Merge remote-tracking branch 'galaxyproject/dev' into gie-generic

Conflicts:
	static/maps/layout/menu.js.map
	static/scripts/bundled/libs.bundled.js
	static/scripts/bundled/libs.bundled.js.map
	static/scripts/layout/menu.js

.ci/flake8_wrapper.sh

@@ -5,4 +5,4 @@ set -e
 flake8 --exclude `paste -sd, .ci/flake8_blacklist.txt` .
 
 # Apply stricter rules for the directories shared with Pulsar
-flake8 --ignore= --max-line-length=150 lib/galaxy/jobs/runners/util/ lib/pulsar/
+flake8 --ignore= --max-line-length=150 lib/galaxy/jobs/runners/util/

.ci/py3_sources.txt

@@ -1,6 +1,5 @@
 lib/galaxy/util/
 lib/galaxy/jobs/runners/util/
-lib/pulsar/
 lib/galaxy/tools/parser/
 lib/galaxy/tools/lint.py
 lib/galaxy/tools/lint_util.py

.gitignore

@@ -14,6 +14,7 @@ database/citations
 database/community_files
 database/compiled_templates
 database/files
+database/jobs_directory
 database/job_working_directory
 database/pbs
 database/tmp

Makefile

@@ -5,12 +5,47 @@ RELEASE_NEXT:=16.04
 #RELEASE_NEXT_BRANCH:=release_$(RELEASE_NEXT)
 RELEASE_NEXT_BRANCH:=dev
 RELEASE_UPSTREAM:=upstream
+# Location of virtualenv used for development.
+VENV?=.venv
+# Source virtualenv to execute command (flake8, sphinx, twine, etc...)
+IN_VENV=if [ -f $(VENV)/bin/activate ]; then . $(VENV)/bin/activate; fi;
+PROJECT_URL?=https://github.com/galaxyproject/galaxy
 GRUNT_DOCKER_NAME:=galaxy/client-builder:16.01
 
 all: help
 	@echo "This makefile is primarily used for building Galaxy's JS client. A sensible all target is not yet implemented."
 
-npm-deps:
+docs: ## generate Sphinx HTML documentation, including API docs
+	$(IN_VENV) $(MAKE) -C doc clean
+	$(IN_VENV) $(MAKE) -C doc html
+
+_open-docs:
+	open doc/_build/html/index.html || xdg-open doc/_build/html/index.html
+
+open-docs: docs _open-docs ## generate Sphinx HTML documentation and open in browser
+
+open-project: ## open project on github
+	open $(PROJECT_URL) || xdg-open $(PROJECT_URL)
+
+lint: ## check style using tox and flake8 for Python 2 and Python 3
+	$(IN_VENV) tox -e py27-lint && tox -e py34-lint
+
+release-issue: ## Create release issue on github
+	$(IN_VENV) python scripts/bootstrap_history.py --create-release-issue $(RELEASE_CURR)
+
+release-check-metadata: ## check github PR metadata for target release
+	$(IN_VENV) python scripts/bootstrap_history.py --check-release $(RELEASE_CURR)
+
+release-check-blocking-issues: ## Check github for release blocking issues
+	$(IN_VENV) python scripts/bootstrap_history.py --check-blocking-issues $(RELEASE_CURR)
+
+release-check-blocking-prs: ## Check github for release blocking PRs
+	$(IN_VENV) python scripts/bootstrap_history.py --check-blocking-prs $(RELEASE_CURR)
+
+release-bootstrap-history: ## bootstrap history for a new release
+	$(IN_VENV) python scripts/bootstrap_history.py --release $(RELEASE_CURR)
+
+npm-deps: ## Install NodeJS dependencies.
 	cd client && npm install
 
 grunt: npm-deps ## Calls out to Grunt to build client
@@ -22,7 +57,7 @@ style: npm-deps ## Calls the style task of Grunt
 webpack: npm-deps ## Pack javascript
 	cd client && node_modules/webpack/bin/webpack.js -p
 
-client: grunt style webpack ## Process all client-side tasks
+client: grunt style webpack ## Rebuild all client-side artifacts
 
 grunt-docker-image: ## Build docker image for running grunt
 	docker build -t ${GRUNT_DOCKER_NAME} client
@@ -35,7 +70,7 @@ clean-grunt-docker-image: ## Remove grunt docker image
 
 
 # Release Targets
-create_release_rc: ## Create a release-candidate branch
+release-create-rc: ## Create a release-candidate branch 
 	git checkout dev
 	git pull --ff-only ${RELEASE_UPSTREAM} dev
 	git push origin dev

README.rst

@@ -56,3 +56,8 @@ Issues and Galaxy Development
 =============================
 
 Please see `CONTRIBUTING.md <CONTRIBUTING.md>`_ .
+
+Roadmap
+=============================
+
+Interested in the next steps for Galaxy? Take a look here: https://github.com/galaxyproject/galaxy/issues/1928

client/galaxy/scripts/layout/masthead.js

@@ -29,7 +29,6 @@ var View = Backbone.View.extend({
 
         // scratchbook
         Galaxy.frame = this.frame = new Scratchbook( { collection: this.collection } );
-        $( 'body' ).append( this.frame.$el );
 
         // set up the quota meter (And fetch the current user data from trans)
         // add quota meter to masthead

client/galaxy/scripts/layout/menu.js

@@ -41,23 +41,19 @@ var Collection = Backbone.Collection.extend({
             url             : 'library/index',
             tooltip         : 'Access published resources',
             menu            : [{
-                    title   : 'Data Libraries deprecated',
-                    url     : 'library/index'
-                },{
                     title   : 'Data Libraries',
-                    url     : 'library/list',
-                    divider : true
+                    url     : 'library/list'
                 },{
-                    title   : 'Published Histories',
+                    title   : 'Histories',
                     url     : 'history/list_published'
                 },{
-                    title   : 'Published Workflows',
+                    title   : 'Workflows',
                     url     : 'workflow/list_published'
                 },{
-                    title   : 'Published Visualizations',
+                    title   : 'Visualizations',
                     url     : 'visualization/list_published'
                 },{
-                    title   : 'Published Pages',
+                    title   : 'Pages',
                     url     : 'page/list_published'
             }]
         });

client/galaxy/scripts/layout/page.js

@@ -32,7 +32,8 @@ var PageLayoutView = Backbone.View.extend( BaseMVC.LoggableMixin ).extend({
         Galaxy.modal = this.modal = new Modal.View();
         this.masthead = new Masthead.View( this.options.config );
         this.$el.attr( 'scroll', 'no' );
-        this.$el.append( this._template() );
+        this.$el.html( this._template() );
+        this.$el.append( this.masthead.frame.$el );
         this.$el.append( this.masthead.$el );
         this.$el.append( this.modal.$el );
         this.$messagebox = this.$( '#messagebox' );
@@ -72,11 +73,11 @@ var PageLayoutView = Backbone.View.extend( BaseMVC.LoggableMixin ).extend({
     renderInactivityBox : function() {
         if( this.options.show_inactivity_warning ){
             var content = this.options.inactivity_box_content || '';
-            var verificationLink = $( '<a/>' ).attr( 'href', Galaxy.root + 'user/resend_verification' ).html( 'Resend verification.' );
+            var verificationLink = $( '<a/>' ).attr( 'href', Galaxy.root + 'user/resend_verification' ).text( 'Resend verification' );
             this.$el.addClass( 'has-inactivity-box' );
             this.$inactivebox
-                .html( content )
-                .append( ' ' + verificationLink )
+                .html( content + ' ' )
+                .append( verificationLink )
                 .toggle( !!content )
                 .show();
         } else {
@@ -93,10 +94,14 @@ var PageLayoutView = Backbone.View.extend( BaseMVC.LoggableMixin ).extend({
             if( _.has( page, panelId ) ){
                 page[ panelId ].setElement( '#' + panelId );
                 page[ panelId ].render();
-            } else if ( panelId !== 'center' ) {
-                page.center.$el.css( panelId, 0 );
             }
         });
+        if( !this.left ){
+            this.center.$el.css( 'left', 0 );
+        }
+        if( !this.right ){
+            this.center.$el.css( 'right', 0 );
+        }
         return this;
     },
 
@@ -106,27 +111,26 @@ var PageLayoutView = Backbone.View.extend( BaseMVC.LoggableMixin ).extend({
             '<div id="everything">',
                 '<div id="background"/>',
                 '<div id="messagebox"/>',
-                '<div id="inactivebox" class="panel-warning-message"/>',
-                '<div id="left"/>',
-                '<div id="center" class="inbound"/>',
-                '<div id="right"/>',
+                '<div id="inactivebox" class="panel-warning-message" />',
+                this.left?   '<div id="left" />' : '',
+                this.center? '<div id="center" class="inbound" />' : '',
+                this.right?  '<div id="right" />' : '',
             '</div>',
-            '<div id="dd-helper"/>',
-            '<noscript>',
-                '<div class="overlay overlay-background noscript-overlay">',
-                    '<div>',
-                        '<h3 class="title">Javascript Required for Galaxy</h3>',
-                        '<div>',
-                            'The Galaxy analysis interface requires a browser with Javascript enabled.<br>',
-                            'Please enable Javascript and refresh this page',
-                        '</div>',
-                    '</div>',
-                '</div>',
-            '</noscript>'
+            '<div id="dd-helper" />',
         ].join('');
     },
 
-    toString : function() { return 'PageLayoutView' }
+    /** hide both side panels if previously shown */
+    hideSidePanels : function(){
+        if( this.left ){
+            this.left.hide();
+        }
+        if( this.right ){
+            this.right.hide();
+        }
+    },
+
+    toString : function() { return 'PageLayoutView'; }
 });
 
 // ============================================================================

client/galaxy/scripts/mvc/form/form-input.js

@@ -3,124 +3,124 @@
 */
 define([], function() {
     return Backbone.View.extend({
-        initialize: function(app, options) {
+        initialize: function( app, options ) {
             this.app = app;
-            this.field = options.field;
+            this.app_options = app.options || {};
+            this.field = options && options.field || new Backbone.View();
+            this.model = options && options.model || new Backbone.Model({
+                text_enable     : this.app_options.text_enable   || 'Enable',
+                text_disable    : this.app_options.text_disable  || 'Disable',
+                cls_enable      : this.app_options.cls_enable    || 'fa fa-caret-square-o-down',
+                cls_disable     : this.app_options.cls_disable   || 'fa fa-caret-square-o-up'
+            }).set( options );
 
-            // set text labels and icons for collapsible button
-            this.text_enable    = app.options.text_enable || 'Enable';
-            this.text_disable   = app.options.text_disable || 'Disable';
-            this.cls_enable     = app.options.cls_enable || 'fa fa-caret-square-o-down';
-            this.cls_disable    = app.options.cls_disable || 'fa fa-caret-square-o-up';
-
-            // set element
-            this.setElement(this._template(options));
-
-            // link elements
-            this.$field = this.$('.ui-form-field');
-            this.$preview = this.$('.ui-form-preview');
-            this.$collapsible = this.$('.ui-form-collapsible');
-            this.$collapsible_icon = this.$('.ui-form-collapsible').find('.icon');
-            this.$error_text = this.$('.ui-form-error-text');
-            this.$error = this.$('.ui-form-error');
-            this.$backdrop = this.$('.ui-form-backdrop');
+            // set element and link components
+            this.setElement( this._template() );
+            this.$field             = this.$( '.ui-form-field' );
+            this.$info              = this.$( '.ui-form-info' );
+            this.$preview           = this.$( '.ui-form-preview' );
+            this.$collapsible       = this.$( '.ui-form-collapsible' );
+            this.$collapsible_text  = this.$( '.ui-form-collapsible-text' );
+            this.$collapsible_icon  = this.$( '.ui-form-collapsible-icon' );
+            this.$title             = this.$( '.ui-form-title' );
+            this.$title_text        = this.$( '.ui-form-title-text' );
+            this.$error_text        = this.$( '.ui-form-error-text' );
+            this.$error             = this.$( '.ui-form-error' );
+            this.$backdrop          = this.$( '.ui-form-backdrop' );
 
             // add field element
-            this.$field.prepend(this.field.$el);
+            this.$field.prepend( this.field.$el );
 
             // decide wether to expand or collapse fields
-            this.field.collapsed = options.collapsible_value !== undefined && JSON.stringify( options.value ) == JSON.stringify( options.collapsible_value );
+            var collapsible_value = this.model.get( 'collapsible_value' );
+            this.field.collapsed = collapsible_value !== undefined && JSON.stringify( this.model.get( 'value' ) ) == JSON.stringify( collapsible_value );
+            this.listenTo( this.model, 'change', this.render, this );
+            this.render();
 
-            // refresh view
-            this._refresh();
-
-            // add collapsible hide/show
+            // add click handler
             var self = this;
-            this.$collapsible.on('click', function() {
+            this.$collapsible.on( 'click', function() {
                 self.field.collapsed = !self.field.collapsed;
-                self._refresh();
+                app.trigger && app.trigger( 'change' );
+                self.render();
             });
         },
 
         /** Disable input element
         */
         disable: function( silent ) {
-            this.$backdrop.show();
-            silent && this.$backdrop.css({ 'opacity': 0, 'cursor': 'default' } );
+            this.model.set( 'backdrop', silent ? 'silent' : 'default' );
         },
 
         /** Set error text
         */
-        error: function(text) {
-            this.$error_text.html(text);
-            this.$error.show();
-            this.$el.addClass('ui-error');
+        error: function( text ) {
+            this.model.set( 'error_text', text );
         },
 
         /** Reset this view
         */
         reset: function() {
-            this.$error.hide();
-            this.$el.removeClass('ui-error');
+            this.model.set( 'error_text', null );
         },
 
-        /** Refresh element
-        */
-        _refresh: function() {
-            this.$collapsible_icon.removeClass().addClass('icon');
-            if (!this.field.collapsed) {
-                this.$field.fadeIn('fast');
-                this.$preview.hide();
-                this._tooltip(this.text_disable, this.cls_disable);
+        render: function() {
+            // render help
+            $( '.tooltip' ).hide();
+            var help_text = this.model.get( 'help', '' );
+            var help_argument = this.model.get( 'argument' );
+            if ( help_argument && help_text.indexOf( '(' + help_argument + ')' ) == -1 ) {
+                help_text += ' (' + help_argument + ')';
+            }
+            this.$info.html( help_text );
+            // render input field
+            this.field.collapsed ? this.$field.hide() : this.$field.fadeIn( 'fast' );
+            // render preview view for collapsed fields
+            this.$preview[ this.field.collapsed && this.model.get( 'collapsible_preview' ) ? 'show' : 'hide' ]()
+                         .html( this.model.get( 'text_value' ) );
+            // render error messages
+            var error_text = this.model.get( 'error_text' );
+            this.$error[ error_text ? 'show' : 'hide' ]();
+            this.$el[ error_text ? 'addClass' : 'removeClass' ]( 'ui-error' );
+            this.$error_text.html( error_text );
+            // render backdrop to disable field
+            this.$backdrop.removeClass()
+                          .addClass( 'ui-form-backdrop' )
+                          .addClass( 'ui-form-backdrop-' + this.model.get( 'backdrop' ) );
+            // render collapsible state and title
+            if ( !this.model.get( 'disabled' ) && this.model.get( 'collapsible_value' ) !== undefined ) {
+                var collapsible_state = this.field.collapsed ? 'enable' : 'disable';
+                this.$title_text.hide();
+                this.$collapsible.show();
+                this.$collapsible_text.text( this.model.get( 'label' ) );
+                this.$collapsible_icon.removeClass().addClass( 'icon' )
+                                      .addClass( this.model.get( 'cls_' +  collapsible_state ) )
+                                      .attr( 'data-original-title', this.model.get( 'text_' + collapsible_state ) )
+                                      .tooltip( { placement: 'bottom' } );
             } else {
-                this.$field.hide();
-                this.$preview.show();
-                this._tooltip(this.text_enable, this.cls_enable);
+                this.$title_text.show().text( this.model.get( 'label' ) );
+                this.$collapsible.hide();
             }
-            this.app.trigger('change');
         },
 
-        /** Set tooltip text
-        */
-        _tooltip: function(title, cls) {
-            this.$collapsible_icon.addClass(cls)
-                               .tooltip({ placement: 'bottom' })
-                               .attr('data-original-title', title)
-                               .tooltip('fixTitle').tooltip('hide');
-        },
-
-        /** Main Template
-        */
-        _template: function(options) {
-            var tmp =   '<div class="ui-form-element">' +
-                            '<div class="ui-form-error ui-error">' +
-                                '<span class="fa fa-arrow-down"/><span class="ui-form-error-text"/>' +
-                            '</div>' +
-                            '<div class="ui-form-title">';
-            if ( !options.disabled && options.collapsible_value !== undefined ) {
-                tmp +=          '<div class="ui-form-collapsible">' +
-                                    '<i class="icon"/>' + options.label +
-                                '</div>';
-            } else {
-                tmp += options.label;
-            }
-            tmp +=          '</div>' +
-                            '<div class="ui-form-field">';
-            tmp +=              '<div class="ui-form-info">';
-            if (options.help) {
-                tmp +=              options.help;
-            }
-            if (options.argument && options.help.indexOf('(' + options.argument + ')') == -1) {
-                tmp +=              ' (' + options.argument + ')';
-            }
-            tmp +=              '</div>' +
-                                '<div class="ui-form-backdrop"/>' +
-                            '</div>';
-            if ( options.collapsible_preview ) {
-                tmp +=      '<div class="ui-form-preview">' + options.text_value + '</div>';
-            }
-            tmp += '</div>';
-            return tmp;
+        _template: function() {
+            return  $( '<div/>' ).addClass( 'ui-form-element' )
+                                 .append( $( '<div/>' ).addClass( 'ui-form-error ui-error' )
+                                    .append( $( '<span/>' ).addClass( 'fa fa-arrow-down' ) )
+                                    .append( $( '<span/>' ).addClass( 'ui-form-error-text' ) )
+                                 )
+                                 .append( $( '<div/>' ).addClass( 'ui-form-title' )
+                                    .append( $( '<div/>' ).addClass( 'ui-form-collapsible' )
+                                        .append( $( '<i/>' ).addClass( 'ui-form-collapsible-icon' ) )
+                                        .append( $( '<span/>' ).addClass( 'ui-form-collapsible-text' ) )
+                                    )
+                                    .append( $( '<span/>' ).addClass( 'ui-form-title-text' ) )
+                                 )
+                                 .append( $( '<div/>' ).addClass( 'ui-form-field' )
+                                    .append( $( '<span/>' ).addClass( 'ui-form-info' ) )
+                                    .append( $( '<span/>' ).addClass( 'ui-form-backdrop' ) )
+                                 )
+                                 .append( $( '<div/>' ).addClass( 'ui-form-preview' ) );
         }
     });
 });

client/galaxy/scripts/mvc/form/form-parameters.js

@@ -3,7 +3,7 @@
 */
 define(['utils/utils',
         'mvc/ui/ui-misc',
-        'mvc/form/form-select-content',
+        'mvc/ui/ui-select-content',
         'mvc/ui/ui-select-library',
         'mvc/ui/ui-select-ftp',
         'mvc/ui/ui-color-picker'],
@@ -54,7 +54,7 @@ define(['utils/utils',
         */
         _fieldData: function( input_def ) {
             var self = this;
-            return new SelectContent.View( this.app, {
+            return new SelectContent.View({
                 id          : 'field-' + input_def.id,
                 extensions  : input_def.extensions,
                 optional    : input_def.optional,

client/galaxy/scripts/mvc/form/form-select-content.js

@@ -1,347 +0,0 @@
-// dependencies
-define(['utils/utils', 'mvc/ui/ui-misc', 'mvc/ui/ui-tabs'], function(Utils, Ui, Tabs) {
-// hda/hdca content selector ui element
-var View = Backbone.View.extend({
-    // initialize
-    initialize : function(app, options) {
-        // link app and options
-        this.app = app;
-        this.options = options;
-
-        // track current history elements
-        this.history = {};
-
-
-        // link this
-        var self = this;
-
-        // add element
-        this.setElement('<div class="ui-select-content"/>');
-
-        // list of select fieldsFormSection
-        this.list = {};
-
-        // radio button options
-        var radio_buttons = [];
-
-        // identify selector type
-        if (options.type == 'data_collection') {
-            this.mode = 'collection';
-        } else {
-            if (options.multiple) {
-                this.mode = 'multiple';
-            } else {
-                this.mode = 'single';
-            }
-        }
-
-        // set initial state
-        this.current = this.mode;
-        this.list = {};
-
-        // error messages
-        var extensions = Utils.textify(options.extensions);
-        var hda_error = 'No dataset available.';
-        if (extensions) {
-            hda_error = 'No ' + extensions + ' dataset available.';
-        }
-        var hdca_error = 'No dataset list available.';
-        if (extensions) {
-            hdca_error = 'No ' + extensions + ' dataset collection available.';
-        }
-
-        // add single dataset selector
-        if (this.mode == 'single') {
-            radio_buttons.push({
-                icon    : 'fa-file-o',
-                value   : 'single',
-                tooltip : 'Single dataset'
-            });
-            this.select_single = new Ui.Select.View({
-                optional    : options.optional,
-                error_text  : hda_error,
-                onchange    : function() {
-                    self.trigger('change');
-                }
-            });
-            this.list['single'] = {
-                field: this.select_single,
-                type : 'hda'
-            };
-        }
-
-        // add multiple dataset selector
-        if (this.mode == 'single' || this.mode == 'multiple') {
-            radio_buttons.push({
-                icon    : 'fa-files-o',
-                value   : 'multiple',
-                tooltip : 'Multiple datasets'
-            });
-            this.select_multiple = new Ui.Select.View({
-                multiple    : true,
-                searchable  : false,
-                optional    : options.optional,
-                error_text  : hda_error,
-                onchange    : function() {
-                    self.trigger('change');
-                }
-            });
-            this.list['multiple'] = {
-                field: this.select_multiple,
-                type : 'hda'
-            };
-        }
-
-        // add collection selector
-        if (this.mode == 'single' || this.mode == 'multiple' || this.mode == 'collection') {
-            radio_buttons.push({
-                icon    : 'fa-folder-o',
-                value   : 'collection',
-                tooltip : 'Dataset collection'
-            });
-            var multiple = this.mode == 'multiple';
-            this.select_collection = new Ui.Select.View({
-                error_text  : hdca_error,
-                multiple    : multiple,
-                searchable  : false,
-                optional    : options.optional,
-                onchange    : function() {
-                    self.trigger('change');
-                }
-            });
-            this.list['collection'] = {
-                field: this.select_collection,
-                type : 'hdca'
-            };
-        }
-
-        // create button
-        this.button_type = new Ui.RadioButton.View({
-            value   : this.current,
-            data    : radio_buttons,
-            onchange: function(value) {
-                self.current = value;
-                self.refresh();
-                self.trigger('change');
-            }
-        });
-
-        // add batch mode information
-        this.$batch = $(this.template_batch());
-
-        // number of radio buttons
-        var n_buttons = _.size(this.list);
-
-        // add button to dom
-        var button_width = 0;
-        if (n_buttons > 1) {
-            this.$el.append(this.button_type.$el);
-            button_width = Math.max(0, _.size(this.list) * 35) + 'px';
-        }
-
-        // append field elements
-        for (var i in this.list) {
-            this.$el.append(this.list[i].field.$el.css({
-                'margin-left': button_width
-            }));
-        }
-
-        // append batch message
-        this.$el.append(this.$batch.css({
-            'margin-left': button_width
-        }));
-
-        // update options
-        this.update(options.data);
-
-        // set initial value
-        if (this.options.value !== undefined) {
-            this.value(this.options.value);
-        }
-
-        // refresh view
-        this.refresh();
-
-        // add change event. fires on trigger
-        this.on('change', function() {
-            if (options.onchange) {
-                options.onchange(self.value());
-            }
-        });
-    },
-
-    /** Indicate that select fields are being updated */
-    wait: function() {
-        for (var i in this.list) {
-            this.list[i].field.wait();
-        }
-    },
-
-    /** Indicate that the options update has been completed */
-    unwait: function() {
-        for (var i in this.list) {
-            this.list[i].field.unwait();
-        }
-    },
-
-    /** Update content selector */
-    update: function(options) {
-        // update a particular select field
-        var self = this;
-        function _update(field, options) {
-            if (field) {
-                // identify available options
-                var select_options = [];
-                for (var i in options) {
-                    var item = options[i];
-                    select_options.push({
-                        hid  : item.hid,
-                        label: item.hid + ': ' + item.name,
-                        value: item.id
-                    });
-                    // backup to local history
-                    self.history[item.id + '_' + item.src] = item;
-                }
-                // update field
-                field.add( select_options, function( a, b ) { return b.hid - a.hid } );
-            }
-        }
-
-        // update available options
-        _update(this.select_single, options.hda);
-        _update(this.select_multiple, options.hda);
-        _update(this.select_collection, options.hdca);
-    },
-
-    /** Return the currently selected dataset values */
-    value : function (new_value) {
-        // update current value
-        if (new_value !== undefined) {
-            if (new_value && new_value.values) {
-                try {
-                    // create list with values
-                    var list = [];
-                    for (var i in new_value.values) {
-                        list.push(new_value.values[i].id);
-                    }
-
-                    // identify suitable select field
-                    if (new_value && new_value.values.length > 0 && new_value.values[0].src == 'hdca') {
-                        this.current = 'collection';
-                        this.select_collection.value(list);
-                    } else {
-                        if (this.mode == 'multiple') {
-                            this.current = 'multiple';
-                            this.select_multiple.value(list);
-                        } else {
-                            this.current = 'single';
-                            this.select_single.value(list[0]);
-                        }
-                    }
-                } catch (err) {
-                    Galaxy.emit.debug('tools-select-content::value()', 'Skipped.');
-                }
-            } else {
-                for (var i in this.list) {
-                    this.list[i].field.value(null);
-                }
-            }
-        }
-
-        // refresh view
-        this.refresh();
-
-        // validate value
-        var id_list = this._select().value();
-        if (id_list === null) {
-            return null;
-        }
-
-        // transform into an array
-        if (!(id_list instanceof Array)) {
-            id_list = [id_list];
-        }
-
-        // check if value exists
-        if (id_list.length === 0) {
-            return null;
-        }
-
-        // prepare result dict
-        var result = {
-            batch   : this._batch(),
-            values  : []
-        }
-
-        // append to dataset ids
-        for (var i in id_list) {
-            var details = this.history[id_list[i] + '_' + this.list[this.current].type];
-            if (details) {
-                result.values.push(details);
-            } else {
-                return null;
-            }
-        }
-
-        // sort by history ids
-        result.values.sort(function(a, b){
-            return a.hid - b.hid;
-        });
-
-        // return
-        return result;
-    },
-
-    /** Refreshes data selection view */
-    refresh: function() {
-        this.button_type.value(this.current);
-        for (var i in this.list) {
-            var $el = this.list[i].field.$el;
-            if (this.current == i) {
-                $el.show();
-            } else {
-                $el.hide();
-            }
-        }
-        if (this._batch()) {
-            this.$batch.show();
-        } else {
-            this.$batch.hide();
-        }
-    },
-
-    /** Assists in selecting the current field */
-    _select: function() {
-        return this.list[this.current].field;
-    },
-
-    /** Assists in identifying the batch mode */
-    _batch: function() {
-        if (this.current == 'collection') {
-            var hdca = this.history[this._select().value() + '_hdca'];
-            if (hdca && hdca.map_over_type) {
-                return true;
-            }
-        }
-        if (this.current != 'single') {
-            if (this.mode == 'single') {
-                return true;
-            }
-        }
-        return false;
-    },
-
-    /** Batch message template */
-    template_batch: function() {
-        return  '<div class="ui-form-info">' +
-                    '<i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>' +
-                    'This is a batch mode input field. A separate job will be triggered for each dataset.' +
-                '</div>';
-    }
-});
-
-return {
-    View: View
-}
-
-});

client/galaxy/scripts/mvc/library/library-dataset-view.js

@@ -30,9 +30,7 @@ var LibraryDatasetView = Backbone.View.extend({
     "click .btn-make-private"             :   "makeDatasetPrivate",
     "click .btn-remove-restrictions"      :   "removeDatasetRestrictions",
     "click .toolbtn_save_permissions"     :   "savePermissions",
-
     "click .toolbtn_save_modifications"   :   "comingSoon",
-    // "click .btn-share-dataset"            :   "comingSoon"
 
   },
 
@@ -217,7 +215,7 @@ var LibraryDatasetView = Backbone.View.extend({
       historyItem.save({ content : this.id, source : 'library' }, {
         success : function(){
             Galaxy.modal.hide();
-          mod_toastr.success('Dataset imported. Click this to start analysing it.', '', {onclick: function() {window.location='/';}});
+          mod_toastr.success('Dataset imported. Click this to start analyzing it.', '', {onclick: function() {window.location='/';}});
         },
         error : function(model, response){
           if (typeof response.responseJSON !== "undefined"){
@@ -585,15 +583,26 @@ var LibraryDatasetView = Backbone.View.extend({
     '<div class="library_style_container">',
       '<div id="library_toolbar">',
         '<button data-toggle="tooltip" data-placement="top" title="Download dataset" class="btn btn-default toolbtn-download-dataset primary-button toolbar-item" type="button">',
-          '<span class="fa fa-download"> Download</span>',
+          '<span class="fa fa-download"></span>',
+          '&nbsp;Download',
+        '</button>',
+        '<button data-toggle="tooltip" data-placement="top" title="Import dataset into history" class="btn btn-default toolbtn-import-dataset primary-button toolbar-item" type="button">',
+          '<span class="fa fa-book"></span>',
+          '&nbsp;to History',
         '</button>',
-        '<button data-toggle="tooltip" data-placement="top" title="Import dataset into history" class="btn btn-default toolbtn-import-dataset primary-button toolbar-item" type="button"><span class="fa fa-book"> to History</span></button>',
         '<% if (item.get("can_user_modify")) { %>',
-          '<button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-default toolbtn_modify_dataset primary-button toolbar-item" type="button"><span class="fa fa-pencil"> Modify</span></button>',
+          '<button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-default toolbtn_modify_dataset primary-button toolbar-item" type="button">',
+            '<span class="fa fa-pencil"></span>',
+            '&nbsp;Modify',
+          '</button>',
         '<% } %>',
         '<% if (item.get("can_user_manage")) { %>',
-          '<a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button toolbar-item" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>',
-          // '<button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button toolbar-item" type="button"><span class="fa fa-share"> Share</span></button>',
+          '<a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions">',
+            '<button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button toolbar-item" type="button">',
+              '<span class="fa fa-group"></span>',
+              '&nbsp;Permissions',
+            '</button>',
+          '</a>',
         '<% } %>',
       '</div>',
 
@@ -613,7 +622,8 @@ var LibraryDatasetView = Backbone.View.extend({
       '<div class="alert alert-info">',
         'This dataset is unrestricted so everybody can access it. Just share the URL of this page. ',
         '<button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button">',
-          '<span class="fa fa-clipboard"> To Clipboard</span>',
+          '<span class="fa fa-clipboard"></span>',
+          '&nbsp;To Clipboard',
         '</button> ',
       '</div>',
     '<% } %>',
@@ -726,7 +736,12 @@ var LibraryDatasetView = Backbone.View.extend({
     // CONTAINER START
     '<div class="library_style_container">',
       '<div id="library_toolbar">',
-        '<a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go to latest dataset" class="btn btn-default primary-button toolbar-item" type="button"><span class="fa fa-caret-left fa-lg"> Latest dataset</span></button><a>',
+        '<a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>">',
+          '<button data-toggle="tooltip" data-placement="top" title="Go to latest dataset" class="btn btn-default primary-button toolbar-item" type="button">',
+            '<span class="fa fa-caret-left fa-lg"></span>',
+            '&nbsp;Latest dataset',
+          '</button>',
+        '<a>',
       '</div>',
 
       // BREADCRUMBS
@@ -838,8 +853,14 @@ var LibraryDatasetView = Backbone.View.extend({
     // CONTAINER START
     '<div class="library_style_container">',
       '<div id="library_toolbar">',
-        '<button data-toggle="tooltip" data-placement="top" title="Cancel modifications" class="btn btn-default toolbtn_cancel_modifications primary-button toolbar-item" type="button"><span class="fa fa-times"> Cancel</span></button>',
-        '<button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button toolbar-item" type="button"><span class="fa fa-floppy-o"> Save</span></button>',
+        '<button data-toggle="tooltip" data-placement="top" title="Cancel modifications" class="btn btn-default toolbtn_cancel_modifications primary-button toolbar-item" type="button">',
+          '<span class="fa fa-times"></span>',
+          '&nbsp;Cancel',
+        '</button>',
+        '<button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button toolbar-item" type="button">',
+          '<span class="fa fa-floppy-o"></span>',
+          '&nbsp;Save',
+        '</button>',
       '</div>',
 
       // BREADCRUMBS
@@ -932,8 +953,18 @@ var LibraryDatasetView = Backbone.View.extend({
     // CONTAINER START
     '<div class="library_style_container">',
       '<div id="library_toolbar">',
-        '<a href="#folders/<%- item.get("folder_id") %>"><button data-toggle="tooltip" data-placement="top" title="Go back to containing folder" class="btn btn-default primary-button toolbar-item" type="button"><span class="fa fa-folder-open-o"> Containing Folder</span></button></a>',
-        '<a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go back to dataset" class="btn btn-default primary-button toolbar-item" type="button"><span class="fa fa-file-o"> Dataset Details</span></button><a>',
+        '<a href="#folders/<%- item.get("folder_id") %>">',
+          '<button data-toggle="tooltip" data-placement="top" title="Go back to containing folder" class="btn btn-default primary-button toolbar-item" type="button">',
+            '<span class="fa fa-folder-open-o"></span>',
+            '&nbsp;Containing Folder',
+          '</button>',
+        '</a>',
+        '<a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>">',
+          '<button data-toggle="tooltip" data-placement="top" title="Go back to dataset" class="btn btn-default primary-button toolbar-item" type="button">',
+            '<span class="fa fa-file-o"></span>',
+            '&nbsp;Dataset Details',
+          '</button>',
+        '<a>',
       '</div>',
 
