[galaxy-commits] commit/galaxy-central: 2 new changesets

5 Dec 2014

2 new commits in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/7114d15a6d22/
Changeset:   7114d15a6d22
Branch:      next-stable
User:        jmchilton
Date:        2014-12-06 01:35:22+00:00
Summary:     Twill tool tests allowed selects specified by display text instead of value.
This didn't work for API tests - restore this functionality and add test case in test/functional/tools/multi_select.xml to verify this behavior is correct.
Affected #:  2 files

diff -r 149784a152afc3d7164eaf7dfa7d5dc97be92671 -r 7114d15a6d2234cb895d058e0e44c86f373c49b2 lib/galaxy/tools/test.py

--- a/lib/galaxy/tools/test.py
+++ b/lib/galaxy/tools/test.py
@@ -196,12 +196,37 @@
                         if not isinstance(param_value, list):
                             param_value = [ param_value ]
                         processed_value = [ self.__add_uploaded_dataset( context.for_state(), v, param_extra, value ) for v in param_value ]
-                    if isinstance( value, basic.DataCollectionToolParameter ):
+                    elif isinstance( value, basic.DataCollectionToolParameter ):
                         assert 'collection' in param_extra
                         collection_def = param_extra[ 'collection' ]
                         for ( name, value, extra ) in collection_def.collect_inputs():
                             require_file( name, value, extra, self.required_files )
                         processed_value = collection_def
+                    elif isinstance( value, basic.SelectToolParameter ):
+                        # Tests may specify values as either raw value or the value
+                        # as they appear in the list - the API doesn't and shouldn't
+                        # accept the text value - so we need to convert the text
+                        # into the form value.
+                        def process_param_value( param_value ):
+                            found_value = False
+                            value_for_text = None
+                            if value.static_options:
+                                for (text, opt_value, selected) in value.static_options:
+                                    if param_value == opt_value:
+                                        found_value = True
+                                    if value_for_text is None and param_value == text:
+                                        value_for_text = opt_value
+                            if not found_value and value_for_text is not None:
+                                processed_value = value_for_text
+                            else:
+                                processed_value = param_value
+                            return processed_value
+                        # Do replacement described above for lists or singleton
+                        # values.
+                        if isinstance( param_value, list ):
+                            processed_value = map( process_param_value, param_value )
+                        else:
+                            processed_value = process_param_value( param_value )
                     else:
                         processed_value = param_value
                     expanded_inputs[ context.for_state() ] = processed_value

diff -r 149784a152afc3d7164eaf7dfa7d5dc97be92671 -r 7114d15a6d2234cb895d058e0e44c86f373c49b2 test/functional/tools/multi_select.xml
--- a/test/functional/tools/multi_select.xml
+++ b/test/functional/tools/multi_select.xml
@@ -25,5 +25,13 @@
         </assert_contents></output></test>
+    <test>
+      <param name="select_ex" value="Ex1" />
+      <output name="output">
+        <assert_contents>
+          <has_line line="--ex1" />
+        </assert_contents>
+      </output>
+    </test></tests></tool>


https://bitbucket.org/galaxy/galaxy-central/commits/719191cd0f3e/
Changeset:   719191cd0f3e
User:        jmchilton
Date:        2014-12-06 01:36:48+00:00
Summary:     Merge next-stable.
Affected #:  31 files

diff -r 46a3d43d779fa7735029449935dad77474adf9b1 -r 719191cd0f3ea8ad2ff02ec303dabf0e22c31e60 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 46a3d43d779fa7735029449935dad77474adf9b1 -r 719191cd0f3ea8ad2ff02ec303dabf0e22c31e60 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 46a3d43d779fa7735029449935dad77474adf9b1 -r 719191cd0f3ea8ad2ff02ec303dabf0e22c31e60 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(''));
+  },
 
 });
 

diff -r 46a3d43d779fa7735029449935dad77474adf9b1 -r 719191cd0f3ea8ad2ff02ec303dabf0e22c31e60 client/galaxy/scripts/mvc/library/library-librarylist-view.js
--- a/client/galaxy/scripts/mvc/library/library-librarylist-view.js
+++ b/client/galaxy/scripts/mvc/library/library-librarylist-view.js
@@ -21,20 +21,19 @@
         'click .sort-libraries-link'    : 'sort_clicked'
     },
 
