Changeset 5731

Timestamp:

Nov 19, 2019, 10:04:42 AM (3 years ago)

Author:

Nicklas Nordborg

Message:

References #1199: Implement Variant calling pipeline

Added a variant calling section to the case summary.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/reports/case-summary.js (modified) (5 diffs)
• resources/reports/case_summary.jsp (modified) (2 diffs)
• src/net/sf/basedb/reggie/servlet/CaseSummaryServlet.java (modified) (4 diffs)

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

@@ -715 +715 @@
           cs.addColumn('rawBioAssays.geneReport', geneReport && geneReport.type == 'FILE' ? 'Yes '+cs.asFileLink(geneReport, 'pdffile.png') : 'No');
           cs.addColumn('rawBioAssays.pilotReport', pilotReport && pilotReport.type == 'FILE' ? 'Yes '+cs.asFileLink(pilotReport, 'pdffile.png') : 'No');
-          cs.addColumn('rawBioAssays.comment', cs.truncate(a.comment, truncateAt));
+          cs.addColumn('rawBioAssays.comment', cs.truncate(raw.comment, truncateAt));
         }
         catch (e)
@@ -730 +730 @@
     }
     
+    var variantCalling = response.variantCalling;
+    if (variantCalling && variantCalling.length > 0)
+    {
+      var truncateAt = TRUNCATE_SIZE[Math.min(variantCalling.length-1, TRUNCATE_SIZE.length)];
+      maxItemsInRightCol = Math.max(maxItemsInRightCol, variantCalling.length);
+      for (var i = 0; i < variantCalling.length; i++)
+      {
+        try
+        {
+          var vcall = variantCalling[i];
+          defaultColClass = cs.getDefaultColClass(vcall, yellowPrefixes);
+          cs.addColumn('variantCalling.name', cs.asLink('RAWBIOASSAY', vcall, 0, true));
+          cs.addColumn('variantCalling.donotuse', cs.asDoNotUse(vcall));
+          cs.addColumn('variantCalling.pipeline', vcall.pipeline);
+          var job = raw.job;
+          cs.addColumn('variantCalling.date', cs.asJob(job, truncateAt));
+          cs.addColumn('variantCalling.result', (vcall.result && vcall.result != 'Successful') ? cs.asFailInfo(vcall.result, 'error.png') : null);
+          cs.addColumn('variantCalling.variants', cs.asVariantsFile(vcall));
+          cs.addColumn('variantCalling.comment', cs.truncate(vcall.comment, truncateAt));
+        }
+        catch (e)
+        {
+          cs.logError('variantCalling-info', e);
+        }
+      }
+      defaultColClass = null;
+    }
+    else
+    {
+      cs.addColumn('variantCalling.name', cs.asNoInfo('No variant calling information has been registered'));
+      Doc.hide('variantCalling-details');
+    }
+
+    
     var linkedItems = document.getElementsByClassName('linked-item');
     for (var itemNo = 0; itemNo < linkedItems.length; itemNo++)
@@ -746 +780 @@
     {
       Events.addEventHandler(linkedVcf[i], 'click', cs.vcfLinkOnClick);
+    }
+
+    var linkedVcf = document.getElementsByClassName('variants-link');
+    for (var i = 0; i < linkedVcf.length; i++)
+    {
+      Events.addEventHandler(linkedVcf[i], 'click', cs.variantsLinkOnClick);
     }
     
@@ -1232 +1272 @@
   }
   
+  cs.asVariantsFile = function(vcall)
+  {
+    var result = cs.asCount(vcall.VariantsPassedFilter);
+    if (vcall.vcfFile)
+    {
+      result += '<span class="link variants-link" data-file-id="'+vcall.vcfFile.id+'" data-item-id="'+vcall.id+'"><img src="'+home+'/images/vcf_file.png" style="margin-left: 2px;"></span>';
+    }
+    return result;
+  }
+
+  
   cs.truncate = function(value, maxLength)
   {
@@ -1303 +1354 @@
   }
   
+  cs.variantsLinkOnClick = function(event)
+  {
+    var fileId = Data.int(event.currentTarget, 'file-id');
+    var itemId = Data.get(event.currentTarget, 'item-id');
+
+    var url = home+'/analysis/view_variants.jsp?ID=' + App.getSessionId();
+    url += '&fileId='+fileId;
+    url += '&itemId='+itemId;
+    Dialogs.openPopup(url, 'ViewVariants', 900, 600);
+  }
+
   cs.columnBalance = function(event)
   {

