[galaxy-commits] commit/galaxy-central: 4 new changesets

14 Dec 2014

4 new commits in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/5edaafeecfed/
Changeset:   5edaafeecfed
User:        abretaud
Date:        2014-11-27 13:18:18+00:00
Summary:     Add an API to remove items from tool data tables
Affected #:  2 files

diff -r 3975b317ffdcbaa6c8dcb4b2b52404bfa34edbc2 -r 5edaafeecfed448ea259adaacf3a4ce6e6da15d1 lib/galaxy/tools/data/__init__.py

--- a/lib/galaxy/tools/data/__init__.py
+++ b/lib/galaxy/tools/data/__init__.py
@@ -211,6 +211,13 @@
                 self.add_entry( entry, allow_duplicates=allow_duplicates, persist=persist, persist_on_error=persist_on_error, entry_source=entry_source, **kwd )
         return self._loaded_content_version
 
+    def _remove_entry(self, values, **kwd):
+        raise NotImplementedError( "Abstract method" )
+
+    def remove_entry(self, values, **kwd):
+        self._remove_entry_and_reload( values,**kwd )
+        return self._update_version()
+
     def is_current_version( self, other_version ):
         return self._loaded_content_version == other_version
 
@@ -506,6 +513,42 @@
                 data_table_fh.write( "%s\n" % ( self.separator.join( fields ) ) )
         return not is_error
 
+    def _remove_entry_and_reload( self, values):
+
+        # update every file
+        for filename in self.filenames:
+
+            if os.path.exists( filename ):
+                values = self._replace_field_separators( values )
+                self.filter_file_fields( filename, values )
+            else:
+                log.warn( "Cannot find index file '%s' for tool data table '%s'" % ( filename, self.name ) )
+        
+        self.reload_from_files()
+
+    def filter_file_fields( self, loc_file, values ):
+        """
+        Reads separated lines from file and print back only the lines that pass a filter.
+        """
+        separator_char = (lambda c: '<TAB>' if c == '\t' else c)(self.separator)
+
+        with open(loc_file) as reader:
+            rval = ""
+            for i, line in enumerate( reader ):
+                if line.lstrip().startswith( self.comment_char ):
+                    rval += line
+                else:
+                    line_s = line.rstrip( "\n\r" )
+                    if line_s:
+                        fields = line_s.split( self.separator )
+                        if fields != values:
+                            rval += line
+        
+        with open(loc_file, 'wb') as writer:
+            writer.write(rval)
+        
+        return rval
+
     def _replace_field_separators( self, fields, separator=None, replace=None, comment_char=None ):
         #make sure none of the fields contain separator
         #make sure separator replace is different from comment_char,

diff -r 3975b317ffdcbaa6c8dcb4b2b52404bfa34edbc2 -r 5edaafeecfed448ea259adaacf3a4ce6e6da15d1 lib/galaxy/webapps/galaxy/api/tool_data.py
--- a/lib/galaxy/webapps/galaxy/api/tool_data.py
+++ b/lib/galaxy/webapps/galaxy/api/tool_data.py
@@ -20,3 +20,44 @@
     @web.expose_api
     def show( self, trans, id, **kwds ):
         return trans.app.tool_data_tables.data_tables[id].to_dict(view='element')
+
+    @web.require_admin
+    @web.expose_api
+    def delete( self, trans, id, **kwd ):
+        """
+        DELETE /api/tool_data/{id}
+        Removes a role from a group
+
+        :type   id:     str
+        :param  id:     the encoded id of the history to delete
+        :type   kwd:    dict
+        :param  kwd:    (required) dictionary structure containing:
+
+            * payload:     a dictionary itself containing:
+                * values:   <TAB> separated list of column contents, there must be a value for all the columns of the data table
+        """
+        decoded_tool_data_id = id
+        
+        try:
+            data_table = trans.app.tool_data_tables.data_tables.get(decoded_tool_data_id)
+        except:
+            data_table = None
+        if not data_table:
+            trans.response.status = 400
+            return "Invalid data table id ( %s ) specified." % str( decoded_tool_data_id )
+        
+        values = None
+        if kwd.get( 'payload', None ):
+            values = kwd['payload'].get( 'values', '' )
+
+        if not values:
+            trans.response.status = 400
+            return "Invalid data table item ( %s ) specified." % str( values )
+        
+        split_values = values.split("\t")
+        
+        if len(split_values) != len(data_table.get_column_name_list()):
+            trans.response.status = 400
+            return "Invalid data table item ( %s ) specified. Wrong number of columns (%s given, %s required)." % ( str( values ), str(len(split_values)), str(len(data_table.get_column_name_list())))
+
+        return data_table.remove_entry(split_values)


https://bitbucket.org/galaxy/galaxy-central/commits/d76253bb22c4/
Changeset:   d76253bb22c4
User:        abretaud
Date:        2014-12-09 14:01:47+00:00
Summary:     Merged galaxy/galaxy-central into default
Affected #:  184 files

diff -r 5edaafeecfed448ea259adaacf3a4ce6e6da15d1 -r d76253bb22c4f64c73523956d119c0c5ab0a357b .hgtags
--- a/.hgtags
+++ b/.hgtags
@@ -20,4 +20,4 @@
 ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11
 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11
 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06
-acc8d1e2bc88530aa8d8651cf5f88649f6769304 latest_2014.10.06
+acb2548443ae42d39ef200d035ccc0481d6b930c latest_2014.10.06

diff -r 5edaafeecfed448ea259adaacf3a4ce6e6da15d1 -r d76253bb22c4f64c73523956d119c0c5ab0a357b client/galaxy/scripts/galaxy.library.js
--- a/client/galaxy/scripts/galaxy.library.js
+++ b/client/galaxy/scripts/galaxy.library.js
@@ -36,7 +36,7 @@
   initialize: function() {
     this.routesHit = 0;
     //keep count of number of routes handled by the application
-    Backbone.history.on('route', function() { this.routesHit++; }, this);
+    Backbone.history.on( 'route', function() { this.routesHit++; }, this );
 },
 
 routes: {
@@ -45,6 +45,7 @@
     "library/:library_id/permissions"                               : "library_permissions",
     "folders/:folder_id/permissions"                                : "folder_permissions",
     "folders/:id"                                                   : "folder_content",
+    "folders/:id/page/:show_page"                                   : "folder_page",
     "folders/:folder_id/datasets/:dataset_id"                       : "dataset_detail",
     "folders/:folder_id/datasets/:dataset_id/permissions"           : "dataset_permissions",
     "folders/:folder_id/datasets/:dataset_id/versions/:ldda_id"     : "dataset_version",
@@ -53,13 +54,13 @@
 },
 
 back: function() {
-    if(this.routesHit > 1) {
+    if( this.routesHit > 1 ) {
       //more than one route hit -> user did not land to current page directly
       window.history.back();
   } else {
       //otherwise go to the home page. Use replaceState if available so
       //the navigation doesn't create an extra history entry
-      this.navigate('#', {trigger:true, replace:true});
+      this.navigate( '#', { trigger:true, replace:true } );
   }
 }
 });
@@ -71,7 +72,8 @@
         with_deleted      : false,
         sort_order        : 'asc',
         sort_by           : 'name',
-        library_page_size : 20
+        library_page_size : 20,
+        folder_page_size  : 15
     }
 });
 
@@ -94,10 +96,10 @@
 
         this.library_router = new LibraryRouter();
 
-        this.library_router.on('route:libraries', function() {
-          Galaxy.libraries.libraryToolbarView = new mod_librarytoolbar_view.LibraryToolbarView();
-          Galaxy.libraries.libraryListView = new mod_librarylist_view.LibraryListView();
-      });
+        this.library_router.on( 'route:libraries', function() {
+            Galaxy.libraries.libraryToolbarView = new mod_librarytoolbar_view.LibraryToolbarView();
+            Galaxy.libraries.libraryListView = new mod_librarylist_view.LibraryListView();
+        });
         
         this.library_router.on('route:libraries_page', function( show_page ) {
             if ( Galaxy.libraries.libraryToolbarView === null ){
@@ -108,66 +110,77 @@
             }
         });
 
-        this.library_router.on('route:folder_content', function(id) {
+        this.library_router.on( 'route:folder_content', function( id ) {
             if (Galaxy.libraries.folderToolbarView){ 
-              Galaxy.libraries.folderToolbarView.$el.unbind('click');
-          }
-          Galaxy.libraries.folderToolbarView = new mod_foldertoolbar_view.FolderToolbarView({id: id});
-          Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView({id: id});
-      });
+                Galaxy.libraries.folderToolbarView.$el.unbind( 'click' );
+            }
+            Galaxy.libraries.folderToolbarView = new mod_foldertoolbar_view.FolderToolbarView( { id: id } );
+            Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView( { id: id } );
+        });
 
-        this.library_router.on('route:download', function(folder_id, format) {
-          if ($('#folder_list_body').find(':checked').length === 0) {
-            mod_toastr.info( 'You must select at least one dataset to download' );
-            Galaxy.libraries.library_router.navigate('folders/' + folder_id, {trigger: true, replace: true});
-        } else {
-            Galaxy.libraries.folderToolbarView.download(folder_id, format);
-            Galaxy.libraries.library_router.navigate('folders/' + folder_id, {trigger: false, replace: true});
-        }
-    });
+        this.library_router.on( 'route:folder_page', function( id, show_page ) {
+            if ( Galaxy.libraries.folderToolbarView === null ){
+                Galaxy.libraries.folderToolbarView = new mod_foldertoolbar_view.FolderToolbarView( {id: id} );
+                Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView( { id: id, show_page: show_page } );
+            } else {
+                Galaxy.libraries.folderListView.render( { id: id, show_page: parseInt( show_page ) } )
+            }
+        });
 
-        this.library_router.on('route:dataset_detail', function(folder_id, dataset_id){
-          if (Galaxy.libraries.datasetView){
-            Galaxy.libraries.datasetView.$el.unbind('click');
-        }
-        Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id});
-    });
-        this.library_router.on('route:dataset_version', function(folder_id, dataset_id, ldda_id){
-          if (Galaxy.libraries.datasetView){
-            Galaxy.libraries.datasetView.$el.unbind('click');
-        }
-        Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id, ldda_id: ldda_id, show_version: true});
-    });
+        this.library_router.on( 'route:download', function( folder_id, format ) {
+            if ( $( '#folder_list_body' ).find( ':checked' ).length === 0 ) {
+                mod_toastr.info( 'You must select at least one dataset to download' );
+                Galaxy.libraries.library_router.navigate( 'folders/' + folder_id, { trigger: true, replace: true } );
+            } else {
+                Galaxy.libraries.folderToolbarView.download( folder_id, format );
+                Galaxy.libraries.library_router.navigate( 'folders/' + folder_id, { trigger: false, replace: true } );
+            }
+        });
 
-        this.library_router.on('route:dataset_permissions', function(folder_id, dataset_id){
-          if (Galaxy.libraries.datasetView){
-            Galaxy.libraries.datasetView.$el.unbind('click');
-        }
-        Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id, show_permissions: true});
-    });
+        this.library_router.on( 'route:dataset_detail', function(folder_id, dataset_id){
+            if (Galaxy.libraries.datasetView){
+                Galaxy.libraries.datasetView.$el.unbind('click');
+            }
+            Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id});
+        });
 
