From 95507c5d02cd56199c232a8cd829e46c3f43ef7a Mon Sep 17 00:00:00 2001
From: Martin Cech <cech.marten@gmail.com>
Date: Mon, 23 Nov 2015 15:07:40 -0500
Subject: [PATCH 1/7] fix whitespace

---
 .../scripts/mvc/library/library-folderrow-view.js      | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/client/galaxy/scripts/mvc/library/library-folderrow-view.js b/client/galaxy/scripts/mvc/library/library-folderrow-view.js
index 6c357d1458d..7d5eef4eedf 100644
--- a/client/galaxy/scripts/mvc/library/library-folderrow-view.js
+++ b/client/galaxy/scripts/mvc/library/library-folderrow-view.js
@@ -66,7 +66,7 @@ var FolderRowView = Backbone.View.extend({
     var dataset_id = $(event.target).closest('tr')[0].id;
     var dataset = Galaxy.libraries.folderListView.collection.get(dataset_id);
     dataset.url = dataset.urlRoot + dataset.id + '?undelete=true';
-    dataset.destroy({ 
+    dataset.destroy({
         success : function(model, response){
           Galaxy.libraries.folderListView.collection.remove(dataset_id);
           var updated_dataset = new mod_library_model.Item(response);
@@ -76,7 +76,7 @@ var FolderRowView = Backbone.View.extend({
             var folder_id = that.model.get('folder_id');
             window.location='#folders/' + folder_id + '/datasets/' + that.id;
           }});
-        }, 
+        },
         error : function(model, response){
           if (typeof response.responseJSON !== "undefined"){
             mod_toastr.error('Dataset was not undeleted. ' + response.responseJSON.err_msg);
@@ -103,7 +103,7 @@ var FolderRowView = Backbone.View.extend({
           Galaxy.libraries.folderListView.collection.add(updated_folder);
           Galaxy.libraries.folderListView.collection.sortByNameAsc();
           mod_toastr.success('Folder undeleted.');
-        }, 
+        },
         error : function(model, response){
           if (typeof response.responseJSON !== "undefined"){
             mod_toastr.error('Folder was not undeleted. ' + response.responseJSON.err_msg);
@@ -157,7 +157,7 @@ var FolderRowView = Backbone.View.extend({
     tmpl_array.push('</tr>');
 
     return _.template(tmpl_array.join(''));
-  },  
+  },
 
   templateRowDeletedFile: function(){
     tmpl_array = [];
@@ -196,7 +196,7 @@ var FolderRowView = Backbone.View.extend({
 
     return _.template(tmpl_array.join(''));
   }
-   
+
 });
 
 return {

From e142beaffe1ee6aa853bbdb211ccf3fe1beb509e Mon Sep 17 00:00:00 2001
From: Martin Cech <cech.marten@gmail.com>
Date: Mon, 23 Nov 2015 15:08:25 -0500
Subject: [PATCH 2/7] replace wrong class name

---
 client/galaxy/scripts/mvc/library/library-folderrow-view.js | 2 +-
 static/maps/mvc/library/library-folderrow-view.js.map       | 2 +-
 static/scripts/mvc/library/library-folderrow-view.js        | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/client/galaxy/scripts/mvc/library/library-folderrow-view.js b/client/galaxy/scripts/mvc/library/library-folderrow-view.js
index 7d5eef4eedf..c58080c7853 100644
--- a/client/galaxy/scripts/mvc/library/library-folderrow-view.js
+++ b/client/galaxy/scripts/mvc/library/library-folderrow-view.js
@@ -180,7 +180,7 @@ var FolderRowView = Backbone.View.extend({
   templateRowDeletedFolder: function(){
     tmpl_array = [];
 
