Changeset 2239

Timestamp:

Feb 21, 2014, 8:50:01 AM (9 years ago)

Author:

Nicklas Nordborg

Message:

References #562: Re-design clustering and sequencing startup wizards

Display a warning icon if the planned SequencingCycles is different from the information in the runParameters.xml file. Registration will overwrite the planned values with the actual values.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/libprep/sequencing_started.jsp (modified) (6 diffs)
• src/net/sf/basedb/reggie/servlet/SequencingRunServlet.java (modified) (3 diffs)

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

@@ -158 +158 @@
   Main.hide('existing-sequencing-runs');
   setInnerHTML('existing-sequencing-runs', '');
+  setInputStatus('sequencingCycles', '', '');
   
   var reader = new FileReader();
@@ -256 +257 @@
   setInnerHTML('flowCellName', Main.encodeTags(flowCell.name));
 
+  if (flowCell.SequencingCycles != info.SequencingCycles)
+  {
+    setInputStatus('sequencingCycles', 'Not same as planned SequencingCycles ('+flowCell.SequencingCycles+').', 'warning');
+  }
+
+  
   var pools = flowCell.pools;
   var html = '';
@@ -558 +565 @@
         </td>
         <td class="status" id="runParametersXml.status"></td>
-        <td class="help" rowspan="12"><span id="runParametersXml.message" class="message" style="display:none;"></span>
-          Select the <b>runParameters.xml</b> file that was created by the HiSeq. Typically found in
-          <b>D:\Illumina\HiSeqTemp\&lt;run-folder&gt;</b> subfolder.
+        <td class="help" rowspan="8"><span id="runParametersXml.message" class="message" style="display:none;"></span>
+          Select the <b>runParameters.xml</b> file that was created by the HiSeq. Typically found 
+          on drive <b>D: or E:</b> in <b>\Illumina\HiSeqTemp\&lt;run-folder&gt;</b> subfolder.
         </td>
       </tr>
@@ -600 +607 @@
         <td class="subprompt">Sequencing cycles</td>
         <td class="input" id="sequencingCycles"></td>
-        <td class="status"></td>
+        <td class="status" id="sequencingCycles.status"></td>
+        <td class="help"><span id="sequencingCycles.message" class="message" style="display: none;"></span></td>
       </tr>
       <tr valign="top" class="fc-info">
         <td class="prompt" colspan="2" id="flowCellName">Flow cell information</td>
         <td class="status"></td>
+        <td class="help"></td>
       </tr>
       <tr valign="top" class="fc-info">
@@ -610 +619 @@
         <td class="input" id="pools"></td>
         <td class="status"></td>
+        <td class="help"></td>
       </tr>
       <tr valign="top" class="fc-info">
@@ -615 +625 @@
         <td class="input" id="libPlate"></td>
         <td class="status"></td>
+        <td class="help"></td>
       </tr>
       <tbody id="existing-sequencing-runs" style="border-bottom: 1em solid transparent;">

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

@@ -282 +282 @@
         String sequencingComments = Values.getStringOrNull((String)jsonSeq.get("comments"));
         String sequencingOperator = Values.getStringOrNull((String)jsonSeq.get("operator"));
+        String sequencingCycles = (String)jsonRunParameters.get("SequencingCycles");
         Date startDate = Reggie.CONVERTER_STRING_TO_DATE.convert((String)jsonRunParameters.get("SequencingStart"));
 
@@ -299 +300 @@
         // Clear result of any previous sequencing runs (eg. FirstBaseReportFailed)
         Annotationtype.SEQUENCING_RESULT.setAnnotationValue(dc, flowCell, null);
+        // Overwrite sequencing cycles on flow cell if different
+        if (!sequencingCycles.equals(Annotationtype.SEQUENCING_CYCLES.getAnnotationValue(dc, flowCell)))
+        {
+          Annotationtype.SEQUENCING_CYCLES.setAnnotationValue(dc, flowCell, sequencingCycles);
+        }
         sequenceRun.addPhysicalBioAssay(flowCell);
         
@@ -305 +311 @@
         Annotationtype.SEQUENCING_START.setAnnotationValue(dc, sequenceRun, startDate);
         Annotationtype.SEQUENCING_RUN_NUMBER.setAnnotationValue(dc, sequenceRun, jsonRunParameters.get("ScanNumber"));
-        Annotationtype.SEQUENCING_CYCLES.setAnnotationValue(dc, sequenceRun, jsonRunParameters.get("SequencingCycles"));
+        Annotationtype.SEQUENCING_CYCLES.setAnnotationValue(dc, sequenceRun, sequencingCycles);
         Annotationtype.DATA_FILES_FOLDER.setAnnotationValue(dc, sequenceRun, jsonRunParameters.get("RunID"));
         dc.commit();