Changeset 3545

Timestamp:

Oct 16, 2015, 9:55:36 AM (7 years ago)

Author:

Nicklas Nordborg

Message:

References #818: Track volumes of RNAQC aliquots

Changes the default RNA volume in the 'DNA/RNA/FlowThrough registration' wizard to 53 (was 51).

The 'Create aliquots on Bioanalyzer/Caliper? plates' has been updated with input fields for the aliquot volumes. The default values are 2µl for normal, and 6µl for HiSense.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/sampleproc/extraction_registration.js (modified) (1 diff)
• resources/sampleproc/rnaqc_aliquot.js (modified) (13 diffs)
• src/net/sf/basedb/reggie/servlet/RnaQcServlet.java (modified) (2 diffs)

extensions/net.sf.basedb.reggie/trunk/resources/sampleproc/extraction_registration.js

@@ -36 +36 @@
   var DEFAULT_LYSATE_USED = 350;
   var DEFAULT_DNA_VOLUME = 95;
-  var DEFAULT_RNA_VOLUME = 51;
+  var DEFAULT_RNA_VOLUME = 53;
   var DEFAULT_FT_VOLUME = 550;
   var MINIMAL_PRE_NORMALIZE_QUANTITY = 0; // µg, =0 since we no longer handle NotEnoughQuantity in this wizard

extensions/net.sf.basedb.reggie/trunk/resources/sampleproc/rnaqc_aliquot.js

@@ -4 +4 @@
   
   var HISENSE_LIMIT = 35.0;
+  var ALIQUOT_VOLUME_NORMAL = 2.0;
+  var ALIQUOT_VOLUME_HISENSE = 6.0;
   
   var selectedRna;
@@ -349 +351 @@
     html += '<th colspan="2" class="dottedleft">' + Strings.encodeTags(selectedBioPlate.name) + '</th>';
     html += '<th class="dottedleft">HiSense</th>';
+    html += '<th>Volume</th>';
     html += '<th>NDConc</th>';
     html += '<th></th>';
@@ -359 +362 @@
     html += '<th>Column</th>';
     html += '<th class="dottedleft">NDConc ‹ ' + HISENSE_LIMIT + '</th>';
+    html += '<th>(µl)</th>';
     html += '<th>(ng/µl)</th>';
     html += '<th></th>';
@@ -370 +374 @@
       var rna = selectedRna[i];
       rna.isValid = false;
+      rna.isValidVolume = true;
       
       var hiSenseChecked = '';
       var ndConc = null;
+      var volume = ALIQUOT_VOLUME_NORMAL;
       if (rna.NDConc)
       {
@@ -379 +385 @@
         {
           hiSenseChecked = 'checked';
+          volume = ALIQUOT_VOLUME_HISENSE;
         }
       }
@@ -388 +395 @@
       html += '<td><input name="column.'+i+'" id="column.'+i+'" type="text" class="required" style="width: 3em;" maxlength="3"></td>';
       html += '<td class="dottedleft"><input name="hiSense.'+i+'" id="hiSense.'+i+'" type="checkbox" value="1" ' + hiSenseChecked + '></td>';
-      html += '<td class="ndconc">'
+      html += '<td>';
+      html += '<input name="volume.'+i+'" id="volume.'+i+'" type="text" class="required" style="width: 3em;" maxlength="3" value="'+volume+'">';
+      html += '</td>';
+      html += '<td class="ndconc">';
       if (ndConc) html += Reggie.formatNumber(ndConc);
       html += '</td>';
@@ -411 +421 @@
     {
       Events.addEventHandler('row.'+i, 'keypress', Wizard.focusOnEnter, { 'next-focus': 'column.'+i });
-      Events.addEventHandler('column.'+i, 'keypress', Wizard.focusOnEnter, { 'next-focus': 'row.'+(i+1) });
+      Events.addEventHandler('column.'+i, 'keypress', Wizard.focusOnEnter, { 'next-focus': 'volume.'+i });
+      Events.addEventHandler('volume.'+i, 'keypress', Wizard.focusOnEnter, { 'next-focus': 'row.'+(i+1) });
+      Events.addEventHandler('volume.'+i, 'keypress', Numbers.numberOnly);
 
