Changeset 2089

Timestamp:

Oct 21, 2013, 9:02:52 AM (9 years ago)

Author:

Nicklas Nordborg

Message:

References #481: Register prepared flow cells

Replaces ReadString with SequencingCycles.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/libprep/flowcell_registration.jsp (modified) (11 diffs)
• src/net/sf/basedb/reggie/servlet/FlowCellServlet.java (modified) (2 diffs)

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

@@ -30 +30 @@
 <script language="JavaScript">
 
-var debug = true;
+var debug = 0;
 var currentStep = 1;
 
@@ -37 +37 @@
 var dateIsValid = [];
 var flowCellIdIsValid = [];
-var readStringIsValid = [];
+var sequencingCyclesIsValid = [];
 
 function init()
@@ -128 +128 @@
     {
       var fc = frm.flowcells[i].flowCell;
-      //Main.debug(fc.name + ':'+ fc.id + ':' + flowCellIsValid['fc.'+fc.id+'.id'] + ':' + flowCellIsValid['fc.'+fc.id+'.readString']);
       if (flowCellIdIsValid['fc-'+index+'.externalId'] != true) return false;
       if (dateIsValid['fc-'+index+'.clusterDate'] != true) return false;
@@ -157 +156 @@
     {
       var fc = frm.flowcells[i].flowCell;
-      //Main.debug(fc.name + ':'+ fc.id + ':' + flowCellIsValid['fc.'+fc.id+'.id'] + ':' + flowCellIsValid['fc.'+fc.id+'.readString']);
-      if (readStringIsValid['fc-'+index+'.readString'] != true) return false;
+      if (sequencingCyclesIsValid['fc-'+index+'.sequencingCycles'] != true) return false;
       index++;
     }
@@ -318 +316 @@
       var fc = frm.flowcells[i].flowCell;
       var prefix = 'fc-'+index;
-      setInnerHTML(prefix+'.name.s', fc.name);
-      setInnerHTML(prefix+'.externalId', '<b>ID:</b> ' + frm[prefix+'.externalId'].value);
-      frm[prefix+'.readString'].value = fc.ReadString;
-      readStringOnBlur(prefix+'.readString');
+      setInnerHTML(prefix+'.externalId', frm[prefix+'.externalId'].value);
+      document.getElementById(prefix+'.externalId').title = fc.name;
+      frm[prefix+'.sequencingCycles'].value = fc.SequencingCycles;
+      sequencingCyclesOnBlur(prefix+'.sequencingCycles');
       index++;
     }
@@ -492 +490 @@
 }
 
-function readStringOnBlur(readStringField)
-{
-  var frm = document.forms['reggie'];
-  
-  setInputStatus(readStringField, '', '');
-  readStringIsValid[readStringField] = false;
-  
-  var readString = frm[readStringField].value;
-  if (readString == '')
-  {
-    setInputStatus(readStringField, 'ReadString is a required value', 'invalid');
+function sequencingCyclesOnBlur(sequencingCyclesField)
+{
+  var frm = document.forms['reggie'];
+  
+  setInputStatus(sequencingCyclesField, '', '');
+  sequencingCyclesIsValid[sequencingCyclesField] = false;
+  
+  var sequencingCycles = frm[sequencingCyclesField].value;
+  if (sequencingCycles == '')
+  {
+    setInputStatus(sequencingCyclesField, 'Sequencing cycles is a required value', 'invalid');
     return;
   }
-  if (!readString.match(/^([YNIJ]\d+)+$/))
-  {
-    setInputStatus(readStringField, 'Not a valid ReadString value', 'invalid');
+  if (!sequencingCycles.match(/^\d+\-\d+\-\d+$/))
+  {
+    setInputStatus(sequencingCyclesField, 'Not a valid Sequencing cycles value', 'invalid');
     return;
   }
   
-  readStringIsValid[readStringField] = true;
-  setInputStatus(readStringField, '', 'valid');
+  sequencingCyclesIsValid[sequencingCyclesField] = true;
+  setInputStatus(sequencingCyclesField, '', 'valid');
 }
 
