Changeset 2232

Timestamp:

Feb 17, 2014, 3:30:06 PM (9 years ago)

Author:

Nicklas Nordborg

Message:

References #575: Add sequencing information to case summary

Include some information about sequencing runs in the case summary.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/reports/case_summary.jsp (modified) (3 diffs)
• src/net/sf/basedb/reggie/dao/SequencingRun.java (modified) (2 diffs)
• src/net/sf/basedb/reggie/servlet/CaseSummaryServlet.java (modified) (6 diffs)

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

@@ -780 +780 @@
     }
   }
+  
+  var sequencingRuns = consentOk ? response.sequencingRun : null;
+  if (sequencingRuns && sequencingRuns.length > 0)
+  {
+    var truncateAt = TRUNCATE_SIZE[Math.min(sequencingRuns.length-1, TRUNCATE_SIZE.length)];
+    for (var i = 0; i < sequencingRuns.length; i++)
+    {
+      var sr = sequencingRuns[i];
+      var fc = sr.flowCell;
+      addColumn('sequencingRun.name', makeLink('DERIVEDBIOASSAY', sr));
+      addColumn('sequencingRun.flowCell', makeLink('PHYSICALBIOASSAY', fc));
+      addColumn('sequencingRun.result', (sr.result && sr.result != 'Successful') ? asFailInfo(sr.result, 'error.png') : null);
+      addColumn('sequencingRun.clusterDate', formatDate(fc.clusterDate));
+      addColumn('sequencingRun.startDate', formatDate(sr.startDate));
+      addColumn('sequencingRun.endDate', formatDate(sr.endDate));
+      addColumn('sequencingRun.comment', truncate(sr.comment, truncateAt));
+    }
+  }
+  else
+  {
+    if (consentOk)
+    {
+      addColumn('sequencingRun.name', asNoInfo('No sequencing information has been registered'));
+      Main.hide('sequencingRun-details');
+    }
+    else
+    {
+      Main.hide('sequencingRun-info');
+    }
+    
+  }
 }
 
@@ -847 +878 @@
     var details = document.getElementById(section.id+'-details');
     // If the details section is 'forcibly' hidden (eg. no items of that type), ignore this call
-    if (details.style.display != 'none')
+    if (details && details.style.display != 'none')
     {
       var headerDiv = document.getElementById(section.id+'-header');
@@ -1514 +1545 @@
           </div>
         </div>
+  
+        <div class="info-section" id="sequencingRun-info">
+          <div>
+          <table class="info-table dynamic-columns">
+          <thead>
+            <tr id="sequencingRun.name">
+              <th id="sequencingRun-header">Sequencing runs</th>
+            </tr>
+          </thead>
+          <tbody id="sequencingRun-details" class="info-details">
+            <tr id="sequencingRun.flowCell">
+              <th>Flow cell</th>
+            </tr>
+            <tr id="sequencingRun.clusterDate">
+              <th>Cluster date</th>
+            </tr>
+            <tr id="sequencingRun.startDate">
+              <th>Start date</th>
+            </tr>
+            <tr id="sequencingRun.endDate">
+              <th>End date</th>
+            </tr>
+            <tr id="sequencingRun.result" class="dynamic-column">
+              <th>Sequencing result</th>
+            </tr>
+            <tr id="sequencingRun.comment" class="comment dynamic-column">
+              <th>Comment</th>
+            </tr>
+          </tbody>
+          </table>
+          </div>
+        </div>
         
       </div>

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

@@ -9 +9 @@
 import net.sf.basedb.core.DbControl;
 import net.sf.basedb.core.DerivedBioAssay;
+import net.sf.basedb.core.Extract;
 import net.sf.basedb.core.ItemQuery;
+import net.sf.basedb.core.Type;
 import net.sf.basedb.core.query.Expressions;
 import net.sf.basedb.core.query.Hql;
@@ -57 +59 @@
   }
   
