(merge dev); Testing, histories: update tests to reflect allowing anon to create/copy histories via the API

Makefile

@@ -0,0 +1,19 @@
+GRUNT_DOCKER_NAME:=galaxy/client-builder:16.01
+
+all:
+	@echo "This makefile is primarily used for building Galaxy's JS client. A sensible all target is not yet implemented."
+
+npm-deps:
+	cd client && npm install
+
+grunt: npm-deps
+	cd client && grunt
+
+grunt-docker-image:
+	docker build -t ${GRUNT_DOCKER_NAME} client
+
+grunt-docker: grunt-docker-image
+	docker run -it -v `pwd`:/data ${GRUNT_DOCKER_NAME}
+
+clean-grunt-docker-image:
+	docker rmi ${GRUNT_DOCKER_NAME}

client/.docker-build.sh

@@ -0,0 +1,4 @@
+#!/bin/bash
+cd /data/client && \
+    npm install && \
+    grunt

client/Dockerfile

@@ -0,0 +1,13 @@
+FROM digitallyseamless/nodejs-bower-grunt
+RUN mkdir /gx
+
+COPY package.json /gx/package.json
+
+RUN cd /gx && \
+    npm install -g && \
+    cd / && \
+    rm -rf /gx
+
+WORKDIR /data/client
+ADD ./.docker-build.sh /build.sh
+CMD ["/build.sh"]

client/galaxy/scripts/apps/analysis.js

@@ -151,7 +151,8 @@ window.app = function app( options, bootstrapped ){
         // page render. It's re-created each time because there is no render function and can't be re-rendered without
         // re-creating it.
         Galaxy.listenTo( analysisPage.right.historyView, 'history-size-change', function(){
-            Galaxy.user.fetch();
+            // fetch to update the quota meter adding 'current' for any anon-user's id
+            Galaxy.user.fetch({ url: Galaxy.user.urlRoot() + '/' + ( Galaxy.user.id || 'current' ) });
         });
         analysisPage.right.historyView.connectToQuotaMeter( analysisPage.masthead.quotaMeter );
 

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

@@ -66,7 +66,7 @@ var SessionStorageModel = Backbone.Model.extend({
 
     _checkEnabledSessionStorage : function(){
         try {
-            return sessionStorage.length;
+            return window.sessionStorage.length >= 0;
         } catch( err ){
             alert( 'Please enable cookies in your browser for this Galaxy site' );
             return false;

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

@@ -2,7 +2,7 @@ define([
     "libs/bibtex",
     "mvc/base-mvc",
     "utils/localization"
-], function( bibtex, baseMVC, _l ){
+], function( BibtexParser, baseMVC, _l ){
 /* global Backbone */
 
 var logNamespace = 'citation';
@@ -14,9 +14,9 @@ var logNamespace = 'citation';
 var Citation = Backbone.Model.extend( baseMVC.LoggableMixin ).extend( {
     _logNamespace : logNamespace,
 
-    initialize: function( ) {
-        var bibtex = this.attributes.content;
-        var entry = new bibtex.BibtexParser(bibtex).entries[0];
+    initialize: function() {
+        var bibtex = this.get( 'content' );
+        var entry = BibtexParser(bibtex).entries[0];
         this.entry = entry;
         this._fields = {};
         var rawFields = entry.Fields;
@@ -61,6 +61,7 @@ var ToolCitationCollection = BaseCitationCollection.extend( {
     partial : false, // If a tool has citations, assume they are complete.
 } );
 
+
 //==============================================================================
 return {
     Citation : Citation,

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

@@ -30,6 +30,7 @@ var View = Backbone.View.extend({
         // link elements
         this.$select = this.$el.find('.select');
         this.$icon_dropdown = this.$el.find('.icon-dropdown');
+        this.$icon_dropdown.on( 'click', function() { self.$select.select2 && self.$select.select2( 'open' ) });
 
         // allow regular multi-select field to be resized
         var minHeight = null;

client/galaxy/scripts/mvc/workflow/workflow-manager.js

@@ -1,4 +1,8 @@
-define(['mvc/workflow/workflow-connector'], function( Connector ) {
+define([
+    'mvc/workflow/workflow-connector',
+    'libs/toastr'
+    ],
+function( Connector, Toastr ) {
     function Workflow( app, canvas_container ) {
         this.app = app;
         this.canvas_container = canvas_container;
@@ -7,10 +11,49 @@ define(['mvc/workflow/workflow-connector'], function( Connector ) {
         this.name = null;
         this.has_changes = false;
         this.active_form_has_changes = false;
+        this.nodeLabels = {}; // TODO: track and enforce output labels also
+
     }
     $.extend( Workflow.prototype, {
-        create_node: function ( type, title_text, tool_id ) {
-            var node = this.app.prebuildNode( type, title_text, tool_id );
+        canLabelNodeWith: function( label ) {
+            if( label ) {
+                return ! (label in this.nodeLabels);
+            } else {
+                // empty labels are non-exclusive, so allow this one.
+                return true;
+            }
+        },
+        registerNodeLabel: function( label ) {
+            if( label ) {
+                this.nodeLabels[label] = true;
+            }
+        },
+        unregisterNodeLabel: function( label ) {
+            if( label ) {
+                delete this.nodeLabels[label];
+            }
+        },
+        updateNodeLabel: function( fromLabel, toLabel ) {
+            if( fromLabel ) {
+                this.unregisterNodeLabel( fromLabel );
+            }
+            if( ! this.canLabelNodeWith( toLabel ) ) {
+                Toastr.warning("Workflow contains duplicate node labels " + toLabel + ". This must be fixed before it can be saved.");
+            }
+            if( toLabel ) {
+                this.registerNodeLabel( toLabel );
+            }
+        },
+        attemptUpdateNodeLabel: function( node, label ) {
+            if( this.canLabelNodeWith( label ) ) {
+                node.setLabel( label );
+                return true;
+            } else {
+                return false;
+            }
+        },
+        create_node: function ( type, title_text, content_id ) {
+            var node = this.app.prebuildNode( type, title_text, content_id );
             this.add_node( node );
             this.fit_canvas_to_nodes();
             this.app.canvas_manager.draw_overview();
@@ -131,7 +174,7 @@ define(['mvc/workflow/workflow-connector'], function( Connector ) {
                 var node_data = {
                     id : node.id,
                     type : node.type,
-                    tool_id : node.tool_id,
+                    tool_id : node.content_id,
                     tool_state : node.tool_state,
                     tool_errors : node.tool_errors,
                     input_connections : input_connections,
@@ -383,4 +426,4 @@ define(['mvc/workflow/workflow-connector'], function( Connector ) {
         }
     });
     return Workflow;
-});
+});

client/galaxy/scripts/mvc/workflow/workflow-node.js

@@ -124,6 +124,10 @@ define(['mvc/workflow/workflow-view-node'], function( NodeView ) {
             // Remove active class
             $(element).removeClass( "toolForm-active" );
         },
+        setLabel: function(label) {
+            this.app.workflow.updateNodeLabel(this.label, label);
+            this.label = label || null;
+        },
         init_field_data : function ( data ) {
             if ( data.type ) {
                 this.type = data.type;
@@ -135,7 +139,7 @@ define(['mvc/workflow/workflow-view-node'], function( NodeView ) {
             this.tooltip = data.tooltip ? data.tooltip : "";
             this.annotation = data.annotation;
             this.post_job_actions = data.post_job_actions ? data.post_job_actions : {};
-            this.label = data.label;
+            this.setLabel(data.label);
             this.uuid = data.uuid;
             this.workflow_outputs = data.workflow_outputs ? data.workflow_outputs : [];
 
@@ -165,6 +169,8 @@ define(['mvc/workflow/workflow-view-node'], function( NodeView ) {
             this.form_html = data.form_html;
             this.tool_errors = data.tool_errors;
             this.annotation = data['annotation'];
+            this.setLabel(data.label);
+
             if( "post_job_actions" in data ) {
                 // Won't be present in response for data inputs
                 var pja_in = $.parseJSON(data.post_job_actions);
@@ -184,6 +190,7 @@ define(['mvc/workflow/workflow-view-node'], function( NodeView ) {
                 unusedView.el.terminal.destroy();
             } );
             nodeView.terminalViews = newTerminalViews;
+            node.nodeView.render();
             // In general workflow editor assumes tool outputs don't change in # or
             // type (not really valid right?) but adding special logic here for
             // data collection input parameters that can have their collection

client/galaxy/scripts/mvc/workflow/workflow-view-node.js

@@ -11,6 +11,14 @@ define(['mvc/workflow/workflow-view-terminals', 'mvc/workflow/workflow-view-data
         },
 
         render: function() {
+            var label = this.node.label;
+            var title;
+            if(label) {
+                title = label; 
+            } else {
+                title = this.node.name;
+            }
+            this.$el.find(".nodeTitle").text(title);
             this.renderToolErrors();
             this.$el.css( "width", Math.min(250, Math.max( this.$el.width(), this.output_width )));
         },

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

@@ -7,7 +7,9 @@ define([
     'mvc/workflow/workflow-node',
     'mvc/tool/tools-form-workflow',
     'utils/async-save-text',
-], function( Utils, Globals, Workflow, WorkflowCanvas, Node, ToolsForm, async_save_text ){
+    'libs/toastr',
+    'ui/editable-text'
+], function( Utils, Globals, Workflow, WorkflowCanvas, Node, ToolsForm, async_save_text, Toastr ){
 
 // Reset tool search to start state.
 function reset_tool_search( initValue ) {
@@ -44,6 +46,21 @@ function reset_tool_search( initValue ) {
     }
 }
 
+NODE_ICONS = {
+    'tool': 'fa-wrench',
+    'data_input': 'fa-file-o',
+    'data_collection_input': 'fa-folder-o',
+    'pause': 'fa-pause'
+}
+
+add_node_icon = function($to_el, nodeType) {
+    var iconStyle = NODE_ICONS[nodeType];
+    if(iconStyle) {
+        var $icon = $('<i class="icon fa">&nbsp;</i>').addClass(iconStyle);
+        $to_el.before($icon);
+    }
+}
+
 
 // Really a shell of a real backbone view, but refactoring in the right
 // direction I think.
@@ -61,7 +78,33 @@ EditorFormView = Backbone.View.extend({
         this.setElement($el);
 
         if (node && node.id != 'no-node') {
-            $el.find('.toolForm:first').after(this._genericStepAttributesTemplate( node ));
+            $el.find('table:first').after(this._genericStepAttributesTemplate( node ));
+            var nodeType = node.type;
+            add_node_icon($el.find('.portlet-title-text'), nodeType);
+            var $titleText = $el.find(".portlet-title-text");
+            $titleText.data('last-value', $titleText.text());
+            $titleText.make_text_editable({
+                on_finish: function( newLabel ){
+                    var lastValue = $titleText.data("last-value");
+                    if( newLabel == lastValue ) {
+                        return;
+                    }
+
+                    var workflow = workflowView.workflow;
+                    if( workflow.attemptUpdateNodeLabel( node, newLabel ) ) {
+                        $el.find("input[name='label']").val(newLabel);
+                        $titleText.data("last-value", newLabel);
+                        $el.find('form').submit();
+                        if(newLabel == "") {
+                            // If label unset restore default name as title.
+                            $titleText.text(node.name);
+                        }
+                    } else {
+                        Toastr.warning("Step label " + newLabel + " already exists, cannot update label.");
+                        $titleText.text(lastValue);
+                    }
+                }
+            });
             ($el.find( 'form' ).length > 0) && $el.find( 'form' ).ajaxForm( {
                 type: 'POST',
                 dataType: 'json',
@@ -525,12 +568,10 @@ EditorFormView = Backbone.View.extend({
             cc.css( { left: left, top: top } );
         },
 
-        // Add a new step to the workflow by tool id
-        add_node_for_tool: function ( id, title ) {
-            node = this.workflow.create_node( 'tool', title, id );
+        _moduleInitAjax: function(node, request_data) {
             $.ajax( {
                 url: this.urls.get_new_module_info,
-                data: { type: "tool", tool_id: id, "_": "true" },
+                data: request_data,
                 global: false,
                 dataType: "json",
                 success: function( data ) {
@@ -546,23 +587,21 @@ EditorFormView = Backbone.View.extend({
             });
         },
 
+        // Add a new step to the workflow by tool id
+        add_node_for_tool: function ( id, title ) {
+            node = this.workflow.create_node( 'tool', title, id );
+            this._moduleInitAjax(node, { type: "tool", content_id: id, "_": "true" });
+        },
+
+        // Add a new step to the workflow by tool id
+        add_node_for_subworkflow: function ( id, title ) {
+            node = this.workflow.create_node( 'subworkflow', title, id );
+            this._moduleInitAjax(node, { type: "subworkflow", subworkflow_id: id, "_": "true" });
+        },
+
         add_node_for_module: function ( type, title ) {
             node = this.workflow.create_node( type, title );
-            $.ajax( {
-                url: this.urls.get_new_module_info,
-                data: { type: type, "_": "true" },
-                dataType: "json",
-                success: function( data ) {
-                    node.init_field_data( data );
-                },
-                error: function( x, e ) {
-                    var m = "error loading field data"
-                    if ( x.status == 0 ) {
-                        m += ", server unavailable"
-                    }
-                    node.error( m );
-                }
-            });
+            this._moduleInitAjax(node, { type: type, "_": "true" });
         },
 