-        this.library_router.on('route:library_permissions', function(library_id){
-          if (Galaxy.libraries.libraryView){
-            Galaxy.libraries.libraryView.$el.unbind('click');
-        }
-        Galaxy.libraries.libraryView = new mod_library_library_view.LibraryView({id: library_id, show_permissions: true});
-    });
+        this.library_router.on( 'route:dataset_version', function(folder_id, dataset_id, ldda_id){
+            if (Galaxy.libraries.datasetView){
+                Galaxy.libraries.datasetView.$el.unbind('click');
+            }
+            Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id, ldda_id: ldda_id, show_version: true});
+        });
 
-        this.library_router.on('route:folder_permissions', function(folder_id){
-          if (Galaxy.libraries.folderView){
-            Galaxy.libraries.folderView.$el.unbind('click');
-        }
-        Galaxy.libraries.folderView = new mod_library_folder_view.FolderView({id: folder_id, show_permissions: true});
-    });
-        this.library_router.on('route:import_datasets', function(folder_id, source){
-          if (Galaxy.libraries.folderToolbarView && Galaxy.libraries.folderListView){
-            Galaxy.libraries.folderToolbarView.showImportModal({source:source});
-        } else {
-            Galaxy.libraries.folderToolbarView = new mod_foldertoolbar_view.FolderToolbarView({id: folder_id});
-            Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView({id: folder_id});
-            Galaxy.libraries.folderToolbarView.showImportModal({source: source});
-        }
-    });
+        this.library_router.on( 'route:dataset_permissions', function(folder_id, dataset_id){
+            if (Galaxy.libraries.datasetView){
+                Galaxy.libraries.datasetView.$el.unbind('click');
+            }
+            Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id, show_permissions: true});
+        });
+
+        this.library_router.on( 'route:library_permissions', function(library_id){
+            if (Galaxy.libraries.libraryView){
+                Galaxy.libraries.libraryView.$el.unbind('click');
+            }
+            Galaxy.libraries.libraryView = new mod_library_library_view.LibraryView({id: library_id, show_permissions: true});
+        });
+
+        this.library_router.on( 'route:folder_permissions', function(folder_id){
+            if (Galaxy.libraries.folderView){
+                Galaxy.libraries.folderView.$el.unbind('click');
+            }
+            Galaxy.libraries.folderView = new mod_library_folder_view.FolderView({id: folder_id, show_permissions: true});
+        });
+
+        this.library_router.on( 'route:import_datasets', function( folder_id, source ){
+            if ( Galaxy.libraries.folderToolbarView && Galaxy.libraries.folderListView ){
+                Galaxy.libraries.folderToolbarView.showImportModal( { source:source } );
+            } else {
+                Galaxy.libraries.folderToolbarView = new mod_foldertoolbar_view.FolderToolbarView( { id: folder_id } );
+                Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView( { id: folder_id } );
+                Galaxy.libraries.folderToolbarView.showImportModal( { source: source } );
+            }
+        });
 
         Backbone.history.start({pushState: false});
     }

diff -r 5edaafeecfed448ea259adaacf3a4ce6e6da15d1 -r d76253bb22c4f64c73523956d119c0c5ab0a357b client/galaxy/scripts/jq-plugins/ui/filter-control.js
--- /dev/null
+++ b/client/galaxy/scripts/jq-plugins/ui/filter-control.js
@@ -0,0 +1,204 @@
+// from: https://raw.githubusercontent.com/umdjs/umd/master/jqueryPlugin.js
+// Uses AMD or browser globals to create a jQuery plugin.
+(function (factory) {
+    if (typeof define === 'function' && define.amd) {
+        // AMD. Register as an anonymous module.
+        define(['jquery'], factory);
+    } else {
+        // Browser globals
+        factory(jQuery);
+    }
+
+}(function ($) {
+	//==============================================================================
+	/**
+	 *  Template function that produces a bootstrap dropdown to replace the
+	 *  vanilla HTML select input. Pass in an array of options and an initial selection:
+	 *  $( '.my-div' ).append( dropDownSelect( [ 'option1', 'option2' ], 'option2' );
+	 *
+	 *  When the user changes the selected option a 'change.dropdown-select' event will
+	 *  fire with both the jq event and the new selection text as arguments.
+	 *
+	 *  Get the currently selected choice using:
+	 *  var userChoice = $( '.my-div .dropdown-select .dropdown-select-selected' ).text();
+	 *
+	 */
+	function dropDownSelect( options, selected ){
+		// replacement for vanilla select element using bootstrap dropdowns instead
+		selected = selected || (( !_.isEmpty( options ) )?( options[0] ):( '' ));
+		var $select = $([
+				'<div class="dropdown-select btn-group">',
+					'<button type="button" class="btn btn-default">',
+						'<span class="dropdown-select-selected">' + selected + '</span>',
+					'</button>',
+				'</div>'
+			].join( '\n' ));
+
+		// if there's only one option, do not style/create as buttons, dropdown - use simple span
+		// otherwise, a dropdown displaying the current selection
+		if( options && options.length > 1 ){
+			$select.find( 'button' )
+				.addClass( 'dropdown-toggle' ).attr( 'data-toggle', 'dropdown' )
+				.append( ' <span class="caret"></span>' );
+			$select.append([
+				'<ul class="dropdown-menu" role="menu">',
+					_.map( options, function( option ){
+						return [
+							'<li><a href="javascript:void(0)">', option, '</a></li>'
+						].join( '' );
+					}).join( '\n' ),
+				'</ul>'
+			].join( '\n' ));
+		}
+
+		// trigger 'change.dropdown-select' when a new selection is made using the dropdown
+		function selectThis( event ){
+			var $this = $( this ),
+				$select = $this.parents( '.dropdown-select' ),
+				newSelection = $this.text();
+			$select.find( '.dropdown-select-selected' ).text( newSelection );
+			$select.trigger( 'change.dropdown-select', newSelection );
+		}
+
+		$select.find( 'a' ).click( selectThis );
+		return $select;
+	}
+
+	//==============================================================================
+    /**
+     *  Creates a three part bootstrap button group (key, op, value) meant to
+     *  allow the user control of filters (e.g. { key: 'name', op: 'contains', value: 'my_history' })
+     *
+     *  Each field uses a dropDownSelect (from ui.js) to allow selection
+     *  (with the 'value' field appearing as an input when set to do so).
+     *
+     *  Any change or update in any of the fields will trigger a 'change.filter-control'
+     *  event which will be passed an object containing those fields (as the example above).
+     *
+     *  Pass in an array of possible filter objects to control what the user can select.
+     *  Each filter object should have:
+     *      key : generally the attribute name on which to filter something
+     *      ops : an array of 1 or more filter operations (e.g. [ 'is', '<', 'contains', '!=' ])
+     *      values (optional) : an array of possible values for the filter (e.g. [ 'true', 'false' ])
+     *  @example:
+     *  $( '.my-div' ).filterControl({
+     *      filters : [
+     *          { key: 'name',    ops: [ 'is exactly', 'contains' ] }
+     *          { key: 'deleted', ops: [ 'is' ], values: [ 'true', 'false' ] }
+     *      ]
+     *  });
+     *  // after initialization, you can prog. get the current value using:
+     *  $( '.my-div' ).filterControl( 'val' )
+     *
+     */
+    function FilterControl( element, options ){
+		return this.init( element, options );
+    }
+    /** the data key that this object will be stored under in the DOM element */
+	FilterControl.prototype.DATA_KEY = 'filter-control';
+
+    /** parses options, sets up instance vars, and does initial render */
+	FilterControl.prototype.init = function _init( element, options ){
+		options = options || { filters: [] };
+		this.$element = $( element ).addClass( 'filter-control btn-group' );
+		this.options = jQuery.extend( true, {}, this.defaults, options );
+
+        this.currFilter = this.options.filters[0];
+		return this.render();
+	};
+
+    /** render (or re-render) the controls on the element */
+	FilterControl.prototype.render = function _render(){
+        this.$element.empty()
+            .append([ this._renderKeySelect(), this._renderOpSelect(), this._renderValueInput() ]);
+        return this;
+    };
+
+    /** render the key dropDownSelect, bind a change event to it, and return it */
+	FilterControl.prototype._renderKeySelect = function __renderKeySelect(){
+        var filterControl = this;
+        var keys = this.options.filters.map( function( filter ){
+            return filter.key;
+        });
+        this.$keySelect = dropDownSelect( keys, this.currFilter.key )
+            .addClass( 'filter-control-key' )
+            .on( 'change.dropdown-select', function( event, selection ){
+                filterControl.currFilter = _.findWhere( filterControl.options.filters, { key: selection });
+                // when the filter/key changes, re-render the control entirely
+                filterControl.render()._triggerChange();
+            });
+        return this.$keySelect;
+    };
+
+    /** render the op dropDownSelect, bind a change event to it, and return it */
+	FilterControl.prototype._renderOpSelect = function __renderOpSelect(){
+        var filterControl = this,
+            ops = this.currFilter.ops;
+        //TODO: search for currOp in avail. ops: use that for selected if there; otherwise: first op
+        this.$opSelect = dropDownSelect( ops, ops[0] )
+            .addClass( 'filter-control-op' )
+            .on( 'change.dropdown-select', function( event, selection ){
+                filterControl._triggerChange();
+            });
+        return this.$opSelect;
+    };
+
+    /** render the value control, bind a change event to it, and return it */
+	FilterControl.prototype._renderValueInput = function __renderValueInput(){
+        var filterControl = this;
+        // if a values attribute is prov. on the filter - make this a dropdown; otherwise, use an input
+        if( this.currFilter.values ){
+            this.$valueSelect = dropDownSelect( this.currFilter.values, this.currFilter.values[0] )
+                .on( 'change.dropdown-select', function( event, selection ){
+                    filterControl._triggerChange();
+                });
+        } else {
+            //TODO: allow setting a value type (mainly for which html5 input to use: range, number, etc.)
+            this.$valueSelect = $( '<input/>' ).addClass( 'form-control' )
+                .on( 'change', function( event, value ){
+                    filterControl._triggerChange();
+                });
+        }
+        this.$valueSelect.addClass( 'filter-control-value' );
+        return this.$valueSelect;
+    };
+
+    /** return the current state/setting for the filter as a three key object: key, op, value */
+	FilterControl.prototype.val = function _val(){
+        var key = this.$element.find( '.filter-control-key .dropdown-select-selected' ).text(),
+            op  = this.$element.find( '.filter-control-op .dropdown-select-selected'  ).text(),
+            // handle either a dropdown or plain input
+            $value = this.$element.find( '.filter-control-value' ),
+            value = ( $value.hasClass( 'dropdown-select' ) )?( $value.find( '.dropdown-select-selected' ).text() )
+                                                            :( $value.val() );
+        return { key: key, op: op, value: value };
+    };
+
+    // single point of change for change event
+	FilterControl.prototype._triggerChange = function __triggerChange(){
+        this.$element.trigger( 'change.filter-control', this.val() );
+    };
+
+    // as jq plugin
+    jQuery.fn.extend({
+        filterControl : function $filterControl( options ){
+			var nonOptionsArgs = jQuery.makeArray( arguments ).slice( 1 );
+            return this.map( function(){
+				var $this = $( this ),
+					data = $this.data( FilterControl.prototype.DATA_KEY );
+
+				if( jQuery.type( options ) === 'object' ){
+					data = new FilterControl( $this, options );
+					$this.data( FilterControl.prototype.DATA_KEY, data );
+				}
+				if( data && jQuery.type( options ) === 'string' ){
+					var fn = data[ options ];
+					if( jQuery.type( fn ) === 'function' ){
+						return fn.apply( data, nonOptionsArgs );
+					}
+				}
+				return this;
+            });
+        }
+    });
+}));

