Changeset 2226

Timestamp:

Feb 13, 2014, 1:44:46 PM (9 years ago)

Author:

Nicklas Nordborg

Message:

References #546: Confirm sequencing as completed

First version of 'Confirm sequencing completed' wizard. It's really simple. After selecting if a sequencing failed or succeeded there is a field for comments and a possibility to mark individual lanes as failed (if the sequencing was otherwise successful).

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/analysis (added)
• resources/analysis/sequencing_confirm.jsp (added)
• resources/index.jsp (modified) (3 diffs)
• src/net/sf/basedb/reggie/dao/Annotationtype.java (modified) (2 diffs)
• src/net/sf/basedb/reggie/plugins/FlowCellSampleSheetExporter.java (modified) (6 diffs)
• src/net/sf/basedb/reggie/servlet/InstallServlet.java (modified) (2 diffs)
• src/net/sf/basedb/reggie/servlet/SequencingRunServlet.java (modified) (5 diffs)

extensions/net.sf.basedb.reggie/trunk/resources/index.jsp

@@ -224 +224 @@
       url = 'SequencingRun.servlet?ID=<%=ID%>&cmd=CountActiveSequencingRuns';
     }
+    else if (what == 'unconfirmed-sequencing-runs')
+    {
+      url = 'SequencingRun.servlet?ID=<%=ID%>&cmd=CountUncomfirmedSequencingRuns';
+    }
     
     if (url)
@@ -390 +394 @@
       var count = error ? -1 : response.count;
       setCount('count.sequencing-run', count, 'sequencing runs', msg);
+      startCounting('unconfirmed-sequencing-runs');
+    }
+    else if (currentCount == 'unconfirmed-sequencing-runs')
+    {
+      var msg = error || 'Number of ended but not confirmed sequencing runs';
+      var count = error ? -1 : response.count;
+      setCount('count.unconfirmed-sequencing-run', count, 'sequencing runs', msg);
     }
     
@@ -687 +698 @@
           <dd>
             <ul>
-            <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/sequencing_end.jsp?ID=<%=ID%>"
-              >Confirm sequencing completed</span> 
+            <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/sequencing_confirm.jsp?ID=<%=ID%>"
+              >Confirm sequencing completed</span> <span class="counter" id="count.unconfirmed-sequencing-run" title="Counting..."><img src="images/loading-small.gif"></span>
+            
             <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/demux_start.jsp?ID=<%=ID%>"
               >Start demux and merge</span> 

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

@@ -674 +674 @@
     new Annotationtype("SequencingCycles", Type.STRING, Item.PHYSICALBIOASSAY, Item.DERIVEDBIOASSAY);
 
-  
+  /**
+    The "FailedLanes" annotation, used for physical bioassays (FlowCell).
+    It is a multi-valued annotation type representing the index numbers
+    of lanes that failed during sequencing of a flow cell. The index numbers
+    go from 1 to the size of the flow cell (eg. 1-8).
+    @since 2.15
+  */
+  public static final Annotationtype FAILED_LANES = 
+    new Annotationtype("FailedLanes", Type.INT, Item.PHYSICALBIOASSAY);
+
   /**
     The "HiSeqPosition" annotation, used for derived bioassays (SequencingRun).
@@ -953 +962 @@
     }
   }
+  
+  /**
+    Set a multi-valued annotation on an item. If the values list is null or 
+    emtpy the annotation will be removed.
+    @since 2.15
+  */
+  public void setAnnotationValues(DbControl dc, Annotatable item, List<?> values)
+  {
+    AnnotationType at = load(dc);
+    if (values == null || values.isEmpty())
+    {
+      if (item.isAnnotated() && item.getAnnotationSet().hasAnnotation(at))
+      {
+        item.getAnnotationSet().removeAnnotation(at);
+      }
+    }
+    else
+    {
+      item.getAnnotationSet().getAnnotation(at).setValues(values);
+    }
+  }
 
   /**

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/plugins/FlowCellSampleSheetExporter.java

