Changeset 1970

Timestamp:

May 8, 2013, 2:55:14 PM (9 years ago)

Author:

Nicklas Nordborg

Message:

References #480: Register pooled libraries

Preliminary registration form which only register the date, protocol and comments. May need to discuss if there is other information to store (freezer location, etc).

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/index.jsp (modified) (1 diff)
• resources/libprep/pool_registration.jsp (added)
• src/net/sf/basedb/reggie/servlet/PoolServlet.java (modified) (3 diffs)

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

@@ -264 +264 @@
             <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</a> (preliminary)
-            <li><a href="libprep/pool_registration.jsp?ID=<%=ID%>" class="not-implemented">Register pooled libraries</a>
+            <li><a href="libprep/pool_protocol.jsp?ID=<%=ID%>">Lab protocols for pooling</a>
+            <li><a href="libprep/pool_registration.jsp?ID=<%=ID%>">Register pooled libraries</a>
             <li><a href="libprep/flowcell_registration.jsp?ID=<%=ID%>" class="not-implemented">Register flow cells</a>
             </ul>

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

@@ -4 +4 @@
 
 import java.util.Arrays;
+import java.util.Date;
 import java.util.List;
 
@@ -25 +26 @@
 import net.sf.basedb.core.ItemQuery;
 import net.sf.basedb.core.ItemSubtype;
+import net.sf.basedb.core.Protocol;
 import net.sf.basedb.core.SessionControl;
 import net.sf.basedb.core.Type;
@@ -385 +387 @@
           jsonMessages.add("Created '" + pool.getName() + "' from " + jsonLibs.size() + " libraries; pool molarity=" + Values.formatNumber(summedPoolMolarity / jsonLibs.size(), 2)); // conc="+Values.formatNumber(poolQuantity * 1000 / poolVolume, 2) + "ng/µl; quantity="+Values.formatNumber(poolQuantity*1000, 2)+"ng; volume="+Values.formatNumber(poolVolume, 2) + "µl");
         }
+        dc.commit();
+      }
+      else if ("RegisterPooledLibraries".equals(cmd))
+      {
+        JSONObject jsonReq = (JSONObject)new JSONParser().parse(req.getReader());
+        dc = sc.newDbControl();
+        
+        Number poolProtocolId = (Number)jsonReq.get("poolProtocol");
+        Date poolDate = Reggie.CONVERTER_STRING_TO_DATE.convert((String)jsonReq.get("poolDate"));
+        String operator = Values.getStringOrNull((String)jsonReq.get("poolOperator"));
+        String comment = Values.getStringOrNull((String)jsonReq.get("comments"));
+        
+        Protocol poolProtocol = poolProtocolId == null ? null : Protocol.getById(dc, poolProtocolId.intValue());
+        
+        JSONArray jsonPools = (JSONArray)jsonReq.get("pools");        
+        for (int i = 0; i < jsonPools.size(); i++)
+        {
+          Number poolId = (Number)jsonPools.get(i);
+          Extract pool = Extract.getById(dc, poolId.intValue());
+          BioMaterialEvent creationEvent = pool.getCreationEvent();
+          
+          creationEvent.setEventDate(poolDate);
+          creationEvent.setProtocol(poolProtocol);
+          pool.setDescription(comment);
+          
+          jsonMessages.add("Pool '" + pool.getName() + "' registered as completed.");
+        }
         
         dc.commit();