         // This function preloads how to display known pja's.
@@ -704,22 +743,27 @@ EditorFormView = Backbone.View.extend({
             return ( this.type_to_type[child] ) && ( parent in this.type_to_type[child] );
         },
 
-        prebuildNode: function ( type, title_text, tool_id ) {
+        $newNodeElement: function(type, title_text) {
+            var $f = $("<div class='toolForm toolFormInCanvas'></div>");
+            var $title = $("<div class='toolFormTitle unselectable'><span class='nodeTitle'>" + title_text + "</div></div>" );
+            add_node_icon($title.find('.nodeTitle'), type);
+            $f.append( $title );
+            $f.css( "left", $(window).scrollLeft() + 20 );
+            $f.css( "top", $(window).scrollTop() + 20 );
+            var $b = $("<div class='toolFormBody'></div>");
+            $f.append($b);
+            return $f
+        },
+
+        prebuildNode: function ( type, title_text, content_id ) {
             var self = this;
-            var f = $("<div class='toolForm toolFormInCanvas'></div>");
-            var node = new Node( this, { element: f } );
+            var $f = this.$newNodeElement( type, title_text );
+            var node = new Node( this, { element: $f } );
             node.type = type;
-            if ( type == 'tool' ) {
-                node.tool_id = tool_id;
-            }
-            var title = $("<div class='toolFormTitle unselectable'>" + title_text + "</div>" );
-            f.append( title );
-            f.css( "left", $(window).scrollLeft() + 20 ); f.css( "top", $(window).scrollTop() + 20 );
-            var b = $("<div class='toolFormBody'></div>");
+            node.content_id = content_id;
             var tmp = "<div><img height='16' align='middle' src='" + Galaxy.root + "static/images/loading_small_white_bg.gif'/> loading tool info...</div>";
-            b.append( tmp );
+            $f.find(".toolFormBody").append(tmp);
             node.form_html = tmp;
-            f.append( b );
             // Fix width to computed width
             // Now add floats
             var buttons = $("<div class='buttons' style='float: right;'></div>");
@@ -727,17 +771,17 @@ EditorFormView = Backbone.View.extend({
                 node.destroy();
             }));
             // Place inside container
-            f.appendTo( "#canvas-container" );
+            $f.appendTo( "#canvas-container" );
             // Position in container
             var o = $("#canvas-container").position();
             var p = $("#canvas-container").parent();
-            var width = f.width();
-            var height = f.height();
-            f.css( { left: ( - o.left ) + ( p.width() / 2 ) - ( width / 2 ), top: ( - o.top ) + ( p.height() / 2 ) - ( height / 2 ) } );
-            buttons.prependTo( title );
+            var width = $f.width();
+            var height = $f.height();
+            $f.css( { left: ( - o.left ) + ( p.width() / 2 ) - ( width / 2 ), top: ( - o.top ) + ( p.height() / 2 ) - ( height / 2 ) } );
+            buttons.prependTo( $f.find(".toolFormTitle" ) );
             width += ( buttons.width() + 10 );
-            f.css( "width", width );
-            $(f).bind( "dragstart", function() {
+            $f.css( "width", width );
+            $f.bind( "dragstart", function() {
                 self.workflow.activate_node( node );
             }).bind( "dragend", function() {
                 self.workflow.node_changed( this );

client/galaxy/scripts/polyfills.js

@@ -51,17 +51,17 @@
     };
 
     // ------------------------------------------------------------------ can't/won't polyfill
-    var incompatibilities = [
+    var features = [
         { name: 'canvas',           compatible: function(){ return window.CanvasRenderingContext2D; } },
         { name: 'sessionStorage',   compatible: function(){
             try {
-                return Number.isInteger( sessionStorage.length );
+                return window.sessionStorage.length >= 0;
             } catch( err ){}
             return false;
         }},
     ];
     // build a list of feature names for features that were not found
-    incompatibilities = incompatibilities
+    var incompatibilities = features
         .filter( function( feature ){ return !feature.compatible(); })
         .map( function( feature ){ return feature.name; });
 
@@ -69,7 +69,7 @@
     if( !!incompatibilities.length ){
         var root = document.querySelectorAll( 'link[rel="index"]' ).item( 0 );
         if( root ){
-            window.location.href = root.href + 'static/incompatible-browser.html';
+            window.location = root.href + 'static/incompatible-browser.html';
         }
         console.log( 'incompatible browser:\n' + incompatibilities.join( '\n' ) );
     }

client/galaxy/style/less/ui.less

@@ -578,6 +578,7 @@
         position: absolute;
         top: 8px;
         right: 8px;
+        cursor: pointer;
     }
     .icon-resize {
         display: none;

doc/source/dev/faq.rst

@@ -10,3 +10,16 @@ to provide relatively concrete answers for specific Galaxy development scenarios
 This can be done with either IPython/Jupyter or a plain python console, depending on your preferences::
 
     python -i scripts/db_shell.py
+
+... build Galaxy Javascript frontend client?
+--------------------------------------------
+
+We've added a makefile which will let you do this. If you have nodejs and npm installed, you can simple run::
+
+    make grunt
+
+If you prefer docker and aren't a JS developer primarily, you can run
+
+    make grunt-docker
+
+

lib/galaxy/datatypes/text.py

@@ -11,7 +11,7 @@ import subprocess
 import tempfile
 
 from galaxy.datatypes.data import get_file_peek, Text
-from galaxy.datatypes.metadata import MetadataElement
+from galaxy.datatypes.metadata import MetadataElement, MetadataParameter
 from galaxy.util import nice_size, string_as_bool
 
 log = logging.getLogger(__name__)
@@ -122,45 +122,98 @@ class Ipynb( Json ):
         pass
 
 
-class Biom1(Json):
+class Biom1( Json ):
+    """
+        BIOM version 1.0 file format description
+        http://biom-format.org/documentation/format_versions/biom-1.0.html
+    """
     file_ext = "biom1"
 
-    def set_peek(self, dataset, is_multi_byte=False):
-        super(Biom1, self).set_peek(dataset, is_multi_byte)
+    MetadataElement( name="table_rows", default=[], desc="table_rows", param=MetadataParameter, readonly=True, visible=False, optional=True, no_value=[] )
+    MetadataElement( name="table_matrix_element_type", default="", desc="table_matrix_element_type", param=MetadataParameter, readonly=True, visible=False, optional=True, no_value="" )
+    MetadataElement( name="table_format", default="", desc="table_format", param=MetadataParameter, readonly=True, visible=False, optional=True, no_value="" )
+    MetadataElement( name="table_generated_by", default="", desc="table_generated_by", param=MetadataParameter, readonly=True, visible=True, optional=True, no_value="" )
+    MetadataElement( name="table_matrix_type", default="", desc="table_matrix_type", param=MetadataParameter, readonly=True, visible=False, optional=True, no_value="" )
+    MetadataElement( name="table_shape", default=[], desc="table_shape", param=MetadataParameter, readonly=True, visible=False, optional=True, no_value=[] )
+    MetadataElement( name="table_format_url", default="", desc="table_format_url", param=MetadataParameter, readonly=True, visible=False, optional=True, no_value="" )
+    MetadataElement( name="table_date", default="", desc="table_date", param=MetadataParameter, readonly=True, visible=True, optional=True, no_value="" )
+    MetadataElement( name="table_type", default="", desc="table_type", param=MetadataParameter, readonly=True, visible=True, optional=True, no_value="" )
+    MetadataElement( name="table_id", default=None, desc="table_id", param=MetadataParameter, readonly=True, visible=True, optional=True, no_value=None )
+    MetadataElement( name="table_columns", default=[], desc="table_columns", param=MetadataParameter, readonly=True, visible=False, optional=True, no_value=[] )
+
+    def set_peek( self, dataset, is_multi_byte=False ):
+        super( Biom1, self ).set_peek( dataset, is_multi_byte )
         if not dataset.dataset.purged:
             dataset.blurb = "Biological Observation Matrix v1"
 
-    def sniff(self, filename):
+    def sniff( self, filename ):
         is_biom = False
         if self._looks_like_json( filename ):
-            is_biom = self._looks_like_biom(filename)
+            is_biom = self._looks_like_biom( filename )
         return is_biom
 
-    def _looks_like_biom(self, filepath, load_size=50000):
+    def _looks_like_biom( self, filepath, load_size=50000 ):
         """
         @param filepath: [str] The path to the evaluated file.
         @param load_size: [int] The size of the file block load in RAM (in
                           bytes).
         """
         is_biom = False
-        segment_size = int(load_size / 2)
+        segment_size = int( load_size / 2 )
         try:
-            with open(filepath, "r") as fh:
+            with open( filepath, "r" ) as fh:
                 prev_str = ""
-                segment_str = fh.read(segment_size)
-                if segment_str.strip().startswith('{'):
-                    while segment_str and not is_biom:
+                segment_str = fh.read( segment_size )
+                if segment_str.strip().startswith( '{' ):
+                    while segment_str:
                         current_str = prev_str + segment_str
                         if '"format"' in current_str:
-                            current_str = re.sub(r'\s', '', current_str)
+                            current_str = re.sub( r'\s', '', current_str )
                             if '"format":"BiologicalObservationMatrix' in current_str:
                                 is_biom = True
+                                break
                         prev_str = segment_str
-                        segment_str = fh.read(segment_size)
-        except:
+                        segment_str = fh.read( segment_size )
+        except Exception:
             pass
         return is_biom
 
+    def set_meta( self, dataset, **kwd ):
+        """
+            Store metadata information from the BIOM file.
+        """
+        if dataset.has_data():
+            with open( dataset.file_name ) as fh:
+                try:
+                    json_dict = json.load( fh )
+                except Exception:
+                    return
+
+                def _transform_dict_list_ids( dict_list ):
+                    if dict_list:
+                        return [ x.get( 'id', None ) for x in dict_list ]
+                    return []
+
+                b_transform = { 'rows': _transform_dict_list_ids, 'columns': _transform_dict_list_ids }
+                for ( m_name, b_name ) in [ ('table_rows', 'rows'),
+                                            ('table_matrix_element_type', 'matrix_element_type'),
+                                            ('table_format', 'format'),
+                                            ('table_generated_by', 'generated_by'),
+                                            ('table_matrix_type', 'matrix_type'),
+                                            ('table_shape', 'shape'),
+                                            ('table_format_url', 'format_url'),
+                                            ('table_date', 'date'),
+                                            ('table_type', 'type'),
+                                            ('table_id', 'id'),
+                                            ('table_columns', 'columns') ]:
+                    try:
+                        metadata_value = json_dict.get( b_name, None )
+                        if b_name in b_transform:
+                            metadata_value = b_transform[ b_name ]( metadata_value )
+                        setattr( dataset.metadata, m_name, metadata_value )
+                    except Exception:
+                        pass
+
 
 class Obo( Text ):
     """

lib/galaxy/managers/base.py

@@ -112,6 +112,16 @@ def get_class( class_name ):
     return item_class
 
 
+def decode_id(app, id):
+    try:
+        # note: use str - occasionally a fully numeric id will be placed in post body and parsed as int via JSON
+        #   resulting in error for valid id
+        return app.security.decode_id( str( id ) )
+    except ( ValueError, TypeError ):
+        msg = "Malformed id ( %s ) specified, unable to decode" % ( str( id ) )
+        raise exceptions.MalformedId( msg, id=str( id ) )
+
+
 def get_object( trans, id, class_name, check_ownership=False, check_accessible=False, deleted=None ):
     """
     Convenience method to get a model object with the specified checks. This is
@@ -119,11 +129,7 @@ def get_object( trans, id, class_name, check_ownership=False, check_accessible=F
     controller mixin code - however whenever possible the managers for a
     particular model should be used to load objects.
     """
-    try:
-        decoded_id = trans.security.decode_id( id )
-    except:
-        raise exceptions.MessageException( "Malformed %s id ( %s ) specified, unable to decode"
-                                           % ( class_name, str( id ) ), type='error' )
+    decoded_id = decode_id(trans.app, id)
     try:
         item_class = get_class( class_name )
         assert item_class is not None

lib/galaxy/managers/users.py

@@ -235,7 +235,7 @@ class UserManager( base.ModelManager, deletable.PurgableManagerMixin ):
         if self.is_anonymous( user ):
             return False
         request_types = self.app.security_agent.get_accessible_request_types( trans, user )
-        return ( user.requests or request_types )
+        return bool( user.requests or request_types )
 
 
 class UserSerializer( base.ModelSerializer, deletable.PurgableSerializerMixin ):
@@ -283,8 +283,7 @@ class UserSerializer( base.ModelSerializer, deletable.PurgableSerializerMixin ):
             'quota_percent' : lambda i, k, **c: self.user_manager.quota( i ),
 
