Changeset 5788


Ignore:
Timestamp:
Dec 13, 2019, 11:49:44 AM (3 years ago)
Author:
Nicklas Nordborg
Message:

Fixes #1216: Finalize the "Confirm MIPs demux" wizard

The wizard now display "Align" as the next step and also put selected items into the "MIPs Alignment Pipeline" list.

Location:
extensions/net.sf.basedb.reggie/trunk
Files:
4 edited

Legend:

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

    r5763 r5788  
    971971            <dt>
    972972              <base:icon image="<%=home+"/images/server.png" %>" />
    973               Demux and merge wizards
     973              Demux wizards
    974974            </dt>
    975975            <dd>
     
    981981             
    982982              <li><span class="require-permission" data-role="MIPsSecondaryAnalysis" data-link="analysis/demux_start.jsp?ID=<%=ID%>&pipeline=MIPS"
    983                 >Start demux and merge</span>
     983                >Start demux</span>
    984984                <span class="counter" data-counter="sequencing-runs-for-demux-mips"
    985985                  title="Number of confirmed MIPs sequencing runs waiting to be demuxed">∙</span>
    986986             
    987987              <li><span class="require-permission" data-role="MIPsSecondaryAnalysis" data-link="mipsanalysis/demux_confirm.jsp?ID=<%=ID%>"
    988                 >Confirm demux and merge completed</span>
     988                >Confirm demux completed</span>
    989989                <span class="counter" data-counter="demux-jobs-not-confirmed-mips"
    990990                  title="Number of MIPs demux jobs waiting for confirmation">∙</span>
  • extensions/net.sf.basedb.reggie/trunk/resources/mipsanalysis/demux_confirm.js

    r5620 r5788  
    199199    url += '&cmd=GetMergedSequences&job='+job.id;
    200200   
    201     Wizard.showLoadingAnimation('Loading merged sequences...');
     201    Wizard.showLoadingAnimation('Loading demuxed sequences...');
    202202    Wizard.asyncJsonRequest(url, demux.mergedSequencesLoaded);
    203203  }
     
    234234    html += '<th class="warning-col"></th>';
    235235    html += '<th class="dottedleft">Flag DNA</th>';
    236     html += '<th>????</th>';
     236    html += '<th>Align</th>';
    237237    html += '<th class="dottedleft"></th>';
    238238    html += '</tr>';
     
    297297        }
    298298         
    299         html += '<td><input type="checkbox" name="nextStepTODO.'+merged.id+'" '+(alignChecked ? ' checked':'')+'></td>';
     299        html += '<td><input type="checkbox" name="mipsAlign.'+merged.id+'" '+(alignChecked ? ' checked':'')+'></td>';
    300300        html += '<td class="dottedleft comment"><input type="text" name="comment.'+merged.id+'"></td>';
    301301      }
     
    351351        demux.resetCheckbox(frm['flag.'+merge.id]);
    352352      }
    353       if (frm['nextStepTODO.'+merge.id])
    354       {
    355         frm['nextStepTODO.'+merge.id].disabled = failed;
    356         demux.resetCheckbox(frm['nextStepTODO.'+merge.id]);
     353      if (frm['mipsAlign.'+merge.id])
     354      {
     355        frm['mipsAlign.'+merge.id].disabled = failed;
     356        demux.resetCheckbox(frm['mipsAlign.'+merge.id]);
    357357      }
    358358      if (frm['comment.'+merge.id])
     
    414414        tmp.id = merge.id;
    415415        tmp.flag = frm['flag.'+merge.id] && frm['flag.'+merge.id].checked;
    416         tmp.nextStepTODO = frm['nextStepTODO.'+merge.id].checked;
     416        tmp.mipsAlign = frm['mipsAlign.'+merge.id].checked;
    417417        tmp.comment = frm['comment.'+merge.id].value;
    418418        merged[merged.length] = tmp;
  • extensions/net.sf.basedb.reggie/trunk/resources/mipsanalysis/demux_confirm.jsp

    r5551 r5788  
    111111  <p:path><p:pathelement
    112112    title="Reggie" href="<%="../index.jsp?ID="+ID%>"
    113     /><p:pathelement title="Confirm demux and merge ended"
     113    /><p:pathelement title="Confirm demux ended"
    114114    /></p:path>
    115115
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/DemuxMergeServlet.java

    r5620 r5788  
    457457        int numHisatAlign = 0;
    458458        int numLegacyAlign = 0;
    459         int numNextStepTODO = 0; // TODO - MIPs
     459        int numMipsAlign = 0;
    460460        int numConfirmed = 0;
    461461        int numFlaggedRna = 0;
     
    466466        ItemList hisatPipeline = BiomaterialList.HISAT_PIPELINE.load(dc);
    467467        ItemList legacyPipeline = BiomaterialList.LEGACY_PIPELINE.load(dc);
    468         ItemList mipsPipeline = null; // TODO - MIPs
     468        ItemList mipsPipeline = BiomaterialList.MIPS_ALIGN_PIPELINE.load(dc);
    469469
    470470        for (int mergeNo = 0; mergeNo < jsonMergedSequences.size(); ++mergeNo)
     
    474474          boolean legacyAlign = !failed && Boolean.TRUE.equals(jsonMerge.get("legacyAlign"));
    475475          boolean hisatAlign = !failed && Boolean.TRUE.equals(jsonMerge.get("hisatAlign"));
    476           boolean nextStepTODO = !failed && Boolean.TRUE.equals(jsonMerge.get("nextStepTODO"));
     476          boolean mipsAlign = !failed && Boolean.TRUE.equals(jsonMerge.get("mipsAlign"));
    477477             
    478           boolean align = legacyAlign || hisatAlign || nextStepTODO;
     478          boolean align = legacyAlign || hisatAlign || mipsAlign;
    479479          if (align) numConfirmed++;
    480480         
     
    526526          else if (pipeline == Pipeline.MIPS)
    527527          {
    528             // TODO - MIPs
    529             if (nextStepTODO)
    530             {
    531 //              mipsPipeline.add(merge);
    532               numNextStepTODO++;
     528            if (mipsAlign)
     529            {
     530              mipsPipeline.add(merge);
     531              numMipsAlign++;
    533532            }
    534533           
     
    570569        else if (pipeline == Pipeline.MIPS)
    571570        {
    572           if (numNextStepTODO > 0)
    573           {
    574             jsonMessages.add(numNextStepTODO + " libraries confirmed for next MIPs step (TODO)");
     571          if (numMipsAlign > 0)
     572          {
     573            jsonMessages.add(numMipsAlign + " libraries confirmed for MIPs alignment");
    575574          }
    576575          else
    577576          {
    578             jsonMessages.add("No libraries confirmed for next MIPs step");
    579           }         
     577            jsonMessages.add("No libraries confirmed for MIPs alignment");
     578          }
    580579        }
    581580       
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