Changeset 6220

Timestamp:

Apr 20, 2021, 3:10:40 PM (2 years ago)

Author:

Nicklas Nordborg

Message:

References #1302: Qubit concentration instead of NanoDrop? on RNA and DNA items

Fixed in case summary, the outtake wizards and release exporter.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/outtake/define.js (modified) (4 diffs)
• resources/outtake/define.jsp (modified) (1 diff)
• resources/outtake/picklist.js (modified) (2 diffs)
• resources/reports/case-summary.js (modified) (2 diffs)
• resources/reports/case_summary.jsp (modified) (2 diffs)
• src/net/sf/basedb/reggie/plugins/release/DnaWriter.java (modified) (2 diffs)
• src/net/sf/basedb/reggie/plugins/release/RnaWriter.java (modified) (2 diffs)
• src/net/sf/basedb/reggie/servlet/CaseSummaryServlet.java (modified) (2 diffs)
• src/net/sf/basedb/reggie/servlet/OuttakeServlet.java (modified) (7 diffs)

extensions/net.sf.basedb.reggie/trunk/resources/outtake/define.js

@@ -66 +66 @@
     Doc.element('listSize').innerHTML = '';
     Doc.element('listRemainingQuantity').innerHTML = '';
-    Doc.element('listNdConc').innerHTML = '';
+    Doc.element('listConc').innerHTML = '';
 
     var list = event.detail;
@@ -85 +85 @@
     Wizard.setInputStatus('sourceList');
     Wizard.setInputStatus('listRemainingQuantity');
-    Wizard.setInputStatus('listNdConc');
+    Wizard.setInputStatus('listConc');
     Wizard.setInputStatus('targetAmount');
     Wizard.setInputStatus('targetVolume');
@@ -118 +118 @@
       }
     }
-    var ndConc = sourceList.ndConc;
-    if (ndConc)
-    {
-      Doc.element('listNdConc').innerHTML = 
-        Reggie.formatNumber(ndConc.min, ' ng/µl (min), ', 2) +
-        Reggie.formatNumber(ndConc.max, ' ng/µl (max)', 2);
-      
-      if (ndConc.nulls > 0)
+    var conc = sourceList.conc;
+    if (conc)
+    {
+      Doc.element('listConc').innerHTML = 
+        Reggie.formatNumber(conc.min, ' ng/µl (min), ', 2) +
+        Reggie.formatNumber(conc.max, ' ng/µl (max)', 2);
+      
+      if (conc.nulls > 0)
       {
-        Wizard.setInputStatus('listNdConc', 'warning', ndConc.nulls + ' items have unknown concentration');
+        Wizard.setInputStatus('listConc', 'warning', conc.nulls + ' items have unknown concentration');
       }
     }
@@ -249 +249 @@
       }
       
-      if (sourceList.ndConc && sourceList.ndConc.min < targetConc)
+      if (sourceList.conc && sourceList.conc.min < targetConc)
       {
-        Wizard.setInputStatus('targetVolume', 'warning', 'Some items in the list has too low concentration: '+ Reggie.formatNumber(sourceList.ndConc.min, ' ng/µl', 2));
+        Wizard.setInputStatus('targetVolume', 'warning', 'Some items in the list has too low concentration: '+ Reggie.formatNumber(sourceList.conc.min, ' ng/µl', 2));
       }
     }

extensions/net.sf.basedb.reggie/trunk/resources/outtake/define.jsp

@@ -101 +101 @@
       <tr>
         <td class="prompt">Concentration</td>
-        <td class="info" id="listNdConc"></td>
-        <td class="status" id="listNdConc.status"></td>
-        <td class="help"><span id="listNdConc.message" class="message"></span></td>
+        <td class="info" id="listConc"></td>
+        <td class="status" id="listConc.status"></td>
+        <td class="help"><span id="listConc.message" class="message"></span></td>
       </tr>
       </tbody>

extensions/net.sf.basedb.reggie/trunk/resources/outtake/picklist.js

@@ -116 +116 @@
       var p = a.parent;
       
