Changeset 2201


Ignore:
Timestamp:
Jan 20, 2014, 9:24:40 AM (9 years ago)
Author:
Nicklas Nordborg
Message:

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

New version of the lab protocol. Both the clustering and sequencing sections are now separate for both flow cells. Added fields to the sequencing section for recording first base report, turnaround and end date+time.

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

Legend:

Unmodified
Added
Removed

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

    r2199 r2201  
    649649         
    650650          <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/flowcell_protocol.jsp?ID=<%=ID%>"
    651             >Lab protocol for clustering and sequencing startup</span> <span class="counter" id="count.flow-cells.1" title="Counting..."><img src="images/loading-small.gif"></span>
     651            >Lab protocol for clustering and sequencing</span> <span class="counter" id="count.flow-cells.1" title="Counting..."><img src="images/loading-small.gif"></span>
    652652         
    653653          <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/flowcell_registration.jsp?ID=<%=ID%>"

  • extensions/net.sf.basedb.reggie/trunk/resources/libprep/flowcell_protocol.jsp

    r2094 r2201  
    233233  <p:path><p:pathelement
    234234    title="Reggie" href="<%="../index.jsp?ID="+ID%>"
    235     /><p:pathelement title="Lab protocol for clustering and sequencing startup"
     235    /><p:pathelement title="Lab protocol for clustering and sequencing"
    236236    /></p:path>
    237237