       // BREADCRUMBS
@@ -964,30 +995,42 @@ var LibraryDatasetView = Backbone.View.extend({
         '<hr/>',
         '<h2>Dataset-related permissions</h2>',
         '<div class="alert alert-warning">Changes made below will affect <strong>every</strong> library item that was created from this dataset and also every history this dataset is part of.</div>',
-
         '<% if (!item.get("is_unrestricted")) { %>',
           '<p>You can remove all access restrictions on this dataset. ',
-          '<button data-toggle="tooltip" data-placement="top" title="Everybody will be able to access the dataset." class="btn btn-default btn-remove-restrictions primary-button" type="button">',
-            '<span class="fa fa-globe"> Remove restrictions</span>',
-          '</button>',
-        '</p>',
+            '<button data-toggle="tooltip" data-placement="top" title="Everybody will be able to access the dataset." class="btn btn-default btn-remove-restrictions primary-button" type="button">',
+              '<span class="fa fa-globe"></span>',
+              '&nbsp;Remove restrictions',
+            '</button>',
+          '</p>',
         '<% } else { %>',
           'This dataset is unrestricted so everybody can access it. Just share the URL of this page.',
-          '<button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"> To Clipboard</span></button> ',
+          '<button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button">',
+            '<span class="fa fa-clipboard"></span>',
+            '&nbsp;To Clipboard',
+            '</button>',
           '<p>You can make this dataset private to you. ',
-            '<button data-toggle="tooltip" data-placement="top" title="Only you will be able to access the dataset." class="btn btn-default btn-make-private primary-button" type="button"><span class="fa fa-key"> Make Private</span></button>',
+            '<button data-toggle="tooltip" data-placement="top" title="Only you will be able to access the dataset." class="btn btn-default btn-make-private primary-button" type="button">',
+              '<span class="fa fa-key"></span>',
+              '&nbsp;Make Private',
+            '</button>',
           '</p>',
-          // '<p>You can share this dataset privately with other Galaxy users. ',
-          // '<button data-toggle="tooltip" data-placement="top" title="Only you and the suers you choose will be able to access the dataset." class="btn btn-default btn-share-dataset primary-button" type="button"><span class="fa fa-share"> Share Privately</span></button>',
-          // '</p>',
         '<% } %>',
         '<h4>Roles that can access the dataset</h4>',
         '<div id="access_perm" class="access_perm roles-selection"></div>',
-        '<div class="alert alert-info roles-selection">User has to have <strong>all these roles</strong> in order to access this dataset. Users without access permission <strong>cannot</strong> have other permissions on this dataset. If there are no access roles set on the dataset it is considered <strong>unrestricted</strong>.</div>',
+        '<div class="alert alert-info roles-selection">',
+          'User has to have <strong>all these roles</strong> in order to access this dataset.',
+          ' Users without access permission <strong>cannot</strong> have other permissions on this dataset.',
+          ' If there are no access roles set on the dataset it is considered <strong>unrestricted</strong>.',
+        '</div>',
         '<h4>Roles that can manage permissions on the dataset</h4>',
         '<div id="manage_perm" class="manage_perm roles-selection"></div>',
-        '<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can manage permissions of this dataset. If you remove yourself you will loose the ability manage this dataset unless you are an admin.</div>',
-        '<button data-toggle="tooltip" data-placement="top" title="Save modifications made on this page" class="btn btn-default toolbtn_save_permissions primary-button" type="button"><span class="fa fa-floppy-o"> Save</span></button>',
+        '<div class="alert alert-info roles-selection">',
+          'User with <strong>any</strong> of these roles can manage permissions of this dataset. If you remove yourself you will loose the ability manage this dataset unless you are an admin.',
+        '</div>',
+        '<button data-toggle="tooltip" data-placement="top" title="Save modifications made on this page" class="btn btn-default toolbtn_save_permissions primary-button" type="button">',
+          '<span class="fa fa-floppy-o"></span>',
+          '&nbsp;Save',
+        '</button>',
       '</div>',
     // CONTAINER END
     '</div>'
@@ -996,7 +1039,7 @@ var LibraryDatasetView = Backbone.View.extend({
 
   templateBulkImportInModal: function(){
     return _.template([
-    '<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">',
+    '<span class="library-modal-item">',
       'Select history: ',
       '<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ',
         '<% _.each(histories, function(history) { %>', //history select btn

client/galaxy/scripts/mvc/library/library-folder-view.js

@@ -211,91 +211,107 @@ var FolderView = Backbone.View.extend({
   },
 
   templateFolder : function(){
-    var tmpl_array = [];
-    // CONTAINER START
-    tmpl_array.push('<div class="library_style_container">');
-
-    tmpl_array.push('  <div id="library_toolbar">');
-    tmpl_array.push('   <button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-default toolbtn_modify_dataset primary-button" type="button"><span class="fa fa-pencil"></span> Modify</span></button>');
-    tmpl_array.push('   <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>');
-    tmpl_array.push('   <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>');
-    tmpl_array.push('  </div>');
-
-    // tmpl_array.push('<% if (item.get("is_unrestricted")) { %>');
-    tmpl_array.push('  <p>');
-    tmpl_array.push('  This dataset is unrestricted so everybody can access it. Just share the URL of this page. ');
-    tmpl_array.push('  <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"></span> To Clipboard</span></button> ');
-    tmpl_array.push('  </p>');
-    // tmpl_array.push('<% } %>');
-
-    tmpl_array.push('<div class="dataset_table">');
-
-    tmpl_array.push('   <table class="grid table table-striped table-condensed">');
-    tmpl_array.push('       <tr>');
-    tmpl_array.push('           <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');
-    tmpl_array.push('           <td><%= _.escape(item.get("name")) %></td>');
-    tmpl_array.push('       </tr>');
-
-    tmpl_array.push('   <% if (item.get("file_ext")) { %>');
-    tmpl_array.push('       <tr>');
-    tmpl_array.push('           <th scope="row">Data type</th>');
-    tmpl_array.push('           <td><%= _.escape(item.get("file_ext")) %></td>');
-    tmpl_array.push('       </tr>');
-    tmpl_array.push('   <% } %>');
-
-    tmpl_array.push('    </table>');
-    tmpl_array.push('</div>');
-
-    // CONTAINER END
-    tmpl_array.push('</div>');
-
-    return _.template(tmpl_array.join(''));
+    return _.template([
+    '<div class="library_style_container">',
+      '<div id="library_toolbar">',
+        '<button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-default toolbtn_modify_dataset primary-button" type="button">',
+          '<span class="fa fa-pencil"/>',
+          '&nbsp;Modify',
+        '</button>',
+        '<a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions">',
+          '<button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button">',
+            '<span class="fa fa-group"/>',
+            '&nbsp;Permissions',
+          '</button>',
+        '</a>',
+        '<button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button">',
+          '<span class="fa fa-share"/>',
+          '&nbsp;Share',
+          '</span>',
+        '</button>',
+      '</div>',
+      '<p>',
+        'This dataset is unrestricted so everybody can access it. Just share the URL of this page. ',
+        '<button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button">',
+          '<span class="fa fa-clipboard"/>',
+          '&nbsp;To Clipboard',
+        '</button> ',
+      '</p>',
+      '<div class="dataset_table">',
+        '<table class="grid table table-striped table-condensed">',
+          '<tr>',
+            '<th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">',
+              'Name',
+            '</th>',
+            '<td>',
+              '<%= _.escape(item.get("name")) %>',
+            '</td>',
+          '</tr>',
+          '<% if (item.get("file_ext")) { %>',
+            '<tr>',
+              '<th scope="row">Data type</th>',
+              '<td>',
+                '<%= _.escape(item.get("file_ext")) %>',
+              '</td>',
+            '</tr>',
+          '<% } %>',
+        '</table>',
+      '</div>',
+    '</div>'
+    ].join(''));
   },
 
   templateFolderPermissions : function(){
-    var tmpl_array = [];
-    // CONTAINER START
-    tmpl_array.push('<div class="library_style_container">');
-
-
-    tmpl_array.push('  <div id="library_toolbar">');
-    tmpl_array.push('   <a href="#/folders/<%= folder.get("parent_id") %>"><button data-toggle="tooltip" data-placement="top" title="Go back to the parent folder" class="btn btn-default primary-button" type="button"><span class="fa fa-caret-left fa-lg"></span> Parent folder</span></button></a>');
-    tmpl_array.push('  </div>');
-
-    tmpl_array.push('<h1>Folder: <%= _.escape(folder.get("name")) %></h1>');
-
-    tmpl_array.push('<div class="alert alert-warning">');
-    tmpl_array.push('<% if (is_admin) { %>');
-    tmpl_array.push('You are logged in as an <strong>administrator</strong> therefore you can manage any folder on this Galaxy instance. Please make sure you understand the consequences.');
-    tmpl_array.push('<% } else { %>');
-    tmpl_array.push('You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.');
-    tmpl_array.push('<% }%>');
-    tmpl_array.push('</div>');
-
-    tmpl_array.push('<div class="dataset_table">');
-
-    tmpl_array.push('<h2>Folder permissions</h2>');
-
-    tmpl_array.push('<h4>Roles that can manage permissions on this folder</h4>');
-    tmpl_array.push('<div id="manage_perm" class="manage_perm roles-selection"></div>');
-    tmpl_array.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can manage permissions on this folder.</div>');
-
-    tmpl_array.push('<h4>Roles that can add items to this folder</h4>');
-    tmpl_array.push('<div id="add_perm" class="add_perm roles-selection"></div>');
-    tmpl_array.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can add items to this folder (folders and datasets).</div>');
-
-    tmpl_array.push('<h4>Roles that can modify this folder</h4>');
-    tmpl_array.push('<div id="modify_perm" class="modify_perm roles-selection"></div>');
-    tmpl_array.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify this folder (name, etc.).</div>');
-
-    tmpl_array.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_permissions primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');
-
-    tmpl_array.push('</div>');
-
-    // CONTAINER END
-    tmpl_array.push('</div>');
-
-    return _.template(tmpl_array.join(''));
+    return _.template([
+    '<div class="library_style_container">',
+      '<div id="library_toolbar">',
+        '<a href="#/folders/<%= folder.get("parent_id") %>">',
+          '<button data-toggle="tooltip" data-placement="top" title="Go back to the parent folder" class="btn btn-default primary-button" type="button">',
+            '<span class="fa fa-caret-left fa-lg"/>',
+            '&nbsp;Parent folder',
+          '</button>',
+        '</a>',
+      '</div>',
+      '<h1>',
+        'Folder: <%= _.escape(folder.get("name")) %>',
+      '</h1>',
+      '<div class="alert alert-warning">',
+        '<% if (is_admin) { %>',
+          'You are logged in as an <strong>administrator</strong> therefore you can manage any folder on this Galaxy instance. Please make sure you understand the consequences.',
+        '<% } else { %>',
+          'You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.',
+        '<% }%>',
+      '</div>',
+      '<div class="dataset_table">',
+        '<h2>Folder permissions</h2>',
+        '<h4>',
+          'Roles that can manage permissions on this folder',
+        '</h4>',
+        '<div id="manage_perm" class="manage_perm roles-selection"/>',
+        '<div class="alert alert-info roles-selection">',
+          'User with <strong>any</strong> of these roles can manage permissions on this folder.',
+        '</div>',
+        '<h4>',
+          'Roles that can add items to this folder',
+        '</h4>',
+        '<div id="add_perm" class="add_perm roles-selection"/>',
+        '<div class="alert alert-info roles-selection">',
+          'User with <strong>any</strong> of these roles can add items to this folder (folders and datasets).',
+        '</div>',
+        '<h4>',
+          'Roles that can modify this folder',
+        '</h4>',
+        '<div id="modify_perm" class="modify_perm roles-selection"/>',
+        '<div class="alert alert-info roles-selection">',
+          'User with <strong>any</strong> of these roles can modify this folder (name, etc.).',
+        '</div>',
+        '<button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_permissions primary-button" type="button">',
+          '<span class="fa fa-floppy-o"/>',
+          '&nbsp;Save',
+        '</button>',
+      '</div>',
+    '</div>'
+    ].join(''));
   }
 
 });

client/galaxy/scripts/mvc/library/library-folderlist-view.js

@@ -254,7 +254,6 @@ var FolderListView = Backbone.View.extend({
      *  Currently supports only sorting by name.
      */
     sortFolder: function(sort_by, order){
-        console.log('sorting');
         // default to asc sort by name
         if (sort_by === 'undefined' && order === 'undefined'){
             return this.collection.sortByNameAsc();
@@ -345,49 +344,52 @@ var FolderListView = Backbone.View.extend({
     },
 
     templateFolder : function (){
-        var tmpl_array = [];
+      return _.template([
+      // BREADCRUMBS
+      '<ol class="breadcrumb">',
+        '<li><a title="Return to the list of libraries" href="#">Libraries</a></li>',
+        '<% _.each(path, function(path_item) { %>',
+          '<% if (path_item[0] != id) { %>',
+            '<li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a> </li> ',
+          '<% } else { %>',
+            '<li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>',
+          '<% } %>',
+        '<% }); %>',
+      '</ol>',
 
-        // 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="sort-icon fa fa-sort-alpha-<%- order %>"></span></th>');
-        tmpl_array.push('       <th style="width:25%;">description</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('           <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(''));
+      // FOLDER CONTENT
+      '<table data-library-id="<%- parent_library_id  %>" id="folder_table" class="grid table table-condensed">',
+        '<thead>',
+          '<th class="button_heading"></th>',
+          '<th style="text-align: center; width: 20px; " title="Check to select all datasets"><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>',
+          '<th><a class="sort-folder-link" title="Click to reverse order" href="#">name</a> <span title="Sorted alphabetically" class="sort-icon fa fa-sort-alpha-<%- order %>"></span></th>',
+          '<th style="width:25%;">description</th>',
+          '<th style="width:5%;">data type</th>',
+          '<th style="width:10%;">size</th>',
+          '<th style="width:160px;">time updated (UTC)</th>',
+          '<th style="width:10%;"></th> ',
+        '</thead>',
+        '<tbody id="folder_list_body">',
+          '<tr id="first_folder_item">',
+          '<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>',
+          '<td></td>',
+          '<td></td>',
+          '<td></td>',
+          '<td></td>',
+          '<td></td>',
+          '<td></td>',
+          '<td></td>',
+          '</tr>',
+        '</tbody>',
+      '</table>',
+      '<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>'
+      ].join(''));
     }
 
 });

client/galaxy/scripts/mvc/library/library-folderrow-view.js

@@ -53,8 +53,8 @@ var FolderRowView = Backbone.View.extend({
         template = this.templateRowFile();
       }
     } else {
-      console.error('Unknown library item type found.');
-      console.error(folder_item.get('type') || folder_item.get('model_class'));
+      Galaxy.emit.error('Unknown library item type found.');
+      Galaxy.emit.error(folder_item.get('type') || folder_item.get('model_class'));
     }
     this.setElement(template({content_item: folder_item, edit_mode: this.options.edit_mode, button_config: this.options.visibility_config}));
     this.$el.show();
@@ -224,7 +224,7 @@ var FolderRowView = Backbone.View.extend({
     return _.template([
       '<tr class="folder_row light library-row" data-id="<%- content_item.id %>">',
         '<td>',
-          '<span title="Folder" class="fa fa-folder-o"></span>',
+          '<span title="Folder" class="fa fa-folder-o"/>',
         '</td>',
         '<td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>',
         '<% if(!edit_mode) { %>',
@@ -245,15 +245,21 @@ var FolderRowView = Backbone.View.extend({
           '</td>',
           '<td>',
             '<% if(edit_mode) { %>',  // start edit mode
-              '<button data-toggle="tooltip" data-placement="top" title="Save changes" class="primary-button btn-xs save_folder_btn" type="button" style="<% if(button_config.save_folder_btn === false) { print("display:none;") } %>"><span class="fa fa-floppy-o"> Save</span></button>',
-              '<button data-toggle="tooltip" data-placement="top" title="Discard changes" class="primary-button btn-xs cancel_folder_btn" type="button" style="<% if(button_config.cancel_folder_btn === false) { print("display:none;") } %>"><span class="fa fa-times"> Cancel</span></button>',
+              '<button data-toggle="tooltip" data-placement="top" title="Save changes" class="primary-button btn-xs save_folder_btn" type="button" style="<% if(button_config.save_folder_btn === false) { print("display:none;") } %>">',
+                '<span class="fa fa-floppy-o"/>',
+                '&nbsp;Save',
+              '</button>',
+              '<button data-toggle="tooltip" data-placement="top" title="Discard changes" class="primary-button btn-xs cancel_folder_btn" type="button" style="<% if(button_config.cancel_folder_btn === false) { print("display:none;") } %>">',
+                '<span class="fa fa-times"/>',
+                '&nbsp;Cancel',
+              '</button>',
             '<% } else if (!edit_mode){%>',  // start no edit mode
               '<button data-toggle="tooltip" data-placement="top" title="Modify \'<%- content_item.get("name") %>\'" class="primary-button btn-xs edit_folder_btn" type="button" style="<% if(button_config.edit_folder_btn === false) { print("display:none;") } %>">',
-                '<span class="fa fa-pencil"></span>',
+                '<span class="fa fa-pencil"/>',
               '</button>',
               '<a href="#/folders/<%- content_item.id %>/permissions">',
                 '<button data-toggle="tooltip" data-placement="top" class="primary-button btn-xs permission_folder_btn" title="Manage \'<%- content_item.get("name") %>\'" style="<% if(button_config.permission_folder_btn === false) { print("display:none;") } %>">',
-                  '<span class="fa fa-group"></span>',
+                  '<span class="fa fa-group"/>',
                 '</button>',
               '</a>',
             '<% } %>',  //end no edit mode
@@ -263,67 +269,107 @@ var FolderRowView = Backbone.View.extend({
   },
 
   templateRowFile: function(){
-    tmpl_array = [];
-
-    tmpl_array.push('<tr class="dataset_row light library-row" data-id="<%- content_item.id %>">');
-    tmpl_array.push('  <td>');
-    tmpl_array.push('    <span title="Dataset" class="fa fa-file-o"></span>');
-    tmpl_array.push('  </td>');
-    tmpl_array.push('  <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');
-    tmpl_array.push('  <td><a href="#folders/<%- content_item.get("folder_id") %>/datasets/<%- content_item.id %>" class="library-dataset"><%- content_item.get("name") %><a></td>'); // dataset
-    tmpl_array.push('  <td><%- content_item.get("message") %></td>');
-    tmpl_array.push('  <td><%= _.escape(content_item.get("file_ext")) %></td>'); // data type
-    tmpl_array.push('  <td><%= _.escape(content_item.get("file_size")) %></td>'); // size
-    tmpl_array.push('  <td><%= _.escape(content_item.get("update_time")) %></td>'); // time updated
-    tmpl_array.push('  <td>');
-    tmpl_array.push('    <% if (content_item.get("is_unrestricted")) { %><span data-toggle="tooltip" data-placement="top" title="Unrestricted dataset" style="color:grey;" class="fa fa-globe fa-lg"></span><% } %>');
-    tmpl_array.push('    <% if (content_item.get("is_private")) { %><span data-toggle="tooltip" data-placement="top" title="Private dataset" style="color:grey;" class="fa fa-key fa-lg"></span><% } %>');
-    tmpl_array.push('    <% if ((content_item.get("is_unrestricted") === false) && (content_item.get("is_private") === false)) { %><span data-toggle="tooltip" data-placement="top" title="Restricted dataset" style="color:grey;" class="fa fa-shield fa-lg"></span><% } %>');
-    tmpl_array.push('    <% if (content_item.get("can_manage")) { %><a href="#folders/<%- content_item.get("folder_id") %>/datasets/<%- content_item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" class="primary-button btn-xs permissions-dataset-btn" title="Manage permissions"><span class="fa fa-group"></span></button></a><% } %>');
-    tmpl_array.push('  </td>');
-    tmpl_array.push('</tr>');
-
-    return _.template(tmpl_array.join(''));
+    return _.template([
+    '<tr class="dataset_row light library-row" data-id="<%- content_item.id %>">',
+      '<td>',
+        '<span title="Dataset" class="fa fa-file-o"/>',
+      '</td>',
+      '<td style="text-align: center; ">',
+        '<input style="margin: 0;" type="checkbox">',
+      '</td>',
+      '<td>',
+        '<a href="#folders/<%- content_item.get("folder_id") %>/datasets/<%- content_item.id %>" class="library-dataset">',
+          '<%- content_item.get("name") %>',
+        '<a>',
+      '</td>',
+      '<td><%- content_item.get("message") %></td>',
+      '<td><%= _.escape(content_item.get("file_ext")) %></td>',
+      '<td><%= _.escape(content_item.get("file_size")) %></td>',
+      '<td><%= _.escape(content_item.get("update_time")) %></td>',
+      '<td>',
+        '<% if (content_item.get("is_unrestricted")) { %>',
+          '<span data-toggle="tooltip" data-placement="top" title="Unrestricted dataset" style="color:grey;" class="fa fa-globe fa-lg"/>',
+        '<% } %>',
+        '<% if (content_item.get("is_private")) { %>',
+          '<span data-toggle="tooltip" data-placement="top" title="Private dataset" style="color:grey;" class="fa fa-key fa-lg"/>',
+        '<% } %>',
+        '<% if ((content_item.get("is_unrestricted") === false) && (content_item.get("is_private") === false)) { %>',
+          '<span data-toggle="tooltip" data-placement="top" title="Restricted dataset" style="color:grey;" class="fa fa-shield fa-lg"/>',
+        '<% } %>',
+        '<% if (content_item.get("can_manage")) { %>',
+          '<a href="#folders/<%- content_item.get("folder_id") %>/datasets/<%- content_item.id %>/permissions">',
+            '<button data-toggle="tooltip" data-placement="top" class="primary-button btn-xs permissions-dataset-btn" title="Manage permissions">',
+              '<span class="fa fa-group"/>',
+            '</button>',
+          '</a>',
+        '<% } %>',
+      '</td>',
+    '</tr>'
+    ].join(''));
   },
 
   templateRowDeletedFile: function(){
-    tmpl_array = [];
-
-    tmpl_array.push('<tr class="active deleted_dataset library-row" data-id="<%- content_item.id %>">');
-    tmpl_array.push('  <td>');
-    tmpl_array.push('    <span title="Dataset" class="fa fa-file-o"></span>');
-    tmpl_array.push('  </td>');
-    tmpl_array.push('  <td></td>');
-    tmpl_array.push('  <td style="color:grey;"><%- content_item.get("name") %></td>'); // dataset
-    tmpl_array.push('  <td><%- content_item.get("message") %></td>');
-    tmpl_array.push('  <td><%= _.escape(content_item.get("file_ext")) %></td>'); // data type
-    tmpl_array.push('  <td><%= _.escape(content_item.get("file_size")) %></td>'); // size
-    tmpl_array.push('  <td><%= _.escape(content_item.get("update_time")) %></td>'); // time updated
-    tmpl_array.push('  <td><span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg"> </span><button data-toggle="tooltip" data-placement="top" title="Undelete <%- content_item.get("name") %>" class="primary-button btn-xs undelete_dataset_btn" type="button" style="margin-left:1em;"><span class="fa fa-unlock"> Undelete</span></button></td>');
-    tmpl_array.push('</tr>');
-
-    return _.template(tmpl_array.join(''));
+    return _.template([
+    '<tr class="active deleted_dataset library-row" data-id="<%- content_item.id %>">',
+      '<td>',
+        '<span title="Dataset" class="fa fa-file-o"/>',
+      '</td>',
+      '<td></td>',
+      '<td style="color:grey;">',
+        '<%- content_item.get("name") %>',
+      '</td>',
+      '<td>',
+        '<%- content_item.get("message") %>',
+      '</td>',
+      '<td>',
+        '<%= _.escape(content_item.get("file_ext")) %>',
+      '</td>',
+      '<td>',
+        '<%= _.escape(content_item.get("file_size")) %>',
+      '</td>',
+      '<td>',
+        '<%= _.escape(content_item.get("update_time")) %>',
+      '</td>',
+      '<td>',
+        '<span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg"/>',
+        '<button data-toggle="tooltip" data-placement="top" title="Undelete <%- content_item.get("name") %>" class="primary-button btn-xs undelete_dataset_btn" type="button" style="margin-left:1em;">',
+          '<span class="fa fa-unlock"/>',
+          '&nbsp;Undelete',
+        '</button>',
+      '</td>',
+    '</tr>'
+    ].join(''));
   },
 
   templateRowDeletedFolder: function(){
-    tmpl_array = [];
-
-    tmpl_array.push('<tr class="active deleted_folder light library-row" data-id="<%- content_item.id %>">');
-    tmpl_array.push('  <td>');
-    tmpl_array.push('    <span title="Folder" class="fa fa-folder-o"></span>');
-    tmpl_array.push('  </td>');
-    tmpl_array.push('  <td></td>');
-    tmpl_array.push('  <td style="color:grey;">');
-    tmpl_array.push('    <%- content_item.get("name") %>');
-    tmpl_array.push('  </td>');
-    tmpl_array.push('  <td><%- content_item.get("description") %></td>');
-    tmpl_array.push('  <td>folder</td>');
-    tmpl_array.push('  <td></td>');
-    tmpl_array.push('  <td><%= _.escape(content_item.get("update_time")) %></td>'); // time updated
-    tmpl_array.push('  <td><span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg"> </span><button data-toggle="tooltip" data-placement="top" title="Undelete <%- content_item.get("name") %>" class="primary-button btn-xs undelete_folder_btn" type="button" style="margin-left:1em;"><span class="fa fa-unlock"> Undelete</span></button></td>');
-    tmpl_array.push('</tr>');
-
-    return _.template(tmpl_array.join(''));
+    return _.template([
+    '<tr class="active deleted_folder light library-row" data-id="<%- content_item.id %>">',
+      '<td>',
+        '<span title="Folder" class="fa fa-folder-o"/>',
+      '</td>',
+      '<td></td>',
+      '<td style="color:grey;">',
+        '<%- content_item.get("name") %>',
+      '</td>',
+      '<td>',
+        '<%- content_item.get("description") %>',
+      '</td>',
+      '<td>',
+        'folder',
+      '</td>',
+      '<td></td>',
+      '<td>',
+        '<%= _.escape(content_item.get("update_time")) %>',
+      '</td>',
+      '<td>',
+        '<span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg"/>',
+        '<button data-toggle="tooltip" data-placement="top" title="Undelete <%- content_item.get("name") %>" class="primary-button btn-xs undelete_folder_btn" type="button" style="margin-left:1em;">',
+          '<span class="fa fa-unlock"/>',
+          '&nbsp;Undelete',
+        '</button>',
+      '</td>',
+    '</tr>'
+    ].join(''));
   }
 
 });

client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js

@@ -21,7 +21,7 @@ var FolderToolbarView = Backbone.View.extend({
     'click #include_deleted_datasets_chk' : 'checkIncludeDeleted',
     'click #toolbtn_bulk_delete'          : 'deleteSelectedItems',
     'click .toolbtn-show-locinfo'         : 'showLocInfo',
-    'click #page_size_prompt'             : 'showPageSizePrompt'
+    'click .page_size_prompt'             : 'showPageSizePrompt'
 
   },
 
@@ -99,7 +99,7 @@ var FolderToolbarView = Backbone.View.extend({
   renderPaginator: function( options ){
       this.options = _.extend( this.options, options );
       var paginator_template = this.templatePaginator();
-      this.$el.find( '#folder_paginator' ).html( paginator_template({
+      $("body").find( '.folder-paginator' ).html( paginator_template({
           id: this.options.id,
           show_page: parseInt( this.options.show_page ),
           page_count: parseInt( this.options.page_count ),
@@ -245,10 +245,30 @@ var FolderToolbarView = Backbone.View.extend({
    */
   importAllIntoHistory : function (){
     this.modal.disableButton('Import');
-    var history_id = $("select[name=dataset_import_bulk] option:selected").val();
-    var history_name = $("select[name=dataset_import_bulk] option:selected").text();
-    // we can save last used history to pre-select it next time
-    this.options.last_used_history_id = history_id;
+    var new_history_name = this.modal.$('input[name=history_name]').val();
+    var that = this;
+    if (new_history_name !== ''){
+      $.post( Galaxy.root + 'api/histories', {name: new_history_name})
+        .done(function( new_history ) {
+          that.options.last_used_history_id = new_history.id;
+          that.processImportToHistory(new_history.id, new_history.name);
+        })
+        .fail(function( xhr, status, error ) {
+          mod_toastr.error('An error ocurred.');
+        })
+        .always(function() {
+          that.modal.enableButton('Import');
+        });
+    } else {
+      var history_id = $("select[name=dataset_import_bulk] option:selected").val();
+      this.options.last_used_history_id = history_id;
+      var history_name = $("select[name=dataset_import_bulk] option:selected").text();
+      this.processImportToHistory(history_id, history_name);
+      this.modal.enableButton('Import');
+    }
+  },
+
+  processImportToHistory: function( history_id, history_name ){
     var dataset_ids = [];
     var folder_ids = [];
     $('#folder_table').find(':checked').each(function(){
@@ -406,6 +426,7 @@ var FolderToolbarView = Backbone.View.extend({
     mod_utils.get({
         url      :  Galaxy.root + "api/datatypes?extension_only=False",
         success  :  function( datatypes ) {
+                        that.list_extensions = [];
                         for (key in datatypes) {
                             that.list_extensions.push({
                                 id              : datatypes[key].extension,
@@ -418,11 +439,13 @@ var FolderToolbarView = Backbone.View.extend({
                             return a.id > b.id ? 1 : a.id < b.id ? -1 : 0;
                         });
                         that.list_extensions.unshift(that.auto);
-                    }
+                    },
+        cache    : true
       });
     mod_utils.get({
         url     :    Galaxy.root + "api/genomes",
         success : function( genomes ) {
+                    that.list_genomes = [];
                     for ( key in genomes ) {
                         that.list_genomes.push({
                             id      : genomes[key][1],
@@ -432,7 +455,8 @@ var FolderToolbarView = Backbone.View.extend({
                     that.list_genomes.sort(function(a, b) {
                         return a.id > b.id ? 1 : a.id < b.id ? -1 : 0;
                     });
-                }
+                },
+        cache   : true
     });
   },
 
@@ -482,6 +506,13 @@ var FolderToolbarView = Backbone.View.extend({
       }
     });
 
+    $('.libimport-select-all').bind("click", function(){
+      $('#jstree_browser').jstree("check_all");
+    });
+    $('.libimport-select-none').bind("click", function(){
+      $('#jstree_browser').jstree("uncheck_all");
+    });
+
     this.renderSelectBoxes();
     options.disabled_jstree_element = 'folders';
     this.renderJstree( options );
@@ -608,7 +639,7 @@ var FolderToolbarView = Backbone.View.extend({
         this.modal.$el.find( '.modal-body' ).html( template( { folder_name : this.options.folder_name } ) );
         break;
       case "deleting_datasets":
-        template = this.templateDeletingDatasetsProgressBar();
+        template = this.templateDeletingItemsProgressBar();
         this.modal.$el.find( '.modal-body' ).html( template() );
         break;
       case "to_history":
@@ -616,7 +647,7 @@ var FolderToolbarView = Backbone.View.extend({
         this.modal.$el.find( '.modal-body' ).html( template( { history_name : options.history_name } ) );
         break;
       default:
-        console.error( 'Wrong action specified.')
+        Galaxy.emit.error( 'Wrong action specified.', 'datalibs');
         break;
     }
 