-    tmpl_array.push('<tr class="active folder_row light library-row" id="<%- content_item.id %>">');
+    tmpl_array.push('<tr class="active deleted_folder light library-row" id="<%- content_item.id %>">');
     tmpl_array.push('  <td>');
     tmpl_array.push('    <span title="Folder" class="fa fa-folder-o"></span>');
     tmpl_array.push('  </td>');
diff --git a/static/maps/mvc/library/library-folderrow-view.js.map b/static/maps/mvc/library/library-folderrow-view.js.map
index ef741012f21..c4122ea9e53 100644
--- a/static/maps/mvc/library/library-folderrow-view.js.map
+++ b/static/maps/mvc/library/library-folderrow-view.js.map
@@ -1 +1 @@
-{"version":3,"file":"library-folderrow-view.js","sources":["../../../src/mvc/library/library-folderrow-view.js"],"names":["define","mod_masthead","mod_utils","mod_toastr","mod_library_model","mod_library_dataset_view","FolderRowView","Backbone","View","extend","lastSelectedHistory","events","click .undelete_dataset_btn","click .undelete_folder_btn","options","type","initialize","folder_item","this","model","render","template","get","templateRowDeletedFolder","templateRowFolder","templateRowDeletedFile","templateRowFile","console","error","setElement","content_item","$el","show","showDatasetDetails","Galaxy","libraries","datasetView","LibraryDatasetView","id","undeleteDataset","event","$","hide","that","dataset_id","target","closest","dataset","folderListView","collection","url","urlRoot","destroy","success","response","remove","updated_dataset","Item","add","sortByNameAsc","onclick","folder_id","window","location","responseJSON","err_msg","undeleteFolder","folder","updated_folder","FolderAsModel","tmpl_array","push","_","join"],"mappings":"AAAAA,QACI,kBACA,cACA,cACA,4BACA,oCACJ,SAASC,EACAC,EACAC,EACAC,EACAC,GAET,GAAIC,GAAgBC,SAASC,KAAKC,QAEhCC,oBAAqB,GAErBC,QACEC,8BAAmC,kBACnCC,6BAAmC,kBAGrCC,SACEC,KAAM,MAGRC,WAAa,SAASC,GACpBC,KAAKC,MAAQF,EACbC,KAAKE,OAAOH,IAGdG,OAAQ,SAASH,GACf,GAAII,GAAW,IAqBf,OApBgC,WAA5BJ,EAAYK,IAAI,SAA2D,kBAAnCL,EAAYK,IAAI,gBAC1DJ,KAAKJ,QAAQC,KAAO,SAElBM,EADEJ,EAAYK,IAAI,WACPJ,KAAKK,2BAELL,KAAKM,qBAEmB,SAA5BP,EAAYK,IAAI,SAAyD,qCAAnCL,EAAYK,IAAI,gBAC/DJ,KAAKJ,QAAQC,KAAO,OAElBM,EADEJ,EAAYK,IAAI,WACPJ,KAAKO,yBAELP,KAAKQ,oBAGlBC,QAAQC,MAAM,oCACdD,QAAQC,MAAMX,EAAYK,IAAI,SAAWL,EAAYK,IAAI,iBAE3DJ,KAAKW,WAAWR,GAAUS,aAAab,KACvCC,KAAKa,IAAIC,OACFd,MAGTe,mBAAqB,WACnBC,OAAOC,UAAUC,YAAc,GAAI/B,GAAyBgC,oBAAoBC,GAAIpB,KAAKoB,MAM3FC,gBAAkB,SAASC,GACzBC,EAAE,YAAYC,MACd,IAAIC,GAAOzB,KACP0B,EAAaH,EAAED,EAAMK,QAAQC,QAAQ,MAAM,GAAGR,GAC9CS,EAAUb,OAAOC,UAAUa,eAAeC,WAAW3B,IAAIsB,EAC7DG,GAAQG,IAAMH,EAAQI,QAAUJ,EAAQT,GAAK,iBAC7CS,EAAQK,SACJC,QAAU,SAASlC,EAAOmC,GACxBpB,OAAOC,UAAUa,eAAeC,WAAWM,OAAOX,EAClD,IAAIY,GAAkB,GAAIpD,GAAkBqD,KAAKH,EACjDpB,QAAOC,UAAUa,eAAeC,WAAWS,IAAIF,GAC/CtB,OAAOC,UAAUa,eAAeC,WAAWU,gBAC3CxD,EAAWkD,QAAQ,2CAA4C,IAAKO,QAAS,WAC3E,GAAIC,GAAYlB,EAAKxB,MAAMG,IAAI,YAC/BwC,QAAOC,SAAS,YAAcF,EAAY,aAAelB,EAAKL,OAGlEV,MAAQ,SAAST,EAAOmC,GAEpBnD,EAAWyB,MADwB,mBAA1B0B,GAASU,aACD,8BAAgCV,EAASU,aAAaC,QAEtD,sEAS3BC,eAAiB,SAAS1B,GACxBC,EAAE,YAAYC,MACd,IACImB,GAAYpB,EAAED,EAAMK,QAAQC,QAAQ,MAAM,GAAGR,GAC7C6B,EAASjC,OAAOC,UAAUa,eAAeC,WAAW3B,IAAIuC,EAC5DM,GAAOjB,IAAMiB,EAAOhB,QAAUgB,EAAO7B,GAAK,iBAC1C6B,EAAOf,SACHC,QAAU,SAASlC,EAAOmC,GACxBpB,OAAOC,UAAUa,eAAeC,WAAWM,OAAOM,EAClD,IAAIO,GAAiB,GAAIhE,GAAkBiE,cAAcf,EACzDpB,QAAOC,UAAUa,eAAeC,WAAWS,IAAIU,GAC/ClC,OAAOC,UAAUa,eAAeC,WAAWU,gBAC3CxD,EAAWkD,QAAQ,sBAErBzB,MAAQ,SAAST,EAAOmC,GAEpBnD,EAAWyB,MADwB,mBAA1B0B,GAASU,aACD,6BAA+BV,EAASU,aAAaC,QAErD,qEAM3BzC,kBAAmB,WAmBjB,MAlBA8C,eAEAA,WAAWC,KAAK,yEAChBD,WAAWC,KAAK,UAChBD,WAAWC,KAAK,2DAChBD,WAAWC,KAAK,WAChBD,WAAWC,KAAK,sFAChBD,WAAWC,KAAK,UAChBD,WAAWC,KAAK,qFAChBD,WAAWC,KAAK,WAChBD,WAAWC,KAAK,qBAChBD,WAAWC,KAAK,eAChBD,WAAWC,KAAK,+DAChBD,WAAWC,KAAK,UAChBD,WAAWC,KAAK,sUAChBD,WAAWC,KAAK,WAChBD,WAAWC,KAAK,SAETC,EAAEnD,SAASiD,WAAWG,KAAK,MAGpC/C,gBAAiB,WAoBf,MAnBA4C,eAEAA,WAAWC,KAAK,0EAChBD,WAAWC,KAAK,UAChBD,WAAWC,KAAK,0DAChBD,WAAWC,KAAK,WAChBD,WAAWC,KAAK,sFAChBD,WAAWC,KAAK,iKAChBD,WAAWC,KAAK,4DAChBD,WAAWC,KAAK,6DAChBD,WAAWC,KAAK,+DAChBD,WAAWC,KAAK,UAChBD,WAAWC,KAAK,kMAChBD,WAAWC,KAAK,sLAChBD,WAAWC,KAAK,2PAChBD,WAAWC,KAAK,oXAChBD,WAAWC,KAAK,WAChBD,WAAWC,KAAK,SAETC,EAAEnD,SAASiD,WAAWG,KAAK,MAGpChD,uBAAwB,WAetB,MAdA6C,eAEAA,WAAWC,KAAK,+EAChBD,WAAWC,KAAK,UAChBD,WAAWC,KAAK,0DAChBD,WAAWC,KAAK,WAChBD,WAAWC,KAAK,eAChBD,WAAWC,KAAK,kEAChBD,WAAWC,KAAK,4DAChBD,WAAWC,KAAK,6DAChBD,WAAWC,KAAK,+DAChBD,WAAWC,KAAK,yZAChBD,WAAWC,KAAK,SAETC,EAAEnD,SAASiD,WAAWG,KAAK,MAGpClD,yBAA0B,WAiBxB,MAhBA+C,eAEAA,WAAWC,KAAK,gFAChBD,WAAWC,KAAK,UAChBD,WAAWC,KAAK,2DAChBD,WAAWC,KAAK,WAChBD,WAAWC,KAAK,eAChBD,WAAWC,KAAK,8BAChBD,WAAWC,KAAK,uCAChBD,WAAWC,KAAK,WAChBD,WAAWC,KAAK,qBAChBD,WAAWC,KAAK,eAChBD,WAAWC,KAAK,+DAChBD,WAAWC,KAAK,wZAChBD,WAAWC,KAAK,SAETC,EAAEnD,SAASiD,WAAWG,KAAK,OAKtC,QACInE,cAAeA"}
\ No newline at end of file
+{"version":3,"file":"library-folderrow-view.js","sources":["../../../src/mvc/library/library-folderrow-view.js"],"names":["define","mod_masthead","mod_utils","mod_toastr","mod_library_model","mod_library_dataset_view","FolderRowView","Backbone","View","extend","lastSelectedHistory","events","click .undelete_dataset_btn","click .undelete_folder_btn","options","type","initialize","folder_item","this","model","render","template","get","templateRowDeletedFolder","templateRowFolder","templateRowDeletedFile","templateRowFile","console","error","setElement","content_item","$el","show","showDatasetDetails","Galaxy","libraries","datasetView","LibraryDatasetView","id","undeleteDataset","event","$","hide","that","dataset_id","target","closest","dataset","folderListView","collection","url","urlRoot","destroy","success","response","remove","updated_dataset","Item","add","sortByNameAsc","onclick","folder_id","window","location","responseJSON","err_msg","undeleteFolder","folder","updated_folder","FolderAsModel","tmpl_array","push","_","join"],"mappings":"AAAAA,QACI,kBACA,cACA,cACA,4BACA,oCACJ,SAASC,EACAC,EACAC,EACAC,EACAC,GAET,GAAIC,GAAgBC,SAASC,KAAKC,QAEhCC,oBAAqB,GAErBC,QACEC,8BAAmC,kBACnCC,6BAAmC,kBAGrCC,SACEC,KAAM,MAGRC,WAAa,SAASC,GACpBC,KAAKC,MAAQF,EACbC,KAAKE,OAAOH,IAGdG,OAAQ,SAASH,GACf,GAAII,GAAW,IAqBf,OApBgC,WAA5BJ,EAAYK,IAAI,SAA2D,kBAAnCL,EAAYK,IAAI,gBAC1DJ,KAAKJ,QAAQC,KAAO,SAElBM,EADEJ,EAAYK,IAAI,WACPJ,KAAKK,2BAELL,KAAKM,qBAEmB,SAA5BP,EAAYK,IAAI,SAAyD,qCAAnCL,EAAYK,IAAI,gBAC/DJ,KAAKJ,QAAQC,KAAO,OAElBM,EADEJ,EAAYK,IAAI,WACPJ,KAAKO,yBAELP,KAAKQ,oBAGlBC,QAAQC,MAAM,oCACdD,QAAQC,MAAMX,EAAYK,IAAI,SAAWL,EAAYK,IAAI,iBAE3DJ,KAAKW,WAAWR,GAAUS,aAAab,KACvCC,KAAKa,IAAIC,OACFd,MAGTe,mBAAqB,WACnBC,OAAOC,UAAUC,YAAc,GAAI/B,GAAyBgC,oBAAoBC,GAAIpB,KAAKoB,MAM3FC,gBAAkB,SAASC,GACzBC,EAAE,YAAYC,MACd,IAAIC,GAAOzB,KACP0B,EAAaH,EAAED,EAAMK,QAAQC,QAAQ,MAAM,GAAGR,GAC9CS,EAAUb,OAAOC,UAAUa,eAAeC,WAAW3B,IAAIsB,EAC7DG,GAAQG,IAAMH,EAAQI,QAAUJ,EAAQT,GAAK,iBAC7CS,EAAQK,SACJC,QAAU,SAASlC,EAAOmC,GACxBpB,OAAOC,UAAUa,eAAeC,WAAWM,OAAOX,EAClD,IAAIY,GAAkB,GAAIpD,GAAkBqD,KAAKH,EACjDpB,QAAOC,UAAUa,eAAeC,WAAWS,IAAIF,GAC/CtB,OAAOC,UAAUa,eAAeC,WAAWU,gBAC3CxD,EAAWkD,QAAQ,2CAA4C,IAAKO,QAAS,WAC3E,GAAIC,GAAYlB,EAAKxB,MAAMG,IAAI,YAC/BwC,QAAOC,SAAS,YAAcF,EAAY,aAAelB,EAAKL,OAGlEV,MAAQ,SAAST,EAAOmC,GAEpBnD,EAAWyB,MADwB,mBAA1B0B,GAASU,aACD,8BAAgCV,EAASU,aAAaC,QAEtD,sEAS3BC,eAAiB,SAAS1B,GACxBC,EAAE,YAAYC,MACd,IACImB,GAAYpB,EAAED,EAAMK,QAAQC,QAAQ,MAAM,GAAGR,GAC7C6B,EAASjC,OAAOC,UAAUa,eAAeC,WAAW3B,IAAIuC,EAC5DM,GAAOjB,IAAMiB,EAAOhB,QAAUgB,EAAO7B,GAAK,iBAC1C6B,EAAOf,SACHC,QAAU,SAASlC,EAAOmC,GACxBpB,OAAOC,UAAUa,eAAeC,WAAWM,OAAOM,EAClD,IAAIO,GAAiB,GAAIhE,GAAkBiE,cAAcf,EACzDpB,QAAOC,UAAUa,eAAeC,WAAWS,IAAIU,GAC/ClC,OAAOC,UAAUa,eAAeC,WAAWU,gBAC3CxD,EAAWkD,QAAQ,sBAErBzB,MAAQ,SAAST,EAAOmC,GAEpBnD,EAAWyB,MADwB,mBAA1B0B,GAASU,aACD,6BAA+BV,EAASU,aAAaC,QAErD,qEAM3BzC,kBAAmB,WAmBjB,MAlBA8C,eAEAA,WAAWC,KAAK,yEAChBD,WAAWC,KAAK,UAChBD,WAAWC,KAAK,2DAChBD,WAAWC,KAAK,WAChBD,WAAWC,KAAK,sFAChBD,WAAWC,KAAK,UAChBD,WAAWC,KAAK,qFAChBD,WAAWC,KAAK,WAChBD,WAAWC,KAAK,qBAChBD,WAAWC,KAAK,eAChBD,WAAWC,KAAK,+DAChBD,WAAWC,KAAK,UAChBD,WAAWC,KAAK,sUAChBD,WAAWC,KAAK,WAChBD,WAAWC,KAAK,SAETC,EAAEnD,SAASiD,WAAWG,KAAK,MAGpC/C,gBAAiB,WAoBf,MAnBA4C,eAEAA,WAAWC,KAAK,0EAChBD,WAAWC,KAAK,UAChBD,WAAWC,KAAK,0DAChBD,WAAWC,KAAK,WAChBD,WAAWC,KAAK,sFAChBD,WAAWC,KAAK,iKAChBD,WAAWC,KAAK,4DAChBD,WAAWC,KAAK,6DAChBD,WAAWC,KAAK,+DAChBD,WAAWC,KAAK,UAChBD,WAAWC,KAAK,kMAChBD,WAAWC,KAAK,sLAChBD,WAAWC,KAAK,2PAChBD,WAAWC,KAAK,oXAChBD,WAAWC,KAAK,WAChBD,WAAWC,KAAK,SAETC,EAAEnD,SAASiD,WAAWG,KAAK,MAGpChD,uBAAwB,WAetB,MAdA6C,eAEAA,WAAWC,KAAK,+EAChBD,WAAWC,KAAK,UAChBD,WAAWC,KAAK,0DAChBD,WAAWC,KAAK,WAChBD,WAAWC,KAAK,eAChBD,WAAWC,KAAK,kEAChBD,WAAWC,KAAK,4DAChBD,WAAWC,KAAK,6DAChBD,WAAWC,KAAK,+DAChBD,WAAWC,KAAK,yZAChBD,WAAWC,KAAK,SAETC,EAAEnD,SAASiD,WAAWG,KAAK,MAGpClD,yBAA0B,WAiBxB,MAhBA+C,eAEAA,WAAWC,KAAK,oFAChBD,WAAWC,KAAK,UAChBD,WAAWC,KAAK,2DAChBD,WAAWC,KAAK,WAChBD,WAAWC,KAAK,eAChBD,WAAWC,KAAK,8BAChBD,WAAWC,KAAK,uCAChBD,WAAWC,KAAK,WAChBD,WAAWC,KAAK,qBAChBD,WAAWC,KAAK,eAChBD,WAAWC,KAAK,+DAChBD,WAAWC,KAAK,wZAChBD,WAAWC,KAAK,SAETC,EAAEnD,SAASiD,WAAWG,KAAK,OAKtC,QACInE,cAAeA"}
\ No newline at end of file
diff --git a/static/scripts/mvc/library/library-folderrow-view.js b/static/scripts/mvc/library/library-folderrow-view.js
index d9683065d0d..f7c503684d7 100644
--- a/static/scripts/mvc/library/library-folderrow-view.js
+++ b/static/scripts/mvc/library/library-folderrow-view.js
@@ -1,2 +1,2 @@
-define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-dataset-view"],function(a,b,c,d,e){var f=Backbone.View.extend({lastSelectedHistory:"",events:{"click .undelete_dataset_btn":"undeleteDataset","click .undelete_folder_btn":"undeleteFolder"},options:{type:null},initialize:function(a){this.model=a,this.render(a)},render:function(a){var b=null;return"folder"===a.get("type")||"LibraryFolder"===a.get("model_class")?(this.options.type="folder",b=a.get("deleted")?this.templateRowDeletedFolder():this.templateRowFolder()):"file"===a.get("type")||"LibraryDatasetDatasetAssociation"===a.get("model_class")?(this.options.type="file",b=a.get("deleted")?this.templateRowDeletedFile():this.templateRowFile()):(console.error("Unknown library item type found."),console.error(a.get("type")||a.get("model_class"))),this.setElement(b({content_item:a})),this.$el.show(),this},showDatasetDetails:function(){Galaxy.libraries.datasetView=new e.LibraryDatasetView({id:this.id})},undeleteDataset:function(a){$(".tooltip").hide();var b=this,e=$(a.target).closest("tr")[0].id,f=Galaxy.libraries.folderListView.collection.get(e);f.url=f.urlRoot+f.id+"?undelete=true",f.destroy({success:function(a,f){Galaxy.libraries.folderListView.collection.remove(e);var g=new d.Item(f);Galaxy.libraries.folderListView.collection.add(g),Galaxy.libraries.folderListView.collection.sortByNameAsc(),c.success("Dataset undeleted. Click this to see it.","",{onclick:function(){var a=b.model.get("folder_id");window.location="#folders/"+a+"/datasets/"+b.id}})},error:function(a,b){c.error("undefined"!=typeof b.responseJSON?"Dataset was not undeleted. "+b.responseJSON.err_msg:"An error occured! Dataset was not undeleted. Please try again.")}})},undeleteFolder:function(a){$(".tooltip").hide();var b=$(a.target).closest("tr")[0].id,e=Galaxy.libraries.folderListView.collection.get(b);e.url=e.urlRoot+e.id+"?undelete=true",e.destroy({success:function(a,e){Galaxy.libraries.folderListView.collection.remove(b);var f=new d.FolderAsModel(e);Galaxy.libraries.folderListView.collection.add(f),Galaxy.libraries.folderListView.collection.sortByNameAsc(),c.success("Folder undeleted.")},error:function(a,b){c.error("undefined"!=typeof b.responseJSON?"Folder was not undeleted. "+b.responseJSON.err_msg:"An error occured! Folder was not undeleted. Please try again.")}})},templateRowFolder:function(){return tmpl_array=[],tmpl_array.push('<tr class="folder_row light library-row" id="<%- content_item.id %>">'),tmpl_array.push("  <td>"),tmpl_array.push('    <span title="Folder" class="fa fa-folder-o"></span>'),tmpl_array.push("  </td>"),tmpl_array.push('  <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>'),tmpl_array.push("  <td>"),tmpl_array.push('    <a href="#folders/<%- content_item.id %>"><%- content_item.get("name") %></a>'),tmpl_array.push("  </td>"),tmpl_array.push("  <td>folder</td>"),tmpl_array.push("  <td></td>"),tmpl_array.push('  <td><%= _.escape(content_item.get("update_time")) %></td>'),tmpl_array.push("  <td>"),tmpl_array.push('    <% if (content_item.get("can_manage")) { %><a href="#/folders/<%- content_item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" class="primary-button btn-xs permissions-folder-btn show_on_hover" title="Manage permissions" style="display:none;"><span class="fa fa-group"></span></button></a><% } %>'),tmpl_array.push("  </td>"),tmpl_array.push("</tr>"),_.template(tmpl_array.join(""))},templateRowFile:function(){return tmpl_array=[],tmpl_array.push('<tr class="dataset_row light library-row" id="<%- content_item.id %>">'),tmpl_array.push("  <td>"),tmpl_array.push('    <span title="Dataset" class="fa fa-file-o"></span>'),tmpl_array.push("  </td>"),tmpl_array.push('  <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>'),tmpl_array.push('  <td><a href="#folders/<%- content_item.get("folder_id") %>/datasets/<%- content_item.id %>" class="library-dataset"><%- content_item.get("name") %><a></td>'),tmpl_array.push('  <td><%= _.escape(content_item.get("file_ext")) %></td>'),tmpl_array.push('  <td><%= _.escape(content_item.get("file_size")) %></td>'),tmpl_array.push('  <td><%= _.escape(content_item.get("update_time")) %></td>'),tmpl_array.push("  <td>"),tmpl_array.push('    <% if (content_item.get("is_unrestricted")) { %><span data-toggle="tooltip" data-placement="top" title="Unrestricted dataset" style="color:grey;" class="fa fa-globe fa-lg"></span><% } %>'),tmpl_array.push('    <% if (content_item.get("is_private")) { %><span data-toggle="tooltip" data-placement="top" title="Private dataset" style="color:grey;" class="fa fa-key fa-lg"></span><% } %>'),tmpl_array.push('    <% if ((content_item.get("is_unrestricted") === false) && (content_item.get("is_private") === false)) { %><span data-toggle="tooltip" data-placement="top" title="Restricted dataset" style="color:grey;" class="fa fa-shield fa-lg"></span><% } %>'),tmpl_array.push('    <% if (content_item.get("can_manage")) { %><a href="#folders/<%- content_item.get("folder_id") %>/datasets/<%- content_item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" class="primary-button btn-xs permissions-dataset-btn show_on_hover" title="Manage permissions" style="display:none;"><span class="fa fa-group"></span></button></a><% } %>'),tmpl_array.push("  </td>"),tmpl_array.push("</tr>"),_.template(tmpl_array.join(""))},templateRowDeletedFile:function(){return tmpl_array=[],tmpl_array.push('<tr class="active deleted_dataset library-row" id="<%- content_item.id %>">'),tmpl_array.push("  <td>"),tmpl_array.push('    <span title="Dataset" class="fa fa-file-o"></span>'),tmpl_array.push("  </td>"),tmpl_array.push("  <td></td>"),tmpl_array.push('  <td style="color:grey;"><%- content_item.get("name") %></td>'),tmpl_array.push('  <td><%= _.escape(content_item.get("file_ext")) %></td>'),tmpl_array.push('  <td><%= _.escape(content_item.get("file_size")) %></td>'),tmpl_array.push('  <td><%= _.escape(content_item.get("update_time")) %></td>'),tmpl_array.push('  <td><span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg"> </span><button data-toggle="tooltip" data-placement="top" title="Undelete <%- content_item.get("name") %>" class="primary-button btn-xs undelete_dataset_btn show_on_hover" type="button" style="display:none; margin-left:1em;"><span class="fa fa-unlock"> Undelete</span></button></td>'),tmpl_array.push("</tr>"),_.template(tmpl_array.join(""))},templateRowDeletedFolder:function(){return tmpl_array=[],tmpl_array.push('<tr class="active folder_row light library-row" id="<%- content_item.id %>">'),tmpl_array.push("  <td>"),tmpl_array.push('    <span title="Folder" class="fa fa-folder-o"></span>'),tmpl_array.push("  </td>"),tmpl_array.push("  <td></td>"),tmpl_array.push('  <td style="color:grey;">'),tmpl_array.push('    <%- content_item.get("name") %>'),tmpl_array.push("  </td>"),tmpl_array.push("  <td>folder</td>"),tmpl_array.push("  <td></td>"),tmpl_array.push('  <td><%= _.escape(content_item.get("update_time")) %></td>'),tmpl_array.push('  <td><span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg"> </span><button data-toggle="tooltip" data-placement="top" title="Undelete <%- content_item.get("name") %>" class="primary-button btn-xs undelete_folder_btn show_on_hover" type="button" style="display:none; margin-left:1em;"><span class="fa fa-unlock"> Undelete</span></button></td>'),tmpl_array.push("</tr>"),_.template(tmpl_array.join(""))}});return{FolderRowView:f}});
+define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-dataset-view"],function(a,b,c,d,e){var f=Backbone.View.extend({lastSelectedHistory:"",events:{"click .undelete_dataset_btn":"undeleteDataset","click .undelete_folder_btn":"undeleteFolder"},options:{type:null},initialize:function(a){this.model=a,this.render(a)},render:function(a){var b=null;return"folder"===a.get("type")||"LibraryFolder"===a.get("model_class")?(this.options.type="folder",b=a.get("deleted")?this.templateRowDeletedFolder():this.templateRowFolder()):"file"===a.get("type")||"LibraryDatasetDatasetAssociation"===a.get("model_class")?(this.options.type="file",b=a.get("deleted")?this.templateRowDeletedFile():this.templateRowFile()):(console.error("Unknown library item type found."),console.error(a.get("type")||a.get("model_class"))),this.setElement(b({content_item:a})),this.$el.show(),this},showDatasetDetails:function(){Galaxy.libraries.datasetView=new e.LibraryDatasetView({id:this.id})},undeleteDataset:function(a){$(".tooltip").hide();var b=this,e=$(a.target).closest("tr")[0].id,f=Galaxy.libraries.folderListView.collection.get(e);f.url=f.urlRoot+f.id+"?undelete=true",f.destroy({success:function(a,f){Galaxy.libraries.folderListView.collection.remove(e);var g=new d.Item(f);Galaxy.libraries.folderListView.collection.add(g),Galaxy.libraries.folderListView.collection.sortByNameAsc(),c.success("Dataset undeleted. Click this to see it.","",{onclick:function(){var a=b.model.get("folder_id");window.location="#folders/"+a+"/datasets/"+b.id}})},error:function(a,b){c.error("undefined"!=typeof b.responseJSON?"Dataset was not undeleted. "+b.responseJSON.err_msg:"An error occured! Dataset was not undeleted. Please try again.")}})},undeleteFolder:function(a){$(".tooltip").hide();var b=$(a.target).closest("tr")[0].id,e=Galaxy.libraries.folderListView.collection.get(b);e.url=e.urlRoot+e.id+"?undelete=true",e.destroy({success:function(a,e){Galaxy.libraries.folderListView.collection.remove(b);var f=new d.FolderAsModel(e);Galaxy.libraries.folderListView.collection.add(f),Galaxy.libraries.folderListView.collection.sortByNameAsc(),c.success("Folder undeleted.")},error:function(a,b){c.error("undefined"!=typeof b.responseJSON?"Folder was not undeleted. "+b.responseJSON.err_msg:"An error occured! Folder was not undeleted. Please try again.")}})},templateRowFolder:function(){return tmpl_array=[],tmpl_array.push('<tr class="folder_row light library-row" id="<%- content_item.id %>">'),tmpl_array.push("  <td>"),tmpl_array.push('    <span title="Folder" class="fa fa-folder-o"></span>'),tmpl_array.push("  </td>"),tmpl_array.push('  <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>'),tmpl_array.push("  <td>"),tmpl_array.push('    <a href="#folders/<%- content_item.id %>"><%- content_item.get("name") %></a>'),tmpl_array.push("  </td>"),tmpl_array.push("  <td>folder</td>"),tmpl_array.push("  <td></td>"),tmpl_array.push('  <td><%= _.escape(content_item.get("update_time")) %></td>'),tmpl_array.push("  <td>"),tmpl_array.push('    <% if (content_item.get("can_manage")) { %><a href="#/folders/<%- content_item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" class="primary-button btn-xs permissions-folder-btn show_on_hover" title="Manage permissions" style="display:none;"><span class="fa fa-group"></span></button></a><% } %>'),tmpl_array.push("  </td>"),tmpl_array.push("</tr>"),_.template(tmpl_array.join(""))},templateRowFile:function(){return tmpl_array=[],tmpl_array.push('<tr class="dataset_row light library-row" id="<%- content_item.id %>">'),tmpl_array.push("  <td>"),tmpl_array.push('    <span title="Dataset" class="fa fa-file-o"></span>'),tmpl_array.push("  </td>"),tmpl_array.push('  <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>'),tmpl_array.push('  <td><a href="#folders/<%- content_item.get("folder_id") %>/datasets/<%- content_item.id %>" class="library-dataset"><%- content_item.get("name") %><a></td>'),tmpl_array.push('  <td><%= _.escape(content_item.get("file_ext")) %></td>'),tmpl_array.push('  <td><%= _.escape(content_item.get("file_size")) %></td>'),tmpl_array.push('  <td><%= _.escape(content_item.get("update_time")) %></td>'),tmpl_array.push("  <td>"),tmpl_array.push('    <% if (content_item.get("is_unrestricted")) { %><span data-toggle="tooltip" data-placement="top" title="Unrestricted dataset" style="color:grey;" class="fa fa-globe fa-lg"></span><% } %>'),tmpl_array.push('    <% if (content_item.get("is_private")) { %><span data-toggle="tooltip" data-placement="top" title="Private dataset" style="color:grey;" class="fa fa-key fa-lg"></span><% } %>'),tmpl_array.push('    <% if ((content_item.get("is_unrestricted") === false) && (content_item.get("is_private") === false)) { %><span data-toggle="tooltip" data-placement="top" title="Restricted dataset" style="color:grey;" class="fa fa-shield fa-lg"></span><% } %>'),tmpl_array.push('    <% if (content_item.get("can_manage")) { %><a href="#folders/<%- content_item.get("folder_id") %>/datasets/<%- content_item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" class="primary-button btn-xs permissions-dataset-btn show_on_hover" title="Manage permissions" style="display:none;"><span class="fa fa-group"></span></button></a><% } %>'),tmpl_array.push("  </td>"),tmpl_array.push("</tr>"),_.template(tmpl_array.join(""))},templateRowDeletedFile:function(){return tmpl_array=[],tmpl_array.push('<tr class="active deleted_dataset library-row" id="<%- content_item.id %>">'),tmpl_array.push("  <td>"),tmpl_array.push('    <span title="Dataset" class="fa fa-file-o"></span>'),tmpl_array.push("  </td>"),tmpl_array.push("  <td></td>"),tmpl_array.push('  <td style="color:grey;"><%- content_item.get("name") %></td>'),tmpl_array.push('  <td><%= _.escape(content_item.get("file_ext")) %></td>'),tmpl_array.push('  <td><%= _.escape(content_item.get("file_size")) %></td>'),tmpl_array.push('  <td><%= _.escape(content_item.get("update_time")) %></td>'),tmpl_array.push('  <td><span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg"> </span><button data-toggle="tooltip" data-placement="top" title="Undelete <%- content_item.get("name") %>" class="primary-button btn-xs undelete_dataset_btn show_on_hover" type="button" style="display:none; margin-left:1em;"><span class="fa fa-unlock"> Undelete</span></button></td>'),tmpl_array.push("</tr>"),_.template(tmpl_array.join(""))},templateRowDeletedFolder:function(){return tmpl_array=[],tmpl_array.push('<tr class="active deleted_folder light library-row" id="<%- content_item.id %>">'),tmpl_array.push("  <td>"),tmpl_array.push('    <span title="Folder" class="fa fa-folder-o"></span>'),tmpl_array.push("  </td>"),tmpl_array.push("  <td></td>"),tmpl_array.push('  <td style="color:grey;">'),tmpl_array.push('    <%- content_item.get("name") %>'),tmpl_array.push("  </td>"),tmpl_array.push("  <td>folder</td>"),tmpl_array.push("  <td></td>"),tmpl_array.push('  <td><%= _.escape(content_item.get("update_time")) %></td>'),tmpl_array.push('  <td><span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg"> </span><button data-toggle="tooltip" data-placement="top" title="Undelete <%- content_item.get("name") %>" class="primary-button btn-xs undelete_folder_btn show_on_hover" type="button" style="display:none; margin-left:1em;"><span class="fa fa-unlock"> Undelete</span></button></td>'),tmpl_array.push("</tr>"),_.template(tmpl_array.join(""))}});return{FolderRowView:f}});
 //# sourceMappingURL=../../../maps/mvc/library/library-folderrow-view.js.map
\ No newline at end of file