@@ -197 +197 @@
         storeValue(job, request, ri.getParameter("Width"));
         storeValue(job, request, ri.getParameter("Concentration"));
+        storeValue(job, request, ri.getParameter("FailedLanes"));
 
         if (request.getParameterValue(SAVE_AS) == null)
@@ -301 +302 @@
       parameters);
   }
+  @SuppressWarnings("unchecked")
   private RequestInformation getConfigureJobParameters(Boolean requireFile)
   {
@@ -346 +348 @@
         parameters.add(getWidthParameter());
         parameters.add(getConcentrationParameter());
+        
+        if (currentBioAssay != null)
+        {
+          List<Integer> failedLanes = new ArrayList<Integer>((List<Integer>)Annotationtype.FAILED_LANES.getAnnotationValues(dc, currentBioAssay));
+          Collections.sort(failedLanes);
+          if (failedLanes.size() > 0)
+          {
+            parameters.add(getFailedLanesParameter(failedLanes));
+          }
+        }
         
       }
@@ -417 +429 @@
     info[18] = flowCell.getName();  // Description
     
+    boolean includeFailedLanes = getParameter(parameters, "FailedLanes", "Exclude").equals("Include");
+    List<Integer> failedLanes = (List<Integer>)(includeFailedLanes ? Collections.emptyList() : Annotationtype.FAILED_LANES.getAnnotationValues(dc, flowCell));
+    
     //Query to get all non-empty wells on the plate
     SpecialQuery<BioMaterialEventSource> query = flowCell.getCreationEvent().getEventSources();
@@ -425 +440 @@
       Extract poolA = (Extract)src.getBioMaterial(); // Aliquot from pool for current lane
       int laneNo = src.getPosition();
+      
+      if (failedLanes.contains(laneNo))
+      {
+        if (progress != null)
+        {
+          progress.display(10 + 80 * laneNo/numLanes, "Skipping failed lane " + laneNo + " of " + flowCell.getSize());
+        }
+        continue; // Do not export failed lanes;
+      }
       
       if (progress != null)
@@ -608 +632 @@
   }
   
+  private PluginParameter<String> getFailedLanesParameter(List<Integer> failedLanes)
+  {
+    Integer lastLane = failedLanes.get(failedLanes.size()-1);
+    String lanes;
+    if (failedLanes.size() == 1)
+    {
+      lanes = "Lane <b>" + lastLane.toString() + "</b>";
+    }
+    else
+    {
+      lanes = "Lanes <b>" + Values.getString(failedLanes.subList(0, failedLanes.size()-1), ", ", true) + " and " + lastLane+"</b>";
+    }
+    
+    PluginParameter<String> parameter = new PluginParameter<String>("FailedLanes", "Failed lanes", 
+        lanes + " failed during sequencing. " +
+        "By default, the exporter <i>Exclude</i> sample information for those lanes.\n" +
+        "Select <i>Include</i> to include sample information for all lanes.", 
+        new StringParameterType(255, "Exclude", false, 1, 0, 0, Arrays.asList("Exclude", "Include"))
+        );
+    return parameter;
+  }
+  
   private String sequencingCycles2ReadString(String sequencingCycles)
   {

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

@@ -331 +331 @@
         jsonChecks.add(checkAnnotationType(dc, Annotationtype.READ_STRING, 1, null, effectivePermissionsUse, createIfMissing));
         jsonChecks.add(checkAnnotationType(dc, Annotationtype.SEQUENCING_CYCLES, 1, null, effectivePermissionsUse, createIfMissing));
+        jsonChecks.add(checkAnnotationType(dc, Annotationtype.FAILED_LANES, 0, null, effectivePermissionsUse, createIfMissing));
 
         jsonChecks.add(checkAnnotationType(dc, Annotationtype.SEQUENCING_START, 1, null, effectivePermissionsUse, createIfMissing));
@@ -427 +428 @@
         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_RESULT));
+
+            Annotationtype.SEQUENCING_CYCLES, Annotationtype.FAILED_LANES,
+            Annotationtype.PLATE_PROCESS_RESULT, Annotationtype.SEQUENCING_RESULT));
         
         jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.SEQUENCING_RUN, createIfMissing, 

