Changeset 2188

Timestamp:

Jan 10, 2014, 2:31:14 PM (8 years ago)

Author:

Nicklas Nordborg

Message:

References #555: Specify amount to use from *.dil items in pool

Implemented the same functionality in the "Create manual pool" wizard. Also discovered and fixed some bugs introduced by #553 (submitting mixingStrategy and target volume as properties of the pool).

Location:

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

Files:

• create_manual_pool.jsp (modified) (8 diffs)
• pool_protocol2.jsp (modified) (3 diffs)

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

@@ -42 +42 @@
 var LIMIT_FOR_AUTO_EXCLUDE = 0.25;
 var LIMIT_FOR_EXTRA_LARGE_MIX;
-var EXTRA_LARGE_MIX_FACTOR;
+var MAX_TARGET_VOLUME = 10;
+var MIN_TARGET_VOLUME = 2;
 
 function init()
@@ -52 +53 @@
   var poolInfo = response.poolInfo;
   TARGET_MOLARITY_IN_POOL = poolInfo.targetMolarity;
-  EXTRA_LARGE_MIX_FACTOR = poolInfo.extraLargeMixFactor;
   LIMIT_FOR_EXTRA_LARGE_MIX = poolInfo.limitForExtraLargeMix;
   setInnerHTML('pool-name', response.names[0]);
@@ -463 +463 @@
   
   targetVolumePerLibIsValid = false;
-  if (targetVolumePerLib < 2 || targetVolumePerLib > 10)
-  {
-    setInputStatus('target_volume', 'Must be between 2 and 10µl', 'invalid');
+  if (targetVolumePerLib < MIN_TARGET_VOLUME || targetVolumePerLib > MAX_TARGET_VOLUME)
+  {
+    setInputStatus('target_volume', 'Must be between '+MIN_TARGET_VOLUME+' and '+MAX_TARGET_VOLUME+'µl', 'invalid');
     return;
   }
@@ -489 +489 @@
   submitInfo.flagged = []; // Always empty
   var frm = document.forms['reggie'];
-  submitInfo.targetVolumeInPoolPerLib = parseFloat(frm.target_volume.value);
-  submitInfo.targetPoolMolarity = TARGET_MOLARITY_IN_POOL;
-  submitInfo.mixingStrategy = Forms.getCheckedRadio(frm.mixing_strategy).value;
+  var mixingStrategy = Forms.getCheckedRadio(frm.mixing_strategy).value;
   
   var pool = {};
@@ -497 +495 @@
   pool.comment = frm.poolComments.value;
   pool.ebVolumeExtra = Math.max(0, poolInfo.ebVolumeExtra);
+  pool.targetVolumeInPoolPerLib = parseFloat(frm.target_volume.value);
+  pool.targetPoolMolarity = TARGET_MOLARITY_IN_POOL;
+  pool.mixingStrategy = mixingStrategy;
   pool.libs = [];
   pool.excluded = [];
@@ -514 +515 @@
       tmp.eb = lib.actualEb;
       tmp.mixFactor = lib.mixFactor;
+      if (lib.mixFactor > 1 && lib.targetVolume && mixingStrategy == 'dynamic') 
+      {
+        tmp.targetVolume = lib.targetVolume;
+      }
       tmp.comment = lib.comment;
       pool.libs[pool.libs.length] = tmp;
@@ -601 +606 @@
   updatePoolData();
 }
+
+//Set target volume on the selected wells
+var lastTargetVolume = null;
+function setTargetVolume()
+{
+  var frm = document.forms['reggie'];
+  var checked = [];
+  var targetVolume;
+  for (var libNo = 0; libNo < selectedLibraries.length; libNo++)
+  {
+    var lib = selectedLibraries[libNo];
+    if (frm['check.'+lib.id].checked && lib.mixFactor > 1)
+    {
+      checked[checked.length] = lib;
+      if (!targetVolume) targetVolume = lib.targetVolume;
+    }
+  }
+  
+  if (checked.length == 0)
+  {
+    alert('No libraries with separate mix have been selected');
+    return;
+  }
+
+  
+  targetVolume = parseFloat(prompt('Volume to use in pool ('+LIMIT_FOR_EXTRA_LARGE_MIX+'--'+MAX_TARGET_VOLUME+' µl)', targetVolume || lastTargetVolume));
+  if (isNaN(targetVolume))
+  {
+    targetVolume = null;
+  }
+  else if (targetVolume > MAX_TARGET_VOLUME)
+  {
+    targetVolume = MAX_TARGET_VOLUME;
+  }
+  else if (targetVolume < LIMIT_FOR_EXTRA_LARGE_MIX)
+  {
+    targetVolume = LIMIT_FOR_EXTRA_LARGE_MIX
+  }
+  lastTargetVolume = targetVolume;
+  if (targetVolume == '') targetVolume = null;
+
+  var targetVolumePerLib = parseFloat(frm.target_volume.value);
+  var mixingStrategy = Forms.getCheckedRadio(frm.mixing_strategy).value;
+  for (var libNo = 0; libNo < checked.length; libNo++)
+  {
+    var lib = checked[libNo];
+    lib.targetVolume = targetVolume;
+    PoolMix.calculateEbVolume(lib, TARGET_MOLARITY_IN_POOL, targetVolumePerLib, mixingStrategy);
+  }
+  
+  updatePoolData();
+}
+
 
 </script>
@@ -823 +881 @@
           onclick="removeSelected()" 
           tooltip="Remove the selected libraries from the pool"
+        />
+        <tbl:button 
+          title="Separate mix volume&hellip;" 
+          image="<%=home+"/images/specimen.png"%>" 
+          onclick="setTargetVolume()" 
+          tooltip="Set volume to use in the pool for separately mixed libraries (dynamic mixing only)" 
         />
         <tbl:button 

extensions/net.sf.basedb.reggie/trunk/resources/libprep/pool_protocol2.jsp

@@ -251 +251 @@
     {
       var pool = pools[poolNo];
-      var realPoolNo = schema.getPoolNumForColumn(pool.libraries[0].bioWell.column);
-
-      var wellsInPool = POOL_CURRENT_SCHEMA ? Plate.getPool(realPoolNo) : null;
+      var wellsInPool = null;
+      if (schema)
+      {
+        var realPoolNo = schema.getPoolNumForColumn(pool.libraries[0].bioWell.column);
+        wellsInPool = Plate.getPool(realPoolNo);
+      }
+
       
       var html = '';
@@ -265 +269 @@
         
         var tr = document.createElement('tr');
-        if (POOL_CURRENT_SCHEMA)
+        if (schema)
         {
           wellIndex = createMissingRows(tbody, wellsInPool, wellIndex, well, barcodeVariant);
@@ -307 +311 @@
         tbody.appendChild(tr);
       }
-      if (POOL_CURRENT_SCHEMA)
+      if (schema)
       {
         createMissingRows(tbody, wellsInPool, wellIndex, null, barcodeVariant);