From 39bc057ef9d9e62f08e3c0dbdb95d14a1ae295d2 Mon Sep 17 00:00:00 2001
From: Martin Cech <cech.marten@gmail.com>
Date: Mon, 23 Nov 2015 15:12:05 -0500
Subject: [PATCH 3/7] fix whitespace

---
 .../mvc/library/library-foldertoolbar-view.js | 50 +++++++++----------
 1 file changed, 25 insertions(+), 25 deletions(-)

diff --git a/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js b/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
index b81a839ed7b..e718ead48b2 100644
--- a/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
+++ b/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
@@ -63,7 +63,7 @@ var FolderToolbarView = Backbone.View.extend({
                     ' to set your data to the format you think it should be.' +
                     ' You can also upload compressed files, which will automatically be decompressed.'
   },
-  
+
   // genomes
   list_genomes : [],
 
@@ -99,7 +99,7 @@ var FolderToolbarView = Backbone.View.extend({
   renderPaginator: function( options ){
       this.options = _.extend( this.options, options );
       var paginator_template = this.templatePaginator();
-      this.$el.find( '#folder_paginator' ).html( paginator_template({ 
+      this.$el.find( '#folder_paginator' ).html( paginator_template({
           id: this.options.id,
           show_page: parseInt( this.options.show_page ),
           page_count: parseInt( this.options.page_count ),
@@ -281,7 +281,7 @@ var FolderToolbarView = Backbone.View.extend({
     }
 
     this.initChainCallControl( { length: datasets_to_import.length, action: 'to_history', history_name: history_name } );
-    // set the used history as current so user will see the last one 
+    // set the used history as current so user will see the last one
     // that he imported into in the history panel on the 'analysis' page
     jQuery.getJSON( galaxy_config.root + 'history/set_as_current?id=' + history_id  );
     this.chainCallImportingIntoHistory( datasets_to_import, history_name );
@@ -360,7 +360,7 @@ var FolderToolbarView = Backbone.View.extend({
             Galaxy.libraries.library_router.back();
           }
       });
-      
+
       // user should always have a history, even anonymous user
       if (self.histories.models.length > 0){
         self.fetchAndDisplayHistoryContents(self.histories.models[0].id);
@@ -393,7 +393,7 @@ var FolderToolbarView = Backbone.View.extend({
           //  TODO: should not trigger routes outside of the router
           Galaxy.libraries.library_router.navigate( 'folders/' + that.id, { trigger: true } );
         }
-    });  
+    });
     this.renderSelectBoxes();
   },
 
@@ -439,7 +439,7 @@ var FolderToolbarView = Backbone.View.extend({
   renderSelectBoxes: function(){
     // This won't work properly unlesss we already have the data fetched.
     // See this.fetchExtAndGenomes()
-    // TODO switch to common resources: 
+    // TODO switch to common resources:
     // https://trello.com/c/dIUE9YPl/1933-ui-common-resources-and-data-into-galaxy-object
     var that = this;
     this.select_genome = new mod_select.View( {
@@ -469,7 +469,7 @@ var FolderToolbarView = Backbone.View.extend({
       title           : 'Please select folders or files',
       body            : template_modal({}),
       buttons         : {
-          'Import'    : function() { 
+          'Import'    : function() {
             that.importFromJstreePath( that, options );
           },
           'Close'     : function() {
@@ -503,7 +503,7 @@ var FolderToolbarView = Backbone.View.extend({
           that.renderJstree( options );
         }
       }
-    );     
+    );
   },
 
   /**
@@ -518,9 +518,9 @@ var FolderToolbarView = Backbone.View.extend({
     var target = options.source || 'userdir';
     var disabled_jstree_element = this.options.disabled_jstree_element;
     this.jstree = new mod_library_model.Jstree();
-    this.jstree.url = this.jstree.urlRoot + 
-                        '?target=' + target + 
-                        '&format=jstree' + 
+    this.jstree.url = this.jstree.urlRoot +
+                        '?target=' + target +
+                        '&format=jstree' +
                         '&disable=' + disabled_jstree_element;
     this.jstree.fetch({
       success: function(model, response){
@@ -583,8 +583,8 @@ var FolderToolbarView = Backbone.View.extend({
       };
       this.initChainCallControl( { length: valid_paths.length, action: 'adding_datasets' } );
       this.chainCallImportingFolders( { paths: valid_paths,
-                                        preserve_dirs: preserve_dirs, 
-                                        link_data: link_data, 
+                                        preserve_dirs: preserve_dirs,
+                                        link_data: link_data,
                                         source: 'admin_path',
                                         file_type: file_type,
                                         dbkey: dbkey } );
@@ -626,9 +626,9 @@ var FolderToolbarView = Backbone.View.extend({
 
   /**
    * Take the selected items from the jstree, create a request queue
-   * and send them one by one to the server for importing into 
-   * the current folder. 
-   * 
+   * and send them one by one to the server for importing into
+   * the current folder.
+   *
    * jstree.js has to be loaded before
    * @see renderJstree
    */
@@ -653,8 +653,8 @@ var FolderToolbarView = Backbone.View.extend({
       if ( selection_type === 'folder' ){
         var full_source = options.source + '_folder';
         this.chainCallImportingFolders( { paths: paths,
-                                          preserve_dirs: preserve_dirs, 
-                                          link_data: link_data, 
+                                          preserve_dirs: preserve_dirs,
+                                          link_data: link_data,
                                           source: full_source,
                                           file_type: file_type,
                                           dbkey: dbkey } );
@@ -767,7 +767,7 @@ var FolderToolbarView = Backbone.View.extend({
       }
       return true;
     }
-    var promise = $.when( $.post( ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/libraries/datasets?encoded_folder_id=' + that.id + 
+    var promise = $.when( $.post( ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/libraries/datasets?encoded_folder_id=' + that.id +
                                                        '&source=' + options.source +
                                                        '&path=' + popped_item +
                                                        '&file_type=' + options.file_type +
@@ -789,7 +789,7 @@ var FolderToolbarView = Backbone.View.extend({
    * @param  {array} paths           paths relative to Galaxy root folder
    * @param  {boolean} preserve_dirs indicates whether to preserve folder structure
    * @param  {boolean} link_data     copy files to Galaxy or link instead
-   * @param  {str} source            string representing what type of folder 
+   * @param  {str} source            string representing what type of folder
    *                                 is the source of import
    */
   chainCallImportingFolders: function( options ){
@@ -825,7 +825,7 @@ var FolderToolbarView = Backbone.View.extend({
   },
 
