Changeset 2239


Ignore:
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:
2 edited

Legend:

Unmodified
Added
Removed
  • extensions/net.sf.basedb.reggie/trunk/resources/libprep/sequencing_started.jsp

    r2237 r2239  
    158158  Main.hide('existing-sequencing-runs');
    159159  setInnerHTML('existing-sequencing-runs', '');
     160  setInputStatus('sequencingCycles', '', '');
    160161 
    161162  var reader = new FileReader();
     
    256257  setInnerHTML('flowCellName', Main.encodeTags(flowCell.name));
    257258
     259  if (flowCell.SequencingCycles != info.SequencingCycles)
     260  {
     261    setInputStatus('sequencingCycles', 'Not same as planned SequencingCycles ('+flowCell.SequencingCycles+').', 'warning');
     262  }
     263
     264 
    258265  var pools = flowCell.pools;
    259266  var html = '';
     
    558565        </td>
    559566        <td class="status" id="runParametersXml.status"></td>
    560         <td class="help" rowspan="12"><span id="runParametersXml.message" class="message" style="display:none;"></span>
    561           Select the <b>runParameters.xml</b> file that was created by the HiSeq. Typically found in
    562           <b>D:\Illumina\HiSeqTemp\&lt;run-folder&gt;</b> subfolder.
     567        <td class="help" rowspan="8"><span id="runParametersXml.message" class="message" style="display:none;"></span>
     568          Select the <b>runParameters.xml</b> file that was created by the HiSeq. Typically found
     569          on drive <b>D: or E:</b> in <b>\Illumina\HiSeqTemp\&lt;run-folder&gt;</b> subfolder.
    563570        </td>
    564571      </tr>
     
    600607        <td class="subprompt">Sequencing cycles</td>
    601608        <td class="input" id="sequencingCycles"></td>
    602         <td class="status"></td>
     609        <td class="status" id="sequencingCycles.status"></td>
     610        <td class="help"><span id="sequencingCycles.message" class="message" style="display: none;"></span></td>
    603611      </tr>
    604612      <tr valign="top" class="fc-info">
    605613        <td class="prompt" colspan="2" id="flowCellName">Flow cell information</td>
    606614        <td class="status"></td>
     615        <td class="help"></td>
    607616      </tr>
    608617      <tr valign="top" class="fc-info">
     
    610619        <td class="input" id="pools"></td>
    611620        <td class="status"></td>
     621        <td class="help"></td>
    612622      </tr>
    613623      <tr valign="top" class="fc-info">
     
    615625        <td class="input" id="libPlate"></td>
    616626        <td class="status"></td>
     627        <td class="help"></td>
    617628      </tr>
    618629      <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

    r2236 r2239  
    282282        String sequencingComments = Values.getStringOrNull((String)jsonSeq.get("comments"));
    283283        String sequencingOperator = Values.getStringOrNull((String)jsonSeq.get("operator"));
     284        String sequencingCycles = (String)jsonRunParameters.get("SequencingCycles");
    284285        Date startDate = Reggie.CONVERTER_STRING_TO_DATE.convert((String)jsonRunParameters.get("SequencingStart"));
    285286
     
    299300        // Clear result of any previous sequencing runs (eg. FirstBaseReportFailed)
    300301        Annotationtype.SEQUENCING_RESULT.setAnnotationValue(dc, flowCell, null);
     302        // Overwrite sequencing cycles on flow cell if different
     303        if (!sequencingCycles.equals(Annotationtype.SEQUENCING_CYCLES.getAnnotationValue(dc, flowCell)))
     304        {
     305          Annotationtype.SEQUENCING_CYCLES.setAnnotationValue(dc, flowCell, sequencingCycles);
     306        }
    301307        sequenceRun.addPhysicalBioAssay(flowCell);
    302308       
     
    305311        Annotationtype.SEQUENCING_START.setAnnotationValue(dc, sequenceRun, startDate);
    306312        Annotationtype.SEQUENCING_RUN_NUMBER.setAnnotationValue(dc, sequenceRun, jsonRunParameters.get("ScanNumber"));
    307         Annotationtype.SEQUENCING_CYCLES.setAnnotationValue(dc, sequenceRun, jsonRunParameters.get("SequencingCycles"));
     313        Annotationtype.SEQUENCING_CYCLES.setAnnotationValue(dc, sequenceRun, sequencingCycles);
    308314        Annotationtype.DATA_FILES_FOLDER.setAnnotationValue(dc, sequenceRun, jsonRunParameters.get("RunID"));
    309315        dc.commit();
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