Changeset 1952

Timestamp:

Apr 24, 2013, 11:33:32 AM (10 years ago)

Author:

Nicklas Nordborg

Message:

References #485: Select libraries for pooling

Calculate volumes in the wizard instead of in the servlet.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/index.jsp (modified) (1 diff)
• resources/libprep/create_pools.jsp (modified) (8 diffs)
• src/net/sf/basedb/reggie/servlet/PoolServlet.java (modified) (3 diffs)

extensions/net.sf.basedb.reggie/trunk/resources/index.jsp

@@ -263 +263 @@
           <dd>
             <ul>
-            <li><a href="libprep/create_pools.jsp?ID=<%=ID%>" class="not-implemented">Create pooled libraries</a>
+            <li><a href="libprep/create_pools.jsp?ID=<%=ID%>">Create pooled libraries</a>
             <li><a href="libprep/pool_protocol.jsp?ID=<%=ID%>">Lab protocols for pooling</a> (preliminary)
             <li><a href="libprep/pool_registration.jsp?ID=<%=ID%>" class="not-implemented">Register pooled libraries</a>

extensions/net.sf.basedb.reggie/trunk/resources/libprep/create_pools.jsp

@@ -34 +34 @@
 var debug = true;
 var currentStep = 1;
+var LIMIT_FOR_5_ML = 1.0;
 
 function init()
@@ -134 +135 @@
     for (var j = 0; j < wells.length; j++)
     {
-      var lib = {};
-      lib.id = wells[j].extract.id;
-      poolInfo.libs[poolInfo.libs.length] = lib;
+      var lib = wells[j].extract;
+      if (lib)
+      {
+        var tmp = {};
+        tmp.id = lib.id;
+        tmp.name = lib.name;
+        tmp.volume = lib.volume;
+        poolInfo.libs[poolInfo.libs.length] = tmp;
+      }
     }
     
@@ -149 +156 @@
 
   var request = Ajax.getXmlHttpRequest();
-  var url = '../Pool.servlet?ID=<%=ID%>';
-  url += '&cmd=CreatePools';
-  request.open("POST", url, false);
-  request.setRequestHeader("Content-Type", "application/json");
-  request.send(JSON.stringify(submitInfo));
+  try
+  {
+    showLoadingAnimation('Creating pools...');
+    var url = '../Pool.servlet?ID=<%=ID%>';
+    url += '&cmd=CreatePools';
+    request.open("POST", url, false);
+    request.setRequestHeader("Content-Type", "application/json");
+    request.send(JSON.stringify(submitInfo));
+  }
+  finally
+  {
+    hideLoadingAnimation();
+  }
 
   if (debug) Main.debug(request.responseText);
@@ -277 +292 @@
   }
   
+  if (lib.molarity)
+  {
+    lib.volume = 10 / lib.molarity;
+    lib.eb = 5-lib.volume;
+    if (lib.speedVacConc != null)
+    {
+      remarks[remarks.length] = 'SpeedVac';
+    }
+    if (lib.volume > 5) 
+    {
+      remarks[remarks.length] = 'Use 5 µl';
+      //lib.volume = 5;
+      //lib.eb = 0;
+    }
+
+    if (lib.volume < LIMIT_FOR_5_ML)
+    {
+      lib.volume *= 2;
+      lib.eb *= 2;
+      remarks[remarks.length] = 'Mix 10µl';
+    }
+
+  }
+  
   lib.remarks = remarks;
 }
@@ -316 +355 @@
     var text = '';
     var lib = well.extract;
-    if (lib && lib.remainingQuantity)
+    if (lib && lib.remainingQuantity && lib.molarity)
     {
       var name = lib.name;
@@ -322 +361 @@
       text += '<div class="lib">'+name.substring(0, i)+'.<br>&nbsp;'+name.substring(i)+'</div>';
       text += '<div class="barcode">'+lib.barcode.name+'</div>';
+      text += '<span class="volume">'+Numbers.formatNumber(lib.volume, 2) + 'µl</span>';
+      text += '<span class="eb">'+Numbers.formatNumber(lib.eb, 2)+'µl</span>';
       text += '<div class="remarks">'+ lib.remarks.join('; ') + '</div>';
     }
@@ -332 +373 @@
 </script>
 <style>
-#export div
-{
-  margin-left: 1em;
+.lib
+{
+  font-weight: bold;
+  margin-bottom: 0.25em;
+}
+
+.volume
+{
+  color: #C80000;
+}
+.eb
+{
+  color: #0000C8;
+  float: right;
+}
+.remarks
+{
+  color: #C80000;
+  font-style: italic;
 }
 </style>
@@ -374 +431 @@
         </td>
         <td class="status" id="bioplate.status"></td>
-        <td class="help" rowspan="2"><span id="bioplate.message" class="message" style="display: none;"></span>
+        <td class="help"><span id="bioplate.message" class="message" style="display: none;"></span>
           Select an existing Library bioplate. The list contain all Library bioplates that
-          has not yet been pooled (determined by ????).
+          contain libraries with no child items.
         </td>
+      </tr>
+      <tr valign="top">
+        <td class="prompt"></td>
+        <td class="input"> - or -</td>
+        <td class="status" id="bioplate.status"></td>
+        <td class="help"></td>
+      </tr>
+      <tr valign="top">
+        <td class="prompt">Manual select</td>
+        <td class="input"> // TODO</td>
+        <td class="status" id="bioplate.status"></td>
+        <td class="help"></td>
       </tr>
       </table>