diff -r 5edaafeecfed448ea259adaacf3a4ce6e6da15d1 -r d76253bb22c4f64c73523956d119c0c5ab0a357b client/galaxy/scripts/jq-plugins/ui/mode-button.js
--- /dev/null
+++ b/client/galaxy/scripts/jq-plugins/ui/mode-button.js
@@ -0,0 +1,191 @@
+// from: https://raw.githubusercontent.com/umdjs/umd/master/jqueryPlugin.js
+// Uses AMD or browser globals to create a jQuery plugin.
+(function (factory) {
+    if (typeof define === 'function' && define.amd) {
+        //TODO: So...this turns out to be an all or nothing thing. If I load jQuery in the define below, it will
+        //  (of course) wipe the old jquery *and all the plugins loaded into it*. So the define below *is still
+        //  relying on jquery being loaded globally* in order to preserve plugins.
+        define([], factory);
+    } else {
+        // Browser globals
+        factory(jQuery);
+    }
+
+}(function () {
+
+    /** Multi 'mode' button (or any element really) that changes the html
+     *      contents of itself when clicked. Pass in an ordered list of
+     *      objects with 'html' and (optional) onclick functions.
+     *
+     *      When clicked in a particular node, the onclick function will
+     *      be called (with the element as this) and the element will
+     *      switch to the next mode, replacing its html content with
+     *      that mode's html.
+     *
+     *      If there is no next mode, the element will switch back to
+     *      the first mode.
+     * @example:
+     *     $( '.myElement' ).modeButton({
+     *         modes : [
+     *             {
+     *                 mode: 'bler',
+     *                 html: '<h5>Bler</h5>',
+     *                 onclick : function(){
+     *                     $( 'body' ).css( 'background-color', 'red' );
+     *                 }
+     *             },
+     *             {
+     *                 mode: 'bloo',
+     *                 html: '<h4>Bloo</h4>',
+     *                 onclick : function(){
+     *                     $( 'body' ).css( 'background-color', 'blue' );
+     *                 }
+     *             },
+     *             {
+     *                 mode: 'blah',
+     *                 html: '<h3>Blah</h3>',
+     *                 onclick : function(){
+     *                     $( 'body' ).css( 'background-color', 'grey' );
+     *                 }
+     *             },
+     *         ]
+     *     });
+     *     $( '.myElement' ).modeButton( 'callModeFn', 'bler' );
+     */
+    /** constructor */
+    function ModeButton( element, options ){
+		this.currModeIndex = 0;
+		return this._init( element, options );
+    }
+
+    /** html5 data key to store this object inside an element */
+	ModeButton.prototype.DATA_KEY = 'mode-button';
+    /** default options */
+	ModeButton.prototype.defaults = {
+        switchModesOnClick : true
+	};
+
+    // ---- private interface
+    /** set up options, intial mode, and the click handler */
+	ModeButton.prototype._init = function _init( element, options ){
+        //console.debug( 'ModeButton._init:', element, options );
+		options = options || {};
+		this.$element = $( element );
+		this.options = $.extend( true, {}, this.defaults, options );
+        if( !options.modes ){
+            throw new Error( 'ModeButton requires a "modes" array' );
+        }
+
+		var modeButton = this;
+		this.$element.click( function _ModeButtonClick( event ){
+			// call the curr mode fn
+			modeButton.callModeFn();
+			// inc the curr mode index
+			if( modeButton.options.switchModesOnClick ){ modeButton._incModeIndex(); }
+			// set the element html
+			$( this ).html( modeButton.options.modes[ modeButton.currModeIndex ].html );
+		});
+		return this.reset();
+	};
+    /** increment the mode index to the next in the array, looping back to zero if at the last */
+	ModeButton.prototype._incModeIndex = function _incModeIndex(){
+		this.currModeIndex += 1;
+		if( this.currModeIndex >= this.options.modes.length ){
+			this.currModeIndex = 0;
+		}
+		return this;
+	};
+    /** get the mode index in the modes array for the given key (mode name) */
+	ModeButton.prototype._getModeIndex = function _getModeIndex( modeKey ){
+		for( var i=0; i<this.options.modes.length; i+=1 ){
+			if( this.options.modes[ i ].mode === modeKey ){ return i; }
+		}
+		throw new Error( 'mode not found: ' + modeKey );
+	};
+    /** set the current mode to the one with the given index and set button html */
+	ModeButton.prototype._setModeByIndex = function _setModeByIndex( index ){
+        var newMode = this.options.modes[ index ];
+        if( !newMode ){
+            throw new Error( 'mode index not found: ' + index );
+        }
+        this.currModeIndex = index;
+        if( newMode.html ){
+            this.$element.html( newMode.html );
+        }
+		return this;
+	};
+
+    // ---- public interface
+    /** get the current mode object (not just the mode name) */
+	ModeButton.prototype.currentMode = function currentMode(){
+		return this.options.modes[ this.currModeIndex ];
+	};
+    /** return the mode key of the current mode */
+	ModeButton.prototype.current = function current(){
+        // sugar for returning mode name
+		return this.currentMode().mode;
+	};
+    /** get the mode with the given modeKey or the current mode if modeKey is undefined */
+	ModeButton.prototype.getMode = function getMode( modeKey ){
+		if( !modeKey ){ return this.currentMode(); }
+		return this.options.modes[( this._getModeIndex( modeKey ) )];
+	};
+    /** T/F if the button has the given mode */
+	ModeButton.prototype.hasMode = function hasMode( modeKey ){
+        try {
+            return !!this.getMode( modeKey );
+        } catch( err ){}
+        return false;
+	};
+    /** set the current mode to the mode with the given name */
+	ModeButton.prototype.setMode = function setMode( modeKey ){
+        return this._setModeByIndex( this._getModeIndex( modeKey ) );
+	};
+    /** reset to the initial mode */
+	ModeButton.prototype.reset = function reset(){
+		this.currModeIndex = 0;
+		if( this.options.initialMode ){
+			this.currModeIndex = this._getModeIndex( this.options.initialMode );
+		}
+        return this._setModeByIndex( this.currModeIndex );
+	};
+    /** manually call the click handler of the given mode */
+	ModeButton.prototype.callModeFn = function callModeFn( modeKey ){
+		var modeFn = this.getMode( modeKey ).onclick;
+		if( modeFn && $.type( modeFn === 'function' ) ){
+            // call with the element as context (std jquery pattern)
+			return modeFn.call( this.$element.get(0) );
+		}
+		return undefined;
+	};
+
+    // as jq plugin
+    $.fn.modeButton = function $modeButton( options ){
+        if( !this.size() ){ return this; }
+
+        //TODO: does map still work with jq multi selection (i.e. $( '.class-for-many-btns' ).modeButton)?
+        if( $.type( options ) === 'object' ){
+            return this.map( function(){
+                var $this = $( this );
+                $this.data( 'mode-button', new ModeButton( $this, options ) );
+                return this;
+            });
+        }
+
+        var $first = $( this[0] ),
+            button = $first.data( 'mode-button' );
+
+        if( !button ){
+            throw new Error( 'modeButton needs an options object or string name of a function' );
+        }
+
+        if( button && $.type( options ) === 'string' ){
+            var fnName = options;
+            if( button && $.type( button[ fnName ] ) === 'function' ){
+                return button[ fnName ].apply( button, $.makeArray( arguments ).slice( 1 ) );
+            }
+        }
+        return button;
+    };
+
+}));

