Changeset 2131

Timestamp:

Nov 11, 2013, 1:43:24 PM (10 years ago)

Author:

Nicklas Nordborg

Message:

References #489: Histology scoring wizard

Added score information to case summary page.

Location:

extensions/net.sf.basedb.reggie/branches/ticket-489

Files:

• resources/reports/case_summary.jsp (modified) (3 diffs)
• src/net/sf/basedb/reggie/servlet/CaseSummaryServlet.java (modified) (2 diffs)

extensions/net.sf.basedb.reggie/branches/ticket-489/resources/reports/case_summary.jsp

@@ -281 +281 @@
 }
 
+function asPercent(value)
+{
+  var result = '';
+  if (value != null)
+  {
+    result = value + '%';
+  }
+  return result;
+}
+
 function init()
 {
@@ -463 +473 @@
 
       var stained = h.stainDate ? true : false;
+      var bestStain = stained ? h.bestStain : null;
+      var scored = bestStain && bestStain.ScoreComplete != null ? true : false;
+        
       addColumn('histology.stained', stained ? formatDate(h.stainDate) : 'No');
       addColumn('histology.nofSlides', stained ? h.numStains : null);
-      addColumn('histology.heGlass', stained ? asBioPlateLocation(h.bestStain) : null);
+      addColumn('histology.heGlass', stained ? asBioPlateLocation(bestStain.bioWell) : null);
       addColumn('histology.stainProtocol', stained ? makeLink('PROTOCOL', h.stainProtocol, truncateAt) : null);
+      
+      addColumn('histology.scored', scored ? (bestStain.ScoreComplete ? 'Complete' : 'In progress') : 'No');
+      addColumn('histology.scoreInvasiveCancer', scored ? asPercent(bestStain.ScoreInvasiveCancer) : null);
+      addColumn('histology.scoreInsituCancer', scored ? asPercent(bestStain.ScoreInsituCancer) : null);
+      addColumn('histology.scoreLymphocytes', scored ? asPercent(bestStain.ScoreLymphocytes) : null);
+      addColumn('histology.scoreNormal', scored ? asPercent(bestStain.ScoreNormal) : null);
+      addColumn('histology.scoreStroma', scored ? asPercent(bestStain.ScoreStroma) : null);
+      addColumn('histology.scoreFat', scored ? asPercent(bestStain.ScoreFat) : null);
+      addColumn('histology.scoreComments', scored ? truncate(bestStain.comments, truncateAt) : null);
     }
   }
@@ -1123 +1145 @@
               <th>Protocol</th>
             </tr>
+            <tr id="histology.scored" class="subtitle">
+              <th>Scored</th>
+            </tr>
+            <tr id="histology.scoreInvasiveCancer" class="dynamic-column">
+              <th>Invasive cancer</th>
+            </tr>
+            <tr id="histology.scoreInsituCancer" class="dynamic-column">
+              <th>Insitu cancer</th>
+            </tr>
+            <tr id="histology.scoreLymphocytes" class="dynamic-column">
+              <th>Lymphocytes</th>
+            </tr>
+            <tr id="histology.scoreNormal" class="dynamic-column">
+              <th>Normal</th>
+            </tr>
+            <tr id="histology.scoreStroma" class="dynamic-column">
+              <th>Stroma</th>
+            </tr>
+            <tr id="histology.scoreFat" class="dynamic-column">
+              <th>Fat</th>
+            </tr>
+            <tr id="histology.scoreComments" class="comment dynamic-column">
+              <th>Comments</th>
+            </tr>
           </tbody>
           </table>

extensions/net.sf.basedb.reggie/branches/ticket-489/src/net/sf/basedb/reggie/servlet/CaseSummaryServlet.java

@@ -430 +430 @@
   }
 
+  @SuppressWarnings("unchecked")
   private void loadHistologyInfo(DbControl dc, Histology his)
   {
@@ -472 +473 @@
       if (goodIsGood)
       {
-        his.setAnnotation("bestStain", JsonUtil.getBioWellAsJSON(good.getBioWell(), true));
+        JSONObject jsonGood = new JSONObject();
+        jsonGood.put("id", good.getId());
+        jsonGood.put("name", good.getName());
+        jsonGood.put("bioWell", JsonUtil.getBioWellAsJSON(good.getBioWell(), true));
+        jsonGood.put("comments", good.getDescription());
+        
+        jsonGood.put("ScoreComplete", Annotationtype.SCORE_COMPLETE.getAnnotationValue(dc, good));
+        jsonGood.put("ScoreInvasiveCancer", Annotationtype.SCORE_INVASIVE_CANCER.getAnnotationValue(dc, good));
+        jsonGood.put("ScoreInsituCancer", Annotationtype.SCORE_INSITU_CANCER.getAnnotationValue(dc, good));
+        jsonGood.put("ScoreLymphocytes", Annotationtype.SCORE_LYMPHOCYTES.getAnnotationValue(dc, good));
+        jsonGood.put("ScoreNormal", Annotationtype.SCORE_NORMAL.getAnnotationValue(dc, good));
+        jsonGood.put("ScoreStroma", Annotationtype.SCORE_STROMA.getAnnotationValue(dc, good));
+        jsonGood.put("ScoreFat", Annotationtype.SCORE_FAT.getAnnotationValue(dc, good));
+        
+        his.setAnnotation("bestStain", jsonGood);
       }
     }