-    /**
-     * Initialize and fetch the libraries from server. 
-     * Async render afterwards.
-     * @param  {object} options an options object
-     */
     defaults: {
         page_count: null,
         show_page: null
     },
 
+    /**
+     * Initialize and fetch the libraries from server. 
+     * Async render afterwards.
+     * @param  {object} options an object with options
+     */
     initialize : function( options ){
         this.options = _.defaults( this.options || {}, this.defaults, options );
-
-        var that = this;  
+        var that = this;
         this.modal = null;
         // map of library model ids to library views = cache
         this.rowViews = {};
@@ -61,19 +60,10 @@
      */
     render: function ( options ) {
         this.options = _.extend( this.options, options );
-
-        if ( ( this.options.page_size != null ) && ( this.options.page_size == parseInt( this.options.page_size ) ) ) {
-            Galaxy.libraries.preferences.set( { 'library_page_size': parseInt( this.options.page_size ) } );
-        }
-
-        $( ".tooltip" ).hide();
-        // this.options.show_page = this.options.show_page || 1;
         var template = this.templateLibraryList();
         var libraries_to_render = null;
         var models = null;
-        if ( this.options.show_page === null || this.options.show_page < 1 ){
-            this.options.show_page = 1;
-        }
+        $( ".tooltip" ).hide();
         if ( typeof options !== 'undefined' ){
             models = typeof options.models !== 'undefined' ? options.models : null;
         }
@@ -89,6 +79,10 @@
         } else {
             libraries_to_render = [];
         }
+        // pagination
+        if ( this.options.show_page === null || this.options.show_page < 1 ){
+            this.options.show_page = 1;
+        }
         this.options.total_libraries_count = libraries_to_render.length
         var page_start = ( Galaxy.libraries.preferences.get( 'library_page_size' ) * ( this.options.show_page - 1 ) );
         this.options.page_count = Math.ceil( this.options.total_libraries_count / Galaxy.libraries.preferences.get( 'library_page_size' ) );

diff -r 46a3d43d779fa7735029449935dad77474adf9b1 -r 719191cd0f3ea8ad2ff02ec303dabf0e22c31e60 client/galaxy/scripts/mvc/tools/tools-tree.js
--- a/client/galaxy/scripts/mvc/tools/tools-tree.js
+++ b/client/galaxy/scripts/mvc/tools/tools-tree.js
@@ -126,7 +126,7 @@
                             // handle default value
                             if (!field.skip) {
                                 if (input.optional && field.validate && !field.validate()) {
-                                    value = 'None';
+                                    value = null;
                                 }
                                 add (job_input_id, input.id, value);
                             }

diff -r 46a3d43d779fa7735029449935dad77474adf9b1 -r 719191cd0f3ea8ad2ff02ec303dabf0e22c31e60 lib/galaxy/managers/folders.py
--- a/lib/galaxy/managers/folders.py
+++ b/lib/galaxy/managers/folders.py
@@ -16,14 +16,14 @@
     Interface/service object for interacting with folders.
     """
 
-    def get( self, trans, decoded_folder_id, check_ownership=False, check_accessible=True):
+    def get( self, trans, decoded_folder_id, check_manageable=False, check_accessible=True):
         """
         Get the folder from the DB.
 
         :param  decoded_folder_id:       decoded folder id
         :type   decoded_folder_id:       int
-        :param  check_ownership:         flag whether the check that user is owner
-        :type   check_ownership:         bool
+        :param  check_manageable:         flag whether the check that user can manage item
+        :type   check_manageable:         bool
         :param  check_accessible:        flag whether to check that user can access item
         :type   check_accessible:        bool
 
@@ -38,17 +38,17 @@
             raise exceptions.RequestParameterInvalidException( 'No folder found with the id provided.' )
         except Exception, e:
             raise exceptions.InternalServerError( 'Error loading from the database.' + str( e ) )
-        folder = self.secure( trans, folder, check_ownership, check_accessible )
+        folder = self.secure( trans, folder, check_manageable, check_accessible )
         return folder
 
-    def secure( self, trans, folder, check_ownership=True, check_accessible=True ):
+    def secure( self, trans, folder, check_manageable=True, check_accessible=True ):
         """
-        Check if (a) user owns folder or (b) folder is accessible to user.
+        Check if (a) user can manage folder or (b) folder is accessible to user.
 
