Changeset 2225

Timestamp:

Feb 13, 2014, 8:44:46 AM (9 years ago)

Author:

Nicklas Nordborg

Message:

References #533: Register sequencing as ended

New version of the 'sequencing ended' wizard. Added an option to specify if first base report failed. If so, the 'sequencing startup' wizard is enabled again for the flow cell. Other changes are mostly related to that there is only a single parent FlowCell for each SequencingRun.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/libprep/sequencing_ended.jsp (modified) (7 diffs)
• resources/libprep/sequencing_started.jsp (modified) (1 diff)
• src/net/sf/basedb/reggie/dao/Annotationtype.java (modified) (1 diff)
• src/net/sf/basedb/reggie/dao/FlowCell.java (modified) (2 diffs)
• src/net/sf/basedb/reggie/dao/SequencingRun.java (modified) (1 diff)
• src/net/sf/basedb/reggie/servlet/FlowCellServlet.java (modified) (2 diffs)
• src/net/sf/basedb/reggie/servlet/InstallServlet.java (modified) (3 diffs)
• src/net/sf/basedb/reggie/servlet/SequencingRunServlet.java (modified) (5 diffs)

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

@@ -124 +124 @@
   var seqRun = frm.seqRuns[frm.seqRuns.selectedIndex].seqRun;
   
-  setInnerHTML('startDate', formatDate(seqRun.sequencingStart));
-  
-  var html = '';
-  for (var fcNo = 0; fcNo < seqRun.flowCells.length; fcNo++)
-  {
-    var fc = seqRun.flowCells[fcNo];
-    if (fcNo > 0) html += '<br>';
-    html += '<b>['+fc.HiSeqPosition+']</b> ' + fc.FlowCellID;
-  }
+  setInnerHTML('startDate', formatDate(seqRun.SequencingStart));
+  
+  var fc = seqRun.flowCell;
+  var html = '<b>['+seqRun.HiSeqPosition+']</b> ' + fc.FlowCellID;
   
   setInnerHTML('flowCellsInRun', html);
@@ -168 +163 @@
   setInnerHTML('step.2.title', seqRun.name);
   
-  // Flow cell comments
-  var html = '';
-  for (var fcNo = 0; fcNo < seqRun.flowCells.length; fcNo++)
-  {
-    var fc = seqRun.flowCells[fcNo];
-    
-    html += '<tr valign="top">';
-    html += '<td class="prompt">Flow cell ['+fc.HiSeqPosition+']</td>';
-    html += '<td class="input"><b>' + fc.FlowCellID + '</b></td>';
-    html += '<td class="status"></td>';
-    html += '<td class="help"></td>';
-    html += '</tr>';
-    
-    html += '<tr valign="top">';
-    html += '<td class="subprompt">Comments</td>';
-    html += '<td class="input"><textarea rows="4" cols="50" style="width: 90%;" name="comments.'+fc.id+'" value=""></textarea></td>';
-    html += '<td class="status"></td>';
-    html += '<td class="help">Comments for the flow cell.</td>';
-    html += '</tr>';
-  }
-  
-  setInnerHTML('flowCells', html);
-  
-  for (var fcNo = 0; fcNo < seqRun.flowCells.length; fcNo++)
-  {
-    var fc = seqRun.flowCells[fcNo];
-    frm['comments.'+fc.id].value = fc.comments;
-  }
-    
   frm.turnAroundDate.focus();
 }
@@ -322 +288 @@
   frm.endTime.disabled = true;
   frm.sequencingComments.disabled = true;
-  
-  
-  var seqRun = frm.seqRuns[frm.seqRuns.selectedIndex].seqRun;
-  for (var fcNo = 0; fcNo < seqRun.flowCells.length; fcNo++)
-  {
-    var fc = seqRun.flowCells[fcNo];
-    frm['comments.'+fc.id].disabled = true;
-    fc.comments = frm['comments.'+fc.id].value;
-  }
+  frm.firstBaseReport[0].disabled = true;
+  frm.firstBaseReport[1].disabled = true;
   
   Main.hide('goregister');
@@ -336 +295 @@
   Main.hide('gonext.message');
   
-  
+  var seqRun = frm.seqRuns[frm.seqRuns.selectedIndex].seqRun;
+  seqRun.firstBaseReportFailed = document.getElementById('firstBaseReportFailed').checked;
   seqRun.turnAroundDate = Main.trimString(frm.turnAroundDate.value + ' ' + frm.turnAroundTime.value);
   seqRun.endDate = Main.trimString(frm.endDate.value + ' ' + frm.endTime.value);
@@ -449 +409 @@
       