   /**
-   * Take the array of hdas and create a request for each. 
+   * Take the array of hdas and create a request for each.
    * Call them in chain and update progress bar in between each.
    * @param  {array} hdas_set array of empty hda objects
    */
@@ -859,7 +859,7 @@ var FolderToolbarView = Backbone.View.extend({
   },
 
   /**
-   * Take the array of lddas, create request for each and 
+   * Take the array of lddas, create request for each and
    * call them in chain. Update progress bar in between each.
    * @param  {array} lddas_set array of lddas to delete
    */
@@ -953,7 +953,7 @@ var FolderToolbarView = Backbone.View.extend({
       var items_total = dataset_ids.length + folder_ids.length
       this.progressStep = 100 / items_total;
       this.progress = 0;
-      
+
       // prepare the dataset items to be added
       var items_to_delete = [];
       for (var i = dataset_ids.length - 1; i >= 0; i--) {
@@ -1017,7 +1017,7 @@ var FolderToolbarView = Backbone.View.extend({
       case "importdir":
         this.importFilesFromGalaxyFolderModal( { source: 'importdir' } );
         break;
-      case "path": 
+      case "path":
         this.importFilesFromPathModal();
         break;
       case "userdir":
@@ -1215,7 +1215,7 @@ var FolderToolbarView = Backbone.View.extend({
     tmpl_array.push('<div class="alert alert-info jstree-files-message">All files you select will be imported into the current folder.</div>');
     tmpl_array.push('<div class="alert alert-info jstree-folders-message" style="display:none;">All files within the selected folders and their subfolders will be imported into the current folder.</div>');
 
-    
+
     tmpl_array.push('<div style="margin-bottom:1em;">');
     tmpl_array.push('<label class="radio-inline">');
     tmpl_array.push('  <input title="Switch to selecting files" type="radio" name="jstree-radio" value="jstree-disable-folders" checked="checked"> Files');

From e19b7f656f6750cc87f7d3e7f0eb12d4292d1987 Mon Sep 17 00:00:00 2001
From: Martin Cech <cech.marten@gmail.com>
Date: Mon, 23 Nov 2015 15:14:15 -0500
Subject: [PATCH 4/7] fix the extra slash in URL when creating folder

---
 client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js | 2 +-
 static/maps/mvc/library/library-foldertoolbar-view.js.map       | 2 +-
 static/scripts/mvc/library/library-foldertoolbar-view.js        | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js b/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
index e718ead48b2..785b2410233 100644
--- a/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
+++ b/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
@@ -163,7 +163,7 @@ var FolderToolbarView = Backbone.View.extend({
           var folder = new mod_library_model.FolderAsModel();
           url_items = Backbone.history.fragment.split('/');
           current_folder_id = url_items[url_items.length-1];
-          folder.url = folder.urlRoot + '/' + current_folder_id ;
+          folder.url = folder.urlRoot + current_folder_id ;
 