         :param  folder:                  folder item
         :type   folder:                  LibraryFolder
-        :param  check_ownership:         flag whether the check that user is owner
-        :type   check_ownership:         bool
+        :param  check_manageable:        flag whether to check that user can manage item
+        :type   check_manageable:        bool
         :param  check_accessible:        flag whether to check that user can access item
         :type   check_accessible:        bool
 
@@ -58,23 +58,26 @@
         # all folders are accessible to an admin
         if trans.user_is_admin():
             return folder
-        if check_ownership:
-            folder = self.check_ownership( trans, folder )
+        if check_manageable:
+            folder = self.check_manageable( trans, folder )
         if check_accessible:
             folder = self.check_accessible( trans, folder )
         return folder
 
-    def check_ownership( self, trans, folder ):
+    def check_manageable( self, trans, folder ):
         """
-        Check whether the user is owner of the folder.
+        Check whether the user can manage the folder.
 
         :returns:   the original folder
         :rtype:     LibraryFolder
+
+        :raises: AuthenticationRequired, InsufficientPermissionsException
         """
         if not trans.user:
-            raise exceptions.AuthenticationRequired( "Must be logged in to manage Galaxy items", type='error' )
-        if folder.user != trans.user:
-            raise exceptions.ItemOwnershipException( "Folder is not owned by the current user", type='error' )
+            raise exceptions.AuthenticationRequired( "Must be logged in to manage Galaxy items.", type='error' )
+        current_user_roles = trans.get_current_user_roles()
+        if not trans.app.security_agent.can_manage_library_item( current_user_roles, folder ):
+            raise exceptions.InsufficientPermissionsException( "You don't have permissions to manage this folder.", type='error' )
         else:
             return folder
 
@@ -135,6 +138,22 @@
         trans.app.security_agent.copy_library_permissions( trans, parent_folder, new_folder )
         return new_folder
 
+    def delete( self, trans, folder, undelete=False ):
+        """
+        Mark given folder deleted/undeleted based on the flag.
+
+        :raises: ItemAccessibilityException
+        """
+        if not trans.user_is_admin():
+            folder = self.check_manageable( trans, folder )
+        if undelete:
+            folder.deleted = False
+        else:
+            folder.deleted = True
+        trans.sa_session.add( folder )
+        trans.sa_session.flush()
+        return folder
+
     def get_current_roles( self, trans, folder ):
         """
         Find all roles currently connected to relevant permissions 

diff -r 46a3d43d779fa7735029449935dad77474adf9b1 -r 719191cd0f3ea8ad2ff02ec303dabf0e22c31e60 lib/galaxy/model/__init__.py
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -2192,7 +2192,7 @@
         return roles
 
 class LibraryFolder( object, Dictifiable, HasName ):
-    dict_element_visible_keys = ( 'id', 'parent_id', 'name', 'description', 'item_count', 'genome_build', 'update_time' )
+    dict_element_visible_keys = ( 'id', 'parent_id', 'name', 'description', 'item_count', 'genome_build', 'update_time', 'deleted' )
     def __init__( self, name=None, description=None, item_count=0, order_id=None ):
         self.name = name or "Unnamed folder"
         self.description = description