       Events.addEventHandler('row.'+i, 'focus', rnaqc.wellOnFocus);
       Events.addEventHandler('row.'+i, 'change', rnaqc.wellOnChange, { 'index': i });
       Events.addEventHandler('column.'+i, 'change', rnaqc.wellOnChange, { 'index': i });
+      Events.addEventHandler('volume.'+i, 'change', rnaqc.wellOnChange, { 'index': i });
+      Events.addEventHandler('hiSense.'+i, 'click', rnaqc.hiSenseOnClick, { 'index': i });
       
       rnaqc.suggestWell(i);
@@ -495 +509 @@
     var row = frm['row.'+index].value;
     var column = frm['column.'+index].value;
+    var volume = frm['volume.'+index].value;
     
     selectedRna[index].isValid = false;
+    selectedRna[index].isValidVolume = false;
     
     if (row == '' || column == '')
@@ -503 +519 @@
       return;
     }
+    
+    if (volume == '')
+    {
+      Wizard.setInputStatus('well.'+index, 'invalid', 'Missing volume');
+      return;
+    }
+    else if (parseFloat(volume) <= 0 || isNaN(parseFloat(volume)))
+    {
+      Wizard.setInputStatus('well.'+index, 'invalid', 'Volume must be &gt; 0');
+      return;
+    }
+    selectedRna[index].isValidVolume = true;
     
     var rowC = Reggie.alphaToWell(row);
@@ -535 +563 @@
     rnaqc.duplicateWellCheck();
   }
-
 
   //  Get a well from a plate given a coordinate.
@@ -586 +613 @@
   }
   
+  rnaqc.hiSenseOnClick = function(event)
+  {
+    var frm = document.forms['reggie'];
+    var index = Data.int(event.currentTarget, 'index');
+    var hiSenseChecked = event.currentTarget.checked;
+    
+    var volume = parseFloat(frm['volume.'+index].value);
+    // Switch default volume when HiSense is toggled (unless the volume has been modified)
+    if (volume == (hiSenseChecked ? ALIQUOT_VOLUME_NORMAL : ALIQUOT_VOLUME_HISENSE))
+    {
+      frm['volume.'+index].value = hiSenseChecked ? ALIQUOT_VOLUME_HISENSE : ALIQUOT_VOLUME_NORMAL;
+      Events.sendChangeEvent(frm['volume.'+index]);
+    }
+    
+  }
   
   rnaqc.printVersion = function()
@@ -607 +649 @@
       if (!rna.isValid || rna.isDuplicate)
       {
-        frm['row.'+i].focus();
         event.preventDefault();
+        // Focus on the 'row' or 'volume' field
+        frm[(rna.isValidVolume ? 'row.' : 'volume.')+i].focus();
         return;
       }
@@ -633 +676 @@
       rnaQc.column = frm['column.'+i].value;
       rnaQc.QCHiSense = frm['hiSense.'+i].checked ? true : false;
+      rnaQc.volume = parseFloat(frm['volume.'+i].value);
       rnaQcExtracts[rnaQcExtracts.length] = rnaQc;
     }

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

@@ -364 +364 @@
           
           Boolean hiSense = (Boolean)jsonRnaQc.get("QCHiSense");
+          Number volume = (Number)jsonRnaQc.get("volume");
           
           // Create a child RNAQC extract
@@ -370 +371 @@
           rnaQc.setName((String)jsonRnaQc.get("name"));
           BioMaterialEventSource evtSrc = rnaQc.getCreationEvent().setSource(parentRna);
-          // TODO - used quantity from parent
-          //evtSrc.setUsedQuantity(...);
+          if (volume != null)
+          {
+            Float ndConc = (Float)Annotationtype.ND_CONC.getAnnotationValue(dc, parentRna);
+            if (ndConc != null)
+            {
+              float usedQuantity = volume.floatValue() * ndConc / 1000;
+              evtSrc.setUsedQuantity(usedQuantity);
+            }
+          }
           
           if (Boolean.TRUE.equals(hiSense))
           {
-            rnaQc.getAnnotationSet().getAnnotation(qcHiSenseType).setValue(hiSense);
+            Annotationtype.QC_HISENSE.setAnnotationValue(dc, rnaQc, hiSense);
           }