Changeset 1939

Timestamp:

Apr 18, 2013, 10:25:10 AM (10 years ago)

Author:

Nicklas Nordborg

Message:

References #424: Select RNA items for library preparation

Added RQS/RIN values to the display. A warning is displayed for scores below 8. This is currently hard-coded, but will be user selectable in the future.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/libprep/select_rna.jsp (modified) (6 diffs)
• src/net/sf/basedb/reggie/dao/Rna.java (modified) (2 diffs)
• src/net/sf/basedb/reggie/servlet/MRnaServlet.java (modified) (2 diffs)

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

@@ -36 +36 @@
 
 <script language="JavaScript">
-var debug = false;
+var debug = true;
 
 var QUANTITY_REGULAR = 1.1;
 var QUANTITY_QC = 1.22;
 var LOW_QUANTITY_WARNING_FACTOR = 1.5;
+var QUALITY_SCORE_WARNING_LIMIT = 8;
 
 var Rna = function()
@@ -219 +220 @@
           if (!warningMsg) warningMsg = 'No quantity';
         }
+        if (info.rqs)
+        {
+          text += '<div class="quality-score">RQS='+Numbers.formatNumber(info.rqs, 1) + '</div>';
+          if (info.rqs < QUALITY_SCORE_WARNING_LIMIT && !warningMsg) warningMsg = 'Low RQS value';
+        }
+        else if (info.rin)
+        {
+          text += '<div class="quality-score">RIN='+Numbers.formatNumber(info.rin, 1) + '</div>';
+          if (info.rin < QUALITY_SCORE_WARNING_LIMIT && !warningMsg) warningMsg = 'Low RIN value';
+        }
+        else
+        {
+          if (!warningMsg) warningMsg = 'No RQS/RIN value';
+        }
         if (info.NDConc)
         {
@@ -1382 +1397 @@
 }
 .plate.hide-ndconc .ndconc
+{
+  display: none;
+}
+.plate.hide-quality-score .quality-score
 {
   display: none;
@@ -1573 +1592 @@
         <td class="input">
           <table>
-          <tr>
+          <tr valign="top">
             <td>
               <input type="checkbox" name="location" id="location" onclick="toggleInfo('location')" checked><label for="location">Bioplate location</label><br>
@@ -1579 +1598 @@
             </td>
             <td>
+              <input type="checkbox" name="quality-score" id="quality-score" onclick="toggleInfo('quality-score')"><label for="quality-score">RQS/RIN</label><br>
               <input type="checkbox" name="ndconc" id="ndconc" onclick="toggleInfo('ndconc')"><label for="ndconc">NDConc</label><br>
               <input type="checkbox" name="volumes" id="volumes" onclick="toggleInfo('volumes')"><label for="volumes">Used volume+water</label><br>
@@ -1675 +1695 @@
         </div>
 
-        <table class="plate hide-volumes hide-ndconc" style="margin: 1em 1em 0 1em;" id="plate"
+        <table class="plate hide-volumes hide-ndconc hide-quality-score" style="margin: 1em 1em 0 1em;" id="plate"
           onmouseup="contextEvent(event)"
           oncontextmenu="contextEvent(event)"

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

@@ -3 +3 @@
 import java.util.ArrayList;
 import java.util.Collection;
+import java.util.Date;
 import java.util.List;
 
 import org.json.simple.JSONObject;
 
+import net.sf.basedb.core.BioPlate;
+import net.sf.basedb.core.BioWell;
 import net.sf.basedb.core.DbControl;
 import net.sf.basedb.core.Extract;
@@ -260 +263 @@
   }
   
+  
+  /**
+    Find the last RNAQC child item that contains either a BA_RIN or CA_RQS value.
+    @return The RNAQC item
+  */
+  public Extract findLastRnaQc(DbControl dc)
+  {
+    Extract rna = getExtract();
+    Extract lastQc = null;
+    
+    // Fetch all child RNAQC items
+    ItemQuery<Extract> rnaqcQuery = rna.getChildExtracts();
+    Subtype.RNAQC.addFilter(dc, rnaqcQuery);
+    rnaqcQuery.include(Reggie.INCLUDE_IN_CURRENT_PROJECT);
+    List<Extract> rnaqc = rnaqcQuery.list(dc);
+    
+    if (rnaqc.size() > 0)
+    {
+      lastQc = rnaqc.get(0);
+      Date lastQcDate = null;
+      // Try to find the last QC run on either Caliper or BioAnalyzer
+      // This should be stored in QC_RUN_DATE annotation on the BioPlate
+      // If no bioplate is associated with the RNA QC item, use the
+      // creation date
+      
+      for (Extract qc : rnaqc)
+      {
+        Float rqs = (Float)Annotationtype.CA_RQS.getAnnotationValue(dc, qc);
+        Float rin = (Float)Annotationtype.BA_RIN.getAnnotationValue(dc, qc);
+        // Skip RNAQC items without any quality score since it may
+        // be a new NanoDrop measurement
+        if (rqs == null && rin == null) continue;
+        
+        BioPlate plate = null;
+        BioWell well = qc.getBioWell();
+        Date qcDate = null;
+        if (well != null)
+        {
+          plate = well.getPlate();
+          qcDate = (Date)Annotationtype.QC_RUN_DATE.getAnnotationValue(dc, plate);
+        }
+        if (qcDate == null)
+        {
+          qcDate = qc.getCreationEvent().getEventDate();
+        }
+        if ((lastQcDate == null && qcDate != null) || (qcDate != null && qcDate.after(lastQcDate)))
+        {
+          lastQcDate = qcDate;
+          lastQc = qc;
+        }
+      }
+    }
+    return lastQc;
+  }
+  
+  
+  public Extract loadRnaQc(DbControl dc)
+  {
+    Extract qc = findLastRnaQc(dc);
+    
+    Float rqs = (Float)Annotationtype.CA_RQS.getAnnotationValue(dc, qc);
+    Float rin = (Float)Annotationtype.BA_RIN.getAnnotationValue(dc, qc);
+    
+    if (rqs != null) setAnnotation("rqs", rqs);
+    if (rin != null) setAnnotation("rin", rin);
+    
+    return qc;
+  }
+  
   /**
     Load information about the plate and location the current RNA

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

@@ -212 +212 @@
             Rna r = Rna.get(rna);
             r.loadBioPlateLocation();
+            r.loadRnaQc(dc);
             r.setAnnotation("remainingQuantity", remainingQuantity);
             r.loadAnnotations(dc, "NDConc", Annotationtype.ND_CONC, null);
@@ -358 +359 @@
         {
           r.loadBioPlateLocation();
+          r.loadRnaQc(dc);
           r.setAnnotation("remainingQuantity", r.getExtract().getRemainingQuantity());
           r.loadAnnotations(dc, "NDConc", Annotationtype.ND_CONC, null);