Changeset 5788

Timestamp:

Dec 13, 2019, 11:49:44 AM (3 years ago)

Author:

Nicklas Nordborg

Message:

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

The wizard now display "Align" as the next step and also put selected items into the "MIPs Alignment Pipeline" list.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/index.jsp (modified) (2 diffs)
• resources/mipsanalysis/demux_confirm.js (modified) (5 diffs)
• resources/mipsanalysis/demux_confirm.jsp (modified) (1 diff)
• src/net/sf/basedb/reggie/servlet/DemuxMergeServlet.java (modified) (5 diffs)

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

@@ -971 +971 @@
             <dt>
               <base:icon image="<%=home+"/images/server.png" %>" />
-              Demux and merge wizards
+              Demux wizards
             </dt>
             <dd>
@@ -981 +981 @@
               
               <li><span class="require-permission" data-role="MIPsSecondaryAnalysis" data-link="analysis/demux_start.jsp?ID=<%=ID%>&pipeline=MIPS"
-                >Start demux and merge</span> 
+                >Start demux</span> 
                 <span class="counter" data-counter="sequencing-runs-for-demux-mips" 
                   title="Number of confirmed MIPs sequencing runs waiting to be demuxed">∙</span>
               
               <li><span class="require-permission" data-role="MIPsSecondaryAnalysis" data-link="mipsanalysis/demux_confirm.jsp?ID=<%=ID%>"
-                >Confirm demux and merge completed</span> 
+                >Confirm demux completed</span> 
                 <span class="counter" data-counter="demux-jobs-not-confirmed-mips"
                   title="Number of MIPs demux jobs waiting for confirmation">∙</span>

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

@@ -199 +199 @@
     url += '&cmd=GetMergedSequences&job='+job.id;
     
-    Wizard.showLoadingAnimation('Loading merged sequences...');
+    Wizard.showLoadingAnimation('Loading demuxed sequences...');
     Wizard.asyncJsonRequest(url, demux.mergedSequencesLoaded);
   }
@@ -234 +234 @@
     html += '<th class="warning-col"></th>';
     html += '<th class="dottedleft">Flag DNA</th>';
-    html += '<th>????</th>';
+    html += '<th>Align</th>';
     html += '<th class="dottedleft"></th>';
     html += '</tr>';
@@ -297 +297 @@
         }
           
-        html += '<td><input type="checkbox" name="nextStepTODO.'+merged.id+'" '+(alignChecked ? ' checked':'')+'></td>';
+        html += '<td><input type="checkbox" name="mipsAlign.'+merged.id+'" '+(alignChecked ? ' checked':'')+'></td>';
         html += '<td class="dottedleft comment"><input type="text" name="comment.'+merged.id+'"></td>';
       }
@@ -351 +351 @@
         demux.resetCheckbox(frm['flag.'+merge.id]);
       }
-      if (frm['nextStepTODO.'+merge.id])
-      {
-        frm['nextStepTODO.'+merge.id].disabled = failed;
-        demux.resetCheckbox(frm['nextStepTODO.'+merge.id]);
+      if (frm['mipsAlign.'+merge.id])
+      {
+        frm['mipsAlign.'+merge.id].disabled = failed;
+        demux.resetCheckbox(frm['mipsAlign.'+merge.id]);
       }
       if (frm['comment.'+merge.id])
@@ -414 +414 @@
         tmp.id = merge.id;
         tmp.flag = frm['flag.'+merge.id] && frm['flag.'+merge.id].checked;
-        tmp.nextStepTODO = frm['nextStepTODO.'+merge.id].checked;
+        tmp.mipsAlign = frm['mipsAlign.'+merge.id].checked;
         tmp.comment = frm['comment.'+merge.id].value;
         merged[merged.length] = tmp;

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

@@ -111 +111 @@
   <p:path><p:pathelement 
     title="Reggie" href="<%="../index.jsp?ID="+ID%>" 
-    /><p:pathelement title="Confirm demux and merge ended" 
+    /><p:pathelement title="Confirm demux ended" 
     /></p:path>
 

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

@@ -457 +457 @@
         int numHisatAlign = 0;
         int numLegacyAlign = 0;
-        int numNextStepTODO = 0; // TODO - MIPs
+        int numMipsAlign = 0;
         int numConfirmed = 0;
         int numFlaggedRna = 0;
@@ -466 +466 @@
         ItemList hisatPipeline = BiomaterialList.HISAT_PIPELINE.load(dc);
         ItemList legacyPipeline = BiomaterialList.LEGACY_PIPELINE.load(dc);
-        ItemList mipsPipeline = null; // TODO - MIPs
+        ItemList mipsPipeline = BiomaterialList.MIPS_ALIGN_PIPELINE.load(dc);
 
         for (int mergeNo = 0; mergeNo < jsonMergedSequences.size(); ++mergeNo)
@@ -474 +474 @@
           boolean legacyAlign = !failed && Boolean.TRUE.equals(jsonMerge.get("legacyAlign"));
           boolean hisatAlign = !failed && Boolean.TRUE.equals(jsonMerge.get("hisatAlign"));
-          boolean nextStepTODO = !failed && Boolean.TRUE.equals(jsonMerge.get("nextStepTODO"));
+          boolean mipsAlign = !failed && Boolean.TRUE.equals(jsonMerge.get("mipsAlign"));
               
-          boolean align = legacyAlign || hisatAlign || nextStepTODO;
+          boolean align = legacyAlign || hisatAlign || mipsAlign;
           if (align) numConfirmed++;
           
@@ -526 +526 @@
           else if (pipeline == Pipeline.MIPS)
           {
-            // TODO - MIPs
-            if (nextStepTODO)
-            {
-//              mipsPipeline.add(merge);
-              numNextStepTODO++;
+            if (mipsAlign)
+            {
+              mipsPipeline.add(merge);
+              numMipsAlign++;
             }
             
@@ -570 +569 @@
         else if (pipeline == Pipeline.MIPS)
         {
-          if (numNextStepTODO > 0)
-          {
-            jsonMessages.add(numNextStepTODO + " libraries confirmed for next MIPs step (TODO)");
+          if (numMipsAlign > 0)
+          {
+            jsonMessages.add(numMipsAlign + " libraries confirmed for MIPs alignment");
           }
           else
           {
-            jsonMessages.add("No libraries confirmed for next MIPs step");
-          }         
+            jsonMessages.add("No libraries confirmed for MIPs alignment");
+          }
         }