Changeset 1942

Timestamp:

Apr 19, 2013, 11:11:26 AM (10 years ago)

Author:

Nicklas Nordborg

Message:

References #424: Select RNA items for library preparation

Added support for setting the RNA quantities to use for regular processing and for QC. Default values are 1.1 and 1.22 µg as before. The auto-select wizard uses the lower quantity when searching for RNA.

Location:

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

Files:

• auto_select_rna.jsp (modified) (4 diffs)
• select_rna.jsp (modified) (13 diffs)

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

@@ -31 +31 @@
 
 <script>
+var QUANTITY_REGULAR = 1.1;
 function autoSelect()
 {
   var options = {};
   var frm = document.forms['options'];
-  if (frm.remainingQuantity.checked) options.remainingQuantity = 1.1;
+  if (frm.remainingQuantity.checked) options.remainingQuantity = QUANTITY_REGULAR;
   if (frm.qualityScore.checked) options.qualityScore = 6.0;
   if (frm.flag.checked) options.flag = 1;
@@ -50 +51 @@
   }
 }
+
+function init()
+{
+  var frm = window.opener.document.forms['reggie'];
+  var qRegular = parseFloat(frm.quantity_regular.value);
+  if (qRegular > 0) QUANTITY_REGULAR = qRegular;
+  
+  setInnerHTML('quantity_regular', QUANTITY_REGULAR);
+}
 </script>
 <style>
@@ -59 +69 @@
 </style>
 </base:head>
-<base:body>
+<base:body onload="init()">
   <h1><%=title %></h1>
 
@@ -70 +80 @@
       <th>Active filters</th>
       <td>
-        <input type="checkbox" name="remainingQuantity" id="remainingQuantity" value="1" checked><label for="remainingQuantity">Remaining quantity ≥ 1.1µg</label><br>
-        <input type="checkbox" name="qualityScore" id="qualityScore" value="1" checked><label for="qualityScore">RQS/RIN ≥ 6</label><br>
+        <input type="checkbox" name="remainingQuantity" id="remainingQuantity" value="1" checked>
+          <label for="remainingQuantity">Remaining quantity ≥ <span id="quantity_regular"></span> µg</label><br>
+        <input type="checkbox" name="qualityScore" id="qualityScore" value="1" checked>
+          <label for="qualityScore">RQS/RIN ≥ 6</label><br>
       </td>
     </tr>

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

@@ -38 +38 @@
 var debug = true;
 
-var QUANTITY_REGULAR = 1.1;
-var QUANTITY_QC = 1.22;
-var LOW_QUANTITY_WARNING_FACTOR = 1.5;
+var quantitiesAreValid = false;
+var QUANTITY_REGULAR;
+var QUANTITY_QC;
+var LOW_QUANTITY_WARNING_FACTOR = 2;
 var QUALITY_SCORE_WARNING_LIMIT = 8;
 
@@ -198 +199 @@
       if (info && info.id && !rna.stratagene && !rna.external)
       {
-        var quantity = 1000 * (rna.qc ? QUANTITY_QC : QUANTITY_REGULAR);
-        var use = Math.ceil(quantity/info.NDConc);
+        var quantity = 10000 * (rna.qc ? QUANTITY_QC : QUANTITY_REGULAR);
+        var use = Math.ceil(quantity/info.NDConc) / 10;
         var water = Math.round(50-use);
         if (info.remainingQuantity)
         {
           text += '<div class="quantity">'+Numbers.formatNumber(info.remainingQuantity, 2) + 'µg</div>';
-          // Must have at least 1.1µg or 1.22µg
+          // Must have at least 1.1µg or 1.22µg (if default values are used)
           var remainLimit = rna.qc ? QUANTITY_QC : QUANTITY_REGULAR;
           if (info.remainingQuantity < remainLimit)
@@ -277 +278 @@
   keepSessionAlive('<%=ID%>', false, '../');
   
+  quantityOnBlur();
+  
   var frm = document.forms['reggie'];
   var schema = PoolSchema.initList(frm.pool_schema);
@@ -1191 +1194 @@
 function goCreate()
 {
+  if (!quantitiesAreValid)
+  {
+    setInnerHTML('gonext.message', 'Invalid RNA quantities');
+    return;
+  }
+  
   var submitInfo = {};
   var plateInfo = {};
@@ -1198 +1207 @@
   submitInfo.flagged = flaggedRnaInfo;
   var frm = document.forms['reggie'];
-  
   var schema = POOL_SCHEMA[frm.pool_schema.selectedIndex];
   
