Changeset 1760

Timestamp:

Nov 30, 2012, 12:45:00 PM (10 years ago)

Author:

Nicklas Nordborg

Message:

References #424: Select RNA items for library preparation

Implemented a simple auto-selection feature that find:

• RNA items with no child mRNA
• A non-empty creation date
• Remaining quantity >= 1.1µg
• Not manually included on the mRNA plate
• Sorted by RNA plate and location: plate, row, column

The user designing the plate need to account for replicates/stratagene by leaving room on each pool and then using copy/paste to duplicate some RNA. The user must also manually assign items for QC.

Location:

extensions/net.sf.basedb.reggie/branches/ticket-422

Files:

• resources/libprep/select_rna.jsp (modified) (8 diffs)
• src/net/sf/basedb/reggie/servlet/MRnaServlet.java (modified) (2 diffs)

extensions/net.sf.basedb.reggie/branches/ticket-422/resources/libprep/select_rna.jsp

@@ -342 +342 @@
     }
     
-    for (var i = 0; i < response.rna.length; i++)
-    {
-      var rna = response.rna[i];
+    rna.cacheInfo(response.rna);
+  }
+  
+  rna.cacheInfo = function(rnaList)
+  {
+    for (var i = 0; i < rnaList.length; i++)
+    {
+      var rna = rnaList[i];
       info['N'+rna.name] = rna;
       info['I'+rna.id] = rna;
@@ -475 +480 @@
       {
         text += '<div class="ndconc">'+Numbers.formatNumber(info.NDConc, 2, 'ng/µl') + '</div>';
-        text += '<div class="volume">'+Numbers.formatNumber(use/10, 1)+' + '+Numbers.formatNumber(water/10, 1)+'µl</div>';
+        text += '<div class="volumes"><span class="volume">'+Numbers.formatNumber(use/10, 1)+'</span> + <span class="water">'+Numbers.formatNumber(water/10, 1)+'µl</span></div>';
       }
       else
@@ -835 +840 @@
 {
   Main.openPopup('select_file.jsp?ID=<%=ID%>', 'SelectFile', 600, 400); 
+}
+
+
+/**
+  Let the wizard automatically select among unprocessed RNA items.
+*/
+function autoSelect()
+{
+
+  var wells = Plate.getWells();
+  var ignore = [];
+  var selected = 0;
+  var notEmpty = 0;
+  
+  // Count selected and non-empty wells and keep track of RNA that is already present
+  for (var i = 0; i < wells.length; i++)
+  {
+    var well = wells[i];
+    if (well.selected) 
+    {
+      selected++;
+      if (well.rna && !well.hasError()) notEmpty++;
+    }
+    if (well.rna && well.rna.id)
+    {
+      ignore[ignore.length] = well.rna.id;
+    }
+  }
+  
+  if (selected == 0)
+  {
+    alert('Please select one or more wells were RNA should be placed.');
+    return;
+  }
+  
+  if (notEmpty > 0)
+  {
+    if (!confirm('Replace RNA in ' + notEmpty + ' wells?'))
+    {
+      return;
+    }
+  }
+
+  var request = Ajax.getXmlHttpRequest();
+  var url = '../MRna.servlet?ID=<%=ID%>&cmd=AutoSelectRnaForMRna&numToSelect='+currentSelected;
+  url += '&ignore='+ignore.join(',');
+  request.open("GET", url, false);
+  request.send(null);
+
+  if (debug) Main.debug(request.responseText);
+  var response = JSON.parse(request.responseText);  
+  if (response.status != 'ok')
+  {
+    setFatalError(response.message);
+    return false;
+  }
+  
+  // Cache RNA information
+  Rna.cacheInfo(response.rna);
+  
+  if (response.rna.length == 0)
+  {
+    alert('Could not find any unprocessed RNA at this time.');
+  }
+  
+  for (var i = 0; i < response.rna.length; i++)
+  {
+    if (i < selected.length)
+    {
+      var well = selected[i];
+      // Create a new RNA object
+      var rna = Rna.createByName(response.rna[i].name);
+      well.setRna(rna);
+      well.selected = false;
+    }
+  }
+  
+  // Check for replicates on the whole plate and repaint it
+  Plate.checkReplicates(null, true);
+  Plate.paint(Plate.getWells());
 }
 
@@ -1158 +1243 @@
   display: none;
 }
-.plate.hide-volume .volume
+.plate.hide-volumes .volumes
 {
   display: none;
@@ -1165 +1250 @@
 {
   display: none;
+}
+
+.volume
+{
+  color: #C80000;
+}
+.water
+{
+  color: #0000C8;
 }
 
