Changeset 1898


Ignore:
Timestamp:
Mar 7, 2013, 9:41:48 AM (7 years ago)
Author:
Nicklas Nordborg
Message:

References #425: Generate a lab protocol for RNA -> cDNA processing

Added possibility to register an 'externalId' and 'NDConc' annotation on external mRNA items which will then be used in the lab protocols. The registration has to be done using the regular BASE interface after the mRNA plate has been created.

IMPORTANT! Do not change the 'name' on external items since then they will not be recognized as external anymore.

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

Legend:

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

    r1894 r1898  
    252252  #listview tr.evencol
    253253  {
    254     background-color: #E8E8E8;
     254    background-color: #F0F0F0;
    255255  }
    256256 
     
    258258  {
    259259    border: 1px solid #000000;
    260     background-color: #E8E8E8;
     260    background-color: #F0F0F0;
    261261  }
    262262 
  • extensions/net.sf.basedb.reggie/trunk/resources/libprep/mrna_protocol2.jsp

    r1892 r1898  
    142142    {
    143143      %>
    144       if (rna.stratagene) rna.NDConc = <%=stratageneConc%>;
     144      if (rna.stratagene && !rna.NDConc) rna.NDConc = <%=stratageneConc%>;
    145145      <%
    146146    }
     
    197197      var mrna = list[i];
    198198      var rna = mrna.rna;
     199      var idSuffix = mrna.bioWell.column + '.' + mrna.bioWell.row;
     200      var tableRow = document.getElementById('row.'+idSuffix);
    199201     
    200       var idSuffix = mrna.bioWell.column + '.' + mrna.bioWell.row;
    201       Main.removeClass(document.getElementById('row.'+idSuffix), 'empty');
    202       setInnerHTML('rna.'+idSuffix, rna.name);
     202      Main.removeClass(tableRow, 'empty');
     203      if (rna.external) Main.addClass(tableRow, 'external');
     204      if (rna.stratagene) Main.addClass(tableRow, 'stratagene');
     205      setInnerHTML('rna.'+idSuffix, rna.external && mrna.externalId ? mrna.externalId : rna.name);
    203206      setInnerHTML('box.'+idSuffix, getPlateCoordinate(rna.bioWell, true));
    204207      setInnerHTML('ndconc.'+idSuffix, Numbers.formatNumber(rna.NDConc, 2));
     
    238241      if (mrna)
    239242      {
    240         if (mrna.rna.qc) cls += ' qc';
     243        var rna = mrna.rna;
     244        if (rna.qc) cls += ' qc';
     245        if (rna.external) cls += ' external';
     246        if (rna.stratagene)cls += ' stratagene';
    241247      }
    242248      return cls;
     
    250256      {
    251257        var rna = mrna.rna;
    252         text += '<div class="rna">'+rna.name+'</div>';
     258        var name = rna.external && mrna.externalId ? mrna.externalId : rna.name;
     259        text += '<div class="rna">'+name+'</div>';
    253260        text += '<div class="box">'+getPlateCoordinate(rna.bioWell, true)+'</div>';
    254261        text += '<div class="remain">'+Numbers.formatNumber(rna.remainingQuantity, 2, 'µg')+'</div>';
     
    296303  #listview tr.evencol
    297304  {
    298     background-color: #E8E8E8;
     305    background-color: #F0F0F0;
    299306  }
    300307 
     
    302309  {
    303310    border: 1px solid #000000;
    304     background-color: #E8E8E8;
     311    background-color: #F0F0F0;
    305312  }
    306313 
     
    344351    color: #666666;
    345352    text-align: center;
     353  }
     354 
     355  .external .rna:before, .stratagene .rna:before
     356  {
     357    content: '[';
     358  }
     359  .external .rna:after, .stratagene .rna:after
     360  {
     361    content: ']';
    346362  }
    347363 
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/dao/MRna.java

    r1867 r1898  
    6363    super.initJSON(json);
    6464    if (jsonWell != null) json.put("bioWell", jsonWell);
    65    
     65    json.put("externalId", getExtract().getExternalId());
    6666  }
    6767
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/MRnaServlet.java

    r1890 r1898  
    258258          Rna rna = r.getRna();
    259259          rna.loadBioPlateLocation();
    260           rna.loadAnnotations(dc, "NDConc", Annotationtype.ND_CONC, null);
     260
     261          if (Rna.isSpecialRna(r.getName()))
     262          {
     263            // Makes it possible to track some info about external RNA in reggie
     264            rna.setAnnotation("NDConc", Annotationtype.ND_CONC.getAnnotationValue(dc, r.getExtract()));
     265          }
     266          else
     267          {
     268            rna.loadAnnotations(dc, "NDConc", Annotationtype.ND_CONC, null);
     269          }
    261270         
    262271          Float used = r.getItem().getCreationEvent().getUsedQuantity(rna.getItem());
     
    386395          mRna.setItemSubtype(mRnaType);
    387396          mRna.setDescription((String)jsonRna.get("comment"));
    388          
     397                 
    389398          int childNum;
    390399          if (childCount.containsKey(rna))
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