@@ -637,7 +668,9 @@ var FolderToolbarView = Backbone.View.extend({
    * @see renderJstree
    */
   importFromJstreePath: function ( that, options ){
-    var selected_nodes = $( '#jstree_browser' ).jstree().get_selected( true );
+    var all_nodes = $( '#jstree_browser' ).jstree().get_selected( true );
+    // remove the disabled elements that could have been trigerred with the 'select all'
+    selected_nodes = _.filter(all_nodes, function(node){ return node.state.disabled == false; })
     var preserve_dirs = this.modal.$el.find( '.preserve-checkbox' ).is( ':checked' );
     var link_data = this.modal.$el.find( '.link-checkbox' ).is( ':checked' );
     var file_type = this.select_extension.value();
@@ -731,7 +764,7 @@ var FolderToolbarView = Backbone.View.extend({
     var popped_item = history_item_set.pop();
     if ( typeof popped_item == "undefined" ) {
       if ( this.options.chain_call_control.failed_number === 0 ){
-        mod_toastr.success( 'Selected datasets imported into history. Click this to start analysing it.', '', { onclick: function() { window.location='/' } } );
+        mod_toastr.success( 'Selected datasets imported into history. Click this to start analyzing it.', '', { onclick: function() { window.location='/' } } );
       } 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 imported into history.' );
       } else if ( this.options.chain_call_control.failed_number < this.options.chain_call_control.total_number ){
@@ -868,8 +901,6 @@ var FolderToolbarView = Backbone.View.extend({
    * @param  {array} lddas_set array of lddas to delete
    */
   chainCallDeletingItems: function( items_to_delete ){
-  console.log('chaincall');
-  console.log(items_to_delete);
   var self = this;
   this.deleted_items = new mod_library_model.Folder();
   var popped_item = items_to_delete.pop();
@@ -897,11 +928,9 @@ var FolderToolbarView = Backbone.View.extend({
               } else if (item.type === 'file' || item.model_class === 'LibraryDataset'){
                 updated_item = new mod_library_model.Item( item );
               } else {
-                console.error('Unknown library item type found.');
-                console.error(item.type || item.model_class);
+                Galaxy.emit.error('Unknown library item type found.', 'datalibs');
+                Galaxy.emit.error(item.type || item.model_class, 'datalibs');
               }
-              console.log('updated item')
-              console.log(updated_item);
               Galaxy.libraries.folderListView.collection.add( updated_item );
             }
             self.chainCallDeletingItems( items_to_delete );
@@ -930,13 +959,13 @@ var FolderToolbarView = Backbone.View.extend({
   deleteSelectedItems: function(){
     var checkedValues = $('#folder_table').find(':checked');
     if(checkedValues.length === 0){
-        mod_toastr.info('You must select at least one dataset for deletion.');
+        mod_toastr.info('You must select at least one item for deletion.');
     } else {
-      var template = this.templateDeletingDatasetsProgressBar();
+      var template = this.templateDeletingItemsProgressBar();
       this.modal = Galaxy.modal;
       this.modal.show({
           closing_events  : true,
-          title           : 'Deleting selected datasets',
+          title           : 'Deleting selected items',
           body            : template({}),
           buttons         : {
               'Close'     : function() {Galaxy.modal.hide();}
@@ -949,7 +978,7 @@ var FolderToolbarView = Backbone.View.extend({
       var dataset_ids = [];
       var folder_ids = [];
       checkedValues.each(function(){
-          if ($(this.parentElement.parentElement).data('id') !== '') {
+          if ($(this.parentElement.parentElement).data('id') !== undefined) {
               if ($(this.parentElement.parentElement).data('id').substring(0,1) == 'F'){
                 folder_ids.push($(this.parentElement.parentElement).data('id'));
               } else {
@@ -972,7 +1001,6 @@ var FolderToolbarView = Backbone.View.extend({
           var folder = new mod_library_model.FolderAsModel({id:folder_ids[i]});
           items_to_delete.push(folder);
       }
-      console.log(items_to_delete);
 
       this.options.chain_call_control.total_number = items_total.length;
       // call the recursive function to call ajax one after each other (request FIFO queue)
@@ -1010,7 +1038,7 @@ var FolderToolbarView = Backbone.View.extend({
     this.modal = Galaxy.modal;
     this.modal.show({
         closing_events  : true,
-        title           : 'Location Information',
+        title           : 'Location Details',
         body            : template({library: library, options: that.options}),
         buttons         : {
             'Close'     : function() {Galaxy.modal.hide();}
@@ -1051,77 +1079,88 @@ var FolderToolbarView = Backbone.View.extend({
   },
 
   templateToolBar: function(){
-    tmpl_array = [];
-
-    // CONTAINER START
-    tmpl_array.push('<div class="library_style_container">');
-    // TOOLBAR START
-    tmpl_array.push(' <div id="library_toolbar">');
-    tmpl_array.push('<form class="form-inline" role="form">');
-    tmpl_array.push('   <span><strong>DATA LIBRARIES</strong></span>');
-    tmpl_array.push('          <span id="folder_paginator" class="library-paginator">');
+    return _.template([
+    // container start
+    '<div class="library_style_container">',
+      // toolbar start
+      '<div id="library_toolbar">',
+        '<form class="form-inline" role="form">',
+          '<span><strong>DATA LIBRARIES</strong></span>',
+          // paginator will append here
+          '<span class="library-paginator folder-paginator"></span>',
+          '<div class="checkbox toolbar-item logged-dataset-manipulation" style="height: 20px; display:none;">',
+            '<label>',
+              '<input id="include_deleted_datasets_chk" type="checkbox">include deleted</input>',
+            '</label>',
+          '</div>',
+          '<button style="display:none;" data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button add-library-items toolbar-item" type="button">',
+            '<span class="fa fa-plus"></span><span class="fa fa-folder"></span>',
+          '</button>',
+          '<% if(mutiple_add_dataset_options) { %>',
+          '<div class="btn-group add-library-items" style="display:none;">',
+            '<button title="Add Datasets to Current Folder" id="" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">',
+              '<span class="fa fa-plus"></span><span class="fa fa-file"></span><span class="caret"></span>',
+            '</button>',
+            '<ul class="dropdown-menu" role="menu">',
+              '<li><a href="#folders/<%= id %>/import/history"> from History</a></li>',
+              '<% if(Galaxy.config.user_library_import_dir !== null) { %>',
+                '<li><a href="#folders/<%= id %>/import/userdir"> from User Directory</a></li>',
+              '<% } %>',
+              '<% if(Galaxy.config.allow_library_path_paste) { %>',
+                '<li class="divider"></li>',
+                '<li class="dropdown-header">Admins only</li>',
+                '<% if(Galaxy.config.library_import_dir !== null) { %>',
+                  '<li><a href="#folders/<%= id %>/import/importdir">from Import Directory</a></li>',
+                '<% } %>',
+                '<% if(Galaxy.config.allow_library_path_paste) { %>',
+                  '<li><a href="#folders/<%= id %>/import/path">from Path</a></li>',
+                '<% } %>',
+              '<% } %>',
+            '</ul>',
+          '</div>',
+          '<% } else { %>',
+            '<a  data-placement="top" title="Add Datasets to Current Folder" style="display:none;" class="btn btn-default add-library-items" href="#folders/<%= id %>/import/history" role="button">',
+              '<span class="fa fa-plus"></span><span class="fa fa-file"></span>',
+            '</a>',
+          '<% } %>',
+          '<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>',
+            '&nbsp;to History',
+          '</button>',
+          '<div class="btn-group dataset-manipulation" style="margin-left: 0.5em; display:none; ">',
+            '<button title="Download selected items as archive" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">',
+              '<span class="fa fa-download"></span> Download <span class="caret"></span>',
+            '</button>',
+            '<ul class="dropdown-menu" role="menu">',
+              '<li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>',
+              '<li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>',
+              '<li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>',
+            '</ul>',
+          '</div>',
+            '<button data-toggle="tooltip" data-placement="top" title="Mark selected items deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button">',
+            '<span class="fa fa-times"></span> Delete</button>',
+            '<button data-id="<%- id %>" data-toggle="tooltip" data-placement="top" title="Show location details" class="primary-button toolbtn-show-locinfo" style="margin-left: 0.5em;" type="button">',
+              '<span class="fa fa-info-circle"></span>',
+              '&nbsp;Details',
+            '</button>',
+            '<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>',
+                  '&nbsp;Help',
+                '</button>',
+              '</a>',
+            '</span>',
+          '</div>',
+        '</form>',
+      // toolbar end
+      '<div id="folder_items_element">',
+      '</div>',
+    // container end
+    '</div>',
     // paginator will append here
-    tmpl_array.push('          </span>');
-    tmpl_array.push('<div class="checkbox toolbar-item logged-dataset-manipulation" style="height: 20px; display:none;">');
-    tmpl_array.push('<label>');
-    tmpl_array.push('<input id="include_deleted_datasets_chk" type="checkbox"> include deleted </input>');
-    tmpl_array.push('</label>');
-    tmpl_array.push('</div>');
-    tmpl_array.push('   <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button add-library-items" type="button"><span class="fa fa-plus"></span> <span class="fa fa-folder"></span></button>');
-
-    tmpl_array.push('<% if(mutiple_add_dataset_options) { %>');
-    tmpl_array.push('   <div class="btn-group add-library-items" style="display:none;">');
-    tmpl_array.push('     <button title="Add Datasets to Current Folder" id="" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');
-    tmpl_array.push('     <span class="fa fa-plus"></span> <span class="fa fa-file"></span> <span class="caret"></span>');
-    tmpl_array.push('     </button>');
-    tmpl_array.push('     <ul class="dropdown-menu" role="menu">');
-    tmpl_array.push('        <li><a href="#folders/<%= id %>/import/history"> from History</a></li>');
-    tmpl_array.push('<% if(Galaxy.config.user_library_import_dir !== null) { %>');
-    tmpl_array.push('        <li><a href="#folders/<%= id %>/import/userdir"> from User Directory</a></li>');
-    tmpl_array.push('<% } %>');
-    tmpl_array.push('<% if(Galaxy.config.allow_library_path_paste) { %>');
-
-    tmpl_array.push('   <li class="divider"></li>');
-    tmpl_array.push('   <li class="dropdown-header">Admins only</li>');
-
-    tmpl_array.push('<% if(Galaxy.config.library_import_dir !== null) { %>');
-    tmpl_array.push('   <li><a href="#folders/<%= id %>/import/importdir">from Import Directory</a></li>');
-    tmpl_array.push('<% } %>');
-
-    tmpl_array.push('<% if(Galaxy.config.allow_library_path_paste) { %>');
-    tmpl_array.push('        <li><a href="#folders/<%= id %>/import/path">from Path</a></li>');
-    tmpl_array.push('<% } %>');
-    tmpl_array.push('<% } %>');
-    tmpl_array.push('     </ul>');
-    tmpl_array.push('   </div>');
-    tmpl_array.push('<% } else { %>');
-    tmpl_array.push(' <a  data-placement="top" title="Add Datasets to Current Folder" style="display:none;" class="btn btn-default add-library-items" href="#folders/<%= id %>/import/history" role="button"><span class="fa fa-plus"></span> <span class="fa fa-file"></span></span></a>');
-    tmpl_array.push('<% } %>');
-
-    tmpl_array.push('  <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to History</button>');
-    tmpl_array.push('   <div id="toolbtn_dl" class="btn-group dataset-manipulation" style="margin-left: 0.5em; display:none; ">');
-    tmpl_array.push('     <button title="Download selected datasets as archive" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');
-    tmpl_array.push('     <span class="fa fa-download"></span> Download <span class="caret"></span>');
-    tmpl_array.push('     </button>');
-    tmpl_array.push('     <ul class="dropdown-menu" role="menu">');
-    tmpl_array.push('        <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');
-    tmpl_array.push('        <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');
-    tmpl_array.push('        <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');
-    tmpl_array.push('     </ul>');
-    tmpl_array.push('   </div>');
-    tmpl_array.push('   <button data-toggle="tooltip" data-placement="top" title="Mark selected items deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button"><span class="fa fa-times"></span> Delete</button>');
-    tmpl_array.push('   <button data-id="<%- id %>" data-toggle="tooltip" data-placement="top" title="Show location information" class="primary-button toolbtn-show-locinfo" style="margin-left: 0.5em;" type="button"><span class="fa fa-info-circle"></span> Location Info</button>');
-    tmpl_array.push('   <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/FolderContents" target="_blank"><button class="primary-button" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>');
-    tmpl_array.push(' </div>');
-    tmpl_array.push('</form>');
-
-    // TOOLBAR END
-    tmpl_array.push(' <div id="folder_items_element">');
-    tmpl_array.push(' </div>');
-    tmpl_array.push('</div>');
-    // CONTAINER END
-
-    return _.template(tmpl_array.join(''));
+    '<div class="folder-paginator paginator-bottom"></div>'
+    ].join(''));
   },
 
   templateLocInfoInModal: function(){
@@ -1188,220 +1227,208 @@ var FolderToolbarView = Backbone.View.extend({
   },
 
   templateNewFolderInModal: function(){
-    tmpl_array = [];
-
-    tmpl_array.push('<div id="new_folder_modal">');
-    tmpl_array.push('<form>');
-    tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');
-    tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');
-    tmpl_array.push('</form>');
-    tmpl_array.push('</div>');
-
-    return _.template(tmpl_array.join(''));
+    return _.template([
+    '<div id="new_folder_modal">',
+      '<form>',
+        '<input type="text" name="Name" value="" placeholder="Name" autofocus>',
+        '<input type="text" name="Description" value="" placeholder="Description">',
+      '</form>',
+    '</div>'
+    ].join(''));
   },
 
 
   templateBulkImportInModal : function(){
-    var tmpl_array = [];
-
-    tmpl_array.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');
-    tmpl_array.push('Select history: ');
-    tmpl_array.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');
-    tmpl_array.push('   <% _.each(histories, function(history) { %>'); //history select box
-    tmpl_array.push('       <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');
-    tmpl_array.push('   <% }); %>');
-    tmpl_array.push('</select>');
-    tmpl_array.push('</span>');
-
-    return _.template(tmpl_array.join(''));
+    return _.template([
+    '<div>',
+      '<div class="library-modal-item">',
+        'Select history: ',
+        '<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; " autofocus>',
+          '<% _.each(histories, function(history) { %>',
+            '<option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>',
+          '<% }); %>',
+        '</select>',
+      '</div>',
+      '<div class="library-modal-item">',
+        'or create new: ',
+        '<input type="text" name="history_name" value="" placeholder="name of the new history" style="width:50%;">',
+        '</input>',
+      '</div>',
+    '</div>'
+    ].join(''));
   },
 
   templateImportIntoHistoryProgressBar : function (){
-    var tmpl_array = [];
-
-    tmpl_array.push('<div class="import_text">');
-    tmpl_array.push('Importing selected datasets to history <b><%= _.escape(history_name) %></b>');
-    tmpl_array.push('</div>');
-    tmpl_array.push('<div class="progress">');
-    tmpl_array.push('   <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');
-    tmpl_array.push('       <span class="completion_span">0% Complete</span>');
-    tmpl_array.push('   </div>');
-    tmpl_array.push('</div>');
-    tmpl_array.push('');
-
-    return _.template(tmpl_array.join(''));
+    return _.template([
+    '<div class="import_text">',
+      'Importing selected items to history <b><%= _.escape(history_name) %></b>',
+    '</div>',
+    '<div class="progress">',
+      '<div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">',
+        '<span class="completion_span">0% Complete</span>',
+      '</div>',
+    '</div>'
+    ].join(''));
   },
 
   templateAddingDatasetsProgressBar: function (){
-    var tmpl_array = [];
-
-    tmpl_array.push('<div class="import_text">');
-    tmpl_array.push('Adding selected datasets to library folder <b><%= _.escape(folder_name) %></b>');
-    tmpl_array.push('</div>');
-    tmpl_array.push('<div class="progress">');
-    tmpl_array.push('   <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');
-    tmpl_array.push('       <span class="completion_span">0% Complete</span>');
-    tmpl_array.push('   </div>');
-    tmpl_array.push('</div>');
-    tmpl_array.push('');
-
-    return _.template(tmpl_array.join(''));
+    return _.template([
+    '<div class="import_text">',
+      'Adding selected datasets to library folder <b><%= _.escape(folder_name) %></b>',
+    '</div>',
+    '<div class="progress">',
+      '<div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">',
+        '<span class="completion_span">0% Complete</span>',
+      '</div>',
+    '</div>'
+    ].join(''));
   },
 
-  templateDeletingDatasetsProgressBar: function (){
-    var tmpl_array = [];
-
-    tmpl_array.push('<div class="import_text">');
-    tmpl_array.push('</div>');
-    tmpl_array.push('<div class="progress">');
-    tmpl_array.push('   <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');
-    tmpl_array.push('       <span class="completion_span">0% Complete</span>');
-    tmpl_array.push('   </div>');
-    tmpl_array.push('</div>');
-    tmpl_array.push('');
-
-    return _.template(tmpl_array.join(''));
+  templateDeletingItemsProgressBar: function (){
+    return _.template([
+    '<div class="import_text">',
+    '</div>',
+    '<div class="progress">',
+      '<div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">',
+        '<span class="completion_span">0% Complete</span>',
+      '</div>',
+    '</div>'
+    ].join(''));
   },
 
   templateBrowserModal: function(){
-    var tmpl_array = [];
-
-    tmpl_array.push('<div id="file_browser_modal">');
-    tmpl_array.push('<div class="alert alert-info jstree-files-message">All files you select will be imported into the current folder.</div>');
-    tmpl_array.push('<div class="alert alert-info jstree-folders-message" style="display:none;">All files within the selected folders and their subfolders will be imported into the current folder.</div>');
-
-
-    tmpl_array.push('<div style="margin-bottom:1em;">');
-    tmpl_array.push('<label class="radio-inline">');
-    tmpl_array.push('  <input title="Switch to selecting files" type="radio" name="jstree-radio" value="jstree-disable-folders" checked="checked"> Files');
-    tmpl_array.push('</label>');
-    tmpl_array.push('<label class="radio-inline">');
-    tmpl_array.push('  <input title="Switch to selecting folders" type="radio" name="jstree-radio" value="jstree-disable-files"> Folders');
-    tmpl_array.push('</label>');
-    tmpl_array.push('</div>');
-    tmpl_array.push('<div style="margin-bottom:1em;">');
-    tmpl_array.push('<label class="checkbox-inline jstree-preserve-structure" style="display:none;">');
-    tmpl_array.push('   <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');
-    tmpl_array.push('Preserve directory structure');
-    tmpl_array.push(' </label>');
-    tmpl_array.push('<label class="checkbox-inline jstree-link-files" style="display:none;">');
-    tmpl_array.push('   <input class="link-checkbox" type="checkbox" value="link_files">');
-    tmpl_array.push('Link files instead of copying');
-    tmpl_array.push(' </label>');
-    tmpl_array.push('</div>');
-    tmpl_array.push('<div id="jstree_browser">');
-    tmpl_array.push('</div>');
-
-    tmpl_array.push('<hr />');
-    tmpl_array.push('<p>You can set extension type and genome for all imported datasets at once:</p>');
-    tmpl_array.push('<div>');
-    tmpl_array.push('Type: <span id="library_extension_select" class="library-extension-select" />');
-    tmpl_array.push('  Genome: <span id="library_genome_select" class="library-genome-select" />');
-    tmpl_array.push('</div>');
-    tmpl_array.push('</div>');
-
-    return _.template(tmpl_array.join(''));
+    return _.template([
+    '<div id="file_browser_modal">',
+      '<div class="alert alert-info jstree-files-message">All files you select will be imported into the current folder ignoring their folder structure.</div>',
+      '<div class="alert alert-info jstree-folders-message" style="display:none;">All files within the selected folders and their subfolders will be imported into the current folder.</div>',
+      '<div style="margin-bottom:1em;">',
+        '<label title="Switch to selecting files" class="radio-inline import-type-switch">',
+          '<input type="radio" name="jstree-radio" value="jstree-disable-folders" checked="checked"> Choose Files',
+        '</label>',
+        '<label title="Switch to selecting folders" class="radio-inline import-type-switch">',
+        '<input type="radio" name="jstree-radio" value="jstree-disable-files"> Choose Folders',
+        '</label>',
+      '</div>',
+      '<div style="margin-bottom:1em;">',
+        '<label class="checkbox-inline jstree-preserve-structure" style="display:none;">',
+          '<input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">',
+          'Preserve directory structure',
+        '</label>',
+        '<label class="checkbox-inline jstree-link-files" style="display:none;">',
+          '<input class="link-checkbox" type="checkbox" value="link_files">',
+          'Link files instead of copying',
+        '</label>',
+      '</div>',
+      '<button title="Select all files" type="button" class="button primary-button libimport-select-all">',
+        'Select all',
+      '</button>',
+      '<button title="Select no files" type="button" class="button primary-button libimport-select-none">',
+        'Select none',
+      '</button>',
+      '<hr />',
+      // append jstree object here
+      '<div id="jstree_browser">',
+      '</div>',
+      '<hr />',
+      '<p>You can set extension type and genome for all imported datasets at once:</p>',
+      '<div>',
+        'Type: <span id="library_extension_select" class="library-extension-select" />',
+        'Genome: <span id="library_genome_select" class="library-genome-select" />',
+        '</div>',
+    '</div>'
+    ].join(''));
   },
 
   templateImportPathModal: function(){
-    var tmpl_array = [];
-
-    tmpl_array.push('<div id="file_browser_modal">');
-    tmpl_array.push('<div class="alert alert-info jstree-folders-message">All files within the given folders and their subfolders will be imported into the current folder.</div>');
-
-    tmpl_array.push('<div style="margin-bottom: 0.5em;">');
-    tmpl_array.push('<label class="checkbox-inline jstree-preserve-structure">');
-    tmpl_array.push('   <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');
-    tmpl_array.push('Preserve directory structure');
-    tmpl_array.push(' </label>');
-    tmpl_array.push('<label class="checkbox-inline jstree-link-files">');
-    tmpl_array.push('   <input class="link-checkbox" type="checkbox" value="link_files">');
-    tmpl_array.push('Link files instead of copying');
-    tmpl_array.push(' </label>');
-    tmpl_array.push('</div>');
-
-    tmpl_array.push('<textarea id="import_paths" class="form-control" rows="5" placeholder="Absolute paths (or paths relative to Galaxy root) separated by newline"></textarea>');
-
-    tmpl_array.push('<hr />');
-    tmpl_array.push('<p>You can set extension type and genome for all imported datasets at once:</p>');
-    tmpl_array.push('<div>');
-    tmpl_array.push('Type: <span id="library_extension_select" class="library-extension-select" />');
-    tmpl_array.push('  Genome: <span id="library_genome_select" class="library-genome-select" />');
-    tmpl_array.push('</div>');
-
-    tmpl_array.push('</div>');
-
-    return _.template(tmpl_array.join(''));
+    return _.template([
+    '<div id="file_browser_modal">',
+      '<div class="alert alert-info jstree-folders-message">All files within the given folders and their subfolders will be imported into the current folder.</div>',
+      '<div style="margin-bottom: 0.5em;">',
+        '<label class="checkbox-inline jstree-preserve-structure">',
+          '<input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">',
+          'Preserve directory structure',
+        '</label>',
+        '<label class="checkbox-inline jstree-link-files">',
+          '<input class="link-checkbox" type="checkbox" value="link_files">',
+          'Link files instead of copying',
+        '</label>',
+      '</div>',
+      '<textarea id="import_paths" class="form-control" rows="5" placeholder="Absolute paths (or paths relative to Galaxy root) separated by newline" autofocus></textarea>',
+      '<hr />',
+      '<p>You can set extension type and genome for all imported datasets at once:</p>',
+      '<div>',
+        'Type: <span id="library_extension_select" class="library-extension-select" />',
+        'Genome: <span id="library_genome_select" class="library-genome-select" />',
+      '</div>',
+    '</div>'
+    ].join(''));
   },
 
   templateAddFilesFromHistory: function (){
-    var tmpl_array = [];
-
-    tmpl_array.push('<div id="add_files_modal">');
-    tmpl_array.push('<div id="history_modal_combo_bulk">');
-    tmpl_array.push('Select history:  ');
-    tmpl_array.push('<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> ');
-    tmpl_array.push('   <% _.each(histories, function(history) { %>'); //history select box
-    tmpl_array.push('       <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');
-    tmpl_array.push('   <% }); %>');
-    tmpl_array.push('</select>');
-    tmpl_array.push('</div>');
-    tmpl_array.push('<br/>');
-    tmpl_array.push('<div id="selected_history_content">');
-
-    tmpl_array.push('</div>');
-    tmpl_array.push('</div>');
-
-    return _.template(tmpl_array.join(''));
+    return _.template([
+    '<div id="add_files_modal">',
+      '<div>',
+        'Select history:  ',
+        '<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> ',
+          '<% _.each(histories, function(history) { %>', //history select box
+            '<option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>',
+          '<% }); %>',
+        '</select>',
+      '</div>',
+      '<br/>',
+      '<div id="selected_history_content">',
+      '</div>',
+    '</div>'
+    ].join(''));
   },
 
   templateHistoryContents: function (){
-    var tmpl_array = [];
-
-    tmpl_array.push('<strong>Choose the datasets to import:</strong>');
-    tmpl_array.push('<ul>');
-    tmpl_array.push(' <% _.each(history_contents, function(history_item) { %>');
-    tmpl_array.push(' <li data-id="<%= _.escape(history_item.get("id")) %>">');
-    tmpl_array.push('   <input style="margin: 0;" type="checkbox"> <%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>');
-    tmpl_array.push(' </li>');
-    tmpl_array.push(' <% }); %>');
-    tmpl_array.push('</ul>');
-
-    return _.template(tmpl_array.join(''));
+    return _.template([
+    '<strong>Choose the datasets to import:</strong>',
+    '<ul>',
+      '<% _.each(history_contents, function(history_item) { %>',
+        '<li data-id="<%= _.escape(history_item.get("id")) %>">',
+          '<input style="margin: 0;" type="checkbox"> <%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>',
+        '</li>',
+      '<% }); %>',
+    '</ul>'
+    ].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(''));
+    return _.template([
+    '<ul class="pagination pagination-sm">',
+      '<% if ( ( show_page - 1 ) > 0 ) { %>',
+        '<% if ( ( show_page - 1 ) > page_count ) { %>', // we are on higher page than total page count
+          '<li><a href="#folders/<%= id %>/page/1"><span class="fa fa-angle-double-left"></span></a></li>',
+          '<li class="disabled"><a href="#folders/<%= id %>/page/<% print( show_page ) %>"><% print( show_page - 1 ) %></a></li>',
+        '<% } else { %>',
+          '<li><a href="#folders/<%= id %>/page/1"><span class="fa fa-angle-double-left"></span></a></li>',
+          '<li><a href="#folders/<%= id %>/page/<% print( show_page - 1 ) %>"><% print( show_page - 1 ) %></a></li>',
+        '<% } %>',
+      '<% } else { %>', // we are on the first page
+        '<li class="disabled"><a href="#folders/<%= id %>/page/1"><span class="fa fa-angle-double-left"></span></a></li>',
+        '<li class="disabled"><a href="#folders/<%= id %>/page/<% print( show_page ) %>"><% print( show_page - 1 ) %></a></li>',
+      '<% } %>',
+      '<li class="active">',
+        '<a href="#folders/<%= id %>/page/<% print( show_page ) %>"><% print( show_page ) %></a>',
+      '</li>',
+      '<% if ( ( show_page ) < page_count ) { %>',
+        '<li><a href="#folders/<%= id %>/page/<% print( show_page + 1 ) %>"><% print( show_page + 1 ) %></a></li>',
+        '<li><a href="#folders/<%= id %>/page/<% print( page_count ) %>"><span class="fa fa-angle-double-right"></span></a></li>',
+      '<% } else { %>',
+        '<li class="disabled"><a href="#folders/<%= id %>/page/<% print( show_page  ) %>"><% print( show_page + 1 ) %></a></li>',
+        '<li class="disabled"><a href="#folders/<%= id %>/page/<% print( page_count ) %>"><span class="fa fa-angle-double-right"></span></a></li>',
+      '<% } %>',
+    '</ul>',
+    '<span>',
+      '&nbsp;showing&nbsp;',
+      '<a data-toggle="tooltip" data-placement="top" title="Click to change the number of items on page" class="page_size_prompt">',
+        '<%- items_shown %>',
+      '</a>',
+      '&nbsp;of <%- total_items_count %> items',
+    '</span>'
+    ].join(''));
   },
 
 });

client/galaxy/scripts/mvc/library/library-library-view.js

@@ -242,95 +242,105 @@ var LibraryView = Backbone.View.extend({
   },
 
   templateLibrary : function(){
-    var tmpl_array = [];
-    // CONTAINER START
-    tmpl_array.push('<div class="library_style_container">');
-
-    tmpl_array.push('  <div id="library_toolbar">');
-    tmpl_array.push('   <button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-default toolbtn_modify_dataset primary-button" type="button"><span class="fa fa-pencil"></span> Modify</span></button>');
-    tmpl_array.push('   <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>');
-    tmpl_array.push('   <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>');
-    tmpl_array.push('  </div>');
-
-    // tmpl_array.push('<% if (item.get("is_unrestricted")) { %>');
-    tmpl_array.push('  <p>');
-    tmpl_array.push('  This dataset is unrestricted so everybody can access it. Just share the URL of this page. ');
-    tmpl_array.push('  <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"></span> To Clipboard</span></button> ');
-    tmpl_array.push('  </p>');
-    // tmpl_array.push('<% } %>');
-
-    tmpl_array.push('<div class="dataset_table">');
-
-    tmpl_array.push('   <table class="grid table table-striped table-condensed">');
-    tmpl_array.push('       <tr>');
-    tmpl_array.push('           <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');
-    tmpl_array.push('           <td><%= _.escape(item.get("name")) %></td>');
-    tmpl_array.push('       </tr>');
-
-    tmpl_array.push('   <% if (item.get("file_ext")) { %>');
-    tmpl_array.push('       <tr>');
-    tmpl_array.push('           <th scope="row">Data type</th>');
-    tmpl_array.push('           <td><%= _.escape(item.get("file_ext")) %></td>');
-    tmpl_array.push('       </tr>');
-    tmpl_array.push('   <% } %>');
-
-    tmpl_array.push('    </table>');
-    tmpl_array.push('</div>');
-
-    // CONTAINER END
-    tmpl_array.push('</div>');
-
-    return _.template(tmpl_array.join(''));
+    return _.template([
+    '<div class="library_style_container">',
+      '<div id="library_toolbar">',
+        '<button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-default toolbtn_modify_dataset primary-button" type="button">',
+          '<span class="fa fa-pencil"/>',
+          '&nbsp;Modify',
+        '</button>',
+        '<a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions">',
+          '<button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button">',
+            '<span class="fa fa-group"/>',
+            '&nbsp;Permissions',
+          '</button>',
+        '</a>',
+        '<button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button">',
+          '<span class="fa fa-share"/>',
+          '&nbsp;Share',
+        '</button>',
+      '</div>',
+      '<p>',
+        'This dataset is unrestricted so everybody can access it. Just share the URL of this page. ',
+        '<button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button">',
+          '<span class="fa fa-clipboard"/>',
+          '&nbsp;To Clipboard',
+        '</button> ',
+      '</p>',
+      '<div class="dataset_table">',
+        '<table class="grid table table-striped table-condensed">',
+          '<tr>',
+            '<th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">',
+              'Name',
+            '</th>',
+            '<td>',
+              '<%= _.escape(item.get("name")) %>',
+            '</td>',
+          '</tr>',
+          '<% if (item.get("file_ext")) { %>',
+            '<tr>',
+              '<th scope="row">Data type</th>',
+              '<td>',
+                '<%= _.escape(item.get("file_ext")) %>',
+              '</td>',
+            '</tr>',
+          '<% } %>',
+        '</table>',
+      '</div>',
+    '</div>',
+    ].join(''));
   },
 
   templateLibraryPermissions : function(){
-    var tmpl_array = [];
-    // CONTAINER START
-    tmpl_array.push('<div class="library_style_container">');
-
-
-    tmpl_array.push('  <div id="library_toolbar">');
-    tmpl_array.push('   <a href="#"><button data-toggle="tooltip" data-placement="top" title="Go back to the list of Libraries" class="btn btn-default primary-button" type="button"><span class="fa fa-list"></span> Libraries</span></button></a>');
-    tmpl_array.push('  </div>');
-
-    tmpl_array.push('<h1>Library: <%= _.escape(library.get("name")) %></h1>');
-
-    tmpl_array.push('<div class="alert alert-warning">');
-    tmpl_array.push('<% if (is_admin) { %>');
-    tmpl_array.push('You are logged in as an <strong>administrator</strong> therefore you can manage any library on this Galaxy instance. Please make sure you understand the consequences.');
-    tmpl_array.push('<% } else { %>');
-    tmpl_array.push('You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.');
-    tmpl_array.push('<% }%>');
-    tmpl_array.push('</div>');
-
-    tmpl_array.push('<div class="dataset_table">');
-
-    tmpl_array.push('<h2>Library permissions</h2>');
-
-    tmpl_array.push('<h4>Roles that can access the library</h4>');
-    tmpl_array.push('<div id="access_perm" class="access_perm roles-selection"></div>');
-    tmpl_array.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can access this library. If there are no access roles set on the library it is considered <strong>unrestricted</strong>.</div>');
-
-    tmpl_array.push('<h4>Roles that can manage permissions on this library</h4>');
-    tmpl_array.push('<div id="manage_perm" class="manage_perm roles-selection"></div>');
-    tmpl_array.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can manage permissions on this library (includes giving access).</div>');
-
-    tmpl_array.push('<h4>Roles that can add items to this library</h4>');
-    tmpl_array.push('<div id="add_perm" class="add_perm roles-selection"></div>');
-    tmpl_array.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can add items to this library (folders and datasets).</div>');
-
-    tmpl_array.push('<h4>Roles that can modify this library</h4>');
-    tmpl_array.push('<div id="modify_perm" class="modify_perm roles-selection"></div>');
-    tmpl_array.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify this library (name, synopsis, etc.).</div>');
-
-    tmpl_array.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications made on this page" class="btn btn-default toolbtn_save_permissions primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');
-
-    tmpl_array.push('</div>');
-
-    // CONTAINER END
-    tmpl_array.push('</div>');
-
-    return _.template(tmpl_array.join(''));
+    return _.template([
+    '<div class="library_style_container">',
+      '<div id="library_toolbar">',
+        '<a href="#">',
+          '<button data-toggle="tooltip" data-placement="top" title="Go back to the list of Libraries" class="btn btn-default primary-button" type="button">',
+            '<span class="fa fa-list"/>',
+            '&nbsp;Libraries',
+          '</button>',
+        '</a>',
+      '</div>',
+      '<h1>',
+        'Library: <%= _.escape(library.get("name")) %>',
+      '</h1>',
+      '<div class="alert alert-warning">',
+        '<% if (is_admin) { %>',
+          'You are logged in as an <strong>administrator</strong> therefore you can manage any library on this Galaxy instance. Please make sure you understand the consequences.',
+        '<% } else { %>',
+          'You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.',
+        '<% }%>',
+      '</div>',
+      '<div class="dataset_table">',
+        '<h2>Library permissions</h2>',
+        '<h4>Roles that can access the library</h4>',
+        '<div id="access_perm" class="access_perm roles-selection"/>',
+        '<div class="alert alert-info roles-selection">',
+          'User with <strong>any</strong> of these roles can access this library. If there are no access roles set on the library it is considered <strong>unrestricted</strong>.',
+        '</div>',
+        '<h4>Roles that can manage permissions on this library</h4>',
+        '<div id="manage_perm" class="manage_perm roles-selection"/>',
+        '<div class="alert alert-info roles-selection">',
+          'User with <strong>any</strong> of these roles can manage permissions on this library (includes giving access).',
+        '</div>',
+        '<h4>Roles that can add items to this library</h4>',
+        '<div id="add_perm" class="add_perm roles-selection"/>',
+        '<div class="alert alert-info roles-selection">',
+          'User with <strong>any</strong> of these roles can add items to this library (folders and datasets).',
+        '</div>',
+        '<h4>Roles that can modify this library</h4>',
+        '<div id="modify_perm" class="modify_perm roles-selection"/>',
+        '<div class="alert alert-info roles-selection">',
+          'User with <strong>any</strong> of these roles can modify this library (name, synopsis, etc.).',
+        '</div>',
+        '<button data-toggle="tooltip" data-placement="top" title="Save modifications made on this page" class="btn btn-default toolbtn_save_permissions primary-button" type="button">',
+          '<span class="fa fa-floppy-o"/>',
+          '&nbsp;Save',
+        '</button>',
+      '</div>',
+    '</div>',
+    ].join(''));
   }
 
 });

client/galaxy/scripts/mvc/library/library-librarylist-view.js

@@ -25,7 +25,8 @@ var LibraryListView = Backbone.View.extend({
 
     defaults: {
         page_count: null,
-        show_page: null
+        show_page: null,
+        all_fetched: false
     },
 
     /**
@@ -39,6 +40,7 @@ var LibraryListView = Backbone.View.extend({
         this.modal = null;
         // collection of {Item}s
         this.collection = new mod_library_model.Libraries();
+        this.collection.url = this.collection.urlRoot + '?deleted=false';
         this.collection.fetch({
           success: function(){
             that.render();
@@ -119,6 +121,29 @@ var LibraryListView = Backbone.View.extend({
         $( "#center" ).css( 'overflow','auto' );
     },
 
+    fetchDeleted: function(){
+      if (this.options.all_fetched){
+        this.render();
+      } else{
+        var that = this;
+        this.collection.url = this.collection.urlRoot + '?deleted=true';
+        this.collection.fetch({
+          remove: false,
+          success: function(){
+            that.options.all_fetched = true;
+            that.render();
+          },
+          error: function( model, response ){
+              if ( typeof response.responseJSON !== "undefined" ){
+                mod_toastr.error( response.responseJSON.err_msg );
+              } else {
+                mod_toastr.error( 'An error ocurred.' );
+              }
+          }
+        });
+      }
+    },
+
     /**
      * Render all given models as rows in the library list
      * @param  {array} libraries_to_render array of library models to render
@@ -197,32 +222,41 @@ var LibraryListView = Backbone.View.extend({
 // MMMMMMMMMMMMMMMMMM
 
     templateLibraryList: function(){
-        tmpl_array = [];
-
-        tmpl_array.push('<div class="library_container table-responsive">');
-        tmpl_array.push('<% if(length === 0) { %>');
-        tmpl_array.push('<% if(search_term.length > 0) { %>');
-        tmpl_array.push('<div>There are no libraries matching your search. Try different keyword.</div>');
-        tmpl_array.push('<% } else{ %>');
-        tmpl_array.push('<div>There are no libraries visible to you here. If you expected some 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>');
-        tmpl_array.push('<% }%>');
-        tmpl_array.push('<% } else{ %>');
-        tmpl_array.push('<table class="grid table table-condensed">');
-        tmpl_array.push('   <thead>');
-        tmpl_array.push('     <th style="width:30%;"><a class="sort-libraries-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:22%;">description</th>');
-        tmpl_array.push('     <th style="width:22%;">synopsis</th> ');
-        tmpl_array.push('     <th style="width:26%;"></th>');
-        tmpl_array.push('   </thead>');
-        tmpl_array.push('   <tbody id="library_list_body">');
-        // library item views will attach here
-        tmpl_array.push('   </tbody>');
-        tmpl_array.push('</table>');
-        tmpl_array.push('<% }%>');
-        tmpl_array.push('</div>');
-
-        return _.template(tmpl_array.join(''));
-    },
+      return _.template([
+      '<div class="library_container table-responsive">',
+        '<% if(length === 0) { %>',
+          '<% if(search_term.length > 0) { %>',
+            '<div>',
+              'There are no libraries matching your search. Try different keyword.',
+            '</div>',
+          '<% } else{ %>',
+            '<div>',
+              'There are no libraries visible to you here. If you expected some 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>',
+          '<% }%>',
+        '<% } else{ %>',
+          '<table class="grid table table-condensed">',
+            '<thead>',
+              '<th style="width:30%;">',
+                '<a class="sort-libraries-link" title="Click to reverse order" href="#">',
+                  'name',
+                '</a>',
+                '<span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"/>',
+              '</th>',
+              '<th style="width:22%;">description</th>',
+              '<th style="width:22%;">synopsis</th> ',
+              '<th style="width:26%;"></th>',
+            '</thead>',
+            '<tbody id="library_list_body">',
+            // library item views will attach here
+            '</tbody>',
+          '</table>',
+        '<% }%>',
+      '</div>'
+      ].join(''));
+    }
 
