Changeset 4976

Timestamp:

Sep 24, 2018, 8:37:21 AM (5 years ago)

Author:

Nicklas Nordborg

Message:

References #1054: Even more functionality in the Flagged alignment wizard

Added an indicator for re-processing that is enabled if there is no other alignment for the same specimen. Alignments from the same RNA (if a Qiacube filter is active) or library (if HET filter or libplate filter is active) are not counted as a separate alignment.

When the High HET filter is active there is also an indicator for DoNotUse that is active if there is another alignement without an "error" condition.

Location:

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

Files:

• search.js (modified) (7 diffs)
• search.jsp (modified) (3 diffs)

extensions/net.sf.basedb.reggie/trunk/resources/flaggedalignment/search.js

@@ -442 +442 @@
       html += '<th class="mode-reprocess num-col">RNA<br>(µg)</th>';
       html += '<th class="mode-reprocess" id="reprocess-header">Re-process</th>';
+      // Note! Two "mode-resolve" columns here to get the same order for grouping
+      html += '<th class="mode-resolve dottedleft">Ok / Do not use?</th>';
+      html += '<th class="mode-resolve comment-col">Comment</th>';
+
       html += '<th class="mode-reprocess comment-col">Comment</th>';
       html += '<th class="mode-reprocess flag-col dottedright">Flag</th>';
-      
-      html += '<th class="mode-resolve dottedleft">Ok / Do not use?</th>';
-      html += '<th class="mode-resolve comment-col">Comment</th>';
     }
     html += '<th></th>';
@@ -467 +468 @@
       var lys = aligned.lysate;
       var sp = aligned.specimen;
+      var recommendReprocess = false;
+      var recommendDoNotUse = false;
       
       var libPlate = lib ? lib.bioWell.bioPlate : null;
@@ -481 +484 @@
       else
       {
-        html += '<tbody class="highlight" id="section.'+aligned.tmpId+'"><tr>';
+        // Try to give a re-process recommendation based on the assumption that the
+        // current alignment is incorrect. We look for other alignments from the same
+        // patient and specimen but with either a different RNA or Library
+        if (filter && aligned.flagged && !aligned.QC_GENOTYPE_VERIFIED && sp)
+        {
+          recommendReprocess = true; 
+          var otherAlignments = alignmentsByPat[sp.patientName];
+          for (var otherNo = 0; otherNo < otherAlignments.length; otherNo++)
+          {
+            var otherA = otherAlignments[otherNo];        
+            if (otherA.bugged && otherA.buglevel > 0) continue; // Ignore items that we "know" to be incorrect
+            
+            var sameLib = otherA.lib && otherA.lib.id == lib.id;
+            var sameRNA = otherA.rna && otherA.rna.id == rna.id;
+            var sameSp = otherA.specimen && otherA.specimen.id == sp.id;
+            if (sameSp)
+            {
+              if (!sameRNA && qiacubefilter || !sameLib && (libplatefilter || highHetFilter)) 
+              {
+                recommendReprocess = false;
+              }
+              if (!sameLib && highHetFilter) recommendDoNotUse = true;
+            }
+          }
+        }
+        
+        html += '<tbody class="highlight'+(recommendReprocess ? ' recommend-reprocess' : '')+(recommendDoNotUse ? ' recommend-donotuse' : '')+'" id="section.'+aligned.tmpId+'"><tr>';
         html += '<td rowspan="'+tbodySpan+'">'+(sp ? HTMLHelper.colorMatch(sp.patientName, null, 'Click to highlight this patient') : '')+'</td>';
         html += '<td rowspan="'+tbodySpan+'" class="'+(qiacubefilter?'':'mode-genotype')+'">'+(sp ? HTMLHelper.qiaCubeLink(rna.QIACUBE_DATE, rna.QIACUBE_RUN_NO, rna.QIACUBE_POSITION, qiacubefilter, false) : '')+'</td>';
@@ -505 +534 @@
           html += '<td rowspan="'+tbodySpan+'" class="mode-reprocess num-col">'+(lys ? Math.round(lys.remainingQuantity) : '')+'</td>';
           html += '<td rowspan="'+tbodySpan+'" class="mode-reprocess num-col">'+(sp ? Reggie.formatNumber(rna.remainingQuantity, null, 2, 2) : '')+'</td>';
-          html += '<td rowspan="'+tbodySpan+'" class="mode-reprocess">'+(sp ? HTMLHelper.reprocessOptions(aligned) : '')+'</td>';
+          html += '<td rowspan="'+tbodySpan+'" class="mode-reprocess">'+(sp ? HTMLHelper.reprocessOptions(aligned, recommendReprocess) : '')+'</td>';
 