diff -r 5edaafeecfed448ea259adaacf3a4ce6e6da15d1 -r d76253bb22c4f64c73523956d119c0c5ab0a357b client/galaxy/scripts/jq-plugins/ui/pagination.js
--- /dev/null
+++ b/client/galaxy/scripts/jq-plugins/ui/pagination.js
@@ -0,0 +1,226 @@
+// from: https://raw.githubusercontent.com/umdjs/umd/master/jqueryPlugin.js
+// Uses AMD or browser globals to create a jQuery plugin.
+(function (factory) {
+    if (typeof define === 'function' && define.amd) {
+        // AMD. Register as an anonymous module.
+        define(['jquery'], factory);
+    } else {
+        // Browser globals
+        factory(jQuery);
+    }
+
+}(function ($) {
+
+    /** Builds (twitter bootstrap styled) pagination controls.
+     *  If the totalDataSize is not null, a horizontal list of page buttons is displayed.
+     *  If totalDataSize is null, two links ('Prev' and 'Next) are displayed.
+     *  When pages are changed, a 'pagination.page-change' event is fired
+     *      sending the event and the (0-based) page requested.
+     */
+    function Pagination( element, options ){
+        /** the total number of pages */
+        this.numPages = null;
+        /** the current, active page */
+		this.currPage = 0;
+		return this.init( element, options );
+    }
+
+    /** data key under which this object will be stored in the element */
+	Pagination.prototype.DATA_KEY = 'pagination';
+    /** default options */
+    Pagination.prototype.defaults = {
+        /** which page to begin at */
+        startingPage    : 0,
+        /** number of data per page */
+        perPage         : 20,
+        /** the total number of data (null == unknown) */
+        totalDataSize   : null,
+        /** size of current data on current page */
+        currDataSize    : null
+	};
+
+    /** init the control, calc numPages if possible, and render
+     *  @param {jQuery} the element that will contain the pagination control
+     *  @param {Object} options a map containing overrides to the pagination default options
+     */
+	Pagination.prototype.init = function _init( $element, options ){
+		options = options || {};
+		this.$element = $element;
+		this.options = jQuery.extend( true, {}, this.defaults, options );
+
+        this.currPage = this.options.startingPage;
+        if( this.options.totalDataSize !== null ){
+            this.numPages = Math.ceil( this.options.totalDataSize / this.options.perPage );
+            // limit currPage by numPages
+            if( this.currPage >= this.numPages ){
+                this.currPage = this.numPages - 1;
+            }
+        }
+        //console.debug( 'Pagination.prototype.init:', this.$element, this.currPage );
+        //console.debug( JSON.stringify( this.options ) );
+
+        // bind to data of element
+        this.$element.data( Pagination.prototype.DATA_KEY, this );
+
+        this._render();
+		return this;
+	};
+
+    /** helper to create a simple li + a combo */
+    function _make$Li( contents ){
+        return $([
+            '<li><a href="javascript:void(0);">', contents, '</a></li>'
+        ].join( '' ));
+    }
+
+    /** render previous and next pagination buttons */
+    Pagination.prototype._render = function __render(){
+        // no data - no pagination
+        if( this.options.totalDataSize === 0 ){ return this; }
+        // only one page
+        if( this.numPages === 1 ){ return this; }
+
+        // when the number of pages are known, render each page as a link
+        if( this.numPages > 0 ){
+            this._renderPages();
+            this._scrollToActivePage();
+
+        // when the number of pages is not known, render previous or next
+        } else {
+            this._renderPrevNext();
+        }
+		return this;
+    };
+
+    /** render previous and next pagination buttons */
+    Pagination.prototype._renderPrevNext = function __renderPrevNext(){
+        var pagination = this,
+            $prev = _make$Li( 'Prev' ),
+            $next = _make$Li( 'Next' ),
+            $paginationContainer = $( '<ul/>' ).addClass( 'pagination pagination-prev-next' );
+
+        // disable if it either end
+        if( this.currPage === 0 ){
+            $prev.addClass( 'disabled' );
+        } else {
+            $prev.click( function(){ pagination.prevPage(); });
+        }
+        if( ( this.numPages && this.currPage === ( this.numPages - 1 ) )
+        ||  ( this.options.currDataSize && this.options.currDataSize < this.options.perPage ) ){
+            $next.addClass( 'disabled' );
+        } else {
+            $next.click( function(){ pagination.nextPage(); });
+        }
+
+        this.$element.html( $paginationContainer.append([ $prev, $next ]) );
+        //console.debug( this.$element, this.$element.html() );
+        return this.$element;
+    };
+
+    /** render page links for each possible page (if we can) */
+    Pagination.prototype._renderPages = function __renderPages(){
+        // it's better to scroll the control and let the user see all pages
+        //  than to force her/him to change pages in order to find the one they want (as traditional << >> does)
+        var pagination = this,
+            $scrollingContainer = $( '<div>' ).addClass( 'pagination-scroll-container' ),
+            $paginationContainer = $( '<ul/>' ).addClass( 'pagination pagination-page-list' ),
+            page$LiClick = function( ev ){
+                pagination.goToPage( $( this ).data( 'page' ) );
+            };
+
+        for( var i=0; i<this.numPages; i+=1 ){
+            // add html5 data tag 'page' for later click event handler use
+            var $pageLi = _make$Li( i + 1 ).attr( 'data-page', i ).click( page$LiClick );
+            // highlight the current page
+            if( i === this.currPage ){
+                $pageLi.addClass( 'active' );
+            }
+            //console.debug( '\t', $pageLi );
+            $paginationContainer.append( $pageLi );
+        }
+        return this.$element.html( $scrollingContainer.html( $paginationContainer ) );
+    };
+
+    /** scroll scroll-container (if any) to show the active page */
+    Pagination.prototype._scrollToActivePage = function __scrollToActivePage(){
+        // scroll to show active page in center of scrollable area
+        var $container = this.$element.find( '.pagination-scroll-container' );
+        // no scroll container : don't scroll
+        if( !$container.size() ){ return this; }
+
+        var $activePage = this.$element.find( 'li.active' ),
+            midpoint = $container.width() / 2;
+        //console.debug( $container, $activePage, midpoint );
+        $container.scrollLeft( $container.scrollLeft() + $activePage.position().left - midpoint );
+        return this;
+    };
+
+    /** go to a certain page */
+    Pagination.prototype.goToPage = function goToPage( page ){
+        if( page <= 0 ){ page = 0; }
+        if( this.numPages && page >= this.numPages ){ page = this.numPages - 1; }
+        if( page === this.currPage ){ return this; }
+
+        //console.debug( '\t going to page ' + page )
+        this.currPage = page;
+        this.$element.trigger( 'pagination.page-change', this.currPage );
+        //console.info( 'pagination:page-change', this.currPage );
+        this._render();
+        return this;
+    };
+
+    /** go to the previous page */
+    Pagination.prototype.prevPage = function prevPage(){
+        return this.goToPage( this.currPage - 1 );
+    };
+
+    /** go to the next page */
+    Pagination.prototype.nextPage = function nextPage(){
+        return this.goToPage( this.currPage + 1 );
+    };
+
+    /** return the current page */
+    Pagination.prototype.page = function page(){
+        return this.currPage;
+    };
+
+    // alternate constructor invocation
+    Pagination.create = function _create( $element, options ){
+        return new Pagination( $element, options );
+    };
+
+    // as jq plugin
+    jQuery.fn.extend({
+        pagination : function $pagination( options ){
+			var nonOptionsArgs = jQuery.makeArray( arguments ).slice( 1 );
+
+            // if passed an object - use that as an options map to create pagination for each selected
+            if( jQuery.type( options ) === 'object' ){
+                return this.map( function(){
+                    Pagination.create( $( this ), options );
+                    return this;
+                });
+            }
+
+            // (other invocations only work on the first element in selected)
+            var $firstElement = $( this[0] ),
+                previousControl = $firstElement.data( Pagination.prototype.DATA_KEY );
+            // if a pagination control was found for this element, either...
+            if( previousControl ){
+                // invoke a function on the pagination object if passed a string (the function name)
+                if( jQuery.type( options ) === 'string' ){
+                    var fn = previousControl[ options ];
+                    if( jQuery.type( fn ) === 'function' ){
+                        return fn.apply( previousControl, nonOptionsArgs );
+                    }
+
+                // if passed nothing, return the previously set control
+                } else {
+                    return previousControl;
+                }
+            }
+            // if there is no control already set, return undefined
+            return undefined;
+        }
+    });
+}));

