Changeset 1792

Timestamp:

Dec 17, 2012, 3:08:17 PM (11 years ago)

Author:

Nicklas Nordborg

Message:

References #424, #425 and #436. Added a 'comments' field on the mRNA plate design wizard. The comment is included in the lab protocol and in the final mRNA registration wizard.

Location:

extensions/net.sf.basedb.reggie/branches/ticket-422

Files:

• resources/css/printable.css (modified) (5 diffs)
• resources/libprep/mrna_protocol.jsp (modified) (3 diffs)
• resources/libprep/mrna_protocol2.jsp (modified) (2 diffs)
• resources/libprep/mrna_registration.jsp (modified) (4 diffs)
• resources/libprep/select_rna.jsp (modified) (2 diffs)
• src/net/sf/basedb/reggie/servlet/MRnaServlet.java (modified) (3 diffs)

extensions/net.sf.basedb.reggie/branches/ticket-422/resources/css/printable.css

@@ -3 +3 @@
 @media print 
 {
+  body
+  {
+    width: 100%;
+    margin: 0;
+    padding: 0;
+  }
+  
   /* Start a new page on all elements with 'pagebreak' class */
   .pagebreak
@@ -18 +25 @@
 @media screen
 {
+  body
+  {
+    width: 210mm;
+    margin-left: 1em;
+    margin-right: 1em;
+  }
+  
   .pagebreak
   {
@@ -30 +44 @@
   body
   {
-    margin-left: 1em;
-    margin-right: 1em;
     font-family: verdana, arial, sans-serif;
     font-size: 75%;
+    padding: 0;
   }
   
@@ -39 +52 @@
   {
     font-size: 1.4em;
+    margin-top: 0;
   }
   
@@ -83 +97 @@
   }
   
+  .reggie
+  {
+    font-size: smaller;
+  }
+  
+  .reggie:before
+  {
+    content: "(";
+  }
+  .reggie:after
+  {
+    content: ")";
+  }
   
 }

extensions/net.sf.basedb.reggie/branches/ticket-422/resources/libprep/mrna_protocol.jsp

@@ -43 +43 @@
       var bioplate = bioplates[i];
       var option = new Option(bioplate.name, bioplate.id);
+      option.comments = bioplate.comments;
       plates.options[plates.length] = option;
     }
     bioplateIsValid = true;
     Main.show('gocreate');
+    bioPlateOnChange();
   }
   else
@@ -121 +123 @@
 }
 
+function bioPlateOnChange()
+{
+  var frm = document.forms['reggie'];
+  setInnerHTML('comments', frm.bioplate[frm.bioplate.selectedIndex].comments);
+}
 </script>
 
@@ -159 +166 @@
         <td class="prompt">mRNA bioplate</td>
         <td class="input"><select style="width:90%" 
-            name="bioplate" id="bioplate"></select>
+            name="bioplate" id="bioplate" onchange="bioPlateOnChange()"></select>
         </td>
         <td class="status" id="bioplate.status"></td>
-        <td class="help"><span id="bioplate.message" class="message" style="display: none;"></span>
+        <td class="help" rowspan="2"><span id="bioplate.message" class="message" style="display: none;"></span>
           Select an existing mRNA bioplate. The list contain all mRNA bioplates that
           has not yet been processed (determined by the absence of a 'creation' date).
         </td>
+      </tr>
+      <tr valign="top">
+        <td class="subprompt">-comments</td>
+        <td class="input" id="comments" style="font-style: italic; background: #E8E8E8; padding: 2px 5px 2px 5px;"></td>
+        <td class="status" id="comments.status"></td>
       </tr>
       <tr valign="top">

extensions/net.sf.basedb.reggie/branches/ticket-422/resources/libprep/mrna_protocol2.jsp

@@ -393 +393 @@
       <img src="../images/print.png">Print&hellip;
     </span>
+    <div>
+      <b>Note!</b> 
+      <%
+      if (view.equals("list"))
+      {
+        %>
+        For better printing reduce margins to about <i>5mm</i> and set page orientation
+        to <i>portrait</i>. To fit everything on a single page, scale down to <i>60-70%</i>.
+        <%
+      }
+      else
+      {
+        %>
+        For better printing reduce margins to about <i>5mm</i> and set page orientation
+        to <i>landscape</i>. The recommended scale is <i>100%</i>.
+        <%
+      }
+      %>
+    </div>
   </div>
   
-  <h1>Lab tracking protocol for mRNA and cDNA preparation</h1>
+  <h1>Lab tracking protocol for mRNA and cDNA preparation <span class="reggie">Reggie <%=reggie.getAbout().getVersion() %></span></h1>
 