           folder.save(folderDetails, {
             success: function (folder) {
diff --git a/static/maps/mvc/library/library-foldertoolbar-view.js.map b/static/maps/mvc/library/library-foldertoolbar-view.js.map
index 1a18c654c8e..f9585700300 100644
--- a/static/maps/mvc/library/library-foldertoolbar-view.js.map
+++ b/static/maps/mvc/library/library-foldertoolbar-view.js.map
@@ -1 +1 @@
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\ No newline at end of file
diff --git a/static/scripts/mvc/library/library-foldertoolbar-view.js b/static/scripts/mvc/library/library-foldertoolbar-view.js
index ec8aae2049f..08d586c46eb 100644
--- a/static/scripts/mvc/library/library-foldertoolbar-view.js
+++ b/static/scripts/mvc/library/library-foldertoolbar-view.js
@@ -1,3 +1,3 @@
-define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(a,b,c,d,e){var f=Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_show_libinfo":"showLibInfo","click #toolbtn_bulk_delete":"deleteSelectedDatasets","click #page_size_prompt":"showPageSizePrompt"},defaults:{can_add_library_item:!1,contains_file_or_folder:!1,chain_call_control:{total_number:0,failed_number:0},disabled_jstree_element:"folders"},modal:null,jstree:null,histories:null,select_genome:null,select_extension:null,list_extensions:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},list_genomes:[],initialize:function(a){this.options=_.defaults(a||{},this.defaults),this.fetchExtAndGenomes(),this.render()},render:function(a){this.options=_.extend(this.options,a);var b=this.templateToolBar(),c={id:this.options.id,is_admin:!1,is_anonym:!0,mutiple_add_dataset_options:!1};Galaxy.currUser&&(c.is_admin=Galaxy.currUser.isAdmin(),c.is_anonym=Galaxy.currUser.isAnonymous(),(null!==Galaxy.config.user_library_import_dir||Galaxy.config.allow_library_path_paste!==!1||null!==Galaxy.config.library_import_dir)&&(c.mutiple_add_dataset_options=!0)),this.$el.html(b(c))},renderPaginator:function(a){this.options=_.extend(this.options,a);var b=this.templatePaginator();this.$el.find("#folder_paginator").html(b({id:this.options.id,show_page:parseInt(this.options.show_page),page_count:parseInt(this.options.page_count),total_items_count:this.options.total_items_count,items_shown:this.options.items_shown}))},configureElements:function(a){this.options=_.extend(this.options,a),this.options.can_add_library_item===!0?$(".add-library-items").show():$(".add-library-items").hide(),this.options.contains_file_or_folder===!0&&Galaxy.currUser?Galaxy.currUser.isAnonymous()?($(".dataset-manipulation").show(),$(".logged-dataset-manipulation").hide()):($(".logged-dataset-manipulation").show(),$(".dataset-manipulation").show()):($(".logged-dataset-manipulation").hide(),$(".dataset-manipulation").hide()),this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(a){a.preventDefault(),a.stopPropagation();var b=this,c=this.templateNewFolderInModal();this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:"Create New Folder",body:c(),buttons:{Create:function(){b.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var a=this.serialize_new_folder();if(this.validate_new_folder(a)){var b=new d.FolderAsModel;url_items=Backbone.history.fragment.split("/"),current_folder_id=url_items[url_items.length-1],b.url=b.urlRoot+"/"+current_folder_id,b.save(a,{success:function(a){Galaxy.modal.hide(),c.success("Folder created."),a.set({type:"folder"}),Galaxy.libraries.folderListView.collection.add(a)},error:function(a,b){Galaxy.modal.hide(),c.error("undefined"!=typeof b.responseJSON?b.responseJSON.err_msg:"An error ocurred.")}})}else c.error("Folder's name is missing.");return!1},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(a){return""!==a.name},modalBulkImport:function(){var a=$("#folder_table").find(":checked");0===a.length?c.info("You must select some datasets first."):this.refreshUserHistoriesList(function(a){var b=a.templateBulkImportInModal();a.modal=Galaxy.modal,a.modal.show({closing_events:!0,title:"Import into History",body:b({histories:a.histories.models}),buttons:{Import:function(){a.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})},refreshUserHistoriesList:function(a){var b=this;this.histories=new d.GalaxyHistories,this.histories.fetch({success:function(){a(b)},error:function(a,b){c.error("undefined"!=typeof b.responseJSON?b.responseJSON.err_msg:"An error ocurred.")}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var a=$("select[name=dataset_import_bulk] option:selected").val(),b=$("select[name=dataset_import_bulk] option:selected").text();this.options.last_used_history_id=a;var c=[],e=[];$("#folder_table").find(":checked").each(function(){""!==this.parentElement.parentElement.id&&this.parentElement.parentElement.classList.contains("dataset_row")?c.push(this.parentElement.parentElement.id):""!==this.parentElement.parentElement.id&&this.parentElement.parentElement.classList.contains("folder_row")&&e.push(this.parentElement.parentElement.id)});for(var f=[],g=c.length-1;g>=0;g--){var h=c[g],i=new d.HistoryItem;i.url=i.urlRoot+a+"/contents",i.content=h,i.source="library",f.push(i)}for(var g=e.length-1;g>=0;g--){var j=e[g],i=new d.HistoryItem;i.url=i.urlRoot+a+"/contents",i.content=j,i.source="library_folder",f.push(i)}this.initChainCallControl({length:f.length,action:"to_history",history_name:b}),jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+a),this.chainCallImportingIntoHistory(f,b)},updateProgress:function(){this.progress+=this.progressStep,$(".progress-bar-import").width(Math.round(this.progress)+"%"),txt_representation=Math.round(this.progress)+"% Complete",$(".completion_span").text(txt_representation)},download:function(a,b){var c=[],d=[];$("#folder_table").find(":checked").each(function(){""!==this.parentElement.parentElement.id&&this.parentElement.parentElement.classList.contains("dataset_row")?c.push(this.parentElement.parentElement.id):""!==this.parentElement.parentElement.id&&this.parentElement.parentElement.classList.contains("folder_row")&&d.push(this.parentElement.parentElement.id)});var e=(window.galaxy_config?galaxy_config.root:"/")+"api/libraries/datasets/download/"+b,f={ld_ids:c,folder_ids:d};this.processDownload(e,f,"get")},processDownload:function(a,b,d){if(a&&b){b="string"==typeof b?b:$.param(b);var e="";$.each(b.split("&"),function(){var a=this.split("=");e+='<input type="hidden" name="'+a[0]+'" value="'+a[1]+'" />'}),$('<form action="'+a+'" method="'+(d||"post")+'">'+e+"</form>").appendTo("body").submit().remove(),c.info("Your download will begin soon.")}else c.error("An error occurred.")},addFilesFromHistoryModal:function(){this.refreshUserHistoriesList(function(a){a.modal=Galaxy.modal;var b=a.templateAddFilesFromHistory(),d=a.options.full_path[a.options.full_path.length-1][1];a.modal.show({closing_events:!0,title:"Adding datasets from your history to folder "+d,body:b({histories:a.histories.models}),buttons:{Add:function(){a.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.back()}}),a.histories.models.length>0?(a.fetchAndDisplayHistoryContents(a.histories.models[0].id),$("#dataset_add_bulk").change(function(b){a.fetchAndDisplayHistoryContents(b.target.value)})):c.error("An error ocurred.")})},importFilesFromPathModal:function(){var a=this;this.modal=Galaxy.modal;var b=this.templateImportPathModal();this.modal.show({closing_events:!0,title:"Please enter paths to import",body:b({}),buttons:{Import:function(){a.importFromPathsClicked(a)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+a.id,{trigger:!0})}}),this.renderSelectBoxes()},fetchExtAndGenomes:function(){var a=this;b.get({url:(window.galaxy_config?galaxy_config.root:"/")+"api/datatypes?extension_only=False",success:function(b){for(key in b)a.list_extensions.push({id:b[key].extension,text:b[key].extension,description:b[key].description,description_url:b[key].description_url});a.list_extensions.sort(function(a,b){return a.id>b.id?1:a.id<b.id?-1:0}),a.list_extensions.unshift(a.auto)}}),b.get({url:(window.galaxy_config?galaxy_config.root:"/")+"api/genomes",success:function(b){for(key in b)a.list_genomes.push({id:b[key][1],text:b[key][0]});a.list_genomes.sort(function(a,b){return a.id>b.id?1:a.id<b.id?-1:0})}})},renderSelectBoxes:function(){var a=this;this.select_genome=new e.View({css:"library-genome-select",data:a.list_genomes,container:Galaxy.modal.$el.find("#library_genome_select"),value:"?"}),this.select_extension=new e.View({css:"library-extension-select",data:a.list_extensions,container:Galaxy.modal.$el.find("#library_extension_select"),value:"auto"})},importFilesFromGalaxyFolderModal:function(a){var b=this,c=this.templateBrowserModal();this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:"Please select folders or files",body:c({}),buttons:{Import:function(){b.importFromJstreePath(b,a)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+b.id,{trigger:!0})}}),this.renderSelectBoxes(),a.disabled_jstree_element="folders",this.renderJstree(a),$("input[type=radio]").change(function(c){"jstree-disable-folders"===c.target.value?(a.disabled_jstree_element="folders",b.renderJstree(a),$(".jstree-folders-message").hide(),$(".jstree-preserve-structure").hide(),$(".jstree-link-files").hide(),$(".jstree-files-message").show()):"jstree-disable-files"===c.target.value&&($(".jstree-files-message").hide(),$(".jstree-folders-message").show(),$(".jstree-link-files").show(),$(".jstree-preserve-structure").show(),a.disabled_jstree_element="files",b.renderJstree(a))})},renderJstree:function(a){this.options=_.extend(this.options,a);var b=a.source||"userdir",e=this.options.disabled_jstree_element;this.jstree=new d.Jstree,this.jstree.url=this.jstree.urlRoot+"?target="+b+"&format=jstree&disable="+e,this.jstree.fetch({success:function(a){define("jquery",function(){return jQuery}),require(["libs/jquery/jstree"],function(){$("#jstree_browser").jstree("destroy"),$("#jstree_browser").jstree({core:{data:a},plugins:["types","checkbox"],types:{folder:{icon:"jstree-folder"},file:{icon:"jstree-file"}},checkbox:{three_state:!1}})})},error:function(a,b){c.error("undefined"!=typeof b.responseJSON?b.responseJSON.err_msg:"An error ocurred.")}})},importFromPathsClicked:function(){var a=this.modal.$el.find(".preserve-checkbox").is(":checked"),b=this.modal.$el.find(".link-checkbox").is(":checked"),d=this.select_extension.value(),e=this.select_genome.value(),f=$("textarea#import_paths").val(),g=[];if(f){this.modal.disableButton("Import"),f=f.split("\n");for(var h=f.length-1;h>=0;h--)trimmed=f[h].trim(),0!==trimmed.length&&g.push(trimmed);this.initChainCallControl({length:g.length,action:"adding_datasets"}),this.chainCallImportingFolders({paths:g,preserve_dirs:a,link_data:b,source:"admin_path",file_type:d,dbkey:e})}else c.info("Please enter a path relative to Galaxy root.")},initChainCallControl:function(a){var b;switch(a.action){case"adding_datasets":b=this.templateAddingDatasetsProgressBar(),this.modal.$el.find(".modal-body").html(b({folder_name:this.options.folder_name}));break;case"deleting_datasets":b=this.templateDeletingDatasetsProgressBar(),this.modal.$el.find(".modal-body").html(b());break;case"to_history":b=this.templateImportIntoHistoryProgressBar(),this.modal.$el.find(".modal-body").html(b({history_name:a.history_name}));break;default:console.error("Wrong action specified.")}this.progress=0,this.progressStep=100/a.length,this.options.chain_call_control.total_number=a.length,this.options.chain_call_control.failed_number=0},importFromJstreePath:function(a,b){var d=$("#jstree_browser").jstree().get_selected(!0),e=this.modal.$el.find(".preserve-checkbox").is(":checked"),f=this.modal.$el.find(".link-checkbox").is(":checked"),g=this.select_extension.value(),h=this.select_genome.value(),i=d[0].type,j=[];if(d.length<1)c.info("Please select some items first.");else{this.modal.disableButton("Import");for(var k=d.length-1;k>=0;k--)void 0!==d[k].li_attr.full_path&&j.push(d[k].li_attr.full_path);if(this.initChainCallControl({length:j.length,action:"adding_datasets"}),"folder"===i){var l=b.source+"_folder";this.chainCallImportingFolders({paths:j,preserve_dirs:e,link_data:f,source:l,file_type:g,dbkey:h})}else if("file"===i){var l=b.source+"_file";this.chainCallImportingUserdirFiles({paths:j,file_type:g,dbkey:h,source:l})}}},fetchAndDisplayHistoryContents:function(a){var b=new d.HistoryContents({id:a}),e=this;b.fetch({success:function(b){var c=e.templateHistoryContents();e.histories.get(a).set({contents:b}),e.modal.$el.find("#selected_history_content").html(c({history_contents:b.models.reverse()}))},error:function(a,b){c.error("undefined"!=typeof b.responseJSON?b.responseJSON.err_msg:"An error ocurred.")}})},addAllDatasetsFromHistory:function(){var a=this.modal.$el.find("#selected_history_content").find(":checked"),b=[],e=[];if(a.length<1)c.info("You must select some datasets first.");else{this.modal.disableButton("Add"),a.each(function(){var a=$(this.parentElement).data("id");a&&b.push(a)});for(var f=b.length-1;f>=0;f--){history_dataset_id=b[f];var g=new d.Item;g.url=(window.galaxy_config?galaxy_config.root:"/")+"api/folders/"+this.options.id+"/contents",g.set({from_hda_id:history_dataset_id}),e.push(g)}this.initChainCallControl({length:e.length,action:"adding_datasets"}),this.chainCallAddingHdas(e)}},chainCallImportingIntoHistory:function(a,b){var d=this,e=a.pop();if("undefined"==typeof e)return 0===this.options.chain_call_control.failed_number?c.success("Selected datasets imported into history. Click this to start analysing it.","",{onclick:function(){window.location="/"}}):this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number?c.error("There was an error and no datasets were imported into history."):this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number&&c.warning("Some of the datasets could not be imported into history. Click this to see what was imported.","",{onclick:function(){window.location="/"}}),Galaxy.modal.hide(),!0;var f=$.when(e.save({content:e.content,source:e.source}));f.done(function(){d.updateProgress(),d.chainCallImportingIntoHistory(a,b)}).fail(function(){d.options.chain_call_control.failed_number+=1,d.updateProgress(),d.chainCallImportingIntoHistory(a,b)})},chainCallImportingUserdirFiles:function(a){var b=this,d=a.paths.pop();if("undefined"==typeof d)return 0===this.options.chain_call_control.failed_number?(c.success("Selected files imported into the current folder"),Galaxy.modal.hide()):c.error("An error occured."),!0;var e=$.when($.post((window.galaxy_config?galaxy_config.root:"/")+"api/libraries/datasets?encoded_folder_id="+b.id+"&source="+a.source+"&path="+d+"&file_type="+a.file_type+"&dbkey="+a.dbkey));e.done(function(){b.updateProgress(),b.chainCallImportingUserdirFiles(a)}).fail(function(){b.options.chain_call_control.failed_number+=1,b.updateProgress(),b.chainCallImportingUserdirFiles(a)})},chainCallImportingFolders:function(a){var b=this,d=a.paths.pop();if("undefined"==typeof d)return 0===this.options.chain_call_control.failed_number?(c.success("Selected folders and their contents imported into the current folder."),Galaxy.modal.hide()):c.error("An error occured."),!0;var e=$.when($.post((window.galaxy_config?galaxy_config.root:"/")+"api/libraries/datasets?encoded_folder_id="+b.id+"&source="+a.source+"&path="+d+"&preserve_dirs="+a.preserve_dirs+"&link_data="+a.link_data+"&file_type="+a.file_type+"&dbkey="+a.dbkey));e.done(function(){b.updateProgress(),b.chainCallImportingFolders(a)}).fail(function(){b.options.chain_call_control.failed_number+=1,b.updateProgress(),b.chainCallImportingFolders(a)})},chainCallAddingHdas:function(a){var b=this;this.added_hdas=new d.Folder;var e=a.pop();if("undefined"==typeof e)return 0===this.options.chain_call_control.failed_number?c.success("Selected datasets from history added to the folder"):this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number?c.error("There was an error and no datasets were added to the folder."):this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number&&c.warning("Some of the datasets could not be added to the folder"),Galaxy.modal.hide(),this.added_hdas;var f=$.when(e.save({from_hda_id:e.get("from_hda_id")}));f.done(function(c){Galaxy.libraries.folderListView.collection.add(c),b.updateProgress(),b.chainCallAddingHdas(a)}).fail(function(){b.options.chain_call_control.failed_number+=1,b.updateProgress(),b.chainCallAddingHdas(a)})},chainCallDeletingItems:function(a){var b=this;this.deleted_items=new d.Folder;var e=a.pop();if("undefined"==typeof e)return 0===this.options.chain_call_control.failed_number?c.success("Selected items were deleted."):this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number?c.error("There was an error and no items were deleted. Please make sure you have sufficient permissions."):this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number&&c.warning("Some of the items could not be deleted. Please make sure you have sufficient permissions."),Galaxy.modal.hide(),this.deleted_items;var f=$.when(e.destroy());f.done(function(c){if(Galaxy.libraries.folderListView.collection.remove(e.id),b.updateProgress(),Galaxy.libraries.folderListView.options.include_deleted){var f=null;"folder"===c.type||"LibraryFolder"===c.model_class?f=new d.FolderAsModel(c):"file"===c.type||"LibraryDataset"===c.model_class?f=new d.Item(c):(console.error("Unknown library item type found."),console.error(c.type||c.model_class)),Galaxy.libraries.folderListView.collection.add(f)}b.chainCallDeletingItems(a)}).fail(function(){b.options.chain_call_control.failed_number+=1,b.updateProgress(),b.chainCallDeletingItems(a)})},checkIncludeDeleted:function(a){Galaxy.libraries.folderListView.fetchFolder(a.target.checked?{include_deleted:!0}:{include_deleted:!1})},deleteSelectedDatasets:function(){var a=$("#folder_table").find(":checked");if(0===a.length)c.info("You must select at least one dataset for deletion.");else{var b=this.templateDeletingDatasetsProgressBar();this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:"Deleting selected datasets",body:b({}),buttons:{Close:function(){Galaxy.modal.hide()}}}),this.options.chain_call_control.total_number=0,this.options.chain_call_control.failed_number=0;var e=[],f=[];a.each(function(){""!==this.parentElement.parentElement.id&&("F"==this.parentElement.parentElement.id.substring(0,1)?f.push(this.parentElement.parentElement.id):e.push(this.parentElement.parentElement.id))});var g=e.length+f.length;this.progressStep=100/g,this.progress=0;for(var h=[],i=e.length-1;i>=0;i--){var j=new d.Item({id:e[i]});h.push(j)}for(var i=f.length-1;i>=0;i--){var k=new d.FolderAsModel({id:f[i]});h.push(k)}this.options.chain_call_control.total_number=g.length,this.chainCallDeletingItems(h)}},showLibInfo:function(){var a=Galaxy.libraries.folderListView.folderContainer.attributes.metadata.parent_library_id,b=null,e=this;null!==Galaxy.libraries.libraryListView?(b=Galaxy.libraries.libraryListView.collection.get(a),this.showLibInfoModal(b)):(b=new d.Library({id:a}),b.fetch({success:function(){e.showLibInfoModal(b)},error:function(a,b){c.error("undefined"!=typeof b.responseJSON?b.responseJSON.err_msg:"An error ocurred.")}}))},showLibInfoModal:function(a){var b=this.templateLibInfoInModal();this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:"Library Information",body:b({library:a}),buttons:{Close:function(){Galaxy.modal.hide()}}})},showImportModal:function(a){switch(a.source){case"history":this.addFilesFromHistoryModal();break;case"importdir":this.importFilesFromGalaxyFolderModal({source:"importdir"});break;case"path":this.importFilesFromPathModal();break;case"userdir":this.importFilesFromGalaxyFolderModal({source:"userdir"});break;default:Galaxy.libraries.library_router.back(),c.error("Invalid import source.")}},showPageSizePrompt:function(){var a=prompt("How many items per page do you want to see?",Galaxy.libraries.preferences.get("folder_page_size"));null!=a&&a==parseInt(a)&&(Galaxy.libraries.preferences.set({folder_page_size:parseInt(a)}),Galaxy.libraries.folderListView.render({id:this.options.id,show_page:1}))},templateToolBar:function(){return tmpl_array=[],tmpl_array.push('<div class="library_style_container">'),tmpl_array.push(' <div id="library_toolbar">'),tmpl_array.push('<form class="form-inline" role="form">'),tmpl_array.push("   <span><strong>DATA LIBRARIES</strong></span>"),tmpl_array.push('          <span id="folder_paginator" class="library-paginator">'),tmpl_array.push("          </span>"),tmpl_array.push('<div class="checkbox toolbar-item logged-dataset-manipulation" style="height: 20px; display:none;">'),tmpl_array.push("<label>"),tmpl_array.push('<input id="include_deleted_datasets_chk" type="checkbox"> include deleted </input>'),tmpl_array.push("</label>"),tmpl_array.push("</div>"),tmpl_array.push('   <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button add-library-items" type="button"><span class="fa fa-plus"></span> <span class="fa fa-folder"></span></button>'),tmpl_array.push("<% if(mutiple_add_dataset_options) { %>"),tmpl_array.push('   <div class="btn-group add-library-items" style="display:none;">'),tmpl_array.push('     <button title="Add Datasets to Current Folder" id="" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">'),tmpl_array.push('     <span class="fa fa-plus"></span> <span class="fa fa-file"></span> <span class="caret"></span>'),tmpl_array.push("     </button>"),tmpl_array.push('     <ul class="dropdown-menu" role="menu">'),tmpl_array.push('        <li><a href="#folders/<%= id %>/import/history"> from History</a></li>'),tmpl_array.push("<% if(Galaxy.config.user_library_import_dir !