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

@@ -83 +83 @@
         */
         dc = sc.newDbControl();
+        
+        // Find Library items with remaining quantity==original quantity
+        ItemQuery<Extract> libQuery = Extract.getQuery();
+        libQuery.setIncludes(Reggie.INCLUDE_IN_CURRENT_PROJECT);
+        Subtype.LIBRARY.addFilter(dc, libQuery);
+        libQuery.restrict(Restrictions.eq(Hql.property("remainingQuantity"), Hql.property("originalQuantity")));
+        
         ItemQuery<BioPlate> query = BioPlate.getQuery();
         query.setIncludes(Reggie.INCLUDE_IN_CURRENT_PROJECT);
         // Only Library bioplates that are not destroyed
         BioplateType.LIBRARY.addFilter(dc, query, true);
-        // Must NOT have a creation date
-        //query.restrict(Restrictions.eq(Hql.property("eventDate"), null));
         // Must have a PLATE_PROCESS_RESULT=Success annotation
         query.join(Annotations.leftJoin(null, Annotationtype.PLATE_PROCESS_RESULT.load(dc), "ppr"));
         query.restrict(Restrictions.eq(Hql.alias("ppr"), Expressions.string(ReactionPlate.PROCESS_SUCCESSFUL)));
+        
+        query.join(Hql.innerJoin("bioWells", "bw"));
+        query.join(Hql.innerJoin("bw", "bioMaterial", "bm"));
+        
+        query.restrict(Restrictions.eq(Hql.alias("bm"), Expressions.any(libQuery)));
+        query.setDistinct(true);
         
         List<BioPlate> plates = query.list(dc);
@@ -118 +129 @@
         query.join(Hql.innerJoin("bw", "bioPlate", "bp"));
         query.restrict(Restrictions.eq(Hql.alias("bp"), Hql.entity(libPlate)));
+        query.restrict(Restrictions.gt(Hql.property("remainingQuantity"), Expressions.aFloat(0f)));
         query.order(Orders.asc(Hql.property("bw", "column")));
         query.order(Orders.asc(Hql.property("bw", "row")));
@@ -211 +223 @@
             Float molarity = (Float)Annotationtype.CA_MOLARITY.getAnnotationValue(dc, lib);
 
-            // TODO - Most of the times 5 µl is used, but sometimes 10µl is used!!
-            // Remember that concentration values are stored in ng/µl
-            Float usedVolume = 10 / molarity;
-            Float usedQuantity = Math.min(usedVolume * usedConc / 1000, lib.getRemainingQuantity());
+            // Get the volume to use from the wizard. This calculated base on the CA_MOLARITY value for each
+            // sample to give a final concentration of 2nM mixed to 5 or 10µl (for high concentration)
+            Number usedVolume = (Number)jsonLib.get("volume");
+            // We never use more than 5µl
+            Float orginalVolume = usedVolume.floatValue();
+            if (usedVolume.floatValue() > 5f) usedVolume = 5f;
+            
+            // Calculate usedQuantity, Remember that concentration values are stored in ng/µl
+            Float usedQuantity = Math.min(usedVolume.floatValue() * usedConc / 1000, lib.getRemainingQuantity());
             src.setUsedQuantity(usedQuantity);
+            
+            jsonMessages.add("Using " + Values.formatNumber(usedQuantity*1000, 2) + "/" + Values.formatNumber(orginalVolume*usedConc, 2) +" of " + Values.formatNumber(lib.getOriginalQuantity()*1000,2) + " from " + lib.getName());
           }