           html += '<td rowspan="'+tbodySpan+'" class="mode-resolve dottedleft">'+(sp ? HTMLHelper.resolveOptions(aligned, filterType) : '')+'</td>';
@@ -703 +732 @@
         
         var otherA = alignmentByName[msg.alignment];
-        if (otherA.bugged && otherA.bugLevel > 0) continue; // The other alignment is a known problem, so we ignore it here
+        if (otherA.bugged && otherA.buglevel > 0) continue; // The other alignment is a known problem, so we ignore it here
         
         // If the other alignment is in the same context it may not be useful unless it is a verified alignment
@@ -1408 +1437 @@
   
   
-  helper.reprocessOptions = function(aligned)
+  helper.reprocessOptions = function(aligned, recommendReprocess)
   {
     var id = 'reprocess.'+aligned.tmpId;
+    var title = '';
+    
     var currentReProcess = null;
     if (aligned.specimen.AutoProcessing == 'ReProcess')
@@ -1426 +1457 @@
     
     var html = '';
-    html += '<select id="'+id+'" name="'+id+'">';
+    html += '<select id="'+id+'" name="'+id+'" '+(recommendReprocess? 'title="Re-processing is recommended"':'')+'>';
     if (!currentReProcess) html += '<option value="" selected>&nbsp;';
     html += '<option '+(currentReProcess=='Specimen'?'value="" selected':'value="specimen"')+'>Specimen';

extensions/net.sf.basedb.reggie/trunk/resources/flaggedalignment/search.jsp

@@ -189 +189 @@
 }
 
-td.mode-reprocess, td.mode-resolve
-{
-  background-color: #fffff0;
-}
-
-.mode-reprocess-header, .mode-resolve-header
-{
-  background-color: #fffff0;
+td.mode-reprocess
+{
+  background-color: #FFFFF0;
+}
+
+.mode-reprocess-header
+{
+  background-color: #FFFFF0;
   border-width: 1px;
   font-size: 120%;
 }
 
+.recommend-reprocess .mode-reprocess select
+{
+  border-right-width: 8px;
+  border-right-color: #2288AA;
+}
+
+td.mode-resolve
+{
+  background-color: #FFFFF0;
+}
+
+.mode-resolve-header
+{
+  background-color: #FFFFF0;
+  border-width: 1px;
+  font-size: 120%;
+}
+
+.recommend-donotuse .mode-resolve select
+{
+  border-right-width: 8px;
+  border-right-color: #2288AA;
+}
 </style>
 </base:head>
@@ -243 +266 @@
           <label><input type="radio" name="mode" id="mode-genotype" checked value="genotype">Genotype analysis</label>
           <label><input type="radio" name="mode" id="mode-reprocess" value="reprocess" disabled>Add comments and schedule re-processing</label>
-          <label><input type="radio" name="mode" id="mode-resolve" value="resolve" disabled>Resolve problems</label>
+          <label><input type="radio" name="mode" id="mode-resolve" value="resolve" disabled>Resolve as <b>DoNotUse</b> or <b>OkToUse</b></label>
         </td>
       </tr>
@@ -258 +281 @@
   <tr>
     <td><base:button id="gocancel" title="Cancel" /></td>
-    <td><base:button id="goreprocess" title="Register" image="<%=home+"/images/gonext.png"%>" /></td>
-    <td><base:button id="goresolve" title="Register" image="<%=home+"/images/gonext.png"%>" /></td>
+    <td><base:button id="goreprocess" title="Register re-processing" image="<%=home+"/images/gonext.png"%>" /></td>
+    <td><base:button id="goresolve" title="Register resolutions" image="<%=home+"/images/gonext.png"%>" /></td>
     <td id="gonext-message" class="message"></td>
   </tr>