== null) { %>"),tmpl_array.push('        <li><a href="#folders/<%= id %>/import/userdir"> from User Directory</a></li>'),tmpl_array.push("<% } %>"),tmpl_array.push("<% if(Galaxy.config.allow_library_path_paste) { %>"),tmpl_array.push('   <li class="divider"></li>'),tmpl_array.push('   <li class="dropdown-header">Admins only</li>'),tmpl_array.push("<% if(Galaxy.config.library_import_dir !== null) { %>"),tmpl_array.push('   <li><a href="#folders/<%= id %>/import/importdir">from Import Directory</a></li>'),tmpl_array.push("<% } %>"),tmpl_array.push("<% if(Galaxy.config.allow_library_path_paste) { %>"),tmpl_array.push('        <li><a href="#folders/<%= id %>/import/path">from Path</a></li>'),tmpl_array.push("<% } %>"),tmpl_array.push("<% } %>"),tmpl_array.push("     </ul>"),tmpl_array.push("   </div>"),tmpl_array.push("<% } else { %>"),tmpl_array.push(' <a  data-placement="top" title="Add Datasets to Current Folder" style="display:none;" class="btn btn-default add-library-items" href="#folders/<%= id %>/import/history" role="button"><span class="fa fa-plus"></span> <span class="fa fa-file"></span></span></a>'),tmpl_array.push("<% } %>"),tmpl_array.push('  <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to History</button>'),tmpl_array.push('   <div id="toolbtn_dl" class="btn-group dataset-manipulation" style="margin-left: 0.5em; display:none; ">'),tmpl_array.push('     <button title="Download selected datasets as archive" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">'),tmpl_array.push('     <span class="fa fa-download"></span> Download <span class="caret"></span>'),tmpl_array.push("     </button>"),tmpl_array.push('     <ul class="dropdown-menu" role="menu">'),tmpl_array.push('        <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>'),tmpl_array.push('        <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>'),tmpl_array.push('        <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>'),tmpl_array.push("     </ul>"),tmpl_array.push("   </div>"),tmpl_array.push('   <button data-toggle="tooltip" data-placement="top" title="Mark selected datasets deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button"><span class="fa fa-times"></span> Delete</button>'),tmpl_array.push('   <button data-id="<%- id %>" data-toggle="tooltip" data-placement="top" title="Show library information" id="toolbtn_show_libinfo" class="primary-button" style="margin-left: 0.5em;" type="button"><span class="fa fa-info-circle"></span> Library Info</button>'),tmpl_array.push('   <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/FolderContents" target="_blank"><button class="primary-button" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>'),tmpl_array.push(" </div>"),tmpl_array.push("</form>"),tmpl_array.push(' <div id="folder_items_element">'),tmpl_array.push(" </div>"),tmpl_array.push("</div>"),_.template(tmpl_array.join(""))},templateLibInfoInModal:function(){return tmpl_array=[],tmpl_array.push('<div id="lif_info_modal">'),tmpl_array.push("<h2>Library name:</h2>"),tmpl_array.push('<p><%- library.get("name") %></p>'),tmpl_array.push("<h3>Library description:</h3>"),tmpl_array.push('<p><%- library.get("description") %></p>'),tmpl_array.push("<h3>Library synopsis:</h3>"),tmpl_array.push('<p><%- library.get("synopsis") %></p>'),tmpl_array.push('<p data-toggle="tooltip" data-placement="top" title="<%- library.get("create_time") %>">created <%- library.get("create_time_pretty") %></p>'),tmpl_array.push("</div>"),_.template(tmpl_array.join(""))},templateNewFolderInModal:function(){return tmpl_array=[],tmpl_array.push('<div id="new_folder_modal">'),tmpl_array.push("<form>"),tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">'),tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">'),tmpl_array.push("</form>"),tmpl_array.push("</div>"),_.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var a=[];return a.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">'),a.push("Select history: "),a.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> '),a.push("   <% _.each(histories, function(history) { %>"),a.push('       <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>'),a.push("   <% }); %>"),a.push("</select>"),a.push("</span>"),_.template(a.join(""))},templateImportIntoHistoryProgressBar:function(){var a=[];return a.push('<div class="import_text">'),a.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>"),a.push("</div>"),a.push('<div class="progress">'),a.push('   <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">'),a.push('       <span class="completion_span">0% Complete</span>'),a.push("   </div>"),a.push("</div>"),a.push(""),_.template(a.join(""))},templateAddingDatasetsProgressBar:function(){var a=[];return a.push('<div class="import_text">'),a.push("Adding selected datasets to library folder <b><%= _.escape(folder_name) %></b>"),a.push("</div>"),a.push('<div class="progress">'),a.push('   <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">'),a.push('       <span class="completion_span">0% Complete</span>'),a.push("   </div>"),a.push("</div>"),a.push(""),_.template(a.join(""))},templateDeletingDatasetsProgressBar:function(){var a=[];return a.push('<div class="import_text">'),a.push("</div>"),a.push('<div class="progress">'),a.push('   <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">'),a.push('       <span class="completion_span">0% Complete</span>'),a.push("   </div>"),a.push("</div>"),a.push(""),_.template(a.join(""))},templateBrowserModal:function(){var a=[];return a.push('<div id="file_browser_modal">'),a.push('<div class="alert alert-info jstree-files-message">All files you select will be imported into the current folder.</div>'),a.push('<div class="alert alert-info jstree-folders-message" style="display:none;">All files within the selected folders and their subfolders will be imported into the current folder.</div>'),a.push('<div style="margin-bottom:1em;">'),a.push('<label class="radio-inline">'),a.push('  <input title="Switch to selecting files" type="radio" name="jstree-radio" value="jstree-disable-folders" checked="checked"> Files'),a.push("</label>"),a.push('<label class="radio-inline">'),a.push('  <input title="Switch to selecting folders" type="radio" name="jstree-radio" value="jstree-disable-files"> Folders'),a.push("</label>"),a.push("</div>"),a.push('<div style="margin-bottom:1em;">'),a.push('<label class="checkbox-inline jstree-preserve-structure" style="display:none;">'),a.push('   <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">'),a.push("Preserve directory structure"),a.push(" </label>"),a.push('<label class="checkbox-inline jstree-link-files" style="display:none;">'),a.push('   <input class="link-checkbox" type="checkbox" value="link_files">'),a.push("Link files instead of copying"),a.push(" </label>"),a.push("</div>"),a.push('<div id="jstree_browser">'),a.push("</div>"),a.push("<hr />"),a.push("<p>You can set extension type and genome for all imported datasets at once:</p>"),a.push("<div>"),a.push('Type: <span id="library_extension_select" class="library-extension-select" />'),a.push('  Genome: <span id="library_genome_select" class="library-genome-select" />'),a.push("</div>"),a.push("</div>"),_.template(a.join(""))},templateImportPathModal:function(){var a=[];return a.push('<div id="file_browser_modal">'),a.push('<div class="alert alert-info jstree-folders-message">All files within the given folders and their subfolders will be imported into the current folder.</div>'),a.push('<div style="margin-bottom: 0.5em;">'),a.push('<label class="checkbox-inline jstree-preserve-structure">'),a.push('   <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">'),a.push("Preserve directory structure"),a.push(" </label>"),a.push('<label class="checkbox-inline jstree-link-files">'),a.push('   <input class="link-checkbox" type="checkbox" value="link_files">'),a.push("Link files instead of copying"),a.push(" </label>"),a.push("</div>"),a.push('<textarea id="import_paths" class="form-control" rows="5" placeholder="Absolute paths (or paths relative to Galaxy root) separated by newline"></textarea>'),a.push("<hr />"),a.push("<p>You can set extension type and genome for all imported datasets at once:</p>"),a.push("<div>"),a.push('Type: <span id="library_extension_select" class="library-extension-select" />'),a.push('  Genome: <span id="library_genome_select" class="library-genome-select" />'),a.push("</div>"),a.push("</div>"),_.template(a.join(""))},templateAddFilesFromHistory:function(){var a=[];return a.push('<div id="add_files_modal">'),a.push('<div id="history_modal_combo_bulk">'),a.push("Select history:  "),a.push('<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> '),a.push("   <% _.each(histories, function(history) { %>"),a.push('       <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>'),
+define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(a,b,c,d,e){var f=Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_show_libinfo":"showLibInfo","click #toolbtn_bulk_delete":"deleteSelectedDatasets","click #page_size_prompt":"showPageSizePrompt"},defaults:{can_add_library_item:!1,contains_file_or_folder:!1,chain_call_control:{total_number:0,failed_number:0},disabled_jstree_element:"folders"},modal:null,jstree:null,histories:null,select_genome:null,select_extension:null,list_extensions:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},list_genomes:[],initialize:function(a){this.options=_.defaults(a||{},this.defaults),this.fetchExtAndGenomes(),this.render()},render:function(a){this.options=_.extend(this.options,a);var b=this.templateToolBar(),c={id:this.options.id,is_admin:!1,is_anonym:!0,mutiple_add_dataset_options:!1};Galaxy.currUser&&(c.is_admin=Galaxy.currUser.isAdmin(),c.is_anonym=Galaxy.currUser.isAnonymous(),(null!==Galaxy.config.user_library_import_dir||Galaxy.config.allow_library_path_paste!==!1||null!==Galaxy.config.library_import_dir)&&(c.mutiple_add_dataset_options=!0)),this.$el.html(b(c))},renderPaginator:function(a){this.options=_.extend(this.options,a);var b=this.templatePaginator();this.$el.find("#folder_paginator").html(b({id:this.options.id,show_page:parseInt(this.options.show_page),page_count:parseInt(this.options.page_count),total_items_count:this.options.total_items_count,items_shown:this.options.items_shown}))},configureElements:function(a){this.options=_.extend(this.options,a),this.options.can_add_library_item===!0?$(".add-library-items").show():$(".add-library-items").hide(),this.options.contains_file_or_folder===!0&&Galaxy.currUser?Galaxy.currUser.isAnonymous()?($(".dataset-manipulation").show(),$(".logged-dataset-manipulation").hide()):($(".logged-dataset-manipulation").show(),$(".dataset-manipulation").show()):($(".logged-dataset-manipulation").hide(),$(".dataset-manipulation").hide()),this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(a){a.preventDefault(),a.stopPropagation();var b=this,c=this.templateNewFolderInModal();this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:"Create New Folder",body:c(),buttons:{Create:function(){b.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var a=this.serialize_new_folder();if(this.validate_new_folder(a)){var b=new d.FolderAsModel;url_items=Backbone.history.fragment.split("/"),current_folder_id=url_items[url_items.length-1],b.url=b.urlRoot+current_folder_id,b.save(a,{success:function(a){Galaxy.modal.hide(),c.success("Folder created."),a.set({type:"folder"}),Galaxy.libraries.folderListView.collection.add(a)},error:function(a,b){Galaxy.modal.hide(),c.error("undefined"!=typeof b.responseJSON?b.responseJSON.err_msg:"An error ocurred.")}})}else c.error("Folder's name is missing.");return!1},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(a){return""!==a.name},modalBulkImport:function(){var a=$("#folder_table").find(":checked");0===a.length?c.info("You must select some datasets first."):this.refreshUserHistoriesList(function(a){var b=a.templateBulkImportInModal();a.modal=Galaxy.modal,a.modal.show({closing_events:!0,title:"Import into History",body:b({histories:a.histories.models}),buttons:{Import:function(){a.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})},refreshUserHistoriesList:function(a){var b=this;this.histories=new d.GalaxyHistories,this.histories.fetch({success:function(){a(b)},error:function(a,b){c.error("undefined"!=typeof b.responseJSON?b.responseJSON.err_msg:"An error ocurred.")}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var a=$("select[name=dataset_import_bulk] option:selected").val(),b=$("select[name=dataset_import_bulk] option:selected").text();this.options.last_used_history_id=a;var c=[],e=[];$("#folder_table").find(":checked").each(function(){""!==this.parentElement.parentElement.id&&this.parentElement.parentElement.classList.contains("dataset_row")?c.push(this.parentElement.parentElement.id):""!==this.parentElement.parentElement.id&&this.parentElement.parentElement.classList.contains("folder_row")&&e.push(this.parentElement.parentElement.id)});for(var f=[],g=c.length-1;g>=0;g--){var h=c[g],i=new d.HistoryItem;i.url=i.urlRoot+a+"/contents",i.content=h,i.source="library",f.push(i)}for(var g=e.length-1;g>=0;g--){var j=e[g],i=new d.HistoryItem;i.url=i.urlRoot+a+"/contents",i.content=j,i.source="library_folder",f.push(i)}this.initChainCallControl({length:f.length,action:"to_history",history_name:b}),jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+a),this.chainCallImportingIntoHistory(f,b)},updateProgress:function(){this.progress+=this.progressStep,$(".progress-bar-import").width(Math.round(this.progress)+"%"),txt_representation=Math.round(this.progress)+"% Complete",$(".completion_span").text(txt_representation)},download:function(a,b){var c=[],d=[];$("#folder_table").find(":checked").each(function(){""!==this.parentElement.parentElement.id&&this.parentElement.parentElement.classList.contains("dataset_row")?c.push(this.parentElement.parentElement.id):""!==this.parentElement.parentElement.id&&this.parentElement.parentElement.classList.contains("folder_row")&&d.push(this.parentElement.parentElement.id)});var e=(window.galaxy_config?galaxy_config.root:"/")+"api/libraries/datasets/download/"+b,f={ld_ids:c,folder_ids:d};this.processDownload(e,f,"get")},processDownload:function(a,b,d){if(a&&b){b="string"==typeof b?b:$.param(b);var e="";$.each(b.split("&"),function(){var a=this.split("=");e+='<input type="hidden" name="'+a[0]+'" value="'+a[1]+'" />'}),$('<form action="'+a+'" method="'+(d||"post")+'">'+e+"</form>").appendTo("body").submit().remove(),c.info("Your download will begin soon.")}else c.error("An error occurred.")},addFilesFromHistoryModal:function(){this.refreshUserHistoriesList(function(a){a.modal=Galaxy.modal;var b=a.templateAddFilesFromHistory(),d=a.options.full_path[a.options.full_path.length-1][1];a.modal.show({closing_events:!0,title:"Adding datasets from your history to folder "+d,body:b({histories:a.histories.models}),buttons:{Add:function(){a.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.back()}}),a.histories.models.length>0?(a.fetchAndDisplayHistoryContents(a.histories.models[0].id),$("#dataset_add_bulk").change(function(b){a.fetchAndDisplayHistoryContents(b.target.value)})):c.error("An error ocurred.")})},importFilesFromPathModal:function(){var a=this;this.modal=Galaxy.modal;var b=this.templateImportPathModal();this.modal.show({closing_events:!0,title:"Please enter paths to import",body:b({}),buttons:{Import:function(){a.importFromPathsClicked(a)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+a.id,{trigger:!0})}}),this.renderSelectBoxes()},fetchExtAndGenomes:function(){var a=this;b.get({url:(window.galaxy_config?galaxy_config.root:"/")+"api/datatypes?extension_only=False",success:function(b){for(key in b)a.list_extensions.push({id:b[key].extension,text:b[key].extension,description:b[key].description,description_url:b[key].description_url});a.list_extensions.sort(function(a,b){return a.id>b.id?1:a.id<b.id?-1:0}),a.list_extensions.unshift(a.auto)}}),b.get({url:(window.galaxy_config?galaxy_config.root:"/")+"api/genomes",success:function(b){for(key in b)a.list_genomes.push({id:b[key][1],text:b[key][0]});a.list_genomes.sort(function(a,b){return a.id>b.id?1:a.id<b.id?-1:0})}})},renderSelectBoxes:function(){var a=this;this.select_genome=new e.View({css:"library-genome-select",data:a.list_genomes,container:Galaxy.modal.$el.find("#library_genome_select"),value:"?"}),this.select_extension=new e.View({css:"library-extension-select",data:a.list_extensions,container:Galaxy.modal.$el.find("#library_extension_select"),value:"auto"})},importFilesFromGalaxyFolderModal:function(a){var b=this,c=this.templateBrowserModal();this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:"Please select folders or files",body:c({}),buttons:{Import:function(){b.importFromJstreePath(b,a)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+b.id,{trigger:!0})}}),this.renderSelectBoxes(),a.disabled_jstree_element="folders",this.renderJstree(a),$("input[type=radio]").change(function(c){"jstree-disable-folders"===c.target.value?(a.disabled_jstree_element="folders",b.renderJstree(a),$(".jstree-folders-message").hide(),$(".jstree-preserve-structure").hide(),$(".jstree-link-files").hide(),$(".jstree-files-message").show()):"jstree-disable-files"===c.target.value&&($(".jstree-files-message").hide(),$(".jstree-folders-message").show(),$(".jstree-link-files").show(),$(".jstree-preserve-structure").show(),a.disabled_jstree_element="files",b.renderJstree(a))})},renderJstree:function(a){this.options=_.extend(this.options,a);var b=a.source||"userdir",e=this.options.disabled_jstree_element;this.jstree=new d.Jstree,this.jstree.url=this.jstree.urlRoot+"?target="+b+"&format=jstree&disable="+e,this.jstree.fetch({success:function(a){define("jquery",function(){return jQuery}),require(["libs/jquery/jstree"],function(){$("#jstree_browser").jstree("destroy"),$("#jstree_browser").jstree({core:{data:a},plugins:["types","checkbox"],types:{folder:{icon:"jstree-folder"},file:{icon:"jstree-file"}},checkbox:{three_state:!1}})})},error:function(a,b){c.error("undefined"!=typeof b.responseJSON?b.responseJSON.err_msg:"An error ocurred.")}})},importFromPathsClicked:function(){var a=this.modal.$el.find(".preserve-checkbox").is(":checked"),b=this.modal.$el.find(".link-checkbox").is(":checked"),d=this.select_extension.value(),e=this.select_genome.value(),f=$("textarea#import_paths").val(),g=[];if(f){this.modal.disableButton("Import"),f=f.split("\n");for(var h=f.length-1;h>=0;h--)trimmed=f[h].trim(),0!==trimmed.length&&g.push(trimmed);this.initChainCallControl({length:g.length,action:"adding_datasets"}),this.chainCallImportingFolders({paths:g,preserve_dirs:a,link_data:b,source:"admin_path",file_type:d,dbkey:e})}else c.info("Please enter a path relative to Galaxy root.")},initChainCallControl:function(a){var b;switch(a.action){case"adding_datasets":b=this.templateAddingDatasetsProgressBar(),this.modal.$el.find(".modal-body").html(b({folder_name:this.options.folder_name}));break;case"deleting_datasets":b=this.templateDeletingDatasetsProgressBar(),this.modal.$el.find(".modal-body").html(b());break;case"to_history":b=this.templateImportIntoHistoryProgressBar(),this.modal.$el.find(".modal-body").html(b({history_name:a.history_name}));break;default:console.error("Wrong action specified.")}this.progress=0,this.progressStep=100/a.length,this.options.chain_call_control.total_number=a.length,this.options.chain_call_control.failed_number=0},importFromJstreePath:function(a,b){var d=$("#jstree_browser").jstree().get_selected(!0),e=this.modal.$el.find(".preserve-checkbox").is(":checked"),f=this.modal.$el.find(".link-checkbox").is(":checked"),g=this.select_extension.value(),h=this.select_genome.value(),i=d[0].type,j=[];if(d.length<1)c.info("Please select some items first.");else{this.modal.disableButton("Import");for(var k=d.length-1;k>=0;k--)void 0!==d[k].li_attr.full_path&&j.push(d[k].li_attr.full_path);if(this.initChainCallControl({length:j.length,action:"adding_datasets"}),"folder"===i){var l=b.source+"_folder";this.chainCallImportingFolders({paths:j,preserve_dirs:e,link_data:f,source:l,file_type:g,dbkey:h})}else if("file"===i){var l=b.source+"_file";this.chainCallImportingUserdirFiles({paths:j,file_type:g,dbkey:h,source:l})}}},fetchAndDisplayHistoryContents:function(a){var b=new d.HistoryContents({id:a}),e=this;b.fetch({success:function(b){var c=e.templateHistoryContents();e.histories.get(a).set({contents:b}),e.modal.$el.find("#selected_history_content").html(c({history_contents:b.models.reverse()}))},error:function(a,b){c.error("undefined"!=typeof b.responseJSON?b.responseJSON.err_msg:"An error ocurred.")