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

@@ -910 +910 @@
           <thead>
             <tr id="rawBioAssays.name">
-              <th id="rawBioAssays-header">Raw bioassays</th>
+              <th id="rawBioAssays-header">Expression profiles</th>
             </tr>
           </thead>
@@ -942 +942 @@
           </div>
         </div>
-        
+
+        <div class="info-section bg-filled-100" id="variantCalling-info">
+          <div>
+          <table class="info-table dynamic-columns">
+          <thead>
+            <tr id="variantCalling.name">
+              <th id="variantCalling-header">Variant calling</th>
+            </tr>
+          </thead>
+          <tbody id="variantCalling-details" class="info-details">
+            <tr id="variantCalling.donotuse" class="dynamic-column">
+              <th>DoNotUse</th>
+            </tr>
+            <tr id="variantCalling.pipeline">
+              <th>Pipeline</th>
+            </tr>
+            <tr id="variantCalling.date">
+              <th>Date</th>
+            </tr>
+            <tr id="variantCalling.result" class="dynamic-column">
+              <th>Result</th>
+            </tr>
+            <tr id="variantCalling.variants">
+              <th>Variants</th>
+            </tr>
+            <tr id="variantCalling.comment" class="comment dynamic-column">
+              <th>Comment</th>
+            </tr>
+          </tbody>
+          </table>
+          </div>
+        </div>        
       </div>
     </div>

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

@@ -49 +49 @@
 import net.sf.basedb.reggie.dao.CDna;
 import net.sf.basedb.reggie.dao.Consent;
+import net.sf.basedb.reggie.dao.Datafiletype;
 import net.sf.basedb.reggie.dao.Dna;
 import net.sf.basedb.reggie.dao.FlowCell;
@@ -61 +62 @@
 import net.sf.basedb.reggie.dao.PooledLibrary;
 import net.sf.basedb.reggie.dao.Rawbioassay;
+import net.sf.basedb.reggie.dao.Rawdatatype;
 import net.sf.basedb.reggie.dao.ReggieItem;
 import net.sf.basedb.reggie.dao.Rna;
@@ -471 +473 @@
         {
           JSONArray jsonRaw = new JSONArray();
+          JSONArray jsonVar = new JSONArray();
           for (Rawbioassay r : raw)
           {
-            loadRawBioAssayInfo(dc, r);
-            jsonRaw.add(r.asJSONObject());
+            if (Rawdatatype.VARIANT_CALL.getRawDataType().equals(r.getItem().getRawDataType()))
+            {
+              loadVariantCallingInfo(dc, r);
+              jsonVar.add(r.asJSONObject());
+            }
+            else
+            {
+              loadRawBioAssayInfo(dc, r);
+              jsonRaw.add(r.asJSONObject());
+            }
           }
           jsonSections.add(loadSectionInfo(sc, "rawBioAssays"));
           json.put("rawBioAssays", jsonRaw);
+          jsonSections.add(loadSectionInfo(sc, "variantCalling"));
+          json.put("variantCalling", jsonVar);
         }
         
@@ -1137 +1150 @@
 
 
+  private void loadVariantCallingInfo(DbControl dc, Rawbioassay raw)
+  {
+    RawBioAssay rba = raw.getRawBioAssay();
+    Job job = rba.getJob();
+    raw.setAnnotation("rawDataType", rba.getRawDataType().getName());
+    raw.loadAnnotations(dc, "pipeline", Annotationtype.PIPELINE, null);
+    raw.setAnnotation("job", JsonUtil.getJobAsJSON(job));
+    raw.setAnnotation("editable", rba.hasPermission(Permission.WRITE));
+    raw.loadDoNotUseAnnotations(dc, null);
+    if (job != null && job.getEnded() != null)
+    {
+      raw.loadAnnotations(dc, "result", Annotationtype.ANALYSIS_RESULT, null);
+      raw.loadAnnotations(dc, "VariantsPassedFilter", Annotationtype.VARIANTS_PASSED_FILTER, null);
+      File vcf = raw.getFile(dc, Datafiletype.VCF);
+      if (vcf != null) raw.setAnnotation("vcfFile", JsonUtil.getFileAsJSON(vcf));
+    }
+    raw.setAnnotation("comment", rba.getDescription());
+  }
+
   
   private BioPlate getBioPlate(MeasuredBioMaterial bioMaterial)