       <tr valign="top">
-        <td class="subprompt">- flow cells</td>
+        <td class="subprompt">- flow cell</td>
         <td class="input" id="flowCellsInRun"></td>
         <td class="status"></td>
@@ -471 +431 @@
       <table>
       <tr valign="top">
+        <td class="prompt">First base report</td>
+        <td class="input">
+          <label><input type="radio" name="firstBaseReport" id="firstBaseReportOk" value="1" checked>Ok</label>
+          <label><input type="radio" name="firstBaseReport" id="firstBaseReportFailed" value="0">Failed</label>
+        </td>
+        <td class="status" id="firstBaseReport.status"></td>
+        <td class="help"><span id="firstBaseReport.message" class="message" style="display: none;"></span>
+          If first base report failed and a restart was possible a new 'sequencing start'
+          must be registered.
+        </td>
+      </tr>
+      <tr valign="top">
         <td class="prompt">Turn-around date</td>
         <td class="input"><input type="text" name="turnAroundDate" value="" size="12" maxlength="10" 
@@ -497 +469 @@
         <td class="help"><span id="sequencingComments.message" class="message" style="display: none;"></span>Comments about the sequencing.</td>
       </tr>
-
-      <tbody id="flowCells"></tbody>
-      
       </table>
     </td>

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

@@ -254 +254 @@
       html += '<tr valign="top" class="fc-info">';
       html += '<td class="subprompt">'+seqRun.name+'</td>';
-      html += '<td class="input">'+formatDate(seqRun.SequencingStart, '(no start date)') + ' -- ' + formatDate(seqRun.SequencingEnd, '(no end date)')+'</td>';
-      html += '<td class="status"></td>';
+      html += '<td class="input" colspan="2">';
+      html += formatDate(seqRun.SequencingStart, '(no start date)') + ' -- ' + formatDate(seqRun.SequencingEnd, '(no end date)');
+      if (seqRun.SequencingResult)
+      {
+        html += ': ' + seqRun.SequencingResult;
+      }
+      html += '</td>';
       html += '<td class="help"></td>';
       html += '</tr>';

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

@@ -728 +728 @@
     new Annotationtype("DataFilesFolder", Type.STRING, Item.DERIVEDBIOASSAY);
 
-  
+  /**
+    The "SequencingResult" annotation, used for derived bioassays (SequencingRun).
+    A value of "Successful" typically means that the process can continue with
+    next step (demux and merge). A value of "Failed" indicates a complete
+    failure that require a new flow cell to be clustered. The pooled
+    libraries on the current flow cell are flagged with "SequencingFailed".
+    A value of "FirstBaseReportFailed" indicates that the first sequencing attempt
+    failed but that it is possible to re-start with the same flow cell. The
+    annotation is also copied to the flow cell.
+    @since 2.15
+  */
+  public static final Annotationtype SEQUENCING_RESULT =
+    new Annotationtype("SequencingResult", Type.STRING, Item.PHYSICALBIOASSAY, Item.DERIVEDBIOASSAY);
+
   /**
     Get the annotation type by name of the static constant defined in this class.

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

@@ -80 +80 @@
   
   /**
-    Load pools used on the flow cell.
+    Load the flow cell on the sequening run.
   */
-  public static List<FlowCell> getBySequencingRun(DbControl dc, SequencingRun sequencingRun)
+  public static FlowCell getBySequencingRun(DbControl dc, SequencingRun sequencingRun)
   {
     ItemQuery<PhysicalBioAssay> fcQuery = PhysicalBioAssay.getQuery();
@@ -96 +96 @@
     List<PhysicalBioAssay> tmp = fcQuery.list(dc);
   
-    return toList(tmp);
+    PhysicalBioAssay fc = null;
+    if (tmp.size() > 1)
+    {
+      throw new InvalidDataException(
+          "More than one flow cell was found on " + sequencingRun.getName() +
+          "This wizard can't be used until that is corrected.");
+    }
+    else if (tmp.size() == 1)
+    {
+      fc = tmp.get(0);
+    }
+    
+    return fc == null ? null : new FlowCell(fc);
   }
 

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

@@ -27 +27 @@
 {
 
+  /**
+    Value for the {@link Annotationtype#SEQUENCING_RESULT} annotation 
+    when the sequencing was successful.
+    @since 2.15
+  */
+  public static final String SEQUENCING_SUCCESSFUL = "Successful";
+  
+  /**
+    Value for the {@link Annotationtype#SEQUENCING_RESULT} annotation when
+    the sequencing failed and a new flow cell must be used for re-sequencing.
+    @since 2.15
+  */
+  public static final String SEQUENCING_FAILED = "Failed";
+  
+  /**
+    Value for the {@link Annotationtype#SEQUENCING_RESULT} annotation when
+    the first base report failed and the same flow cell can be used 
+    for re-sequencing.
+    @since 2.15
+  */
+  public static final String SEQUENCING_FIRST_BASE_REPORT_FAILED = "FirstBaseReportFailed";
+  
   /**
     Get a sequencing run when the id is known.

