Changeset 1934

Timestamp:

Apr 17, 2013, 10:35:45 AM (10 years ago)

Author:

Nicklas Nordborg

Message:

References #485: Select libraries for pooling

Very preliminary wizard for creating pooled library items. Expect it to change a lot in the future. For safety reasons, it will not save any information in the database. It would cause incorrect calculations in the (also preliminary) lab protocols for the pooling.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/index.jsp (modified) (1 diff)
• resources/libprep/create_pools.jsp (added)
• resources/libprep/lib_registration.jsp (modified) (1 diff)
• resources/libprep/plate.js (modified) (1 diff)
• src/net/sf/basedb/reggie/dao/PooledLibrary.java (added)
• src/net/sf/basedb/reggie/servlet/PoolServlet.java (modified) (5 diffs)

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

@@ -263 +263 @@
           <dd>
             <ul>
+            <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 and flow cell preparation</a>
             <li><a href="libprep/pool_registration.jsp?ID=<%=ID%>">Register pooled libraries</a>

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

@@ -653 +653 @@
         <td class="input"><textarea rows="4" cols="50" style="width: 90%;" name="libComments" value="" onblur="libCommentsOnChange()"></textarea></td>
         <td class="status" id="libComments.status"></td>
-        <td class="help"><span id="libComments.message" class="message" style="display: none;"></span>Comments about the quality control results.</td>
+        <td class="help"><span id="libComments.message" class="message" style="display: none;"></span>Comments about the library preparation.</td>
       </tr>
       </table>

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

@@ -66 +66 @@
   plate.getPools = function()
   {
-    return plate.poolSchema ? plate.poolSchema.getPools() : 0;
+    return plate.poolSchema ? plate.poolSchema.numPools : 0;
   }
   

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

@@ -15 +15 @@
 import org.json.simple.JSONArray;
 import org.json.simple.JSONObject;
+import org.json.simple.parser.JSONParser;
 
 
 
 import net.sf.basedb.core.Application;
+import net.sf.basedb.core.BioMaterialEvent;
+import net.sf.basedb.core.BioMaterialEventSource;
 import net.sf.basedb.core.BioPlate;
 import net.sf.basedb.core.DbControl;
@@ -25 +28 @@
 import net.sf.basedb.core.InvalidDataException;
 import net.sf.basedb.core.ItemQuery;
+import net.sf.basedb.core.ItemSubtype;
 import net.sf.basedb.core.SessionControl;
 import net.sf.basedb.core.query.Annotations;
@@ -35 +39 @@
 import net.sf.basedb.reggie.dao.BioplateType;
 import net.sf.basedb.reggie.dao.Library;
+import net.sf.basedb.reggie.dao.PooledLibrary;
 import net.sf.basedb.reggie.dao.ReactionPlate;
+import net.sf.basedb.reggie.dao.Subtype;
 import net.sf.basedb.util.Values;
 import net.sf.basedb.util.error.ThrowableUtil;
@@ -130 +136 @@
         json.put("libraries", jsonLibs);
       }
+      else if ("GetNextAutoGeneratedPoolNames".equals(cmd))
+      {
+        dc = sc.newDbControl();
+        int numNames = Values.getInt(req.getParameter("numNames"));
+        json.put("names", PooledLibrary.generateNamesForBatch(dc, 1, numNames));
+
+      }
     }
     catch (Throwable t)
@@ -166 +179 @@
     try
     {
-      if ("CreateBarcodedLibraries".equals(cmd))
-      {
+      if ("CreatePools".equals(cmd))
+      {
+        JSONObject jsonReq = (JSONObject)new JSONParser().parse(req.getReader());
+        JSONArray jsonPools = (JSONArray)jsonReq.get("pools");
+        
+        dc = sc.newDbControl();
+        ItemSubtype pooledLibraryType = Subtype.POOLED_LIBRARY.load(dc);
+        
+        for (int i = 0; i < jsonPools.size(); i++)
+        {
+          JSONObject jsonPool = (JSONObject)jsonPools.get(i);
+          JSONArray jsonLibs = (JSONArray)jsonPool.get("libs");
+          
+          Extract pool = Extract.getNew(dc);
+          pool.setItemSubtype(pooledLibraryType);
+          pool.setName((String)jsonPool.get("name"));
+          
+          BioMaterialEvent poolEvent = pool.getCreationEvent();
+          
+          for (int j = 0; j < jsonLibs.size(); j++)
+          {
+            JSONObject jsonLib = (JSONObject)jsonLibs.get(j);
+            Number libId = (Number)jsonLib.get("id");
+
+            Extract lib = Extract.getById(dc, libId.intValue());
+            BioMaterialEventSource src = poolEvent.addSource(lib);
+            
+            Float originalConc = (Float)Annotationtype.QUBIT_CONC.getAnnotationValue(dc, lib);
+            Float speedVacConc = (Float)Annotationtype.QUBIT_CONC_AFTER_SPEEDVAC.getAnnotationValue(dc, lib);
+            Float usedConc = speedVacConc == null ? originalConc : speedVacConc;
+            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());
+            src.setUsedQuantity(usedQuantity);
+          }
+          
+          // TODO - how to calculate the original quantity of the pool
+          // pool.setOriginalQuantity(????);
+          
+          dc.saveItem(pool);
+          
+          jsonMessages.add("Created '" + pool.getName() + "' from " + jsonLibs.size() + " libraries");
+        }
+        
+        //dc.commit();
       }
       json.put("messages", jsonMessages);