@@ -1213 +1307 @@
             <td>
               <input type="checkbox" name="ndconc" id="ndconc" onclick="toggleInfo('ndconc')"><label for="ndconc">NDConc</label><br>
-              <input type="checkbox" name="volume" id="volume" onclick="toggleInfo('volume')"><label for="volume">Used volume+water</label><br>
+              <input type="checkbox" name="volumes" id="volumes" onclick="toggleInfo('volumes')"><label for="volumes">Used volume+water</label><br>
             </td>
           </tr>
@@ -1236 +1330 @@
         
         <tbl:button 
-          title="Auto-select&hellip;" 
+          title="Auto-select" 
           image="<%=home+"/images/wizard.png"%>" 
           onclick="autoSelect()" 
@@ -1278 +1372 @@
         />
       </tbl:toolbar>
-        <table class="plate hide-volume hide-ndconc" style="margin: 1em 1em 0 1em;" id="plate">
+        <table class="plate hide-volumes hide-ndconc" style="margin: 1em 1em 0 1em;" id="plate">
         <%
         int columns = 12;

extensions/net.sf.basedb.reggie/branches/ticket-422/src/net/sf/basedb/reggie/servlet/MRnaServlet.java

@@ -2 +2 @@
 
 import java.io.IOException;
+import java.util.Arrays;
 import java.util.Date;
 import java.util.HashMap;
@@ -111 +112 @@
         json.put("bioplates", jsonLists);
       }
+      else if ("AutoSelectRnaForMRna".equals(cmd))
+      {
+        dc = sc.newDbControl();
+        
+        int numToSelect = Values.getInt(req.getParameter("numToSelect"));
+        Integer[] ignore = Values.getInt(req.getParameter("ignore").split(","));
+        ItemQuery<Extract> query = Extract.getQuery();
+        query.setIncludes(Reggie.INCLUDE_IN_CURRENT_PROJECT);
+        Subtype.RNA.addFilter(dc, query);
+        // Filter for RNA already included on the plate
+        if (ignore != null && ignore.length > 0)
+        {
+          query.restrict(Restrictions.not(Restrictions.in(Hql.property("id"), Expressions.parameter("ignore"))));
+          query.setParameter("ignore", Arrays.asList(ignore), Type.INT);
+        }
+        
+        // Filter for non-empty creation date
+        query.join(Hql.innerJoin("creationEvent", "ce"));
+        query.restrict(Restrictions.neq(Hql.property("ce", "eventDate"), null));
+        
+        // Filter for enough remaining quantity >= 1.1 µg
+        query.restrict(Restrictions.gteq(Hql.property("remainingQuantity"), Expressions.aFloat(1.1f)));
+        
+        // Create a query that load all RNA extracts that has at least one mRNA child extract
+        ItemQuery<Extract> subquery = Extract.getQuery();
+        subquery.setIncludes(Reggie.INCLUDE_IN_CURRENT_PROJECT);
+        // Filter on RNA subtype
+        Subtype.RNA.addFilter(dc, subquery);
+        
+        // Join child items and filter on RNAQC subtype
+        subquery.join(Hql.innerJoin("childCreationEvents", "cce"));
+        subquery.join(Hql.innerJoin("cce", "event", "evt", null, false));
+        subquery.join(Hql.innerJoin("evt", "bioMaterial", "bm", null, false));
+        Subtype.MRNA.addFilter(dc, subquery, "bm");
+        
+        // Filter on id not equal to any that has a mRNA child
+        query.restrict(Restrictions.neq(Hql.property("id"), Expressions.all(subquery)));
+        
+        // Order by RNA plate and location: plate - row - column
+        query.join(Hql.innerJoin(null, "bioWell", "w", true));
+        query.join(Hql.innerJoin("w", "bioPlate", "bp", true));
+        query.order(Orders.asc(Hql.property("bp", "name")));
+        query.order(Orders.asc(Hql.property("w", "row")));
+        query.order(Orders.asc(Hql.property("w", "column")));
+        query.setMaxResults(numToSelect);
+        
+        json.put("query", query.toQl(dc));
+        
+        List<Rna> rna = Rna.toRna(query.list(dc));
+        JSONArray jsonRna = new JSONArray();
+        
+        for (Rna r : rna)
+        {
+          r.loadBioPlateLocation();
+          r.setAnnotation("remainingQuantity", r.getExtract().getRemainingQuantity());
+          r.loadAnnotations(dc, "NDConc", Annotationtype.ND_CONC, null);
+          jsonRna.add(r.asJSONObject());
+        }
+        
+        json.put("rna", jsonRna);
+        
+      }
       else if ("GetMRnaInfoForPlate".equals(cmd))
       {