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

@@ -45 +45 @@
 import net.sf.basedb.reggie.dao.ReactionPlate;
 import net.sf.basedb.reggie.dao.ReggieRole;
+import net.sf.basedb.reggie.dao.SequencingRun;
 import net.sf.basedb.reggie.dao.Subtype;
 import net.sf.basedb.util.Values;
@@ -250 +251 @@
         query.join(Annotations.leftJoin(null, Annotationtype.PLATE_PROCESS_RESULT.load(dc), "ppr"));
         query.restrict(Restrictions.eq(Hql.alias("ppr"), Expressions.string(ReactionPlate.PROCESS_SUCCESSFUL)));
-        // but no child SequencingRun items
+        // but no child SequencingRun items (unless SequencingResult=FirstBaseReportFailed is set)
+        query.join(Annotations.leftJoin(null, Annotationtype.SEQUENCING_RESULT.load(dc), "sqr"));
         query.join(Hql.leftJoin("derivedBioAssays", "ssr"));
-        query.restrict(Restrictions.eq(Hql.alias("ssr"), null));
-        
+        query.restrict(
+          Restrictions.or(
+            Restrictions.eq(Hql.alias("ssr"), null), 
+            Restrictions.eq(Hql.alias("sqr"), Expressions.string(SequencingRun.SEQUENCING_FIRST_BASE_REPORT_FAILED))
+          ));
+
         long count = query.count(dc);
         json.put("count", count);

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

@@ -64 +64 @@
 import net.sf.basedb.reggie.dao.ReggieRole;
 import net.sf.basedb.reggie.dao.Rna;
+import net.sf.basedb.reggie.dao.SequencingRun;
 import net.sf.basedb.reggie.dao.Subtype;
 import net.sf.basedb.reggie.plugins.CaliperLibPrepParametersExporter;
@@ -340 +341 @@
             effectivePermissionsUse, createIfMissing));
         jsonChecks.add(checkAnnotationType(dc, Annotationtype.DATA_FILES_FOLDER, 1, null, effectivePermissionsUse, createIfMissing));
+        jsonChecks.add(checkAnnotationType(dc, Annotationtype.SEQUENCING_RESULT, 1, 
+            new ValueOptions(SequencingRun.SEQUENCING_SUCCESSFUL, SequencingRun.SEQUENCING_FIRST_BASE_REPORT_FAILED, SequencingRun.SEQUENCING_FAILED),
+            effectivePermissionsUse, createIfMissing));
         
         // Annotation type categories
@@ -423 +427 @@
         jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.FLOW_CELL, createIfMissing, 
             Annotationtype.FLOWCELL_ID, Annotationtype.CLUSTER_START, Annotationtype.CLUSTER_OPERATOR,
-            Annotationtype.SEQUENCING_CYCLES, Annotationtype.PLATE_PROCESS_RESULT));
+            Annotationtype.SEQUENCING_CYCLES, Annotationtype.PLATE_PROCESS_RESULT, Annotationtype.SEQUENCING_RESULT));
         
         jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.SEQUENCING_RUN, createIfMissing, 
             Annotationtype.SEQUENCING_START, Annotationtype.SEQUENCING_TURN_AROUND, Annotationtype.SEQUENCING_END,
             Annotationtype.SEQUENCING_OPERATOR, Annotationtype.SEQUENCING_RUN_NUMBER, Annotationtype.SEQUENCING_CYCLES,
-            Annotationtype.HISEQ_POSITION, Annotationtype.DATA_FILES_FOLDER
+            Annotationtype.HISEQ_POSITION, Annotationtype.DATA_FILES_FOLDER, Annotationtype.SEQUENCING_RESULT
           ));
         

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

@@ -90 +90 @@
         query.join(Annotations.leftJoin(null, Annotationtype.SEQUENCING_END.load(dc), "sse"));
         query.restrict(Restrictions.eq(Hql.alias("sse"), null));
-        
-        
+
         JSONArray jsonRuns = new JSONArray();
         List<SequencingRun> runs = SequencingRun.toList(query.list(dc));
         for (SequencingRun run : runs)
         {
-          run.loadAnnotations(dc, "sequencingStart", Annotationtype.SEQUENCING_START, Reggie.CONVERTER_DATE_TO_STRING);
+          run.loadAnnotations(dc, "SequencingStart", Annotationtype.SEQUENCING_START, Reggie.CONVERTER_DATE_TO_STRING);
+          run.loadAnnotations(dc, "HiSeqPosition", Annotationtype.HISEQ_POSITION, null);
           run.setAnnotation("comments", run.getDerivedBioAssay().getDescription());
           