  • extensions/net.sf.basedb.reggie/trunk/resources/libprep/flowcell_protocol2.jsp

    r2112 r2201  
    5757<html>
    5858<head>
    59   <title id="pageTitle">Lab protocol for flow cells></title>
     59  <title id="pageTitle">Lab protocol for clustering and sequencing</title>
    6060  <link rel="SHORTCUT ICON" href="<%=home%>/images/flowcell.png">
    6161  <link rel="stylesheet" type="text/css" href="<%=home %>/css/reggie.css">
    … …  
    120120    var flowCellNo = -1;
    121121    var flowCellNameList = '';
    122     var poolColors = [];
     122    var allColors = [];
    123123    var useDarker = false;
    124     var numPools = 0;
    125     var poolsRow = document.getElementById('all-pools');
    126124    for (var index in flowCellInfoArray)
    127125    {
     126      var poolColors = [];
     127      var poolsRow = document.getElementById('all-pools-'+index);
    128128      flowCellNo++;
    129129      var flowCell = flowCellInfoArray[index];
    … …  
    134134      }
    135135      flowCellNameList += flowCellName;
    136       setInnerHTML('flowCellName.'+flowCellNo, flowCellName);       
    137       setInnerHTML('flowCellName2.'+flowCellNo, flowCellName);       
    138       setInnerHTML('flowCellDescription.'+flowCellNo, flowCell.description);       
     136      setInnerHTML('flowCellName.'+flowCellNo, flowCellName);     
     137      setInnerHTML('flowCellDescription.'+flowCellNo, flowCell.description || '<i style="color: #999999;">Clustering comments</i>');       
    139138      setInnerHTML('sequencingCycles.'+flowCellNo, flowCell.SequencingCycles);
    140139      setInnerHTML('flowCellId.'+flowCellNo, flowCell.externalId);
    … …  
    146145        if (!color)
    147146        {
    148           numPools++;
    149           color = COLORS[nextColor] + (useDarker ? ' darker' : '');
     147          color = allColors[poolName];
     148          if (!color)
     149          {
     150            color = COLORS[nextColor] + (useDarker ? ' darker' : '');
     151            allColors[poolName] = color;
     152            nextColor++;
     153            if (nextColor == COLORS.length)
     154            {
     155              nextColor = 0;
     156              useDarker = !useDarker;
     157            }
     158          }
    150159          poolColors[poolName] = color;
    151160          var td = document.createElement('td');
    … …  
    153162          td.innerHTML = poolName;
    154163          poolsRow.appendChild(td);
    155           nextColor++;
    156           if (nextColor == COLORS.length)
    157           {
    158             nextColor = 0;
    159             useDarker = !useDarker;
    160           }
    161164        }
    162165        var row = laneKey - 1;
    … …  
    165168        setInnerHTML('fcPoolName.'+idSuffix, poolName);       
    166169      }
     170     
     171      if (poolColors.length <= 6)
     172      {
     173        // White-space at end to avoid pools getting to wide
     174        var td = document.createElement('td');
     175        td.innerHTML = '';
     176        poolsRow.appendChild(td);
     177      }
    167178    }
    168179
    169     if (numPools <= 6)
    170     {
    171       var td = document.createElement('td');
    172       td.innerHTML = '';
    173       poolsRow.appendChild(td);
    174     }
    175180   
    176181    var pageTitle = 'Lab protocol for ' + flowCellNameList;
    … …  
    181186  </script>
    182187  <style>
     188 
     189  h1
     190  {
     191    margin-top: 1em;
     192  }
    183193 
    184194  h2
    … …  
    208218    max-height: 2.5em;
    209219    border-bottom: 1px solid #000000;
     220    border-top: 1px solid #000000;
    210221  }
    211222
    … …  
    236247  {
    237248    display: inline-block;
    238     width: 0.8em;
    239     height: 0.8em;
     249    width: 0.75em;
     250    height: 0.75em;
    240251    border: 1px solid #000000;
    241     margin-left: 1em;
     252    margin-left: 0em;
    242253    margin-right: 0.5em;
    243254  }
    … …  
    343354  </div>
    344355 
    345   <h1>Lab protocol for clustering and sequencing startup <span class="reggie">Reggie <%=reggie.getAbout().getVersion() %></span></h1>
    346 
    347356  <input type="hidden" name="fcIdList" value="<%=flowCellIdList%>">
    348357
    … …  
    351360  <div id="listviewcontainer" style="display: none;">
    352361 
    353   <table class="protocolheader">
    354   <tr id="all-pools">
    355     <th style="width: 15%;">Used pools</th>
    356   </tr>
    357   </table>
    358  
    359   <h2>1. Clustering</h2>
    360362  <%
    361363  // Note: Variable 'c' here indicates a flow cell, not a table column
    … …  
    364366  {
    365367    %>
     368    <h1>Lab protocol for clustering and sequencing <span class="reggie">Reggie <%=reggie.getAbout().getVersion() %></span></h1>
     369
     370    <table class="protocolheader">
     371    <tr id="all-pools-<%=c%>">
     372      <th style="width: 15%;">Used pools</th>
     373    </tr>
     374    </table>
     375   
     376    <h2>1. Clustering</h2>
    366377    <table style="width: 100%;" class="protocolheader flowcell">
    367     <tr>
     378    <tr style="">
    368379      <th style="width: 15%;">Flow cell</th>
    369380      <td style="width: 35%;"><div id="flowCellName.<%=c%>" >Flow cell name <%=c%></div></td>
    … …  
    392403        </tbody>
    393404        </table>
    394      
    395      
    396405      </td>
    397406    </tr>
    … …  
    414423   
    415424    <tr style="max-height: 100%; height: auto; vertical-align: top;">
    416       <td colspan="2" id="flowCellDescription.<%=c%>"></td>
     425      <td colspan="2" id="flowCellDescription.<%=c%>">Clustering comments</td>
    417426    </tr>
    418427    </table>
     428   
     429   
     430    <h2>2. Sequencing</h2>
     431     
     432    <table class="protocolheader">
     433    <tr>
     434      <th style="width: 25%;">Start date</th>
     435      <td style="width: 75%;" colspan="2"></td>
     436    </tr>
     437    <tr>
     438      <th>Operator</th>
     439      <td colspan="2"></td>
     440    </tr>
     441
     442    <tr>
     443      <th>Sequencing machine</th>
     444      <td colspan="2"></td>
     445    </tr>
     446
     447    <tr>
     448      <th>HiSeq position</th>
     449      <td colspan="2"><b><div class="colorbox"></div>A <div class="colorbox" style="margin-left: 2em;"></div>B</b></td>
     450    </tr>
     451
     452    <tr>
     453      <th>Sequencing cycles</th>
     454      <td id="sequencingCycles.<%=c%>" style="width: 30%;"></td>
     455      <th>(Read 1 - Index - Read 2)</th>
     456    </tr>
     457   
     458    <tr>
     459      <th>First base report</th>
     460      <td colspan="2"><b><div class="colorbox"></div>Ok <div class="colorbox" style="margin-left: 2em;"></div>Not ok</b></td>
     461    </tr>
     462
     463    <tr>
     464      <th style="width: 25%;">Turn-around date+time</th>
     465      <td style="width: 75%;" colspan="2"></td>
     466    </tr>
     467
     468    <tr>
     469      <th style="width: 25%;">End date+time</th>
     470      <td style="width: 75%;" colspan="2"></td>
     471    </tr>
     472
     473    <tr style="height: 10em; vertical-align: top;">
     474      <th>Comments</th>
     475      <td colspan="2"></td>
     476    </tr>
     477    </table>
     478    <div class="pagebreak"></div>
    419479    <%
    420480  }
    421481  %>
    422482 
    423   <h2>2. Sequencing startup</h2>
    424  
    425   <table class="protocolheader">
    426   <tr>
    427     <th style="width: 25%;">Sequencing machine</th>
    428     <td style="width: 75%;" colspan="2"></td>
    429   </tr>
    430   <tr>
    431     <th>Date</th>
    432     <td colspan="2"></td>
    433   </tr>
    434   <tr>
    435     <th>Operator</th>
    436     <td colspan="2"></td>
    437   </tr>
    438  
    439   <tr>
    440     <th></th>
    441     <th style="width: 20%; border-right: 0;">HiSeq position</th>
    442     <th>Sequencing cycles (Read 1 - Index - Read 2)</th>
    443   </tr>
    444 
    445   <%
    446   // Note: Variable 'c' here indicates a flow cell, not a table column
    447   // Each flow cell is shown in its own table
    448   for (int c = 0; c < nFlowCells; ++c)
    449   {
    450     %>
    451     <tr>
    452       <th id="flowCellName2.<%=c%>" class="subprompt">Flowcell<%=c %></th>
    453       <td><b><div class="colorbox"></div>A <div class="colorbox"></div>B</b></td>
    454       <td><div id="sequencingCycles.<%=c%>"></div></td>
    455     </tr>
    456     <%
    457   }
    458   %>
    459   <tr style="height: 7em; vertical-align: top;">
    460     <th>Comments</th>
    461     <td colspan="2"></td>
    462   </tr>
    463   </table>
    464483  </div>
    465484  </form>
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