Changeset 2137

Timestamp:

Nov 13, 2013, 3:53:05 PM (7 years ago)

Author:

Nicklas Nordborg

Message:

References #527: Implement manual pooled library selection

This should now be functional. Need some more testing for border cases.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/libprep/create_manual_pool.jsp (added)
• resources/libprep/create_pools.jsp (modified) (2 diffs)
• resources/libprep/pools.js (modified) (4 diffs)
• src/net/sf/basedb/reggie/servlet/PoolServlet.java (modified) (7 diffs)

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

@@ -96 +96 @@
   }
   return response.bioplates;
+}
+
+function createManualPool()
+{
+  location.replace('create_manual_pool.jsp?ID=<%=ID%>');
 }
 
@@ -874 +879 @@
       </tr>
       <tr valign="top">
-        <td class="prompt">Manual select</td>
-        <td class="input"> // TODO</td>
+        <td class="prompt"></td>
+        <td class="input">
+          <table><tr><td>
+            <base:button title="Create manual pool" onclick="createManualPool()" image="<%=home+"/images/gonext.png"%>" />
+          </td></tr></table>
+        
+        </td>
         <td class="status"></td>
         <td class="help"></td>

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

@@ -307 +307 @@
   pm.calculateLibVolume = function(lib, targetMolarity, targetVolume, mixingStrategy)
   {
-    var maxVolume = lib.speedVacConc != null ? AVAILABLE_VOLUME_AFTER_SPEEDVAC : AVAILABLE_VOLUME;
+    var maxVolume = lib.remainingVolume;
     if (mixingStrategy == 'fixed' && maxVolume > targetVolume)
     {
@@ -387 +387 @@
       // Calculate the total volume needed to get to the
       // target molarity for the pooled libs
-      var totalPoolVolume = totalLibAmount / targetMolarity;
-      var totalEbVolume = totalPoolVolume - totalLibVolume - fixedEbVolume;
+      // Round all summarized values to avoid precision problems (eg. 4.0 --> 3.999999998)
+      var totalPoolVolume = pm.round(totalLibAmount / targetMolarity);
+      totalLibVolume = pm.round(totalLibVolume);
+      fixedEbVolume = pm.round(fixedEbVolume);
+      var totalEbVolume = pm.round(totalPoolVolume - totalLibVolume - fixedEbVolume);
 
       // Divide EB volume among the libs (rounded to 1 decimal)
@@ -405 +408 @@
       }
       
+      usedEb = pm.round(usedEb);
+      
       // If the used EB doesn't add up to the total amount needed (due to rounding)
       // add the extra amount to the last lib
-      if (Math.abs(totalEbVolume - usedEb) > 0.1 && adjustableLib)
+      if (Math.abs(totalEbVolume - usedEb) >= 0.05 && adjustableLib)
       {
         adjustableLib.eb += totalEbVolume - usedEb;
@@ -427 +432 @@
       var lib = libs[libNo];
       var vol = lib.maxVolume < lib.volume ? lib.maxVolume : lib.volume;
-      var eb = Math.max(0, lib.eb);
       libVolume += vol;
-      ebVolume += eb;
+      ebVolume += lib.eb;
       if (mixingStrategy == 'dynamic' && (!lib.mixFactor || lib.mixFactor == 1)) 
       {
-        ebFinalMix += eb; 
+        ebFinalMix += lib.eb;
       }
       libAmount += vol * lib.molarity;

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

@@ -184 +184 @@
         
       }
+      else if ("GetLibraryInfo".equals(cmd))
+      {
+        // Get information about a single library
+        int libId = Values.getInt(req.getParameter("libraryId"));
+        dc = sc.newDbControl();
+        
+        Library lib = Library.getById(dc, libId);
+        lib.loadBioPlateLocation();
+        addPoolingCalculationsToLib(dc, lib, null);
+        lib.setAnnotation("comment", lib.getExtract().getDescription());
+        
+        json.put("library", lib.asJSONObject());
+        
+      }
       else if ("GetLibraryInfoForPlate".equals(cmd))
       {
@@ -208 +222 @@
         {
           lib.loadBioPlateLocation();
-          addPoolingCalculationsToLib(dc, lib, null, libs.size());
+          addPoolingCalculationsToLib(dc, lib, null);
           lib.setAnnotation("comment", lib.getExtract().getDescription());
           jsonLibs.add(lib.asJSONObject());
@@ -230 +244 @@
         int numNames = Values.getInt(req.getParameter("numNames"));
         json.put("names", PooledLibrary.generateNamesForBatch(dc, 1, numNames));
+        JSONObject poolInfo = new JSONObject();
+        poolInfo.put("targetMolarity", TARGET_MOLARITY_IN_POOL);
+        poolInfo.put("targetVolumePerLib", DEFAULT_TARGET_VOLUME_IN_POOL_PER_LIB);
+        poolInfo.put("extraLargeMixFactor", EXTRA_LARGE_MIX_FACTOR);
+        poolInfo.put("limitForExtraLargeMix", LIMIT_FOR_EXTRA_LARGE_MIX);
+        json.put("poolInfo", poolInfo);
       }
       else if ("CountUnprocessedPools".equals(cmd))
@@ -283 +303 @@
           {
             lib.loadBioPlateLocation();
-            addPoolingCalculationsToLib(dc, lib, pool, libs.size());
+            addPoolingCalculationsToLib(dc, lib, pool);
             lib.setAnnotation("comment", lib.getExtract().getDescription());
             jsonLibs.add(lib.asJSONObject());
@@ -597 +617 @@
   
   
-  private void addPoolingCalculationsToLib(DbControl dc, Library lib, PooledLibrary pool, int numLibs)
+  private void addPoolingCalculationsToLib(DbControl dc, Library lib, PooledLibrary pool)
   {
     // Load original and SpeedVac:ed concentrations
@@ -612 +632 @@
     
     // Load remaining quantity of the lib
-    lib.setAnnotation("remainingQuantity", libEx.getRemainingQuantity());
+    Float remain = libEx.getRemainingQuantity();
+    lib.setAnnotation("remainingQuantity", remain);
+    if (remain != null && (originalConc != null || speedVacConc != null))
+    {
+      // Remaining volume in µl
+      Float conc = speedVacConc == null ? originalConc : speedVacConc;
+      lib.setAnnotation("remainingVolume", 1000 * remain / conc);
+    }
 
     if (pool != null)
@@ -642 +669 @@
   }
   
+  
   @SuppressWarnings("unchecked")
   private JSONObject getJSONForLibPlate(DbControl dc, BioPlate libPlate)