Changeset 2243

Timestamp:

Feb 21, 2014, 1:42:15 PM (9 years ago)

Author:

Nicklas Nordborg

Message:

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

The scoring wizard now support unchecking the GoodStain option without selecting a new one. Histology items are automatically added to or removed from the Flagged histology list depending on if a good stain exists or not.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/sampleproc/histology_score.jsp (modified) (10 diffs)
• src/net/sf/basedb/reggie/servlet/HistologyServlet.java (modified) (5 diffs)

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

@@ -35 +35 @@
 
 <script language="JavaScript">
-var debug = 0;
+var debug = false;
 var currentStep = 1;
 var selectedSample;
@@ -80 +80 @@
         
         // Save the first GoodStain sample so we can select it later
-        if (sample.GoodStain && firstGoodSample == null)
+        if (sample.GoodStain)
         {
-          firstGoodSample = sample;
+          if (firstGoodSample == null) firstGoodSample = sample;
         }
         
@@ -287 +287 @@
     className += ' good-stain';
   }
+  else
+  {
+    if (getGoodStainedSampleForLocation(sample.well.location) == null)
+    {
+      className += ' warning';
+    }
+  }
   
   if (sample.ScoreTotal == null)
@@ -313 +320 @@
   var td = document.getElementById(sample.heGlassId+'-'+sample.well.location);
   td.className = className;
+}
+
+function getGoodStainedSampleForLocation(location)
+{
+  // Find sample on given location that has GoodStain annotation
+  for (var glassNo = 0; glassNo < heGlass.length; glassNo++)
+  {
+    var glass = heGlass[glassNo];
+    for (var sampleNo = 0; sampleNo < glass.samples.length; sampleNo++)
+    {
+      var sample = glass.samples[sampleNo];
+      if (sample.well.location == location && sample.GoodStain)
+      {
+        return sample;
+      }
+    }
+  }
+  return null;
 }
 
@@ -357 +382 @@
   {
     frm.good_stain.checked = true;
-    frm.good_stain.disabled = true;
   }
   else
   {
     frm.good_stain.checked = false;
-    frm.good_stain.disabled = false;
   }
   
@@ -478 +501 @@
   var frm = document.forms['reggie'];
   
-  // Reset GoodStain on other samples on same location
+  var goodSample = getGoodStainedSampleForLocation(selectedSample.well.location);
+  if (goodSample != null && goodSample != selectedSample)
+  {
+    // Reset the current GoodStain sample
+    goodSample.GoodStain = null;
+    saveToLocalStorage(goodSample);
+  }
+  
+  selectedSample.GoodStain = frm.good_stain.checked ? true : null;
+  saveToLocalStorage(selectedSample);
+  
+  // Repaint samples on current location
   for (var glassNo = 0; glassNo < heGlass.length; glassNo++)
   {
@@ -488 +522 @@
       if (sample.well.location == selectedSample.well.location)
       {
-        sample.GoodStain = null;
         setSampleClassName(sample);
-        saveToLocalStorage(sample);
       }
     }
   }
-  
-  selectedSample.GoodStain = frm.good_stain.checked ? true : null;
-  frm.good_stain.disabled = true;
-  setSampleClassName(selectedSample);
-  saveToLocalStorage(selectedSample);
 }
 
@@ -797 +824 @@
   display: inline-block;
   border: 1px solid #A0A0A0;
-  margin: 1em;
+  margin: 1em 1em 0.5em 1em;
   width: 20em;
   background: #E8E8E8;
@@ -904 +931 @@
 {
   background-image: url('../images/score-complete.png');
+}
+
+.he-table td.warning
+{
+  background-image: url('../images/warning.png');
 }
 
@@ -1030 +1062 @@
       <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
       </div>
 

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

@@ -4 +4 @@
 import java.io.PrintWriter;
 import java.util.Date;
+import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
@@ -31 +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;
@@ -829 +831 @@
         JSONArray jsonHeGlass = (JSONArray)jsonReq.get("heGlass");
 
+        Set<Sample> histologyItems = new HashSet<Sample>();
+
         // Update scores on samples
         for (int sampleNo = 0; sampleNo < jsonSamples.size(); ++sampleNo)
@@ -849 +853 @@
           he.setDescription(Values.getStringOrNull((String)jsonSample.get("comments")));
           
+          // Get parent Histology item for later checking of good stains
+          histologyItems.add((Sample)he.getParent());
+          
           if (Boolean.TRUE.equals(scoreComplete))
           {
@@ -885 +892 @@
         }
         
+        // Check flagged histology items
+        int numFlagged = 0;
+        int numUnflagged = 0;
+        BioMaterialList flaggedHistology = BiomaterialList.FLAGGED_HISTOLOGY.load(dc);
+        for (Sample histology : histologyItems)
+        {
+          String flag = (String)Annotationtype.FLAG.getAnnotationValue(dc, histology);
+          
+          ItemQuery<Sample> heQuery = histology.getChildSamples();
+          Subtype.STAINED.addFilter(dc, heQuery);
+          heQuery.include(Reggie.INCLUDE_IN_CURRENT_PROJECT);
+          boolean hasGoodStain = false;
+          for (Sample stained : heQuery.list(dc))
+          {
+            if (Boolean.TRUE.equals(Annotationtype.GOOD_STAIN.getAnnotationValue(dc, stained)))
+            {
+              hasGoodStain = true;
+              break;
+            }
+          }
+          
+          if (hasGoodStain)
+          {
+            if (flag != null)
+            {
+              // Remove the flag
+              numUnflagged++;
+              Annotationtype.FLAG.setAnnotationValue(dc, histology, null);
+              flaggedHistology.remove(histology);
+            }
+          }
+          else
+          {
+            if (flag == null)
+            {
+              // Flag the histology since it has no good stain and is not already flagged
+              numFlagged++;
+              Annotationtype.FLAG.setAnnotationValue(dc, histology, Histology.FLAG_NO_GOOD_STAIN);
+              flaggedHistology.add(histology);
+            }
+          }
+          
+        }
+        
+        if (numFlagged > 0)
+        {
+          jsonMessages.add(numFlagged + " items added to Flagged histology list.");
+        }
+        if (numUnflagged > 0)
+        {
+          jsonMessages.add(numUnflagged + " items removed from Flagged histology list.");         
+        }
+
         dc.commit();
       }