-      var storageBox = p.bioWell.bioPlate;
+      var storageBox = p.bioWell ? p.bioWell.bioPlate : { 'name': 'Unknown box', 'id': 0 };
       var aliquotBox = a.bioWell.bioPlate;
       var markNewBox = false;
@@ -181 +181 @@
         {
           // Happens when source concentration is lower that target concentration
-          remarks[remarks.length] = 'Conc: ' + Reggie.formatNumber(p.NdConc, ' ng/µl', 2);
+          remarks[remarks.length] = 'Conc: ' + Reggie.formatNumber(p.conc, ' ng/µl', 2);
           dilution.water = null;
         }

extensions/net.sf.basedb.reggie/trunk/resources/reports/case-summary.js

@@ -386 +386 @@
           cs.addColumn('rna.remainingQuantity', cs.asQuantity(r.remainingQuantity, ' µg'));
           cs.addColumn('rna.originalQuantity', cs.asQuantity(r.originalQuantity, ' µg'));
-          cs.addColumn('rna.ndConc', cs.asQuantity(r.ndConc, ' ng/µl'));
+          cs.addColumn('rna.conc', cs.asQuantity(r.conc, ' ng/µl'));
           cs.addColumn('rna.comment', cs.truncate(r.comment, truncateAt));
           
@@ -430 +430 @@
           cs.addColumn('dna.remainingQuantity', cs.asQuantity(d.remainingQuantity, ' µg'));
           cs.addColumn('dna.originalQuantity', cs.asQuantity(d.originalQuantity, ' µg'));
-          cs.addColumn('dna.ndConc', cs.asQuantity(d.ndConc, ' ng/µl'));
+          cs.addColumn('dna.conc', cs.asQuantity(d.conc, ' ng/µl'));
           cs.addColumn('dna.comment', cs.truncate(d.comment, truncateAt));
         }

extensions/net.sf.basedb.reggie/trunk/resources/reports/case_summary.jsp

@@ -557 +557 @@
               <th>Original quantity</th>
             </tr>
-            <tr id="rna.ndConc">
-              <th>ND Conc.</th>
+            <tr id="rna.conc">
+              <th>Conc.</th>
             </tr>
             <tr id="rna.comment" class="comment dynamic-column">
@@ -619 +619 @@
               <th>Original quantity</th>
             </tr>
-            <tr id="dna.ndConc">
-              <th>ND Conc.</th>
+            <tr id="dna.conc">
+              <th>Conc.</th>
             </tr>
             <tr id="dna.comment" class="comment dynamic-column">

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/plugins/release/DnaWriter.java

@@ -69 +69 @@
       jsonAnnotations.add(item.createAnnotationJSON("DNAOriginalQuantity", dna.getOriginalQuantity()));
       jsonAnnotations.add(item.createAnnotationJSON("DNARemainingQuantity", dna.getRemainingQuantity()));
+      jsonAnnotations.add(item.getAnnotationJSON(Annotationtype.QUBIT_CONC, dna, null));
       jsonAnnotations.add(item.getAnnotationJSON(Annotationtype.ND_CONC, dna, null));
       jsonAnnotations.add(item.getAnnotationJSON(Annotationtype.ND_260_BY_230, dna, null));
@@ -92 +93 @@
     dnaFactory.createAnnotationType("DNAOriginalQuantity", Type.FLOAT).setUnit(µg);
     dnaFactory.createAnnotationType("DNARemainingQuantity", Type.FLOAT).setUnit(µg).setProjectSpecificValues(true);
+    dnaFactory.createAnnotationType(Annotationtype.QUBIT_CONC).setUnit(UnitUtil.getUnit(dc, Quantity.DENSITY, "ng/µl"));
     dnaFactory.createAnnotationType(Annotationtype.ND_CONC).setUnit(UnitUtil.getUnit(dc, Quantity.DENSITY, "ng/µl"));
     dnaFactory.createAnnotationType(Annotationtype.ND_260_BY_230);

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/plugins/release/RnaWriter.java

@@ -74 +74 @@
       jsonAnnotations.add(item.createAnnotationJSON("RNARemainingQuantity", rna.getRemainingQuantity()));
 
+      jsonAnnotations.add(item.getAnnotationJSON(Annotationtype.QUBIT_CONC, rna, null));
       jsonAnnotations.add(item.getAnnotationJSON(Annotationtype.ND_CONC, rna, null));
       jsonAnnotations.add(item.getAnnotationJSON(Annotationtype.ND_260_BY_230, rna, null));
@@ -101 +102 @@
     rnaFactory.createAnnotationType("RNAOriginalQuantity", Type.FLOAT).setUnit(µg);
     rnaFactory.createAnnotationType("RNARemainingQuantity", Type.FLOAT).setUnit(µg).setProjectSpecificValues(true);
+    rnaFactory.createAnnotationType(Annotationtype.QUBIT_CONC).setUnit(UnitUtil.getUnit(dc, Quantity.DENSITY, "ng/µl"));
     rnaFactory.createAnnotationType(Annotationtype.ND_CONC).setUnit(UnitUtil.getUnit(dc, Quantity.DENSITY, "ng/µl"));
     rnaFactory.createAnnotationType(Annotationtype.ND_260_BY_230);