diff -r 5edaafeecfed448ea259adaacf3a4ce6e6da15d1 -r d76253bb22c4f64c73523956d119c0c5ab0a357b client/galaxy/scripts/jq-plugins/ui/peek-column-selector.js
--- /dev/null
+++ b/client/galaxy/scripts/jq-plugins/ui/peek-column-selector.js
@@ -0,0 +1,317 @@
+// from: https://raw.githubusercontent.com/umdjs/umd/master/jqueryPlugin.js
+// Uses AMD or browser globals to create a jQuery plugin.
+(function (factory) {
+    if (typeof define === 'function' && define.amd) {
+        // AMD. Register as an anonymous module.
+        define(['jquery'], factory);
+    } else {
+        // Browser globals
+        factory(jQuery);
+    }
+
+}(function ($) {
+    //==============================================================================
+    /** Column selection using the peek display as the control.
+     *  Adds rows to the bottom of the peek with clickable areas in each cell
+     *      to allow the user to select columns.
+     *  Column selection can be limited to a single column or multiple.
+     *  (Optionally) adds a left hand column of column selection prompts.
+     *  (Optionally) allows the column headers to be clicked/renamed
+     *      and set to some initial value.
+     *  (Optionally) hides comment rows.
+     *  (Optionally) allows pre-selecting and disabling certain columns for
+     *      each row control.
+     *
+     *  Construct by selecting a peek table to be used with jQuery and
+     *      calling 'peekColumnSelector' with options.
+     *  Options must include a 'controls' array and can include other options
+     *      listed below.
+     *  @example:
+     *  $( 'pre.peek' ).peekColumnSelector({
+     *          columnNames : ["Chromosome", "Start", "Base", "", "", "Qual" ],
+     *          controls : [
+     *              { label: 'X Column',  id: 'xColumn' },
+     *              { label: 'Y Column',  id: 'yColumn', selected: 2 },
+     *              { label: 'ID Column', id: 'idColumn', selected: 4, disabled: [ 1, 5 ] },
+     *              { label: 'Heatmap',   id: 'heatmap', selected: [ 2, 4 ], disabled: [ 0, 1 ], multiselect: true,
+     *                selectedText: 'Included', unselectedText: 'Excluded' }
+     *          ],
+     *          renameColumns       : true,
+     *          hideCommentRows     : true,
+     *          includePrompts      : true,
+     *          topLeftContent      : 'Data sample:'
+     *      }).on( 'peek-column-selector.change', function( ev, selection ){
+     *          console.info( 'new selection:', selection );
+     *          //{ yColumn: 2 }
+     *      }).on( 'peek-column-selector.rename', function( ev, names ){
+     *          console.info( 'column names', names );
+     *          //[ 'Bler', 'Start', 'Base', '', '', 'Qual' ]
+     *      });
+     *
+     *  An event is fired when column selection is changed and the event
+     *      is passed an object in the form: { the row id : the new selection value }.
+     *  An event is also fired when the table headers are re-named and
+     *      is passed the new array of column names.
+     */
+
+    /** option defaults */
+    var defaults = {
+            /** does this control allow renaming headers? */
+            renameColumns   : false,
+            /** does this control allow renaming headers? */
+            columnNames     : [],
+            /** the comment character used by the peek's datatype */
+            commentChar     : '#',
+            /** should comment rows be shown or hidden in the peek */
+            hideCommentRows : false,
+            /** should a column of row control prompts be used */
+            includePrompts  : true,
+            /** what is the content of the top left cell (often a title) */
+            topLeftContent  : 'Columns:'
+        },
+        /** class added to the pre.peek element (to allow css on just the control) */
+        PEEKCONTROL_CLASS = 'peek-column-selector',
+        /** the string of the event fired when a control row changes */
+        CHANGE_EVENT   = 'peek-column-selector.change',
+        /** the string of the event fired when a column is renamed */
+        RENAME_EVENT   = 'peek-column-selector.rename',
+        /** class added to the control rows */
+        ROW_CLASS      = 'control',
+        /** class added to the left-hand cells that serve as row prompts */
+        PROMPT_CLASS   = 'control-prompt',
+        /** class added to selected _cells_/tds */
+        SELECTED_CLASS = 'selected',
+        /** class added to disabled/un-clickable cells/tds */
+        DISABLED_CLASS = 'disabled',
+        /** class added to the clickable surface within a cell to select it */
+        BUTTON_CLASS   = 'button',
+        /** class added to peek table header (th) cells to indicate they can be clicked and are renamable */
+        RENAMABLE_HEADER_CLASS = 'renamable-header',
+        /** the data key used for each cell to store the column index ('data-...') */
+        COLUMN_INDEX_DATA_KEY = 'column-index',
+        /** renamable header data key used to store the column name (w/o the number and dot: '1.Bler') */
+        COLUMN_NAME_DATA_KEY = 'column-name';
+
+    //TODO: not happy with pure functional here - rows should polymorph (multi, single, etc.)
+    //TODO: needs clean up, move handlers to outer scope
+
+    // ........................................................................
+    /** validate the control data sent in for each row */
+    function validateControl( control ){
+        if( control.disabled && jQuery.type( control.disabled ) !== 'array' ){
+            throw new Error( '"disabled" must be defined as an array of indeces: ' + JSON.stringify( control ) );
+        }
+        if( control.multiselect && control.selected && jQuery.type( control.selected ) !== 'array' ){
+            throw new Error( 'Mulitselect rows need an array for "selected": ' + JSON.stringify( control ) );
+        }
+        if( !control.label || !control.id ){
+            throw new Error( 'Peek controls need a label and id for each control row: ' + JSON.stringify( control ) );
+        }
+        if( control.disabled && control.disabled.indexOf( control.selected ) !== -1 ){
+            throw new Error( 'Selected column is in the list of disabled columns: ' + JSON.stringify( control ) );
+        }
+        return control;
+    }
+
+    /** build the inner control surface (i.e. button-like) */
+    function buildButton( control, columnIndex ){
+        return $( '<div/>' ).addClass( BUTTON_CLASS ).text( control.label );
+    }
+
+    /** build the basic (shared) cell structure */
+    function buildControlCell( control, columnIndex ){
+        var $td = $( '<td/>' )
+            .html( buildButton( control, columnIndex ) )
+            .attr( 'data-' + COLUMN_INDEX_DATA_KEY, columnIndex );
+
+        // disable if index in disabled array
+        if( control.disabled && control.disabled.indexOf( columnIndex ) !== -1 ){
+            $td.addClass( DISABLED_CLASS );
+        }
+        return $td;
+    }
+
+    /** set the text of the control based on selected/un */
+    function setSelectedText( $cell, control, columnIndex ){
+        var $button = $cell.children( '.' + BUTTON_CLASS );
+        if( $cell.hasClass( SELECTED_CLASS ) ){
+            $button.html( ( control.selectedText !== undefined )?( control.selectedText ):( control.label ) );
+        } else {
+            $button.html( ( control.unselectedText !== undefined )?( control.unselectedText ):( control.label ) );
+        }
+    }
+
+    /** build a cell for a row that only allows one selection */
+    function buildSingleSelectCell( control, columnIndex ){
+        // only one selection - selected is single index
+        var $cell = buildControlCell( control, columnIndex );
+        if( control.selected === columnIndex ){
+            $cell.addClass( SELECTED_CLASS );
+        }
+        setSelectedText( $cell, control, columnIndex );
+
+        // only add the handler to non-disabled controls
+        if( !$cell.hasClass( DISABLED_CLASS ) ){
+            $cell.click( function selectClick( ev ){
+                var $cell = $( this );
+                // don't re-select or fire event if already selected
+                if( !$cell.hasClass( SELECTED_CLASS ) ){
+                    // only one can be selected - remove selected on all others, add it here
+                    var $otherSelected = $cell.parent().children( '.' + SELECTED_CLASS ).removeClass( SELECTED_CLASS );
+                    $otherSelected.each( function(){
+                        setSelectedText( $( this ), control, columnIndex );
+                    });
+
+                    $cell.addClass( SELECTED_CLASS );
+                    setSelectedText( $cell, control, columnIndex );
+
+                    // fire the event from the table itself, passing the id and index of selected
+                    var eventData = {},
+                        key = $cell.parent().attr( 'id' ),
+                        val = $cell.data( COLUMN_INDEX_DATA_KEY );
+                    eventData[ key ] = val;
+                    $cell.parents( '.peek' ).trigger( CHANGE_EVENT, eventData );
+                }
+            });
+        }
+        return $cell;
+    }
+
+    /** build a cell for a row that allows multiple selections */
+    function buildMultiSelectCell( control, columnIndex ){
+        var $cell = buildControlCell( control, columnIndex );
+        // multiple selection - selected is an array
+        if( control.selected && control.selected.indexOf( columnIndex ) !== -1 ){
+            $cell.addClass( SELECTED_CLASS );
+        }
+        setSelectedText( $cell, control, columnIndex );
+
+        // only add the handler to non-disabled controls
+        if( !$cell.hasClass( DISABLED_CLASS ) ){
+            $cell.click( function multiselectClick( ev ){
+                var $cell = $( this );
+                // can be more than one selected - toggle selected on this cell
+                $cell.toggleClass( SELECTED_CLASS );
+                setSelectedText( $cell, control, columnIndex );
+                var selectedColumnIndeces = $cell.parent().find( '.' + SELECTED_CLASS ).map( function( i, e ){
+                    return $( e ).data( COLUMN_INDEX_DATA_KEY );
+                });
+                // fire the event from the table itself, passing the id and index of selected
+                var eventData = {},
+                    key = $cell.parent().attr( 'id' ),
+                    val = jQuery.makeArray( selectedColumnIndeces );
+                eventData[ key ] = val;
+                $cell.parents( '.peek' ).trigger( CHANGE_EVENT, eventData );
+            });
+        }
+        return $cell;
+    }
+
+    /** iterate over columns in peek and create a control for each */
+    function buildControlCells( count, control ){
+        var $cells = [];
+        // build a control for each column - using a build fn based on control
+        for( var columnIndex=0; columnIndex<count; columnIndex+=1 ){
+            $cells.push( control.multiselect?  buildMultiSelectCell( control, columnIndex )
+                                            : buildSingleSelectCell( control, columnIndex ) );
+        }
+        return $cells;
+    }
+
+    /** build a row of controls for the peek */
+    function buildControlRow( cellCount, control, includePrompts ){
+        var $controlRow = $( '<tr/>' ).attr( 'id', control.id ).addClass( ROW_CLASS );
+        if( includePrompts ){
+            var $promptCell = $( '<td/>' ).addClass( PROMPT_CLASS ).text( control.label + ':' );
+            $controlRow.append( $promptCell );
+        }
+        $controlRow.append( buildControlCells( cellCount, control ) );
+        return $controlRow;
+    }
+
+    // ........................................................................
+    /** add to the peek, using options for configuration, return the peek */
+    function peekColumnSelector( options ){
+        options = jQuery.extend( true, {}, defaults, options );
+
+        var $peek = $( this ).addClass( PEEKCONTROL_CLASS ),
+            $peektable = $peek.find( 'table' ),
+            // get the size of the tables - width and height, number of comment rows
+            columnCount = $peektable.find( 'th' ).size(),
+            rowCount = $peektable.find( 'tr' ).size(),
+            // get the rows containing text starting with the comment char (also make them grey)
+            $commentRows = $peektable.find( 'td[colspan]' ).map( function( e, i ){
+                var $this = $( this );
+                if( $this.text() && $this.text().match( new RegExp( '^' + options.commentChar ) ) ){
+                    return $( this ).css( 'color', 'grey' ).parent().get(0);
+                }
+                return null;
+            });
+
+        // should comment rows in the peek be hidden?
+        if( options.hideCommentRows ){
+            $commentRows.hide();
+            rowCount -= $commentRows.size();
+        }
+        //console.debug( 'rowCount:', rowCount, 'columnCount:', columnCount, '$commentRows:', $commentRows );
+
+        // should a first column of control prompts be added?
+        if( options.includePrompts ){
+            var $topLeft = $( '<th/>' ).addClass( 'top-left' ).text( options.topLeftContent )
+                .attr( 'rowspan', rowCount );
+            $peektable.find( 'tr' ).first().prepend( $topLeft );
+        }
+
+        // save either the options column name or the parsed text of each column header in html5 data attr and text
+        var $headers = $peektable.find( 'th:not(.top-left)' ).each( function( i, e ){
+            var $this = $( this ),
+                // can be '1.name' or '1'
+                text  = $this.text().replace( /^\d+\.*/, '' ),
+                name  = options.columnNames[ i ] || text;
+            $this.attr( 'data-' + COLUMN_NAME_DATA_KEY, name )
+                .text( ( i + 1 ) + (( name )?( '.' + name ):( '' )) );
+        });
+
+        // allow renaming of columns when the header is clicked
+        if( options.renameColumns ){
+            $headers.addClass( RENAMABLE_HEADER_CLASS )
+                .click( function renameColumn(){
+                    // prompt for new name
+                    var $this = $( this ),
+                        index = $this.index() + ( options.includePrompts? 0: 1 ),
+                        prevName = $this.data( COLUMN_NAME_DATA_KEY ),
+                        newColumnName = prompt( 'New column name:', prevName );
+                    if( newColumnName !== null && newColumnName !== prevName ){
+                        // set the new text and data
+                        $this.text( index + ( newColumnName?( '.' + newColumnName ):'' ) )
+                            .data( COLUMN_NAME_DATA_KEY, newColumnName )
+                            .attr( 'data-', COLUMN_NAME_DATA_KEY, newColumnName );
+                        // fire event for new column names
+                        var columnNames = jQuery.makeArray(
+                                $this.parent().children( 'th:not(.top-left)' ).map( function(){
+                                    return $( this ).data( COLUMN_NAME_DATA_KEY );
+                                }));
+                        $this.parents( '.peek' ).trigger( RENAME_EVENT, columnNames );
+                    }
+                });
+        }
+
+        // build a row for each control
+        options.controls.forEach( function( control, i ){
+            validateControl( control );
+            var $controlRow = buildControlRow( columnCount, control, options.includePrompts );
+            $peektable.find( 'tbody' ).append( $controlRow );
+        });
+        return this;
+    }
+
+    // ........................................................................
+    // as jq plugin
+    jQuery.fn.extend({
+        peekColumnSelector : function $peekColumnSelector( options ){
+            return this.map( function(){
+                return peekColumnSelector.call( this, options );
+            });
+        }
+    });
+}));

diff -r 5edaafeecfed448ea259adaacf3a4ce6e6da15d1 -r d76253bb22c4f64c73523956d119c0c5ab0a357b client/galaxy/scripts/mvc/history/multi-panel.js
--- a/client/galaxy/scripts/mvc/history/multi-panel.js
+++ b/client/galaxy/scripts/mvc/history/multi-panel.js
@@ -2,7 +2,8 @@
     "mvc/history/history-model",
     "mvc/history/history-panel-edit",
     "mvc/base-mvc",
-    "utils/ajax-queue"
+    "utils/ajax-queue",
+    "jq-plugins/ui/mode-button"
 ], function( HISTORY_MODEL, HPANEL_EDIT, baseMVC, ajaxQueue ){
 window.HISTORY_MODEL = HISTORY_MODEL;
 //==============================================================================

diff -r 5edaafeecfed448ea259adaacf3a4ce6e6da15d1 -r d76253bb22c4f64c73523956d119c0c5ab0a357b client/galaxy/scripts/mvc/library/library-folderlist-view.js
--- a/client/galaxy/scripts/mvc/library/library-folderlist-view.js
+++ b/client/galaxy/scripts/mvc/library/library-folderlist-view.js
@@ -15,322 +15,359 @@
          ) {
 
 var FolderListView = Backbone.View.extend({
-  el : '#folder_items_element',
-  defaults: {
-    'include_deleted' : false
-  },
-  // progress percentage
-  progress: 0,
-  // progress rate per one item
-  progressStep: 1,
-  // self modal
-  modal : null,
+    el : '#folder_items_element',
+    // progress percentage
+    progress: 0,
+    // progress rate per one item
+    progressStep: 1,
 
-  folderContainer: null,
+    folderContainer: null,
 
-  sort: 'asc',
+    sort: 'asc',
 
-  events: {
-    'click #select-all-checkboxes'  : 'selectAll',
-    'click .dataset_row'            : 'selectClickedRow',
-    'click .sort-folder-link'       : 'sortColumnClicked'
-  },
+    events: {
+        'click #select-all-checkboxes'  : 'selectAll',
+        'click .dataset_row'            : 'selectClickedRow',
+        'click .sort-folder-link'       : 'sortColumnClicked'
+    },
 