   <table style="width: 100%; border: 0px;" class="protocolheader">
-  <tr>
-    <td colspan="2">Reggie <%=reggie.getAbout().getVersion() %></td>
+  <tr valign="top">
+    <th style="width: 30%;">Work plate: <%=HTML.encodeTags(plate.getName())%></th>
+    <th style="width: 20%; text-align: right;">Comments:&nbsp;</th>
+    <td rowspan="3"><%=HTML.encodeTags(plate.getDescription()) %></td>
   </tr>
   <tr>
-    <th>Work plate: <%=plate.getName()%></th>
+    <th style="width: 50%;" colspan="2">Date+operator for mRNA:</th>
   </tr>
   <tr>
-    <th style="width: 50%;">Date for mRNA fragmentation:</th>
-    <th style="width: 50%;">Operator:</th>
-  </tr>
-  <tr>
-    <th style="width: 50%;">Date for cDNA preparation:</th>
-    <th style="width: 50%;">Operator:</th>
+    <th style="width: 50%;" colspan="2">Date+operator for cDNA:</th>
   </tr>
   </table>
@@ -416 +432 @@
   <div class="loading" id="loading" style="display: none;"><table><tr><td><img src="../images/loading.gif"></td><td id="loading.msg">Please wait...</td></tr></table></div>
   <div class="messagecontainer error" id="errorMessage" style="display: none;"></div>
-
   <%
   if (view.equals("list"))

extensions/net.sf.basedb.reggie/branches/ticket-422/resources/libprep/mrna_registration.jsp

@@ -48 +48 @@
       var bioplate = bioplates[i];
       var option = new Option(bioplate.name, bioplate.id);
+      option.comments = bioplate.comments;
       plates.options[plates.length] = option;
     }
     bioplateIsValid = true;
     setInputStatus('bioplate', '', 'valid');
+    bioPlateOnChange();
   }
   else
@@ -130 +132 @@
 }
 
+function bioPlateOnChange()
+{
+  var frm = document.forms['reggie'];
+  frm.comments.value = frm.bioplate[frm.bioplate.selectedIndex].comments;
+}
 
 function browseOnClick(extension)
@@ -282 +289 @@
   <p:path><p:pathelement 
     title="Reggie" href="<%="../index.jsp?ID="+ID%>" 
-    /><p:pathelement title="Lab tracking protocol for mRNA and cDNA preparation" 
+    /><p:pathelement title="mRNA registration and quality control results" 
     /></p:path>
 
@@ -312 +319 @@
         <td class="prompt">mRNA bioplate</td>
         <td class="input"><select class="required" style="width:90%" 
-            name="bioplate" id="bioplate"></select>
+            name="bioplate" id="bioplate" onchange="bioPlateOnChange()"></select>
         </td>
         <td class="status" id="bioplate.status"></td>

extensions/net.sf.basedb.reggie/branches/ticket-422/resources/libprep/select_rna.jsp

@@ -1202 +1202 @@
   var plateInfo = {};
   submitInfo.bioplate = plateInfo;
+  var frm = document.forms['reggie'];
   
   plateInfo.name = Plate.name;
+  plateInfo.comments = frm.comments.value;
   plateInfo.wells = [];
 
@@ -1464 +1466 @@
         <td class="input" id="plateName"></td>
         <td class="help">Select RNA items to use for the new mRNA plate.</td>
+      </tr>
+      <tr valign="top">
+        <td class="prompt">Comments</td>
+        <td class="input">
+          <textarea rows="2" style="width: 90%;" name="comments" value=""></textarea>
+        </td>
+        <td class="help">Comments about the new mRNA plate.</td>
       </tr>
       <tr style="vertical-align: top;">

extensions/net.sf.basedb.reggie/branches/ticket-422/src/net/sf/basedb/reggie/servlet/MRnaServlet.java

@@ -101 +101 @@
         
         List<BioPlate> result = query.list(dc);
-        JSONArray jsonLists = new JSONArray();
+        JSONArray jsonPlates = new JSONArray();
         for (BioPlate plate: result)
         {
-          JSONObject jsonList = new JSONObject();
-          
-          jsonList.put("id", plate.getId());
-          jsonList.put("name", plate.getName());
-          
-          jsonLists.add(jsonList);
-        }
-        json.put("bioplates", jsonLists);
+          JSONObject jsonPlate = new JSONObject();
+          
+          jsonPlate.put("id", plate.getId());
+          jsonPlate.put("name", plate.getName());
+          jsonPlate.put("comments", plate.getDescription());
+          
+          jsonPlates.add(jsonPlate);
+        }
+        json.put("bioplates", jsonPlates);
       }
       else if ("AutoSelectRnaForMRna".equals(cmd))
@@ -294 +295 @@
         BioPlate mRnaPlate = BioPlate.getNew(dc, geometry, plateType);
         mRnaPlate.setName(plateName);
+        mRnaPlate.setDescription(Values.getStringOrNull((String)jsonPlate.get("comments")));
         dc.saveItem(mRnaPlate);
         
@@ -398 +400 @@
         
         // Comment about the plate
-        mrnaPlate.setDescription((String)jsonReq.get("comment"));
+        mrnaPlate.setDescription((String)jsonReq.get("comments"));
 
         // Flag so that it will not appear in the wizards next time