             'tags_used'     : lambda i, k, **c: self.user_manager.tags_used( i ),
-            # TODO: 'has_requests' is more apt
-            'requests'      : lambda i, k, trans=None, **c: self.user_manager.has_requests( i, trans )
+            'has_requests'  : lambda i, k, trans=None, **c: self.user_manager.has_requests( i, trans )
         })
 
 

lib/galaxy/managers/workflows.py

@@ -2,12 +2,18 @@ from __future__ import absolute_import
 
 from collections import namedtuple
 import json
+import uuid
+
+from sqlalchemy import and_
 
 from galaxy import model
+from galaxy import util
 from galaxy import exceptions
 from galaxy.model.item_attrs import UsesAnnotations
 from galaxy.workflow import modules
 
+from .base import decode_id
+
 # For WorkflowContentManager
 from galaxy.util.sanitize_html import sanitize_html
 from galaxy.workflow.steps import attach_ordered_steps
@@ -26,6 +32,38 @@ class WorkflowsManager( object ):
     def __init__( self, app ):
         self.app = app
 
+    def get_stored_workflow( self, trans, workflow_id ):
+        """ Use a supplied ID (UUID or encoded stored workflow ID) to find
+        a workflow.
+        """
+        if util.is_uuid(workflow_id):
+            # see if they have passed in the UUID for a workflow that is attached to a stored workflow
+            workflow_uuid = uuid.UUID(workflow_id)
+            stored_workflow = trans.sa_session.query(trans.app.model.StoredWorkflow).filter( and_(
+                trans.app.model.StoredWorkflow.latest_workflow_id == trans.app.model.Workflow.id,
+                trans.app.model.Workflow.uuid == workflow_uuid
+            )).first()
+            if stored_workflow is None:
+                raise exceptions.ObjectNotFound( "Workflow not found: %s" % workflow_id )
+        else:
+            workflow_id = decode_id( self.app, workflow_id )
+            query = trans.sa_session.query( trans.app.model.StoredWorkflow )
+            stored_workflow = query.get( workflow_id )
+        if stored_workflow is None:
+            raise exceptions.ObjectNotFound( "No such workflow found." )
+        return stored_workflow
+
+    def get_stored_accessible_workflow( self, trans, workflow_id ):
+        stored_workflow = self.get_stored_workflow( trans, workflow_id )
+
+        # check to see if user has permissions to selected workflow
+        if stored_workflow.user != trans.user and not trans.user_is_admin():
+            if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0:
+                message = "Workflow is not owned by or shared with current user"
+                raise exceptions.ItemAccessibilityException( message )
+
+        return stored_workflow
+
     def check_security( self, trans, has_workflow, check_ownership=True, check_accessible=True):
         """ check accessibility or ownership of workflows, storedworkflows, and
         workflowinvocations. Throw an exception or returns True if user has
@@ -352,7 +390,7 @@ class WorkflowContentsManager(UsesAnnotations):
             step_dict = {
                 'id': step.order_index,
                 'type': module.type,
-                'tool_id': module.get_tool_id(),
+                'tool_id': module.get_content_id(),
                 'name': module.get_name(),
                 'tool_state': module.get_state(),
                 'tooltip': module.get_tooltip( static_path=url_for( '/static' ) ),
@@ -395,11 +433,13 @@ class WorkflowContentsManager(UsesAnnotations):
                         action_arguments=pja.action_arguments
                     )
                 step_dict['post_job_actions'] = pja_dict
-                # workflow outputs
-                outputs = []
-                for output in step.workflow_outputs:
-                    outputs.append({"output_name": output.output_name})
-                step_dict['workflow_outputs'] = outputs
+
+            # workflow outputs
+            outputs = []
+            for output in step.workflow_outputs:
+                outputs.append({"output_name": output.output_name})
+            step_dict['workflow_outputs'] = outputs
+
             # Encode input connections as dictionary
             input_conn_dict = {}
             for conn in input_connections:
@@ -453,7 +493,7 @@ class WorkflowContentsManager(UsesAnnotations):
             step_dict = {
                 'id': step.order_index,
                 'type': module.type,
-                'tool_id': module.get_tool_id(),
+                'tool_id': module.get_content_id(),
                 'tool_version': step.tool_version,
                 'name': module.get_name(),
                 'tool_state': module.get_state( secure=False ),

lib/galaxy/web/base/controller.py

@@ -11,7 +11,6 @@ from paste.httpexceptions import HTTPBadRequest, HTTPInternalServerError
 from paste.httpexceptions import HTTPNotImplemented, HTTPRequestRangeNotSatisfiable
 from galaxy.exceptions import ItemAccessibilityException, ItemDeletionException, ItemOwnershipException
 from galaxy.exceptions import MessageException
-from galaxy import exceptions
 
 from galaxy import web
 from galaxy import model
@@ -94,13 +93,7 @@ class BaseController( object ):
 
     # ---- parsing query params
     def decode_id( self, id ):
-        try:
-            # note: use str - occasionally a fully numeric id will be placed in post body and parsed as int via JSON
-            #   resulting in error for valid id
-            return self.app.security.decode_id( str( id ) )
-        except ( ValueError, TypeError ):
-            msg = "Malformed id ( %s ) specified, unable to decode" % ( str( id ) )
-            raise exceptions.MalformedId( msg, id=str( id ) )
+        return managers_base.decode_id( self.app, id )
 
     def encode_all_ids( self, trans, rval, recursive=False ):
         """

lib/galaxy/webapps/galaxy/api/workflows.py

@@ -4,11 +4,10 @@ API operations for Workflows
 
 from __future__ import absolute_import
 
-import uuid
 import logging
 import copy
 import urllib
-from sqlalchemy import and_, desc, false, or_, true
+from sqlalchemy import desc, false, or_, true
 from galaxy import exceptions, util
 from galaxy.model.item_attrs import UsesAnnotations
 from galaxy.managers import histories
@@ -570,33 +569,10 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
         )
 
     def __get_stored_accessible_workflow( self, trans, workflow_id ):
-        stored_workflow = self.__get_stored_workflow( trans, workflow_id )
-
-        # check to see if user has permissions to selected workflow
-        if stored_workflow.user != trans.user and not trans.user_is_admin():
-            if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0:
-                message = "Workflow is not owned by or shared with current user"
-                raise exceptions.ItemAccessibilityException( message )
-
-        return stored_workflow
+        return self.workflow_manager.get_stored_accessible_workflow( trans, workflow_id )
 
     def __get_stored_workflow( self, trans, workflow_id ):
-        if util.is_uuid(workflow_id):
-            # see if they have passed in the UUID for a workflow that is attached to a stored workflow
-            workflow_uuid = uuid.UUID(workflow_id)
-            stored_workflow = trans.sa_session.query(trans.app.model.StoredWorkflow).filter( and_(
-                trans.app.model.StoredWorkflow.latest_workflow_id == trans.app.model.Workflow.id,
-                trans.app.model.Workflow.uuid == workflow_uuid
-            )).first()
-            if stored_workflow is None:
-                raise exceptions.ObjectNotFound( "Workflow not found: %s" % workflow_id )
-        else:
-            workflow_id = self.decode_id( workflow_id )
-            query = trans.sa_session.query( trans.app.model.StoredWorkflow )
-            stored_workflow = query.get( workflow_id )
-        if stored_workflow is None:
-            raise exceptions.ObjectNotFound( "No such workflow found." )
-        return stored_workflow
+        return self.workflow_manager.get_stored_workflow( trans, workflow_id )
 
     def __encode_invocation( self, trans, invocation, view="element", step_details=False ):
         return self.encode_all_ids(

lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py

@@ -503,7 +503,7 @@ class AdminToolshed( AdminGalaxy ):
         if err_msg:
             message += err_msg
             status = 'error'
-        message += "Installed tool dependencies: %s" % ','.join( td.name for td in installed_tool_dependencies )
+        message += "Installed tool dependencies: %s" % ', '.join( td.name for td in installed_tool_dependencies )
         td_ids = [ trans.security.encode_id( td.id ) for td in tool_shed_repository.tool_dependencies ]
         return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
                                                           action='manage_tool_dependencies',
@@ -1919,8 +1919,8 @@ class AdminToolshed( AdminGalaxy ):
                             if new_repository_dependencies == original_repository_dependencies:
                                 for new_repository_tup in new_repository_dependencies:
                                     # Make sure all dependencies are installed.
-                                    # TODO: Repository dependencies that are not installed should be displayed to to the user,
-                                    # giving them the option to install them or now.  This is the same behavior as when initially
+                                    # TODO: Repository dependencies that are not installed should be displayed to the user,
+                                    # giving them the option to install them or not. This is the same behavior as when initially
                                     # installing and when re-installing.
                                     new_tool_shed, new_name, new_owner, new_changeset_revision, new_pir, new_oicct = \
                                         common_util.parse_repository_dependency_tuple( new_repository_tup )

lib/galaxy/webapps/galaxy/controllers/root.py

@@ -281,14 +281,6 @@ class RootController( controller.JSAppLauncher, UsesAnnotations ):
             yield "No data with id=%d" % id
 
     # ---- History management -----------------------------------------------
-    @web.expose
-    def history_options( self, trans ):
-        """Displays a list of history related actions.
-        """
-        return trans.fill_template( "/history/options.mako",
-                                    user=trans.get_user(),
-                                    history=trans.get_history( create=True ) )
-
     @web.expose
     def history_delete( self, trans, id ):
         """Backward compatibility with check_galaxy script.

lib/galaxy/webapps/galaxy/controllers/workflow.py

@@ -613,7 +613,7 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
         return trans.fill_template( "workflow/editor.mako", stored=stored, annotation=self.get_item_annotation_str( trans.sa_session, trans.user, stored ) )
 
     @web.json
-    def editor_form_post( self, trans, type='tool', tool_id=None, annotation=None, **incoming ):
+    def editor_form_post( self, trans, type='tool', tool_id=None, annotation=None, label=None, **incoming ):
         """
         Accepts a tool state and incoming values, and generates a new tool
         form and some additional information, packed into a json dictionary.
@@ -625,12 +625,14 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
         module = module_factory.from_dict( trans, {
             'type': type,
             'tool_id': tool_id,
-            'tool_state': tool_state
+            'tool_state': tool_state,
+            'label': label or None,
         } )
         # update module state
         module.update_state( incoming )
         if type == 'tool':
             return {
+                'label': module.label,
                 'tool_state': module.get_state(),
                 'data_inputs': module.get_data_inputs(),
                 'data_outputs': module.get_data_outputs(),
@@ -641,6 +643,7 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
             }
         else:
             return {
+                'label': module.label,
                 'tool_state': module.get_state(),
                 'data_inputs': module.get_data_inputs(),
                 'data_outputs': module.get_data_outputs(),
@@ -664,7 +667,7 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
         return {
             'type': module.type,
             'name': module.get_name(),
-            'tool_id': module.get_tool_id(),
+            'tool_id': module.get_content_id(),
             'tool_state': module.get_state(),
             'tool_model': tool_model,
             'tooltip': module.get_tooltip( static_path=url_for( '/static' ) ),

lib/galaxy/webapps/tool_shed/model/__init__.py

@@ -462,6 +462,7 @@ class WorkflowStep( object ):
         self.position = None
         self.input_connections = []
         self.config = None
+        self.label = None
 
 
 class WorkflowStepConnection( object ):

lib/galaxy/workflow/modules.py

@@ -42,7 +42,7 @@ class WorkflowModule( object ):
     # ---- Creating modules from various representations ---------------------
 
     @classmethod
-    def new( Class, trans, tool_id=None ):
+    def new( Class, trans, content_id=None ):
         """
         Create a new instance of the module with default state
         """
@@ -73,7 +73,10 @@ class WorkflowModule( object ):
     def get_name( self ):
         return self.name
 
-    def get_tool_id( self ):
+    def get_content_id( self ):
+        """ If this component has an identifier external to the step (such
+        as a tool or another workflow) return the identifier for that content.
+        """
         return None
 
     def get_tooltip( self, static_path='' ):
@@ -194,9 +197,10 @@ class WorkflowModule( object ):
 class SimpleWorkflowModule( WorkflowModule ):
 
     @classmethod
-    def new( Class, trans, tool_id=None ):
+    def new( Class, trans, content_id=None ):
         module = Class( trans )
         module.state = Class.default_state()
+        module.label = None
         return module
 
     @classmethod
@@ -204,12 +208,14 @@ class SimpleWorkflowModule( WorkflowModule ):
         module = Class( trans )
         state = loads( d["tool_state"] )
         module.recover_state( state )
+        module.label = d.get("label", None) or None
         return module
 
     @classmethod
     def from_workflow_step( Class, trans, step ):
         module = Class( trans )
         module.recover_state( step.tool_inputs )
+        module.label = step.label
         return module
 
     @classmethod
@@ -502,12 +508,13 @@ class ToolModule( WorkflowModule ):
             self.errors[ tool_id ] = 'Tool unavailable'
 
     @classmethod
-    def new( Class, trans, tool_id=None ):
-        module = Class( trans, tool_id )
+    def new( Class, trans, content_id=None ):
+        module = Class( trans, content_id )
         if module.tool is None:
-            error_message = "Attempted to create new workflow module for invalid tool_id, no tool with id - %s." % tool_id
+            error_message = "Attempted to create new workflow module for invalid tool_id, no tool with id - %s." % content_id
             raise Exception( error_message )
         module.state = module.tool.new_state( trans )
+        module.label = None
         return module
 
