Changeset 4989

Timestamp:

Sep 28, 2018, 1:44:07 PM (4 years ago)

Author:

Nicklas Nordborg

Message:

References #1054: Even more functionality in the Flagged alignment wizard

The "Start Hisat alignment" wizard now checks for items marked with DoNotUse. It will display a warning that must be confirmed before using such items.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/analysis/hisat_start.js (modified) (5 diffs)
• src/net/sf/basedb/reggie/servlet/HisatServlet.java (modified) (2 diffs)

extensions/net.sf.basedb.reggie/trunk/resources/analysis/hisat_start.js

@@ -5 +5 @@
   var subtypeMergedSequences = null;
   var clusterIsValid = false;
+  var manuallySelected = [];
   
   // Page initialization
@@ -13 +14 @@
     Buttons.addClickHandler('btnSelectMergedSequences', hisat.selectMergedSequences);
     Events.addEventHandler('mergedSequences', 'base-selected', hisat.setMergedSequenceCallback);
+    Events.addEventHandler('mergedSequences', 'change', hisat.mergedSequencesOnChange);
     Events.addEventHandler('step-1', 'wizard-validate', hisat.validateStep1);
 
@@ -49 +51 @@
       {
         var ms = mergedSequences[msNo];
-        var lib = ms.lib;
-        var isYellow = lib.specimen && lib.specimen.YellowLabel != null;
-        var libPlate = lib.bioWell ? lib.bioWell.bioPlate : null;
+        var libPlate = ms.lib.bioWell ? ms.lib.bioWell.bioPlate : null;
         if (firstPlate == null && libPlate != null) firstPlate = libPlate.name;
-        
-        var name = (msNo+1) + ': ';
-        if (libPlate) name += libPlate.name + ' - ';
-        name += ms.name;
-        if (ms.AutoProcess == 'ReProcess')
-        {
-          name += ' [R]';
-        }
-        
-        var option = new Option(name, ms.id, false, libPlate != null && libPlate.name==firstPlate);
-        if (isYellow) option.className = 'yellow';
-        option.mergedSequences = ms;
+        var option = hisat.createListOption(msNo+1, ms, ms.DO_NOT_USE == null && libPlate != null && libPlate.name==firstPlate)
         frm.mergedSequences.options[frm.mergedSequences.length] = option;
       }
@@ -101 +90 @@
     }
     
+    // Reset list
+    manuallySelected = [];
     var url = '&resetTemporary=1';
     url += '&tmpfilter:INT:itemSubtype='+subtypeMergedSequences.id;
@@ -109 +100 @@
   {
     var ms = event.detail;
-    
-    var frm = document.forms['reggie'];
-    var mergedSequences = frm.mergedSequences;
-    for (var i = 0; i < mergedSequences.length; i++)
-    {
-      if (mergedSequences[i].value == ms.id)
-      {
-        mergedSequences[i].selected = true;
-        Wizard.setInputStatus('mergedSequences');
-        return;
-      }
-    }
-
-    var ms = event.detail;
-    var option = new Option(ms.name, ms.id);
-    option.mergedSequences = ms;
-    option.selected = true;
-    mergedSequences[mergedSequences.length] = option;
-    Wizard.setInputStatus('mergedSequences');
-  }
-
+    manuallySelected[manuallySelected.length] = ms.id;
+    
+    if (ms.remaining == 0)
+    {
+      var url = '../Hisat.servlet?ID='+App.getSessionId();
+      url += '&cmd=GetMergedSequencesForHisat';
+      url += '&items='+manuallySelected.join(',');
+      Wizard.showLoadingAnimation('Loading bioassays...');
+      Wizard.asyncJsonRequest(url, hisat.manuallySelected);
+    }
+  }
+
+  hisat.manuallySelected = function(response)
+  {
+    var mergedSequences = response.mergedSequences;
+    var frm = document.forms['reggie']; 
+
+    if (mergedSequences != null && mergedSequences.length > 0)
+    {
+      var offset = frm.mergedSequences.length+1;
+      for (var msNo=0; msNo < mergedSequences.length; msNo++)
+      {
+        var ms = mergedSequences[msNo];
+        var option = hisat.createListOption(msNo+offset, ms, ms.DO_NOT_USE == null);
+        frm.mergedSequences.options[frm.mergedSequences.length] = option;
+      }
+    }
+  }
+  
+  hisat.createListOption = function(index, mergedItem, selected)
+  {
+    var lib = mergedItem.lib;
+    var isYellow = lib.specimen && lib.specimen.YellowLabel != null;
+    var libPlate = lib.bioWell ? lib.bioWell.bioPlate : null;
+    
+    var tooltip = null;
+    var name = (index) + ': ';
+    if (libPlate) name += libPlate.name + ' - ';
+    name += mergedItem.name;
+    
+    if (mergedItem.DO_NOT_USE)
+    {
+      name += ' [DoNotUse]';
+      tooltip = 'DoNotUse-'+Strings.encodeTags(mergedItem.DO_NOT_USE+': '+mergedItem.DO_NOT_USE_COMMENT);
+    }
+    else if (mergedItem.AutoProcess == 'ReProcess')
+    {
+      name += ' [R]';
+    }
+    
+    var option = new Option(name, mergedItem.id, false, selected);
+    if (isYellow) option.className = 'yellow';
+    if (tooltip) option.title = tooltip;
+    option.mergedSequences = mergedItem;
+    return option;
+  }
+  
+  hisat.mergedSequencesOnChange = function()
+  {
+    var frm = document.forms['reggie'];
+    
+    var numDoNotUse = 0;
+    for (var msNo = 0; msNo < frm.mergedSequences.length; msNo++)
+    {
+      if (frm.mergedSequences[msNo].selected) 
+      {
+        var ms = frm.mergedSequences[msNo].mergedSequences;
+        if (ms.DO_NOT_USE) numDoNotUse++;
+      }
+    }
+    
+    if (numDoNotUse > 0)
+    {
+      Wizard.setInputStatus('mergedSequences', 'warning', numDoNotUse + ' selected items marked as DoNotUse');
+      Wizard.showGoNextConfirmation(true, 'Confirm ' + numDoNotUse + ' items marked as DoNotUse');
+    }
+    else
+    {
+      Wizard.setInputStatus('mergedSequences');
+      Wizard.hideGoNextConfirmation();
+    }
+  }
   
