Changeset 5797

Timestamp:

Dec 18, 2019, 8:33:26 AM (2 years ago)

Author:

Nicklas Nordborg

Message:

References #1216: Finalize the "Confirm MIPs demux" wizard

Added some more columns: Plate, Barcode and MIPS_Panel. Also changed the sort order to sort by plate location.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/mipsanalysis/demux_confirm.js (modified) (6 diffs)
• src/net/sf/basedb/reggie/servlet/DemuxMergeServlet.java (modified) (2 diffs)

extensions/net.sf.basedb.reggie/trunk/resources/mipsanalysis/demux_confirm.js

@@ -198 +198 @@
     var url = '../DemuxMerge.servlet?ID='+App.getSessionId();
     url += '&cmd=GetMergedSequences&job='+job.id;
+    url += '&pipeline=MIPS';
     
     Wizard.showLoadingAnimation('Loading demuxed sequences...');
@@ -214 +215 @@
     
     var mergedSeq = response.mergedSequences;
-    mergedSeq.sort(demux.sortByPool);
+    mergedSeq.sort(demux.sortByLibPlate);
     job.mergedSequences = mergedSeq;
       
@@ -221 +222 @@
     // Header row
     html += '<tr>';
+    html += '<th></th>';
+    html += '<th></th>';
+    html += '<th></th>';
     html += '<th></th>';
     html += '<th class="dottedleft"></th>';
@@ -228 +232 @@
     html += '</tr>';
     html += '<tr>';
+    html += '<th>Plate</th>';
     html += '<th>Library</th>';
-    html += '<th class="dottedleft">Pools</th>';
+    html += '<th>MIPS_Panel</th>';
+    html += '<th>Barcode</th>';
+    html += '<th class="dottedleft">Pool</th>';
     html += '<th class="dottedleft">READS</th>';
     html += '<th>PF_READS</th>';
@@ -267 +274 @@
         html += 'style="border-top: 1px solid #000000;"';
       }
-      html += '><td class="prompt if-yellow">'+img+Strings.encodeTags(merged.name)+'</td>';
+      html += '><td>'+Strings.encodeTags(lib.bioWell.bioPlate.name+' '+lib.bioWell.location)+'</td>';
+      html += '<td class="prompt if-yellow">'+img+Strings.encodeTags(merged.name)+'</td>';
+      html += '<td>'+Strings.encodeTags(lib.MIPSPanel)+'</td>';
+      html += '<td>'+Strings.encodeTags(lib.barcode.name)+'</td>';
       html += '<td class="dottedleft">';
       for (var poolNo = 0; poolNo < pools.length; poolNo++)
@@ -329 +339 @@
     return a.id - b.id;
   }
+  
+  /**
+    Sort by library plate location.
+  */
+  demux.sortByLibPlate = function(a, b)
+  {
+    var p1 = a.lib.bioWell.bioPlate.name;
+    var p2 = b.lib.bioWell.bioPlate.name;
+    if (p1 < p2) return -1;
+    if (p1 > p2) return 1;
+    var w1 = a.lib.bioWell;
+    var w2 = b.lib.bioWell;
+    if (w1.column != w2.column) return w1.column - w2.column;
+    return w1.row - w2.row;
+  }
 
   demux.outcomeOnChange = function()

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

@@ -221 +221 @@
       {
         int jobId = Values.getInt(req.getParameter("job"));
+        Pipeline pipeline = Pipeline.getByCName(req.getParameter("pipeline"));
         dc = sc.newDbControl();
         
@@ -239 +240 @@
         {
           Library lib = mg.getLibrary(dc);
+          lib.loadBioPlateLocation();
+          if (pipeline == Pipeline.MIPS)
+          {
+            Extract dna = (Extract)lib.findSingleParent(dc, Subtype.DNA_NORMALIZED_ALIQUOT);
+            lib.setAnnotation("MIPSPanel", Annotationtype.MIPS_PANEL.getAnnotationValue(dc, dna));
+          }
           // All pools for the library, but we only keep those used in the demux
           List<PooledLibrary> pools = lib.getPools(dc);