-          JSONArray jsonFlowCells = new JSONArray();
-          List<FlowCell> flowCells = FlowCell.getBySequencingRun(dc, run);
-          for (FlowCell fc : flowCells)
-          {
-            fc.loadAnnotations(dc, "FlowCellID", Annotationtype.FLOWCELL_ID, null);
-            fc.loadAnnotations(dc, "HiSeqPosition", Annotationtype.HISEQ_POSITION, null);
-            fc.setAnnotation("comments", fc.getItem().getDescription());
-            jsonFlowCells.add(fc.asJSONObject());
-          }
-          run.setAnnotation("flowCells", jsonFlowCells);
+          FlowCell fc = FlowCell.getBySequencingRun(dc, run);
+          fc.loadAnnotations(dc, "FlowCellID", Annotationtype.FLOWCELL_ID, null);
+          fc.setAnnotation("comments", fc.getItem().getDescription());
+          
+          run.setAnnotation("flowCell", fc.asJSONObject());
           jsonRuns.add(run.asJSONObject());
         }
@@ -126 +121 @@
           seqRun.loadAnnotations(dc, "SequencingStart", Annotationtype.SEQUENCING_START, Reggie.CONVERTER_DATE_TO_STRING);
           seqRun.loadAnnotations(dc, "SequencingEnd", Annotationtype.SEQUENCING_END, Reggie.CONVERTER_DATE_TO_STRING);
+          seqRun.loadAnnotations(dc, "SequencingResult", Annotationtype.SEQUENCING_RESULT, null);
           seqRun.loadAnnotations(dc, "DataFilesFolder", Annotationtype.DATA_FILES_FOLDER, null);
           jsonSeqRuns.add(seqRun.asJSONObject());
@@ -197 +193 @@
         Number flowCellId = (Number)jsonFlowCell.get("id");
         PhysicalBioAssay flowCell = PhysicalBioAssay.getById(dc, flowCellId.intValue());
+        // Clear result of any previous sequencing runs (eg. FirstBaseReportFailed)
+        Annotationtype.SEQUENCING_RESULT.setAnnotationValue(dc, flowCell, null);
         sequenceRun.addPhysicalBioAssay(flowCell);
         
@@ -218 +216 @@
         JSONObject jsonReq = (JSONObject)new JSONParser().parse(req.getReader());
         JSONObject jsonSeq = (JSONObject)jsonReq.get("sequencingRun");
-        JSONArray jsonFlowCells = (JSONArray)jsonSeq.get("flowCells");
+        JSONObject jsonFlowCell = (JSONObject)jsonSeq.get("flowCell");
 
         Number seqId = (Number)jsonSeq.get("id");
         DerivedBioAssay seqRun = DerivedBioAssay.getById(dc, seqId.intValue());
+        Number flowCellId = (Number)jsonFlowCell.get("id");
+        PhysicalBioAssay fc = PhysicalBioAssay.getById(dc, flowCellId.intValue());
         
         Date turnAroundDate = Reggie.CONVERTER_STRING_TO_DATETIME.convert((String)jsonSeq.get("turnAroundDate"));
@@ -227 +227 @@
         Annotationtype.SEQUENCING_TURN_AROUND.setAnnotationValue(dc, seqRun, turnAroundDate);
         Annotationtype.SEQUENCING_END.setAnnotationValue(dc, seqRun, endDate);
-        
         seqRun.setDescription((String)jsonSeq.get("comments"));
         
-        for (int fcNo = 0; fcNo < jsonFlowCells.size(); ++fcNo)
-        {
-          JSONObject jsonFlowCell = (JSONObject)jsonFlowCells.get(fcNo);
-          Number fcId = (Number)jsonFlowCell.get("id");
-
-          PhysicalBioAssay flowCell = PhysicalBioAssay.getById(dc, fcId.intValue());
-          flowCell.setDescription((String)jsonFlowCell.get("comments"));
-        }
-        
-        jsonMessages.add(seqRun.getName() + " registered as ended.");
+        if (Boolean.TRUE.equals(jsonSeq.get("firstBaseReportFailed")))
+        {
+          Annotationtype.SEQUENCING_RESULT.setAnnotationValue(dc, seqRun, SequencingRun.SEQUENCING_FIRST_BASE_REPORT_FAILED);
+          Annotationtype.SEQUENCING_RESULT.setAnnotationValue(dc, fc, SequencingRun.SEQUENCING_FIRST_BASE_REPORT_FAILED);
+          jsonMessages.add(seqRun.getName() + " registered as ended with status: " + SequencingRun.SEQUENCING_FIRST_BASE_REPORT_FAILED);
+        }
+        else
+        {
+          Annotationtype.SEQUENCING_RESULT.setAnnotationValue(dc, fc, null);
+          jsonMessages.add(seqRun.getName() + " registered as ended.");
+        }
+        
         dc.commit();
       }