diff -r 46a3d43d779fa7735029449935dad77474adf9b1 -r 719191cd0f3ea8ad2ff02ec303dabf0e22c31e60 lib/galaxy/tools/test.py
--- a/lib/galaxy/tools/test.py
+++ b/lib/galaxy/tools/test.py
@@ -196,12 +196,37 @@
                         if not isinstance(param_value, list):
                             param_value = [ param_value ]
                         processed_value = [ self.__add_uploaded_dataset( context.for_state(), v, param_extra, value ) for v in param_value ]
-                    if isinstance( value, basic.DataCollectionToolParameter ):
+                    elif isinstance( value, basic.DataCollectionToolParameter ):
                         assert 'collection' in param_extra
                         collection_def = param_extra[ 'collection' ]
                         for ( name, value, extra ) in collection_def.collect_inputs():
                             require_file( name, value, extra, self.required_files )
                         processed_value = collection_def
+                    elif isinstance( value, basic.SelectToolParameter ):
+                        # Tests may specify values as either raw value or the value
+                        # as they appear in the list - the API doesn't and shouldn't
+                        # accept the text value - so we need to convert the text
+                        # into the form value.
+                        def process_param_value( param_value ):
+                            found_value = False
+                            value_for_text = None
+                            if value.static_options:
+                                for (text, opt_value, selected) in value.static_options:
+                                    if param_value == opt_value:
+                                        found_value = True
+                                    if value_for_text is None and param_value == text:
+                                        value_for_text = opt_value
+                            if not found_value and value_for_text is not None:
+                                processed_value = value_for_text
+                            else:
+                                processed_value = param_value
+                            return processed_value
+                        # Do replacement described above for lists or singleton
+                        # values.
+                        if isinstance( param_value, list ):
+                            processed_value = map( process_param_value, param_value )
+                        else:
+                            processed_value = process_param_value( param_value )
                     else:
                         processed_value = param_value
                     expanded_inputs[ context.for_state() ] = processed_value

diff -r 46a3d43d779fa7735029449935dad77474adf9b1 -r 719191cd0f3ea8ad2ff02ec303dabf0e22c31e60 lib/galaxy/webapps/galaxy/api/folders.py
--- a/lib/galaxy/webapps/galaxy/api/folders.py
+++ b/lib/galaxy/webapps/galaxy/api/folders.py
@@ -44,7 +44,7 @@
         :rtype:     dict
         """
         folder_id = self.folder_manager.cut_and_decode( trans, id )
-        folder = self.folder_manager.get( trans, folder_id, check_ownership=False, check_accessible=True )
+        folder = self.folder_manager.get( trans, folder_id, check_manageable=False, check_accessible=True )
         return_dict = self.folder_manager.get_folder_dict( trans, folder )
         return return_dict
 
@@ -229,6 +229,32 @@
                                 'Allowed values are: "set_permissions"' )
         return self.folder_manager.get_current_roles( trans, folder )
 
+    @expose_api
+    def delete( self, trans, id, **kwd ):
+        """
+        delete( self, trans, id, **kwd )
+        * DELETE /api/folders/{id}
+            marks the folder with the given ``id`` as `deleted` (or removes the `deleted` mark if the `undelete` param is true)
+
+        .. note:: Currently, only admin users can un/delete folders.
+
+        :param  id:     the encoded id of the folder to un/delete
+        :type   id:     an encoded id string
+
+        :param  undelete:    (optional) flag specifying whether the item should be deleted or undeleted, defaults to false:
+        :type   undelete:    bool
+
+        :returns:   detailed folder information
+        :rtype:     dictionary
+
+        :raises: ItemAccessibilityException, MalformedId, ObjectNotFound
+        """
+        folder = self.folder_manager.get( trans, self.folder_manager.cut_and_decode( trans, id ), True )
+        undelete = util.string_as_bool( kwd.get( 'undelete', False ) )
+        folder = self.folder_manager.delete( trans, folder, undelete )
+        folder_dict = self.folder_manager.get_folder_dict( trans, folder )
+        return folder_dict
+
     @web.expose_api
     def update( self, trans, id,  library_id, payload, **kwd ):
         """