-  // cache of rendered views
-  rowViews: {},
-  
-  initialize : function(options){
-    this.options = _.defaults(this.options || {}, options);
-    this.fetchFolder();
-  },
+    collection: null,
 
-  fetchFolder: function(options){
-    var options = options || {};
-    this.options.include_deleted = options.include_deleted;
-    var that = this;
+    defaults: {
+        include_deleted: false,
+        page_count: null,
+        show_page: null
+    },
 
-    this.collection = new mod_library_model.Folder();
+    /**
+     * Initialize and fetch the folder from the server.
+     * @param  {object} options an object with options
+     */
+    initialize : function( options ){
+        this.options = _.defaults( this.options || {}, this.defaults, options );
+        this.modal = null;
+        // map of folder item ids to item views = cache
+        this.rowViews = {};
 
-    // start to listen if someone modifies collection
-    this.listenTo(this.collection, 'add', this.renderOne);
-    this.listenTo(this.collection, 'remove', this.removeOne);
+        // create a collection of folder items for this view
+        this.collection = new mod_library_model.Folder();
 
-    this.folderContainer = new mod_library_model.FolderContainer({id: this.options.id});
-    this.folderContainer.url = this.folderContainer.attributes.urlRoot + this.options.id + '/contents';
-    if (this.options.include_deleted){
-      this.folderContainer.url = this.folderContainer.url + '?include_deleted=true';
-    }
-    this.folderContainer.fetch({
-        success: function(folder_container) {
-          that.folder_container = folder_container;
-          that.render();
-          that.addAll(folder_container.get('folder').models);
-          if (that.options.dataset_id){
-            row = _.findWhere(that.rowViews, {id: that.options.dataset_id});
-            if (row) {
+        // start to listen if someone modifies the collection
+        this.listenTo( this.collection, 'add', this.renderOne );
+        this.listenTo( this.collection, 'remove', this.removeOne );
+
+        this.fetchFolder();
+    },
+
+    fetchFolder: function( options ){
+        var options = options || {};
+        this.options.include_deleted = options.include_deleted;
+        var that = this;
+
+        this.folderContainer = new mod_library_model.FolderContainer( { id: this.options.id } );
+        this.folderContainer.url = this.folderContainer.attributes.urlRoot + this.options.id + '/contents';
+
+        if ( this.options.include_deleted ){
+            this.folderContainer.url = this.folderContainer.url + '?include_deleted=true';
+        }
+        this.folderContainer.fetch({
+            success: function( folder_container ) {
+              that.folder_container = folder_container;
+              that.render();
+            },
+            error: function( model, response ){
+              if ( typeof response.responseJSON !== "undefined" ){
+                mod_toastr.error( response.responseJSON.err_msg + ' Click this to go back.', '', { onclick: function() { Galaxy.libraries.library_router.back(); } } );
+              } else {
+                mod_toastr.error( 'An error ocurred. Click this to go back.', '', { onclick: function() { Galaxy.libraries.library_router.back(); } } );
+              }
+            }
+        });
+    },
+
+    render: function ( options ){
+        this.options = _.extend( this.options, options );
+        var template = this.templateFolder();
+        $(".tooltip").hide();
+
+        // find the upper id in the full path
+        var path = this.folderContainer.attributes.metadata.full_path;
+        var upper_folder_id;
+        if ( path.length === 1 ){ // the library is above us
+          upper_folder_id = 0;
+        } else {
+          upper_folder_id = path[ path.length-2 ][ 0 ];
+        }
+
+        this.$el.html( template( { 
+            path: this.folderContainer.attributes.metadata.full_path,
+            parent_library_id: this.folderContainer.attributes.metadata.parent_library_id,
+            id: this.options.id,
+            upper_folder_id: upper_folder_id,
+            order: this.sort
+        } ) );
+
+        // when dataset_id is present render its details too
+        if ( this.options.dataset_id ){
+            row = _.findWhere( that.rowViews, { id: this.options.dataset_id } );
+            if ( row ) {
               row.showDatasetDetails();
             } else {
-              mod_toastr.error('Dataset not found. Showing folder instead.');
+              mod_toastr.error( 'Requested dataset not found. Showing folder instead.' );
             }
+        } else {
+            if ( this.options.show_page === null || this.options.show_page < 1 ){
+                this.options.show_page = 1;
+            }
+            this.paginate();
+        }
+        $("#center [data-toggle]").tooltip();
+        $("#center").css('overflow','auto');
+    },
+
+    paginate: function( options ){
+        this.options = _.extend( this.options, options );
+
+        if ( this.options.show_page === null || this.options.show_page < 1 ){
+            this.options.show_page = 1;
+        }
+        this.options.total_items_count = this.folder_container.get( 'folder' ).models.length;
+        this.options.page_count = Math.ceil( this.options.total_items_count / Galaxy.libraries.preferences.get( 'folder_page_size' ) );
+        var page_start = ( Galaxy.libraries.preferences.get( 'folder_page_size' ) * ( this.options.show_page - 1 ) );
+        var items_to_render = null;
+        items_to_render = this.folder_container.get( 'folder' ).models.slice( page_start, page_start + Galaxy.libraries.preferences.get( 'folder_page_size' ) );
+        this.options.items_shown = items_to_render.length;
+        // User requests page with no items
+        if ( Galaxy.libraries.preferences.get( 'folder_page_size' ) * this.options.show_page > ( this.options.total_items_count + Galaxy.libraries.preferences.get( 'folder_page_size' ) ) ){
+            items_to_render = [];
+        }
+        Galaxy.libraries.folderToolbarView.renderPaginator( this.options );
+        this.collection.reset();
+        this.addAll( items_to_render )
+    },
+
+    /**
+     * Adds all given models to the collection.
+     * @param {array of Item or FolderAsModel} array of models that should
+     *  be added to the view's collection.
+     */
+    addAll: function( models ){
+        _.each(models, function( model ) {
+            Galaxy.libraries.folderListView.collection.add( model );
+        });
+        $( "#center [data-toggle]" ).tooltip();
+        this.checkEmptiness();
+        this.postRender();
+    },
+
+    /**
+     * Call this after all models are added to the collection
+     * to ensure that the folder toolbar will show proper options
+     * and that event will be bound on all subviews.
+     */
+    postRender: function(){
+        var fetched_metadata = this.folderContainer.attributes.metadata;
+        fetched_metadata.contains_file = typeof this.collection.findWhere({type: 'file'}) !== 'undefined';
+        Galaxy.libraries.folderToolbarView.configureElements(fetched_metadata);
+        $('.library-row').hover(function() {
+          $(this).find('.show_on_hover').show();
+        }, function () {
+          $(this).find('.show_on_hover').hide();
+        });
+    },
+
+    /**
+     * Iterates this view's collection and calls the render
+     * function for each. Also binds the hover behavior.
+     */
+    renderAll: function(){
+        var that = this;
+        _.each( this.collection.models.reverse(), function( model ) {
+          that.renderOne( model );
+        });
+        this.postRender();
+    },
+
+    /**
+     * Creates a view for the given model and adds it to the folder view.
+     * @param {Item or FolderAsModel} model of the view that will be rendered
+     */
+    renderOne: function(model){
+        if (model.get('type') !== 'folder'){
+            this.options.contains_file = true;
+            // model.set('readable_size', this.size_to_string(model.get('file_size')));
           }
-        },
-        error: function(model, response){
-          if (typeof response.responseJSON !== "undefined"){
-            mod_toastr.error(response.responseJSON.err_msg + ' Click this to go back.', '', {onclick: function() {Galaxy.libraries.library_router.back();}});
-          } else {
-            mod_toastr.error('An error ocurred. Click this to go back.', '', {onclick: function() {Galaxy.libraries.library_router.back();}});
-          }
+        model.set('folder_id', this.id);
+        var rowView = new mod_library_folderrow_view.FolderRowView(model);
+
+        // save new rowView to cache
+        this.rowViews[model.get('id')] = rowView;
+
+        this.$el.find('#first_folder_item').after(rowView.el);
+
+        $('.library-row').hover(function() {
+          $(this).find('.show_on_hover').show();
+        }, function () {
+          $(this).find('.show_on_hover').hide();
+        });
+    },
+
+    /**
+     * removes the view of the given model from the DOM
+     * @param {Item or FolderAsModel} model of the view that will be removed
+     */
+    removeOne: function( model ){
+       this.$el.find( '#' + model.id ).remove();
+    },
+
+    /** Checks whether the list is empty and adds/removes the message */
+    checkEmptiness : function(){
+        if ((this.$el.find('.dataset_row').length === 0) && (this.$el.find('.folder_row').length === 0)){
+          this.$el.find('.empty-folder-message').show();
+        } else {
+          this.$el.find('.empty-folder-message').hide();
         }
-    });
-  },
+    },
 
-  render: function (options) {
-    this.options = _.defaults(this.options, options);
-    var template = this.templateFolder();
-    $(".tooltip").hide();
+    /** User clicked the table heading = he wants to sort stuff */
+    sortColumnClicked : function(event){
+        event.preventDefault();
+        if (this.sort === 'asc'){
+            this.sortFolder('name','desc');
+            this.sort = 'desc';
+        } else {
+            this.sortFolder('name','asc');
+            this.sort = 'asc';
+        }
+        this.render();
+        this.renderAll();
+        this.checkEmptiness();
+    },
 
