Changeset 2031 for extensions/net.sf.basedb.reggie/trunk/resources/libprep/flowcell_registration.jsp

Timestamp:

Oct 1, 2013, 2:07:24 PM (9 years ago)

Author:

Nicklas Nordborg

Message:

References #481: Register prepared flow cells

Added fields for "FlowCellID", "ReadString?" and sequence start date/operator when registering flow cells. But so far, only some of the information is saved in the database.

Not sure if we should introduce a DERIVEDBIOASSAY to represent the sequencing already at this point. If so, it would make sense to register the start date and operator on this item instead of on the flow cells.

Failure to cluster a flow cell is also not handled vere well at the moment.

File:

• extensions/net.sf.basedb.reggie/trunk/resources/libprep/flowcell_registration.jsp (modified) (14 diffs)

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

@@ -34 +34 @@
 
 var dateIsValid = [];
+var flowCellIsValid = [];
 var commentsIsValid = false;
 
@@ -49 +50 @@
       var flowCell = flowCells[i];
       var option = new Option(flowCell.name, flowCell.id, i < 2);
-      option.comments = flowCell.comments;
+      option.flowCell = flowCell;
       frm.flowcells.options[frm.flowcells.length] = option;
     }
-    flowCellIsValid = true;
     setInputStatus('flowcells', '', 'valid');
     outcomeOnChange();
@@ -114 +114 @@
 function gotoStep2()
 {
-  var frm = document.forms['reggie']; 
+  var frm = document.forms['reggie'];
+  
+  var selectedFlowCells = [];
+  for (var i = 0; i < frm.flowcells.length; i++)
+  {
+    if (frm.flowcells[i].selected)
+    {
+      selectedFlowCells[selectedFlowCells.length] = frm.flowcells[i].flowCell;
+    }
+  }
+  
+  if (selectedFlowCells.length == 0)
+  {
+    setInputStatus('flowcells', 'Select at least 1 flow cell', 'invalid');
+    return;
+  }
+
+  
   frm.flowcells.disabled = true;
   frm.outcome[0].disabled = true;
   frm.outcome[1].disabled = true;
 
-  
   currentStep = 2;
   Main.show('step.2.section');
@@ -127 +143 @@
   Main.show('goregister');
   
+  var html = '<tr valign="top">';
+  html += '<td class="prompt">Flow cell</td>';
+  html += '<td style="width: 11em;"><b>ID</b></td>';
+  html += '<td><b>ReadString</b></td>';
+  html += '<td class="status"></td>';
+  html += '<td class="help" rowspan="' + (selectedFlowCells.length+1) +'">';
+  html += 'ID and ReadString is required for registration. ';
+  html += 'ReadString must be a sequence of letters <b>Y</b>, <b>N</b>, <b>I</b>, <b>J</b> followed by digits.';
+  html += '</td>';
+  html += '</tr>';
+  
+  for (var i = 0; i < selectedFlowCells.length; i++)
+  {
+    var fc = selectedFlowCells[i];
+    var prefix = 'fc.'+fc.id;
+    html += '<tr>';
+    html += '<td class="subprompt">'+fc.name+'</td>';
+    html += '<td><input type="text" class="required" name="'+prefix+'.id" onblur="flowCellIdOnBlur('+fc.id+')"></td>';
+    html += '<td><input type="text" class="required" name="'+prefix+'.readString" onblur="readStringOnBlur('+fc.id+')" value="'+fc.ReadString+'"></td>';
+    html += '<td class="status" id="'+prefix+'.status">';
+    html += '</tr>';
+  }
+  
+  setInnerHTML('fc-data', html);
+  
   // Load mRNA protocols
   var clusterProtocols = getProtocols('CLUSTER_PROTOCOL');
@@ -140 +181 @@
   }
 
-  frm.clusterDate.focus();
+  frm['fc.'+selectedFlowCells[0].id+'.id'].focus();
 }
 
@@ -228 +269 @@
 }
 
+function flowCellIdOnBlur(flowCellId)
+{
+  checkFlowCellData(flowCellId);
+}
+
+function readStringOnBlur(flowCellId)
+{
+  checkFlowCellData(flowCellId);
+}
+
+function checkFlowCellData(flowCellId)
+{
+  var frm = document.forms['reggie'];
+    
+  var prefix = 'fc.'+flowCellId;
+  setInputStatus(prefix, '', '');
+  
+  flowCellIsValid[prefix+'.id'] = false;
+  flowCellIsValid[prefix+'.readString'] = false;
+  
+  var id = frm[prefix+'.id'].value;
+  if (id == '')
+  {
+    setInputStatus(prefix, 'ID is a required value', 'invalid');
+    return;
+  }
+  
+  flowCellIsValid[prefix+'.id'] = true;
+  
+  var readString = frm[prefix+'.readString'].value;
+  if (readString == '')
+  {
+    setInputStatus(prefix, 'ReadString is a required value', 'invalid');
+    return;
+  }
+
+  if (!readString.match(/^([YNIJ]\d+)+$/))
+  {
+    setInputStatus(prefix, 'Not a valid ReadString value', 'invalid');
+    return;
+  }
+  
+  flowCellIsValid[prefix+'.readString'] = true;
+  setInputStatus(prefix, '', 'valid');
+}
+
 function step2IsValid()
 {
@@ -233 +320 @@
   
