Changeset 2087

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:

• resources/libprep/create_flowcells.jsp (modified) (1 diff)
• resources/libprep/flowcell_protocol2.jsp (modified) (3 diffs)
• src/net/sf/basedb/reggie/dao/Annotationtype.java (modified) (1 diff)
• src/net/sf/basedb/reggie/servlet/FlowCellServlet.java (modified) (3 diffs)
• src/net/sf/basedb/reggie/servlet/InstallServlet.java (modified) (2 diffs)

extensions/net.sf.basedb.reggie/trunk/resources/libprep/create_flowcells.jsp

@@ -703 +703 @@
       <table>
       <tr valign="top">
-        <td class="prompt">Number of reads</td>
+        <td class="prompt">Sequencing cycles</td>
         <td class="input">(planned)</td>
         <td class="status"></td>
         <td class="help" rowspan="4">
-          Planned number of reads. The actual numbers used may be changed in the
+          Planned number of sequencing cycles. The actual numbers used may be changed in the
           registration wizard.<br>
         </td>

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

@@ -130 +130 @@
       setInnerHTML('flowCellName2.'+flowCellNo, flowCellName);        
       setInnerHTML('flowCellDescription.'+flowCellNo, flowCell.description);        
-      setInnerHTML('sequenceString.'+flowCellNo, flowCell.SequenceString);
+      setInnerHTML('sequencingCycles.'+flowCellNo, flowCell.SequencingCycles);
       setInnerHTML('flowCellId.'+flowCellNo, flowCell.externalId);
       var flowCellLanes = flowCell['lanes'];
@@ -351 +351 @@
     <th></th>
     <th style="width: 20%; border-right: 0;">HiSeq position</th>
-    <th>SequenceString (Read 1 - Index - Read 2)</th>
+    <th>Sequencing cycles (Read 1 - Index - Read 2)</th>
   </tr>
 
@@ -363 +363 @@
       <th id="flowCellName2.<%=c%>" class="subprompt">Flowcell<%=c %></th>
       <td><b><div class="colorbox"></div>A <div class="colorbox"></div>B</b></td>
-      <td><div id="sequenceString.<%=c%>">SequenceString</div></td>
+      <td><div id="sequencingCycles.<%=c%>"></div></td>
     </tr>
     <%

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/dao/Annotationtype.java

@@ -589 +589 @@
 
   /**
-    The "SequenceString" annotation, used for physical bioassays (FlowCell).
-    @since 2.13
-  */
-  public static final Annotationtype SEQUENCE_STRING = 
-    new Annotationtype("SequenceString", Type.STRING, Item.PHYSICALBIOASSAY);
+    The "SequencingCycles" annotation, used for physical bioassays (FlowCell).
+    @since 2.13
+  */
+  public static final Annotationtype SEQUENCING_CYCLES = 
+    new Annotationtype("SequencingCycles", Type.STRING, Item.PHYSICALBIOASSAY);
 
   

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/FlowCellServlet.java

@@ -197 +197 @@
           fc.setAnnotation("description", physBA.getDescription());
           fc.setAnnotation("numLanes", physBA.getSize());
-          fc.loadAnnotations(dc, "SequenceString", Annotationtype.SEQUENCE_STRING, null);
+          fc.loadAnnotations(dc, "SequencingCycles", Annotationtype.SEQUENCING_CYCLES, null);
           fc.loadAnnotations(dc, "externalId", Annotationtype.FLOWCELL_ID, null);
           
@@ -258 +258 @@
         Number read2 = (Number)jsonReq.get("read2");
         // Sequence string is concatenated: read1-index-read2
-        String sequenceString = read1 + "-" + indexRead + "-" + read2;
+        String sequencingCycles = read1 + "-" + indexRead + "-" + read2;
             
         dc = sc.newDbControl();
@@ -277 +277 @@
           flowCell.setSize(jsonLanes.size());
           dc.saveItem(flowCell);
-          Annotationtype.SEQUENCE_STRING.setAnnotationValue(dc, flowCell, sequenceString);
+          Annotationtype.SEQUENCING_CYCLES.setAnnotationValue(dc, flowCell, sequencingCycles);
           
           Map<Number, Extract> poolCache = new HashMap<Number, Extract>();

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/InstallServlet.java

@@ -290 +290 @@
         jsonChecks.add(checkAnnotationType(dc, Annotationtype.CLUSTER_OPERATOR, 1, null, effectiveOptions, createIfMissing));
         jsonChecks.add(checkAnnotationType(dc, Annotationtype.READ_STRING, 1, null, effectiveOptions, createIfMissing));
-        jsonChecks.add(checkAnnotationType(dc, Annotationtype.SEQUENCE_STRING, 1, null, effectiveOptions, createIfMissing));
+        jsonChecks.add(checkAnnotationType(dc, Annotationtype.SEQUENCING_CYCLES, 1, null, effectiveOptions, createIfMissing));
         jsonChecks.add(checkAnnotationType(dc, Annotationtype.HISEQ_POSITION, 1, 
             new ValueOptions("A", "B"),
@@ -375 +375 @@
         jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.FLOW_CELL, createIfMissing, 
             Annotationtype.FLOWCELL_ID, Annotationtype.CLUSTER_START, Annotationtype.CLUSTER_OPERATOR,
-            Annotationtype.SEQUENCE_STRING, Annotationtype.READ_STRING, Annotationtype.HISEQ_POSITION,
+            Annotationtype.SEQUENCING_CYCLES, Annotationtype.READ_STRING, Annotationtype.HISEQ_POSITION,
             Annotationtype.PLATE_PROCESS_RESULT));