@@ -1289 +1297 @@
 
   if (debug) Main.debug(JSON.stringify(submitInfo));
-  
+
   var request = Ajax.getXmlHttpRequest();
   var url = '../MRna.servlet?ID=<%=ID%>';
@@ -1340 +1348 @@
   Plate.paint(Plate.getWells());
   PoolSchema.buildPoolTableRow(schema, Plate.columns, true);
+}
+
+function quantityOnBlur()
+{
+  var frm = document.forms['reggie'];
+  quantitiesAreValid = false;
+  setInnerHTML('gonext.message', '');
+  
+  var qRegular = parseFloat(frm.quantity_regular.value);
+  if (!(qRegular > 0))
+  {
+    setInputStatus('quantities', 'Amount must be ≥ 0.', 'invalid');
+    return;
+  }
+  var qQc = parseFloat(frm.quantity_qc.value);
+  if (!(qQc > qRegular))
+  {
+    setInputStatus('quantities', 'Amount QC must be &gt; ' + qRegular + '.', 'invalid');
+    return;
+  }
+  
+  quantitiesAreValid = true;
+  QUANTITY_REGULAR = qRegular;
+  QUANTITY_QC = qQc;
+  setInputStatus('quantities', '', 'valid');
+  Plate.paint(Plate.getWells());
 }
 
@@ -1552 +1586 @@
         <td class="prompt">Name</td>
         <td class="input" id="plateName"></td>
+        <td class="status"></td>
         <td class="help">Select RNA items to use for the new mRNA plate.</td>
+      </tr>
+      <tr valign="top">
+        <td class="prompt">Preliminary pool layout</td>
+        <td class="input">
+          <select name="pool_schema" onchange="poolSchemaOnChange()" style="width: 25em;" class="required"></select>
+        </td>
+        <td class="status"></td>
+        <td class="help">Preliminary pool layout (can be changed later).</td>
       </tr>
       <tr valign="top">
         <td class="prompt">Stratagene to use</td>
         <td class="input">
-          <select name="stratagene" style="width: 25em;"></select>
+          <select name="stratagene" style="width: 25em;" class="required"></select>
         </td>
+        <td class="status"></td>
         <td class="help">
           Select the Stratagene tube to use. If not known, the
@@ -1565 +1609 @@
       </tr>
       <tr valign="top">
-        <td class="prompt">Preliminary pool layout</td>
+        <td class="prompt">Amount of RNA</td>
         <td class="input">
-          <select name="pool_schema" onchange="poolSchemaOnChange()" style="width: 25em;"></select>
+          Normal <input type="text" class="text required" name="quantity_regular" 
+            value="1.1" style="width: 4em;"
+            onblur="quantityOnBlur()"
+            onkeypress="return Numbers.numberOnly(event)">µg,
+          QC <input type="text" class="text required" name="quantity_qc" 
+            value="1.22" style="width: 4em;"
+            onblur="quantityOnBlur()"
+            onkeypress="return Numbers.numberOnly(event)">µg
         </td>
-        <td class="help">Preliminary pool layout (can be changed later).</td>
+        <td class="status" id="quantities.status"></td>
+        <td class="help">
+          <span id="quantities.message" class="message" style="display: none;"></span>
+          Specify the amount of RNA to use. Aliquots for QC usually need 0.12µg extra.
+        </td>
       </tr>
       <tr valign="top">
@@ -1576 +1631 @@
           <textarea rows="2" style="width: 90%;" name="comments" value=""></textarea>
         </td>
+        <td class="status"></td>
         <td class="help">Comments about the new mRNA plate.</td>
       </tr>
@@ -1595 +1651 @@
           </table>
         </td>
+        <td class="status"></td>
         <td class="help">Toggles visiblity of the selected information inside each well on the plate.</td>
       </tr>
@@ -1604 +1661 @@
           <br>
         </td>
+        <td class="status"></td>
         <td class="help">Use the selected mouse button to display a context-menu when clicking on the plate.</td>
       </tr>
@@ -1772 +1830 @@
     <td><base:button id="gocreate" title="Create" image="<%=home+"/images/gonext.png"%>" onclick="goCreate()" /></td>
     <td><base:button id="gorestart" title="Restart" image="<%=home+"/images/goback.png"%>" onclick="goRestart(true)" style="display: none;"/></td>
+    <td id="gonext.message" class="message"></td>
   </tr>
   </table>