-    // TODO move to server
-    // find the upper id in the full path
-    var path = this.folderContainer.attributes.metadata.full_path;
-    var upper_folder_id;
-    if (path.length === 1){ // the library is above us
-      upper_folder_id = 0;
-    } else {
-      upper_folder_id = path[path.length-2][0];
+    /**
+     *  Sorts the underlying collection according to the parameters received. 
+     *  Currently supports only sorting by name. 
+     */
+    sortFolder: function(sort_by, order){
+        if (sort_by === 'name'){
+            if (order === 'asc'){
+                return this.collection.sortByNameAsc();
+            } else if (order === 'desc'){
+                return this.collection.sortByNameDesc();
+            }
+        }
+    },
+
+    /**
+     * User clicked the checkbox in the table heading
+     * @param  {context} event
+     */
+    selectAll : function (event) {
+         var selected = event.target.checked;
+         that = this;
+         // Iterate each checkbox
+         $(':checkbox', '#folder_list_body').each(function() {
+            this.checked = selected;
+            $row = $(this.parentElement.parentElement);
+            // Change color of selected/unselected
+            if (selected) {
+              that.makeDarkRow($row);
+            } else {
+              that.makeWhiteRow($row);
+            } 
+        });
+     },
+
+    /** 
+     * Check checkbox if user clicks on the whole row or 
+     *  on the checkbox itself 
+     */
+    selectClickedRow : function (event) {
+        var checkbox = '';
+        var $row;
+        var source;
+        if (event.target.localName === 'input'){
+            checkbox = event.target;
+            $row = $(event.target.parentElement.parentElement);
+            source = 'input';
+        } else if (event.target.localName === 'td') {
+            checkbox = $("#" + event.target.parentElement.id).find(':checkbox')[0];
+            $row = $(event.target.parentElement);
+            source = 'td';
+        }
+        if (checkbox.checked){
+            if (source==='td'){
+                checkbox.checked = '';
+                this.makeWhiteRow($row);
+            } else if (source==='input') {
+                this.makeDarkRow($row);
+            }
+        } else {
+            if (source==='td'){
+                checkbox.checked = 'selected';
+                this.makeDarkRow($row);
+            } else if (source==='input') {
+                this.makeWhiteRow($row);
+            }
+        }
+    },
+
+    makeDarkRow: function($row){
+        $row.removeClass('light').addClass('dark');
+        $row.find('a').removeClass('light').addClass('dark');
+        $row.find('.fa-file-o').removeClass('fa-file-o').addClass('fa-file');
+    },
+
+    makeWhiteRow: function($row){
+        $row.removeClass('dark').addClass('light');
+        $row.find('a').removeClass('dark').addClass('light');
+        $row.find('.fa-file').removeClass('fa-file').addClass('fa-file-o');
+    },
+
+    templateFolder : function (){
+        var tmpl_array = [];
+
+        // BREADCRUMBS
+        tmpl_array.push('<ol class="breadcrumb">');
+        tmpl_array.push('   <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');
+        tmpl_array.push('   <% _.each(path, function(path_item) { %>');
+        tmpl_array.push('   <% if (path_item[0] != id) { %>');
+        tmpl_array.push('   <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');
+        tmpl_array.push(    '<% } else { %>');
+        tmpl_array.push('   <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>');
+        tmpl_array.push('   <% } %>');
+        tmpl_array.push('   <% }); %>');
+        tmpl_array.push('</ol>');
+
+        // FOLDER CONTENT
+        tmpl_array.push('<table data-library-id="<%- parent_library_id  %>" id="folder_table" class="grid table table-condensed">');
+        tmpl_array.push('   <thead>');
+        tmpl_array.push('       <th class="button_heading"></th>');
+        tmpl_array.push('       <th style="text-align: center; width: 20px; " title="Check to select all datasets"><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');
+        tmpl_array.push('       <th><a class="sort-folder-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');
+        tmpl_array.push('       <th style="width:5%;">data type</th>');
+        tmpl_array.push('       <th style="width:10%;">size</th>');
+        tmpl_array.push('       <th style="width:160px;">time updated (UTC)</th>');
+        tmpl_array.push('       <th style="width:10%;"></th> ');
+        tmpl_array.push('   </thead>');
+        tmpl_array.push('   <tbody id="folder_list_body">');
+        tmpl_array.push('       <tr id="first_folder_item">');
+        tmpl_array.push('           <td><a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..<a></td>');
+        tmpl_array.push('           <td></td>');
+        tmpl_array.push('           <td></td>');
+        tmpl_array.push('           <td></td>');
+        tmpl_array.push('           <td></td>');
+        tmpl_array.push('           <td></td>');
+        tmpl_array.push('           <td></td>');
+        tmpl_array.push('       </tr>');
+
+        tmpl_array.push('   </tbody>');
+        tmpl_array.push('</table>');
+        tmpl_array.push('<div class="empty-folder-message" style="display:none;">This folder is either empty or you do not have proper access permissions to see the contents. If you expected something to show up please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity" target="_blank">library security wikipage</a> or visit the <a href="https://biostar.usegalaxy.org/" target="_blank">Galaxy support site</a>.</div>');
+
+        return _.template(tmpl_array.join(''));
     }
-
-    this.$el.html(template({ path: this.folderContainer.attributes.metadata.full_path, parent_library_id: this.folderContainer.attributes.metadata.parent_library_id, id: this.options.id, upper_folder_id: upper_folder_id, order: this.sort}));
-
-    // initialize the library tooltips
-    $("#center [data-toggle]").tooltip();
-    //hack to show scrollbars
-    $("#center").css('overflow','auto');
-  },
-
-  /**
-   * Call this after all models are added to the collection
-   * to ensure that the folder toolbar will show proper options
-   * and that event will be bound on all subviews.
-   */
-  postRender: function(){
-    var fetched_metadata = this.folderContainer.attributes.metadata;
-    fetched_metadata.contains_file = typeof this.collection.findWhere({type: 'file'}) !== 'undefined';
-    Galaxy.libraries.folderToolbarView.configureElements(fetched_metadata);
-    $('.library-row').hover(function() {
-      $(this).find('.show_on_hover').show();
-    }, function () {
-      $(this).find('.show_on_hover').hide();
-    });
-  },
-
-  /**
-   * Adds all given models to the collection.
-   * @param {array of Item or FolderAsModel} array of models that should
-   *  be added to the view's collection.
-   */
-  addAll: function(models){
-    _.each(models.reverse(), function(model) {
-      Galaxy.libraries.folderListView.collection.add(model);
-    });
-
-    $("#center [data-toggle]").tooltip();
-    this.checkEmptiness();
-
-    this.postRender();
-  },
-
-  /**
-   * Iterates this view's collection and calls the render
-   * function for each. Also binds the hover behavior.
-   */
-  renderAll: function(){
-    var that = this;
-    _.each(this.collection.models.reverse(), function(model) {
-      that.renderOne(model);
-    });
-    this.postRender();
-  },
-
-  /**
-   * Creates a view for the given model and adds it to the folder view.
-   * @param {Item or FolderAsModel} model of the view that will be rendered
-   */
-  renderOne: function(model){
-    if (model.get('type') !== 'folder'){
-        this.options.contains_file = true;
-        // model.set('readable_size', this.size_to_string(model.get('file_size')));
-      }
-    model.set('folder_id', this.id);
-    var rowView = new mod_library_folderrow_view.FolderRowView(model);
-
-    // save new rowView to cache
-    this.rowViews[model.get('id')] = rowView;
-
-    this.$el.find('#first_folder_item').after(rowView.el);
-
-    $('.library-row').hover(function() {
-      $(this).find('.show_on_hover').show();
-    }, function () {
-      $(this).find('.show_on_hover').hide();
-    });
-  },
-
-  /**
-   * removes the view of the given model from the DOM
-   * @param {Item or FolderAsModel} model of the view that will be removed
-   */
-  removeOne: function(model){
-    this.$el.find('#' + model.id).remove();
-  },
-
-  /** Checks whether the list is empty and adds/removes the message */
-  checkEmptiness : function(){
-    if ((this.$el.find('.dataset_row').length === 0) && (this.$el.find('.folder_row').length === 0)){
-      this.$el.find('.empty-folder-message').show();
-    } else {
-      this.$el.find('.empty-folder-message').hide();
-    }
-  },
-
-  /** User clicked the table heading = he wants to sort stuff */
-  sortColumnClicked : function(event){
-    event.preventDefault();
-    if (this.sort === 'asc'){
-        this.sortFolder('name','desc');
-        this.sort = 'desc';
-    } else {
-        this.sortFolder('name','asc');
-        this.sort = 'asc';
-    }
-    this.render();
-    this.renderAll();
-    this.checkEmptiness();
-  },
-
-  /**
-   *  Sorts the underlying collection according to the parameters received. 
-   *  Currently supports only sorting by name. 
-   */
-  sortFolder: function(sort_by, order){
-      if (sort_by === 'name'){
-          if (order === 'asc'){
-              return this.collection.sortByNameAsc();
-          } else if (order === 'desc'){
-              return this.collection.sortByNameDesc();
-          }
-      }
-  },
-
-  /**
-   * User clicked the checkbox in the table heading
-   * @param  {context} event
-   */
-  selectAll : function (event) {
-       var selected = event.target.checked;
-       that = this;
-       // Iterate each checkbox
-       $(':checkbox', '#folder_list_body').each(function() {
-          this.checked = selected;
-          $row = $(this.parentElement.parentElement);
-          // Change color of selected/unselected
-          if (selected) {
-            that.makeDarkRow($row);
-          } else {
-            that.makeWhiteRow($row);
-          } 
-      });
-   },
-
-  /** 
-   * Check checkbox if user clicks on the whole row or 
-   *  on the checkbox itself 
-   */
-  selectClickedRow : function (event) {
-    var checkbox = '';
-    var $row;
-    var source;
-    if (event.target.localName === 'input'){
-        checkbox = event.target;
-        $row = $(event.target.parentElement.parentElement);
-        source = 'input';
-    } else if (event.target.localName === 'td') {
-        checkbox = $("#" + event.target.parentElement.id).find(':checkbox')[0];
-        $row = $(event.target.parentElement);
-        source = 'td';
-    }
-    if (checkbox.checked){
-        if (source==='td'){
-            checkbox.checked = '';
-            this.makeWhiteRow($row);
-        } else if (source==='input') {
-            this.makeDarkRow($row);
-        }
-    } else {
-        if (source==='td'){
-            checkbox.checked = 'selected';
-            this.makeDarkRow($row);
-        } else if (source==='input') {
-            this.makeWhiteRow($row);
-        }
-    }
-  },
-
-  makeDarkRow: function($row){
-    $row.removeClass('light').addClass('dark');
-    $row.find('a').removeClass('light').addClass('dark');
-    $row.find('.fa-file-o').removeClass('fa-file-o').addClass('fa-file');
-  },
-
-  makeWhiteRow: function($row){
-    $row.removeClass('dark').addClass('light');
-    $row.find('a').removeClass('dark').addClass('light');
-    $row.find('.fa-file').removeClass('fa-file').addClass('fa-file-o');
-  },
-
-  templateFolder : function (){
-      var tmpl_array = [];
-
-      // BREADCRUMBS
-      tmpl_array.push('<ol class="breadcrumb">');
-      tmpl_array.push('   <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');
-      tmpl_array.push('   <% _.each(path, function(path_item) { %>');
-      tmpl_array.push('   <% if (path_item[0] != id) { %>');
-      tmpl_array.push('   <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');
-      tmpl_array.push(    '<% } else { %>');
-      tmpl_array.push('   <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>');
-      tmpl_array.push('   <% } %>');
-      tmpl_array.push('   <% }); %>');
-      tmpl_array.push('</ol>');
-
-      // FOLDER CONTENT
-      tmpl_array.push('<table data-library-id="<%- parent_library_id  %>" id="folder_table" class="grid table table-condensed">');
-      tmpl_array.push('   <thead>');
-      tmpl_array.push('       <th class="button_heading"></th>');
-      tmpl_array.push('       <th style="text-align: center; width: 20px; " title="Check to select all datasets"><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');
-      tmpl_array.push('       <th><a class="sort-folder-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');
-      tmpl_array.push('       <th style="width:5%;">data type</th>');
-      tmpl_array.push('       <th style="width:10%;">size</th>');
-      tmpl_array.push('       <th style="width:160px;">time updated (UTC)</th>');
-      tmpl_array.push('       <th style="width:10%;"></th> ');
-      tmpl_array.push('   </thead>');
-      tmpl_array.push('   <tbody id="folder_list_body">');
-      tmpl_array.push('       <tr id="first_folder_item">');
-      tmpl_array.push('           <td><a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..<a></td>');
-      tmpl_array.push('           <td></td>');
-      tmpl_array.push('           <td></td>');
-      tmpl_array.push('           <td></td>');
-      tmpl_array.push('           <td></td>');
-      tmpl_array.push('           <td></td>');
-      tmpl_array.push('           <td></td>');
-      tmpl_array.push('       </tr>');
-
-      tmpl_array.push('   </tbody>');
-      tmpl_array.push('</table>');
-      tmpl_array.push('<div class="empty-folder-message" style="display:none;">This folder is either empty or you do not have proper access permissions to see the contents. If you expected something to show up please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity" target="_blank">library security wikipage</a> or visit the <a href="https://biostar.usegalaxy.org/" target="_blank">Galaxy support site</a>.</div>');
-
-      return _.template(tmpl_array.join(''));
-  }
-  
+    
 });
 
 return {

diff -r 5edaafeecfed448ea259adaacf3a4ce6e6da15d1 -r d76253bb22c4f64c73523956d119c0c5ab0a357b client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
--- a/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
+++ b/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
@@ -20,7 +20,9 @@
     'click #toolbtn_bulk_import'          : 'modalBulkImport',
     'click #include_deleted_datasets_chk' : 'checkIncludeDeleted',
     'click #toolbtn_show_libinfo'         : 'showLibInfo',
-    'click #toolbtn_bulk_delete'          : 'deleteSelectedDatasets'
+    'click #toolbtn_bulk_delete'          : 'deleteSelectedDatasets',
+    'click #page_size_prompt'             : 'showPageSizePrompt'
+
   },
 
   defaults: {
@@ -90,6 +92,22 @@
     this.$el.html(toolbar_template(template_defaults));
   },
 