     @classmethod
@@ -516,6 +523,7 @@ class ToolModule( WorkflowModule ):
         tool_version = str( d.get( 'tool_version', None ) )
         module = Class( trans, tool_id, tool_version=tool_version )
         module.state = galaxy.tools.DefaultToolState()
+        module.label = d.get("label", None) or None
         if module.tool is not None:
             message = ""
             if tool_id != module.tool_id:
@@ -560,6 +568,7 @@ class ToolModule( WorkflowModule ):
             module.recover_state( step.tool_inputs )
             module.errors = step.tool_errors
             module.workflow_outputs = step.workflow_outputs
+            module.label = step.label or None
             pjadict = {}
             for pja in step.post_job_actions:
                 pjadict[pja.action_type] = pja
@@ -623,7 +632,7 @@ class ToolModule( WorkflowModule ):
             return self.tool.name
         return 'unavailable'
 
-    def get_tool_id( self ):
+    def get_content_id( self ):
         return self.tool_id
 
     def get_tool_version( self ):
@@ -735,6 +744,7 @@ class ToolModule( WorkflowModule ):
         # set. We also need to make sure all datasets have a dummy value
         # for dependencies to see
 
+        self.label = incoming.get("label", None) or None
         self.post_job_actions = ActionBox.handle_incoming(incoming)
 
         make_runtime_key = incoming.get( 'make_runtime', None )
@@ -951,13 +961,13 @@ class WorkflowModuleFactory( object ):
     def __init__( self, module_types ):
         self.module_types = module_types
 
-    def new( self, trans, type, tool_id=None ):
+    def new( self, trans, type, content_id=None ):
         """
         Return module for type and (optional) tool_id intialized with
         new / default state.
         """
         assert type in self.module_types
-        return self.module_types[type].new( trans, tool_id )
+        return self.module_types[type].new( trans, content_id )
 
     def from_dict( self, trans, d, **kwargs ):
         """

lib/galaxy/workflow/run.py

@@ -235,8 +235,8 @@ class WorkflowProgress( object ):
             if not hasattr( step, 'module' ):
                 self.module_injector.inject( step )
                 if step_id not in step_states:
-                    template = "Workflow invocation [%s] has no step state for step id [%s]. States are [%s]."
-                    message = template % (self.workflow_invocation.id, step_id, step_states)
+                    template = "Workflow invocation [%s] has no step state for step id [%s]. States ids are %s."
+                    message = template % (self.workflow_invocation.id, step_id, step_states.keys())
                     raise Exception(message)
                 runtime_state = step_states[ step_id ].value
                 step.state = step.module.recover_runtime_state( runtime_state )

lib/tool_shed/galaxy_install/install_manager.py

@@ -126,10 +126,10 @@ class InstallToolDependencyManager( object ):
             # Since there was an installation error, update the tool dependency status to Error. The remove_installation_path option must
             # be left False here.
             error_message = '%s\n%s' % ( self.format_traceback(), str( e ) )
-            tool_dependency = tool_dependency_util.handle_tool_dependency_installation_error( self.app,
-                                                                                              tool_dependency,
-                                                                                              error_message,
-                                                                                              remove_installation_path=False )
+            tool_dependency = tool_dependency_util.set_tool_dependency_attributes(self.app,
+                                                                                  tool_dependency=tool_dependency,
+                                                                                  status=self.app.install_model.ToolDependency.installation_status.ERROR,
+                                                                                  error_message=error_message)
         tool_dependency = self.mark_tool_dependency_installed( tool_dependency )
         return tool_dependency
 
@@ -204,10 +204,10 @@ class InstallToolDependencyManager( object ):
                                 # Since there was an installation error, update the tool dependency status to Error. The
                                 # remove_installation_path option must be left False here.
                                 tool_dependency = \
-                                    tool_dependency_util.handle_tool_dependency_installation_error( self.app,
-                                                                                                    tool_dependency,
-                                                                                                    error_message,
-                                                                                                    remove_installation_path=False )
+                                    tool_dependency_util.set_tool_dependency_attributes(self.app,
+                                                                                        tool_dependency=tool_dependency,
+                                                                                        status=self.app.install_model.ToolDependency.installation_status.ERROR,
+                                                                                        error_message=error_message)
                         if tool_dependency and tool_dependency.status in [ self.install_model.ToolDependency.installation_status.INSTALLED,
                                                                            self.install_model.ToolDependency.installation_status.ERROR ]:
                             installed_packages.append( tool_dependency )
@@ -422,9 +422,7 @@ class InstallToolDependencyManager( object ):
             status = self.install_model.ToolDependency.installation_status.INSTALLED
             tool_dependency = tool_dependency_util.set_tool_dependency_attributes( self.app,
                                                                                    tool_dependency=tool_dependency,
-                                                                                   status=status,
-                                                                                   error_message=None,
-                                                                                   remove_from_disk=False )
+                                                                                   status=status )
         return tool_dependency
 
 

lib/tool_shed/galaxy_install/repair_repository_manager.py

@@ -204,9 +204,7 @@ class RepairRepositoryManager():
                         tool_dependency = \
                             tool_dependency_util.set_tool_dependency_attributes( self.app,
                                                                                  tool_dependency=tool_dependency,
-                                                                                 status=self.app.install_model.ToolDependency.installation_status.UNINSTALLED,
-                                                                                 error_message=None,
-                                                                                 remove_from_disk=True )
+                                                                                 status=self.app.install_model.ToolDependency.installation_status.UNINSTALLED )
                 # Install tool dependencies.
                 irm.update_tool_shed_repository_status( repository,
                                                         self.app.install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES )

lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py

@@ -19,7 +19,7 @@ from galaxy.util import unicodify
 
 from tool_shed.galaxy_install.tool_dependencies.recipe import asynchronous_reader
 
-from tool_shed.util import basic_util
+from tool_shed.util import basic_util, tool_dependency_util
 
 log = logging.getLogger( __name__ )
 
@@ -113,7 +113,6 @@ class InstallEnvironment( object ):
 
     def handle_command( self, tool_dependency, cmd, return_output=False, job_name="" ):
         """Handle a command and log the results."""
-        context = self.app.install_model.context
         command = str( cmd )
         output = self.handle_complex_command( command, job_name=job_name )
         self.log_results( cmd, output, os.path.join( self.install_dir, basic_util.INSTALLATION_LOG ) )
@@ -126,17 +125,19 @@ class InstallEnvironment( object ):
             log.warn( "Length of stderr > %s, so only a portion will be saved in the database." % str( DATABASE_MAX_STRING_SIZE_PRETTY ) )
             stderr = shrink_string_by_size( stderr, DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True )
         if output.return_code not in [ 0 ]:
-            tool_dependency.status = self.app.install_model.ToolDependency.installation_status.ERROR
+            status = self.app.install_model.ToolDependency.installation_status.ERROR
             if stderr:
-                tool_dependency.error_message = unicodify( stderr )
+                error_message = unicodify( stderr )
             elif stdout:
-                tool_dependency.error_message = unicodify( stdout )
+                error_message = unicodify( stdout )
             else:
                 # We have a problem if there was no stdout and no stderr.
-                tool_dependency.error_message = "Unknown error occurred executing shell command %s, return_code: %s" % \
+                error_message = "Unknown error occurred executing shell command %s, return_code: %s" % \
                     ( str( cmd ), str( output.return_code ) )
-            context.add( tool_dependency )
-            context.flush()
+            tool_dependency_util.set_tool_dependency_attributes(self.app,
+                                                                tool_dependency=tool_dependency,
+                                                                status=status,
+                                                                error_message=error_message)
         if return_output:
             return output
         return output.return_code
@@ -156,6 +157,8 @@ class InstallEnvironment( object ):
         if len( job_name ) > 0:
             llog_name += ':' + job_name
         llog = logging.getLogger( llog_name )
+        # Print the command we're about to execute, ``set -x`` style.
+        llog.debug('+ ' + str( command ) )
         # Launch the command as subprocess.  A bufsize of 1 means line buffered.
         process_handle = subprocess.Popen( str( command ),
                                            stdout=subprocess.PIPE,

lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py

@@ -284,8 +284,7 @@ class AssertDirectoryExecutable( RecipeStep ):
             tool_dependency = tool_dependency_util.set_tool_dependency_attributes( self.app,
                                                                                    tool_dependency,
                                                                                    status=status,
-                                                                                   error_message=error_message,
-                                                                                   remove_from_disk=False )
+                                                                                   error_message=error_message )
         return tool_dependency, None, None
 
     def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
@@ -330,8 +329,7 @@ class AssertDirectoryExists( RecipeStep ):
             tool_dependency = tool_dependency_util.set_tool_dependency_attributes( self.app,
                                                                                    tool_dependency,
                                                                                    status=status,
-                                                                                   error_message=error_message,
-                                                                                   remove_from_disk=False )
+                                                                                   error_message=error_message )
         return tool_dependency, None, None
 
     def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
@@ -380,8 +378,7 @@ class AssertFileExecutable( RecipeStep ):
             tool_dependency = tool_dependency_util.set_tool_dependency_attributes( self.app,
                                                                                    tool_dependency,
                                                                                    status=status,
-                                                                                   error_message=error_message,
-                                                                                   remove_from_disk=False )
+                                                                                   error_message=error_message )
         return tool_dependency, None, None
 
     def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
@@ -427,8 +424,7 @@ class AssertFileExists( RecipeStep ):
             tool_dependency = tool_dependency_util.set_tool_dependency_attributes( self.app,
                                                                                    tool_dependency,
                                                                                    status=status,
-                                                                                   error_message=error_message,
-                                                                                   remove_from_disk=False )
+                                                                                   error_message=error_message )
         return tool_dependency, None, None
 
     def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):

lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py

@@ -180,10 +180,10 @@ class Install( RecipeTag, SyncDatabase ):
                     error_message += 'tag set.'
                     # Since there was an installation error, update the tool dependency status to Error.
                     # The remove_installation_path option must be left False here.
-                    tool_dependency = tool_dependency_util.handle_tool_dependency_installation_error( self.app,
-                                                                                                      tool_dependency,
-                                                                                                      error_message,
-                                                                                                      remove_installation_path=False )
+                    tool_dependency = tool_dependency_util.set_tool_dependency_attributes(self.app,
+                                                                                          tool_dependency=tool_dependency,
+                                                                                          status=self.app.install_model.ToolDependency.installation_status.ERROR,
+                                                                                          error_message=error_message)
             else:
                 raise NotImplementedError( 'Only install version 1.0 is currently supported (i.e., change your tag to be <install version="1.0">).' )
         return tool_dependency, proceed_with_install, actions_elem_tuples
@@ -213,9 +213,7 @@ class Package( RecipeTag ):
                 tool_dependency = \
                     tool_dependency_util.set_tool_dependency_attributes( self.app,
                                                                          tool_dependency=tool_dependency,
-                                                                         status=self.app.install_model.ToolDependency.installation_status.ERROR,
-                                                                         error_message=None,
-                                                                         remove_from_disk=False )
+                                                                         status=self.app.install_model.ToolDependency.installation_status.ERROR )
             else:
                 proceed_with_install = True
         return tool_dependency, proceed_with_install, action_elem_tuples
@@ -329,18 +327,18 @@ class Repository( RecipeTag, SyncDatabase ):
                                 error_message = 'Error defining env.sh file for package %s, return_code: %s' % \
                                     ( str( package_name ), str( return_code ) )
                                 tool_dependency = \
-                                    tool_dependency_util.handle_tool_dependency_installation_error( self.app,
-                                                                                                    tool_dependency,
-                                                                                                    error_message,
-                                                                                                    remove_installation_path=False )
+                                    tool_dependency_util.set_tool_dependency_attributes(self.app,
+                                                                                        tool_dependency=tool_dependency,
+                                                                                        status=self.app.install_model.ToolDependency.installation_status.ERROR,
+                                                                                        error_message=error_message)
                             elif required_tool_dependency is not None and required_tool_dependency.in_error_state:
                                 error_message = "This tool dependency's required tool dependency %s version %s has status %s." % \
                                     ( str( required_tool_dependency.name ), str( required_tool_dependency.version ), str( required_tool_dependency.status ) )
                                 tool_dependency = \
-                                    tool_dependency_util.handle_tool_dependency_installation_error( self.app,
-                                                                                                    tool_dependency,
-                                                                                                    error_message,
-                                                                                                    remove_installation_path=False )
+                                    tool_dependency_util.set_tool_dependency_attributes(self.app,
+                                                                                        tool_dependency=tool_dependency,
+                                                                                        status=self.app.install_model.ToolDependency.installation_status.ERROR,
+                                                                                        error_message=error_message)
                             else:
                                 tool_dependency = \
                                     tool_dependency_util.set_tool_dependency_attributes( self.app,
@@ -556,18 +554,10 @@ class SetEnvironment( RecipeTag ):
         else:
             attr_tups_of_dependencies_for_install = [ ( td.name, td.version, td.type ) for td in tool_dependency_db_records ]
         try:
-            tool_dependencies = self.set_environment( package_elem, tool_shed_repository, attr_tups_of_dependencies_for_install )
+            self.set_environment( package_elem, tool_shed_repository, attr_tups_of_dependencies_for_install )
         except Exception, e:
             error_message = "Error setting environment for tool dependency: %s" % str( e )
             log.debug( error_message )
-        for tool_dependency in tool_dependencies:
-            if tool_dependency and tool_dependency.status == self.app.install_model.ToolDependency.installation_status.ERROR:
-                # Since there was an installation error, update the tool dependency status to Error. The
-                # remove_installation_path option must be left False here.
-                tool_dependency = tool_dependency_util.handle_tool_dependency_installation_error( self.app,
-                                                                                                  tool_dependency,
-                                                                                                  error_message,
-                                                                                                  remove_installation_path=False )
         return tool_dependency, proceed_with_install, action_elem_tuples
 
