Changeset 2112

Timestamp:

Oct 30, 2013, 11:31:42 AM (9 years ago)

Author:

Nicklas Nordborg

Message:

References #501: Generate lab protocol for clustering

Added a section with used pools at the top of the protocol. Color coded the pools to make it easier to find the corresponding pools on the flow cells.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/libprep/flowcell_protocol2.jsp (modified) (7 diffs)
• src/net/sf/basedb/reggie/servlet/FlowCellServlet.java (modified) (1 diff)

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

@@ -66 +66 @@
   
   <script language="JavaScript">
-  var debug = false;
+  var debug = 0;
   var currentStep = 1;
+  
+  var COLORS = ['blue', 'green', 'yellow', 'red'];
+  var nextColor = 0;
   
   function init()
@@ -117 +120 @@
     var flowCellNo = -1;
     var flowCellNameList = '';
+    var poolColors = [];
+    var useDarker = false;
+    var numPools = 0;
+    var poolsRow = document.getElementById('all-pools');
     for (var index in flowCellInfoArray)
     {
@@ -135 +142 @@
       for (laneKey in flowCellLanes)
       {
-        var poolId = flowCellLanes[laneKey];
+        var poolName = flowCellLanes[laneKey];
+        var color = poolColors[poolName];
+        if (!color)
+        {
+          numPools++;
+          color = COLORS[nextColor] + (useDarker ? ' darker' : '');
+          poolColors[poolName] = color;
+          var td = document.createElement('td');
+          td.className = 'pool-legend ' + color;
+          td.innerHTML = poolName;
+          poolsRow.appendChild(td);
+          nextColor++;
+          if (nextColor == COLORS.length)
+          {
+            nextColor = 0;
+            useDarker = !useDarker;
+          }
+        }
         var row = laneKey - 1;
         var idSuffix = flowCellNo + '.' + row;
-        setInnerHTML('fcPoolName.'+idSuffix, poolId);       
+        Main.addClass(document.getElementById('fcPoolName.'+idSuffix), color);
+        setInnerHTML('fcPoolName.'+idSuffix, poolName);       
       }
     }
+
+    if (numPools <= 6)
+    {
+      var td = document.createElement('td');
+      td.innerHTML = '';
+      poolsRow.appendChild(td);
+    }
+    
     var pageTitle = 'Lab protocol for ' + flowCellNameList;
     setInnerHTML('pageTitle', pageTitle);       
@@ -161 +194 @@
     margin-bottom: 1em;
     border-collapse: collapse;
+  }
+  
+  table.flowcell
+  {
     min-height: 20em;
     height: 20em;
@@ -245 +282 @@
   {
     width: 8em;
-  }
+    text-align: center;
+  }
+  
+  .pool-legend
+  {
+    width: 8em;
+    text-align: center !important;
+  }
+  
+  .green
+  {
+    background-color: #D8F8D8;
+  }
+  .green.darker
+  {
+    background-color: #A0F8A0;
+  }
+  
+  .blue
+  {
+    background-color: #D8E8FF;
+  }
+  .blue.darker
+  {
+    background-color: #B8B8FF;
+  }
+  
+  .yellow
+  {
+    background-color: #FFFFD8;
+  }
+  .yellow.darker
+  {
+    background-color: #FFFFA0;
+  }
+  
+  .red
+  {
+    background-color: #FFC8C8;
+  }
+  .red.darker
+  {
+    background-color: #F8A0A0;
+  }
+
   
   </style>
@@ -270 +351 @@
   <div id="listviewcontainer" style="display: none;">
   
+  <table class="protocolheader">
+  <tr id="all-pools">
+    <th style="width: 15%;">Used pools</th>
+  </tr>
+  </table>
   
   <h2>1. Clustering</h2>
-  
   <%
   // Note: Variable 'c' here indicates a flow cell, not a table column
@@ -279 +364 @@
   {
     %>
-    <table style="width: 100%;" class="protocolheader">
+    <table style="width: 100%;" class="protocolheader flowcell">
     <tr>
       <th style="width: 15%;">Flow cell</th>

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

@@ -213 +213 @@
           for (BioMaterialEventSource eventSource : physBA.getCreationEvent().getEventSources().list(dc))
           {
-            Extract pool = (Extract)eventSource.getBioMaterial();
+            Extract poolAliquot = (Extract)eventSource.getBioMaterial();
+            Extract pool = (Extract)poolAliquot.getParent();
             jsonFlowCellLanes.put(eventSource.getPosition(), pool.getName());
           }