diff -r 46a3d43d779fa7735029449935dad77474adf9b1 -r 719191cd0f3ea8ad2ff02ec303dabf0e22c31e60 lib/galaxy/webapps/galaxy/controllers/dataset.py
--- a/lib/galaxy/webapps/galaxy/controllers/dataset.py
+++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py
@@ -932,11 +932,14 @@
     @web.expose
     def show_params( self, trans, dataset_id=None, from_noframe=None, **kwd ):
         """
-        Show the parameters used for an HDA
+        Show the parameters used for the job associated with an HDA
         """
-        hda = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.security.decode_id( dataset_id ) )
+        try:
+            hda = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.security.decode_id( dataset_id ) )
+        except ValueError:
+            hda = None
         if not hda:
-            raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable( "Invalid reference dataset id: %s." % str( dataset_id ) )
+            raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable( "Invalid reference dataset id: %s." % escape( str( dataset_id ) ) )
         if not self._can_access_dataset( trans, hda ):
             return trans.show_error_message( "You are not allowed to access this dataset" )
 
@@ -961,19 +964,30 @@
                     toolbox = self.get_toolbox()
                     tool = toolbox.get_tool( job.tool_id )
                     assert tool is not None, 'Requested tool has not been loaded.'
-                    #Load parameter objects, if a parameter type has changed, it's possible for the value to no longer be valid
+                    # Load parameter objects, if a parameter type has changed, it's possible for the value to no longer be valid
                     try:
                         params_objects = job.get_param_values( trans.app, ignore_errors=False )
                     except:
                         params_objects = job.get_param_values( trans.app, ignore_errors=True )
-                        upgrade_messages = tool.check_and_update_param_values( job.get_param_values( trans.app, ignore_errors=True ), trans, update_values=False ) #use different param_objects here, since we want to display original values as much as possible
+                        # use different param_objects in the following line, since we want to display original values as much as possible
+                        upgrade_messages = tool.check_and_update_param_values( job.get_param_values( trans.app, ignore_errors=True ),
+                                                                               trans,
+                                                                               update_values=False )
                         has_parameter_errors = True
                 except:
                     pass
         if job is None:
             return trans.show_error_message( "Job information is not available for this dataset." )
-        #TODO: we should provide the basic values along with the objects, in order to better handle reporting of old values during upgrade
-        return trans.fill_template( "show_params.mako", inherit_chain=inherit_chain, history=trans.get_history(), hda=hda, job=job, tool=tool, params_objects=params_objects, upgrade_messages=upgrade_messages, has_parameter_errors=has_parameter_errors )
+        # TODO: we should provide the basic values along with the objects, in order to better handle reporting of old values during upgrade
+        return trans.fill_template( "show_params.mako",
+                                    inherit_chain=inherit_chain,
+                                    history=trans.get_history(),
+                                    hda=hda,
+                                    job=job,
+                                    tool=tool,
+                                    params_objects=params_objects,
+                                    upgrade_messages=upgrade_messages,
+                                    has_parameter_errors=has_parameter_errors )
 
     @web.expose
     def copy_datasets( self, trans, source_history=None, source_content_ids="", target_history_id=None, target_history_ids="", new_history_name="", do_copy=False, **kwd ):

diff -r 46a3d43d779fa7735029449935dad77474adf9b1 -r 719191cd0f3ea8ad2ff02ec303dabf0e22c31e60 lib/galaxy/webapps/galaxy/controllers/search.py
--- a/lib/galaxy/webapps/galaxy/controllers/search.py
+++ b/lib/galaxy/webapps/galaxy/controllers/search.py
@@ -1,4 +1,3 @@
-
 """
 Contains a basic search interface for Galaxy
 """
@@ -8,7 +7,13 @@
 
 log = logging.getLogger( __name__ )
 
+
 class SearchController( BaseUIController ):
+
     @web.expose
     def index(self, trans):
-        return trans.fill_template( "search/index.mako")
+        """
+        Per the message, this is not ready for human consumption, yet.  Power
+        users can still use the search API.
+        """
+        return trans.show_message("Sorry, the search interface isn't quite ready for use, yet.  Watch the release notes and check back later!")

diff -r 46a3d43d779fa7735029449935dad77474adf9b1 -r 719191cd0f3ea8ad2ff02ec303dabf0e22c31e60 static/scripts/galaxy.library.js
--- a/static/scripts/galaxy.library.js
+++ b/static/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});
     }

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

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

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