     def set_environment( self, elem, tool_shed_repository, attr_tups_of_dependencies_for_install ):
@@ -613,7 +603,7 @@ class SetEnvironment( RecipeTag ):
             # <requirement type="set_environment">R_SCRIPT_PATH</requirement>).
             env_var_action = env_var_elem.get( 'action', None )
             if env_var_name and env_var_action:
-                # Tool dependencies of type "set_environmnet" always have the version attribute set to None.
+                # Tool dependencies of type "set_environment" always have the version attribute set to None.
                 attr_tup = ( env_var_name, None, 'set_environment' )
                 if attr_tup in attr_tups_of_dependencies_for_install:
                     install_dir = \
@@ -654,8 +644,7 @@ class SetEnvironment( RecipeTag ):
                                     tool_dependency_util.set_tool_dependency_attributes( self.app,
                                                                                          tool_dependency=tool_dependency,
                                                                                          status=status,
-                                                                                         error_message=error_message,
-                                                                                         remove_from_disk=False )
+                                                                                         error_message=error_message )
                             else:
                                 if tool_dependency.status not in [ self.app.install_model.ToolDependency.installation_status.ERROR,
                                                                    self.app.install_model.ToolDependency.installation_status.INSTALLED ]:
@@ -663,9 +652,7 @@ class SetEnvironment( RecipeTag ):
                                     tool_dependency = \
                                         tool_dependency_util.set_tool_dependency_attributes( self.app,
                                                                                              tool_dependency=tool_dependency,
-                                                                                             status=status,
-                                                                                             error_message=None,
-                                                                                             remove_from_disk=False )
+                                                                                             status=status )
                                     log.debug( 'Environment variable %s set in %s for tool dependency %s.' %
                                         ( str( env_var_name ), str( install_dir ), str( tool_dependency.name ) ) )
                         else:
@@ -675,7 +662,6 @@ class SetEnvironment( RecipeTag ):
                                 tool_dependency_util.set_tool_dependency_attributes( self.app,
                                                                                      tool_dependency=tool_dependency,
                                                                                      status=status,
-                                                                                     error_message=error_message,
-                                                                                     remove_from_disk=False )
+                                                                                     error_message=error_message )
             tool_dependencies.append( tool_dependency )
         return tool_dependencies

lib/tool_shed/util/tool_dependency_util.py

@@ -48,14 +48,7 @@ def create_or_update_tool_dependency( app, tool_shed_repository, name, version,
         # In some cases we should not override the current status of an existing tool_dependency, so do so only
         # if set_status is True.
         if set_status:
-            if str( tool_dependency.status ) != str( status ):
-                debug_msg = 'Updating an existing record for version %s of tool dependency %s for revision %s of repository %s ' % \
-                    ( str( version ), str( name ), str( tool_shed_repository.changeset_revision ), str( tool_shed_repository.name ) )
-                debug_msg += 'by updating the status from %s to %s.' % ( str( tool_dependency.status ), str( status ) )
-                log.debug( debug_msg )
-            tool_dependency.status = status
-            context.add( tool_dependency )
-            context.flush()
+            set_tool_dependency_attributes(app, tool_dependency=tool_dependency, status=status)
     else:
         # Create a new tool_dependency record for the tool_shed_repository.
         debug_msg = 'Creating a new record for version %s of tool dependency %s for revision %s of repository %s.  ' % \
@@ -227,38 +220,6 @@ def get_tool_dependency_install_dir( app, repository_name, repository_owner, rep
                                               repository_changeset_revision ) )
 
 
-def handle_tool_dependency_installation_error( app, tool_dependency, error_message, remove_installation_path=False ):
-    # Since there was an installation error, remove the installation directory because the install_package method uses
-    # this: "if os.path.exists( install_dir ):". Setting remove_installation_path to True should rarely occur. It is
-    # currently set to True only to handle issues with installing tool dependencies into an Amazon S3 bucket.
-    sa_session = app.install_model.context
-    tool_shed_repository = tool_dependency.tool_shed_repository
-    install_dir = get_tool_dependency_install_dir( app=app,
-                                                   repository_name=tool_shed_repository.name,
-                                                   repository_owner=tool_shed_repository.owner,
-                                                   repository_changeset_revision=tool_shed_repository.installed_changeset_revision,
-                                                   tool_dependency_type=tool_dependency.type,
-                                                   tool_dependency_name=tool_dependency.name,
-                                                   tool_dependency_version=tool_dependency.version )
-    if remove_installation_path:
-        # This will be True only in the case where an exception was encountered during the installation process after
-        # the installation path was created but before any information was written to the installation log and the
-        # tool dependency status was not set to "Installed" or "Error".
-        if os.path.exists( install_dir ):
-            log.debug( 'Attempting to remove installation directory %s for version %s of tool dependency %s %s' %
-                ( str( install_dir ), str( tool_dependency.version ), str( tool_dependency.type ), str( tool_dependency.name ) ) )
-            log.debug( 'due to the following installation error:\n%s' % str( error_message ) )
-            try:
-                shutil.rmtree( install_dir )
-            except Exception, e:
-                log.exception( 'Error removing existing installation directory %s: %s', (install_dir, str(e)) )
-    tool_dependency.status = app.install_model.ToolDependency.installation_status.ERROR
-    tool_dependency.error_message = error_message
-    sa_session.add( tool_dependency )
-    sa_session.flush()
-    return tool_dependency
-
-
 def parse_package_elem( package_elem, platform_info_dict=None, include_after_install_actions=True ):
     """
     Parse a <package> element within a tool dependency definition and return a list of action tuples.
@@ -405,19 +366,25 @@ def remove_tool_dependency_installation_directory( dependency_install_dir ):
         except Exception, e:
             removed = False
             error_message = "Error removing tool dependency installation directory %s: %s" % ( str( dependency_install_dir ), str( e ) )
-            log.debug( error_message )
+            log.warn( error_message )
     else:
         removed = True
         error_message = ''
     return removed, error_message
 
 
-def set_tool_dependency_attributes( app, tool_dependency, status, error_message=None, remove_from_disk=False ):
+def set_tool_dependency_attributes( app, tool_dependency, status, error_message=None ):
     sa_session = app.install_model.context
-    if remove_from_disk:
+    if status == app.install_model.ToolDependency.installation_status.UNINSTALLED:
         installation_directory = tool_dependency.installation_directory( app )
-        removed, err_msg = remove_tool_dependency_installation_directory( installation_directory )
+        remove_tool_dependency_installation_directory( installation_directory )
     tool_dependency.error_message = error_message
+    if str( tool_dependency.status ) != str( status ):
+        tool_shed_repository = tool_dependency.tool_shed_repository
+        debug_msg = 'Updating an existing record for version %s of tool dependency %s for revision %s of repository %s ' % \
+            ( str( tool_dependency.version ), str( tool_dependency.name ), str( tool_shed_repository.changeset_revision ), str( tool_shed_repository.name ) )
+        debug_msg += 'by updating the status from %s to %s.' % ( str( tool_dependency.status ), str( status ) )
+        log.debug( debug_msg )
     tool_dependency.status = status
     sa_session.add( tool_dependency )
     sa_session.flush()

lib/tool_shed/util/workflow_util.py

@@ -267,6 +267,7 @@ def get_workflow_from_dict( trans, workflow_dict, tools_metadata, repository_id,
     for step_dict in workflow_dict[ 'steps' ].itervalues():
         # Create the model class for the step
         step = trans.model.WorkflowStep()
+        step.label = step_dict.get('label', None)
         step.name = step_dict[ 'name' ]
         step.position = step_dict[ 'position' ]
         module = module_factory.from_dict( trans, repository_id, changeset_revision, step_dict, tools_metadata=tools_metadata, secure=False )

run_tests.sh

@@ -68,7 +68,7 @@ ensure_grunt() {
 }
 
 
-DOCKER_DEFAULT_IMAGE='galaxy/testing-base:15.10.2'
+DOCKER_DEFAULT_IMAGE='galaxy/testing-base:15.10.3'
 
 test_script="./scripts/functional_tests.py"
 report_file="run_functional_tests.html"

static/maps/mvc/citation/citation-model.js.map

@@ -1 +1 @@
-{"version":3,"file":"citation-model.js","sources":["../../../src/mvc/citation/citation-model.js"],"names":["define","bibtex","baseMVC","logNamespace","Citation","Backbone","Model","extend","LoggableMixin","_logNamespace","initialize","this","attributes","content","entry","BibtexParser","entries","_fields","rawFields","Fields","key","value","lowerKey","toLowerCase","entryType","EntryType","fields","BaseCitationCollection","Collection","urlRoot","Galaxy","root","partial","model","HistoryCitationCollection","url","history_id","ToolCitationCollection","tool_id"],"mappings":"AAAAA,QACI,cACA,eACA,sBACD,SAAUC,EAAQC,GAGrB,GAAIC,GAAe,WAMfC,EAAWC,SAASC,MAAMC,OAAQL,EAAQM,eAAgBD,QAC1DE,cAAgBN,EAEhBO,WAAY,WACR,GAAIT,GAASU,KAAKC,WAAWC,QACzBC,EAAQ,GAAIb,GAAOc,aAAad,GAAQe,QAAQ,EACpDL,MAAKG,MAAQA,EACbH,KAAKM,UACL,IAAIC,GAAYJ,EAAMK,MACtB,KAAI,GAAIC,KAAOF,GAAW,CACtB,GAAIG,GAAQH,EAAWE,GACnBE,EAAWF,EAAIG,aACnBZ,MAAKM,QAASK,GAAaD,IAGnCG,UAAW,WACP,MAAOb,MAAKG,MAAMW,WAEtBC,OAAQ,WACJ,MAAOf,MAAKM,WAOhBU,EAAyBtB,SAASuB,WAAWrB,OAAQL,EAAQM,eAAgBD,QAC7EE,cAAgBN,EAGhB0B,QAAUC,OAAOC,KAAO,MACxBC,SAAU,EACVC,MAAQ7B,IAGR8B,EAA4BP,EAAuBpB,QAEnD4B,IAAM,WACF,MAAOxB,MAAKkB,QAAU,cAAgBlB,KAAKyB,WAAa,gBAI5DC,EAAyBV,EAAuBpB,QAEhD4B,IAAM,WACF,MAAOxB,MAAKkB,QAAU,UAAYlB,KAAK2B,QAAU,cAErDN,SAAU,GAId,QACI5B,SAAWA,EACX8B,0BAA6BA,EAC7BG,uBAAwBA"}
+{"version":3,"file":"citation-model.js","sources":["../../../src/mvc/citation/citation-model.js"],"names":["define","BibtexParser","baseMVC","logNamespace","Citation","Backbone","Model","extend","LoggableMixin","_logNamespace","initialize","bibtex","this","get","entry","entries","_fields","rawFields","Fields","key","value","lowerKey","toLowerCase","entryType","EntryType","fields","BaseCitationCollection","Collection","urlRoot","Galaxy","root","partial","model","HistoryCitationCollection","url","history_id","ToolCitationCollection","tool_id"],"mappings":"AAAAA,QACI,cACA,eACA,sBACD,SAAUC,EAAcC,GAG3B,GAAIC,GAAe,WAMfC,EAAWC,SAASC,MAAMC,OAAQL,EAAQM,eAAgBD,QAC1DE,cAAgBN,EAEhBO,WAAY,WACR,GAAIC,GAASC,KAAKC,IAAK,WACnBC,EAAQb,EAAaU,GAAQI,QAAQ,EACzCH,MAAKE,MAAQA,EACbF,KAAKI,UACL,IAAIC,GAAYH,EAAMI,MACtB,KAAI,GAAIC,KAAOF,GAAW,CACtB,GAAIG,GAAQH,EAAWE,GACnBE,EAAWF,EAAIG,aACnBV,MAAKI,QAASK,GAAaD,IAGnCG,UAAW,WACP,MAAOX,MAAKE,MAAMU,WAEtBC,OAAQ,WACJ,MAAOb,MAAKI,WAOhBU,EAAyBrB,SAASsB,WAAWpB,OAAQL,EAAQM,eAAgBD,QAC7EE,cAAgBN,EAGhByB,QAAUC,OAAOC,KAAO,MACxBC,SAAU,EACVC,MAAQ5B,IAGR6B,EAA4BP,EAAuBnB,QAEnD2B,IAAM,WACF,MAAOtB,MAAKgB,QAAU,cAAgBhB,KAAKuB,WAAa,gBAI5DC,EAAyBV,EAAuBnB,QAEhD2B,IAAM,WACF,MAAOtB,MAAKgB,QAAU,UAAYhB,KAAKyB,QAAU,cAErDN,SAAU,GAKd,QACI3B,SAAWA,EACX6B,0BAA6BA,EAC7BG,uBAAwBA"}