   // --- Step 2 -----------------------------------

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

@@ -82 +82 @@
       {
         dc = sc.newDbControl();
-        ItemList hisatPipeline = BiomaterialList.HISAT_PIPELINE.load(dc);
-        
-        ItemQuery<DerivedBioAssay> query = (ItemQuery<DerivedBioAssay>)hisatPipeline.getMembers();
-        query.setIncludes(Reggie.INCLUDE_IN_CURRENT_PROJECT);
-        Subtype.MERGED_SEQUENCES.addFilter(dc, query);
-        // Join LibPlate for sorting
-        query.join(Hql.innerJoin(null, "extract", "lib", true));
-        query.join(Hql.innerJoin("lib", "bioWell", "bw", true));
-        query.join(Hql.innerJoin("bw", "bioPlate", "libPlate", true));
-        query.order(Orders.asc(Hql.property("libPlate", "id")));
-        query.order(Orders.asc(Hql.property("name")));
-        query.setMaxResults(250);
-
-        List<MergedSequences> list = MergedSequences.toList(query.list(dc));
+        
+        List<MergedSequences> list = null;
+        String items = Values.getStringOrNull(req.getParameter("items"));
+        if (items == null)
+        {
+          // Load items from the pipeline list
+          ItemList hisatPipeline = BiomaterialList.HISAT_PIPELINE.load(dc);
+          ItemQuery<DerivedBioAssay> query = (ItemQuery<DerivedBioAssay>)hisatPipeline.getMembers();
+          query.setIncludes(Reggie.INCLUDE_IN_CURRENT_PROJECT);
+          Subtype.MERGED_SEQUENCES.addFilter(dc, query);
+          // Join LibPlate for sorting
+          query.join(Hql.innerJoin(null, "extract", "lib", true));
+          query.join(Hql.innerJoin("lib", "bioWell", "bw", true));
+          query.join(Hql.innerJoin("bw", "bioPlate", "libPlate", true));
+          query.order(Orders.asc(Hql.property("libPlate", "id")));
+          query.order(Orders.asc(Hql.property("name")));
+          query.setMaxResults(250);
+          list = MergedSequences.toList(query.list(dc));
+        }
+        else
+        {
+          Integer[] ids = Values.getInt(items.split(","));
+          list = new ArrayList<MergedSequences>();
+          for (Integer id : ids)
+          {
+            list.add(MergedSequences.getById(dc, id));
+          }
+        }
+
         SnapshotManager manager = new SnapshotManager();
         JSONArray jsonMergedSequences = new JSONArray();
@@ -106 +121 @@
           ms.setAnnotation("lib", lib.asJSONObject());
           ms.loadAnnotations(dc, manager, "AutoProcess", Annotationtype.AUTO_PROCESSING, null);
+          ms.loadDoNotUseAnnotations(dc, manager);
           jsonMergedSequences.add(ms.asJSONObject());
         }