Changeset 1929


Ignore:
Timestamp:
Apr 12, 2013, 2:34:01 PM (7 years ago)
Author:
Nicklas Nordborg
Message:

References #424, #425, #457, #479. Re-designed protocols to make the header section a bit more compact when the comment text is large. Display a warning when the remaining RNA quanitity is below 1.5 times the required amount (eg. 1.1µg or 1.22µg).

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

Legend:

Unmodified
Added
Removed
  • extensions/net.sf.basedb.reggie/trunk/resources/libprep/libprep_protocol2.jsp

    r1927 r1929  
    374374  <table style="width: 100%; border: 0px;" class="protocolheader">
    375375  <tr valign="top">
    376     <th style="width: 30%;">Work plate: <%=HTML.encodeTags(plate.getName())%></th>
    377     <th style="width: 20%; text-align: right;">Comments:&nbsp;</th>
    378     <td rowspan="3"><%=HTML.niceFormat(plate.getDescription()) %></td>
     376    <th style="width: 40%;">Work plate: <%=HTML.encodeTags(plate.getName())%></th>
     377    <th style="width: 60%;">Comments:</th>
    379378  </tr>
    380   <tr>
    381     <th style="width: 50%;" colspan="2">Date+operator for library preparation:</th>
     379  <tr valign="top">
     380    <th style="width: 40%; padding-bottom: 1.5em;">Date+operator for library preparation:</th>
     381    <td><%=HTML.niceFormat(plate.getDescription()) %></td>
    382382  </tr>
    383383  </table>
  • extensions/net.sf.basedb.reggie/trunk/resources/libprep/mrna_protocol2.jsp

    r1927 r1929  
    6161  var debug = false;
    6262  var currentStep = 1;
    63  
     63
     64  var QUANTITY_REGULAR = 1.1;
     65  var QUANTITY_QC = 1.22;
     66  var LOW_QUANTITY_WARNING_FACTOR = 1.5;
     67
    6468  function init()
    6569  {
     
    139143    rna.external = rna.name == EXTERNAL_RNA_NAME;
    140144   
    141     // Set the 'QC' flag if more than 1.2µg is used
    142     rna.qc = rna.usedQuantity > 1.2;
     145    // Set the 'QC' flag if more than 1.1µg is used
     146    rna.qc = rna.usedQuantity > QUANTITY_REGULAR;
    143147   
    144148    <%
     
    171175        remarks[remarks.length] = 'No quantity';
    172176      }
    173       else if (rna.remainingQuantity < (rna.qc ? 1.22 : 1.1))
     177      else if (rna.remainingQuantity < (rna.qc ? QUANTITY_QC : QUANTITY_REGULAR) * LOW_QUANTITY_WARNING_FACTOR)
    174178      {
    175179        remarks[remarks.length] = 'Low quantity';
     
    495499  <h1>Lab protocol for mRNA and cDNA preparation <span class="reggie">Reggie <%=reggie.getAbout().getVersion() %></span></h1>
    496500
    497   <table style="width: 100%; border: 0px;" class="protocolheader">
     501  <table style="width: 100%;" class="protocolheader">
    498502  <tr valign="top">
    499     <th style="width: 30%;">Work plate: <%=HTML.encodeTags(plate.getName())%></th>
    500     <th style="width: 20%; text-align: right;">Comments:&nbsp;</th>
    501     <td rowspan="3"><%=HTML.niceFormat(plate.getDescription()) %></td>
     503    <th style="width: 40%;">Work plate: <%=HTML.encodeTags(plate.getName())%></th>
     504    <th style="width: 60%;">Comments:</th>
    502505  </tr>
    503   <tr>
    504     <th style="width: 50%;" colspan="2">Date+operator for mRNA:</th>
     506  <tr valign="top">
     507    <th style="width: 40%; padding-bottom: 1.5em;">Date+operator for mRNA:</th>
     508    <td rowspan="2"><%=HTML.niceFormat(plate.getDescription()) %></td>
    505509  </tr>
    506   <tr>
    507     <th style="width: 50%;" colspan="2">Date+operator for cDNA:</th>
     510  <tr valign="top">
     511    <th style="width: 40%; padding-bottom: 1.5em;">Date+operator for cDNA:</th>
    508512  </tr>
    509513  </table>
  • extensions/net.sf.basedb.reggie/trunk/resources/libprep/pool_protocol2.jsp

    r1927 r1929  
    449449  <table style="width: 100%; border: 0px;" class="protocolheader">
    450450  <tr valign="top">
    451     <th style="width: 30%;">Work plate: <%=HTML.encodeTags(plate.getName())%></th>
    452     <th style="width: 20%; text-align: right;">Comments:&nbsp;</th>
    453     <td rowspan="3"><%=HTML.niceFormat(plate.getDescription()) %></td>
     451    <th style="width: 40%;">Work plate: <%=HTML.encodeTags(plate.getName())%></th>
     452    <th style="width: 60%">Comments:</th>
    454453  </tr>
    455   <tr>
    456     <th style="width: 50%;" colspan="2">Date+operator:</th>
     454  <tr valign="top">
     455    <th style="width: 40%; padding-bottom: 1.5em;">Date+operator:</th>
     456    <td><%=HTML.niceFormat(plate.getDescription()) %></td>
    457457  </tr>
    458458  </table>
  • extensions/net.sf.basedb.reggie/trunk/resources/libprep/select_rna.jsp

    r1897 r1929  
    4040var QUANTITY_REGULAR = 1.1;
    4141var QUANTITY_QC = 1.22;
     42var LOW_QUANTITY_WARNING_FACTOR = 1.5;
    4243
    4344var Rna = function()
     
    201202        {
    202203          text += '<div class="quantity">'+Numbers.formatNumber(info.remainingQuantity, 2) + 'µg</div>';
    203           if (info.remainingQuantity < (rna.qc ? QUANTITY_QC : QUANTITY_REGULAR))
     204          // Must have at least 1.1µg or 1.22µg
     205          var remainLimit = rna.qc ? QUANTITY_QC : QUANTITY_REGULAR;
     206          if (info.remainingQuantity < remainLimit)
     207          {
     208            if (!warningMsg) warningMsg = 'Low quantity';
     209          }
     210          // Warning if near the limit
     211          if (info.remainingQuantity < remainLimit *  LOW_QUANTITY_WARNING_FACTOR)
    204212          {
    205213            if (!warningMsg) warningMsg = 'Low quantity';
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