static/maps/mvc/ui/ui-select-default.js.map

@@ -1 +1 @@
-{"version":3,"file":"ui-select-default.js","sources":["../../../src/mvc/ui/ui-select-default.js"],"names":["define","Utils","Buttons","View","Backbone","extend","optionsDefault","id","uid","cls","error_text","empty_text","visible","wait","multiple","searchable","optional","initialize","options","self","this","merge","setElement","_template","$select","$el","find","$icon_dropdown","minHeight","$","on","event","currentY","pageY","currentHeight","height","show","Math","max","hide","off","all_button","ButtonCheck","onclick","new_value","value","_availableOptions","trigger","prepend","addClass","prop","remove","update","data","undefined","onchange","exists","val","select2","current","_getValue","isArray","length","_size","first","text","unwait","removeClass","disabled","is","enable","disable","append","_templateOption","label","key","closeOnSelect","setOnChange","callback","validate","available","each","i","e","push","attr","_","escape"],"mappings":"AAGAA,QAAQ,cAAe,qBAAsB,SAASC,EAAOC,GAC7D,GAAIC,GAAOC,SAASD,KAAKE,QAErBC,gBACIC,GAAcN,EAAMO,MACpBC,IAAc,YACdC,WAAc,uBACdC,WAAc,mBACdC,SAAc,EACdC,MAAc,EACdC,UAAc,EACdC,YAAc,EACdC,UAAc,GAIlBC,WAAY,SAASC,GAEjB,GAAIC,GAAOC,IAGXA,MAAKF,QAAUjB,EAAMoB,MAAMH,EAASE,KAAKd,gBAGzCc,KAAKE,WAAWF,KAAKG,UAAUH,KAAKF,UAGpCE,KAAKI,QAAUJ,KAAKK,IAAIC,KAAK,WAC7BN,KAAKO,eAAiBP,KAAKK,IAAIC,KAAK,iBAGpC,IAAIE,GAAY,IAChBR,MAAKS,EAAE,gBAAgBC,GAAG,YAAa,SAASC,GAC5C,GAAIC,GAAWD,EAAME,MACjBC,EAAgBf,EAAKK,QAAQW,QACjCP,GAAYA,GAAaM,EACzBL,EAAE,cAAcO,OAAON,GAAG,YAAa,SAASC,GAC5CZ,EAAKK,QAAQW,OAAOE,KAAKC,IAAIJ,GAAiBH,EAAME,MAAQD,GAAWJ,MACxEE,GAAG,qBAAsB,WACxBD,EAAE,cAAcU,OAAOC,UAK3BpB,KAAKF,QAAQJ,WAETM,KAAKF,QAAQH,YACbK,KAAKqB,WAAa,GAAIvC,GAAQwC,aAC1BC,QAAS,WACL,GAAIC,KAC4B,KAA5BzB,EAAKsB,WAAWI,UAChBD,EAAYzB,EAAK2B,qBAErB3B,EAAK0B,MAAMD,GACXzB,EAAK4B,QAAQ,aAGrB3B,KAAKK,IAAIuB,QAAQ5B,KAAKqB,WAAWhB,MAEjCL,KAAKK,IAAIwB,SAAS,sBAEtB7B,KAAKI,QAAQ0B,KAAK,YAAY,GAC9B9B,KAAKO,eAAewB,UAIxB/B,KAAKgC,OAAOhC,KAAKF,QAAQmC,MAGEC,SAAvBlC,KAAKF,QAAQ2B,OACbzB,KAAKyB,MAAMzB,KAAKF,QAAQ2B,OAIvBzB,KAAKF,QAAQN,SACdQ,KAAKmB,OAILnB,KAAKF,QAAQL,KACbO,KAAKP,OAELO,KAAKgB,OAIThB,KAAKI,QAAQM,GAAG,SAAU,WACtBX,EAAK4B,QAAQ,YAIjB3B,KAAKU,GAAG,SAAU,WACdX,EAAKD,QAAQqC,UAAYpC,EAAKD,QAAQqC,SAASnC,KAAKyB,YAM5DA,MAAO,SAAUD,GAEKU,SAAdV,IACkB,OAAdA,IACAA,EAAY,aAEZxB,KAAKoC,OAAOZ,IAAcxB,KAAKF,QAAQJ,YACvCM,KAAKI,QAAQiC,IAAIb,GACbxB,KAAKI,QAAQkC,SACbtC,KAAKI,QAAQkC,QAAQ,MAAOd,IAKxC,IAAIe,GAAUvC,KAAKwC,WAInB,OAHIxC,MAAKqB,YACLrB,KAAKqB,WAAWI,MAAMhB,EAAEgC,QAAQF,IAAYA,EAAQG,QAAU,EAAG1C,KAAK2C,SAEnEJ,GAKXK,MAAO,WACH,GAAI9C,GAAUE,KAAKI,QAAQE,KAAK,UAAUsC,OAC1C,OAAI9C,GAAQ4C,OAAS,EACV5C,EAAQuC,MAER,MAMfQ,KAAM,WACF,MAAO7C,MAAKI,QAAQE,KAAK,mBAAmBuC,QAKhD7B,KAAM,WACFhB,KAAK8C,SACL9C,KAAKI,QAAQY,OACbhB,KAAKK,IAAIW,QAKbG,KAAM,WACFnB,KAAKK,IAAIc,QAKb1B,KAAM,WACFO,KAAKO,eAAewC,cACpB/C,KAAKO,eAAesB,SAAS,wCAKjCiB,OAAQ,WACJ9C,KAAKO,eAAewC,cACpB/C,KAAKO,eAAesB,SAAS,mCAKjCmB,SAAU,WACN,MAAOhD,MAAKI,QAAQ6C,GAAG,cAK3BC,OAAQ,WACJlD,KAAKI,QAAQ0B,KAAK,YAAY,IAKlCqB,QAAS,WACLnD,KAAKI,QAAQ0B,KAAK,YAAY,IAKlCE,OAAQ,SAASlC,GAEb,GAAIyC,GAAUvC,KAAKwC,WAGnBxC,MAAKI,QAAQE,KAAK,UAAUyB,UAGvB/B,KAAKF,QAAQJ,UAAYM,KAAKF,QAAQF,UACvCI,KAAKI,QAAQgD,OAAOpD,KAAKqD,iBAAiB5B,MAAQ,WAAY6B,MAAQtD,KAAKF,QAAQP,aAIvF,KAAK,GAAIgE,KAAOzD,GACZE,KAAKI,QAAQgD,OAAOpD,KAAKqD,gBAAgBvD,EAAQyD,IAIjC,IAAhBvD,KAAK2C,SAEL3C,KAAKmD,UAGLnD,KAAKI,QAAQgD,OAAOpD,KAAKqD,iBAAiB5B,MAAQ,WAAY6B,MAAQtD,KAAKF,QAAQR,eAGnFU,KAAKkD,SAILlD,KAAKF,QAAQH,aACbK,KAAKI,QAAQkC,QAAQ,WACrBtC,KAAKI,QAAQkC,SAAUkB,eAAgBxD,KAAKF,QAAQJ,WACpDM,KAAKS,EAAG,4CAA6CW,IAAK,SAI9DpB,KAAKyB,MAAMc,GAGc,OAArBvC,KAAKwC,aAA0BxC,KAAKF,QAAQJ,UAAYM,KAAKF,QAAQF,UACrEI,KAAKyB,MAAMzB,KAAK4C,UAMxBa,YAAa,SAASC,GAClB1D,KAAKF,QAAQqC,SAAWuB,GAK5BtB,OAAQ,SAASX,GACb,MAAOzB,MAAKI,QAAQE,KAAK,iBAAmBmB,EAAQ,MAAMiB,OAAS,GAKvEF,UAAW,WACP,GAAIH,GAAMrC,KAAKI,QAAQiC,KACvB,OAAKxD,GAAM8E,SAAStB,GAGbA,EAFI,MAOfX,kBAAmB,WACf,GAAIkC,KAIJ,OAHA5D,MAAKI,QAAQE,KAAK,UAAUuD,KAAK,SAASC,EAAGC,GACzCH,EAAUI,KAAKvD,EAAEsD,GAAGE,KAAK,YAEtBL,GAKXjB,MAAO,WACH,MAAO3C,MAAKI,QAAQE,KAAK,UAAUoC,QAKvCW,gBAAiB,SAASvD,GACtB,MAAO,kBAAoBA,EAAQ2B,MAAQ,KAAOyC,EAAEC,OAAOrE,EAAQwD,OAAS,aAKhFnD,UAAW,SAASL,GAChB,MAAQ,YAAcA,EAAQX,GAAK,YAAcW,EAAQT,IAAM,iBAClCS,EAAQX,GAAK,iJASlD,QACIJ,KAAMA"}
+{"version":3,"file":"ui-select-default.js","sources":["../../../src/mvc/ui/ui-select-default.js"],"names":["define","Utils","Buttons","View","Backbone","extend","optionsDefault","id","uid","cls","error_text","empty_text","visible","wait","multiple","searchable","optional","initialize","options","self","this","merge","setElement","_template","$select","$el","find","$icon_dropdown","on","select2","minHeight","$","event","currentY","pageY","currentHeight","height","show","Math","max","hide","off","all_button","ButtonCheck","onclick","new_value","value","_availableOptions","trigger","prepend","addClass","prop","remove","update","data","undefined","onchange","exists","val","current","_getValue","isArray","length","_size","first","text","unwait","removeClass","disabled","is","enable","disable","append","_templateOption","label","key","closeOnSelect","setOnChange","callback","validate","available","each","i","e","push","attr","_","escape"],"mappings":"AAGAA,QAAQ,cAAe,qBAAsB,SAASC,EAAOC,GAC7D,GAAIC,GAAOC,SAASD,KAAKE,QAErBC,gBACIC,GAAcN,EAAMO,MACpBC,IAAc,YACdC,WAAc,uBACdC,WAAc,mBACdC,SAAc,EACdC,MAAc,EACdC,UAAc,EACdC,YAAc,EACdC,UAAc,GAIlBC,WAAY,SAASC,GAEjB,GAAIC,GAAOC,IAGXA,MAAKF,QAAUjB,EAAMoB,MAAMH,EAASE,KAAKd,gBAGzCc,KAAKE,WAAWF,KAAKG,UAAUH,KAAKF,UAGpCE,KAAKI,QAAUJ,KAAKK,IAAIC,KAAK,WAC7BN,KAAKO,eAAiBP,KAAKK,IAAIC,KAAK,kBACpCN,KAAKO,eAAeC,GAAI,QAAS,WAAaT,EAAKK,QAAQK,SAAWV,EAAKK,QAAQK,QAAS,SAG5F,IAAIC,GAAY,IAChBV,MAAKW,EAAE,gBAAgBH,GAAG,YAAa,SAASI,GAC5C,GAAIC,GAAWD,EAAME,MACjBC,EAAgBhB,EAAKK,QAAQY,QACjCN,GAAYA,GAAaK,EACzBJ,EAAE,cAAcM,OAAOT,GAAG,YAAa,SAASI,GAC5Cb,EAAKK,QAAQY,OAAOE,KAAKC,IAAIJ,GAAiBH,EAAME,MAAQD,GAAWH,MACxEF,GAAG,qBAAsB,WACxBG,EAAE,cAAcS,OAAOC,UAK3BrB,KAAKF,QAAQJ,WAETM,KAAKF,QAAQH,YACbK,KAAKsB,WAAa,GAAIxC,GAAQyC,aAC1BC,QAAS,WACL,GAAIC,KAC4B,KAA5B1B,EAAKuB,WAAWI,UAChBD,EAAY1B,EAAK4B,qBAErB5B,EAAK2B,MAAMD,GACX1B,EAAK6B,QAAQ,aAGrB5B,KAAKK,IAAIwB,QAAQ7B,KAAKsB,WAAWjB,MAEjCL,KAAKK,IAAIyB,SAAS,sBAEtB9B,KAAKI,QAAQ2B,KAAK,YAAY,GAC9B/B,KAAKO,eAAeyB,UAIxBhC,KAAKiC,OAAOjC,KAAKF,QAAQoC,MAGEC,SAAvBnC,KAAKF,QAAQ4B,OACb1B,KAAK0B,MAAM1B,KAAKF,QAAQ4B,OAIvB1B,KAAKF,QAAQN,SACdQ,KAAKoB,OAILpB,KAAKF,QAAQL,KACbO,KAAKP,OAELO,KAAKiB,OAITjB,KAAKI,QAAQI,GAAG,SAAU,WACtBT,EAAK6B,QAAQ,YAIjB5B,KAAKQ,GAAG,SAAU,WACdT,EAAKD,QAAQsC,UAAYrC,EAAKD,QAAQsC,SAASpC,KAAK0B,YAM5DA,MAAO,SAAUD,GAEKU,SAAdV,IACkB,OAAdA,IACAA,EAAY,aAEZzB,KAAKqC,OAAOZ,IAAczB,KAAKF,QAAQJ,YACvCM,KAAKI,QAAQkC,IAAIb,GACbzB,KAAKI,QAAQK,SACbT,KAAKI,QAAQK,QAAQ,MAAOgB,IAKxC,IAAIc,GAAUvC,KAAKwC,WAInB,OAHIxC,MAAKsB,YACLtB,KAAKsB,WAAWI,MAAMf,EAAE8B,QAAQF,IAAYA,EAAQG,QAAU,EAAG1C,KAAK2C,SAEnEJ,GAKXK,MAAO,WACH,GAAI9C,GAAUE,KAAKI,QAAQE,KAAK,UAAUsC,OAC1C,OAAI9C,GAAQ4C,OAAS,EACV5C,EAAQwC,MAER,MAMfO,KAAM,WACF,MAAO7C,MAAKI,QAAQE,KAAK,mBAAmBuC,QAKhD5B,KAAM,WACFjB,KAAK8C,SACL9C,KAAKI,QAAQa,OACbjB,KAAKK,IAAIY,QAKbG,KAAM,WACFpB,KAAKK,IAAIe,QAKb3B,KAAM,WACFO,KAAKO,eAAewC,cACpB/C,KAAKO,eAAeuB,SAAS,wCAKjCgB,OAAQ,WACJ9C,KAAKO,eAAewC,cACpB/C,KAAKO,eAAeuB,SAAS,mCAKjCkB,SAAU,WACN,MAAOhD,MAAKI,QAAQ6C,GAAG,cAK3BC,OAAQ,WACJlD,KAAKI,QAAQ2B,KAAK,YAAY,IAKlCoB,QAAS,WACLnD,KAAKI,QAAQ2B,KAAK,YAAY,IAKlCE,OAAQ,SAASnC,GAEb,GAAIyC,GAAUvC,KAAKwC,WAGnBxC,MAAKI,QAAQE,KAAK,UAAU0B,UAGvBhC,KAAKF,QAAQJ,UAAYM,KAAKF,QAAQF,UACvCI,KAAKI,QAAQgD,OAAOpD,KAAKqD,iBAAiB3B,MAAQ,WAAY4B,MAAQtD,KAAKF,QAAQP,aAIvF,KAAK,GAAIgE,KAAOzD,GACZE,KAAKI,QAAQgD,OAAOpD,KAAKqD,gBAAgBvD,EAAQyD,IAIjC,IAAhBvD,KAAK2C,SAEL3C,KAAKmD,UAGLnD,KAAKI,QAAQgD,OAAOpD,KAAKqD,iBAAiB3B,MAAQ,WAAY4B,MAAQtD,KAAKF,QAAQR,eAGnFU,KAAKkD,SAILlD,KAAKF,QAAQH,aACbK,KAAKI,QAAQK,QAAQ,WACrBT,KAAKI,QAAQK,SAAU+C,eAAgBxD,KAAKF,QAAQJ,WACpDM,KAAKW,EAAG,4CAA6CU,IAAK,SAI9DrB,KAAK0B,MAAMa,GAGc,OAArBvC,KAAKwC,aAA0BxC,KAAKF,QAAQJ,UAAYM,KAAKF,QAAQF,UACrEI,KAAK0B,MAAM1B,KAAK4C,UAMxBa,YAAa,SAASC,GAClB1D,KAAKF,QAAQsC,SAAWsB,GAK5BrB,OAAQ,SAASX,GACb,MAAO1B,MAAKI,QAAQE,KAAK,iBAAmBoB,EAAQ,MAAMgB,OAAS,GAKvEF,UAAW,WACP,GAAIF,GAAMtC,KAAKI,QAAQkC,KACvB,OAAKzD,GAAM8E,SAASrB,GAGbA,EAFI,MAOfX,kBAAmB,WACf,GAAIiC,KAIJ,OAHA5D,MAAKI,QAAQE,KAAK,UAAUuD,KAAK,SAASC,EAAGC,GACzCH,EAAUI,KAAKrD,EAAEoD,GAAGE,KAAK,YAEtBL,GAKXjB,MAAO,WACH,MAAO3C,MAAKI,QAAQE,KAAK,UAAUoC,QAKvCW,gBAAiB,SAASvD,GACtB,MAAO,kBAAoBA,EAAQ4B,MAAQ,KAAOwC,EAAEC,OAAOrE,EAAQwD,OAAS,aAKhFnD,UAAW,SAASL,GAChB,MAAQ,YAAcA,EAAQX,GAAK,YAAcW,EAAQT,IAAM,iBAClCS,EAAQX,GAAK,iJASlD,QACIJ,KAAMA"}