}})},addAllDatasetsFromHistory:function(){var a=this.modal.$el.find("#selected_history_content").find(":checked"),b=[],e=[];if(a.length<1)c.info("You must select some datasets first.");else{this.modal.disableButton("Add"),a.each(function(){var a=$(this.parentElement).data("id");a&&b.push(a)});for(var f=b.length-1;f>=0;f--){history_dataset_id=b[f];var g=new d.Item;g.url=(window.galaxy_config?galaxy_config.root:"/")+"api/folders/"+this.options.id+"/contents",g.set({from_hda_id:history_dataset_id}),e.push(g)}this.initChainCallControl({length:e.length,action:"adding_datasets"}),this.chainCallAddingHdas(e)}},chainCallImportingIntoHistory:function(a,b){var d=this,e=a.pop();if("undefined"==typeof e)return 0===this.options.chain_call_control.failed_number?c.success("Selected datasets imported into history. Click this to start analysing it.","",{onclick:function(){window.location="/"}}):this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number?c.error("There was an error and no datasets were imported into history."):this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number&&c.warning("Some of the datasets could not be imported into history. Click this to see what was imported.","",{onclick:function(){window.location="/"}}),Galaxy.modal.hide(),!0;var f=$.when(e.save({content:e.content,source:e.source}));f.done(function(){d.updateProgress(),d.chainCallImportingIntoHistory(a,b)}).fail(function(){d.options.chain_call_control.failed_number+=1,d.updateProgress(),d.chainCallImportingIntoHistory(a,b)})},chainCallImportingUserdirFiles:function(a){var b=this,d=a.paths.pop();if("undefined"==typeof d)return 0===this.options.chain_call_control.failed_number?(c.success("Selected files imported into the current folder"),Galaxy.modal.hide()):c.error("An error occured."),!0;var e=$.when($.post((window.galaxy_config?galaxy_config.root:"/")+"api/libraries/datasets?encoded_folder_id="+b.id+"&source="+a.source+"&path="+d+"&file_type="+a.file_type+"&dbkey="+a.dbkey));e.done(function(){b.updateProgress(),b.chainCallImportingUserdirFiles(a)}).fail(function(){b.options.chain_call_control.failed_number+=1,b.updateProgress(),b.chainCallImportingUserdirFiles(a)})},chainCallImportingFolders:function(a){var b=this,d=a.paths.pop();if("undefined"==typeof d)return 0===this.options.chain_call_control.failed_number?(c.success("Selected folders and their contents imported into the current folder."),Galaxy.modal.hide()):c.error("An error occured."),!0;var e=$.when($.post((window.galaxy_config?galaxy_config.root:"/")+"api/libraries/datasets?encoded_folder_id="+b.id+"&source="+a.source+"&path="+d+"&preserve_dirs="+a.preserve_dirs+"&link_data="+a.link_data+"&file_type="+a.file_type+"&dbkey="+a.dbkey));e.done(function(){b.updateProgress(),b.chainCallImportingFolders(a)}).fail(function(){b.options.chain_call_control.failed_number+=1,b.updateProgress(),b.chainCallImportingFolders(a)})},chainCallAddingHdas:function(a){var b=this;this.added_hdas=new d.Folder;var e=a.pop();if("undefined"==typeof e)return 0===this.options.chain_call_control.failed_number?c.success("Selected datasets from history added to the folder"):this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number?c.error("There was an error and no datasets were added to the folder."):this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number&&c.warning("Some of the datasets could not be added to the folder"),Galaxy.modal.hide(),this.added_hdas;var f=$.when(e.save({from_hda_id:e.get("from_hda_id")}));f.done(function(c){Galaxy.libraries.folderListView.collection.add(c),b.updateProgress(),b.chainCallAddingHdas(a)}).fail(function(){b.options.chain_call_control.failed_number+=1,b.updateProgress(),b.chainCallAddingHdas(a)})},chainCallDeletingItems:function(a){var b=this;this.deleted_items=new d.Folder;var e=a.pop();if("undefined"==typeof e)return 0===this.options.chain_call_control.failed_number?c.success("Selected items were deleted."):this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number?c.error("There was an error and no items were deleted. Please make sure you have sufficient permissions."):this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number&&c.warning("Some of the items could not be deleted. Please make sure you have sufficient permissions."),Galaxy.modal.hide(),this.deleted_items;var f=$.when(e.destroy());f.done(function(c){if(Galaxy.libraries.folderListView.collection.remove(e.id),b.updateProgress(),Galaxy.libraries.folderListView.options.include_deleted){var f=null;"folder"===c.type||"LibraryFolder"===c.model_class?f=new d.FolderAsModel(c):"file"===c.type||"LibraryDataset"===c.model_class?f=new d.Item(c):(console.error("Unknown library item type found."),console.error(c.type||c.model_class)),Galaxy.libraries.folderListView.collection.add(f)}b.chainCallDeletingItems(a)}).fail(function(){b.options.chain_call_control.failed_number+=1,b.updateProgress(),b.chainCallDeletingItems(a)})},checkIncludeDeleted:function(a){Galaxy.libraries.folderListView.fetchFolder(a.target.checked?{include_deleted:!0}:{include_deleted:!1})},deleteSelectedDatasets:function(){var a=$("#folder_table").find(":checked");if(0===a.length)c.info("You must select at least one dataset for deletion.");else{var b=this.templateDeletingDatasetsProgressBar();this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:"Deleting selected datasets",body:b({}),buttons:{Close:function(){Galaxy.modal.hide()}}}),this.options.chain_call_control.total_number=0,this.options.chain_call_control.failed_number=0;var e=[],f=[];a.each(function(){""!==this.parentElement.parentElement.id&&("F"==this.parentElement.parentElement.id.substring(0,1)?f.push(this.parentElement.parentElement.id):e.push(this.parentElement.parentElement.id))});var g=e.length+f.length;this.progressStep=100/g,this.progress=0;for(var h=[],i=e.length-1;i>=0;i--){var j=new d.Item({id:e[i]});h.push(j)}for(var i=f.length-1;i>=0;i--){var k=new d.FolderAsModel({id:f[i]});h.push(k)}this.options.chain_call_control.total_number=g.length,this.chainCallDeletingItems(h)}},showLibInfo:function(){var a=Galaxy.libraries.folderListView.folderContainer.attributes.metadata.parent_library_id,b=null,e=this;null!==Galaxy.libraries.libraryListView?(b=Galaxy.libraries.libraryListView.collection.get(a),this.showLibInfoModal(b)):(b=new d.Library({id:a}),b.fetch({success:function(){e.showLibInfoModal(b)},error:function(a,b){c.error("undefined"!=typeof b.responseJSON?b.responseJSON.err_msg:"An error ocurred.")}}))},showLibInfoModal:function(a){var b=this.templateLibInfoInModal();this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:"Library Information",body:b({library:a}),buttons:{Close:function(){Galaxy.modal.hide()}}})},showImportModal:function(a){switch(a.source){case"history":this.addFilesFromHistoryModal();break;case"importdir":this.importFilesFromGalaxyFolderModal({source:"importdir"});break;case"path":this.importFilesFromPathModal();break;case"userdir":this.importFilesFromGalaxyFolderModal({source:"userdir"});break;default:Galaxy.libraries.library_router.back(),c.error("Invalid import source.")}},showPageSizePrompt:function(){var a=prompt("How many items per page do you want to see?",Galaxy.libraries.preferences.get("folder_page_size"));null!=a&&a==parseInt(a)&&(Galaxy.libraries.preferences.set({folder_page_size:parseInt(a)}),Galaxy.libraries.folderListView.render({id:this.options.id,show_page:1}))},templateToolBar:function(){return tmpl_array=[],tmpl_array.push('<div class="library_style_container">'),tmpl_array.push(' <div id="library_toolbar">'),tmpl_array.push('<form class="form-inline" role="form">'),tmpl_array.push("   <span><strong>DATA LIBRARIES</strong></span>"),tmpl_array.push('          <span id="folder_paginator" class="library-paginator">'),tmpl_array.push("          </span>"),tmpl_array.push('<div class="checkbox toolbar-item logged-dataset-manipulation" style="height: 20px; display:none;">'),tmpl_array.push("<label>"),tmpl_array.push('<input id="include_deleted_datasets_chk" type="checkbox"> include deleted </input>'),tmpl_array.push("</label>"),tmpl_array.push("</div>"),tmpl_array.push('   <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button add-library-items" type="button"><span class="fa fa-plus"></span> <span class="fa fa-folder"></span></button>'),tmpl_array.push("<% if(mutiple_add_dataset_options) { %>"),tmpl_array.push('   <div class="btn-group add-library-items" style="display:none;">'),tmpl_array.push('     <button title="Add Datasets to Current Folder" id="" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">'),tmpl_array.push('     <span class="fa fa-plus"></span> <span class="fa fa-file"></span> <span class="caret"></span>'),tmpl_array.push("     </button>"),tmpl_array.push('     <ul class="dropdown-menu" role="menu">'),tmpl_array.push('        <li><a href="#folders/<%= id %>/import/history"> from History</a></li>'),tmpl_array.push("<% if(Galaxy.config.user_library_import_dir !== null) { %>"),tmpl_array.push('        <li><a href="#folders/<%= id %>/import/userdir"> from User Directory</a></li>'),tmpl_array.push("<% } %>"),tmpl_array.push("<% if(Galaxy.config.allow_library_path_paste) { %>"),tmpl_array.push('   <li class="divider"></li>'),tmpl_array.push('   <li class="dropdown-header">Admins only</li>'),tmpl_array.push("<% if(Galaxy.config.library_import_dir !== null) { %>"),tmpl_array.push('   <li><a href="#folders/<%= id %>/import/importdir">from Import Directory</a></li>'),tmpl_array.push("<% } %>"),tmpl_array.push("<% if(Galaxy.config.allow_library_path_paste) { %>"),tmpl_array.push('        <li><a href="#folders/<%= id %>/import/path">from Path</a></li>'),tmpl_array.push("<% } %>"),tmpl_array.push("<% } %>"),tmpl_array.push("     </ul>"),tmpl_array.push("   </div>"),tmpl_array.push("<% } else { %>"),tmpl_array.push(' <a  data-placement="top" title="Add Datasets to Current Folder" style="display:none;" class="btn btn-default add-library-items" href="#folders/<%= id %>/import/history" role="button"><span class="fa fa-plus"></span> <span class="fa fa-file"></span></span></a>'),tmpl_array.push("<% } %>"),tmpl_array.push('  <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to History</button>'),tmpl_array.push('   <div id="toolbtn_dl" class="btn-group dataset-manipulation" style="margin-left: 0.5em; display:none; ">'),tmpl_array.push('     <button title="Download selected datasets as archive" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">'),tmpl_array.push('     <span class="fa fa-download"></span> Download <span class="caret"></span>'),tmpl_array.push("     </button>"),tmpl_array.push('     <ul class="dropdown-menu" role="menu">'),tmpl_array.push('        <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>'),tmpl_array.push('        <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>'),tmpl_array.push('        <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>'),tmpl_array.push("     </ul>"),tmpl_array.push("   </div>"),tmpl_array.push('   <button data-toggle="tooltip" data-placement="top" title="Mark selected datasets deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button"><span class="fa fa-times"></span> Delete</button>'),tmpl_array.push('   <button data-id="<%- id %>" data-toggle="tooltip" data-placement="top" title="Show library information" id="toolbtn_show_libinfo" class="primary-button" style="margin-left: 0.5em;" type="button"><span class="fa fa-info-circle"></span> Library Info</button>'),tmpl_array.push('   <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/FolderContents" target="_blank"><button class="primary-button" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>'),tmpl_array.push(" </div>"),tmpl_array.push("</form>"),tmpl_array.push(' <div id="folder_items_element">'),tmpl_array.push(" </div>"),tmpl_array.push("</div>"),_.template(tmpl_array.join(""))},templateLibInfoInModal:function(){return tmpl_array=[],tmpl_array.push('<div id="lif_info_modal">'),tmpl_array.push("<h2>Library name:</h2>"),tmpl_array.push('<p><%- library.get("name") %></p>'),tmpl_array.push("<h3>Library description:</h3>"),tmpl_array.push('<p><%- library.get("description") %></p>'),tmpl_array.push("<h3>Library synopsis:</h3>"),tmpl_array.push('<p><%- library.get("synopsis") %></p>'),tmpl_array.push('<p data-toggle="tooltip" data-placement="top" title="<%- library.get("create_time") %>">created <%- library.get("create_time_pretty") %></p>'),tmpl_array.push("</div>"),_.template(tmpl_array.join(""))},templateNewFolderInModal:function(){return tmpl_array=[],tmpl_array.push('<div id="new_folder_modal">'),tmpl_array.push("<form>"),tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">'),tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">'),tmpl_array.push("</form>"),tmpl_array.push("</div>"),_.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var a=[];return a.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">'),a.push("Select history: "),a.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> '),a.push("   <% _.each(histories, function(history) { %>"),a.push('       <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>'),a.push("   <% }); %>"),a.push("</select>"),a.push("</span>"),_.template(a.join(""))},templateImportIntoHistoryProgressBar:function(){var a=[];return a.push('<div class="import_text">'),a.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>"),a.push("</div>"),a.push('<div class="progress">'),a.push('   <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">'),a.push('       <span class="completion_span">0% Complete</span>'),a.push("   </div>"),a.push("</div>"),a.push(""),_.template(a.join(""))},templateAddingDatasetsProgressBar:function(){var a=[];return a.push('<div class="import_text">'),a.push("Adding selected datasets to library folder <b><%= _.escape(folder_name) %></b>"),a.push("</div>"),a.push('<div class="progress">'),a.push('   <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">'),a.push('       <span class="completion_span">0% Complete</span>'),a.push("   </div>"),a.push("</div>"),a.push(""),_.template(a.join(""))},templateDeletingDatasetsProgressBar:function(){var a=[];return a.push('<div class="import_text">'),a.push("</div>"),a.push('<div class="progress">'),a.push('   <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">'),a.push('       <span class="completion_span">0% Complete</span>'),a.push("   </div>"),a.push("</div>"),a.push(""),_.template(a.join(""))},templateBrowserModal:function(){var a=[];return a.push('<div id="file_browser_modal">'),a.push('<div class="alert alert-info jstree-files-message">All files you select will be imported into the current folder.</div>'),a.push('<div class="alert alert-info jstree-folders-message" style="display:none;">All files within the selected folders and their subfolders will be imported into the current folder.</div>'),a.push('<div style="margin-bottom:1em;">'),a.push('<label class="radio-inline">'),a.push('  <input title="Switch to selecting files" type="radio" name="jstree-radio" value="jstree-disable-folders" checked="checked"> Files'),a.push("</label>"),a.push('<label class="radio-inline">'),a.push('  <input title="Switch to selecting folders" type="radio" name="jstree-radio" value="jstree-disable-files"> Folders'),a.push("</label>"),a.push("</div>"),a.push('<div style="margin-bottom:1em;">'),a.push('<label class="checkbox-inline jstree-preserve-structure" style="display:none;">'),a.push('   <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">'),a.push("Preserve directory structure"),a.push(" </label>"),a.push('<label class="checkbox-inline jstree-link-files" style="display:none;">'),a.push('   <input class="link-checkbox" type="checkbox" value="link_files">'),a.push("Link files instead of copying"),a.push(" </label>"),a.push("</div>"),a.push('<div id="jstree_browser">'),a.push("</div>"),a.push("<hr />"),a.push("<p>You can set extension type and genome for all imported datasets at once:</p>"),a.push("<div>"),a.push('Type: <span id="library_extension_select" class="library-extension-select" />'),a.push('  Genome: <span id="library_genome_select" class="library-genome-select" />'),a.push("</div>"),a.push("</div>"),_.template(a.join(""))},templateImportPathModal:function(){var a=[];return a.push('<div id="file_browser_modal">'),a.push('<div class="alert alert-info jstree-folders-message">All files within the given folders and their subfolders will be imported into the current folder.</div>'),a.push('<div style="margin-bottom: 0.5em;">'),a.push('<label class="checkbox-inline jstree-preserve-structure">'),a.push('   <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">'),a.push("Preserve directory structure"),a.push(" </label>"),a.push('<label class="checkbox-inline jstree-link-files">'),a.push('   <input class="link-checkbox" type="checkbox" value="link_files">'),a.push("Link files instead of copying"),a.push(" </label>"),a.push("</div>"),a.push('<textarea id="import_paths" class="form-control" rows="5" placeholder="Absolute paths (or paths relative to Galaxy root) separated by newline"></textarea>'),a.push("<hr />"),a.push("<p>You can set extension type and genome for all imported datasets at once:</p>"),a.push("<div>"),a.push('Type: <span id="library_extension_select" class="library-extension-select" />'),a.push('  Genome: <span id="library_genome_select" class="library-genome-select" />'),a.push("</div>"),a.push("</div>"),_.template(a.join(""))},templateAddFilesFromHistory:function(){var a=[];return a.push('<div id="add_files_modal">'),a.push('<div id="history_modal_combo_bulk">'),a.push("Select history:  "),a.push('<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> '),a.push("   <% _.each(histories, function(history) { %>"),a.push('       <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>'),
 a.push("   <% }); %>"),a.push("</select>"),a.push("</div>"),a.push("<br/>"),a.push('<div id="selected_history_content">'),a.push("</div>"),a.push("</div>"),_.template(a.join(""))},templateHistoryContents:function(){var a=[];return a.push("<strong>Choose the datasets to import:</strong>"),a.push("<ul>"),a.push(" <% _.each(history_contents, function(history_item) { %>"),a.push(' <li data-id="<%= _.escape(history_item.get("id")) %>">'),a.push('   <input style="margin: 0;" type="checkbox"> <%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>'),a.push(" </li>"),a.push(" <% }); %>"),a.push("</ul>"),_.template(a.join(""))},templatePaginator:function(){return tmpl_array=[],tmpl_array.push('   <ul class="pagination pagination-sm">'),tmpl_array.push("       <% if ( ( show_page - 1 ) > 0 ) { %>"),tmpl_array.push("           <% if ( ( show_page - 1 ) > page_count ) { %>"),tmpl_array.push('               <li><a href="#folders/<%= id %>/page/1"><span class="fa fa-angle-double-left"></span></a></li>'),tmpl_array.push('               <li class="disabled"><a href="#folders/<%= id %>/page/<% print( show_page ) %>"><% print( show_page - 1 ) %></a></li>'),tmpl_array.push("           <% } else { %>"),tmpl_array.push('               <li><a href="#folders/<%= id %>/page/1"><span class="fa fa-angle-double-left"></span></a></li>'),tmpl_array.push('               <li><a href="#folders/<%= id %>/page/<% print( show_page - 1 ) %>"><% print( show_page - 1 ) %></a></li>'),tmpl_array.push("           <% } %>"),tmpl_array.push("       <% } else { %>"),tmpl_array.push('           <li class="disabled"><a href="#folders/<%= id %>/page/1"><span class="fa fa-angle-double-left"></span></a></li>'),tmpl_array.push('           <li class="disabled"><a href="#folders/<%= id %>/page/<% print( show_page ) %>"><% print( show_page - 1 ) %></a></li>'),tmpl_array.push("       <% } %>"),tmpl_array.push('       <li class="active">'),tmpl_array.push('       <a href="#folders/<%= id %>/page/<% print( show_page ) %>"><% print( show_page ) %></a>'),tmpl_array.push("       </li>"),tmpl_array.push("       <% if ( ( show_page ) < page_count ) { %>"),tmpl_array.push('           <li><a href="#folders/<%= id %>/page/<% print( show_page + 1 ) %>"><% print( show_page + 1 ) %></a></li>'),tmpl_array.push('           <li><a href="#folders/<%= id %>/page/<% print( page_count ) %>"><span class="fa fa-angle-double-right"></span></a></li>'),tmpl_array.push("       <% } else { %>"),tmpl_array.push('           <li class="disabled"><a href="#folders/<%= id %>/page/<% print( show_page  ) %>"><% print( show_page + 1 ) %></a></li>'),tmpl_array.push('           <li class="disabled"><a href="#folders/<%= id %>/page/<% print( page_count ) %>"><span class="fa fa-angle-double-right"></span></a></li>'),tmpl_array.push("       <% } %>"),tmpl_array.push("   </ul>"),tmpl_array.push("   <span>"),tmpl_array.push('       showing <a data-toggle="tooltip" data-placement="top" title="Click to change the number of items on page" id="page_size_prompt"><%- items_shown %></a> of <%- total_items_count %> items'),tmpl_array.push("   </span>"),_.template(tmpl_array.join(""))}});return{FolderToolbarView:f}});
 //# sourceMappingURL=../../../maps/mvc/library/library-foldertoolbar-view.js.map
\ No newline at end of file