 });
 

client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js

@@ -15,7 +15,7 @@ var LibraryToolbarView = Backbone.View.extend({
   },
 
   events: {
-    'click #create_new_library_btn' : 'showLibraryModal',
+    'click #create_new_library_btn' : 'createLibraryFromModal',
     'click #include_deleted_chk'    : 'includeDeletedChecked',
     'click #lib_page_size_prompt'   : 'showPageSizePrompt',
     'keyup .library-search-input'   : 'searchLibraries'
@@ -58,7 +58,7 @@ var LibraryToolbarView = Backbone.View.extend({
    * User clicked on 'New library' button. Show modal to
    * satisfy the wish.
    */
-  showLibraryModal : function (event){
+  createLibraryFromModal : function (event){
     event.preventDefault();
     event.stopPropagation();
     var self = this;
@@ -148,7 +148,7 @@ var LibraryToolbarView = Backbone.View.extend({
   includeDeletedChecked: function( event ){
     if (event.target.checked){
         Galaxy.libraries.preferences.set( { 'with_deleted': true } );
-        Galaxy.libraries.libraryListView.render();
+        Galaxy.libraries.libraryListView.fetchDeleted();
     } else{
         Galaxy.libraries.preferences.set( { 'with_deleted': false } );
         Galaxy.libraries.libraryListView.render();
@@ -182,7 +182,9 @@ var LibraryToolbarView = Backbone.View.extend({
               '<% if(admin_user === true) { %>',
                   '<div class="checkbox toolbar-item" style="height: 20px;">',
                     '<label>',
-                      '<input id="include_deleted_chk" type="checkbox"> include deleted </input>',
+                      '<input id="include_deleted_chk" type="checkbox">',
+                        '&nbsp;include deleted ',
+                      '</input>',
                     '</label>',
                   '</div>',
                   '<span class="toolbar-item" data-toggle="tooltip" data-placement="top" title="Create New Library">',
@@ -240,7 +242,7 @@ var LibraryToolbarView = Backbone.View.extend({
     return _.template([
       '<div id="new_library_modal">',
         '<form>',
-          '<input type="text" name="Name" value="" placeholder="Name">',
+          '<input type="text" name="Name" value="" placeholder="Name" autofocus>',
           '<input type="text" name="Description" value="" placeholder="Description">',
           '<input type="text" name="Synopsis" value="" placeholder="Synopsis">',
         '</form>',

client/galaxy/scripts/mvc/library/library-model.js

@@ -19,7 +19,7 @@ define([], function() {
     });
 
     var Libraries = Backbone.Collection.extend({
-      url: Galaxy.root + 'api/libraries',
+      urlRoot: Galaxy.root + 'api/libraries',
 
       model: Library,
 
@@ -182,7 +182,7 @@ define([], function() {
               var file_item = new Ldda(obj.folder_contents[i])
               this.get("folder").add(file_item);
             } else{
-              console.error('Unknown folder item type encountered while parsing response.');
+              Galaxy.emit.error('Unknown folder item type encountered while parsing response.');
             }
           };
         return obj;

client/galaxy/scripts/mvc/tool/tool-form-base.js

@@ -79,7 +79,12 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view',
                 url     : build_url,
                 data    : build_data,
                 success : function(new_model) {
-                    self._buildForm(new_model['tool_model'] || new_model);
+                    new_model = new_model.tool_model || new_model;
+                    if( !new_model.display ) {
+                        window.location = Galaxy.root;
+                        return;
+                    }
+                    self._buildForm(new_model);
                     !hide_message && self.message.update({
                         status      : 'success',
                         message     : 'Now you are using \'' + self.options.name + '\' version ' + self.options.version + ', id \'' + self.options.id + '\'.',
@@ -87,11 +92,12 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view',
                     });
                     Galaxy.emit.debug('tool-form-base::initialize()', 'Initial tool model ready.', new_model);
                     process.resolve();
-
                 },
-                error   : function(response) {
+                error   : function(response, xhr) {
                     var error_message = ( response && response.err_msg ) || 'Uncaught error.';
-                    if ( self.$el.is(':empty') ) {
+                    if ( xhr.status == 401 ) {
+                        window.location = Galaxy.root + 'user/login?' + $.param({ redirect : Galaxy.root + '?tool_id=' + self.options.id });
+                    } else if ( self.$el.is(':empty') ) {
                         self.$el.prepend((new Ui.Message({
                             message     : error_message,
                             status      : 'danger',

client/galaxy/scripts/mvc/tool/tool-form-workflow.js

@@ -98,7 +98,7 @@ define(['utils/utils', 'mvc/tool/tool-form-base'],
                     type        : 'boolean',
                     value       : String(Boolean(this.post_job_actions['EmailAction' + output_id])),
                     ignore      : 'false',
-                    help        : 'An email notification will be send when the job has completed.',
+                    help        : 'An email notification will be sent when the job has completed.',
                     payload     : {
                         'host'  : window.location.host
                     }

client/galaxy/scripts/mvc/ui/ui-select-content.js

@@ -0,0 +1,249 @@
+define([ 'utils/utils', 'mvc/ui/ui-misc', 'mvc/ui/ui-select-default' ], function( Utils, Ui, Select ) {
+
+/** List of available content selectors options */
+var Configurations = {
+    'data': [
+        { src: 'hda',  icon: 'fa-file-o',   tooltip: 'Single dataset',       batchmode: false, multiple: false },
+        { src: 'hda',  icon: 'fa-files-o',  tooltip: 'Multiple datasets',    batchmode: true,  multiple: true  },
+        { src: 'hdca', icon: 'fa-folder-o', tooltip: 'Dataset collection',   batchmode: true,  multiple: false } ],
+    'data_multiple': [
+        { src: 'hda',  icon: 'fa-files-o',  tooltip: 'Multiple datasets',    batchmode: false, multiple: true  },
+        { src: 'hdca', icon: 'fa-folder-o', tooltip: 'Dataset collection',   batchmode: false, multiple: false } ],
+    'data_collection': [
+        { src: 'hdca', icon: 'fa-folder-o', tooltip: 'Dataset collection',   batchmode: false, multiple: false } ],
+    'workflow_data': [
+        { src: 'hda',  icon: 'fa-file-o',   tooltip: 'Single dataset',       batchmode: false, multiple: false },
+        { src: 'hda',  icon: 'fa-files-o',  tooltip: 'Multiple datasets',    batchmode: true,  multiple: true  } ],
+    'workflow_collection': [
+        { src: 'hdca', icon: 'fa-folder-o', tooltip: 'Dataset collection',   batchmode: false, multiple: false },
+        { src: 'hdca', icon: 'fa-folder',   tooltip: 'Multiple collections', batchmode: true,  multiple: true } ]
+};
+
+/** View for hda and hdca content selector ui elements */
+var View = Backbone.View.extend({
+    initialize : function( options ) {
+        var self = this;
+        this.model = options && options.model || new Backbone.Model({
+            src_labels: { 'hda' : 'dataset', 'hdca': 'dataset collection' }
+        }).set( options );
+        this.setElement( $( '<div/>' ).addClass( 'ui-select-content' ) );
+        this.$batch = $( '<div/>' ).addClass( 'ui-form-info' )
+                        .append( $( '<i/>' ).addClass( 'fa fa-sitemap' ) )
+                        .append( $( '<span/>' ).html( 'This is a batch mode input field. A separate job will be triggered for each dataset.' ) );
+
+        // track current history elements
+        this.history = {};
+
+        // add listeners
+        this.listenTo( this.model, 'change:data', this._changeData, this );
+        this.listenTo( this.model, 'change:wait', this._changeWait, this );
+        this.listenTo( this.model, 'change:current', this._changeCurrent, this );
+        this.listenTo( this.model, 'change:value', this._changeValue, this );
+        this.listenTo( this.model, 'change:type change:optional change:multiple change:extensions', this._changeType, this );
+        this.render();
+
+        // add change event
+        this.on( 'change', function() { options.onchange && options.onchange( self.value() ) } );
+    },
+
+    render: function() {
+        this._changeType();
+        this._changeValue();
+        this._changeWait();
+    },
+
+    /** Indicate that select fields are being updated */
+    wait: function() {
+        this.model.set( 'wait', true );
+    },
+
+    /** Indicate that the options update has been completed */
+    unwait: function() {
+        this.model.set( 'wait', false );
+    },
+
+    /** Update data representing selectable options */
+    update: function( options ) {
+        this.model.set( 'data', options );
+    },
+
+    /** Return the currently selected dataset values */
+    value: function ( new_value ) {
+        new_value !== undefined && this.model.set( 'value', new_value );
+        var current = this.model.get( 'current' );
+        if ( this.config[ current ] ) {
+            var id_list = this.fields[ current ].value();
+            if (id_list !== null) {
+                id_list = $.isArray( id_list ) ? id_list : [ id_list ];
+                if ( id_list.length > 0 ) {
+                    var result = { batch: this._batch(), values: [] };
+                    for ( var i in id_list ) {
+                        var details = this.history[ id_list[ i ] + '_' + this.config[ current ].src ];
+                        if ( details ) {
+                            result.values.push( details );
+                        } else {
+                            Galaxy.emit.debug( 'tools-select-content::value()', 'Requested details not found for \'' + id_list[ i ] + '\'.'  );
+                            return null;
+                        }
+                    }
+                    result.values.sort( function( a, b ) { return a.hid - b.hid } );
+                    return result;
+                }
+            }
+        } else {
+            Galaxy.emit.debug( 'tools-select-content::value()', 'Invalid value/source \'' + new_value + '\'.'  );
+        }
+        return null;
+    },
+
+    /** Change of current select field */
+    _changeCurrent: function() {
+        var self = this;
+        _.each( this.fields, function( field, i ) {
+            if ( self.model.get( 'current' ) == i ) {
+                field.$el.show();
+                self.$batch[ self.config[ i ].batchmode && 'show' || 'hide' ]();
+                self.button_type.value( i );
+            } else {
+                field.$el.hide();
+            }
+        });
+    },
+
+    /** Change of type */
+    _changeType: function() {
+        var self = this;
+
+        // identify selector type
+        var config_id = String( this.model.get( 'type' ) ) + ( this.model.get( 'multiple' ) ? '_multiple' : '' );
+        if ( Configurations[ config_id ] ) {
+            this.config = Configurations[ config_id ];
+        } else {
+            this.config = Configurations[ 'data' ];
+            Galaxy.emit.debug( 'tools-select-content::_changeType()', 'Invalid configuration/type id \'' + config_id + '\'.'  );
+        }
+
+        // prepare extension component of error message
+        var extensions = Utils.textify( this.model.get( 'extensions' ) );
+        var src_labels = this.model.get( 'src_labels' );
+
+        // build views
+        this.fields = [];
+        this.button_data = [];
+        _.each( this.config, function( c, i ) {
+            self.button_data.push({
+                value   : i,
+                icon    : c.icon,
+                tooltip : c.tooltip
+            });
+            self.fields.push(
+                new Select.View({
+                    optional    : self.model.get( 'optional' ),
+                    multiple    : c.multiple,
+                    searchable  : !c.multiple,
+                    error_text  : 'No ' + ( extensions ? extensions + ' ' : '' ) + ( src_labels[ c.src ] || 'content' ) + ' available.',
+                    onchange    : function() {
+                        self.trigger( 'change' );
+                    }
+                })
+            );
+        });
+        this.button_type = new Ui.RadioButton.View({
+            value   : this.model.get( 'current' ),
+            data    : this.button_data,
+            onchange: function( value ) {
+                self.model.set( 'current', value );
+                self.trigger( 'change' );
+            }
+        });
+
+        // append views
+        this.$el.empty();
+        var button_width = 0;
+        if ( this.fields.length > 1 ) {
+            this.$el.append( this.button_type.$el );
+            button_width = Math.max( 0, this.fields.length * 35 ) + 'px';
+        }
+        _.each( this.fields, function( field ) {
+            self.$el.append( field.$el.css( { 'margin-left': button_width } ) );
+        });
+        this.$el.append( this.$batch.css( { 'margin-left': button_width } ) );
+        this.model.set( 'current', 0 );
+        this._changeCurrent();
+        this._changeData();
+    },
+
+    /** Change of wait flag */
+    _changeWait: function() {
+        var self = this;
+        _.each( this.fields, function( field ) { field[ self.model.get( 'wait' ) ? 'wait' : 'unwait' ]() } );
+    },
+
+    /** Change of available options */
+    _changeData: function() {
+        var options = this.model.get( 'data' );
+        var self = this;
+        var select_options = {};
+        _.each( options, function( items, src ) {
+            select_options[ src ] = [];
+            _.each( items, function( item ) {
+                select_options[ src ].push({
+                    hid  : item.hid,
+                    label: item.hid + ': ' + item.name,
+                    value: item.id
+                });
+                self.history[ item.id + '_' + src ] = item;
+            });
+        });
+        _.each( this.config, function( c, i ) {
+            select_options[ c.src ] && self.fields[ i ].add( select_options[ c.src ], function( a, b ) { return b.hid - a.hid } );
+        });
+    },
+
+    /** Change of incoming value */
+    _changeValue: function () {
+        var new_value = this.model.get( 'value' );
+        if ( new_value && new_value.values && new_value.values.length > 0 ) {
+            // create list with content ids
+            var list = [];
+            _.each( new_value.values, function( value ) {
+                list.push( value.id );
+            });
+            // sniff first suitable field type from config list
+            var src = new_value.values[ 0 ].src;
+            var multiple = new_value.values.length > 1;
+            for( var i = 0; i < this.config.length; i++ ) {
+                var field = this.fields[ i ];
+                var c = this.config[ i ];
+                if ( c.src == src && [ multiple, true ].indexOf( c.multiple ) !== -1 ) {
+                    this.model.set( 'current', i );
+                    field.value( list );
+                    break;
+                }
+            }
+        } else {
+            _.each( this.fields, function( field ) {
+                field.value( null );
+            });
+        }
+    },
+
+    /** Assists in identifying the batch mode */
+    _batch: function() {
+        var current = this.model.get( 'current' );
+        var config = this.config[ current ];
+        if ( config.src == 'hdca' && !config.multiple ) {
+            var hdca = this.history[ this.fields[ current ].value() + '_hdca' ];
+            if ( hdca && hdca.map_over_type ) {
+                return true;
+            }
+        }
+        return config.batchmode;
+    }
+});
+
+return {
+    View: View
+}
+
+});

client/galaxy/scripts/mvc/ui/ui-select-default.js

@@ -191,7 +191,7 @@ var View = Backbone.View.extend({
         _.each( this.model.get( 'options' ), function( v ) {
             !_.findWhere( options, v ) && options.push( v );
         });
-        sorter && options.sort( sorter );
+        sorter && options && options.sort( sorter );
         this.update( options );
     },
     update: function(options) {

client/galaxy/scripts/utils/utils.js

@@ -64,13 +64,12 @@ function validate ( value ) {
  * Convert list to pretty string
  * @param{String}   lst - List of strings to be converted in human readable list sentence
  */
-function textify(lst) {
-    var lst = lst.toString();
-    if (lst) {
-        lst = lst.replace(/,/g, ', ');
-        var pos = lst.lastIndexOf(', ');
-        if (pos != -1) {
-            lst = lst.substr(0, pos) + ' or ' + lst.substr(pos+1);
+function textify( lst ) {
+    if ( $.isArray( lst ) ) {
+        var lst = lst.toString().replace( /,/g, ', ' );
+        var pos = lst.lastIndexOf( ', ' );
+        if ( pos != -1 ) {
+            lst = lst.substr( 0, pos ) + ' or ' + lst.substr( pos + 2 );
         }
         return lst;
     }

client/galaxy/scripts/viz/trackster/tracks.js

@@ -2507,7 +2507,7 @@ extend(Track.prototype, Drawable.prototype, {
             var data = result.data;
 
             // Tracks may not have stat data either because there is no data or data is not yet ready.
-            if (data !== undefined && data.min !== undefined && data.max !== undefined) {
+            if (data && data.min !== undefined && data.max !== undefined) {
                 // Compute default minimum and maximum values
                 var min_value = data.min,
                     max_value = data.max;

client/galaxy/style/less/library.less

@@ -1,6 +1,14 @@
 @import "galaxy_bootstrap/variables.less";
 @import "galaxy_variables.less";
 
+.library_style_container .fa{
+    font-size: 12px;
+}
+.library_style_container .fa-globe{
+    font-size: initial;
+    margin-left: 0.6em;
+}
+
 .libraryRow {
     background-color: @table-heading-bg;
 }
@@ -229,3 +237,21 @@ span.expandLink {
 .library-paginator {
     margin-left: 2em;
 }
+.paginator-bottom{
+    width: 27em;
+    margin-left: auto;
+    margin-right: auto;
+    margin-top: 2em;
+}
+.import-type-switch{
+    text-decoration: underline;
+}
+.libimport-select-none,
+.libimport-select-all{
+    margin-left: 0.5em;
+}
+.library-modal-item{
+    width:90%;
+    margin-left: 1em;
+    margin-right: 1em;
+}

client/galaxy/style/less/ui.less

@@ -263,14 +263,22 @@
             top: 0px;
             width: 100%;
             height: 100%;
-            opacity: 0.2;
             background: @white;
+        }
+        .ui-form-backdrop-default {
+            display: block;
+            opacity: 0.2;
             cursor: not-allowed;
         }
+        .ui-form-backdrop-silent {
+            display: block;
+            opacity: 0.0;
+            cursor: default;
+        }
     }
     .ui-form-preview {
         &:extend(.ui-input);
-        margin-top: 5px;
+        margin-top: @ui-margin-vertical;
         border-color: transparent !important;
         box-shadow: none !important;
     }
@@ -286,8 +294,12 @@
 }
 
 .ui-form-info {
-        &:extend(.toolParamHelp);
-        clear: both !important;
+    &:extend(.toolParamHelp);
+    clear: both !important;
+    i {
+        font-size: 1.2em;
+        padding: 2px 5px;
+    }
 }
 
 .ui-form-footer-info {

config/datatypes_conf.xml.sample

@@ -440,9 +440,58 @@
     <datatype extension="vtkascii" type="galaxy.datatypes.constructive_solid_geometry:VtkAscii" display_in_upload="true" />
     <datatype extension="vtkbinary" type="galaxy.datatypes.constructive_solid_geometry:VtkBinary" display_in_upload="true" />
     <!-- Metagenomic Datatype -->
-    <datatype extension="biom1" type="galaxy.datatypes.text:Biom1" display_in_upload="True" subclass="True" mimetype="application/json" />
+    <datatype extension="biom1" type="galaxy.datatypes.text:Biom1" display_in_upload="True" subclass="True" mimetype="application/json">
+        <display file="biom/biom_simple.xml" />
+    </datatype>
     <!-- Strand-specific Coordinate Count Datatype used by the Center for Eukaryotic Gene Regulation labs at Penn State -->
     <datatype extension="scidx" type="galaxy.datatypes.interval:ScIdx" display_in_upload="true" />
+
+    <!--Cheminformatics Datatypes -->
+    <datatype extension="smi" type="galaxy.datatypes.molecules:SMILES" display_in_upload="True">
+        <!-- The ordering is important. The first one is considered as default converter in the build-in conversion function -> (as sdf)-->
+        <converter file="smi_to_sdf_converter.xml" target_datatype="sdf"/>
+        <converter file="smi_to_inchi_converter.xml" target_datatype="inchi"/>
+        <converter file="smi_to_cml_converter.xml" target_datatype="cml"/>
+        <converter file="smi_to_mol_converter.xml" target_datatype="mol"/>
+        <converter file="smi_to_mol2_converter.xml" target_datatype="mol2"/>
+        <converter file="smi_to_smi_converter.xml" target_datatype="smi"/>
+    </datatype>
+    <datatype extension="sdf" type="galaxy.datatypes.molecules:SDF" display_in_upload="True">
+        <converter file="sdf_to_smi_converter.xml" target_datatype="smi"/>
+        <converter file="sdf_to_inchi_converter.xml" target_datatype="inchi"/>
+        <converter file="sdf_to_mol2_converter.xml" target_datatype="mol2"/>
+        <converter file="sdf_to_cml_converter.xml" target_datatype="cml"/>
+    </datatype>
+    <datatype extension="inchi" type="galaxy.datatypes.molecules:InChI" display_in_upload="True">
+        <converter file="inchi_to_smi_converter.xml" target_datatype="smi"/>
+        <converter file="inchi_to_sdf_converter.xml" target_datatype="sdf"/>
+        <converter file="inchi_to_mol_converter.xml" target_datatype="mol"/>
+        <converter file="inchi_to_mol2_converter.xml" target_datatype="mol2"/>
+        <converter file="inchi_to_cml_converter.xml" target_datatype="cml"/>
+    </datatype>
+    <datatype extension="mol" type="galaxy.datatypes.molecules:MOL" display_in_upload="True">
+        <converter file="mol_to_smi_converter.xml" target_datatype="smi"/>
+        <converter file="mol_to_inchi_converter.xml" target_datatype="inchi"/>
+        <converter file="mol_to_mol2_converter.xml" target_datatype="mol2"/>
+        <converter file="mol_to_cml_converter.xml" target_datatype="cml"/>
+    </datatype>
+    <datatype extension="mol2" type="galaxy.datatypes.molecules:MOL2" display_in_upload="False">
+        <converter file="mol2_to_smi_converter.xml" target_datatype="smi"/>
+        <converter file="mol2_to_sdf_converter.xml" target_datatype="sdf"/>
+        <converter file="mol2_to_inchi_converter.xml" target_datatype="inchi"/>
+        <converter file="mol2_to_mol_converter.xml" target_datatype="mol"/>
+        <converter file="mol2_to_cml_converter.xml" target_datatype="cml"/>
+    </datatype>
+    <datatype extension="cml" type="galaxy.datatypes.molecules:CML" display_in_upload="True">
+        <converter file="cml_to_smi_converter.xml" target_datatype="smi"/>
+        <converter file="cml_to_inchi_converter.xml" target_datatype="inchi"/>
+        <converter file="cml_to_sdf_converter.xml" target_datatype="sdf"/>
+        <converter file="cml_to_mol2_converter.xml" target_datatype="mol2"/>
+        </datatype>
+    <datatype extension="fps" type="galaxy.datatypes.molecules:FPS" mimetype="text/html" display_in_upload="True" />
+    <datatype extension="obfs" type="galaxy.datatypes.molecules:OBFS" mimetype="text/html" display_in_upload="True" />
+    <datatype extension="phar" type="galaxy.datatypes.molecules:PHAR" display_in_upload="False" />
+    <datatype extension="pdb" type="galaxy.datatypes.molecules:PDB" display_in_upload="True" />
   </registration>
   <sniffers>
     <!--
@@ -484,6 +533,7 @@
     <sniffer type="galaxy.datatypes.proteomics:Msp"/>
     <sniffer type="galaxy.datatypes.proteomics:SPLib"/>
     <sniffer type="galaxy.datatypes.proteomics:ThermoRAW"/>
+    <sniffer type="galaxy.datatypes.molecules:CML"/>
     <sniffer type="galaxy.datatypes.xml:GenericXml"/>
     <sniffer type="galaxy.datatypes.triples:Turtle"/>
     <sniffer type="galaxy.datatypes.triples:NTriples"/>
@@ -493,6 +543,12 @@
     <sniffer type="galaxy.datatypes.sequence:csFasta"/>
     <sniffer type="galaxy.datatypes.qualityscore:QualityScoreSOLiD"/>
     <sniffer type="galaxy.datatypes.qualityscore:QualityScore454"/>
+    <sniffer type="galaxy.datatypes.molecules:SDF"/>
+    <sniffer type="galaxy.datatypes.molecules:PDB"/>
+    <sniffer type="galaxy.datatypes.molecules:MOL2"/>
+    <sniffer type="galaxy.datatypes.molecules:InChI"/>
+    <sniffer type="galaxy.datatypes.molecules:FPS"/>
+    <!-- TODO: see molecules.py <sniffer type="galaxy.datatypes.molecules:SMILES"/>-->
     <sniffer type="galaxy.datatypes.sequence:Fasta"/>
     <sniffer type="galaxy.datatypes.sequence:Fastq"/>
     <sniffer type="galaxy.datatypes.interval:Wiggle"/>

config/galaxy.ini.sample

@@ -656,6 +656,13 @@ nglims_config_file = tool-data/nglims.yaml
 # log_events and log_actions functionality will eventually be merged.
 #log_actions = True
 
+
+# Fluentd configuration.  Various events can be logged to the fluentd instance
+# configured below by enabling fluent_log.
+#fluent_log = False
+#fluent_host = localhost
+#fluent_port = 24224
+
 # Sanitize all HTML tool output.  By default, all tool output served as
 # 'text/html' will be sanitized thoroughly.  This can be disabled if you have
 # special tools that require unaltered output.  WARNING: disabling this does

config/job_conf.xml.sample_advanced

@@ -98,6 +98,26 @@
                deprecated and will disappear with a future release of Galaxy.
           -->
         </plugin>
+        <plugin id="pulsar_embedded" type="runner" load="galaxy.jobs.runners.pulsar:PulsarEmbeddedJobRunner">
+          <!-- The embedded Pulsar runner starts a Pulsar app
+               internal to Galaxy and communicates it directly.
+               This maybe be useful for instance when Pulsar
+               staging is important but a Pulsar server is
+               unneeded (most obviously for instance if compute
+               servers cannot mount Galaxy's files but Galaxy
+               can mount a scratch directory available on
+               compute). -->
+          <!-- Specify a complete description of the Pulsar app
+               to create. Currently this configuration (if set)
+               must create exactly on job manager. For more
+               information on configuring a Pulsar app see:
+
+               https://github.com/galaxyproject/pulsar/blob/master/app.yml.sample
+               http://pulsar.readthedocs.org/en/latest/configure.html
+          -->
+          <!-- <param id="pulsar_conf">path/to/pulsar/app.yml</param> -->
+        </plugin>
+
     </plugins>
     <handlers default="handlers">
         <!-- Additional job handlers - the id should match the name of a

config/tool_data_table_conf.xml.sample

@@ -85,4 +85,9 @@
         <columns>value, name, url</columns>
         <file path="tool-data/vcf_iobio.loc" />
     </table>
+    <!-- simple biom servers -->
+    <table name="biom_simple_display" comment_char="#">
+        <columns>value, name, url</columns>
+        <file path="tool-data/biom_simple_display.loc" />
+    </table>
 </tables>

config/tool_shed.ini.sample

@@ -35,6 +35,9 @@ database_file = database/community.sqlite
 # The default is the Galaxy installation directory.
 #hgweb_config_dir = None
 
+# Disable Mercurial pushing to repositories.
+#disable_push = True
+
 # Where tool shed repositories are stored.
 file_path = database/community_files
 # Temporary storage for additional datasets,

display_applications/biom/biom_simple.xml

@@ -0,0 +1,7 @@
+<?xml version="1.0"?>
+<display id="biom_simple" version="1.0.0" name="view biom at">
+    <dynamic_links from_data_table="biom_simple_display" skip_startswith="#" id="value" name="name">
+        <url>${ url % { 'biom_file_url_qp': $biom_file.qp } }</url>
+        <param type="data" name="biom_file" url="galaxy_${DATASET_HASH}.biom" />
+    </dynamic_links>
+</display>

doc/source/lib/modules.rst

@@ -10,5 +10,4 @@ lib
    log_tempfile
    mimeparse
    psyco_full
-   pulsar
    tool_shed

doc/source/lib/pulsar.client.rst

@@ -1,132 +0,0 @@
-pulsar.client package
-=====================
-
-.. automodule:: pulsar.client
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-Subpackages
------------
-
-.. toctree::
-
-    pulsar.client.staging
-    pulsar.client.transport
-
-Submodules
-----------
-
-pulsar.client.action_mapper module
-----------------------------------
-
-.. automodule:: pulsar.client.action_mapper
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-pulsar.client.amqp_exchange module
-----------------------------------
-
-.. automodule:: pulsar.client.amqp_exchange
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-pulsar.client.amqp_exchange_factory module
-------------------------------------------
-
-.. automodule:: pulsar.client.amqp_exchange_factory
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-pulsar.client.client module
----------------------------
-
-.. automodule:: pulsar.client.client
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-pulsar.client.config_util module
---------------------------------
-
-.. automodule:: pulsar.client.config_util
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-pulsar.client.decorators module
--------------------------------
-
-.. automodule:: pulsar.client.decorators
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-pulsar.client.destination module
---------------------------------
-
-.. automodule:: pulsar.client.destination
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-pulsar.client.interface module
-------------------------------
-
-.. automodule:: pulsar.client.interface
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-pulsar.client.job_directory module
-----------------------------------
-
-.. automodule:: pulsar.client.job_directory
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-pulsar.client.manager module
-----------------------------
-
-.. automodule:: pulsar.client.manager
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-pulsar.client.object_client module
-----------------------------------
-
-.. automodule:: pulsar.client.object_client
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-pulsar.client.path_mapper module
---------------------------------
-
-.. automodule:: pulsar.client.path_mapper
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-pulsar.client.setup_handler module
-----------------------------------
-
-.. automodule:: pulsar.client.setup_handler
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-pulsar.client.util module
--------------------------
-
-.. automodule:: pulsar.client.util
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-

doc/source/lib/pulsar.client.staging.rst

@@ -1,28 +0,0 @@
-pulsar.client.staging package
-=============================
-
-.. automodule:: pulsar.client.staging
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-Submodules
-----------
-
-pulsar.client.staging.down module
----------------------------------
-
-.. automodule:: pulsar.client.staging.down
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-pulsar.client.staging.up module
--------------------------------
-
-.. automodule:: pulsar.client.staging.up
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-

doc/source/lib/pulsar.client.transport.rst

@@ -1,52 +0,0 @@
-pulsar.client.transport package
-===============================
-
-.. automodule:: pulsar.client.transport
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-Submodules
-----------
-
-pulsar.client.transport.curl module
------------------------------------
-
-.. automodule:: pulsar.client.transport.curl
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-pulsar.client.transport.poster module
--------------------------------------
-
-.. automodule:: pulsar.client.transport.poster
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-pulsar.client.transport.requests module
----------------------------------------
-
-.. automodule:: pulsar.client.transport.requests
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-pulsar.client.transport.ssh module
-----------------------------------
-
-.. automodule:: pulsar.client.transport.ssh
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-pulsar.client.transport.standard module
----------------------------------------
-
-.. automodule:: pulsar.client.transport.standard
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-

doc/source/lib/pulsar.rst

@@ -1,15 +0,0 @@
-pulsar package
-==============
-
-.. automodule:: pulsar
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-Subpackages
------------
-
-.. toctree::
-
-    pulsar.client
-

doc/source/releases/index.rst

@@ -4,6 +4,8 @@ Releases
 .. toctree::
    :maxdepth: 1
 
+.. annoucements
+   16.04_announce
    16.01_announce
    15.10_announce
    15.07_announce

lib/galaxy/config.py

@@ -91,7 +91,6 @@ class Configuration( object ):
         self.tool_data_path = resolve_path( kwargs.get( "tool_data_path", "tool-data" ), os.getcwd() )
         self.builds_file_path = resolve_path( kwargs.get( "builds_file_path", os.path.join( self.tool_data_path, 'shared', 'ucsc', 'builds.txt') ), self.root )
         self.len_file_path = resolve_path( kwargs.get( "len_file_path", os.path.join( self.tool_data_path, 'shared', 'ucsc', 'chrom') ), self.root )
-        self.test_conf = resolve_path( kwargs.get( "test_conf", "" ), self.root )
         # The value of migrated_tools_config is the file reserved for containing only those tools that have been eliminated from the distribution
         # and moved to the tool shed.
         self.integrated_tool_panel_config = resolve_path( kwargs.get( 'integrated_tool_panel_config', 'integrated_tool_panel.xml' ), self.root )

lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml

@@ -0,0 +1,22 @@
+<tool id="CONVERTER_cml_to_inchi" name="CML to InChI" version="1.0.0">
+    <description></description>
+    <parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
+    <requirements>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
+    </requirements>
+    <command>
+<![CDATA[
+        obabel -icml "${input}" -oinchi -O "${output}" -e 2>&1
+]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="cml" label="Molecules in CML-format"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="inchi"/>
+    </outputs>
+    <help>
+<![CDATA[
+]]>
+    </help>
+</tool>

lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml

@@ -0,0 +1,22 @@
+<tool id="CONVERTER_cml_to_mol2" name="CML to mol2" version="1.0.0">
+    <description></description>
+    <parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
+    <requirements>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
+    </requirements>
+    <command>
+<![CDATA[
+        obabel -icml "${input}" -omol2 -O "${output}" -e 2>&1
+]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="cml" label="Molecules in CML-format"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="mol2"/>
+    </outputs>
+    <help>
+<![CDATA[
+]]>
+    </help>
+</tool>

lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml

@@ -0,0 +1,22 @@
+<tool id="CONVERTER_cml_to_sdf" name="CML to SDF" version="1.0.0">
+    <description></description>
+    <parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
+    <requirements>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
+    </requirements>
+    <command>
+<![CDATA[
+        obabel -icml "${input}" -osdf "${output}" -e 2>&1
+]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="cml" label="Molecules in CML-format"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="sdf"/>
+    </outputs>
+    <help>
+<![CDATA[
+]]>
+    </help>
+</tool>

lib/galaxy/datatypes/converters/cml_to_smi_converter.xml

@@ -0,0 +1,48 @@
+<tool id="CONVERTER_cml_to_smiles" name="CML to SMILES" version="1.0.0">
+    <description></description>
+    <parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
+    <requirements>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
+    </requirements>
+    <command >
+<![CDATA[
+        obabel
+            -icml "${input}"
+            #if $can:
+                -ocan
+            #else:
+                -osmi
+            #end if
+            -O "${output}"
+            -e
+            $remove_h
+            #if $iso_chi or $can or $exp_h:
+                -x$iso_chi$exp_h$can
+            #end if
+            #if $dative_bonds:
+                -b
+            #end if
+            #if int($ph) >= 0:
+                -p $ph
+            #end if
+
+            2>&1
+]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="cml" label="Molecules in CML-format"/>
+        <param name="iso_chi" type="boolean" label="Do not include isotopic or chiral markings (-xi)" truevalue="i" falsevalue="" checked="false" />
+        <param name="can" type="boolean" label="Output in canonical form (-xc)" truevalue="c" falsevalue="" checked="false" />
+        <param name="exp_h" type="boolean" label="Output explicit hydrogens as such (-xh)" truevalue="h" falsevalue="" checked="false" />
+        <param name="remove_h" type="boolean" label="Delete hydrogen atoms (-d)" truevalue="-d" falsevalue="" />
+        <param name="ph" type="float" value="-1" label="Add hydrogens appropriate for pH (-p)" help="-1 means deactivated"/>
+        <param name="dative_bonds" type="boolean" label="Convert dative bonds (e.g. [N+]([O-])=O to N(=O)=O) (-b)" truevalue="-b" falsevalue="" />
+    </inputs>
+    <outputs>
+        <data name="output" format="smi"/>
+    </outputs>
+    <help>
+<![CDATA[
+]]>
+    </help>
+</tool>

lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml

@@ -0,0 +1,22 @@
+<tool id="CONVERTER_inchi_to_cml" name="InChI to CML" version="1.0.0">
+    <description></description>
+    <parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
+    <requirements>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
+    </requirements>
+    <command>
+<![CDATA[
+        obabel -iinchi "${input}" -ocml -O "${output}" -e 2>&1
+]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="inchi" label="Molecules in InChI format"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="cml"/>
+    </outputs>
+    <help>
+<![CDATA[
+]]>
+    </help>
+</tool>

lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml

@@ -0,0 +1,22 @@
+<tool id="CONVERTER_inchi_to_mol2" name="InChI to MOL2" version="1.0.0">
+    <description></description>
+    <parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
+    <requirements>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
+    </requirements>
+    <command>
+<![CDATA[
+        obabel -iinchi "${input}" -omol2 -O "${output}" -e 2>&1
+]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="inchi" label="Molecules in InChI format"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="mol2"/>
+    </outputs>
+    <help>
+<![CDATA[
+]]>
+    </help>
+</tool>

lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml

@@ -0,0 +1,22 @@
+<tool id="CONVERTER_inchi_to_mol" name="InChI to MOL" version="1.0.0">
+    <description></description>
+    <parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
+    <requirements>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
+    </requirements>
+    <command>
+<![CDATA[
+        obabel -iinchi "${input}" -omol -O "${output}" -e 2>&1
+]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="inchi" label="Molecules in InChI-format"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="mol"/>
+    </outputs>
+    <help>
+<![CDATA[
+]]>
+    </help>
+</tool>

lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml

@@ -0,0 +1,22 @@
+<tool id="CONVERTER_inchi_to_sdf" name="InChI to SDF" version="1.0.0">
+    <description></description>
+    <parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
+    <requirements>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
+    </requirements>
+    <command>
+<![CDATA[
+        obabel -iinchi "${input}" -osdf -O "${output}" -e 2>&1
+]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="inchi" label="Molecules in InChI format"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="sdf"/>
+    </outputs>
+    <help>
+<![CDATA[
+]]>
+    </help>
+</tool>

lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml

@@ -0,0 +1,22 @@
+<tool id="CONVERTER_inchi_to_smi" name="InChI to SMILES" version="1.0.0">
+    <description></description>
+    <parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
+    <requirements>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
+    </requirements>
+    <command>
+<![CDATA[
+        obabel -iinchi "${input}" -osmi -O "${output}" -e 2>&1
+]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="inchi" label="Molecules in InChI format"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="smi"/>
+    </outputs>
+    <help>
+<![CDATA[
+]]>
+    </help>
+</tool>

lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml

@@ -0,0 +1,22 @@
+<tool id="CONVERTER_mol2_to_cml" name="MOL2 to CML" version="1.0.0">
+    <description></description>
+    <parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
+    <requirements>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
+    </requirements>
+    <command>
+<![CDATA[
+        obabel -imol2 "${input}" -ocml -O "${output}" -e 2>&1
+]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="mol2" label="Molecules in MOL2-format"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="cml"/>
+    </outputs>
+    <help>
+<![CDATA[
+]]>
+    </help>
+</tool>

lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml

@@ -0,0 +1,22 @@
+<tool id="CONVERTER_mol2_to_inchi" name="MOL2 to InChI" version="1.0.0">
+    <description></description>
+    <parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
+    <requirements>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
+    </requirements>
+    <command>
+<![CDATA[
+        obabel -imol2 "${input}" -oinchi -O "${output}" -e 2>&1
+]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="mol2" label="Molecules in MOL2-format"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="inchi"/>
+    </outputs>
+    <help>
+<![CDATA[
+]]>
+    </help>
+</tool>

lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml

@@ -0,0 +1,22 @@
+<tool id="CONVERTER_mol2_to_mol" name="MOL2 to MOL" version="1.0.0">
+    <description></description>
+    <parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
+    <requirements>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
+    </requirements>
+    <command>
+<![CDATA[
+        obabel -imol2 "${input}" -omol -O "${output}" -e 2>&1
+]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="mol2" label="Molecules in MOL2-format"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="mol"/>
+    </outputs>
+    <help>
+<![CDATA[
+]]>
+    </help>
+</tool>

lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml

@@ -0,0 +1,22 @@
+<tool id="CONVERTER_mol2_to_sdf" name="MOL2 to SDF" version="1.0.0">
+    <description></description>
+    <parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
+    <requirements>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
+    </requirements>
+    <command>
+<![CDATA[
+        obabel -imol2 "${input}" -osdf "${output}" -e 2>&1
+]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="mol2" label="Molecules in MOL2-format"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="sdf"/>
+    </outputs>
+    <help>
+<![CDATA[
+]]>
+    </help>
+</tool>

lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml

@@ -0,0 +1,22 @@
+<tool id="CONVERTER_mol2_to_smi" name="MOL2 to SMILES" version="1.0.0">
+    <description></description>
+    <parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
+    <requirements>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
+    </requirements>
+    <command>
+<![CDATA[
+        obabel -imol2 "${input}" -omol "${output}" -e 2>&1
+]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="mol2" label="Molecules in MOL2-format"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="smi"/>
+    </outputs>
+    <help>
+<![CDATA[
+]]>
+    </help>
+</tool>

lib/galaxy/datatypes/converters/mol_to_cml_converter.xml

@@ -0,0 +1,21 @@
+<tool id="CONVERTER_mol_to_cml" name="MOL to CML" version="1.0.0">
+    <description></description>
+    <requirements>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
+    </requirements>
+    <command>
+<![CDATA[
+        obabel -imol "${input}" -ocml -O "${output}" -e 2>&1
+]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="mol" label="Molecules in MOL-format"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="cml"/>
+    </outputs>
+    <help>
+<![CDATA[
+]]>
+    </help>
+</tool>

lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml

@@ -0,0 +1,21 @@
+<tool id="CONVERTER_mol_to_mol2" name="MOL to MOL2" version="1.0.0">
+    <description></description>
+    <requirements>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
+    </requirements>
+    <command>
+<![CDATA[
+        obabel -imol "${input}" -omol2 -O "${output}" -e 2>&1
+]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="mol" label="Molecules in MOL-format"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="mol2"/>
+    </outputs>
+    <help>
+<![CDATA[
+]]>
+    </help>
+</tool>

lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml

@@ -0,0 +1,21 @@
+<tool id="CONVERTER_mol_to_mol2" name="MOL to MOL2" version="1.0.0">
+    <description></description>
+    <requirements>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
+    </requirements>
+    <command>
+<![CDATA[
+        obabel -imol "${input}" -omol2 -O "${output}" -e 2>&1
+]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="mol" label="Molecules in MOL-format"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="mol2"/>
+    </outputs>
+    <help>
+<![CDATA[
+]]>
+    </help>
+</tool>

lib/galaxy/datatypes/converters/mol_to_smi_converter.xml

@@ -0,0 +1,21 @@
+<tool id="CONVERTER_mol_to_smi" name="MOL to SMILES" version="1.0.0">
+    <description></description>
+    <requirements>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
+    </requirements>
+    <command>
+<![CDATA[
+        obabel -imol "${input}" -osmi  -O "${output}" -e 2>&1
+]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="mol" label="Molecules in MOL-format"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="smi"/>
+    </outputs>
+    <help>
+<![CDATA[
+]]>
+    </help>
+</tool>

lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml

@@ -0,0 +1,22 @@
+<tool id="CONVERTER_sdf_to_cml" name="SDF to CML" version="1.0.0">
+    <description></description>
+    <parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
+    <requirements>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
+    </requirements>
+    <command>
+<![CDATA[
+        obabel -isdf "${input}" -ocml -O "${output}" -e 2>&1
+]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="sdf" label="Molecules in SDF-format"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="cml"/>
+    </outputs>
+    <help>
+<![CDATA[
+]]>
+    </help>
+</tool>

lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml

@@ -0,0 +1,22 @@
+<tool id="CONVERTER_sdf_to_inchi" name="SDF to InChI" version="1.0.0">
+    <description></description>
+    <parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
+    <requirements>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
+    </requirements>
+    <command>
+<![CDATA[
+        obabel -isdf "${input}" -oinchi -O "${output}" -e 2>&1
+]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="sdf" label="Molecules in SDF-format"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="inchi"/>
+    </outputs>
+    <help>
+<![CDATA[
+]]>
+    </help>
+</tool>

lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml

@@ -0,0 +1,22 @@
+<tool id="CONVERTER_sdf_to_mol2" name="SDF to mol2" version="1.0.0">
+    <description></description>
+    <parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
+    <requirements>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
+    </requirements>
+    <command>
+<![CDATA[
+        obabel -isdf "${input}" -omol2 -O "${output}" -e 2>&1
+]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="sdf" label="Molecules in SDF-format"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="mol2"/>
+    </outputs>
+    <help>
+<![CDATA[
+]]>
+    </help>
+</tool>

lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml

@@ -0,0 +1,27 @@
+<tool id="CONVERTER_sdf_to_smiles" name="SDF to SMILES" version="1.0.1">
+    <description></description>
+    <parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
+    <requirements>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
+    </requirements>
+    <command >
+<![CDATA[
+        obabel
+            -isdf "${input}"
+            -ocan
+            -O "${output}"
+            -e
+        2>&1
+]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="sdf" label="Molecules in SDF-format"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="smi"/>
+    </outputs>
+    <help>
+<![CDATA[
+]]>
+    </help>
+</tool>

lib/galaxy/datatypes/converters/smi_to_cml_converter.xml

@@ -0,0 +1,22 @@
+<tool id="CONVERTER_SMILES_to_cml" name="SMILES to CML" version="1.0.0">
+    <description></description>
+    <parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
+    <requirements>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
+    </requirements>
+    <command>
+<![CDATA[
+        obabel -ismi "${input}" -ocml -O "${output}" -e 2>&1
+]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="smi" label="Molecules in SMILES format"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="cml"/>
+    </outputs>
+    <help>
+<![CDATA[
+]]>
+    </help>
+</tool>

lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml

@@ -0,0 +1,22 @@
+<tool id="CONVERTER_SMILES_to_inchi" name="SMILES to InChI" version="1.0.0">
+    <description></description>
+    <parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
+    <requirements>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
+    </requirements>
+    <command>
+<![CDATA[
+        obabel -ismi "${input}" -oinchi -O "${output}" -e 2>&1
+]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="smi" label="Molecules in SMILES format"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="inchi"/>
+    </outputs>
+    <help>
+<![CDATA[
+]]>
+    </help>
+</tool>

lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml

@@ -0,0 +1,22 @@
+<tool id="CONVERTER_SMILES_to_MOL2" name="SMILES to MOL2" version="1.0.0">
+    <description></description>
+    <parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
+    <requirements>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
+    </requirements>
+    <command>
+<![CDATA[
+        obabel -ismi "${input}" -omol2 -O "${output}" -e 2>&1
+]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="smi" label="Molecules in SMILES format"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="mol2"/>
+    </outputs>
+    <help>
+<![CDATA[
+]]>
+    </help>
+</tool>

lib/galaxy/datatypes/converters/smi_to_mol_converter.xml

@@ -0,0 +1,22 @@
+<tool id="CONVERTER_SMILES_to_MOL" name="SMILES to MOL" version="1.0.0">
+    <description></description>
+    <parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
+    <requirements>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
+    </requirements>
+    <command>
+<![CDATA[
+        obabel -ismi "${input}" -omol -O "${output}" -e 2>&1
+]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="smi" label="Molecules in SMILES format"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="mol"/>
+    </outputs>
+    <help>
+<![CDATA[
+]]>
+    </help>
+</tool>

lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml

@@ -0,0 +1,22 @@
+<tool id="CONVERTER_SMILES_to_sdf" name="SMILES to SDF" version="1.0.0">
+    <description></description>
+    <parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
+    <requirements>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
+    </requirements>
+    <command>
+<![CDATA[
+    obabel -ismi "${input}" -osdf -O "${output}" -e 2>&1
+]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="smi" label="Molecules in SMILES format"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="sdf"/>
+    </outputs>
+    <help>
+<![CDATA[
+]]>
+    </help>
+</tool>

lib/galaxy/datatypes/converters/smi_to_smi_converter.xml

@@ -0,0 +1,48 @@
+<tool id="CONVERTER_smiles_to_smiles" name="SMILES to SMILES" version="1.0.0">
+    <description></description>
+    <parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
+    <requirements>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
+    </requirements>
+    <command >
+<![CDATA[
+        obabel
+            -ismi "${input}"
+            #if $can:
+                -ocan
+            #else:
+                -osmi
+            #end if
+            -O "${output}"
+            -e
+            $remove_h
+            #if $iso_chi or $can or $exp_h:
+                -x$iso_chi$exp_h$can
+            #end if
+            #if $dative_bonds:
+                -b
+            #end if
+            #if int($ph) >= 0:
+                -p $ph
+            #end if
+
+            2>&1
+]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="smi" label="Molecules in SD-format"/>
+        <param name="iso_chi" type="boolean" label="Do not include isotopic or chiral markings (-xi)" truevalue="i" falsevalue="" checked="false" />
+        <param name="can" type="boolean" label="Output in canonical form (-xc)" truevalue="c" falsevalue="" checked="false" />
+        <param name="exp_h" type="boolean" label="Output explicit hydrogens as such (-xh)" truevalue="h" falsevalue="" checked="false" />
+        <param name="remove_h" type="boolean" label="Delete hydrogen atoms (-d)" truevalue="-d" falsevalue="" />
+        <param name="ph" type="float" value="-1" label="Add hydrogens appropriate for pH (-p)" help="-1 means deactivated"/>
+        <param name="dative_bonds" type="boolean" label="Convert dative bonds (e.g. [N+]([O-])=O to N(=O)=O) (-b)" truevalue="-b" falsevalue="" />
+    </inputs>
+    <outputs>
+        <data name="output" format="smi"/>
+    </outputs>
+    <help>
+<![CDATA[
+]]>
+    </help>
+</tool>

lib/galaxy/datatypes/molecules.py

@@ -0,0 +1,769 @@
+# -*- coding: utf-8 -*-
+
+from galaxy.datatypes import data
+import logging
+from galaxy.datatypes.sniff import get_headers
+from galaxy.datatypes.data import get_file_peek
+from galaxy.datatypes.tabular import Tabular
+from galaxy.datatypes.binary import Binary
+from galaxy.datatypes.xml import GenericXml
+import subprocess
+import os
+
+from galaxy.datatypes.metadata import MetadataElement
+from galaxy.datatypes import metadata
+
+log = logging.getLogger(__name__)
+
+
+def count_special_lines(word, filename, invert=False):
+    """
+        searching for special 'words' using the grep tool
+        grep is used to speed up the searching and counting
+        The number of hits is returned.
+    """
+    try:
+        cmd = ["grep", "-c"]
+        if invert:
+            cmd.append('-v')
+        cmd.extend([word, filename])
+        out = subprocess.Popen(cmd, stdout=subprocess.PIPE)
+        return int(out.communicate()[0].split()[0])
+    except:
+        pass
+    return 0
+
+
+def count_lines(filename, non_empty=False):
+    """
+        counting the number of lines from the 'filename' file
+    """
+    try:
+        if non_empty:
+            out = subprocess.Popen(['grep', '-cve', '^\s*$', filename], stdout=subprocess.PIPE)
+        else:
+            out = subprocess.Popen(['wc', '-l', filename], stdout=subprocess.PIPE)
+        return int(out.communicate()[0].split()[0])
+    except:
+        pass
+    return 0
+
+
+class GenericMolFile(data.Text):
+    """
+        abstract class for most of the molecule files
+    """
+    MetadataElement(name="number_of_molecules", default=0, desc="Number of molecules", readonly=True, visible=True, optional=True, no_value=0)
+
+    def set_peek(self, dataset, is_multi_byte=False):
+        if not dataset.dataset.purged:
+            dataset.peek = get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
+            if (dataset.metadata.number_of_molecules == 1):
+                dataset.blurb = "1 molecule"
+            else:
+                dataset.blurb = "%s molecules" % dataset.metadata.number_of_molecules
+            dataset.peek = data.get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disk'
+
+    def get_mime(self):
+        return 'text/plain'
+
+
+class MOL(GenericMolFile):
+    file_ext = "mol"
+
+    def set_meta(self, dataset, **kwd):
+        """
+        Set the number molecules, in the case of MOL its always one.
+        """
+        dataset.metadata.number_of_molecules = 1
+
+
+class SDF(GenericMolFile):
+    file_ext = "sdf"
+
+    def sniff(self, filename):
+        """
+        Try to guess if the file is a SDF2 file.
+
+        >>> from galaxy.datatypes.sniff import get_test_fname
+        >>> fname = get_test_fname('drugbank_drugs.sdf')
+        >>> SDF().sniff(fname)
+        True
+
+        >>> fname = get_test_fname('drugbank_drugs.cml')
+        >>> SDF().sniff(fname)
+        False
+        """
+        counter = count_special_lines("^M\s*END", filename) + count_special_lines("^\$\$\$\$", filename)
+        if counter > 0 and counter % 2 == 0:
+            return True
+        else:
+            return False
+
+    def set_meta(self, dataset, **kwd):
+        """
+        Set the number of molecules in dataset.
+        """
+        dataset.metadata.number_of_molecules = count_special_lines("^\$\$\$\$", dataset.file_name)
+
+    def split(cls, input_datasets, subdir_generator_function, split_params):
+        """
+        Split the input files by molecule records.
+        """
+        if split_params is None:
+            return None
+
+        if len(input_datasets) > 1:
+            raise Exception("SD-file splitting does not support multiple files")
+        input_files = [ds.file_name for ds in input_datasets]
+
+        chunk_size = None
+        if split_params['split_mode'] == 'number_of_parts':
+            raise Exception('Split mode "%s" is currently not implemented for SD-files.' % split_params['split_mode'])
+        elif split_params['split_mode'] == 'to_size':
+            chunk_size = int(split_params['split_size'])
+        else:
+            raise Exception('Unsupported split mode %s' % split_params['split_mode'])
+
+        def _read_sdf_records(filename):
+            lines = []
+            with open(filename) as handle:
+                for line in handle:
+                    lines.append(line)
+                    if line.startswith("$$$$"):
+                        yield lines
+                        lines = []
+
+        def _write_part_sdf_file(accumulated_lines):
+            part_dir = subdir_generator_function()
+            part_path = os.path.join(part_dir, os.path.basename(input_files[0]))
+            part_file = open(part_path, 'w')
+            part_file.writelines(accumulated_lines)
+            part_file.close()
+
+        try:
+            sdf_records = _read_sdf_records(input_files[0])
+            sdf_lines_accumulated = []
+            for counter, sdf_record in enumerate(sdf_records, start=1):
+                sdf_lines_accumulated.extend(sdf_record)
+                if counter % chunk_size == 0:
+                    _write_part_sdf_file(sdf_lines_accumulated)
+                    sdf_lines_accumulated = []
+            if sdf_lines_accumulated:
+                _write_part_sdf_file(sdf_lines_accumulated)
+        except Exception, e:
+            log.error('Unable to split files: %s' % str(e))
+            raise
+    split = classmethod(split)
+
+
+class MOL2(GenericMolFile):
+    file_ext = "mol2"
+
+    def sniff(self, filename):
+        """
+        Try to guess if the file is a MOL2 file.
+
+        >>> from galaxy.datatypes.sniff import get_test_fname
+        >>> fname = get_test_fname('drugbank_drugs.mol2')
+        >>> MOL2().sniff(fname)
+        True
+
+        >>> fname = get_test_fname('drugbank_drugs.cml')
+        >>> MOL2().sniff(fname)
+        False
+        """
+        if count_special_lines("@<TRIPOS>MOLECULE", filename) > 0:
+            return True
+        else:
+            return False
+
+    def set_meta(self, dataset, **kwd):
+        """
+        Set the number of lines of data in dataset.
+        """
+        dataset.metadata.number_of_molecules = count_special_lines("@<TRIPOS>MOLECULE", dataset.file_name)
+
+    def split(cls, input_datasets, subdir_generator_function, split_params):
+        """
+        Split the input files by molecule records.
+        """
+        if split_params is None:
+            return None
+
+        if len(input_datasets) > 1:
+            raise Exception("MOL2-file splitting does not support multiple files")
+        input_files = [ds.file_name for ds in input_datasets]
+
+        chunk_size = None
+        if split_params['split_mode'] == 'number_of_parts':
+            raise Exception('Split mode "%s" is currently not implemented for MOL2-files.' % split_params['split_mode'])
+        elif split_params['split_mode'] == 'to_size':
+            chunk_size = int(split_params['split_size'])
+        else:
+            raise Exception('Unsupported split mode %s' % split_params['split_mode'])
+
+        def _read_mol2_records(filename):
+            lines = []
+            start = True
+            with open(filename) as handle:
+                for line in handle:
+                    if line.startswith("@<TRIPOS>MOLECULE"):
+                        if start:
+                            start = False
+                        else:
+                            yield lines
+                            lines = []
+                    lines.append(line)
+
+        def _write_part_mol2_file(accumulated_lines):
+            part_dir = subdir_generator_function()
+            part_path = os.path.join(part_dir, os.path.basename(input_files[0]))
+            part_file = open(part_path, 'w')
+            part_file.writelines(accumulated_lines)
+            part_file.close()
+
+        try:
+            mol2_records = _read_mol2_records(input_files[0])
+            mol2_lines_accumulated = []
+            for counter, mol2_record in enumerate(mol2_records, start=1):
+                mol2_lines_accumulated.extend(mol2_record)
+                if counter % chunk_size == 0:
+                    _write_part_mol2_file(mol2_lines_accumulated)
+                    mol2_lines_accumulated = []
+            if mol2_lines_accumulated:
+                _write_part_mol2_file(mol2_lines_accumulated)
+        except Exception, e:
+            log.error('Unable to split files: %s' % str(e))
+            raise
+    split = classmethod(split)
+
+
+class FPS(GenericMolFile):
+    """
+    chemfp fingerprint file: http://code.google.com/p/chem-fingerprints/wiki/FPS
+    """
+    file_ext = "fps"
+
+    def sniff(self, filename):
+        """
+        Try to guess if the file is a FPS file.
+
+        >>> from galaxy.datatypes.sniff import get_test_fname
+        >>> fname = get_test_fname('q.fps')
+        >>> FPS().sniff(fname)
+        True
+
+        >>> fname = get_test_fname('drugbank_drugs.cml')
+        >>> FPS().sniff(fname)
+        False
+        """
+        header = get_headers(filename, sep='\t', count=1)
+        if header[0][0].strip() == '#FPS1':
+            return True
+        else:
+            return False
+
+    def set_meta(self, dataset, **kwd):
+        """
+        Set the number of lines of data in dataset.
+        """
+        dataset.metadata.number_of_molecules = count_special_lines('^#', dataset.file_name, invert=True)
+
+    def split(cls, input_datasets, subdir_generator_function, split_params):
+        """
+        Split the input files by fingerprint records.
+        """
+        if split_params is None:
+            return None
+
+        if len(input_datasets) > 1:
+            raise Exception("FPS-file splitting does not support multiple files")
+        input_files = [ds.file_name for ds in input_datasets]
+
+        chunk_size = None
+        if split_params['split_mode'] == 'number_of_parts':
+            raise Exception('Split mode "%s" is currently not implemented for MOL2-files.' % split_params['split_mode'])
+        elif split_params['split_mode'] == 'to_size':
+            chunk_size = int(split_params['split_size'])
+        else:
+            raise Exception('Unsupported split mode %s' % split_params['split_mode'])
+
+        def _write_part_fingerprint_file(accumulated_lines):
+            part_dir = subdir_generator_function()
+            part_path = os.path.join(part_dir, os.path.basename(input_files[0]))
+            part_file = open(part_path, 'w')
+            part_file.writelines(accumulated_lines)
+            part_file.close()
+
+        try:
+            header_lines = []
+            lines_accumulated = []
+            fingerprint_counter = 0
+            for line in open(input_files[0]):
+                if not line.strip():
+                    continue
+                if line.startswith('#'):
+                    header_lines.append(line)
+                else:
+                    fingerprint_counter += 1
+                    lines_accumulated.append(line)
+                if fingerprint_counter != 0 and fingerprint_counter % chunk_size == 0:
+                    _write_part_fingerprint_file(header_lines + lines_accumulated)
+                    lines_accumulated = []
+            if lines_accumulated:
+                _write_part_fingerprint_file(header_lines + lines_accumulated)
+        except Exception, e:
+            log.error('Unable to split files: %s' % str(e))
+            raise
+    split = classmethod(split)
+
+    def merge(split_files, output_file):
+        """
+        Merging fps files requires merging the header manually.
+        We take the header from the first file.
+        """
+        if len(split_files) == 1:
+            # For one file only, use base class method (move/copy)
+            return data.Text.merge(split_files, output_file)
+        if not split_files:
+            raise ValueError("No fps files given, %r, to merge into %s"
+                             % (split_files, output_file))
+        out = open(output_file, "w")
+        first = True
+        for filename in split_files:
+            with open(filename) as handle:
+                for line in handle:
+                    if line.startswith('#'):
+                        if first:
+                            out.write(line)
+                    else:
+                        # line is no header and not a comment, we assume the first header is written to out and we set 'first' to False
+                        first = False
+                        out.write(line)
+        out.close()
+    merge = staticmethod(merge)
+
+
+class OBFS(Binary):
+    """OpenBabel Fastsearch format (fs)."""
+    file_ext = 'fs'
+    composite_type = 'basic'
+    allow_datatype_change = False
+
+    MetadataElement(name="base_name", default='OpenBabel Fastsearch Index',
+                    readonly=True, visible=True, optional=True,)
+
+    def __init__(self, **kwd):
+        """
+            A Fastsearch Index consists of a binary file with the fingerprints
+            and a pointer the actual molecule file.
+        """
+        Binary.__init__(self, **kwd)
+        self.add_composite_file('molecule.fs', is_binary=True,
+                                description='OpenBabel Fastsearch Index')
+        self.add_composite_file('molecule.sdf', optional=True,
+                                is_binary=False, description='Molecule File')
+        self.add_composite_file('molecule.smi', optional=True,
+                                is_binary=False, description='Molecule File')
+        self.add_composite_file('molecule.inchi', optional=True,
+                                is_binary=False, description='Molecule File')
+        self.add_composite_file('molecule.mol2', optional=True,
+                                is_binary=False, description='Molecule File')
+        self.add_composite_file('molecule.cml', optional=True,
+                                is_binary=False, description='Molecule File')
+
+    def set_peek(self, dataset, is_multi_byte=False):
+        """Set the peek and blurb text."""
+        if not dataset.dataset.purged:
+            dataset.peek = "OpenBabel Fastsearch Index"
+            dataset.blurb = "OpenBabel Fastsearch Index"
+        else:
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
+
+    def display_peek(self, dataset):
+        """Create HTML content, used for displaying peek."""
+        try:
+            return dataset.peek
+        except:
+            return "OpenBabel Fastsearch Index"
+
+    def display_data(self, trans, data, preview=False, filename=None,
+                     to_ext=None, size=None, offset=None, **kwd):
+        """Apparently an old display method, but still gets called.
+
+        This allows us to format the data shown in the central pane via the "eye" icon.
+        """
+        return "This is a OpenBabel Fastsearch format. You can speed up your similarity and substructure search with it."
+
+    def get_mime(self):
+        """Returns the mime type of the datatype (pretend it is text for peek)"""
+        return 'text/plain'
+
+    def merge(split_files, output_file, extra_merge_args):
+        """Merging Fastsearch indices is not supported."""
+        raise NotImplementedError("Merging Fastsearch indices is not supported.")
+
+    def split(cls, input_datasets, subdir_generator_function, split_params):
+        """Splitting Fastsearch indices is not supported."""
+        if split_params is None:
+            return None
+        raise NotImplementedError("Splitting Fastsearch indices is not possible.")
+
+
+class DRF(GenericMolFile):
+    file_ext = "drf"
+
+    def set_meta(self, dataset, **kwd):
+        """
+        Set the number of lines of data in dataset.
+        """
+        dataset.metadata.number_of_molecules = count_special_lines('\"ligand id\"', dataset.file_name, invert=True)
+
+
+class PHAR(GenericMolFile):
+    """
+    Pharmacophore database format from silicos-it.
+    """
+    file_ext = "phar"
+
+    def set_peek(self, dataset, is_multi_byte=False):
+        if not dataset.dataset.purged:
+            dataset.peek = get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
+            dataset.blurb = "pharmacophore"
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disk'
+
+
+class PDB(GenericMolFile):
+    """
+    Protein Databank format.
+    http://www.wwpdb.org/documentation/format33/v3.3.html
+    """
+    file_ext = "pdb"
+
+    def sniff(self, filename):
+        """
+        Try to guess if the file is a PDB file.
+
+        >>> from galaxy.datatypes.sniff import get_test_fname
+        >>> fname = get_test_fname('5e5z.pdb')
+        >>> PDB().sniff(fname)
+        True
+
+        >>> fname = get_test_fname('drugbank_drugs.cml')
+        >>> PDB().sniff(fname)
+        False
+        """
+        headers = get_headers(filename, sep=' ', count=300)
+        h = t = c = s = k = e = False
+        for line in headers:
+            section_name = line[0].strip()
+            if section_name == 'HEADER':
+                h = True
+            elif section_name == 'TITLE':
+                t = True
+            elif section_name == 'COMPND':
+                c = True
+            elif section_name == 'SOURCE':
+                s = True
+            elif section_name == 'KEYWDS':
+                k = True
+            elif section_name == 'EXPDTA':
+                e = True
+
+        if h * t * c * s * k * e:
+            return True
+        else:
+            return False
+
+    def set_peek(self, dataset, is_multi_byte=False):
+        if not dataset.dataset.purged:
+            atom_numbers = count_special_lines("^ATOM", dataset.file_name)
+            hetatm_numbers = count_special_lines("^HETATM", dataset.file_name)
+            dataset.peek = get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
+            dataset.blurb = "%s atoms and %s HET-atoms" % (atom_numbers, hetatm_numbers)
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disk'
+
+
+class grd(data.Text):
+    file_ext = "grd"
+
+    def set_peek(self, dataset, is_multi_byte=False):
+        if not dataset.dataset.purged:
+            dataset.peek = get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
+            dataset.blurb = "grids for docking"
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disk'
+
+
+class grdtgz(Binary):
+    file_ext = "grd.tgz"
+
+    def set_peek(self, dataset, is_multi_byte=False):
+        if not dataset.dataset.purged:
+            dataset.peek = 'binary data'
+            dataset.blurb = "compressed grids for docking"
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disk'
+
+
+class InChI(Tabular):
+    file_ext = "inchi"
+    column_names = ['InChI']
+    MetadataElement(name="columns", default=2, desc="Number of columns", readonly=True, visible=False)
+    MetadataElement(name="column_types", default=['str'], param=metadata.ColumnTypesParameter, desc="Column types", readonly=True, visible=False)
+    MetadataElement(name="number_of_molecules", default=0, desc="Number of molecules", readonly=True, visible=True, optional=True, no_value=0)
+
+    def set_meta(self, dataset, **kwd):
+        """
+        Set the number of lines of data in dataset.
+        """
+        dataset.metadata.number_of_molecules = self.count_data_lines(dataset)
+
+    def set_peek(self, dataset, is_multi_byte=False):
+        if not dataset.dataset.purged:
+            dataset.peek = get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
+            if (dataset.metadata.number_of_molecules == 1):
+                dataset.blurb = "1 molecule"
+            else:
+                dataset.blurb = "%s molecules" % dataset.metadata.number_of_molecules
+            dataset.peek = data.get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disk'
+
+    def sniff(self, filename):
+        """
+        Try to guess if the file is a InChI file.
+
+        >>> from galaxy.datatypes.sniff import get_test_fname
+        >>> fname = get_test_fname('drugbank_drugs.inchi')
+        >>> InChI().sniff(fname)
+        True
+
+        >>> fname = get_test_fname('drugbank_drugs.cml')
+        >>> InChI().sniff(fname)
+        False
+        """
+        inchi_lines = get_headers(filename, sep=' ', count=10)
+        for inchi in inchi_lines:
+            if not inchi[0].startswith('InChI='):
+                return False
+        return True
+
+
+class SMILES(Tabular):
+    file_ext = "smi"
+    column_names = ['SMILES', 'TITLE']
+    MetadataElement(name="columns", default=2, desc="Number of columns", readonly=True, visible=False)
+    MetadataElement(name="column_types", default=['str', 'str'], param=metadata.ColumnTypesParameter, desc="Column types", readonly=True, visible=False)
+    MetadataElement(name="number_of_molecules", default=0, desc="Number of molecules", readonly=True, visible=True, optional=True, no_value=0)
+
+    def set_meta(self, dataset, **kwd):
+        """
+        Set the number of lines of data in dataset.
+        """
+        dataset.metadata.number_of_molecules = self.count_data_lines(dataset)
+
+    def set_peek(self, dataset, is_multi_byte=False):
+        if not dataset.dataset.purged:
+            dataset.peek = get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
+            if dataset.metadata.number_of_molecules == 1:
+                dataset.blurb = "1 molecule"
+            else:
+                dataset.blurb = "%s molecules" % dataset.metadata.number_of_molecules
+            dataset.peek = data.get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disk'
+
+    '''
+    def sniff(self, filename):
+        """
+        Its hard or impossible to sniff a SMILES File. We can
+        try to import the first SMILES and check if it is a molecule, but
+        currently its not possible to use external libraries in datatype definition files.
+        Moreover it seems mpossible to inlcude OpenBabel as python library because OpenBabel
+        is GPL licensed.
+        """
+        self.molecule_number = count_lines(filename, non_empty = True)
+        word_count = count_lines(filename)
+
+        if self.molecule_number != word_count:
+            return False
+
+        if self.molecule_number > 0:
+            # test first 3 SMILES
+            smiles_lines = get_headers(filename, sep='\t', count=3)
+            for smiles_line in smiles_lines:
+                if len(smiles_line) > 2:
+                    return False
+                smiles = smiles_line[0]
+                try:
+                    # if we have atoms, we have a molecule
+                    if not len(pybel.readstring('smi', smiles).atoms) > 0:
+                        return False
+                except:
+                    # if convert fails its not a smiles string
+                    return False
+            return True
+        else:
+            return False
+    '''
+
+
+class CML(GenericXml):
+    """
+    Chemical Markup Language
+    http://cml.sourceforge.net/
+    """
+    file_ext = "cml"
+    MetadataElement(name="number_of_molecules", default=0, desc="Number of molecules", readonly=True, visible=True, optional=True, no_value=0)
+
+    def set_meta(self, dataset, **kwd):
+        """
+        Set the number of lines of data in dataset.
+        """
+        dataset.metadata.number_of_molecules = count_special_lines('^\s*<molecule', dataset.file_name)
+
+    def set_peek(self, dataset, is_multi_byte=False):
+        if not dataset.dataset.purged:
+            dataset.peek = get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
+            if (dataset.metadata.number_of_molecules == 1):
+                dataset.blurb = "1 molecule"
+            else:
+                dataset.blurb = "%s molecules" % dataset.metadata.number_of_molecules
+            dataset.peek = data.get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disk'
+
+    def sniff(self, filename):
+        """
+        Try to guess if the file is a CML file.
+
+        >>> from galaxy.datatypes.sniff import get_test_fname
+        >>> fname = get_test_fname('interval.interval')
+        >>> CML().sniff(fname)
+        False
+
+        >>> fname = get_test_fname('drugbank_drugs.cml')
+        >>> CML().sniff(fname)
+        True
+        """
+        handle = open(filename)
+        line = handle.readline()
+        if line.strip() != '<?xml version="1.0"?>':
+            handle.close()
+            return False
+        line = handle.readline()
+        if line.strip().find('http://www.xml-cml.org/schema') == -1:
+            handle.close()
+            return False
+        handle.close()
+        return True
+
+    def split(cls, input_datasets, subdir_generator_function, split_params):
+        """
+        Split the input files by molecule records.
+        """
+        if split_params is None:
+            return None
+
+        if len(input_datasets) > 1:
+            raise Exception("CML-file splitting does not support multiple files")
+        input_files = [ds.file_name for ds in input_datasets]
+
+        chunk_size = None
+        if split_params['split_mode'] == 'number_of_parts':
+            raise Exception('Split mode "%s" is currently not implemented for CML-files.' % split_params['split_mode'])
+        elif split_params['split_mode'] == 'to_size':
+            chunk_size = int(split_params['split_size'])
+        else:
+            raise Exception('Unsupported split mode %s' % split_params['split_mode'])
+
+        def _read_cml_records(filename):
+            lines = []
+            with open(filename) as handle:
+                for line in handle:
+                    if line.lstrip().startswith('<?xml version="1.0"?>') or \
+                       line.lstrip().startswith('<cml xmlns="http://www.xml-cml.org/schema') or \
+                       line.lstrip().startswith('</cml>'):
+                            continue
+                    lines.append(line)
+                    if line.lstrip().startswith('</molecule>'):
+                        yield lines
+                        lines = []
+
+        header_lines = ['<?xml version="1.0"?>\n', '<cml xmlns="http://www.xml-cml.org/schema">\n']
+        footer_line = ['</cml>\n']
+
+        def _write_part_cml_file(accumulated_lines):
+            part_dir = subdir_generator_function()
+            part_path = os.path.join(part_dir, os.path.basename(input_files[0]))
+            part_file = open(part_path, 'w')
+            part_file.writelines(header_lines)
+            part_file.writelines(accumulated_lines)
+            part_file.writelines(footer_line)
+            part_file.close()
+
+        try:
+            cml_records = _read_cml_records(input_files[0])
+            cml_lines_accumulated = []
+            for counter, cml_record in enumerate(cml_records, start=1):
+                cml_lines_accumulated.extend(cml_record)
+                if counter % chunk_size == 0:
+                    _write_part_cml_file(cml_lines_accumulated)
+                    cml_lines_accumulated = []
+            if cml_lines_accumulated:
+                _write_part_cml_file(cml_lines_accumulated)
+        except Exception, e:
+            log.error('Unable to split files: %s' % str(e))
+            raise
+    split = classmethod(split)
+
+    def merge(split_files, output_file):
+        """
+        Merging CML files.
+        """
+        if len(split_files) == 1:
+            # For one file only, use base class method (move/copy)
+            return data.Text.merge(split_files, output_file)
+        if not split_files:
+            raise ValueError("Given no CML files, %r, to merge into %s"
+                             % (split_files, output_file))
+        with open(output_file, "w") as out:
+            for filename in split_files:
+                with open(filename) as handle:
+                    header = handle.readline()
+                    if not header:
+                        raise ValueError("CML file %s was empty" % filename)
+                    if not header.lstrip().startswith('<?xml version="1.0"?>'):
+                        out.write(header)
+                        raise ValueError("%s is not a valid XML file!" % filename)
+                    line = handle.readline()
+                    header += line
+                    if not line.lstrip().startswith('<cml xmlns="http://www.xml-cml.org/schema'):
+                        out.write(header)
+                        raise ValueError("%s is not a CML file!" % filename)
+                    molecule_found = False
+                    for line in handle.readlines():
+                        # We found two required header lines, the next line should start with <molecule >
+                        if line.lstrip().startswith('</cml>'):
+                            continue
+                        if line.lstrip().startswith('<molecule'):
+                            molecule_found = True
+                        if molecule_found:
+                            out.write(line)
+            out.write("</cml>\n")
+    merge = staticmethod(merge)

lib/galaxy/datatypes/sniff.py

@@ -263,8 +263,9 @@ def guess_ext( fname, sniff_order, is_multi_byte=False ):
 