static/maps/mvc/workflow/workflow-view-node.js.map

@@ -1 +1 @@
-{"version":3,"file":"workflow-view-node.js","sources":["../../../src/mvc/workflow/workflow-view-node.js"],"names":["define","TerminalViews","DataViews","Backbone","View","extend","initialize","options","this","node","output_width","Math","max","$el","width","tool_body","find","remove","newInputsDiv","appendTo","terminalViews","outputTerminlViews","render","renderToolErrors","css","min","tool_errors","addClass","removeClass","$","updateMaxWidth","newWidth","addRule","append","addDataInput","input","body","skipResize","terminalView","name","terminalViewClass","input_type","InputCollectionTerminalView","InputTerminalView","el","terminal","destroy","update","destroyInvalidConnections","terminalElement","inputView","DataInputView","nodeView","ib","prepend","terminalElements","addDataOutput","output","OutputCollectionTerminalView","OutputTerminalView","outputView","DataOutputView","updateDataOutput","outputTerminal","output_terminals"],"mappings":"AAAAA,QAAQ,uCAAwC,mCAAoC,SAAUC,EAAeC,GACzG,MAAOC,UAASC,KAAKC,QACjBC,WAAY,SAAUC,GAClBC,KAAKC,KAAOF,EAAQE,KACpBD,KAAKE,aAAeC,KAAKC,IAAI,IAAKJ,KAAKK,IAAIC,SAC3CN,KAAKO,UAAYP,KAAKK,IAAIG,KAAM,iBAChCR,KAAKO,UAAUC,KAAM,OAAQC,SAC7BT,KAAKU,eAAeC,SAAUX,KAAKO,WACnCP,KAAKY,iBACLZ,KAAKa,uBAGTC,OAAQ,WACJd,KAAKe,mBACLf,KAAKK,IAAIW,IAAK,QAASb,KAAKc,IAAI,IAAKd,KAAKC,IAAKJ,KAAKK,IAAIC,QAASN,KAAKE,iBAG1Ea,iBAAkB,WACTf,KAAKC,KAAKiB,YACXlB,KAAKK,IAAIc,SAAU,mBAEnBnB,KAAKK,IAAIe,YAAa,oBAI9BV,aAAc,WACV,MAAOW,GAAE,+BAGbC,eAAgB,SAAUC,GACtBvB,KAAKE,aAAeC,KAAKC,IAAKJ,KAAKE,aAAcqB,IAGrDC,QAAS,WACLxB,KAAKO,UAAUkB,OAAQJ,EAAG,8BAG9BK,aAAc,SAAUC,EAAOC,GAC3B,GAAIC,IAAa,CACXD,KACFA,EAAO5B,KAAKqB,EAAG,WAGfQ,GAAa,EAEjB,IAAIC,GAAe9B,KAAKY,cAAee,EAAMI,MACzCC,EAA0C,sBAApBL,EAAMM,WAAuCxC,EAAcyC,4BAA8BzC,EAAc0C,iBAKjI,KAJIL,GAAoBA,YAAwBE,KAC5CF,EAAaM,GAAGC,SAASC,UACzBR,EAAe,MAEbA,EAKC,CACH,GAAIO,GAAWP,EAAaM,GAAGC,QAC/BA,GAASE,OAAQZ,GACjBU,EAASG,gCAPTV,GAAe,GAAIE,IACf/B,KAAMD,KAAKC,KACX0B,MAAOA,GAOf3B,MAAKY,cAAee,EAAMI,MAASD,CACnC,IAAIW,GAAkBX,EAAaM,GAC/BM,EAAY,GAAIhD,GAAUiD,eAC1BF,gBAAiBA,EACjBd,MAAOA,EACPiB,SAAU5C,KACV6B,WAAYA,IAEZgB,EAAKH,EAAUrC,GAEnB,OADAuB,GAAKH,OAAQoB,EAAGC,QAAShB,EAAaiB,qBAC/BjB,GAGXkB,cAAe,SAAUC,GACrB,GAAIjB,GAAsBiB,EAAkB,WAAIxD,EAAcyD,6BAA+BzD,EAAc0D,mBACvGrB,EAAe,GAAIE,IACnB/B,KAAMD,KAAKC,KACXgD,OAAQA,IAERG,EAAa,GAAI1D,GAAU2D,gBAC3BJ,OAAUA,EACVR,gBAAmBX,EAAaM,GAChCQ,SAAY5C,MAEhBA,MAAKO,UAAUkB,OAAQ2B,EAAW/C,IAAIoB,OAAQK,EAAaiB,sBAG/DO,iBAAkB,SAAUL,GACxB,GAAIM,GAAiBvD,KAAKC,KAAKuD,iBAAkBP,EAAOlB,KACxDwB,GAAehB,OAAQU"}
+{"version":3,"file":"workflow-view-node.js","sources":["../../../src/mvc/workflow/workflow-view-node.js"],"names":["define","TerminalViews","DataViews","Backbone","View","extend","initialize","options","this","node","output_width","Math","max","$el","width","tool_body","find","remove","newInputsDiv","appendTo","terminalViews","outputTerminlViews","render","title","label","name","text","renderToolErrors","css","min","tool_errors","addClass","removeClass","$","updateMaxWidth","newWidth","addRule","append","addDataInput","input","body","skipResize","terminalView","terminalViewClass","input_type","InputCollectionTerminalView","InputTerminalView","el","terminal","destroy","update","destroyInvalidConnections","terminalElement","inputView","DataInputView","nodeView","ib","prepend","terminalElements","addDataOutput","output","OutputCollectionTerminalView","OutputTerminalView","outputView","DataOutputView","updateDataOutput","outputTerminal","output_terminals"],"mappings":"AAAAA,QAAQ,uCAAwC,mCAAoC,SAAUC,EAAeC,GACzG,MAAOC,UAASC,KAAKC,QACjBC,WAAY,SAAUC,GAClBC,KAAKC,KAAOF,EAAQE,KACpBD,KAAKE,aAAeC,KAAKC,IAAI,IAAKJ,KAAKK,IAAIC,SAC3CN,KAAKO,UAAYP,KAAKK,IAAIG,KAAM,iBAChCR,KAAKO,UAAUC,KAAM,OAAQC,SAC7BT,KAAKU,eAAeC,SAAUX,KAAKO,WACnCP,KAAKY,iBACLZ,KAAKa,uBAGTC,OAAQ,WACJ,GACIC,GADAC,EAAQhB,KAAKC,KAAKe,KAGlBD,GADDC,EACSA,EAEAhB,KAAKC,KAAKgB,KAEtBjB,KAAKK,IAAIG,KAAK,cAAcU,KAAKH,GACjCf,KAAKmB,mBACLnB,KAAKK,IAAIe,IAAK,QAASjB,KAAKkB,IAAI,IAAKlB,KAAKC,IAAKJ,KAAKK,IAAIC,QAASN,KAAKE,iBAG1EiB,iBAAkB,WACTnB,KAAKC,KAAKqB,YACXtB,KAAKK,IAAIkB,SAAU,mBAEnBvB,KAAKK,IAAImB,YAAa,oBAI9Bd,aAAc,WACV,MAAOe,GAAE,+BAGbC,eAAgB,SAAUC,GACtB3B,KAAKE,aAAeC,KAAKC,IAAKJ,KAAKE,aAAcyB,IAGrDC,QAAS,WACL5B,KAAKO,UAAUsB,OAAQJ,EAAG,8BAG9BK,aAAc,SAAUC,EAAOC,GAC3B,GAAIC,IAAa,CACXD,KACFA,EAAOhC,KAAKyB,EAAG,WAGfQ,GAAa,EAEjB,IAAIC,GAAelC,KAAKY,cAAemB,EAAMd,MACzCkB,EAA0C,sBAApBJ,EAAMK,WAAuC3C,EAAc4C,4BAA8B5C,EAAc6C,iBAKjI,KAJIJ,GAAoBA,YAAwBC,KAC5CD,EAAaK,GAAGC,SAASC,UACzBP,EAAe,MAEbA,EAKC,CACH,GAAIM,GAAWN,EAAaK,GAAGC,QAC/BA,GAASE,OAAQX,GACjBS,EAASG,gCAPTT,GAAe,GAAIC,IACflC,KAAMD,KAAKC,KACX8B,MAAOA,GAOf/B,MAAKY,cAAemB,EAAMd,MAASiB,CACnC,IAAIU,GAAkBV,EAAaK,GAC/BM,EAAY,GAAInD,GAAUoD,eAC1BF,gBAAiBA,EACjBb,MAAOA,EACPgB,SAAU/C,KACViC,WAAYA,IAEZe,EAAKH,EAAUxC,GAEnB,OADA2B,GAAKH,OAAQmB,EAAGC,QAASf,EAAagB,qBAC/BhB,GAGXiB,cAAe,SAAUC,GACrB,GAAIjB,GAAsBiB,EAAkB,WAAI3D,EAAc4D,6BAA+B5D,EAAc6D,mBACvGpB,EAAe,GAAIC,IACnBlC,KAAMD,KAAKC,KACXmD,OAAQA,IAERG,EAAa,GAAI7D,GAAU8D,gBAC3BJ,OAAUA,EACVR,gBAAmBV,EAAaK,GAChCQ,SAAY/C,MAEhBA,MAAKO,UAAUsB,OAAQ0B,EAAWlD,IAAIwB,OAAQK,EAAagB,sBAG/DO,iBAAkB,SAAUL,GACxB,GAAIM,GAAiB1D,KAAKC,KAAK0D,iBAAkBP,EAAOnC,KACxDyC,GAAehB,OAAQU"}

