Changeset 2235

Timestamp:

Feb 19, 2014, 3:39:52 PM (9 years ago)

Author:

Nicklas Nordborg

Message:

References #546: Confirm sequencing as completed

Adding an option to let the user decide if a pool should be flagged or not.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/analysis/sequencing_confirm.jsp (modified) (5 diffs)
• src/net/sf/basedb/reggie/servlet/SequencingRunServlet.java (modified) (2 diffs)

extensions/net.sf.basedb.reggie/trunk/resources/analysis/sequencing_confirm.jsp

@@ -130 +130 @@
   
   Forms.checkRadio(frm.outcome, seqRun.SequencingResult || 'Successful');
+  outcomeOnChange();
   
   var html = '';
@@ -139 +140 @@
 }
 
+function outcomeOnChange()
+{
+  var frm = document.forms['reggie']; 
+
+  frm.flagPools.disabled = !document.getElementById('outcomeFailed').checked;
+}
 
 function formatDate(value)
@@ -220 +227 @@
   var outcome = Forms.getCheckedRadio(frm, 'outcome').value;
   var submitInfo = {};
+  
+  submitInfo.flagPools = !frm.flagPools.disabled && frm.flagPools.checked ? true : false;
 
   seqRun.comments = frm.sequencingComments.value;
@@ -383 +392 @@
         <td class="input" colspan="2">
           <label><input type="radio" name="outcome" id="outcomeSuccess" value="Successful"
+            onclick="outcomeOnChange()"
             checked>Success</label> - continue with demux<br>
           <label><input type="radio" name="outcome" id="outcomeFirstBaseReportFailed" value="FirstBaseReportFailed"
+            onclick="outcomeOnChange()"
             >FirstBaseReportFailed</label> - re-start sequencing<br>
           <label><input type="radio" name="outcome" id="outcomeFailed" value="Failed"
-            >Failure</label> - flag pools for re-clustering
+            onclick="outcomeOnChange()"
+            >Failure</label><br>
+          <img src="../images/joinbottom.gif"><label><input type="checkbox" name="flagPools" value="1" disabled checked>Flag pools for re-clustering</label>
+          
         </td>
         <td class="help">
@@ -394 +408 @@
           is made from this run.<br>
           Select the <b>Failure</b> option if further analysis of the data is not possible.
-          No child bioassay set will be created and existing pooled libraries will
+          No child bioassay set will be created. Existing pooled libraries can optionally
           be flagged for re-clustering on a new flow cell.
         </td>

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

@@ -319 +319 @@
         JSONObject jsonSeq = (JSONObject)jsonReq.get("sequencingRun");
         JSONObject jsonFlowCell = (JSONObject)jsonSeq.get("flowCell");
+        boolean flagPools = Boolean.TRUE.equals(jsonReq.get("flagPools"));
         
         Number seqId = (Number)jsonSeq.get("id");
@@ -329 +330 @@
         PhysicalBioAssay flowCell = PhysicalBioAssay.getById(dc, fcId.intValue());
 
-        if (SequencingRun.SEQUENCING_FAILED.equals(outcome))
+        if (SequencingRun.SEQUENCING_FAILED.equals(outcome) && flagPools)
         {
           BioMaterialList flaggedPools = null;