+  
+  /**
+    Find all sequencing runs that include the library with the given case name.
+    This method will check for {@link Subtype#SEQUENCING_RUN} derived bioassays
+    that have a parent flow cell that include pools that contains libraries
+    with the given name.
+    @since 2.15
+  */
+  public static List<SequencingRun> findByCaseName(DbControl dc, String name)
+  {
+    // Get rid of suffixes in the name (eg. 'C' which is used for pre-neoadjuvant forms)
+    if (name.length() > 7) name = name.substring(0, 7);   
+  
+    // Find all 'Pooled library aliquot':s where the lib we are looking for is present
+    ItemQuery<Extract> poolQuery = Extract.getQuery();
+    Subtype.POOLED_LIBRARY_ALIQUOT.addFilter(dc, poolQuery);
+    poolQuery.setIncludes(Reggie.INCLUDE_IN_CURRENT_PROJECT);
+    poolQuery.join(Hql.innerJoin("parent", "pool"));
+    poolQuery.join(Hql.innerJoin("pool", "creationEvent", "poolc"));
+    poolQuery.join(Hql.innerJoin("poolc", "sources", "poolsrc"));
+    poolQuery.join(Hql.innerJoin("poolsrc", "bioMaterial", "lib"));
+    poolQuery.restrict(Restrictions.like(Hql.property("lib", "name"), Expressions.parameter("name", name+".%", Type.STRING)));
+    
+    // Find all Sequencing run items for flow cells that include any of the pools.
+    ItemQuery<DerivedBioAssay> query = DerivedBioAssay.getQuery();
+    Subtype.SEQUENCING_RUN.addFilter(dc, query);
+    query.setIncludes(Reggie.INCLUDE_IN_CURRENT_PROJECT);
+    query.join(Hql.innerJoin(null, "physicalBioAssays", "fc", true));
+    query.join(Hql.innerJoin("fc", "creationEvent", "fcc", true));
+    query.join(Hql.innerJoin("fcc", "sources", "src"));
+    query.join(Hql.innerJoin("src", "bioMaterial", "poolA"));
+    query.restrict(Restrictions.eq(Hql.alias("poolA"), Expressions.any(poolQuery)));
+    
+    return toList(query.list(dc));
+  }
+
   
   public static List<SequencingRun> findByFlowCell(DbControl dc, FlowCell fc)

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

@@ -23 +23 @@
 import net.sf.basedb.core.BioWell;
 import net.sf.basedb.core.DbControl;
+import net.sf.basedb.core.DerivedBioAssay;
 import net.sf.basedb.core.Extract;
 import net.sf.basedb.core.File;
@@ -29 +30 @@
 import net.sf.basedb.core.Permission;
 import net.sf.basedb.core.PermissionDeniedException;
+import net.sf.basedb.core.PhysicalBioAssay;
 import net.sf.basedb.core.Sample;
 import net.sf.basedb.core.SessionControl;
@@ -40 +42 @@
 import net.sf.basedb.reggie.dao.Consent;
 import net.sf.basedb.reggie.dao.Dna;
+import net.sf.basedb.reggie.dao.FlowCell;
 import net.sf.basedb.reggie.dao.FlowThrough;
 import net.sf.basedb.reggie.dao.Histology;
@@ -49 +52 @@
 import net.sf.basedb.reggie.dao.PooledLibrary;
 import net.sf.basedb.reggie.dao.Rna;
+import net.sf.basedb.reggie.dao.SequencingRun;
 import net.sf.basedb.reggie.dao.SpecimenTube;
 import net.sf.basedb.reggie.dao.Subtype;
@@ -331 +335 @@
           json.put("pooledlib", jsonPooledLib);
         }
+        
+        List<SequencingRun> sequencingRuns = SequencingRun.findByCaseName(dc, caseName);
+        if (sequencingRuns.size() > 0)
+        {
+          JSONArray jsonSequencingRun = new JSONArray();
+          for (SequencingRun sr : sequencingRuns)
+          {
+            loadSequencingRunInfo(dc, sr);
+            jsonSequencingRun.add(sr.asJSONObject());
+          }
+          jsonSections.add(loadSectionInfo(sc, "sequencingRun"));
+          json.put("sequencingRun", jsonSequencingRun);
+        }
+        
       }
     }
@@ -802 +820 @@
   }
   
+  private void loadSequencingRunInfo(DbControl dc, SequencingRun sr)
+  {
+    DerivedBioAssay dba = sr.getDerivedBioAssay();
+    
+    sr.setAnnotation("editable", dba.hasPermission(Permission.WRITE));
+    sr.loadAnnotations(dc, "startDate", Annotationtype.SEQUENCING_START, Reggie.CONVERTER_DATE_TO_STRING);
+    sr.loadAnnotations(dc, "endDate", Annotationtype.SEQUENCING_END, Reggie.CONVERTER_DATE_TO_STRING);
+    sr.loadAnnotations(dc, "result", Annotationtype.SEQUENCING_RESULT, null);
+    sr.setAnnotation("comment", dba.getDescription());
+    
+    FlowCell fc = FlowCell.getBySequencingRun(dc, sr);
+    PhysicalBioAssay pba = fc.getPhysicalBioAssay();
+    
+    fc.setAnnotation("editable", pba.hasPermission(Permission.WRITE));
+    fc.loadAnnotations(dc, "clusterDate", Annotationtype.CLUSTER_START, Reggie.CONVERTER_DATE_TO_STRING);
+    sr.setAnnotation("flowCell", fc.asJSONObject());
+  }
+  
   private BioPlate getBioPlate(MeasuredBioMaterial bioMaterial)
   {