Changeset 4981

Timestamp:

Sep 25, 2018, 2:11:48 PM (4 years ago)

Author:

Nicklas Nordborg

Message:

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

Added an option to keep an alignment that was marked as DoNotUse available for future genotype checks (eg. QC_GENOTYPE_STATUS=Checked instead of QC_GENOTYPE_STATUS=Disabled).

For example, if we have a QiaCube shift on positions 8-12, a verified RNA on position 6 but no information about the RNA at position 7 (and no remaining specimen) we can mark it as DoNotUse but keep it enabled for genotype checks in case we get a second sample from the same patient in the future.

Note that there is no possibility yet to change the DoNotUse to OkToUse if the second sample confirms that the original sample was correct.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/flaggedalignment/search.js (modified) (12 diffs)
• src/net/sf/basedb/reggie/servlet/GenotypeServlet.java (modified) (4 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>';
+      // Note! "mode-resolve" columns here to get the same order for grouping
+      html += '<th class="mode-resolve dottedleft">Ok</th>';
+      html += '<th class="mode-resolve">DoNotUse</th>';
+      html += '<th class="mode-resolve">FutureGT</th>';
       html += '<th class="mode-resolve comment-col">Comment</th>';
 
@@ -536 +538 @@
           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>';
+          html += '<td rowspan="'+tbodySpan+'" class="mode-resolve dottedleft">'+(sp ? HTMLHelper.okToUseOptions(aligned, filterType) : '')+'</td>';
+          html += '<td rowspan="'+tbodySpan+'" class="mode-resolve">'+(sp ? HTMLHelper.resolveOptions(aligned, filterType) : '')+'</td>';
+          html += '<td rowspan="'+tbodySpan+'" class="mode-resolve">'+(sp ? HTMLHelper.futureGtOptions(aligned, filterType) : '')+'</td>';
           html += '<td rowspan="'+tbodySpan+'" class="mode-resolve comment-col dottedright">'+(sp ? HTMLHelper.resolveComment(aligned) : '')+'</td>';
         }
@@ -850 +854 @@
     var tmpId = event.currentTarget.id.replace('oktouse.', '');
     var doNotUseList = Doc.element('donotuse.'+tmpId);
+    var futureGtCheck = Doc.element('futuregt.'+tmpId);
     var commentField = Doc.element('resolvecomment.'+tmpId);
     if (event.currentTarget.checked)
@@ -857 +862 @@
       Doc.removeClass(commentField, 'required');
       doNotUseList.disabled = true;
+      futureGtCheck.disabled = true;
     }
     else
@@ -871 +877 @@
     var tmpId = event.currentTarget.id.replace('donotuse.', '');
     var value = event.currentTarget.value;    
+    var futureGtCheck = Doc.element('futuregt.'+tmpId);
+    futureGtCheck.disabled = value == '';
     var commentField = Doc.element('resolvecomment.'+tmpId);
     Doc.addOrRemoveClass(commentField, 'required', value != '');
@@ -935 +943 @@
     {
       var img = bugIcons[alignment.buglevel];
-      var imgTitle = alignment.buglevel > 0 && alignment.bugText.length > 0 ? alignment.bugText[0] : '';
+      // .replace will strip simple HTML tags
+      var imgTitle = alignment.buglevel > 0 && alignment.bugText.length > 0 ? alignment.bugText[0].replace(/<\/?[^>]+(>|$)/g, '') : '';
       icons += '<img src="../images/'+img+'" title="'+imgTitle+'">';
     }
@@ -1116 +1125 @@
       var okToUse = Doc.element('oktouse.'+aligned.tmpId);
       var doNotUse = Doc.element('donotuse.'+aligned.tmpId);
+      var futureGt = Doc.element('futuregt.'+aligned.tmpId);
       var comment = Doc.element('resolvecomment.'+aligned.tmpId);
       
@@ -1153 +1163 @@
           Doc.addClass('section.'+aligned.tmpId, 'invalid');
           numInvalid++;
+        }
+        if (doNotUse.value && futureGt)
+        {
+          item.futureGt = futureGt.checked;
         }
       }
@@ -1551 +1565 @@
   }
 