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

@@ -3 +3 @@
 import java.io.IOException;
 import java.util.Date;
+import java.util.HashSet;
 import java.util.List;
+import java.util.Set;
 
 import javax.servlet.ServletException;
@@ -15 +17 @@
 
 import net.sf.basedb.core.Application;
+import net.sf.basedb.core.BioMaterialList;
 import net.sf.basedb.core.DbControl;
 import net.sf.basedb.core.DerivedBioAssay;
+import net.sf.basedb.core.Extract;
 import net.sf.basedb.core.Hardware;
 import net.sf.basedb.core.ItemQuery;
@@ -27 +31 @@
 import net.sf.basedb.reggie.Reggie;
 import net.sf.basedb.reggie.dao.Annotationtype;
+import net.sf.basedb.reggie.dao.BiomaterialList;
 import net.sf.basedb.reggie.dao.FlowCell;
+import net.sf.basedb.reggie.dao.PooledLibrary;
 import net.sf.basedb.reggie.dao.ReggieRole;
 import net.sf.basedb.reggie.dao.SequencingRun;
@@ -102 +108 @@
           fc.loadAnnotations(dc, "FlowCellID", Annotationtype.FLOWCELL_ID, null);
           fc.setAnnotation("comments", fc.getItem().getDescription());
+          
+          run.setAnnotation("flowCell", fc.asJSONObject());
+          jsonRuns.add(run.asJSONObject());
+        }
+        
+        json.put("sequencingRuns", jsonRuns);
+      }
+      else if ("CountUncomfirmedSequencingRuns".equals(cmd))
+      {
+        dc = sc.newDbControl();
+        ItemQuery<DerivedBioAssay> query = DerivedBioAssay.getQuery();
+        query.setIncludes(Reggie.INCLUDE_IN_CURRENT_PROJECT);
+        Subtype.SEQUENCING_RUN.addFilter(dc, query);
+        // Must have a SEQUENCING_END annotation
+        query.join(Annotations.leftJoin(null, Annotationtype.SEQUENCING_END.load(dc), "sse"));
+        query.restrict(Restrictions.neq(Hql.alias("sse"), null));
+        // Must NOT have a SEQUENCING_RESULT annotation
+        query.join(Annotations.leftJoin(null, Annotationtype.SEQUENCING_RESULT.load(dc), "ssr"));
+        query.restrict(Restrictions.eq(Hql.alias("ssr"), null));
+        long count = query.count(dc);
+        json.put("count", count);
+      }
+      else if ("GetUnconfirmedSequencingRuns".equals(cmd))
+      {
+        dc = sc.newDbControl();
+        ItemQuery<DerivedBioAssay> query = DerivedBioAssay.getQuery();
+        query.setIncludes(Reggie.INCLUDE_IN_CURRENT_PROJECT);
+        Subtype.SEQUENCING_RUN.addFilter(dc, query);
+        // Must have a SEQUENCING_END annotation
+        query.join(Annotations.leftJoin(null, Annotationtype.SEQUENCING_END.load(dc), "sse"));
+        query.restrict(Restrictions.neq(Hql.alias("sse"), null));
+        // Must NOT have a SEQUENCING_RESULT annotation
+        query.join(Annotations.leftJoin(null, Annotationtype.SEQUENCING_RESULT.load(dc), "ssr"));
+        query.restrict(Restrictions.eq(Hql.alias("ssr"), 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, "SequencingTurnAround", Annotationtype.SEQUENCING_TURN_AROUND, Reggie.CONVERTER_DATETIME_TO_STRING);
+          run.loadAnnotations(dc, "SequencingEnd", Annotationtype.SEQUENCING_END, Reggie.CONVERTER_DATETIME_TO_STRING);
+          run.loadAnnotations(dc, "HiSeqPosition", Annotationtype.HISEQ_POSITION, null);
+          run.setAnnotation("comments", run.getDerivedBioAssay().getDescription());
+          
+          FlowCell fc = FlowCell.getBySequencingRun(dc, run);
+          PhysicalBioAssay pba = fc.getItem();
+          fc.loadAnnotations(dc, "FlowCellID", Annotationtype.FLOWCELL_ID, null);
+          fc.setAnnotation("numLanes", pba.getSize());
+          fc.setAnnotation("comments", pba.getDescription());
           