     >>> fname = get_test_fname('megablast_xml_parser_test1.blastxml')
     >>> from galaxy.datatypes import registry
+    >>> sample_conf = os.path.join(util.galaxy_directory(), "config", "datatypes_conf.xml.sample")
     >>> datatypes_registry = registry.Registry()
-    >>> datatypes_registry.load_datatypes()
+    >>> datatypes_registry.load_datatypes(root_dir=util.galaxy_directory(), config=sample_conf)
     >>> sniff_order = datatypes_registry.sniff_order
     >>> guess_ext(fname, sniff_order)
     'xml'
@@ -324,6 +325,24 @@ def guess_ext( fname, sniff_order, is_multi_byte=False ):
     >>> fname = get_test_fname('test.mz5')
     >>> guess_ext(fname, sniff_order)
     'h5'
+    >>> fname = get_test_fname('drugbank_drugs.cml')
+    >>> guess_ext(fname, sniff_order)
+    'cml'
+    >>> fname = get_test_fname('q.fps')
+    >>> guess_ext(fname, sniff_order)
+    'fps'
+    >>> fname = get_test_fname('drugbank_drugs.inchi')
+    >>> guess_ext(fname, sniff_order)
+    'inchi'
+    >>> fname = get_test_fname('drugbank_drugs.mol2')
+    >>> guess_ext(fname, sniff_order)
+    'mol2'
+    >>> fname = get_test_fname('drugbank_drugs.sdf')
+    >>> guess_ext(fname, sniff_order)
+    'sdf'
+    >>> fname = get_test_fname('5e5z.pdb')
+    >>> guess_ext(fname, sniff_order)
+    'pdb'
     """
     for datatype in sniff_order:
         """

lib/galaxy/datatypes/test/5e5z.pdb

@@ -0,0 +1,357 @@
+HEADER    DE NOVO PROTEIN, MEMBRANE PROTEIN       09-OCT-15   5E5Z              
+TITLE     STRUCTURE OF THE AMYLOID FORMING PEPTIDE LVHSSN (RESIDUES             
+COMPND    MOL_ID: 1;                                                            
+COMPND   2 MOLECULE: LVHSSN (RESIDUES 16-21) FROM ISLET AMYLOID POLYPEPTIDE;    
+COMPND   3 CHAIN: A;                                                            
+COMPND   4 ENGINEERED: YES                                                      
+SOURCE    MOL_ID: 1;                                                            
+SOURCE   2 SYNTHETIC: YES;                                                      
+SOURCE   3 ORGANISM_SCIENTIFIC: HOMO SAPIENS;                                   
+SOURCE   4 ORGANISM_TAXID: 9606                                                 
+KEYWDS    AMYLOID-LIKE PROTOFIBRIL, DE NOVO PROTEIN, MEMBRANE PROTEIN, PROTEIN  
+KEYWDS   2 FIBRIL                                                               
+EXPDTA    X-RAY DIFFRACTION                                                     
+AUTHOR    A.B.SORIAGA,D.EISENBERG                                               
+REVDAT   2   20-JAN-16 5E5Z    1       JRNL                                     
+REVDAT   1   16-DEC-15 5E5Z    0                                                
+JRNL        AUTH   A.B.SORIAGA,S.SANGWAN,R.MACDONALD,M.R.SAWAYA,D.EISENBERG     
+JRNL        TITL   CRYSTAL STRUCTURES OF IAPP AMYLOIDOGENIC SEGMENTS REVEAL A   
+JRNL        TITL 2 NOVEL PACKING MOTIF OF OUT-OF-REGISTER BETA SHEETS.          
+JRNL        REF    J.PHYS.CHEM.B                              2016              
+JRNL        REFN                   ISSN 1089-5647                               
+JRNL        PMID   26629790                                                     
+JRNL        DOI    10.1021/ACS.JPCB.5B09981                                     
+REMARK   2                                                                      
+REMARK   2 RESOLUTION.    1.66 ANGSTROMS.                                       
+REMARK   3                                                                      
+REMARK   3 REFINEMENT.                                                          
+REMARK   3   PROGRAM     : PHENIX 1.6.4_486                                     
+REMARK   3   AUTHORS     : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN            
+REMARK   3               : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,           
+REMARK   3               : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,            
+REMARK   3               : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,              
+REMARK   3               : REETAL PAI,RANDY READ,JANE RICHARDSON,               
+REMARK   3               : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,           
+REMARK   3               : NICHOLAS SAUTER,JACOB SMITH,LAURENT                  
+REMARK   3               : STORONI,TOM TERWILLIGER,PETER ZWART                  
+REMARK   3                                                                      
+REMARK   3    REFINEMENT TARGET : LS_WUNIT_K1                                   
+REMARK   3                                                                      
+REMARK   3  DATA USED IN REFINEMENT.                                            
+REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.66                           
+REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 9.46                           
+REMARK   3   MIN(FOBS/SIGMA_FOBS)              : 0.000                          
+REMARK   3   COMPLETENESS FOR RANGE        (%) : 89.1                           
+REMARK   3   NUMBER OF REFLECTIONS             : 391                            
+REMARK   3                                                                      
+REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
+REMARK   3   R VALUE     (WORKING + TEST SET) : 0.170                           
+REMARK   3   R VALUE            (WORKING SET) : 0.167                           
+REMARK   3   FREE R VALUE                     : 0.198                           
+REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 4.600                           
+REMARK   3   FREE R VALUE TEST SET COUNT      : 18                              
+REMARK   3                                                                      
+REMARK   3  FIT TO DATA USED IN REFINEMENT (IN BINS).                           
+REMARK   3   BIN  RESOLUTION RANGE  COMPL.    NWORK NFREE   RWORK  RFREE        
+REMARK   3     1  9.4587 -  1.6644    0.89      373    18  0.1673 0.1983        
+REMARK   3                                                                      
+REMARK   3  BULK SOLVENT MODELLING.                                             
+REMARK   3   METHOD USED        : FLAT BULK SOLVENT MODEL                       
+REMARK   3   SOLVENT RADIUS     : 0.00                                          
+REMARK   3   SHRINKAGE RADIUS   : 0.00                                          
+REMARK   3   K_SOL              : 0.60                                          
+REMARK   3   B_SOL              : 251.4                                         
+REMARK   3                                                                      
+REMARK   3  ERROR ESTIMATES.                                                    
+REMARK   3   COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED)     : 0.310            
+REMARK   3   PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.270           
+REMARK   3                                                                      
+REMARK   3  B VALUES.                                                           
+REMARK   3   FROM WILSON PLOT           (A**2) : NULL                           
+REMARK   3   MEAN B VALUE      (OVERALL, A**2) : NULL                           
+REMARK   3   OVERALL ANISOTROPIC B VALUE.                                       
+REMARK   3    B11 (A**2) : 0.51090                                              
+REMARK   3    B22 (A**2) : -3.44720                                             
+REMARK   3    B33 (A**2) : -8.26450                                             
+REMARK   3    B12 (A**2) : 0.00000                                              
+REMARK   3    B13 (A**2) : 0.77970                                              
+REMARK   3    B23 (A**2) : 0.00000                                              
+REMARK   3                                                                      
+REMARK   3  TWINNING INFORMATION.                                               
+REMARK   3   FRACTION: NULL                                                     
+REMARK   3   OPERATOR: NULL                                                     
+REMARK   3                                                                      
+REMARK   3  DEVIATIONS FROM IDEAL VALUES.                                       
+REMARK   3                 RMSD          COUNT                                  
+REMARK   3   BOND      :  0.004             46                                  
+REMARK   3   ANGLE     :  0.975             62                                  
+REMARK   3   CHIRALITY :  0.056              8                                  
+REMARK   3   PLANARITY :  0.004              8                                  
+REMARK   3   DIHEDRAL  : 10.740             15                                  
+REMARK   3                                                                      
+REMARK   3  TLS DETAILS                                                         
+REMARK   3   NUMBER OF TLS GROUPS  : 1                                          
+REMARK   3   TLS GROUP : 1                                                      
+REMARK   3    SELECTION: ALL                                                    
+REMARK   3    ORIGIN FOR THE GROUP (A):   4.5323   0.1096   3.9760              
+REMARK   3    T TENSOR                                                          
+REMARK   3      T11:  -0.1260 T22:  -0.0788                                     
+REMARK   3      T33:  -0.0487 T12:   0.0821                                     
+REMARK   3      T13:  -0.0518 T23:   0.0723                                     
+REMARK   3    L TENSOR                                                          
+REMARK   3      L11:   0.1003 L22:   0.0184                                     
+REMARK   3      L33:   0.0647 L12:  -0.0319                                     
+REMARK   3      L13:   0.0506 L23:  -0.0233                                     
+REMARK   3    S TENSOR                                                          
+REMARK   3      S11:   0.0084 S12:  -0.0300 S13:  -0.0565                       
+REMARK   3      S21:   0.0231 S22:   0.0090 S23:   0.0127                       
+REMARK   3      S31:  -0.0046 S32:  -0.0049 S33:  -0.0009                       
+REMARK   3                                                                      
+REMARK   3  NCS DETAILS                                                         
+REMARK   3   NUMBER OF NCS GROUPS : NULL                                        
+REMARK   3                                                                      
+REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
+REMARK   4                                                                      
+REMARK   4 5E5Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
+REMARK 100                                                                      
+REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-OCT-15.                  
+REMARK 100 THE DEPOSITION ID IS D_1000214421.                                   
+REMARK 200                                                                      
+REMARK 200 EXPERIMENTAL DETAILS                                                 
+REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
+REMARK 200  DATE OF DATA COLLECTION        : 10-MAR-10                          
+REMARK 200  TEMPERATURE           (KELVIN) : 291                                
+REMARK 200  PH                             : NULL                               
+REMARK 200  NUMBER OF CRYSTALS USED        : NULL                               
+REMARK 200                                                                      
+REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
+REMARK 200  RADIATION SOURCE               : APS                                
+REMARK 200  BEAMLINE                       : 24-ID-E                            
+REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
+REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
+REMARK 200  WAVELENGTH OR RANGE        (A) : 0.979                              
+REMARK 200  MONOCHROMATOR                  : NULL                               
+REMARK 200  OPTICS                         : NULL                               
+REMARK 200                                                                      
+REMARK 200  DETECTOR TYPE                  : CCD                                
+REMARK 200  DETECTOR MANUFACTURER          : ADSC QUANTUM 315                   
+REMARK 200  INTENSITY-INTEGRATION SOFTWARE : DENZO                              
+REMARK 200  DATA SCALING SOFTWARE          : NULL                               
+REMARK 200                                                                      
+REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 1136                               
+REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.600                              
+REMARK 200  RESOLUTION RANGE LOW       (A) : 100.000                            
+REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL                               
+REMARK 200                                                                      
+REMARK 200 OVERALL.                                                             
+REMARK 200  COMPLETENESS FOR RANGE     (%) : 92.9                               
+REMARK 200  DATA REDUNDANCY                : 2.900                              
+REMARK 200  R MERGE                    (I) : 0.07600                            
+REMARK 200  R SYM                      (I) : NULL                               
+REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 17.8600                            
+REMARK 200                                                                      
+REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
+REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL                     
+REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : NULL                     
+REMARK 200  COMPLETENESS FOR SHELL     (%) : NULL                               
+REMARK 200  DATA REDUNDANCY IN SHELL       : NULL                               
+REMARK 200  R MERGE FOR SHELL          (I) : NULL                               
+REMARK 200  R SYM FOR SHELL            (I) : NULL                               
+REMARK 200  <I/SIGMA(I)> FOR SHELL         : NULL                               
+REMARK 200                                                                      
+REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
+REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT        
+REMARK 200 SOFTWARE USED: PHASER                                                
+REMARK 200 STARTING MODEL: NULL                                                 
+REMARK 200                                                                      
+REMARK 200 REMARK: NULL                                                         
+REMARK 280                                                                      
+REMARK 280 CRYSTAL                                                              
+REMARK 280 SOLVENT CONTENT, VS   (%): 6.59                                      
+REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.32                     
+REMARK 280                                                                      
+REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MG/ML IN WATER AND MIXED WITH 0.09    
+REMARK 280  M HEPES PH 7.5, 1.26M TRI-SODIUM CITRATE, AND 10% GLYCEROL,         
+REMARK 280  VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K                     
+REMARK 290                                                                      
+REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
+REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1                         
+REMARK 290                                                                      
+REMARK 290      SYMOP   SYMMETRY                                                
+REMARK 290     NNNMMM   OPERATOR                                                
+REMARK 290       1555   X,Y,Z                                                   
+REMARK 290       2555   -X,Y+1/2,-Z                                             
+REMARK 290                                                                      
+REMARK 290     WHERE NNN -> OPERATOR NUMBER                                     
+REMARK 290           MMM -> TRANSLATION VECTOR                                  
+REMARK 290                                                                      
+REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS                            
+REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM             
+REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY                
+REMARK 290 RELATED MOLECULES.                                                   
+REMARK 290   SMTRY1   1  1.000000  0.000000  0.000000        0.00000            
+REMARK 290   SMTRY2   1  0.000000  1.000000  0.000000        0.00000            
+REMARK 290   SMTRY3   1  0.000000  0.000000  1.000000        0.00000            
+REMARK 290   SMTRY1   2 -1.000000  0.000000  0.000000        0.00000            
+REMARK 290   SMTRY2   2  0.000000  1.000000  0.000000        4.80450            
+REMARK 290   SMTRY3   2  0.000000  0.000000 -1.000000        0.00000            
+REMARK 290                                                                      
+REMARK 290 REMARK: NULL                                                         
+REMARK 300                                                                      
+REMARK 300 BIOMOLECULE: 1                                                       
+REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM                
+REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN                  
+REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON               
+REMARK 300 BURIED SURFACE AREA.                                                 
+REMARK 350                                                                      
+REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN           
+REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE                
+REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS          
+REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC AND                          
+REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.                               
+REMARK 350                                                                      
+REMARK 350 BIOMOLECULE: 1                                                       
+REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DECAMERIC                         
+REMARK 350 APPLY THE FOLLOWING TO CHAINS: A                                     
+REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000            
+REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000        0.00000            
+REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000        0.00000            
+REMARK 350   BIOMT1   2  1.000000  0.000000  0.000000        0.00000            
+REMARK 350   BIOMT2   2  0.000000  1.000000  0.000000       -9.60900            
+REMARK 350   BIOMT3   2  0.000000  0.000000  1.000000        0.00000            
+REMARK 350   BIOMT1   3  1.000000  0.000000  0.000000        0.00000            
+REMARK 350   BIOMT2   3  0.000000  1.000000  0.000000        9.60900            
+REMARK 350   BIOMT3   3  0.000000  0.000000  1.000000        0.00000            
+REMARK 350   BIOMT1   4  1.000000  0.000000  0.000000        9.64300            
+REMARK 350   BIOMT2   4  0.000000  1.000000  0.000000        0.00000            
+REMARK 350   BIOMT3   4  0.000000  0.000000  1.000000        0.00000            
+REMARK 350   BIOMT1   5  1.000000  0.000000  0.000000        9.64300            
+REMARK 350   BIOMT2   5  0.000000  1.000000  0.000000       -9.60900            
+REMARK 350   BIOMT3   5  0.000000  0.000000  1.000000        0.00000            
+REMARK 350   BIOMT1   6  1.000000  0.000000  0.000000        9.64300            
+REMARK 350   BIOMT2   6  0.000000  1.000000  0.000000        9.60900            
+REMARK 350   BIOMT3   6  0.000000  0.000000  1.000000        0.00000            
+REMARK 350   BIOMT1   7 -1.000000  0.000000  0.000000        9.64300            
+REMARK 350   BIOMT2   7  0.000000  1.000000  0.000000       -4.80450            
+REMARK 350   BIOMT3   7  0.000000  0.000000 -1.000000        0.00000            
+REMARK 350   BIOMT1   8 -1.000000  0.000000  0.000000        9.64300            
+REMARK 350   BIOMT2   8  0.000000  1.000000  0.000000        4.80450            
+REMARK 350   BIOMT3   8  0.000000  0.000000 -1.000000        0.00000            
+REMARK 350   BIOMT1   9 -1.000000  0.000000  0.000000       19.28600            
+REMARK 350   BIOMT2   9  0.000000  1.000000  0.000000       -4.80450            
+REMARK 350   BIOMT3   9  0.000000  0.000000 -1.000000        0.00000            
+REMARK 350   BIOMT1  10 -1.000000  0.000000  0.000000       19.28600            
+REMARK 350   BIOMT2  10  0.000000  1.000000  0.000000        4.80450            
+REMARK 350   BIOMT3  10  0.000000  0.000000 -1.000000        0.00000            
+REMARK 900                                                                      
+REMARK 900 RELATED ENTRIES                                                      
+REMARK 900 RELATED ID: 5E5V   RELATED DB: PDB                                   
+REMARK 900 RELATED ID: 5E5X   RELATED DB: PDB                                   
+REMARK 900 RELATED ID: 5E61   RELATED DB: PDB                                   
+DBREF  5E5Z A    1     6  PDB    5E5Z     5E5Z             1      6             
+SEQRES   1 A    6  LEU VAL HIS SER SER ASN                                      
+FORMUL   2  HOH   *(H2 O)                                                       
+CRYST1    9.643    9.609   19.029  90.00 101.22  90.00 P 1 21 1      2          
+ORIGX1      1.000000  0.000000  0.000000        0.00000                         
+ORIGX2      0.000000  1.000000  0.000000        0.00000                         
+ORIGX3      0.000000  0.000000  1.000000        0.00000                         
+SCALE1      0.103702  0.000000  0.020579        0.00000                         
+SCALE2      0.000000  0.104069  0.000000        0.00000                         
+SCALE3      0.000000  0.000000  0.053576        0.00000                         
+ATOM      1  N   LEU A   1       6.078  -0.306  -5.753  1.00  0.00           N  
+ANISOU    1  N   LEU A   1        0      0      0      0      0      0       N  
+ATOM      2  CA  LEU A   1       5.166  -0.026  -4.647  1.00  2.42           C  
+ANISOU    2  CA  LEU A   1      307    307    307      0      0      0       C  
+ATOM      3  C   LEU A   1       5.682  -0.642  -3.356  1.00  3.48           C  
+ANISOU    3  C   LEU A   1      435    443    445      1      1      9       C  
+ATOM      4  O   LEU A   1       6.056  -1.814  -3.322  1.00  3.52           O  
+ANISOU    4  O   LEU A   1      436    449    454      2      2     16       O  
+ATOM      5  CB  LEU A   1       3.755  -0.555  -4.967  1.00  1.86           C  
+ANISOU    5  CB  LEU A   1      232    237    238      1      1      5       C  
+ATOM      6  CG  LEU A   1       2.596  -0.354  -3.975  1.00  6.87           C  
+ANISOU    6  CG  LEU A   1      861    873    877      2      2     14       C  
+ATOM      7  CD1 LEU A   1       2.753  -1.182  -2.704  1.00 11.83           C  
+ANISOU    7  CD1 LEU A   1     1481   1504   1512      4      4     27       C  
+ATOM      8  CD2 LEU A   1       2.404   1.122  -3.638  1.00  4.27           C  
+ANISOU    8  CD2 LEU A   1      537    543    544      1      2      7       C  
+ATOM      9  N   VAL A   2       5.715   0.161  -2.297  1.00  0.61           N  
+ANISOU    9  N   VAL A   2       71     80     82      2      2     11       N  
+ATOM     10  CA  VAL A   2       5.968  -0.352  -0.960  1.00  0.12           C  
+ANISOU   10  CA  VAL A   2        1     20     24      4      4     22       C  
+ATOM     11  C   VAL A   2       4.976   0.281   0.000  1.00  3.40           C  
+ANISOU   11  C   VAL A   2      413    437    440      5      5     27       C  
+ATOM     12  O   VAL A   2       4.746   1.489  -0.046  1.00  3.22           O  
+ANISOU   12  O   VAL A   2      395    414    414      4      5     20       O  
+ATOM     13  CB  VAL A   2       7.400  -0.027  -0.475  1.00  3.56           C  
+ANISOU   13  CB  VAL A   2      440    456    458      3      3     18       C  
+ATOM     14  CG1 VAL A   2       7.566  -0.421   0.993  1.00  7.93           C  
+ANISOU   14  CG1 VAL A   2      986   1012   1016      5      5     30       C  
+ATOM     15  CG2 VAL A   2       8.429  -0.722  -1.342  1.00  6.71           C  
+ANISOU   15  CG2 VAL A   2      841    853    856      2      2     14       C  
+ATOM     16  N   HIS A   3       4.367  -0.537   0.850  1.00  0.22           N  
+ANISOU   16  N   HIS A   3        1     38     44      7      8     41       N  
+ATOM     17  CA  HIS A   3       3.603  -0.011   1.971  1.00  1.73           C  
+ANISOU   17  CA  HIS A   3      189    233    237     10     10     48       C  
+ATOM     18  C   HIS A   3       4.003  -0.675   3.280  1.00  1.84           C  
+ANISOU   18  C   HIS A   3      194    250    255     12     12     61       C  
+ATOM     19  O   HIS A   3       4.208  -1.889   3.338  1.00  0.73           O  
+ANISOU   19  O   HIS A   3       47    109    120     11     12     69       O  
+ATOM     20  CB  HIS A   3       2.095  -0.177   1.781  1.00  2.62           C  
+ANISOU   20  CB  HIS A   3      296    346    351     11     11     54       C  
+ATOM     21  CG  HIS A   3       1.324   0.074   3.040  1.00  2.97           C  
+ANISOU   21  CG  HIS A   3      335    396    399     14     14     66       C  
+ATOM     22  ND1 HIS A   3       0.950  -0.937   3.900  1.00  4.29           N  
+ANISOU   22  ND1 HIS A   3      491    566    573     16     17     82       N  
+ATOM     23  CD2 HIS A   3       0.921   1.230   3.620  1.00  4.90           C  
+ANISOU   23  CD2 HIS A   3      581    642    639     16     16     64       C  
+ATOM     24  CE1 HIS A   3       0.321  -0.417   4.940  1.00  5.53           C  
+ANISOU   24  CE1 HIS A   3      644    727    729     20     20     89       C  
+ATOM     25  NE2 HIS A   3       0.290   0.896   4.794  1.00  6.02           N  
+ANISOU   25  NE2 HIS A   3      714    790    785     20     19     78       N  
+ATOM     26  N   SER A   4       4.099   0.141   4.326  1.00  0.34           N  
+ANISOU   26  N   SER A   4        3     63     63     14     14     62       N  
+ATOM     27  CA  SER A   4       4.357  -0.330   5.683  1.00  1.49           C  
+ANISOU   27  CA  SER A   4      141    213    213     16     16     75       C  
+ATOM     28  C   SER A   4       3.814   0.686   6.681  1.00  2.14           C  
+ANISOU   28  C   SER A   4      222    299    292     20     19     78       C  
+ATOM     29  O   SER A   4       4.008   1.889   6.507  1.00  3.47           O  
+ANISOU   29  O   SER A   4      397    465    454     19     18     68       O  
+ATOM     30  CB  SER A   4       5.858  -0.513   5.905  1.00  5.61           C  
+ANISOU   30  CB  SER A   4      665    734    734     15     15     72       C  
+ATOM     31  OG  SER A   4       6.132  -0.771   7.272  1.00  9.89           O  
+ANISOU   31  OG  SER A   4     1200   1280   1278     18     18     83       O  
+ATOM     32  N   SER A   5       3.138   0.213   7.725  1.00  2.34           N  
+ANISOU   32  N   SER A   5      239    330    322     24     23     93       N  
+ATOM     33  CA  SER A   5       2.651   1.119   8.765  1.00  0.66           C  
+ANISOU   33  CA  SER A   5       24    123    106     28     26     97       C  
+ATOM     34  C   SER A   5       3.677   1.311   9.885  1.00  2.66           C  
+ANISOU   34  C   SER A   5      275    378    356     30     27    100       C  
+ATOM     35  O   SER A   5       3.411   2.024  10.851  1.00  2.02           O  
+ANISOU   35  O   SER A   5      193    303    273     35     30    104       O  
+ATOM     36  CB  SER A   5       1.318   0.639   9.350  1.00  2.68           C  
+ANISOU   36  CB  SER A   5      269    383    365     32     29    113       C  
+ATOM     37  OG  SER A   5       1.478  -0.544  10.117  1.00  2.49           O  
+ANISOU   37  OG  SER A   5      236    363    349     33     31    128       O  
+ATOM     38  N   ASN A   6       4.838   0.672   9.758  1.00  2.94           N  
+ANISOU   38  N   ASN A   6      311    412    394     28     25     98       N  
+ATOM     39  CA  ASN A   6       5.912   0.838  10.741  1.00  4.68           C  
+ANISOU   39  CA  ASN A   6      530    634    613     29     26    100       C  
+ATOM     40  C   ASN A   6       6.574   2.203  10.638  1.00 10.84           C  
+ANISOU   40  C   ASN A   6     1320   1413   1387     28     24     87       C  
+ATOM     41  O   ASN A   6       7.335   2.594  11.519  1.00 13.68           O  
+ANISOU   41  O   ASN A   6     1680   1775   1745     30     26     88       O  
+ATOM     42  CB  ASN A   6       6.986  -0.243  10.589  1.00  5.08           C  
+ANISOU   42  CB  ASN A   6      579    682    668     27     25    102       C  
+ATOM     43  CG  ASN A   6       6.592  -1.558  11.236  1.00  8.08           C  
+ANISOU   43  CG  ASN A   6      948   1067   1057     28     27    120       C  
+ATOM     44  OD1 ASN A   6       5.576  -1.644  11.923  1.00  8.72           O  
+ANISOU   44  OD1 ASN A   6     1022   1152   1139     32     30    131       O  
+ATOM     45  ND2 ASN A   6       7.409  -2.588  11.030  1.00  9.89           N  
+ANISOU   45  ND2 ASN A   6     1174   1293   1290     25     25    122       N  
+ATOM     46  OXT ASN A   6       6.383   2.933   9.667  1.00 14.02           O  
+ANISOU   46  OXT ASN A   6     1730   1811   1787     25     22     75       O  
+TER      47      ASN A   6                                                      
+HETATM   48  O   HOH A 101       8.203   1.052  -4.564  1.00 12.67           O  
+ANISOU   48  O   HOH A 101     1605   1605   1605      0      0      0       O  
+MASTER      227    0    0    0    0    0    0    6   47    1    0    1          
+END                                                                             