From 87b9d1a5f44a6e42397694e16f17c97c504c1b27 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <ghv2@psu.edu>
Date: Sat, 28 Nov 2015 14:28:38 -0500
Subject: [PATCH 5/7] Add support for Strand-specific COordinate Count datatype

---
 lib/galaxy/datatypes/interval.py | 77 ++++++++++++++++++++++++++++++++
 1 file changed, 77 insertions(+)

diff --git a/lib/galaxy/datatypes/interval.py b/lib/galaxy/datatypes/interval.py
index 998ee9318a6..d3d630c66eb 100644
--- a/lib/galaxy/datatypes/interval.py
+++ b/lib/galaxy/datatypes/interval.py
@@ -1485,6 +1485,83 @@ class ChromatinInteractions( Interval ):
         return False
 
 
+class ScIdx(Tabular):
+    """
+    Support for the Strand-specific coordinate count datatype which is used
+    by tools within the Chip-exo Galaxy flavor.  The Chip-exo Galaxy flavor
+    is used by the Center for Eukaryotic Gene Regulation labs at Penn State
+    University.
+
+    ScIdx files are 1-based and consist of strand-specific coordinate counts.
+    They always have 5 columns, and the first row is the column labels:
+    'chrom', 'index', 'forward', 'reverse', 'value'.
+    Each line following the first consists of data:
+    chromosome name (type str), peak index (type int), Forward strand peak
+    count (type int), Reverse strand peak count (type int) and value (type int).
+    The value of the 5th 'value' column is the sum of the forward and end
+    reverse peak count values.
+    """
+    file_ext = "scidx"
+
+    MetadataElement(name="columns", default=0, desc="Number of columns", readonly=True, visible=False)
+    MetadataElement(name="column_types", default=[], param=metadata.ColumnTypesParameter, desc="Column types", readonly=True, visible=False, no_value=[])
+
+    def __init__(self, **kwd):
+        """
+        Initialize scidx datatype.
+        """
+        Tabular.__init__(self, **kwd)
+        # Don't set column names since the first
+        # line of the dataset displays them.
+        self.column_names = []
+
+    def sniff(self, filename):
+        """
+        Checks for 'scidx-ness.'
+        """
+        try:
+            count = 0
+            fh = open(filename, "r")
+            while True:
+                line = fh.readline()
+                line = line.strip()
+                if not line:
+                    # EOF
+                    if count > 1:
+                        # We need at least the column labels and a data line.
+                        return True
+                    return False
+                # Skip first line.
+                if count > 0:
+                    items = line.split('\t')
+                    if len(items) != 5:
+                        return False
+                    index = items[1]
+                    if not index.isdigit():
+                        return False
+                    forward = items[2]
+                    if not forward.isdigit():
+                        return False
+                    reverse = items[3]
+                    if not reverse.isdigit():
+                        return False
+                    value = items[4]
+                    if not value.isdigit():
+                        return False
+                    if int(forward) + int(reverse) != int(value):
+                        return False
+                if count == 100:
+                    return True
+                count += 1
+            if count < 100 and count > 0:
+                return True
+        except:
+            return False
+        finally:
+            fh.close()
+        return False
+
+
 if __name__ == '__main__':
     import doctest
     doctest.testmod(sys.modules[__name__])

From 6fdff2d2f88458cef6f29ee3cb8bb895babab62c Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <ghv2@psu.edu>
Date: Sat, 28 Nov 2015 14:32:12 -0500
Subject: [PATCH 6/7] Add Strand-specific Coordinate Count datatype entry to
 the datatypes config.

---
 config/datatypes_conf.xml.sample | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/config/datatypes_conf.xml.sample b/config/datatypes_conf.xml.sample
index db44f9072dd..128ead09c8b 100644
--- a/config/datatypes_conf.xml.sample
+++ b/config/datatypes_conf.xml.sample
@@ -418,6 +418,8 @@
     <datatype extension="oxlist" type="galaxy.datatypes.binary:OxliStopTags" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="oxliss" type="galaxy.datatypes.binary:OxliSubset" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="oxligl" type="galaxy.datatypes.binary:OxliGraphLabels" mimetype="application/octet-stream" display_in_upload="true"/>
+    <!-- Strand-specific Coordinate Count Datatype used by the Center for Eukaryotic Gene Regulation labs at Penn State -->
+    <datatype extension="scidx" type="galaxy.datatypes.interval:ScIdx" display_in_upload="true" />
   </registration>
   <sniffers>
     <!--
@@ -427,6 +429,7 @@
     defined format first, followed by next-most rigidly defined,
     and so on.
     -->
+    <sniffer type="galaxy.datatypes.interval:ScIdx"/>
     <sniffer type="galaxy.datatypes.tabular:Vcf"/>
     <sniffer type="galaxy.datatypes.binary:TwoBit"/>
     <sniffer type="galaxy.datatypes.binary:GeminiSQLite"/>

From 21fad8ac88a46996b2ff2719527709374f0c9913 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <ghv2@psu.edu>
Date: Mon, 30 Nov 2015 07:48:08 -0500
Subject: [PATCH 7/7] Set the column names and edit the comments section

---
 lib/galaxy/datatypes/interval.py | 11 +++--------
 1 file changed, 3 insertions(+), 8 deletions(-)

diff --git a/lib/galaxy/datatypes/interval.py b/lib/galaxy/datatypes/interval.py
index d3d630c66eb..13160aa7b3e 100644
--- a/lib/galaxy/datatypes/interval.py
+++ b/lib/galaxy/datatypes/interval.py
@@ -1487,19 +1487,14 @@ class ChromatinInteractions( Interval ):
 
 class ScIdx(Tabular):
     """
-    Support for the Strand-specific coordinate count datatype which is used
-    by tools within the Chip-exo Galaxy flavor.  The Chip-exo Galaxy flavor
-    is used by the Center for Eukaryotic Gene Regulation labs at Penn State
-    University.
-
     ScIdx files are 1-based and consist of strand-specific coordinate counts.
     They always have 5 columns, and the first row is the column labels:
     'chrom', 'index', 'forward', 'reverse', 'value'.
     Each line following the first consists of data:
     chromosome name (type str), peak index (type int), Forward strand peak
     count (type int), Reverse strand peak count (type int) and value (type int).
-    The value of the 5th 'value' column is the sum of the forward and end
-    reverse peak count values.
+    The value of the 5th 'value' column is the sum of the forward and reverse
+    peak count values.
     """
     file_ext = "scidx"
 
@@ -1513,7 +1508,7 @@ class ScIdx(Tabular):
         Tabular.__init__(self, **kwd)
         # Don't set column names since the first
         # line of the dataset displays them.
-        self.column_names = []
+        self.column_names = ['chrom', 'index', 'forward', 'reverse', 'value']
 
     def sniff(self, filename):
         """