Changeset 2087


Ignore:
Timestamp:
Oct 18, 2013, 1:42:49 PM (9 years ago)
Author:
Nicklas Nordborg
Message:

References #502 and #501. Renamed SequenceString to SequencingCycles since it should better describe what is stored in that annotation. Changes to the text in the registration interface and lab protocol as well.

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

Legend:

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

    r2085 r2087  
    703703      <table>
    704704      <tr valign="top">
    705         <td class="prompt">Number of reads</td>
     705        <td class="prompt">Sequencing cycles</td>
    706706        <td class="input">(planned)</td>
    707707        <td class="status"></td>
    708708        <td class="help" rowspan="4">
    709           Planned number of reads. The actual numbers used may be changed in the
     709          Planned number of sequencing cycles. The actual numbers used may be changed in the
    710710          registration wizard.<br>
    711711        </td>
  • extensions/net.sf.basedb.reggie/trunk/resources/libprep/flowcell_protocol2.jsp

    r2086 r2087  
    130130      setInnerHTML('flowCellName2.'+flowCellNo, flowCellName);       
    131131      setInnerHTML('flowCellDescription.'+flowCellNo, flowCell.description);       
    132       setInnerHTML('sequenceString.'+flowCellNo, flowCell.SequenceString);
     132      setInnerHTML('sequencingCycles.'+flowCellNo, flowCell.SequencingCycles);
    133133      setInnerHTML('flowCellId.'+flowCellNo, flowCell.externalId);
    134134      var flowCellLanes = flowCell['lanes'];
     
    351351    <th></th>
    352352    <th style="width: 20%; border-right: 0;">HiSeq position</th>
    353     <th>SequenceString (Read 1 - Index - Read 2)</th>
     353    <th>Sequencing cycles (Read 1 - Index - Read 2)</th>
    354354  </tr>
    355355
     
    363363      <th id="flowCellName2.<%=c%>" class="subprompt">Flowcell<%=c %></th>
    364364      <td><b><div class="colorbox"></div>A <div class="colorbox"></div>B</b></td>
    365       <td><div id="sequenceString.<%=c%>">SequenceString</div></td>
     365      <td><div id="sequencingCycles.<%=c%>"></div></td>
    366366    </tr>
    367367    <%
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/dao/Annotationtype.java

    r2085 r2087  
    589589
    590590  /**
    591     The "SequenceString" annotation, used for physical bioassays (FlowCell).
    592     @since 2.13
    593   */
    594   public static final Annotationtype SEQUENCE_STRING =
    595     new Annotationtype("SequenceString", Type.STRING, Item.PHYSICALBIOASSAY);
     591    The "SequencingCycles" annotation, used for physical bioassays (FlowCell).
     592    @since 2.13
     593  */
     594  public static final Annotationtype SEQUENCING_CYCLES =
     595    new Annotationtype("SequencingCycles", Type.STRING, Item.PHYSICALBIOASSAY);
    596596
    597597 
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/FlowCellServlet.java

    r2086 r2087  
    197197          fc.setAnnotation("description", physBA.getDescription());
    198198          fc.setAnnotation("numLanes", physBA.getSize());
    199           fc.loadAnnotations(dc, "SequenceString", Annotationtype.SEQUENCE_STRING, null);
     199          fc.loadAnnotations(dc, "SequencingCycles", Annotationtype.SEQUENCING_CYCLES, null);
    200200          fc.loadAnnotations(dc, "externalId", Annotationtype.FLOWCELL_ID, null);
    201201         
     
    258258        Number read2 = (Number)jsonReq.get("read2");
    259259        // Sequence string is concatenated: read1-index-read2
    260         String sequenceString = read1 + "-" + indexRead + "-" + read2;
     260        String sequencingCycles = read1 + "-" + indexRead + "-" + read2;
    261261           
    262262        dc = sc.newDbControl();
     
    277277          flowCell.setSize(jsonLanes.size());
    278278          dc.saveItem(flowCell);
    279           Annotationtype.SEQUENCE_STRING.setAnnotationValue(dc, flowCell, sequenceString);
     279          Annotationtype.SEQUENCING_CYCLES.setAnnotationValue(dc, flowCell, sequencingCycles);
    280280         
    281281          Map<Number, Extract> poolCache = new HashMap<Number, Extract>();
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/InstallServlet.java

    r2085 r2087  
    290290        jsonChecks.add(checkAnnotationType(dc, Annotationtype.CLUSTER_OPERATOR, 1, null, effectiveOptions, createIfMissing));
    291291        jsonChecks.add(checkAnnotationType(dc, Annotationtype.READ_STRING, 1, null, effectiveOptions, createIfMissing));
    292         jsonChecks.add(checkAnnotationType(dc, Annotationtype.SEQUENCE_STRING, 1, null, effectiveOptions, createIfMissing));
     292        jsonChecks.add(checkAnnotationType(dc, Annotationtype.SEQUENCING_CYCLES, 1, null, effectiveOptions, createIfMissing));
    293293        jsonChecks.add(checkAnnotationType(dc, Annotationtype.HISEQ_POSITION, 1,
    294294            new ValueOptions("A", "B"),
     
    375375        jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.FLOW_CELL, createIfMissing,
    376376            Annotationtype.FLOWCELL_ID, Annotationtype.CLUSTER_START, Annotationtype.CLUSTER_OPERATOR,
    377             Annotationtype.SEQUENCE_STRING, Annotationtype.READ_STRING, Annotationtype.HISEQ_POSITION,
     377            Annotationtype.SEQUENCING_CYCLES, Annotationtype.READ_STRING, Annotationtype.HISEQ_POSITION,
    378378            Annotationtype.PLATE_PROCESS_RESULT));
    379379       
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