lib/galaxy/datatypes/test/drugbank_drugs.cml

@@ -0,0 +1,385 @@
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+   <bond atomRefs2="a76 a79" order="1"/>
+   <bond atomRefs2="a76 a81" order="2"/>
+   <bond atomRefs2="a77 a85" order="2"/>
+   <bond atomRefs2="a79 a84" order="2"/>
+   <bond atomRefs2="a81 a86" order="1"/>
+   <bond atomRefs2="a82 a88" order="1"/>
+   <bond atomRefs2="a83 a89" order="2"/>
+   <bond atomRefs2="a84 a87" order="1"/>
+   <bond atomRefs2="a86 a87" order="2"/>
+   <bond atomRefs2="a88 a91" order="2"/>
+   <bond atomRefs2="a89 a91" order="1"/>
+  </bondArray>
+ </molecule>
+ <molecule id="Desmopressin">
+  <atomArray>
+   <atom id="a1" elementType="N" x2="0.000000" y2="-7.864600"/>
+   <atom id="a2" elementType="C" x2="0.674100" y2="-7.460100"/>
+   <atom id="a3" elementType="C" x2="1.393200" y2="-7.864600"/>
+   <atom id="a4" elementType="N" x2="2.112200" y2="-7.460100"/>
+   <atom id="a5" elementType="C" x2="2.831300" y2="-7.864600"/>
+   <atom id="a6" elementType="C" x2="3.550300" y2="-7.460100">
+    <atomParity atomRefs4="a6 a12 a7 a5">1</atomParity>
+   </atom>
+   <atom id="a7" elementType="N" x2="4.269300" y2="-7.864600"/>
+   <atom id="a8" elementType="C" x2="4.943500" y2="-7.460100"/>
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+   <atom id="a14" elementType="C" x2="2.831300" y2="-5.437800"/>
+   <atom id="a15" elementType="N" x2="2.112200" y2="-5.033300"/>
+   <atom id="a16" elementType="C" x2="4.943500" y2="-6.651200">
+    <atomParity atomRefs4="a16 a8 a17 a18">1</atomParity>
+   </atom>
+   <atom id="a17" elementType="C" x2="4.314300" y2="-6.156800"/>
+   <atom id="a18" elementType="N" x2="5.617600" y2="-6.156800"/>
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+    <atomParity atomRefs4="a22 a21 a28 a23">1</atomParity>
+   </atom>
+   <atom id="a23" elementType="N" x2="7.774700" y2="-6.561300"/>
+   <atom id="a24" elementType="C" x2="8.448800" y2="-6.156800"/>
+   <atom id="a25" elementType="C" x2="9.167800" y2="-6.561300">
+    <atomParity atomRefs4="a25 a32 a26 a24">1</atomParity>
+   </atom>
+   <atom id="a26" elementType="N" x2="9.886900" y2="-6.156800"/>
+   <atom id="a27" elementType="O" x2="6.336600" y2="-7.415200"/>
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+   <atom id="a29" elementType="S" x2="6.336600" y2="-4.943500"/>
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+   <atom id="a34" elementType="O" x2="9.886900" y2="-8.628600"/>
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+   <atom id="a37" elementType="C" x2="10.606000" y2="-4.943500">
+    <atomParity atomRefs4="a37 a39 a44 a36">1</atomParity>
+   </atom>
+   <atom id="a38" elementType="O" x2="9.167800" y2="-4.943500"/>
+   <atom id="a39" elementType="C" x2="11.325000" y2="-5.347900"/>
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+   <atom id="a43" elementType="O" x2="12.763100" y2="-6.201800"/>
+   <atom id="a44" elementType="N" x2="10.606000" y2="-4.134500"/>
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+   <atom id="a48" elementType="C" x2="9.886900" y2="-2.876200">
+    <atomParity atomRefs4="a48 a47 a61 a49">1</atomParity>
+   </atom>
+   <atom id="a49" elementType="C" x2="9.886900" y2="-3.730000"/>
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+   <atom id="a59" elementType="O" x2="8.448800" y2="-3.730000"/>
+   <atom id="a60" elementType="C" x2="7.774700" y2="-2.471700">
+    <atomParity atomRefs4="a60 a63 a54 a58">1</atomParity>
+   </atom>
+   <atom id="a61" elementType="N" x2="9.167800" y2="-2.471700"/>
+   <atom id="a62" elementType="O" x2="9.167800" y2="-4.134500"/>
+   <atom id="a63" elementType="C" x2="7.774700" y2="-1.662800"/>
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+   <atom id="a65" elementType="C" x2="8.448800" y2="-1.258300"/>
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+   <atom id="a67" elementType="C" x2="9.886900" y2="-0.404500"/>
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+   <atom id="a70" elementType="O" x2="6.336600" y2="-1.662800"/>
+   <atom id="a71" elementType="O" x2="10.606000" y2="0.000000"/>
+   <atom id="a72" elementType="C" x2="1.393200" y2="-5.437800"/>
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+   <atom id="a74" elementType="N" x2="0.674100" y2="-5.033300"/>
+  </atomArray>
+  <bondArray>
+   <bond atomRefs2="a1 a2" order="1"/>
+   <bond atomRefs2="a2 a3" order="1"/>
+   <bond atomRefs2="a2 a10" order="2"/>
+   <bond atomRefs2="a3 a4" order="1"/>
+   <bond atomRefs2="a4 a5" order="1"/>
+   <bond atomRefs2="a5 a6" order="1"/>
+   <bond atomRefs2="a5 a11" order="2"/>
+   <bond atomRefs2="a6 a7" order="1"/>
+   <bond atomRefs2="a6 a12" order="1"/>
+   <bond atomRefs2="a7 a8" order="1"/>
+   <bond atomRefs2="a8 a9" order="2"/>
+   <bond atomRefs2="a16 a8" order="1"/>
+   <bond atomRefs2="a12 a13" order="1"/>
+   <bond atomRefs2="a13 a14" order="1"/>
+   <bond atomRefs2="a14 a15" order="1"/>
+   <bond atomRefs2="a15 a72" order="1"/>
+   <bond atomRefs2="a16 a17" order="1"/>
+   <bond atomRefs2="a16 a18" order="1"/>
+   <bond atomRefs2="a17 a19" order="1"/>
+   <bond atomRefs2="a18 a20" order="1"/>
+   <bond atomRefs2="a18 a21" order="1"/>
+   <bond atomRefs2="a19 a20" order="1"/>
+   <bond atomRefs2="a22 a21" order="1"/>
+   <bond atomRefs2="a21 a27" order="2"/>
+   <bond atomRefs2="a22 a23" order="1"/>
+   <bond atomRefs2="a22 a28" order="1"/>
+   <bond atomRefs2="a23 a24" order="1"/>
+   <bond atomRefs2="a24 a25" order="1"/>
+   <bond atomRefs2="a24 a31" order="2"/>
+   <bond atomRefs2="a25 a26" order="1"/>
+   <bond atomRefs2="a25 a32" order="1"/>
+   <bond atomRefs2="a26 a36" order="1"/>
+   <bond atomRefs2="a28 a29" order="1"/>
+   <bond atomRefs2="a29 a30" order="1"/>
+   <bond atomRefs2="a30 a57" order="1"/>
+   <bond atomRefs2="a32 a33" order="1"/>
+   <bond atomRefs2="a33 a34" order="2"/>
+   <bond atomRefs2="a33 a35" order="1"/>
+   <bond atomRefs2="a36 a37" order="1"/>
+   <bond atomRefs2="a36 a38" order="2"/>
+   <bond atomRefs2="a37 a39" order="1"/>
+   <bond atomRefs2="a37 a44" order="1"/>
+   <bond atomRefs2="a39 a40" order="1"/>
+   <bond atomRefs2="a40 a41" order="1"/>
+   <bond atomRefs2="a41 a42" order="1"/>
+   <bond atomRefs2="a41 a43" order="2"/>
+   <bond atomRefs2="a44 a49" order="1"/>
+   <bond atomRefs2="a45 a47" order="1"/>
+   <bond atomRefs2="a45 a52" order="1"/>
+   <bond atomRefs2="a45 a46" order="2"/>
+   <bond atomRefs2="a46 a53" order="1"/>
+   <bond atomRefs2="a48 a47" order="1"/>
+   <bond atomRefs2="a48 a61" order="1"/>
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+   <bond atomRefs2="a49 a62" order="2"/>
+   <bond atomRefs2="a50 a51" order="1"/>
+   <bond atomRefs2="a50 a52" order="2"/>
+   <bond atomRefs2="a51 a53" order="2"/>
+   <bond atomRefs2="a54 a55" order="1"/>
+   <bond atomRefs2="a54 a60" order="1"/>
+   <bond atomRefs2="a55 a56" order="1"/>
+   <bond atomRefs2="a55 a70" order="2"/>
+   <bond atomRefs2="a56 a57" order="1"/>
+   <bond atomRefs2="a58 a59" order="2"/>
+   <bond atomRefs2="a58 a60" order="1"/>
+   <bond atomRefs2="a58 a61" order="1"/>
+   <bond atomRefs2="a60 a63" order="1"/>
+   <bond atomRefs2="a63 a65" order="1"/>
+   <bond atomRefs2="a64 a66" order="2"/>
+   <bond atomRefs2="a64 a65" order="1"/>
+   <bond atomRefs2="a65 a68" order="2"/>
+   <bond atomRefs2="a66 a67" order="1"/>
+   <bond atomRefs2="a67 a69" order="2"/>
+   <bond atomRefs2="a67 a71" order="1"/>
+   <bond atomRefs2="a68 a69" order="1"/>
+   <bond atomRefs2="a72 a73" order="2"/>
+   <bond atomRefs2="a72 a74" order="1"/>
+  </bondArray>
+ </molecule>
+</cml>

lib/galaxy/datatypes/test/drugbank_drugs.inchi

@@ -0,0 +1,2 @@
+InChI=1S/C59H84N18O14/c1-31(2)22-40(49(82)68-39(12-8-20-64-57(60)61)56(89)77-21-9-13-46(77)55(88)75-76-58(62)90)69-54(87)45(29-91-59(3,4)5)74-50(83)41(23-32-14-16-35(79)17-15-32)70-53(86)44(28-78)73-51(84)42(24-33-26-65-37-11-7-6-10-36(33)37)71-52(85)43(25-34-27-63-30-66-34)72-48(81)38-18-19-47(80)67-38/h6-7,10-11,14-17,26-27,30-31,38-46,65,78-79H,8-9,12-13,18-25,28-29H2,1-5H3,(H,63,66)(H,67,80)(H,68,82)(H,69,87)(H,70,86)(H,71,85)(H,72,81)(H,73,84)(H,74,83)(H,75,88)(H4,60,61,64)(H3,62,76,90)/t38-,39-,40-,41-,42-,43-,44-,45+,46-/m0/s1
+InChI=1S/C46H64N14O12S2/c47-35(62)15-14-29-40(67)58-32(22-36(48)63)43(70)59-33(45(72)60-18-5-9-34(60)44(71)56-28(8-4-17-52-46(50)51)39(66)53-23-37(49)64)24-74-73-19-16-38(65)54-30(21-26-10-12-27(61)13-11-26)41(68)57-31(42(69)55-29)20-25-6-2-1-3-7-25/h1-3,6-7,10-13,28-34,61H,4-5,8-9,14-24H2,(H2,47,62)(H2,48,63)(H2,49,64)(H,53,66)(H,54,65)(H,55,69)(H,56,71)(H,57,68)(H,58,67)(H,59,70)(H4,50,51,52)/t28-,29-,30-,31-,32-,33-,34-/m0/s1

lib/galaxy/datatypes/test/drugbank_drugs.mol2

@@ -0,0 +1,354 @@
+@<TRIPOS>MOLECULE
+Goserelin
+ 91 96 0 0 0
+SMALL
+GASTEIGER
+
+@<TRIPOS>ATOM
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+      2 O          13.9726   -2.5226    0.0000 O.2     4  UNK4       -0.2699
+      3 O          10.1766   -3.9327    0.0000 O.2     4  UNK4       -0.2715
+      4 O          11.2019   -0.7961    0.0000 O.3     4  UNK4       -0.3562
+      5 O           8.7800   -1.3064    0.0000 O.2     4  UNK4       -0.2714
+      6 O          16.8589   -3.2421    0.0000 O.2     4  UNK4       -0.2457
+      7 O          10.3562    1.2163    0.0000 O.2     4  UNK4       -0.2715
+      8 O           3.2702    4.8341    0.0000 O.2     1  UNK1       -0.2715
+      9 O           2.3500    8.2734    0.0000 O.2     1  UNK1       -0.2733
+     10 O           3.8213    4.2201    0.0000 O.2     2  HIS2       -0.2715
+     11 O           5.2178    1.5938    0.0000 O.2     3  TRP3       -0.2715
+     12 O           7.8960    2.8883    0.0000 O.2     4  UNK4       -0.2714
+     13 O           7.1271    0.5358    0.0000 O.3     4  UNK4       -0.2179
+     14 O          12.4834    3.1249    0.0000 O.3     4  UNK4       -0.2866
+     15 N          13.1495   -4.0364    0.0000 N.am    4  UNK4       -0.2715
+     16 N          11.2402   -2.9784    0.0000 N.am    4  UNK4       -0.1964
+     17 N          15.2089   -3.2393    0.0000 N.am    4  UNK4       -0.0850
+     18 N          10.1383   -1.7503    0.0000 N.am    4  UNK4       -0.1963
+     19 N          15.6226   -2.5255    0.0000 N.am    4  UNK4       -0.0678
+     20 N          12.3806   -6.3890    0.0000 N.pl3   4  UNK4       -0.0865
+     21 N           9.2926    0.2619    0.0000 N.am    4  UNK4       -0.1937
+     22 N           3.1485    7.0391    0.0000 N.am    1  UNK1       -0.1978
+     23 N           4.3338    5.7884    0.0000 N.am    2  HIS2       -0.1959
+     24 N          16.8613   -1.8132    0.0000 N.am    4  UNK4       -0.0665
+     25 N           8.1907    1.4900    0.0000 N.am    4  UNK4       -0.1959
+     26 N           5.1795    3.7761    0.0000 N.am    3  TRP3       -0.1960
+     27 N           6.2814    2.5480    0.0000 N.am    4  UNK4       -0.1936
+     28 N          11.3170   -7.3433    0.0000 N.pl3   4  UNK4        0.1354
+     29 N          12.6753   -7.7873    0.0000 N.pl3   4  UNK4        0.1354
+     30 NE1         3.8596    0.7098    0.0000 N.ar    3  TRP3       -0.2442
+     31 ND1         6.7335    6.3823    0.0000 N.ar    2  HIS2       -0.2267
+     32 NE2         5.9507    7.4636    0.0000 N.ar    2  HIS2       -0.2212
+     33 C          13.9701   -3.9516    0.0000 C.3     4  UNK4        0.1552
+     34 C          14.3043   -4.7058    0.0000 C.3     4  UNK4        0.0311
+     35 C          13.6903   -5.2569    0.0000 C.3     4  UNK4        0.0237
+     36 C          12.9766   -4.8431    0.0000 C.3     4  UNK4        0.0939
+     37 C          12.5984   -3.4224    0.0000 C.2     4  UNK4        0.2458
+     38 C          11.7912   -3.5925    0.0000 C.3     4  UNK4        0.1714
+     39 C          14.3838   -3.2378    0.0000 C.2     4  UNK4        0.2788
+     40 C          11.5349   -4.3767    0.0000 C.3     4  UNK4        0.0347
+     41 C          12.0859   -4.9907    0.0000 C.3     4  UNK4        0.0492
+     42 C           9.8819   -2.5345    0.0000 C.3     4  UNK4        0.1728
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+     44 C           9.0747   -2.7046    0.0000 C.3     4  UNK4        0.0311
+     45 C           8.8184   -3.4889    0.0000 C.3     4  UNK4        0.0022
+     46 C          11.8295   -5.7750    0.0000 C.3     4  UNK4        0.2205
+     47 C           8.0112   -3.6590    0.0000 C.3     4  UNK4        0.0001
+     48 C           9.3694   -4.1029    0.0000 C.3     4  UNK4        0.0001
+     49 C           9.5873   -1.1363    0.0000 C.2     4  UNK4        0.2642
+     50 C           9.8436   -0.3521    0.0000 C.3     4  UNK4        0.2021
+     51 C          10.6509   -0.1820    0.0000 C.3     4  UNK4        0.1729
+     52 C          16.4476   -2.5269    0.0000 C.2     4  UNK4        0.3786
+     53 C           2.9756    6.2324    0.0000 C.3     1  UNK1        0.1732
+     54 C          12.0091   -0.6259    0.0000 C.3     4  UNK4        0.0931
+     55 C           8.9979    1.6602    0.0000 C.3     4  UNK4        0.1771
+     56 C           9.5489    1.0461    0.0000 C.2     4  UNK4        0.2620
+     57 C          12.1242   -7.1732    0.0000 C.cat   4  UNK4        0.5346
+     58 C           2.1549    6.1475    0.0000 C.3     1  UNK1        0.0407
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+     60 CA          4.9232    2.9920    0.0000 C.3     3  TRP3        0.1771
+     61 C           1.8207    6.9019    0.0000 C.3     1  UNK1        0.0891
+     62 C           9.2542    2.4444    0.0000 C.3     4  UNK4        0.0574
+     63 CB          4.1159    2.8219    0.0000 C.3     3  TRP3        0.0590
+     64 C           3.5266    5.6183    0.0000 C.2     1  UNK1        0.2616
+     65 C           2.4348    7.4528    0.0000 C.2     1  UNK1        0.2418
+     66 CB          5.6921    5.3445    0.0000 C.3     2  HIS2        0.0785
+     67 C           6.8324    1.9340    0.0000 C.3     4  UNK4        0.2055
+     68 C           4.6285    4.3902    0.0000 C.2     2  HIS2        0.2620
+     69 C          12.1793   -1.4332    0.0000 C.3     4  UNK4        0.0296
+     70 C          12.8164   -0.4557    0.0000 C.3     4  UNK4        0.0296
+     71 C          11.8389    0.1814    0.0000 C.3     4  UNK4        0.0296
+     72 CG          3.8596    2.0376    0.0000 C.ar    3  TRP3        0.0006
+     73 C           5.4742    2.3779    0.0000 C.2     3  TRP3        0.2620
+     74 C           7.6397    2.1041    0.0000 C.2     4  UNK4        0.2643
+     75 C          10.0615    2.6145    0.0000 C.ar    4  UNK4       -0.0198
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+     79 CE2         3.0790    0.9612    0.0000 C.ar    3  TRP3        0.0810
+     80 C           6.5761    1.1498    0.0000 C.3     4  UNK4        0.2130
+     81 CE3         2.3645    2.1987    0.0000 C.ar    3  TRP3        0.0012
+     82 C          10.3178    3.3987    0.0000 C.ar    4  UNK4       -0.0009
+     83 C          10.6125    2.0005    0.0000 C.ar    4  UNK4       -0.0009
+     84 CZ2         2.3645    0.5487    0.0000 C.ar    3  TRP3        0.0191
+     85 CD2         5.4646    6.7970    0.0000 C.ar    2  HIS2        0.1154
+     86 CZ3         1.6500    1.7862    0.0000 C.ar    3  TRP3        0.0001
+     87 CH2         1.6500    0.9612    0.0000 C.ar    3  TRP3        0.0015
+     88 C          11.1251    3.5688    0.0000 C.ar    4  UNK4        0.0417
+     89 C          11.4198    2.1706    0.0000 C.ar    4  UNK4        0.0417
+     90 CE1         6.7349    7.2073    0.0000 C.ar    2  HIS2        0.1986
+     91 C          11.6761    2.9548    0.0000 C.ar    4  UNK4        0.1957
+@<TRIPOS>BOND
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+@<TRIPOS>MOLECULE
+Desmopressin
+ 74 77 0 0 0
+SMALL
+GASTEIGER
+
+@<TRIPOS>ATOM
+      1 N           0.0000   -7.8646    0.0000 N.am    1  LIG1       -0.0862
+      2 C           0.6741   -7.4601    0.0000 C.2     1  LIG1        0.2828
+      3 C           1.3932   -7.8646    0.0000 C.3     1  LIG1        0.2031
+      4 N           2.1122   -7.4601    0.0000 N.am    1  LIG1       -0.1939
+      5 C           2.8313   -7.8646    0.0000 C.2     1  LIG1        0.2617
+      6 C           3.5503   -7.4601    0.0000 C.3     1  LIG1        0.1729
+      7 N           4.2693   -7.8646    0.0000 N.am    1  LIG1       -0.1964
+      8 C           4.9435   -7.4601    0.0000 C.2     1  LIG1        0.2598
+      9 O           5.6625   -7.8646    0.0000 O.2     1  LIG1       -0.2715
+     10 O           0.6741   -6.6512    0.0000 O.2     1  LIG1       -0.2697
+     11 O           2.8313   -8.7184    0.0000 O.2     1  LIG1       -0.2715
+     12 C           3.5503   -6.6512    0.0000 C.3     1  LIG1        0.0348
+     13 C           2.8313   -6.2467    0.0000 C.3     1  LIG1        0.0492
+     14 C           2.8313   -5.4378    0.0000 C.3     1  LIG1        0.2205
+     15 N           2.1122   -5.0333    0.0000 N.pl3   1  LIG1       -0.0865
+     16 C           4.9435   -6.6512    0.0000 C.3     1  LIG1        0.1536
+     17 C           4.3143   -6.1568    0.0000 C.3     1  LIG1        0.0310
+     18 N           5.6176   -6.1568    0.0000 N.am    1  LIG1       -0.2715
+     19 C           4.5390   -5.3929    0.0000 C.3     1  LIG1        0.0237
+     20 C           5.3479   -5.3929    0.0000 C.3     1  LIG1        0.0939
+     21 C           6.3366   -6.5613    0.0000 C.2     1  LIG1        0.2467
+     22 C           7.0557   -6.1568    0.0000 C.3     1  LIG1        0.1828
+     23 N           7.7747   -6.5613    0.0000 N.am    1  LIG1       -0.1954
+     24 C           8.4488   -6.1568    0.0000 C.2     1  LIG1        0.2621
+     25 C           9.1678   -6.5613    0.0000 C.3     1  LIG1        0.1819
+     26 N           9.8869   -6.1568    0.0000 N.am    1  LIG1       -0.1958
+     27 O           6.3366   -7.4152    0.0000 O.2     1  LIG1       -0.2730
+     28 C           7.0557   -5.3479    0.0000 C.3     1  LIG1        0.0996
+     29 S           6.3366   -4.9435    0.0000 S.3     1  LIG1       -0.0798
+     30 S           6.3366   -4.1345    0.0000 S.3     1  LIG1       -0.0816
+     31 O           8.4488   -5.3479    0.0000 O.2     1  LIG1       -0.2715
+     32 C           9.1678   -7.4152    0.0000 C.3     1  LIG1        0.1195
+     33 C           9.8869   -7.8197    0.0000 C.2     1  LIG1        0.2630
+     34 O           9.8869   -8.6286    0.0000 O.2     1  LIG1       -0.2716
+     35 N          10.6060   -7.4152    0.0000 N.am    1  LIG1       -0.0877
+     36 C           9.8869   -5.3479    0.0000 C.2     1  LIG1        0.2616
+     37 C          10.6060   -4.9435    0.0000 C.3     1  LIG1        0.1733
+     38 O           9.1678   -4.9435    0.0000 O.2     1  LIG1       -0.2715
+     39 C          11.3250   -5.3479    0.0000 C.3     1  LIG1        0.0408
+     40 C          12.0441   -4.9435    0.0000 C.3     1  LIG1        0.0908
+     41 C          12.7631   -5.3479    0.0000 C.2     1  LIG1        0.2608
+     42 N          13.4822   -4.9435    0.0000 N.am    1  LIG1       -0.0878
+     43 O          12.7631   -6.2018    0.0000 O.2     1  LIG1       -0.2717
+     44 N          10.6060   -4.1345    0.0000 N.am    1  LIG1       -0.1963
+     45 C          11.3250   -2.8762    0.0000 C.ar    1  LIG1       -0.0200
+     46 C          11.3250   -3.7300    0.0000 C.ar    1  LIG1       -0.0042
+     47 C          10.6060   -2.4717    0.0000 C.3     1  LIG1        0.0574
+     48 C           9.8869   -2.8762    0.0000 C.3     1  LIG1        0.1771
+     49 C           9.8869   -3.7300    0.0000 C.2     1  LIG1        0.2619
+     50 C          12.7631   -2.8762    0.0000 C.ar    1  LIG1       -0.0003
+     51 C          12.7631   -3.7300    0.0000 C.ar    1  LIG1       -0.0000
+     52 C          12.0441   -2.4717    0.0000 C.ar    1  LIG1       -0.0042
+     53 C          12.0441   -4.1345    0.0000 C.ar    1  LIG1       -0.0003
+     54 N           7.0557   -2.8762    0.0000 N.am    1  LIG1       -0.1974
+     55 C           6.3366   -2.4717    0.0000 C.2     1  LIG1        0.2427
+     56 C           5.6176   -2.8762    0.0000 C.3     1  LIG1        0.0993
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+     60 C           7.7747   -2.4717    0.0000 C.3     1  LIG1        0.1770
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+     71 O          10.6060    0.0000    0.0000 O.3     1  LIG1       -0.2866
+     72 C           1.3932   -5.4378    0.0000 C.cat   1  LIG1        0.5346
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+     74 N           0.6741   -5.0333    0.0000 N.pl3   1  LIG1        0.1354
+@<TRIPOS>BOND
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lib/galaxy/datatypes/test/drugbank_drugs.sdf

@@ -0,0 +1,491 @@
+Goserelin
+  Mrv0541 04221219462D          
+
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+ 89 91  1  0  0  0  0
+M  END
+> <DRUGBANK_ID>
+DB00014
+
+> <DRUG_GROUPS>
+approved
+
+> <GENERIC_NAME>
+Goserelin
+
+> <SALTS>
+Goserelin acetate
+
+> <BRANDS>
+Zoladex
+
+> <CHEMICAL_FORMULA>
+C59H84N18O14
+
+> <MOLECULAR_WEIGHT>
+1269.4105
+
+> <EXACT_MASS>
+1268.641439486
+
+> <IUPAC_NAME>
+(2S)-1-[(2S)-2-[(2S)-2-[(2R)-3-(tert-butoxy)-2-[(2S)-2-[(2S)-3-hydroxy-2-[(2S)-2-[(2S)-3-(1H-imidazol-5-yl)-2-{[(2S)-5-oxopyrrolidin-2-yl]formamido}propanamido]-3-(1H-indol-3-yl)propanamido]propanamido]-3-(4-hydroxyphenyl)propanamido]propanamido]-4-methylpentanamido]-5-[(diaminomethylidene)amino]pentanoyl]-N-(carbamoylamino)pyrrolidine-2-carboxamide
+
+> <INCHI_IDENTIFIER>
+InChI=1S/C59H84N18O14/c1-31(2)22-40(49(82)68-39(12-8-20-64-57(60)61)56(89)77-21-9-13-46(77)55(88)75-76-58(62)90)69-54(87)45(29-91-59(3,4)5)74-50(83)41(23-32-14-16-35(79)17-15-32)70-53(86)44(28-78)73-51(84)42(24-33-26-65-37-11-7-6-10-36(33)37)71-52(85)43(25-34-27-63-30-66-34)72-48(81)38-18-19-47(80)67-38/h6-7,10-11,14-17,26-27,30-31,38-46,65,78-79H,8-9,12-13,18-25,28-29H2,1-5H3,(H,63,66)(H,67,80)(H,68,82)(H,69,87)(H,70,86)(H,71,85)(H,72,81)(H,73,84)(H,74,83)(H,75,88)(H4,60,61,64)(H3,62,76,90)/t38-,39-,40-,41-,42-,43-,44-,45+,46-/m0/s1
+
+> <INCHI_KEY>
+InChIKey=BLCLNMBMMGCOAS-URPVMXJPSA-N
+
+> <SMILES>
+CC(C)C[C@H](NC(=O)[C@@H](COC(C)(C)C)NC(=O)[C@H](CC1=CC=C(O)C=C1)NC(=O)[C@H](CO)NC(=O)[C@H](CC1=CNC2=CC=CC=C12)NC(=O)[C@H](CC1=CN=CN1)NC(=O)[C@@H]1CCC(=O)N1)C(=O)N[C@@H](CCCN=C(N)N)C(=O)N1CCC[C@H]1C(=O)NNC(N)=O
+
+> <JCHEM_ACCEPTOR_COUNT>
+18
+
+> <JCHEM_DONOR_COUNT>
+17
+
+> <JCHEM_ACIDIC_PKA>
+9.82
+
+> <ALOGPS_LOGP>
+0.3
+
+> <JCHEM_LOGP>
+-5.2
+
+> <ALOGPS_LOGS>
+-4.7
+
+> <JCHEM_POLARIZABILITY>
+131.22
+
+> <JCHEM_POLAR_SURFACE_AREA>
+495.89
+
+> <JCHEM_REFRACTIVITY>
+325.84
+
+> <JCHEM_ROTATABLE_BOND_COUNT>
+33
+
+> <ALOGPS_SOLUBILITY>
+2.83e-02 g/l
+
+$$$$
+Desmopressin
+  Mrv0541 04221221522D          
+
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+M  END
+> <DRUGBANK_ID>
+DB00035
+
+> <DRUG_GROUPS>
+approved
+
+> <GENERIC_NAME>
+Desmopressin
+
+> <SYNONYMS>
+1-Desamino-8-D-arginine vasopressin; Desmopresina [INN-Spanish]; Desmopressine [INN-French]; Desmopressinum [INN-Latin]
+
+> <SALTS>
+Desmopressin acetate
+
+> <BRANDS>
+Adiuretin; Concentraid; DDAVP; Minirin; Stimate
+
+> <CHEMICAL_FORMULA>
+C46H64N14O12S2
+
+> <MOLECULAR_WEIGHT>
+1069.217
+
+> <EXACT_MASS>
+1068.426954962
+
+> <IUPAC_NAME>
+(2S)-2-{[(2S)-1-{[(4R,7S,10S,13S,16S)-13-benzyl-10-(2-carbamoylethyl)-7-(carbamoylmethyl)-16-[(4-hydroxyphenyl)methyl]-6,9,12,15,18-pentaoxo-1,2-dithia-5,8,11,14,17-pentaazacycloicosan-4-yl]carbonyl}pyrrolidin-2-yl]formamido}-5-carbamimidamido-N-(carbamoylmethyl)pentanamide
+
+> <INCHI_IDENTIFIER>
+InChI=1S/C46H64N14O12S2/c47-35(62)15-14-29-40(67)58-32(22-36(48)63)43(70)59-33(45(72)60-18-5-9-34(60)44(71)56-28(8-4-17-52-46(50)51)39(66)53-23-37(49)64)24-74-73-19-16-38(65)54-30(21-26-10-12-27(61)13-11-26)41(68)57-31(42(69)55-29)20-25-6-2-1-3-7-25/h1-3,6-7,10-13,28-34,61H,4-5,8-9,14-24H2,(H2,47,62)(H2,48,63)(H2,49,64)(H,53,66)(H,54,65)(H,55,69)(H,56,71)(H,57,68)(H,58,67)(H,59,70)(H4,50,51,52)/t28-,29-,30-,31-,32-,33-,34-/m0/s1
+
+> <INCHI_KEY>
+InChIKey=NFLWUMRGJYTJIN-NXBWRCJVSA-N
+
+> <SMILES>
+NC(=O)CC[C@@H]1NC(=O)[C@H](CC2=CC=CC=C2)NC(=O)[C@H](CC2=CC=C(O)C=C2)NC(=O)CCSSC[C@H](NC(=O)[C@H](CC(N)=O)NC1=O)C(=O)N1CCC[C@H]1C(=O)N[C@@H](CCCNC(N)=N)C(=O)NCC(N)=O
+
+> <JCHEM_ACCEPTOR_COUNT>
+15
+
+> <JCHEM_DONOR_COUNT>
+14
+
+> <JCHEM_ACIDIC_PKA>
+11.34
+
+> <ALOGPS_LOGP>
+-1
+
+> <JCHEM_LOGP>
+-6.1
+
+> <ALOGPS_LOGS>
+-4
+
+> <JCHEM_POLARIZABILITY>
+106.19
+
+> <JCHEM_POLAR_SURFACE_AREA>
+435.41
+
+> <JCHEM_REFRACTIVITY>
+279.78
+
+> <JCHEM_ROTATABLE_BOND_COUNT>
+19
+
+> <ALOGPS_SOLUBILITY>
+1.10e-01 g/l
+
+$$$$

lib/galaxy/datatypes/test/drugbank_drugs.smi

@@ -0,0 +1,2 @@
+O=C(N1[C@@H](CCC1)C(=O)NNC(=O)N)[C@@H](NC(=O)[C@@H](NC(=O)[C@H](NC(=O)[C@@H](NC(=O)[C@@H](NC(=O)[C@@H](NC(=O)[C@@H](NC(=O)[C@H]1NC(=O)CC1)Cc1[nH]cnc1)Cc1c2c([nH]c1)cccc2)CO)Cc1ccc(O)cc1)COC(C)(C)C)CC(C)C)CCCN=C(N)N	Goserelin
+NC(=O)CNC(=O)[C@@H](NC(=O)[C@@H]1CCCN1C(=O)[C@H]1NC(=O)[C@@H](NC(=O)[C@H](CCC(=O)N)NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@@H](NC(=O)CCSSC1)Cc1ccc(cc1)O)CC(=O)N)CCCNC(=N)N	Desmopressin

lib/galaxy/datatypes/test/q.fps

@@ -0,0 +1,7 @@
+#FPS1
+#num_bits=881
+#type=CACTVS-E_SCREEN/1.0 extended=2
+#software=CACTVS/unknown
+#source=CID_28434379.sdf
+#date=2012-02-03T13:08:39
+07ce04000000000000000000000000000080060000000c060000000000001a800f0000780008100000101487e9608c0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800000000000100200000040080000010000002000000000000	28434379

lib/galaxy/dependencies/pinned-requirements.txt

@@ -3,8 +3,7 @@ bx-python==0.7.3
 MarkupSafe==0.23
 PyYAML==3.11
 SQLAlchemy==1.0.8
-# Mercurial >= 3.5 changed the bundle format, which breaks hg push of TS repositories
-mercurial==3.4.2
+mercurial==3.7.3
 numpy==1.9.2
 pycrypto==2.6.1
 
@@ -25,6 +24,7 @@ Mako==1.0.2
 pytz==2015.4
 Babel==2.0
 Beaker==1.7.0
+dictobj==0.3.1
 
 # Cheetah and dependencies
 Cheetah==2.4.4
@@ -41,13 +41,16 @@ kombu==3.0.30
 amqp==1.4.8
 anyjson==0.3.3
 
+# Pulsar requirements
+psutil==4.1.0
+pulsar-galaxy-lib==0.7.0.dev1
+
 # sqlalchemy-migrate and dependencies
 sqlalchemy-migrate==0.10.0
 decorator==4.0.2
 Tempita==0.5.3dev
 sqlparse==0.1.16
 pbr==1.8.0
-# six is also a Pulsar client dep
 six==1.9.0
 Parsley==1.3
 nose==1.3.7

lib/galaxy/dependencies/requirements.txt

@@ -26,6 +26,7 @@ Mako
 pytz
 Babel
 Beaker
+dictobj
 
 # Cheetah and dependencies
 Cheetah
@@ -38,6 +39,10 @@ requests
 # kombu and dependencies
 kombu
 
+# Pulsar requirements
+psutil
+pulsar-galaxy-lib==0.7.0.dev1
+
 # sqlalchemy-migrate and dependencies
 sqlalchemy-migrate
 decorator

lib/galaxy/jobs/__init__.py

@@ -1662,10 +1662,13 @@ class JobWrapper( object ):
                                                                          **kwds )
         if resolve_metadata_dependencies:
             metadata_tool = self.app.toolbox.get_tool("__SET_METADATA__")
-            dependency_shell_commands = metadata_tool.build_dependency_shell_commands(job_directory=self.working_directory)
-            if dependency_shell_commands:
-                dependency_shell_commands = "; ".join(dependency_shell_commands)
-                command = "%s; %s" % (dependency_shell_commands, command)
+            if metadata_tool is not None:
+                # Due to tool shed hacks for migrate and installed tool tests...
+                # see (``setup_shed_tools_for_test`` in test/base/driver_util.py).
+                dependency_shell_commands = metadata_tool.build_dependency_shell_commands(job_directory=self.working_directory)
+                if dependency_shell_commands:
+                    dependency_shell_commands = "; ".join(dependency_shell_commands)
+                    command = "%s; %s" % (dependency_shell_commands, command)
         return command
 
     @property

lib/galaxy/jobs/handler.py

@@ -186,7 +186,7 @@ class JobHandlerQueue( object ):
         jobs (either from the database or from its own queue), then iterates
         over all new and waiting jobs to check the state of the jobs each
         depends on. If the job has dependencies that have not finished, it
-        it goes to the waiting queue. If the job has dependencies with errors,
+        goes to the waiting queue. If the job has dependencies with errors,
         it is marked as having errors and removed from the queue. If the job
         belongs to an inactive user it is ignored.
         Otherwise, the job is dispatched.

lib/galaxy/jobs/runners/__init__.py

@@ -322,7 +322,7 @@ class BaseJobRunner( object ):
         compute_job_directory=None
     ):
         if not compute_working_directory:
-            compute_working_directory = job_wrapper.working_directory
+            compute_working_directory = job_wrapper.tool_working_directory
 
         if not compute_tool_directory:
             compute_tool_directory = job_wrapper.tool.tool_dir

lib/galaxy/jobs/runners/pbs.py

@@ -272,7 +272,7 @@ class PBSJobRunner( AsynchronousJobRunner ):
         # write the job script
         if self.app.config.pbs_stage_path != '':
             # touch the ecfile so that it gets staged
-            with file(ecfile, 'a'):
+            with open(ecfile, 'a'):
                 os.utime(ecfile, None)
 
             stage_commands = pbs_symlink_template % (

lib/galaxy/jobs/runners/pulsar.py

@@ -1,6 +1,26 @@
+"""Job runner used to execute Galaxy jobs through Pulsar.
+
+More infromation on Pulsar can be found at http://pulsar.readthedocs.org/.
+"""
 from __future__ import absolute_import  # Need to import pulsar_client absolutely.
 
