Changeset 1946

Timestamp:

Apr 19, 2013, 3:48:04 PM (10 years ago)

Author:

Nicklas Nordborg

Message:

References #424: Select RNA items for library preparation

Added support for manually flagging an RNA item.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/libprep/select_rna.jsp (modified) (10 diffs)
• resources/libprep/show_flagged_rna.jsp (modified) (4 diffs)
• src/net/sf/basedb/reggie/dao/Rna.java (modified) (1 diff)
• src/net/sf/basedb/reggie/servlet/InstallServlet.java (modified) (1 diff)
• src/net/sf/basedb/reggie/servlet/MRnaServlet.java (modified) (2 diffs)

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

@@ -145 +145 @@
     }
     return true;
+  }
+  
+  rna.flag = function(r, flag)
+  {
+    if (!r.info || r.info.flag) return false;
+    r.info.flag = flag;
+    flagged[flagged.length] = r.info;
   }
   
@@ -253 +260 @@
         text += '<div class="comment">'+Main.encodeTags(rna.comment)+'</div>';
       }
+      if (info && info.comment)
+      {
+        text += '<div class="comment">'+Main.encodeTags(info.comment)+'</div>';
+      }
       if (warningMsg)
       {
@@ -751 +762 @@
   Plate.paint(wells);
 }
+
+//Flag the selected RNA
+function flagSelected(flag)
+{
+  var wells = Plate.getSelected();
+  
+  if (wells.length == 0)
+  {
+    alert('No wells have been selected');
+    return;
+  }
+  
+  var comment = null;
+  if (flag == 'ManualFlag')
+  {
+    // Check if a comment has been set on any of the RNA
+    for (var i = 0; i < wells.length; i++)
+    {
+      var well = wells[i];
+      if (well.extract && well.extract.info) 
+      {
+        if (well.extract.info.comment) comment = well.extract.info.comment;
+      }
+    }
+    comment = prompt('Comment', comment || '');
+  }
+  
+  var count = 0;
+  for (var i = 0; i < wells.length; i++)
+  {
+    var well = wells[i];
+    var rna = well.extract;
+    if (rna && !rna.stratagene && !rna.external)
+    {
+      Rna.flag(rna, flag);
+      rna.info.comment = comment;
+      well.setExtract(null);
+      count++;
+    }
+    well.selected = false;
+  }
+  
+  updateNumFlaggedRna();
+  Plate.paint(wells);
+}
+
 
 /**
@@ -1157 +1214 @@
 {
   var frm = document.forms['reggie'];
-  var showContext = false;
-  
-  if (frm.contextMenu[0].checked)
-  {
-    // Context menu on 'right' mouse button
-    // Can't just check the button since two events are sent ('mouseup' and 'contextmenu')
-    showContext = event.type == 'contextmenu' && event.button == 2;
-  }
-  else
-  {
-    // Context menu on 'middle' mouse button
-    showContext = event.button == 1;
-  }
+  // Context menu on 'right' mouse button
+  // Can't just check the button since two events are sent ('mouseup' and 'contextmenu')
+  var showContext = event.type == 'contextmenu' && event.button == 2;
   
   if (showContext)
@@ -1258 +1305 @@
     tmp.id = rna.id;
     tmp.flag = rna.flag;
+    tmp.comment = rna.comment;
     flaggedRnaInfo[flaggedRnaInfo.length] = tmp;
   }
@@ -1338 +1386 @@
 
   var flagged = Rna.getFlagged();
-  Main.openPopup('show_flagged_rna.jsp?ID=<%=ID%>&numFlagged='+flagged.length+'&numSelected='+currentSelected.length, 'FlaggedRna', 700, 500);
+  Main.openPopup('show_flagged_rna.jsp?ID=<%=ID%>&numFlagged='+flagged.length+'&numSelected='+currentSelected.length, 'FlaggedRna', 800, 500);
 }
 
