diffs)

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/CaseSummaryServlet.java

@@ -24 +24 @@
 import net.sf.basedb.core.File;
 import net.sf.basedb.core.ItemQuery;
+import net.sf.basedb.core.MeasuredBioMaterial;
 import net.sf.basedb.core.Permission;
 import net.sf.basedb.core.Sample;
@@ -648 +649 @@
     mrna.setAnnotation("comment", e.getDescription());
     
-    // Get BioPlate CleanupDate annotation
-    BioPlate plate = mrna.getItem().getBioWell().getPlate();
-    Date cleanupDate = (Date) Annotationtype.CLEANUP_DATE.getAnnotationValue(dc, plate);
-    mrna.setAnnotation("cleanupDate", Reggie.CONVERTER_DATE_TO_STRING.convert(cleanupDate));
-    // Get BioPlate PlateProcessResult annotation
-    String result = (String) Annotationtype.PLATE_PROCESS_RESULT.getAnnotationValue(dc, plate);
-    mrna.setAnnotation("result", result);
+    // Get BioPlate annotations
+    BioPlate plate = getBioPlate(e);
+    if (plate != null)
+    {
+      Date cleanupDate = (Date) Annotationtype.CLEANUP_DATE.getAnnotationValue(dc, plate);
+      mrna.setAnnotation("cleanupDate", Reggie.CONVERTER_DATE_TO_STRING.convert(cleanupDate));
+      // Get BioPlate PlateProcessResult annotation
+      String result = (String) Annotationtype.PLATE_PROCESS_RESULT.getAnnotationValue(dc, plate);
+      mrna.setAnnotation("result", result);
+    }
   }
 
@@ -665 +669 @@
     cdna.setAnnotation("editable", e.hasPermission(Permission.WRITE));  
     cdna.setAnnotation("comment", e.getDescription());
-    // Get BioPlate SynthesisDate annotation
-    BioPlate plate = cdna.getItem().getBioWell().getPlate();
-    Date synthesisDate = (Date) Annotationtype.SYNTHESIS_DATE.getAnnotationValue(dc, plate);
-    cdna.setAnnotation("synthesisDate", Reggie.CONVERTER_DATE_TO_STRING.convert(synthesisDate));
-    // Get BioPlate PlateProcessResult annotation
-    String result = (String) Annotationtype.PLATE_PROCESS_RESULT.getAnnotationValue(dc, plate);
-    cdna.setAnnotation("result", result);
+    
+    // Get BioPlate annotations
+    BioPlate plate = getBioPlate(e);
+    if (plate != null)
+    {
+      Date synthesisDate = (Date) Annotationtype.SYNTHESIS_DATE.getAnnotationValue(dc, plate);
+      cdna.setAnnotation("synthesisDate", Reggie.CONVERTER_DATE_TO_STRING.convert(synthesisDate));
+      // Get BioPlate PlateProcessResult annotation
+      String result = (String) Annotationtype.PLATE_PROCESS_RESULT.getAnnotationValue(dc, plate);
+      cdna.setAnnotation("result", result);
+    }
   }
 
@@ -681 +689 @@
     lib.setAnnotation("registrationDate", Reggie.CONVERTER_DATE_TO_STRING.convert(e.getEntryDate()));
     lib.setAnnotation("editable", e.hasPermission(Permission.WRITE)); 
-    // Get BioPlate CleanupDate annotation
-    BioPlate plate = lib.getItem().getBioWell().getPlate();
-    Date cleanupDate = (Date) Annotationtype.CLEANUP_DATE.getAnnotationValue(dc, plate);
-    lib.setAnnotation("cleanupDate", Reggie.CONVERTER_DATE_TO_STRING.convert(cleanupDate));
     lib.setAnnotation("originalQuantity", e.getOriginalQuantity());
     lib.setAnnotation("remainingQuantity", e.getRemainingQuantity());
@@ -691 +695 @@
     lib.loadAnnotations(dc, "qubitconc", Annotationtype.QUBIT_CONC, null);
     lib.setAnnotation("comment", e.getDescription());
-    // Get BioPlate PlateProcessResult annotation
-    String result = (String) Annotationtype.PLATE_PROCESS_RESULT.getAnnotationValue(dc, plate);
-    lib.setAnnotation("result", result);
+    
+    // Get BioPlate annotations
+    BioPlate plate = getBioPlate(e);
+    if (plate != null)
+    {
+      Date cleanupDate = (Date) Annotationtype.CLEANUP_DATE.getAnnotationValue(dc, plate);
+      lib.setAnnotation("cleanupDate", Reggie.CONVERTER_DATE_TO_STRING.convert(cleanupDate));
+      // Get BioPlate PlateProcessResult annotation
+      String result = (String) Annotationtype.PLATE_PROCESS_RESULT.getAnnotationValue(dc, plate);
+      lib.setAnnotation("result", result);
+    }
   }
 
@@ -710 +722 @@
     lib.setAnnotation("comment", e.getDescription());
   }
+  
+  private BioPlate getBioPlate(MeasuredBioMaterial bioMaterial)
+  {
+    BioWell well = bioMaterial.getBioWell();
+    return well == null ? null : well.getPlate();
+  }
+  
 }