   if (dateIsValid['clusterDate'] == false) return false;
+  if (dateIsValid['sequenceStartDate'] == false) return false;
+  
+  var frm = document.forms['reggie'];
+  for (var i = 0; i < frm.flowcells.length; i++)
+  {
+    if (frm.flowcells[i].selected)
+    {
+      var fc = frm.flowcells[i].flowCell;
+      Main.debug(fc.name + ':'+ fc.id + ':' + flowCellIsValid['fc.'+fc.id+'.id'] + ':' + flowCellIsValid['fc.'+fc.id+'.readString']);
+      if (flowCellIsValid['fc.'+fc.id+'.id'] != true) return false;
+      if (flowCellIsValid['fc.'+fc.id+'.readString'] != true) return false;
+    }
+  }
   
   return true;
@@ -240 +340 @@
 {
   if (!step2IsValid()) return;
-
   var frm = document.forms['reggie'];
   
@@ -249 +348 @@
   frm.clusterDate.disabled = true;
   frm.clusterOperator.disabled = true;
+  frm.sequenceStartDate.disabled = true;
+  frm.sequenceOperator.disabled = true;
   frm.clusterProtocol.disabled = true;
   frm.comments.disabled = true;
@@ -256 +357 @@
   for (var i = 0; i < frm.flowcells.length; i++)
   {
-    if (frm.flowcells[i].selected) submitInfo.flowCells[submitInfo.flowCells.length] = parseInt(frm.flowcells[i].value);
+    if (frm.flowcells[i].selected) 
+    {
+      var fc = frm.flowcells[i].flowCell;
+      fc.externalId = frm['fc.'+fc.id+'.id'].value;
+      fc.ReadString = frm['fc.'+fc.id+'.readString'].value;
+      submitInfo.flowCells[submitInfo.flowCells.length] = fc;
+    }
   }
   
@@ -263 +370 @@
   submitInfo.clusterDate = frm.clusterDate.value;
   submitInfo.clusterOperator = frm.clusterOperator.value;
+  submitInfo.sequenceStartDate = frm.sequenceStartDate.value;
+  submitInfo.sequenceOperator = frm.sequenceOperator.value;
   submitInfo.comments = frm.comments.value;
   
@@ -390 +499 @@
     <td class="stepfields">
       <table>
+      <tbody id="fc-data"></tbody>
       <tr valign="top">
         <td class="prompt">Step</td>
@@ -395 +505 @@
         <td><b>Operator</b></td>
         <td class="status"></td>
-        <td class="help" rowspan="2">
-          <span id="mrnaDate.message" class="message" style="display: none;"></span>
-          Enter date and operator for each step in the clustering.
+        <td class="help" rowspan="3">
+          Enter date and operator for each step in the clustering and sequencing startup.
           (YYYYMMDD or MMDD)
         </td>
@@ -415 +524 @@
         <td>
           <input type="text" name="clusterOperator" value="<%=HTML.encodeTags(user.getName()) %>" 
+            style="width: 95%;" maxlength="255" onkeypress="focusOnEnter(event, 'sequenceStartDate')">
+        </td>
+        <td class="status" id="clusterDate.status"></td>
+      </tr>
+      <tr>
+        <td class="subprompt">Sequence start</td>
+        <td>
+          <input type="text" name="sequenceStartDate" maxlength="10" style="width: 8em;"
+            onblur="dateOnChange('sequenceStartDate')" onkeypress="focusOnEnter(event, 'sequenceOperator')">
+            <base:icon 
+              onclick="Dates.selectDate('Sequence start date', 'reggie', 'sequenceStartDate', 'setDate', 'yyyyMMdd')"
+              image="calendar.png" 
+              tooltip="Select a date from a calendar" 
+              tabindex="-1"
+            />
+        </td>
+        <td>
+          <input type="text" name="sequenceOperator" value="<%=HTML.encodeTags(user.getName()) %>" 
             style="width: 95%;" maxlength="255" onkeypress="focusOnEnter(event, 'clusterProtocol')">
         </td>
-        <td class="status" id="clusterDate.status"></td>
+        <td class="status" id="sequenceStartDate.status"></td>
       </tr>
       <tr valign="top">