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

@@ -892 +892 @@
     rna.setAnnotation("comment", e.getDescription());
     rna.loadAnnotations(dc, "ndConc", Annotationtype.ND_CONC, null);
+    rna.loadAnnotations(dc, "QubitConc", Annotationtype.QUBIT_CONC, null);
+    rna.coalesceInto("conc", "ndConc", "QubitConc");
     
     List<RnaQc> rnaqc = RnaQc.findByRna(dc, rna);
@@ -943 +945 @@
     dna.setAnnotation("comment", e.getDescription());
     dna.loadAnnotations(dc, "ndConc", Annotationtype.ND_CONC, null);
+    dna.loadAnnotations(dc, "QubitConc", Annotationtype.QUBIT_CONC, null);
+    dna.coalesceInto("conc", "ndConc", "QubitConc");
   }
 

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

@@ -110 +110 @@
           
           MinMax remainingQuantity = new MinMax();
-          MinMax ndConc = new MinMax();
+          MinMax conc = new MinMax();
                     
           Iterator<Extract> it = memberQuery.iterate(dc);
@@ -117 +117 @@
             Extract e = it.next();
             remainingQuantity.add(e.getRemainingQuantity());
-            ndConc.add((Float)Annotationtype.ND_CONC.getAnnotationValue(dc, e));
+            Float c = (Float)Annotationtype.ND_CONC.getAnnotationValue(dc, e);
+            if (c == null) c = (Float)Annotationtype.QUBIT_CONC.getAnnotationValue(dc, e);
+            conc.add(c);
             
             ItemSubtype subtype = e.getItemSubtype();
@@ -129 +131 @@
           
           jsonList.put("remainingQuantity", remainingQuantity.asJSONObject());
-          jsonList.put("ndConc", ndConc.asJSONObject());
+          jsonList.put("conc", conc.asJSONObject());
           jsonList.put("numDoNotUse", numDoNotUse);
         }
@@ -293 +295 @@
 
           Float remain = parent.getRemainingQuantity();
-          Float ndConc = (Float)Annotationtype.ND_CONC.getAnnotationValue(dc, parent);
-          
-          if (remain != null && ndConc != null)
-          {
-            Dilution d = new Dilution(targetAmount, targetVolume, ndConc, remain);
+          Float conc = (Float)Annotationtype.ND_CONC.getAnnotationValue(dc, parent);
+          if (conc == null) conc = (Float)Annotationtype.QUBIT_CONC.getAnnotationValue(dc, parent);
+          
+          if (remain != null && conc != null)
+          {
+            Dilution d = new Dilution(targetAmount, targetVolume, conc, remain);
             jsonA.put("dilution", d.asJSONObject());
           }
@@ -305 +308 @@
           jsonP.put("name", parent.getName());
           jsonP.put("bioWell", JsonUtil.getBioWellAsJSON(parent.getBioWell(), true));
-          jsonP.put("NdConc", ndConc);
+          jsonP.put("conc", conc);
           jsonP.put("remainingQuantity", remain);
           
@@ -579 +582 @@
           
           Float remain = parent.getRemainingQuantity();
-          Float ndConc = (Float)Annotationtype.ND_CONC.getAnnotationValue(dc, parent);
-          
-          if (remain != null && ndConc != null)
+          Float conc = (Float)Annotationtype.ND_CONC.getAnnotationValue(dc, parent);
+          if (conc == null) conc = (Float)Annotationtype.QUBIT_CONC.getAnnotationValue(dc, parent);
+          
+          if (remain != null && conc != null)
           {
             boolean isException = except.contains(aliquot.getId());
@@ -588 +592 @@
             if (sampleConsumed != isException)
             {
-              Dilution d = new Dilution(targetAmount, targetVolume, ndConc, remain);
+              Dilution d = new Dilution(targetAmount, targetVolume, conc, remain);
               creationEvent.getEventSource(parent).setUsedQuantity(d.amount);
               aliquot.setOriginalQuantity(d.amount);