+  helper.okToUseOptions = function(aligned, filterType)
+  {
+    var html = '';
+    if (aligned.flagged && !aligned.DO_NOT_USE) 
+    {
+      var idOkToUse = 'oktouse.'+aligned.tmpId;
+      var okValue = filterType == 'QIACUBE' ? 'ok-rna' : 'ok-library';
+      html += '<input type="checkbox" value="'+okValue+'" id="'+idOkToUse+'" name="'+idOkToUse+'" class="oktouse" title="Check this to indicate that the flagged item is ok to use.">';
+    }
+    return html;
+  }
+  
   /**
     We generate a checkbox (if the item is flagged) and a 
@@ -1560 +1586 @@
     if (aligned.DO_NOT_USE) 
     {
-      html += '<input type="checkbox" style="visibility: hidden;">';
       html += aligned.DO_NOT_USE;
     }
@@ -1566 +1591 @@
     {
       var idDoNotUse = 'donotuse.'+aligned.tmpId;
-      var idOkToUse = 'oktouse.'+aligned.tmpId;
       var cls = aligned.flagged && filterType != 'HET' ? 'required' : '';
-  
-      if (aligned.flagged)
-      {
-        var okValue = filterType == 'QIACUBE' ? 'ok-rna' : 'ok-library';
-        html += '<input type="checkbox" value="'+okValue+'" id="'+idOkToUse+'" name="'+idOkToUse+'" class="oktouse" title="Check this to indicate that the flagged item is ok to use.">';
-      }
-      else
-      {
-        // Dummy checkbox that is hidden. Used to make the selection lists align
-        html += '<input type="checkbox" style="visibility: hidden;">';
-      }
-      
+    
       html += '<select id="'+idDoNotUse+'" name="'+idDoNotUse+'" class="donotuse-options '+cls+'">';
       html += '<option value="">&nbsp;';
@@ -1594 +1607 @@
     return html;
   }
+  
+  helper.futureGtOptions = function(aligned, filterType)
+  {
+    var html = '';
+    if (!aligned.DO_NOT_USE) 
+    {
+      var idFutureGt = 'futuregt.'+aligned.tmpId;
+      html += '<input type="checkbox" id="'+idFutureGt+'" name="'+idFutureGt+'" disabled title="Check this to use the alignment in future genotype checks.">';
+    }
+    return html;
+  }
+
 
   helper.resolveComment = function(aligned)

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

@@ -531 +531 @@
         int numUnflagged = 0;
         int numDisabled = 0;
+        int numFutureGt = 0;
         int numOkToUse = 0;
         int numAutoUnflagged = 0;
@@ -546 +547 @@
           String doNotUse = (String)jsonItem.get("doNotUse");
           boolean okToUse = Boolean.TRUE.equals(jsonItem.get("okToUse"));
+          boolean futureGt = Boolean.TRUE.equals(jsonItem.get("futureGt"));
           String comment = (String)jsonItem.get("comment");
           
@@ -646 +648 @@
                 if (doNotUse != null)
                 {
-                  Annotationtype.QC_GENOTYPE_STATUS.setAnnotationValue(dc, dba, "Disabled");
-                  jsonDebug.add("[Debug]Disabled: " + basicItem);
-                  numDisabled++;
+                  if (futureGt)
+                  {
+                    Annotationtype.QC_GENOTYPE_STATUS.setAnnotationValue(dc, dba, "Checked");
+                    jsonDebug.add("[Debug]FutureGT: " + basicItem);
+                    numFutureGt++;
+                  }
+                  else
+                  {
+                    Annotationtype.QC_GENOTYPE_STATUS.setAnnotationValue(dc, dba, "Disabled");
+                    jsonDebug.add("[Debug]Disabled: " + basicItem);
+                    numDisabled++;
+                  }
                 }
                 else if (okToUse)
@@ -713 +724 @@
         }
         
-        if (numDisabled > 0)
-        {
-          jsonMessages.add(countMessage(numDisabled, "alignment has", "alignments have") + " been disabled for future genotype checks.");
+        if (numDisabled > 0 || numFutureGt > 0)
+        {
+          StringBuilder msg = new StringBuilder();
+          if (numDisabled > 0)
+          {
+            msg.append(countMessage(numDisabled, "alignment has", "alignments have")).append(" been disabled");
+          }
+          if (numFutureGt > 0)
+          {
+            if (msg.length() > 0) msg.append(" and ");
+            msg.append(countMessage(numFutureGt, "alignment has", "alignments have")).append(" been retained");
+          }
+          msg.append(" for future genotype checks.");
+          jsonMessages.add(msg.toString());
         }