+import errno
 import logging
+import os
+from time import sleep
+
+from pulsar.client import build_client_manager
+from pulsar.client import url_to_destination_params
+from pulsar.client import finish_job as pulsar_finish_job
+from pulsar.client import submit_job as pulsar_submit_job
+from pulsar.client import ClientJobDescription
+from pulsar.client import PulsarOutputs
+from pulsar.client import ClientOutputs
+from pulsar.client import PathMapper
+
+import pulsar.core
+
+import yaml
 
 from galaxy import model
 from galaxy.jobs.runners import AsynchronousJobState, AsynchronousJobRunner
@@ -12,22 +32,15 @@ from galaxy.util import string_as_bool_or_none
 from galaxy.util.bunch import Bunch
 from galaxy.util import specs
 
-import errno
-from time import sleep
-import os
-
-from pulsar.client import build_client_manager
-from pulsar.client import url_to_destination_params
-from pulsar.client import finish_job as pulsar_finish_job
-from pulsar.client import submit_job as pulsar_submit_job
-from pulsar.client import ClientJobDescription
-from pulsar.client import PulsarOutputs
-from pulsar.client import ClientOutputs
-from pulsar.client import PathMapper
 
 log = logging.getLogger( __name__ )
 
-__all__ = [ 'PulsarLegacyJobRunner', 'PulsarRESTJobRunner', 'PulsarMQJobRunner' ]
+__all__ = [
+    'PulsarLegacyJobRunner',
+    'PulsarRESTJobRunner',
+    'PulsarMQJobRunner',
+    'PulsarEmbeddedJobRunner',
+]
 
 NO_REMOTE_GALAXY_FOR_METADATA_MESSAGE = "Pulsar misconfiguration - Pulsar client configured to set metadata remotely, but remote Pulsar isn't properly configured with a galaxy_home directory."
 NO_REMOTE_DATATYPES_CONFIG = "Pulsar client is configured to use remote datatypes configuration when setting metadata externally, but Pulsar is not configured with this information. Defaulting to datatypes_conf.xml."
@@ -57,6 +70,10 @@ PULSAR_PARAM_SPECS = dict(
         map=specs.to_str_or_none,
         default=None,
     ),
+    pulsar_config=dict(
+        map=specs.to_str_or_none,
+        default=None,
+    ),
     manager=dict(
         map=specs.to_str_or_none,
         default=None,
@@ -133,13 +150,13 @@ PARAMETER_SPECIFICATION_IGNORED = object()
 
 
 class PulsarJobRunner( AsynchronousJobRunner ):
-    """
-    Pulsar Job Runner
-    """
+    """Base class for pulsar job runners."""
+
     runner_name = "PulsarJobRunner"
+    default_build_pulsar_app = False
 
     def __init__( self, app, nworkers, **kwds ):
-        """Start the job runner """
+        """Start the job runner."""
         super( PulsarJobRunner, self ).__init__( app, nworkers, runner_param_specs=PULSAR_PARAM_SPECS, **kwds )
         self._init_worker_threads()
         galaxy_url = self.runner_params.galaxy_url
@@ -156,16 +173,42 @@ class PulsarJobRunner( AsynchronousJobRunner ):
         self._init_monitor_thread()
 
     def __init_client_manager( self ):
+        pulsar_conf = self.runner_params.get('pulsar_conf', None)
+        self.__init_pulsar_app(pulsar_conf)
+
         client_manager_kwargs = {}
         for kwd in 'manager', 'cache', 'transport', 'persistence_directory':
             client_manager_kwargs[ kwd ] = self.runner_params[ kwd ]
+        if self.pulsar_app is not None:
+            # TODO: Make this more generic and configurable - client_manager
+            # should define an app and client (destination) should reference
+            # a job manager.
+            job_manager = self.pulsar_app.only_manager
+            client_manager_kwargs[ "job_manager" ] = job_manager
+            # TODO: Hack remove this following line pulsar lib update
+            # that includes https://github.com/galaxyproject/pulsar/commit/ce0636a5b64fae52d165bcad77b2caa3f0e9c232
+            client_manager_kwargs[ "file_cache" ] = None
+
         for kwd in self.runner_params.keys():
             if kwd.startswith( 'amqp_' ):
                 client_manager_kwargs[ kwd ] = self.runner_params[ kwd ]
         self.client_manager = build_client_manager(**client_manager_kwargs)
 
+    def __init_pulsar_app( self, pulsar_conf_path ):
+        if pulsar_conf_path is None and not self.default_build_pulsar_app:
+            self.pulsar_app = None
+            return
+        conf = {}
+        if pulsar_conf_path is None:
+            log.info("Creating a Pulsar app with default configuration (no pulsar_conf specified).")
+        else:
+            log.info("Loading Pulsar app configuration from %s" % pulsar_conf_path)
+            with open(pulsar_conf_path, "r") as f:
+                conf.update(yaml.load(f) or {})
+        self.pulsar_app = pulsar.core.PulsarApp(**conf)
+
     def url_to_destination( self, url ):
-        """Convert a legacy URL to a job destination"""
+        """Convert a legacy URL to a job destination."""
         return JobDestination( runner="pulsar", params=url_to_destination_params( url ) )
 
     def check_watched_item(self, job_state):
@@ -217,7 +260,7 @@ class PulsarJobRunner( AsynchronousJobRunner ):
                 command_line=command_line,
                 input_files=self.get_input_files(job_wrapper),
                 client_outputs=self.__client_outputs(client, job_wrapper),
-                working_directory=job_wrapper.working_directory,
+                working_directory=job_wrapper.tool_working_directory,
                 tool=job_wrapper.tool,
                 config_files=job_wrapper.extra_filenames,
                 dependencies_description=dependencies_description,
@@ -243,7 +286,7 @@ class PulsarJobRunner( AsynchronousJobRunner ):
         self.monitor_job(pulsar_job_state)
 
     def __prepare_job(self, job_wrapper, job_destination):
-        """ Build command-line and Pulsar client for this job. """
+        """Build command-line and Pulsar client for this job."""
         command_line = None
         client = None
         remote_job_config = None
@@ -424,9 +467,7 @@ class PulsarJobRunner( AsynchronousJobRunner ):
             job_wrapper.fail("Unable to finish job", exception=True)
 
     def fail_job( self, job_state, message=GENERIC_REMOTE_ERROR ):
-        """
-        Seperated out so we can use the worker threads for it.
-        """
+        """Seperated out so we can use the worker threads for it."""
         self.stop_job( self.sa_session.query( self.app.model.Job ).get( job_state.job_wrapper.job_id ) )
         job_state.job_wrapper.fail( getattr( job_state, "fail_message", message ) )
 
@@ -475,7 +516,7 @@ class PulsarJobRunner( AsynchronousJobRunner ):
             client.kill()
 
     def recover( self, job, job_wrapper ):
-        """Recovers jobs stuck in the queued/running state when Galaxy started"""
+        """Recover jobs stuck in the queued/running state when Galaxy started."""
         job_state = self._job_state( job, job_wrapper )
         job_wrapper.command_line = job.get_command_line()
         state = job.get_state()
@@ -538,7 +579,9 @@ class PulsarJobRunner( AsynchronousJobRunner ):
 
     @staticmethod
     def __use_remote_datatypes_conf( pulsar_client ):
-        """ When setting remote metadata, use integrated datatypes from this
+        """Use remote metadata datatypes instead of Galaxy's.
+
+        When setting remote metadata, use integrated datatypes from this
         Galaxy instance or use the datatypes config configured via the remote
         Pulsar.
 
@@ -604,6 +647,8 @@ class PulsarJobRunner( AsynchronousJobRunner ):
 
 
 class PulsarLegacyJobRunner( PulsarJobRunner ):
+    """Flavor of Pulsar job runner mimicking behavior of old LWR runner."""
+
     destination_defaults = dict(
         rewrite_parameters="false",
         dependency_resolution="local",
@@ -611,6 +656,8 @@ class PulsarLegacyJobRunner( PulsarJobRunner ):
 
 
 class PulsarMQJobRunner( PulsarJobRunner ):
+    """Flavor of Pulsar job runner with sensible defaults for message queue communication."""
+
     destination_defaults = dict(
         default_file_action="remote_transfer",
         rewrite_parameters="true",
@@ -640,6 +687,8 @@ class PulsarMQJobRunner( PulsarJobRunner ):
 
 
 class PulsarRESTJobRunner( PulsarJobRunner ):
+    """Flavor of Pulsar job runner with sensible defaults for RESTful usage."""
+
     destination_defaults = dict(
         default_file_action="transfer",
         rewrite_parameters="true",
@@ -648,6 +697,21 @@ class PulsarRESTJobRunner( PulsarJobRunner ):
     )
 
 
+class PulsarEmbeddedJobRunner(PulsarJobRunner):
+    """Flavor of Puslar job runnner that runs Pulsar's server code directly within Galaxy.
+
+    This is an appropriate job runner for when the desire is to use Pulsar staging
+    but their is not need to run a remote service.
+    """
+
+    destination_defaults = dict(
+        default_file_action="copy",
+        rewrite_parameters="true",
+        dependency_resolution="remote",
+    )
+    default_build_pulsar_app = True
+
+
 class PulsarComputeEnvironment( ComputeEnvironment ):
 
     def __init__( self, pulsar_client, job_wrapper, remote_job_config ):

lib/galaxy/managers/base.py

@@ -930,6 +930,9 @@ class ModelFilterParser( HasAModelManager ):
         super( ModelFilterParser, self ).__init__( app, **kwargs )
         self.app = app
 
+        #: regex for testing/dicing iso8601 date strings, with optional time and ms, but allowing only UTC timezone
+        self.date_string_re = re.compile( r'^(\d{4}\-\d{2}\-\d{2})[T| ]{0,1}(\d{2}:\d{2}:\d{2}(?:\.\d{1,6}){0,1}){0,1}Z{0,1}$' )
+
         # dictionary containing parsing data for ORM/SQLAlchemy-based filters
         # ..note: although kind of a pain in the ass and verbose, opt-in/whitelisting allows more control
         #   over potentially expensive queries
@@ -1121,19 +1124,21 @@ class ModelFilterParser( HasAModelManager ):
 
     def parse_date( self, date_string ):
         """
-        Attempts to get an SQL-able(?) date string for a query filter.
+        Reformats a string containing either seconds from epoch or an iso8601 formated
+        date string into a new date string usable within a filter query.
+
+        Seconds from epoch can be a floating point value as well (i.e containing ms).
         """
-        # Attempts to parse epoch int back into date string
+        # assume it's epoch if no date separator is present
         try:
-            epoch = int( date_string )
-            date = datetime.datetime.fromtimestamp( epoch )
-            return date.isoformat().replace( 'T', ' ', 1 )
+            epoch = float( date_string )
+            datetime_obj = datetime.datetime.fromtimestamp( epoch )
+            return datetime_obj.isoformat( sep=' ' )
         except ValueError:
             pass
-        # or removes T from date string
-        if not hasattr( self, 'date_string_re' ):
-            self.date_string_re = re.compile( r'^\d{4}\-\d{2}\-\d{2}T' )
-        if self.date_string_re.match( date_string ):
-            return date_string.replace( 'T', ' ', 1 )
-        # or as is
-        return date_string
+
+        match = self.date_string_re.match( date_string )
+        if match:
+            date_string = ' '.join([ group for group in match.groups() if group ])
+            return date_string
+        raise ValueError( 'datetime strings must be in the ISO 8601 format and in the UTC' )

lib/galaxy/model/__init__.py

@@ -961,8 +961,13 @@ class PostJobAction( object ):
 
 
 class PostJobActionAssociation( object ):
-    def __init__(self, pja, job):
-        self.job = job
+    def __init__(self, pja, job=None, job_id=None ):
+        if job is not None:
+            self.job = job
+        elif job_id is not None:
+            self.job_id = job_id
+        else:
+            raise Exception("PostJobActionAssociation must be created with a job or a job_id.")
         self.post_job_action = pja
 
 
@@ -1173,7 +1178,7 @@ class History( object, Dictifiable, UsesAnnotations, HasName ):
         dataset.history = self
         if genome_build not in [None, '?']:
             self.genome_build = genome_build
-        self.datasets.append( dataset )
+        dataset.history_id = self.id
         return dataset
 
     def add_datasets( self, sa_session, datasets, parent_id=None, genome_build=None, set_hid=True, quota=True, flush=False ):
@@ -1208,7 +1213,8 @@ class History( object, Dictifiable, UsesAnnotations, HasName ):
             dataset.history = self
             if set_genome:
                 self.genome_build = genome_build
-        self.datasets.extend( datasets )
+        for dataset in datasets:
+            dataset.history_id = self.id
         return datasets
 
     def add_dataset_collection( self, history_dataset_collection, set_hid=True ):

lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py

@@ -4,7 +4,7 @@ Migration script to support subworkflows and workflow request input parameters
 import datetime
 import logging
 
-from sqlalchemy import Column, Integer, ForeignKey, MetaData, Table
+from sqlalchemy import Column, Integer, ForeignKey, MetaData, Table, Index, ForeignKeyConstraint
 
 from galaxy.model.custom_types import TrimmedString, UUIDType, JSONType
 
@@ -15,22 +15,33 @@ metadata = MetaData()
 WorkflowInvocationToSubworkflowInvocationAssociation_table = Table(
     "workflow_invocation_to_subworkflow_invocation_association", metadata,
     Column( "id", Integer, primary_key=True ),
-    Column( "workflow_invocation_id", Integer, ForeignKey( "workflow_invocation.id" ), index=True ),
-    Column( "subworkflow_invocation_id", Integer, ForeignKey( "workflow_invocation.id" ), index=True ),
-    Column( "workflow_step_id", Integer, ForeignKey("workflow_step.id") ),
+    Column( "workflow_invocation_id", Integer ),
+    Column( "subworkflow_invocation_id", Integer ),
+    Column( "workflow_step_id", Integer ),
+    ForeignKeyConstraint(['workflow_invocation_id'], ['workflow_invocation.id'], name='fk_wfi_swi_wfi'),
+    ForeignKeyConstraint(['subworkflow_invocation_id'], ['workflow_invocation.id'], name='fk_wfi_swi_swi'),
+    ForeignKeyConstraint(['workflow_step_id'], ['workflow_step.id'], name='fk_wfi_swi_ws')
 )
 
-WorkflowRequestInputStepParmeter_table = Table(
+WorkflowRequestInputStepParameter_table = Table(
     "workflow_request_input_step_parameter", metadata,
     Column( "id", Integer, primary_key=True ),
-    Column( "workflow_invocation_id", Integer, ForeignKey( "workflow_invocation.id" ), index=True ),
-    Column( "workflow_step_id", Integer, ForeignKey("workflow_step.id") ),
+    Column( "workflow_invocation_id", Integer ),
+    Column( "workflow_step_id", Integer ),
     Column( "parameter_value", JSONType ),
+    ForeignKeyConstraint(['workflow_invocation_id'], ['workflow_invocation.id'], name='fk_wfreq_isp_wfi'),
+    ForeignKeyConstraint(['workflow_step_id'], ['workflow_step.id'], name='fk_wfreq_isp_ws')
 )
 
 TABLES = [
     WorkflowInvocationToSubworkflowInvocationAssociation_table,
-    WorkflowRequestInputStepParmeter_table,
+    WorkflowRequestInputStepParameter_table,
+]
+
+INDEXES = [
+    Index( "ix_wfinv_swfinv_wfi", WorkflowInvocationToSubworkflowInvocationAssociation_table.c.workflow_invocation_id),
+    Index( "ix_wfinv_swfinv_swfi", WorkflowInvocationToSubworkflowInvocationAssociation_table.c.subworkflow_invocation_id),
+    Index( "ix_wfreq_inputstep_wfi", WorkflowRequestInputStepParameter_table.c.workflow_invocation_id)
 ]
 
 
@@ -38,16 +49,17 @@ def upgrade(migrate_engine):
     metadata.bind = migrate_engine
     print __doc__
     metadata.reflect()
-
-    subworkflow_id_column = Column( "subworkflow_id", Integer, ForeignKey("workflow.id"), nullable=True )
+    if migrate_engine.name in ['postgres', 'postgresql']:
+        subworkflow_id_column = Column( "subworkflow_id", Integer, ForeignKey("workflow.id"), nullable=True )
+        input_subworkflow_step_id_column = Column( "input_subworkflow_step_id", Integer, ForeignKey("workflow_step.id"), nullable=True )
+        parent_workflow_id_column = Column( "parent_workflow_id", Integer, ForeignKey("workflow.id"), nullable=True )
+    else:
+        subworkflow_id_column = Column( "subworkflow_id", Integer, nullable=True )
+        input_subworkflow_step_id_column = Column( "input_subworkflow_step_id", Integer, nullable=True )
+        parent_workflow_id_column = Column( "parent_workflow_id", Integer, nullable=True )
     __add_column( subworkflow_id_column, "workflow_step", metadata )
-
-    input_subworkflow_step_id_column = Column( "input_subworkflow_step_id", Integer, ForeignKey("workflow_step.id"), nullable=True )
     __add_column( input_subworkflow_step_id_column, "workflow_step_connection", metadata )
-
-    parent_workflow_id_column = Column( "parent_workflow_id", Integer, ForeignKey("workflow.id"), nullable=True )
     __add_column( parent_workflow_id_column, "workflow", metadata )
-
     workflow_output_label_column = Column( "label", TrimmedString(255) )
     workflow_output_uuid_column = Column( "uuid", UUIDType, nullable=True )
     __add_column( workflow_output_label_column, "workflow_output", metadata )
@@ -58,6 +70,7 @@ def upgrade(migrate_engine):
     __alter_column("workflow", "stored_workflow_id", metadata, nullable=True)
 
     for table in TABLES:
+        # Indexes are automatically created when the tables are.
         __create(table)
 
 
@@ -66,15 +79,13 @@ def downgrade(migrate_engine):
     metadata.reflect()
 
     __drop_column( "subworkflow_id", "workflow_step", metadata )
-    __drop_column( "parent_workflow_id", "workflow_step", metadata )
+    __drop_column( "parent_workflow_id", "workflow", metadata )
 
     __drop_column( "input_subworkflow_step_id", "workflow_step_connection", metadata )
 
     __drop_column( "label", "workflow_output", metadata )
     __drop_column( "uuid", "workflow_output", metadata )
 
-    __alter_column("workflow", "stored_workflow_id", metadata, nullable=False)
-
     for table in TABLES:
         __drop(table)
 

lib/galaxy/model/util.py

@@ -10,25 +10,24 @@ def pgcalc( sa_session, id, dryrun=False ):
     TODO: Check against the recently updated versions of sqlalchemy if this
     'special' postgresql version is even necessary.
     """
-    sql = """
-           UPDATE galaxy_user
-              SET disk_usage = (SELECT COALESCE(SUM(total_size), 0)
-                                  FROM (  SELECT DISTINCT ON (d.id) d.total_size, d.id
-                                            FROM history_dataset_association hda
-                                                 JOIN history h ON h.id = hda.history_id
-                                                 JOIN dataset d ON hda.dataset_id = d.id
-                                           WHERE h.user_id = :id
-                                                 AND h.purged = false
-                                                 AND hda.purged = false
-                                                 AND d.purged = false
-                                                 AND d.id NOT IN (SELECT dataset_id
-                                                                    FROM library_dataset_dataset_association)
-                                         ) sizes)
-            WHERE id = :id
-        RETURNING disk_usage;
-    """
-    r = sa_session.execute(sql, {'id': id})
-    new = r.fetchone()[0]
+    sql_calc = """SELECT COALESCE(SUM(total_size), 0)
+                  FROM (  SELECT DISTINCT ON (d.id) d.total_size, d.id
+                          FROM history_dataset_association hda
+                               JOIN history h ON h.id = hda.history_id
+                               JOIN dataset d ON hda.dataset_id = d.id
+                          WHERE h.user_id = :id
+                                AND h.purged = false
+                                AND hda.purged = false
+                                AND d.purged = false
+                                AND d.id NOT IN (SELECT dataset_id
+                                                 FROM library_dataset_dataset_association)
+                  ) sizes"""
+    sql_update = """UPDATE galaxy_user
+                    SET disk_usage = (%s)
+                    WHERE id = :id
+                    RETURNING disk_usage;""" % sql_calc
     if dryrun:
-        sa_session.rollback()
-    return new
+        r = sa_session.execute(sql_calc, {'id': id})
+    else:
+        r = sa_session.execute(sql_update, {'id': id})
+    return r.fetchone()[0]

lib/galaxy/tools/__init__.py

@@ -407,6 +407,8 @@ class Tool( object, Dictifiable ):
         """
         :returns: bool -- Whether the user is allowed to access the tool.
         """
+        if self.require_login and user is None:
+            return False
         return True
 
     def parse( self, tool_source, guid=None ):
@@ -1426,7 +1428,7 @@ class Tool( object, Dictifiable ):
         return output_collect.collect_dynamic_collections( self, output, **kwds )
 
     def to_archive(self):
-        tool = self.tool
+        tool = self
         tarball_files = []
         temp_files = []
         tool_xml = open( os.path.abspath( tool.config_file ), 'r' ).read()
@@ -1643,7 +1645,8 @@ class Tool( object, Dictifiable ):
         # expand incoming parameters (parameters might trigger multiple tool executions,
         # here we select the first execution only in order to resolve dynamic parameters)
         expanded_incomings, _ = expand_meta_parameters( trans, self, params.__dict__ )
-        params.__dict__ = expanded_incomings[ 0 ]
+        if expanded_incomings:
+            params.__dict__ = expanded_incomings[ 0 ]
 
         # do param translation here, used by datasource tools
         if self.input_translator:
@@ -1659,12 +1662,6 @@ class Tool( object, Dictifiable ):
         tool_model[ 'inputs' ] = {}
         populate_model( self.inputs, state_inputs, tool_model[ 'inputs' ] )
 
-        # sanitize tool state
-        def value_to_basic( input, value, parent, **kwargs ):
-            parent[ input.name ] = input.value_to_basic( value, self.app )
-
-        visit_input_values( self.inputs, state_inputs, value_to_basic )
-
         # create tool help
         tool_help = ''
         if self.help:
@@ -1690,10 +1687,11 @@ class Tool( object, Dictifiable ):
             'versions'      : tool_versions,
             'requirements'  : [ { 'name' : r.name, 'version' : r.version } for r in self.requirements ],
             'errors'        : state_errors,
-            'state_inputs'  : state_inputs,
+            'state_inputs'  : params_to_strings( self.inputs, state_inputs, self.app ),
             'job_id'        : trans.security.encode_id( job.id ) if job else None,
             'job_remap'     : self._get_job_remap( job ),
-            'history_id'    : trans.security.encode_id( history.id )
+            'history_id'    : trans.security.encode_id( history.id ),
+            'display'       : self.display_interface
         })
         return tool_model
 
@@ -1753,12 +1751,26 @@ class Tool( object, Dictifiable ):
                     rep_prefix = '%s_%d|' % ( key, rep_index )
                     self.populate_state( request_context, input.inputs, incoming, rep_state, errors, prefix=rep_prefix, context=context )
             else:
-                param_value = incoming.get( key, state.get( input.name ) )
+                param_value = self._get_incoming_value( incoming, key, state.get( input.name ) )
                 value, error = check_param( request_context, input, param_value, context )
                 if error:
                     errors[ key ] = error
                 state[ input.name ] = value
 
+    def _get_incoming_value( self, incoming, key, default ):
+        """
+        Fetch value from incoming dict directly or check special nginx upload
+        created variants of this key.
+        """
+        if '__' + key + '__is_composite' in incoming:
+            composite_keys = incoming[ '__' + key + '__keys' ].split()
+            value = dict()
+            for composite_key in composite_keys:
+                value[ composite_key ] = incoming[ key + '_' + composite_key ]
+            return value
+        else:
+            return incoming.get( key, default )
+
     def _get_job_remap( self, job):
         if job:
             if job.state == job.states.ERROR:

lib/galaxy/tools/actions/__init__.py

@@ -439,6 +439,7 @@ class DefaultToolAction( object ):
                     handle_output( name, output )
                     log.info("Handled output named %s for tool %s %s" % (name, tool.id, handle_output_timer))
 
+        add_datasets_timer = ExecutionTimer()
         # Add all the top-level (non-child) datasets to the history unless otherwise specified
         datasets_to_persist = []
         for name in out_data.keys():
@@ -461,6 +462,8 @@ class DefaultToolAction( object ):
             child_dataset = out_data[ child_name ]
             parent_dataset.children.append( child_dataset )
 
+        log.info("Added output datasets to history %s" % add_datasets_timer)
+        job_setup_timer = ExecutionTimer()
         # Create the job object
         job, galaxy_session = self._new_job_for_session( trans, tool, history )
         self._record_inputs( trans, tool, job, incoming, inp_data, inp_dataset_collections, current_user_roles )
@@ -509,7 +512,12 @@ class DefaultToolAction( object ):
                     trans.sa_session.add(jtod)
             except Exception:
                 log.exception('Cannot remap rerun dependencies.')
+
+        log.info("Setup for job %s complete, ready to flush %s" % (job.log_str(), job_setup_timer))
+
+        job_flush_timer = ExecutionTimer()
         trans.sa_session.flush()
+        log.info("Flushed transaction for job %s %s" % (job.log_str(), job_flush_timer))
         # Some tools are not really executable, but jobs are still created for them ( for record keeping ).
         # Examples include tools that redirect to other applications ( epigraph ).  These special tools must
         # include something that can be retrieved from the params ( e.g., REDIRECT_URL ) to keep the job

lib/galaxy/tools/data/__init__.py

@@ -318,6 +318,10 @@ class TabularToolDataTable( ToolDataTable, Dictifiable ):
                 filename = os.path.join( tool_data_path, filename )
             if os.path.exists( filename ):
                 found = True
+            elif os.path.exists( "%s.sample" % filename ) and not from_shed_config:
+                log.info("Could not find tool data %s, reading sample" % filename)
+                filename = "%s.sample" % filename
+                found = True
             else:
                 # Since the path attribute can include a hard-coded path to a specific directory
                 # (e.g., <file path="tool-data/cg_crr_files.loc" />) which may not be the same value

lib/galaxy/tools/deps/containers.py

@@ -298,7 +298,7 @@ class DockerContainer(Container):
             defaults = "$job_directory:ro,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw"
         elif self.app_info.outputs_to_working_directory:
             # Should need default_file_path (which is a course estimate given
-            # object stores anyway.
+            # object stores anyway).
             defaults = "$galaxy_root:ro,$tool_directory:ro,$working_directory:rw,$default_file_path:ro"
         else:
             defaults = "$galaxy_root:ro,$tool_directory:ro,$working_directory:rw,$default_file_path:rw"

lib/galaxy/tools/evaluation.py

@@ -131,7 +131,7 @@ class ToolEvaluator( object ):
         param_dict.update( incoming )
 
         input_dataset_paths = dataset_path_rewrites( input_paths )
-        self.__populate_wrappers(param_dict, input_dataset_paths, job_working_directory)
+        self.__populate_wrappers(param_dict, input_datasets, input_dataset_paths, job_working_directory)
         self.__populate_input_dataset_wrappers(param_dict, input_datasets, input_dataset_paths)
         self.__populate_output_dataset_wrappers(param_dict, output_datasets, output_paths, job_working_directory)
         self.__populate_output_collection_wrappers(param_dict, output_collections, output_paths, job_working_directory)
@@ -167,7 +167,7 @@ class ToolEvaluator( object ):
 
         do_walk( inputs, input_values )
 
-    def __populate_wrappers(self, param_dict, input_dataset_paths, job_working_directory):
+    def __populate_wrappers(self, param_dict, input_datasets, input_dataset_paths, job_working_directory):
 
         def wrap_input( input_values, input ):
             if isinstance( input, DataToolParameter ) and input.multiple:
@@ -219,14 +219,16 @@ class ToolEvaluator( object ):
                     tool=self,
                     name=input.name
                 )
-                identifier_key = "%s|__identifier__" % input.name
-                if identifier_key in param_dict:
-                    wrapper_kwds["identifier"] = param_dict[identifier_key]
                 if dataset:
                     # A None dataset does not have a filename
                     real_path = dataset.file_name
                     if real_path in input_dataset_paths:
                         wrapper_kwds[ "dataset_path" ] = input_dataset_paths[ real_path ]
+                identifier_key = param_dict[ "identifier_key" ].get( dataset, None )
+                if identifier_key:
+                    element_identifier = param_dict.get(identifier_key, None)
+                    if element_identifier:
+                        wrapper_kwds[ "identifier" ] = element_identifier
                 input_values[ input.name ] = \
                     DatasetFilenameWrapper( dataset, **wrapper_kwds )
             elif isinstance( input, DataCollectionToolParameter ):
@@ -254,6 +256,7 @@ class ToolEvaluator( object ):
         #       tools where the inputs don't even get passed through. These
         #       tools (e.g. UCSC) should really be handled in a special way.
         if self.tool.check_values:
+            param_dict[ "identifier_key" ] = dict((v, "%s|__identifier__" % k) for k, v in input_datasets.iteritems())  # allows lookup of identifier through HDA.
             self.__walk_inputs( self.tool.inputs, param_dict, wrap_input )
 
     def __populate_input_dataset_wrappers(self, param_dict, input_datasets, input_dataset_paths):

lib/galaxy/tools/execute.py

@@ -72,6 +72,7 @@ def execute( trans, tool, param_combinations, history, rerun_remap_job_id=None,
     log.debug("Executed %d job(s) for tool %s request: %s" % (job_count, tool.id, all_jobs_timer))
     if collection_info:
         history = history or tool.get_default_history_by_trans( trans )
+        params = param_combinations[0]
         execution_tracker.create_output_collections( trans, history, params )
 
     return execution_tracker

lib/galaxy/tools/parameters/__init__.py

@@ -24,7 +24,7 @@ def visit_input_values( inputs, input_values, callback, name_prefix='', label_pr
     >>> from xml.etree.ElementTree import XML
     >>> from galaxy.util.bunch import Bunch
     >>> from galaxy.util.odict import odict
-    >>> from galaxy.tools.parameters.basic import TextToolParameter
+    >>> from galaxy.tools.parameters.basic import TextToolParameter, BooleanToolParameter
     >>> from galaxy.tools.parameters.grouping import Repeat
     >>> a = TextToolParameter( None, XML( '<param name="a"/>' ) )
     >>> b = Repeat()
@@ -32,7 +32,7 @@ def visit_input_values( inputs, input_values, callback, name_prefix='', label_pr
     >>> d = Repeat()
     >>> e = TextToolParameter( None, XML( '<param name="e"/>' ) )
     >>> f = Conditional()
-    >>> g = TextToolParameter( None, XML( '<param name="g"/>' ) )
+    >>> g = BooleanToolParameter( None, XML( '<param name="g"/>' ) )
     >>> h = TextToolParameter( None, XML( '<param name="h"/>' ) )
     >>> i = TextToolParameter( None, XML( '<param name="i"/>' ) )
     >>> b.name = 'b'
@@ -45,12 +45,16 @@ def visit_input_values( inputs, input_values, callback, name_prefix='', label_pr
     >>>
     >>> def visitor( input, value, prefix, prefixed_name, **kwargs ):
     ...     print 'name=%s, prefix=%s, prefixed_name=%s, value=%s' % ( input.name, prefix, prefixed_name, value )
-    >>> visit_input_values( odict([('a',a),('b',b)]), odict([ ('a', 1), ('b', [ odict([('c', 3), ( 'd', [odict([ ('e',5), ('f', odict([ ('g','true'), ('h',7) ])) ]) ])]) ]) ]), visitor )
+    >>> inputs = odict([('a',a),('b',b)])
+    >>> nested = odict([ ('a', 1), ('b', [ odict([('c', 3), ( 'd', [odict([ ('e', 5), ('f', odict([ ('g', True), ('h', 7) ])) ]) ])]) ]) ])
+    >>> visit_input_values( inputs, nested, visitor )
     name=a, prefix=, prefixed_name=a, value=1
     name=c, prefix=b_0|, prefixed_name=b_0|c, value=3
     name=e, prefix=b_0|d_0|, prefixed_name=b_0|d_0|e, value=5
-    name=g, prefix=b_0|d_0|, prefixed_name=b_0|d_0|f|g, value=true
+    name=g, prefix=b_0|d_0|, prefixed_name=b_0|d_0|f|g, value=True
     name=h, prefix=b_0|d_0|, prefixed_name=b_0|d_0|f|h, value=7
+    >>> params_from_strings( inputs, params_to_strings( inputs, nested, None ), None )[ 'b' ][ 0 ][ 'd' ][ 0 ][ 'f' ][ 'g' ] is True
+    True
     """
     def callback_helper( input, input_values, name_prefix, label_prefix, parent_prefix, context=None, error=None ):
         args = {

lib/galaxy/tools/parameters/basic.py

@@ -187,9 +187,10 @@ class ToolParameter( object, Dictifiable ):
         return value
 
     def validate( self, value, trans=None ):
-        if value is not '' or not self.optional:
-            for validator in self.validators:
-                validator.validate( value, trans )
+        if value in ["", None] and self.optional:
+            return
+        for validator in self.validators:
+            validator.validate( value, trans )
 
     def to_dict( self, trans, view='collection', value_mapper=None, other_values={} ):
         """ to_dict tool parameter. This can be overridden by subclasses. """
@@ -476,7 +477,7 @@ class BooleanToolParameter( ToolParameter ):
         return ( value in [ True, 'True', 'true' ] )
 
     def to_json( self, value, app=None ):
-        if value is True:
+        if self.to_python( value, app ):
             return 'true'
         else:
             return 'false'
@@ -1873,6 +1874,8 @@ class DataToolParameter( BaseDataToolParameter ):
             raise ValueError( "History does not include a dataset of the required format / build" )
         if value in [ None, "None", '' ]:
             return None
+        if isinstance( value, dict ) and 'values' in value:
+            value = self.to_python( value, trans.app )
         if isinstance( value, string_types ) and value.find( "," ) > 0:
             value = [ int( value_part ) for value_part in value.split( "," ) ]
         if isinstance( value, list ):
@@ -1954,7 +1957,7 @@ class DataToolParameter( BaseDataToolParameter ):
         dataset_count = 0
         for validator in self.validators:
             def do_validate( v ):
-                if validator.requires_dataset_metadata and v and v.dataset.state != galaxy.model.Dataset.states.OK:
+                if validator.requires_dataset_metadata and v and hasattr( v, 'dataset' ) and v.dataset.state != galaxy.model.Dataset.states.OK:
                     return
                 else:
                     validator.validate( v, trans )
@@ -2149,6 +2152,8 @@ class DataCollectionToolParameter( BaseDataToolParameter ):
             raise ValueError( "History does not include a dataset collection of the correct type or containing the correct types of datasets" )
         if value in [None, "None"]:
             return None
+        if isinstance( value, dict ) and 'values' in value:
+            value = self.to_python( value, trans.app )
         if isinstance( value, string_types ) and value.find( "," ) > 0:
             value = [ int( value_part ) for value_part in value.split( "," ) ]
         elif isinstance( value, trans.app.model.HistoryDatasetCollectionAssociation ):

lib/galaxy/tools/parameters/wrapped_json.py

@@ -63,6 +63,9 @@ def _json_wrap_input(input, value, handle_files="SKIP"):
         json_value = _cast_if_not_none(value, int, empty_to_none=True)
     elif input_type == "boolean":
         json_value = _cast_if_not_none(value, bool)
+    elif input_type == "data_column":
+        # value is a SelectToolParameterWrapper()
+        json_value = map(int, _cast_if_not_none(value.value, list))
     else:
         raise NotImplementedError("input_type [%s] not implemented" % input_type)
 

lib/galaxy/tools/parser/interface.py

@@ -347,10 +347,11 @@ class TestCollectionDef( object ):
 
 
 class TestCollectionOutputDef( object ):
-    # TODO: do not require XML directly here.
 
     def __init__( self, name, attrib, element_tests ):
         self.name = name
         self.collection_type = attrib.get( "type", None )
+        count = attrib.get("count", None)
+        self.count = int(count) if count is not None else None
         self.attrib = attrib
         self.element_tests = element_tests

lib/galaxy/tools/toolbox/base.py

@@ -126,13 +126,10 @@ class AbstractToolBox( Dictifiable, ManagesIntegratedToolPanelMixin, object ):
         log.info( "Parsing the tool configuration %s" % config_filename )
         tool_conf_source = get_toolbox_parser(config_filename)
         tool_path = tool_conf_source.parse_tool_path()
-        if tool_path:
-            # We're parsing a shed_tool_conf file since we have a tool_path attribute.
-            parsing_shed_tool_conf = True
+        parsing_shed_tool_conf = tool_conf_source.is_shed_tool_conf()
+        if parsing_shed_tool_conf:
             # Keep an in-memory list of xml elements to enable persistence of the changing tool config.
             config_elems = []
-        else:
-            parsing_shed_tool_conf = False
         tool_path = self.__resolve_tool_path(tool_path, config_filename)
         # Only load the panel_dict under certain conditions.
         load_panel_dict = not self._integrated_tool_panel_config_has_contents