@@ -1539 +1587 @@
       tooltip="Add a comment to the selected wells"
     />
+    <m:menuitem 
+      title="Toggle QC" 
+      icon="<%=home+"/images/mrnaqc.png"%>" 
+      onclick="toggleQc()" 
+      tooltip="Select/deselect RNA for QC" 
+    />
     <m:menuseparator />
     <m:menuitem 
@@ -1565 +1619 @@
     />
     <m:menuseparator />
+    <m:submenu
+      subid="flagMenu"
+      title="Flag"
+      icon="<%=home+"/images/flag.png"%>"
+    />
+  </m:menu>
+
+  <m:menu
+    id="flagMenu"
+    style="display: none;"
+    >
     <m:menuitem 
-      title="Toggle QC" 
-      icon="<%=home+"/images/mrnaqc.png"%>" 
-      onclick="toggleQc()" 
-      tooltip="Select/deselect RNA for QC" 
+      title="LowQualityScore" 
+      onclick="flagSelected('LowQualityScore')"
+      tooltip="Flag the selected RNA"
+    />
+    <m:menuitem 
+      title="NotEnoughRemainingQuantity" 
+      onclick="flagSelected('NotEnoughRemainingQuantity')"
+      tooltip="Flag the selected RNA"
+    />
+    <m:menuitem 
+      title="Other..." 
+      onclick="flagSelected('ManualFlag')"
+      tooltip="Flag the selected RNA"
     />
   </m:menu>
@@ -1605 +1679 @@
         <td class="help">
           Select the Stratagene tube to use. If not known, the
-          generic <b>Stratagene.r</b> (last in the list) should be used.
+          generic <b>Stratagene.r</b> should be used.
         </td>
       </tr>
@@ -1653 +1727 @@
         <td class="status"></td>
         <td class="help">Toggles visiblity of the selected information inside each well on the plate.</td>
-      </tr>
-      <tr style="vertical-align: top;">
-        <td class="prompt">Context menu</td>
-        <td class="input">
-          <input type="radio" name="contextMenu" id="contextMenuRight" checked><label for="contextMenuRight">Right</label>
-          <input type="radio" name="contextMenu" id="contextMenuMiddle"><label for="contextMenuMiddle">Middle</label> mouse button<br>
-          <br>
-        </td>
-        <td class="status"></td>
-        <td class="help">Use the selected mouse button to display a context-menu when clicking on the plate.</td>
       </tr>
       </table>

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

@@ -48 +48 @@
     document.getElementById('remainingQuantity.'+i).innerHTML = rna.remainingQuantity;
     document.getElementById('qualityScore.'+i).innerHTML = rna.rqs || rna.rin;
+    document.getElementById('comment.'+i).innerHTML = rna.comment;
     document.getElementById('flag.'+i).innerHTML = rna.flag;
     if (rna.flag == 'NotEnoughRemainingQuantity')
@@ -56 +57 @@
     {
       makeBold('qualityScore.'+i)
+    }
+    else
+    {
+      makeBold('comment.'+i);
     }
     frm['use.'+i].rna = rna;
@@ -101 +106 @@
     <tbl:columndef id="remainingQuanity" title="Remaining (µg)" />
     <tbl:columndef id="qualityScore" title="RQS/RIN" />
+    <tbl:columndef id="comment" title="Comment" />
     <tbl:columndef id="flag" title="Flag" />
   
@@ -121 +127 @@
           <tbl:cell column="remainingQuanity" id="<%="remainingQuantity."+i%>"></tbl:cell>
           <tbl:cell column="qualityScore" id="<%="qualityScore."+i%>"></tbl:cell>
+          <tbl:cell column="comment" id="<%="comment."+i%>"></tbl:cell>
           <tbl:cell column="flag" id="<%="flag."+i%>"></tbl:cell>
         </tbl:row>

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/dao/Rna.java

@@ -47 +47 @@
   */
   public static final String FLAG_LOW_QUALITY_SCORE = "LowQualityScore";
+
+  /**
+    Flag value for the {@link Annotationtype#FLAG} annotation when a RNA
+    has been manually flagged for some other reason. The desription of
+    the RNA item should contain more information.
+    @since 2.12
+  */
+  public static final String FLAG_MANUAL = "ManualFlag";
   
   /**

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

@@ -233 +233 @@
         jsonChecks.add(checkAnnotationType(dc, Annotationtype.FLAG, 1, 
             new ValueOptions(Rna.FLAG_NOT_ENOUGH_REMAINING_QUANTITY, Rna.FLAG_LOW_QUALITY_SCORE,
+              Rna.FLAG_MANUAL,
               Rna.FLAG_MRNA_PLATE_FAILED, Rna.FLAG_CDNA_PLATE_FAILED, Rna.FLAG_LIB_PLATE_FAILED),
             effectiveOptions, createIfMissing));

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

@@ -243 +243 @@
           r.setAnnotation("remainingQuantity", r.getExtract().getRemainingQuantity());
           r.loadAnnotations(dc, "NDConc", Annotationtype.ND_CONC, null);
+          r.setAnnotation("comment", r.getExtract().getDescription());
           jsonRna.add(r.asJSONObject());
         }
@@ -460 +461 @@
             Number rnaId = (Number)jsonRna.get("id");
             Extract rna = Extract.getById(dc, rnaId.intValue());
+            rna.setDescription((String)jsonRna.get("comment"));
             
             // Safety check in case a flagged RNA is also on the plate