+  /**
+   * Called from FolderListView when needed.
+   * @param  {object} options common options
+   */
+  renderPaginator: function( options ){
+      this.options = _.extend( this.options, options );
+      var paginator_template = this.templatePaginator();
+      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 ),
+          total_items_count: this.options.total_items_count,
+          items_shown: this.options.items_shown
+      }));
+  },
+
   configureElements: function(options){
     this.options = _.extend(this.options, options);
 
@@ -833,11 +851,11 @@
   var popped_item = lddas_set.pop();
   if ( typeof popped_item === "undefined" ) {
     if ( this.options.chain_call_control.failed_number === 0 ){
-      mod_toastr.success( 'Selected datasets deleted' );
+      mod_toastr.success( 'Selected datasets were deleted.' );
     } else if ( this.options.chain_call_control.failed_number === this.options.chain_call_control.total_number ){
-      mod_toastr.error( 'There was an error and no datasets were deleted.' );
+      mod_toastr.error( 'There was an error and no datasets were deleted. Please make sure you have sufficient permissions.' );
     } else if ( this.options.chain_call_control.failed_number < this.options.chain_call_control.total_number ){
-      mod_toastr.warning( 'Some of the datasets could not be deleted' );
+      mod_toastr.warning( 'Some of the datasets could not be deleted. Please make sure you have sufficient permissions.' );
     }
     Galaxy.modal.hide();
     return this.deleted_lddas;
@@ -976,6 +994,14 @@
     }
   },
 
+  showPageSizePrompt: function(){
+    var folder_page_size = prompt( 'How many items per page do you want to see?', Galaxy.libraries.preferences.get( 'folder_page_size' ) );
+    if ( ( folder_page_size != null ) && ( folder_page_size == parseInt( folder_page_size ) ) ) {
+        Galaxy.libraries.preferences.set( { 'folder_page_size': parseInt( folder_page_size ) } );
+        Galaxy.libraries.folderListView.render( { id: this.options.id, show_page: 1 } );
+    }
+  },
+
   templateToolBar: function(){
     tmpl_array = [];
 
@@ -1016,7 +1042,6 @@
     tmpl_array.push('     <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="btn btn-default toolbtn_add_files primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>');
     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">');
@@ -1032,6 +1057,10 @@
     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('          <span id="folder_paginator" class="library-paginator">');
+    // paginator will append here
+    tmpl_array.push('          </span>');
+
     tmpl_array.push(' </div>');
     // TOOLBAR END
     tmpl_array.push(' <div id="folder_items_element">');
@@ -1239,7 +1268,41 @@
     tmpl_array.push('</ul>');
 
     return _.template(tmpl_array.join(''));
-  }
+  },
+
+  templatePaginator: function(){
+    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 ) { %>'); // we are on higher page than total 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 { %>'); // we are on the first page
+    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>');
+
+    return _.template(tmpl_array.join(''));
+  },
 
 });
 

This diff is so big that we needed to truncate the remainder.

https://bitbucket.org/galaxy/galaxy-central/commits/a0bbd59cb420/
Changeset:   a0bbd59cb420
User:        abretaud
Date:        2014-12-11 16:02:05+00:00
Summary:     fix method names and api doc
Affected #:  2 files

diff -r d76253bb22c4f64c73523956d119c0c5ab0a357b -r a0bbd59cb420442c2fb518540fd2fdfbb2b2da0a lib/galaxy/tools/data/__init__.py
--- a/lib/galaxy/tools/data/__init__.py
+++ b/lib/galaxy/tools/data/__init__.py
@@ -211,11 +211,11 @@
                 self.add_entry( entry, allow_duplicates=allow_duplicates, persist=persist, persist_on_error=persist_on_error, entry_source=entry_source, **kwd )
         return self._loaded_content_version
 
-    def _remove_entry(self, values, **kwd):
+    def _remove_entry(self, values):
         raise NotImplementedError( "Abstract method" )
 
-    def remove_entry(self, values, **kwd):
-        self._remove_entry_and_reload( values,**kwd )
+    def remove_entry(self, values):
+        self._remove_entry( values )
         return self._update_version()
 
     def is_current_version( self, other_version ):
@@ -513,7 +513,7 @@
                 data_table_fh.write( "%s\n" % ( self.separator.join( fields ) ) )
         return not is_error
 
-    def _remove_entry_and_reload( self, values):
+    def _remove_entry( self, values):
 
         # update every file
         for filename in self.filenames:

diff -r d76253bb22c4f64c73523956d119c0c5ab0a357b -r a0bbd59cb420442c2fb518540fd2fdfbb2b2da0a lib/galaxy/webapps/galaxy/api/tool_data.py
--- a/lib/galaxy/webapps/galaxy/api/tool_data.py
+++ b/lib/galaxy/webapps/galaxy/api/tool_data.py
@@ -26,10 +26,10 @@
     def delete( self, trans, id, **kwd ):
         """
         DELETE /api/tool_data/{id}
-        Removes a role from a group
+        Removes an item from a data table
 
         :type   id:     str
-        :param  id:     the encoded id of the history to delete
+        :param  id:     the id of the data table containing the item to delete
         :type   kwd:    dict
         :param  kwd:    (required) dictionary structure containing:
 


https://bitbucket.org/galaxy/galaxy-central/commits/6363c839528c/
Changeset:   6363c839528c
User:        jmchilton
Date:        2014-12-15 05:17:31+00:00
Summary:     Merged in abretaud/galaxy-central (pull request #577)

Add an API to remove items from tool data tables
Affected #:  2 files

diff -r ac537b0a4167cbd14e0cb93175cc85c096275697 -r 6363c839528ca8bbbbc60c1b3784c788468d9445 lib/galaxy/tools/data/__init__.py
--- a/lib/galaxy/tools/data/__init__.py
+++ b/lib/galaxy/tools/data/__init__.py
@@ -211,6 +211,13 @@
                 self.add_entry( entry, allow_duplicates=allow_duplicates, persist=persist, persist_on_error=persist_on_error, entry_source=entry_source, **kwd )
         return self._loaded_content_version
 
+    def _remove_entry(self, values):
+        raise NotImplementedError( "Abstract method" )
+
+    def remove_entry(self, values):
+        self._remove_entry( values )
+        return self._update_version()
+
     def is_current_version( self, other_version ):
         return self._loaded_content_version == other_version
 
@@ -506,6 +513,42 @@
                 data_table_fh.write( "%s\n" % ( self.separator.join( fields ) ) )
         return not is_error
 
+    def _remove_entry( self, values):
+
+        # update every file
+        for filename in self.filenames:
+
+            if os.path.exists( filename ):
+                values = self._replace_field_separators( values )
+                self.filter_file_fields( filename, values )
+            else:
+                log.warn( "Cannot find index file '%s' for tool data table '%s'" % ( filename, self.name ) )
+        
+        self.reload_from_files()
+
+    def filter_file_fields( self, loc_file, values ):
+        """
+        Reads separated lines from file and print back only the lines that pass a filter.
+        """
+        separator_char = (lambda c: '<TAB>' if c == '\t' else c)(self.separator)
+
+        with open(loc_file) as reader:
+            rval = ""
+            for i, line in enumerate( reader ):
+                if line.lstrip().startswith( self.comment_char ):
+                    rval += line
+                else:
+                    line_s = line.rstrip( "\n\r" )
+                    if line_s:
+                        fields = line_s.split( self.separator )
+                        if fields != values:
+                            rval += line
+        
+        with open(loc_file, 'wb') as writer:
+            writer.write(rval)
+        
+        return rval
+
     def _replace_field_separators( self, fields, separator=None, replace=None, comment_char=None ):
         #make sure none of the fields contain separator
         #make sure separator replace is different from comment_char,

diff -r ac537b0a4167cbd14e0cb93175cc85c096275697 -r 6363c839528ca8bbbbc60c1b3784c788468d9445 lib/galaxy/webapps/galaxy/api/tool_data.py
--- a/lib/galaxy/webapps/galaxy/api/tool_data.py
+++ b/lib/galaxy/webapps/galaxy/api/tool_data.py
@@ -20,3 +20,44 @@
     @web.expose_api
     def show( self, trans, id, **kwds ):
         return trans.app.tool_data_tables.data_tables[id].to_dict(view='element')
+
+    @web.require_admin
+    @web.expose_api
+    def delete( self, trans, id, **kwd ):
+        """
+        DELETE /api/tool_data/{id}
+        Removes an item from a data table
+
+        :type   id:     str
+        :param  id:     the id of the data table containing the item to delete
+        :type   kwd:    dict
+        :param  kwd:    (required) dictionary structure containing:
+
+            * payload:     a dictionary itself containing:
+                * values:   <TAB> separated list of column contents, there must be a value for all the columns of the data table
+        """
+        decoded_tool_data_id = id
+        
+        try:
+            data_table = trans.app.tool_data_tables.data_tables.get(decoded_tool_data_id)
+        except:
+            data_table = None
+        if not data_table:
+            trans.response.status = 400
+            return "Invalid data table id ( %s ) specified." % str( decoded_tool_data_id )
+        
+        values = None
+        if kwd.get( 'payload', None ):
+            values = kwd['payload'].get( 'values', '' )
+
+        if not values:
+            trans.response.status = 400
+            return "Invalid data table item ( %s ) specified." % str( values )
+        
+        split_values = values.split("\t")
+        
+        if len(split_values) != len(data_table.get_column_name_list()):
+            trans.response.status = 400
+            return "Invalid data table item ( %s ) specified. Wrong number of columns (%s given, %s required)." % ( str( values ), str(len(split_values)), str(len(data_table.get_column_name_list())))
+
+        return data_table.remove_entry(split_values)

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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[galaxy-commits] commit/galaxy-central: 4 new changesets

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