Changeset 2244

Timestamp:

Feb 21, 2014, 2:58:47 PM (9 years ago)

Author:

Nicklas Nordborg

Message:

References #577: Flag histology items in HE glass/scoring wizard

Added comment field for each histology item in the HE glass wizard.

Use a 'flag' icon instead of 'warning' icon to indicate that histology items are flagged when no good stain is selected.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/css/reggie.css (modified) (1 diff)
• resources/sampleproc/histology_glass.jsp (modified) (10 diffs)
• resources/sampleproc/histology_score.jsp (modified) (3 diffs)
• src/net/sf/basedb/reggie/dao/ReactionPlate.java (modified) (1 diff)
• src/net/sf/basedb/reggie/servlet/HistologyServlet.java (modified) (4 diffs)

extensions/net.sf.basedb.reggie/trunk/resources/css/reggie.css

@@ -150 +150 @@
 {
   content: url('../images/warning.png');
+}
+.status.flag:before
+{
+  content: url('../images/flag.png');
 }
 .status.valid:before

extensions/net.sf.basedb.reggie/trunk/resources/sampleproc/histology_glass.jsp

@@ -260 +260 @@
         checkIndexValue(field);
       }
+      frm['comment.'+well.row+'.'+well.column].value = well.bioMaterial.comment;
       numWells++;
     }
@@ -388 +389 @@
   if (indexValue == 0)
   {
-    setInputStatus(field, 'No good stain! Sample will be flagged and saved to Flagged Histology list.', 'warning');
+    setInputStatus(field, 'No good stain! Sample will be flagged and saved to Flagged Histology list.', 'flag');
   }
   else
@@ -610 +611 @@
     {
       well.GoodStain = parseInt(frm[field].value, 10);
+      well.bioMaterial.comment = frm['comment.'+well.row+'.'+well.column].value;
     }
   }
@@ -700 +702 @@
     vertical-align: middle;
     border: 1px solid #A0A0A0;
-    padding: 2px 2px 2px 1em;
+    padding: 0.5em;
   }
 
@@ -725 +727 @@
   {
     padding: 2px;
+  }
+  
+  .comment
+  {
+    width: 95%; 
+    margin: 0.5em 0 0.5em 0;
+  }
+  
+  .comment input
+  {
+    width: 100%;
   }
 
@@ -845 +858 @@
                   onkeypress="focusOnEnter(event, 'idx.1.0');return Numbers.integerOnly(event)" size="2">
                 <span id="idx.0.0.status" class="status"></span>
+                <div class="comment">
+                  <input type="text" name="comment.0.0" placeholder="Comments">
+                </div>
               </td>
               <td>
@@ -856 +872 @@
                   onkeypress="focusOnEnter(event, 'idx.1.1');return Numbers.integerOnly(event)" size="2">
                 <span id="idx.1.0.status" class="status"></span>
+                <div class="comment">
+                  <input type="text" name="comment.1.0" placeholder="Comments">
+                </div>
               </td>
               <td>
@@ -863 +882 @@
                   onkeypress="focusOnEnter(event, 'idx.2.0');return Numbers.integerOnly(event)" size="2">
                 <span id="idx.1.1.status" class="status"></span>
+                <div class="comment">
+                  <input type="text" name="comment.1.1" placeholder="Comments">
+                </div>
               </td>
             </tr>
@@ -872 +894 @@
                   onkeypress="focusOnEnter(event, 'idx.2.1');return Numbers.integerOnly(event)" size="2">
                 <span id="idx.2.0.status" class="status"></span>
+                <div class="comment">
+                  <input type="text" name="comment.2.0" placeholder="Comments">
+                </div>
               </td>
               <td>
@@ -879 +904 @@
                   onkeypress="return Numbers.integerOnly(event)" size="2">
                 <span id="idx.2.1.status" class="status"></span>
+                <div class="comment">
+                  <input type="text" name="comment.2.1" placeholder="Comments">
+                </div>
               </td>
               </tr>

extensions/net.sf.basedb.reggie/trunk/resources/sampleproc/histology_score.jsp

@@ -291 +291 @@
     if (getGoodStainedSampleForLocation(sample.well.location) == null)
     {
-      className += ' warning';
+      className += ' flag';
     }
   }
@@ -933 +933 @@
 }
 
-.he-table td.warning
-{
-  background-image: url('../images/warning.png');
+.he-table td.flag
+{
+  background-image: url('../images/flag.png');
 }
 
@@ -1061 +1061 @@
       
       <div id="he-glass-container" style="display: none;">
-        
       </div>
+      
       <div style="margin-left: 1em; margin-bottom: 0.5em;">
-        <base:icon image="warning.png" /> = No GoodStain sample for that location
+        <base:icon image="<%=home + "/images/flag.png"%>" /> = No GoodStain sample for that location. 
+        The Histology piece will be added to the <i>Flagged histology</i> list.
       </div>
 

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/dao/ReactionPlate.java

@@ -204 +204 @@
             jsonBm.put("id", bm.getId());
             jsonBm.put("name", bm.getName());
+            jsonBm.put("comment", bm.getDescription());
             jsonWell.put("bioMaterial", jsonBm);
           }

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

@@ -32 +32 @@
 import net.sf.basedb.core.Item;
 import net.sf.basedb.core.ItemQuery;
-import net.sf.basedb.core.ItemSubtype;
 import net.sf.basedb.core.MeasuredBioMaterial;
 import net.sf.basedb.core.PlateGeometry;
@@ -245 +244 @@
         // Filter on id not equal to any that has a STAINED child
         query.restrict(Restrictions.neq(Hql.property("id"), Expressions.all(subquery)));
-        
+                
         List<Sample> samples = query.list(dc);
         Set<BioPlate> plates = new TreeSet<BioPlate>(new NameableComparator<BioPlate>(false));
@@ -674 +673 @@
         {
           JSONObject jsonWell = (JSONObject)jsonWells.get(i);
-          Number goodStain = (Number)jsonWell.get("GoodStain");
-          
-          Number wellId = (Number)jsonWell.get("id");
-          BioWell hisWell = BioWell.getById(dc, wellId.intValue());
-          MeasuredBioMaterial histology = hisWell.getBioMaterial();
-          if (histology != null)
-          {
+          JSONObject jsonHistology = (JSONObject)jsonWell.get("bioMaterial");
+          if (jsonHistology != null)
+          {
+            Number goodStain = (Number)jsonWell.get("GoodStain");
+            Number hisId = (Number)jsonHistology.get("id");
+            MeasuredBioMaterial histology = Sample.getById(dc, hisId.intValue());
+
             jsonWell.put("histology", histology);
+            histology.setDescription((String)jsonHistology.get("comment"));
             String flag = (String)Annotationtype.FLAG.getAnnotationValue(dc, histology);
             if (goodStain.intValue() == 0)
@@ -776 +776 @@
                 stained.setName(stainedName);
                 stained.setBioWell(heGlass.getBioWell(heCoordinate));
+                stained.setDescription(histology.getDescription());
                 dc.saveItem(stained);