Changeset 1944

Timestamp:

Apr 19, 2013, 11:41:04 AM (10 years ago)

Author:

Nicklas Nordborg

Message:

References #425: Generate a lab protocol for RNA -> cDNA processing

The protocol wizard now find out the actual regular quantity and marks all higher that that as items selected for QC.

File:

• extensions/net.sf.basedb.reggie/trunk/resources/libprep/mrna_protocol2.jsp (modified) (7 diffs)

extensions/net.sf.basedb.reggie/trunk/resources/libprep/mrna_protocol2.jsp

@@ -50 +50 @@
   <title>Lab protocol for <%=HTML.encodeTags(plate.getName())%> - <%=view.equals("list") ? "list" : "table"%></title>
   <link rel="SHORTCUT ICON" href="<%=home%>/images/pipette.png">
+  <link rel="stylesheet" type="text/css" href="<%=home %>/css/reggie.css">
   <link rel="stylesheet" type="text/css" href="<%=home %>/css/printable.css">
   <link rel="stylesheet" type="text/css" href="<%=home %>/css/plate.css">
@@ -63 +64 @@
 
   var QUANTITY_REGULAR = 1.1;
-  var QUANTITY_QC = 1.22;
-  var LOW_QUANTITY_WARNING_FACTOR = 1.5;
+  var LOW_QUANTITY_WARNING_FACTOR = 2;
 
   function init()
@@ -91 +91 @@
     
     var list = response.mrna;
+    // Find QUANTITY_REGULAR = lowest used value
+    QUANTITY_REGULAR = findLowestUsedQuantity(list);
+    
     // Pre-process the return mRNA items
     for (var i = 0; i < list.length; i++)
@@ -133 +136 @@
   
   /**
+    Find the lowest used quantity. This is the QUANTITY_REGULAR
+    value. RNA with larger used quantities are assumed to be selected
+    for QC.
+  */
+  function findLowestUsedQuantity(mrnaList)
+  {
+    var lowestQuantity = mrnaList[0].rna.usedQuantity;
+    for (var i = 1; i < mrnaList.length; i++)
+    {
+      var rna = mrnaList[i].rna;
+      if (rna.usedQuantity < lowestQuantity)
+      {
+        lowestQuantity = rna.usedQuantity;
+      }
+    }
+    return lowestQuantity;
+  }
+  
+  /**
     Check the mRNA and RNA items for problems and calculate derived
     information such as volume and water, qc/stratagene flags.
@@ -175 +197 @@
         remarks[remarks.length] = 'No quantity';
       }
-      else if (rna.remainingQuantity < (rna.qc ? QUANTITY_QC : QUANTITY_REGULAR) * LOW_QUANTITY_WARNING_FACTOR)
+      else if (rna.remainingQuantity < QUANTITY_REGULAR * LOW_QUANTITY_WARNING_FACTOR)
       {
         remarks[remarks.length] = 'Low quantity';
@@ -270 +292 @@
         text += '<div class="ndconc">'+Numbers.formatNumber(rna.NDConc, 2, 'ng/µl') + '</div>';
 
-        if (rna.volume && rna.water)
+        if (rna.volume >= 0 && rna.water >= 0)
         {
           text += '<div><span class="volume">'+Numbers.formatNumber(rna.volume, 1)+'µl</span>';
@@ -631 +653 @@
   }
   %>
+  <i>Low quantity = The remaining quantity is too low for the RNA to be re-processed one more time</i>
   </div>
 </body>