Changeset 1951

Timestamp:

Apr 24, 2013, 11:13:27 AM (10 years ago)

Author:

Nicklas Nordborg

Message:

References #424: Select RNA items for library preparation

Add link to "Case summary" in the context menu in the "Select RNA" wizard and in the "Flagged RNA" dialog.

Add support for showing the "Case summary" as a popup window.

Location:

extensions/net.sf.basedb.reggie/trunk/resources

Files:

• libprep/select_rna.jsp (modified) (10 diffs)
• libprep/show_flagged_rna.jsp (modified) (3 diffs)
• reports/case_summary.jsp (modified) (3 diffs)

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

@@ -36 +36 @@
 
 <script language="JavaScript">
-var debug = true;
+var debug = false;
 
 var quantitiesAreValid = false;
@@ -193 +193 @@
       text += '<div class="name">'+rna.name+'</div>';
       
-      var warningMsg = null;
+      var warningMsg = [];
       if (info.bioWell)
       {
@@ -201 +201 @@
       else if (!rna.stratagene && !rna.external)
       {
-        if (!warningMsg) warningMsg = 'No location';
+        warningMsg[warningMsg.length] = 'No location';
       }
 
@@ -221 +221 @@
           if (info.remainingQuantity < LOW_QUANTITY_WARNING_LIMIT)
           {
-            if (!warningMsg) warningMsg = 'Low quantity';
+            warningMsg[warningMsg.length] = 'Low quantity';
           }
         }
         else
         {
-          if (!warningMsg) warningMsg = 'No quantity';
+          warningMsg[warningMsg.length] = 'No quantity';
         }
         if (info.rqs)
         {
           text += '<div class="quality-score">RQS='+Numbers.formatNumber(info.rqs, 1) + '</div>';
-          if (info.rqs < QUALITY_SCORE_WARNING_LIMIT && !warningMsg) warningMsg = 'Low RQS value';
+          if (info.rqs < QUALITY_SCORE_WARNING_LIMIT) warningMsg[warningMsg.length] = 'Low RQS value';
         }
         else if (info.rin)
         {
           text += '<div class="quality-score">RIN='+Numbers.formatNumber(info.rin, 1) + '</div>';
-          if (info.rin < QUALITY_SCORE_WARNING_LIMIT && !warningMsg) warningMsg = 'Low RIN value';
+          if (info.rin < QUALITY_SCORE_WARNING_LIMIT) warningMsg[warningMsg.length] = 'Low RIN value';
         }
         else
         {
-          if (!warningMsg) warningMsg = 'No RQS/RIN value';
+          warningMsg[warningMsg.length] = 'No RQS/RIN value';
         }
         if (info.NDConc)
@@ -249 +249 @@
         else
         {
-          if (!warningMsg) warningMsg = 'No NDConc value';
+          warningMsg[warningMsg.length] = 'No NDConc value';
         }
       }
@@ -264 +264 @@
         text += '<div class="comment">'+Main.encodeTags(info.comment)+'</div>';
       }
-      if (warningMsg)
+      if (warningMsg.length > 0)
       {
-        well.setWarning(warningMsg);
+        well.setWarning(warningMsg.join('; '));
       }
     }
@@ -1208 +1208 @@
 }
 
+var contextRNA = null;
 /**
   Reacts to 'mouseup' and 'contextmenu' events for the bioplate. 
@@ -1219 +1220 @@
   // Can't just check the button since two events are sent ('mouseup' and 'contextmenu')
   var showContext = event.type == 'contextmenu' && event.button == 2;
-  
+    
   if (showContext)
   {
     event.preventDefault(); // Prevents the default right-click menu from appearing
+    
+    // Get the well that is right-clicked and the RNA that is in it
+    contextRNA = null;
+    var well = event.target;
+    while (well && (!well.id || well.id.indexOf('well') != 0))
+    {
+      well = well.parentNode;
+    }
+    if (well)
+    {
+      var c = well.id.split(/\./);
+      contextRNA = Plate.getWell(parseInt(c[1]), parseInt(c[2])).extract;
+    }
+    // Update the context meny
+    var caseSummaryMenu = document.getElementById('mnuCaseSummary');
+    if (contextRNA)
+    {
+      caseSummaryMenu.title = 'Show case summary for ' + contextRNA.name;
+      Main.show('sepCaseSummary');
+      Main.show('mnuCaseSummary');
+    }
+    else
+    {
+      Main.hide('sepCaseSummary');
+      Main.hide('mnuCaseSummary');
+    }
+    
     var menu = document.getElementById('menuContext');
     // 1 pixel offset to avoid losing well focus outline
@@ -1232 +1260 @@
     setTimeout(showContextMenu, 100);
   }
+}
+
+function showCaseSummary()
+{
+  if (!contextRNA) return;
+  var caseName = contextRNA.name.substring(0, 7);
+  var url = '../reports/case_summary.jsp?ID=<%=ID%>&caseName='+encodeURIComponent(caseName);
+  url += '&pageType=popup';
+  Main.openPopup(url, 'CaseSummary'+caseName, 1000, 700);
 }
 