@@ -563 +561 @@
     {
       var fc = frm.flowcells[i].flowCell;
-      frm['fc-'+index+'.readString'].disabled = true;
+      frm['fc-'+index+'.sequencingCycles'].disabled = true;
       fc.externalId = frm['fc-'+index+'.externalId'].value;
       fc.clusterDate = frm['fc-'+index+'.clusterDate'].value;
@@ -570 +568 @@
       if (!failed)
       {
-        fc.ReadString = frm['fc-'+index+'.readString'].value;
+        fc.SequencingCycles = frm['fc-'+index+'.sequencingCycles'].value;
         fc.HiSeqPosition = Forms.getCheckedRadio(frm['fc-'+index+'.pos']).value;
       }
@@ -910 +908 @@
         <td class="prompt"></td>
         <td style="font-weight: bold;">HiSeq position</td>
-        <td style="font-weight: bold;">ReadString</td>
+        <td style="font-weight: bold;">Sequencing cycles</td>
         <td class="status"></td>
         <td class="help"></td>
       </tr>
+      <tr valign="top">
+        <td class="prompt"></td>
+        <td></td>
+        <td style="font-style: italic;">(Read 1 - Index - Read 2)</td>
+        <td class="status"></td>
+        <td class="help"></td>
+      </tr>
       <tr valign="top" class="fc-0">
-        <td class="subprompt"><span id="fc-0.name.s"></span></td>
+        <td class="subprompt"><span id="fc-0.externalId"></span></td>
         <td>&nbsp;
           <label><input type="radio" name="fc-0.pos" value="A" onclick="hiseqPosOnClick(0)" checked>A</label>
@@ -921 +926 @@
           <label><input type="radio" name="fc-0.pos" value="B" onclick="hiseqPosOnClick(0)">B</label>
         </td>
-        <td><input type="text" class="required" name="fc-0.readString" onblur="readStringOnBlur(this.name)"></td>
-        <td class="status" id="fc-0.readString.status"></td>
-        <td class="help"><span id="fc-0.readString.message" class="message"></span><span id="fc-0.externalId"></span></td>
+        <td><input type="text" class="required" name="fc-0.sequencingCycles" onblur="sequencingCyclesOnBlur(this.name)"></td>
+        <td class="status" id="fc-0.sequencingCycles.status"></td>
+        <td class="help"><span id="fc-0.sequencingCycles.message" class="message"></span></td>
       </tr>
       <tr valign="top" class="fc-1">
-        <td class="subprompt"><span id="fc-1.name.s"></span></td>
+        <td class="subprompt"><span id="fc-1.externalId"></span></td>
         <td>&nbsp;
           <label><input type="radio" name="fc-1.pos" value="A" onclick="hiseqPosOnClick(1)">A</label>
@@ -932 +937 @@
           <label><input type="radio" name="fc-1.pos" value="B" onclick="hiseqPosOnClick(1)" checked>B</label>
         </td>
-        <td><input type="text" class="required" name="fc-1.readString" onblur="readStringOnBlur(this.name)"></td>
-        <td class="status" id="fc-1.readString.status"></td>
-        <td class="help"><span id="fc-1.readString.message" class="message"></span><span id="fc-1.externalId"></span></td>
+        <td><input type="text" class="required" name="fc-1.sequencingCycles" onblur="sequencingCyclesOnBlur(this.name)"></td>
+        <td class="status" id="fc-1.sequencingCycles.status"></td>
+        <td class="help"><span id="fc-1.sequencingCycles.message" class="message"></span></td>
       </tr>
 

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

@@ -165 +165 @@
         for (FlowCell fc : flowCells)
         {
-          fc.loadAnnotations(dc, "ReadString", Annotationtype.READ_STRING, null);
+          fc.loadAnnotations(dc, "SequencingCycles", Annotationtype.SEQUENCING_CYCLES, null);
           fc.loadAnnotations(dc, "externalId", Annotationtype.FLOWCELL_ID, null);
           fc.setAnnotation("comments", fc.getPhysicalBioAssay().getDescription());
@@ -429 +429 @@
           {
             sequenceRun.addPhysicalBioAssay(flowCell);
-            Annotationtype.READ_STRING.setAnnotationValue(dc, flowCell, jsonFlowCell.get("ReadString"));
+            Annotationtype.SEQUENCING_CYCLES.setAnnotationValue(dc, flowCell, jsonFlowCell.get("SequencingCycles"));
             Annotationtype.HISEQ_POSITION.setAnnotationValue(dc, flowCell, jsonFlowCell.get("HiSeqPosition"));