           run.setAnnotation("flowCell", fc.asJSONObject());
@@ -243 +299 @@
         dc.commit();
       }
+      else if ("ConfirmSequencingEnded".equals(cmd))
+      {
+        dc = sc.newDbControl();
+
+        ReggieRole.checkPermission(dc, "'" + cmd + "' wizard", ReggieRole.SECONDARY_ANALYSIS, ReggieRole.ADMINISTRATOR);
+
+        JSONObject jsonReq = (JSONObject)new JSONParser().parse(req.getReader());
+        JSONObject jsonSeq = (JSONObject)jsonReq.get("sequencingRun");
+        JSONObject jsonFlowCell = (JSONObject)jsonSeq.get("flowCell");
+        boolean failed = Boolean.TRUE.equals(jsonReq.get("failed"));
+
+        Number seqId = (Number)jsonSeq.get("id");
+        DerivedBioAssay seqRun = DerivedBioAssay.getById(dc, seqId.intValue());
+        seqRun.setDescription((String)jsonSeq.get("comments"));
+        
+        BioMaterialList flaggedPools = null;
+        Set<Extract> pools = null;
+        int numFlagged = 0;
+        if (failed)
+        {
+          flaggedPools = BiomaterialList.FLAGGED_POOL.load(dc);
+          pools = new HashSet<Extract>();
+        }
+        
+        Number fcId = (Number)jsonFlowCell.get("id");
+        PhysicalBioAssay flowCell = PhysicalBioAssay.getById(dc, fcId.intValue());
+          
+        if (failed)
+        {
+          // Load pool aliquots and pools for all lanes 
+          ItemQuery<Extract> aliquotQuery = flowCell.getExtracts(0);
+          aliquotQuery.setIncludes(Reggie.INCLUDE_IN_CURRENT_PROJECT);
+          List<Extract> aliquots = aliquotQuery.list(dc);
+
+          // If sequencing failed, we flag the pools and add them to the 'Flagged pools' list.
+          // Typically, most pools have enough material to try clustering again but that
+          // the responsibility of another wizard
+          for (Extract poolA : aliquots)
+          {
+            Extract pool = (Extract)poolA.getParent();
+            if (!pools.contains(pool))
+            {
+              pools.add(pool);
+              flaggedPools.add(pool);
+              numFlagged++;
+              Annotationtype.FLAG.setAnnotationValue(dc, pool, PooledLibrary.FLAG_SEQUENCING_FAILED);
+              Annotationtype.AUTO_PROCESSING.setAnnotationValue(dc, pool, "Disable");
+            }
+          }
+        }
+        else
+        {
+          JSONArray jsonFailedLanes = (JSONArray)jsonFlowCell.get("failedLanes");
+          Annotationtype.FAILED_LANES.setAnnotationValues(dc, flowCell, jsonFailedLanes);
+          if (jsonFailedLanes.size() > 0)
+          {
+            Object lastLane = jsonFailedLanes.get(jsonFailedLanes.size()-1);
+            String lanes;
+            if (jsonFailedLanes.size() == 1)
+            {
+              lanes = "Lane " + lastLane.toString();
+            }
+            else
+            {
+              lanes = "Lanes " + Values.getString(jsonFailedLanes.subList(0, jsonFailedLanes.size()-1), ", ", true) + " and " + lastLane;
+            }
+
+            jsonMessages.add(lanes + " registered as failed.");
+          }
+        }
+        
+        if (failed)
+        {
+          Annotationtype.SEQUENCING_RESULT.setAnnotationValue(dc, seqRun, SequencingRun.SEQUENCING_FAILED);
+          jsonMessages.add(seqRun.getName() + " confirmed as failed.");
+        }
+        else
+        {
+          Annotationtype.SEQUENCING_RESULT.setAnnotationValue(dc, seqRun, SequencingRun.SEQUENCING_SUCCESSFUL);
+          jsonMessages.add(seqRun.getName() + " confirmed as successful.");
+        }
+        
+        if (numFlagged > 0)
+        {
+          jsonMessages.add("Added " + numFlagged + " pools to '" + flaggedPools.getName() + "' list.");
+        }
+
+        dc.commit();
+      }
 
       json.put("messages", jsonMessages);