@@ -1649 +1686 @@
       title="Flag"
       icon="<%=home+"/images/flag.png"%>"
+    />
+    <m:menuseparator id="sepCaseSummary" />
+    <m:menuitem
+      id="mnuCaseSummary"
+      icon="<%=home+"/images/case_summary.png"%>"
+      onclick="showCaseSummary()"
+      tooltip="Show case summary"
+      title="Case summary&hellip;"
     />
   </m:menu>

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

@@ -40 +40 @@
   {
     var rna = flagged[i];
-    document.getElementById('rna.'+i).innerHTML = rna.name;
+    document.getElementById('rna.'+i).innerHTML = rna.name+'<img class="link case-summary" onclick="showCaseSummary(\''+rna.name+'\')" src="../images/case_summary.png">';
     if (rna.bioWell)
     {
@@ -102 +102 @@
   window.close();
 }
+
+function showCaseSummary(name)
+{
+  var caseName = name.substring(0, 7);
+  var url = '../reports/case_summary.jsp?ID=<%=ID%>&caseName='+encodeURIComponent(caseName);
+  url += '&pageType=popup';
+  Main.openPopup(url, 'CaseSummary'+caseName, 1000, 700);
+}
+
 </script>
 
@@ -109 +118 @@
   color: #C80000;
   font-weight: bold;
+}
+
+.case-summary
+{
+  padding-left: 4px;
 }
 </style>

extensions/net.sf.basedb.reggie/trunk/resources/reports/case_summary.jsp

@@ -59 +59 @@
   final String caseName = request.getParameter("caseName");
   final String pageType = Values.getString(request.getParameter("pageType"), "default");
-  boolean fullPage = "default".equals(pageType);
+  
+  boolean iframe = "iframe".equals(pageType);
+  boolean popup = "popup".equals(pageType);
+  boolean fullPage = !iframe && !popup;
 %>
 <base:page type="<%=pageType %>" >
@@ -579 +582 @@
 <base:body onload="init()">
   <div id="all-content">
-  <p:path style="<%=fullPage ? "" : "display: none;"%>"><p:pathelement id="path-reggie" clazz="noprint"
-    title="Reggie" href="<%="../index.jsp?ID="+ID%>"
-    /><p:pathelement id="path-case-summary" title="<%="Case summary - " + HTML.encodeTags(caseName)%>" 
-    /></p:path>
-
+  <%
+  if (fullPage)
+  {
+    %>
+    <p:path><p:pathelement id="path-reggie" clazz="noprint"
+      title="Reggie" href="<%="../index.jsp?ID="+ID%>"
+      /><p:pathelement id="path-case-summary" title="<%="Case summary - " + HTML.encodeTags(caseName)%>" 
+      /></p:path>
+    <%
+  }
+  else if (popup)
+  {
+    %>
+    <h1>Case summary - <%= HTML.encodeTags(caseName)%></h1>
+    <%
+  }
+  %>
   <div class="content">
   <form name="reggie" onsubmit="return false;">
   <%
-  if (fullPage)
+  if (fullPage || popup)
   {
     %>
@@ -975 +990 @@
   </div>
   </div>
+  <%
+  if (popup)
+  {
+    %>
+    <base:buttongroup subclass="dialogbuttons topborder" id="dialogbuttons">
+      <base:button onclick="window.close()" title="Close" />
+    </base:buttongroup>
+    <%
+  }
+  %>
 </base:body>
 </base:page>