static/maps/polyfills.js.map

@@ -1 +1 @@
-{"version":3,"file":"polyfills.js","sources":["../src/polyfills.js"],"names":["window","console","log","debug","info","warn","error","assert","Object","assign","_","extend","lastTime","vendors","x","length","requestAnimationFrame","cancelRequestAnimationFrame","callback","currTime","Date","getTime","timeToCall","Math","max","id","setTimeout","cancelAnimationFrame","clearTimeout","incompatibilities","name","compatible","CanvasRenderingContext2D","Number","isInteger","sessionStorage","err","filter","feature","map","root","document","querySelectorAll","item","location","href","join"],"mappings":"CAKA,WAMI,YAKAA,QAAOC,QAAUD,OAAOC,UACpBC,IAAU,aACVC,MAAU,aACVC,KAAU,aACVC,KAAU,aACVC,MAAU,aACVC,OAAU,cAIdC,OAAOC,OAASD,OAAOC,QAAUC,EAAEC,MAKnC,KAAI,GAFAC,GAAW,EACXC,GAAW,KAAM,MAAO,SAAU,KAC9BC,EAAI,EAAGA,EAAID,EAAQE,SAAWf,OAAOgB,wBAAyBF,EAClEd,OAAOgB,sBAAwBhB,OAAOa,EAAQC,GAAG,yBACjDd,OAAOiB,4BAA8BjB,OAAOa,EAAQC,GAClD,8BAGDd,QAAOgB,wBACRhB,OAAOgB,sBAAwB,SAASE,GACpC,GAAIC,IAAW,GAAIC,OAAOC,UACtBC,EAAaC,KAAKC,IAAI,EAAG,IAAML,EAAWP,IAC1Ca,EAAKzB,OAAO0B,WAAW,WAAaR,EAASC,EAAWG,IAC1DA,EAEF,OADAV,GAAWO,EAAWG,EACfG,IAGVzB,OAAO2B,uBACR3B,OAAO2B,qBAAuB,SAASF,GACnCG,aAAaH,IAIrB,IAAII,KACEC,KAAM,SAAoBC,WAAY,WAAY,MAAO/B,QAAOgC,4BAChEF,KAAM,iBAAoBC,WAAY,WACpC,IACI,MAAOE,QAAOC,UAAWC,eAAepB,QAC1C,MAAOqB,IACT,OAAO,IASf,IALAP,EAAoBA,EACfQ,OAAQ,SAAUC,GAAW,OAAQA,EAAQP,eAC7CQ,IAAK,SAAUD,GAAW,MAAOA,GAAQR,OAGxCD,EAAkBd,OAAQ,CAC5B,GAAIyB,GAAOC,SAASC,iBAAkB,qBAAsBC,KAAM,EAC9DH,KACAxC,OAAO4C,SAASC,KAAOL,EAAKK,KAAO,oCAEvC5C,QAAQC,IAAK,0BAA4B2B,EAAkBiB,KAAM"}
+{"version":3,"file":"polyfills.js","sources":["../src/polyfills.js"],"names":["window","console","log","debug","info","warn","error","assert","Object","assign","_","extend","lastTime","vendors","x","length","requestAnimationFrame","cancelRequestAnimationFrame","callback","currTime","Date","getTime","timeToCall","Math","max","id","setTimeout","cancelAnimationFrame","clearTimeout","features","name","compatible","CanvasRenderingContext2D","sessionStorage","err","incompatibilities","filter","feature","map","root","document","querySelectorAll","item","location","href","join"],"mappings":"CAKA,WAMI,YAKAA,QAAOC,QAAUD,OAAOC,UACpBC,IAAU,aACVC,MAAU,aACVC,KAAU,aACVC,KAAU,aACVC,MAAU,aACVC,OAAU,cAIdC,OAAOC,OAASD,OAAOC,QAAUC,EAAEC,MAKnC,KAAI,GAFAC,GAAW,EACXC,GAAW,KAAM,MAAO,SAAU,KAC9BC,EAAI,EAAGA,EAAID,EAAQE,SAAWf,OAAOgB,wBAAyBF,EAClEd,OAAOgB,sBAAwBhB,OAAOa,EAAQC,GAAG,yBACjDd,OAAOiB,4BAA8BjB,OAAOa,EAAQC,GAClD,8BAGDd,QAAOgB,wBACRhB,OAAOgB,sBAAwB,SAASE,GACpC,GAAIC,IAAW,GAAIC,OAAOC,UACtBC,EAAaC,KAAKC,IAAI,EAAG,IAAML,EAAWP,IAC1Ca,EAAKzB,OAAO0B,WAAW,WAAaR,EAASC,EAAWG,IAC1DA,EAEF,OADAV,GAAWO,EAAWG,EACfG,IAGVzB,OAAO2B,uBACR3B,OAAO2B,qBAAuB,SAASF,GACnCG,aAAaH,IAIrB,IAAII,KACEC,KAAM,SAAoBC,WAAY,WAAY,MAAO/B,QAAOgC,4BAChEF,KAAM,iBAAoBC,WAAY,WACpC,IACI,MAAO/B,QAAOiC,eAAelB,QAAU,EACzC,MAAOmB,IACT,OAAO,KAIXC,EAAoBN,EACnBO,OAAQ,SAAUC,GAAW,OAAQA,EAAQN,eAC7CO,IAAK,SAAUD,GAAW,MAAOA,GAAQP,MAG9C,IAAMK,EAAkBpB,OAAQ,CAC5B,GAAIwB,GAAOC,SAASC,iBAAkB,qBAAsBC,KAAM,EAC9DH,KACAvC,OAAO2C,SAAWJ,EAAKK,KAAO,oCAElC3C,QAAQC,IAAK,0BAA4BiC,EAAkBU,KAAM"}

static/scripts/mvc/citation/citation-model.js

@@ -1,2 +1,2 @@
-define(["libs/bibtex","mvc/base-mvc","utils/localization"],function(a,b){var c="citation",d=Backbone.Model.extend(b.LoggableMixin).extend({_logNamespace:c,initialize:function(){var a=this.attributes.content,b=new a.BibtexParser(a).entries[0];this.entry=b,this._fields={};var c=b.Fields;for(var d in c){var e=c[d],f=d.toLowerCase();this._fields[f]=e}},entryType:function(){return this.entry.EntryType},fields:function(){return this._fields}}),e=Backbone.Collection.extend(b.LoggableMixin).extend({_logNamespace:c,urlRoot:Galaxy.root+"api",partial:!0,model:d}),f=e.extend({url:function(){return this.urlRoot+"/histories/"+this.history_id+"/citations"}}),g=e.extend({url:function(){return this.urlRoot+"/tools/"+this.tool_id+"/citations"},partial:!1});return{Citation:d,HistoryCitationCollection:f,ToolCitationCollection:g}});
+define(["libs/bibtex","mvc/base-mvc","utils/localization"],function(a,b){var c="citation",d=Backbone.Model.extend(b.LoggableMixin).extend({_logNamespace:c,initialize:function(){var b=this.get("content"),c=a(b).entries[0];this.entry=c,this._fields={};var d=c.Fields;for(var e in d){var f=d[e],g=e.toLowerCase();this._fields[g]=f}},entryType:function(){return this.entry.EntryType},fields:function(){return this._fields}}),e=Backbone.Collection.extend(b.LoggableMixin).extend({_logNamespace:c,urlRoot:Galaxy.root+"api",partial:!0,model:d}),f=e.extend({url:function(){return this.urlRoot+"/histories/"+this.history_id+"/citations"}}),g=e.extend({url:function(){return this.urlRoot+"/tools/"+this.tool_id+"/citations"},partial:!1});return{Citation:d,HistoryCitationCollection:f,ToolCitationCollection:g}});
 //# sourceMappingURL=../../../maps/mvc/citation/citation-model.js.map

static/scripts/mvc/ui/ui-select-default.js

@@ -1,2 +1,2 @@
-define(["utils/utils","mvc/ui/ui-buttons"],function(a,b){var c=Backbone.View.extend({optionsDefault:{id:a.uid(),cls:"ui-select",error_text:"No options available",empty_text:"Nothing selected",visible:!0,wait:!1,multiple:!1,searchable:!0,optional:!1},initialize:function(c){var d=this;this.options=a.merge(c,this.optionsDefault),this.setElement(this._template(this.options)),this.$select=this.$el.find(".select"),this.$icon_dropdown=this.$el.find(".icon-dropdown");var e=null;this.$(".icon-resize").on("mousedown",function(a){var b=a.pageY,c=d.$select.height();e=e||c,$("#dd-helper").show().on("mousemove",function(a){d.$select.height(Math.max(c+(a.pageY-b),e))}).on("mouseup mouseleave",function(){$("#dd-helper").hide().off()})}),this.options.multiple&&(this.options.searchable?(this.all_button=new b.ButtonCheck({onclick:function(){var a=[];0!==d.all_button.value()&&(a=d._availableOptions()),d.value(a),d.trigger("change")}}),this.$el.prepend(this.all_button.$el)):this.$el.addClass("ui-select-multiple"),this.$select.prop("multiple",!0),this.$icon_dropdown.remove()),this.update(this.options.data),void 0!==this.options.value&&this.value(this.options.value),this.options.visible||this.hide(),this.options.wait?this.wait():this.show(),this.$select.on("change",function(){d.trigger("change")}),this.on("change",function(){d.options.onchange&&d.options.onchange(this.value())})},value:function(a){void 0!==a&&(null===a&&(a="__null__"),(this.exists(a)||this.options.multiple)&&(this.$select.val(a),this.$select.select2&&this.$select.select2("val",a)));var b=this._getValue();return this.all_button&&this.all_button.value($.isArray(b)&&b.length||0,this._size()),b},first:function(){var a=this.$select.find("option").first();return a.length>0?a.val():null},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait(),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon_dropdown.removeClass(),this.$icon_dropdown.addClass("icon-dropdown fa fa-spinner fa-spin")},unwait:function(){this.$icon_dropdown.removeClass(),this.$icon_dropdown.addClass("icon-dropdown fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},update:function(a){var b=this._getValue();this.$select.find("option").remove(),!this.options.multiple&&this.options.optional&&this.$select.append(this._templateOption({value:"__null__",label:this.options.empty_text}));for(var c in a)this.$select.append(this._templateOption(a[c]));0==this._size()?(this.disable(),this.$select.append(this._templateOption({value:"__null__",label:this.options.error_text}))):this.enable(),this.options.searchable&&(this.$select.select2("destroy"),this.$select.select2({closeOnSelect:!this.options.multiple}),this.$(".select2-container .select2-search input").off("blur")),this.value(b),null!==this._getValue()||this.options.multiple&&this.options.optional||this.value(this.first())},setOnChange:function(a){this.options.onchange=a},exists:function(a){return this.$select.find('option[value="'+a+'"]').length>0},_getValue:function(){var b=this.$select.val();return a.validate(b)?b:null},_availableOptions:function(){var a=[];return this.$select.find("option").each(function(b,c){a.push($(c).attr("value"))}),a},_size:function(){return this.$select.find("option").length},_templateOption:function(a){return'<option value="'+a.value+'">'+_.escape(a.label)+"</option>"},_template:function(a){return'<div id="'+a.id+'" class="'+a.cls+'"><select id="'+a.id+'_select" class="select"/><div class="icon-dropdown"/><div class="icon-resize"><i class="fa fa-angle-double-right fa-rotate-45"/></div></div>'}});return{View:c}});
+define(["utils/utils","mvc/ui/ui-buttons"],function(a,b){var c=Backbone.View.extend({optionsDefault:{id:a.uid(),cls:"ui-select",error_text:"No options available",empty_text:"Nothing selected",visible:!0,wait:!1,multiple:!1,searchable:!0,optional:!1},initialize:function(c){var d=this;this.options=a.merge(c,this.optionsDefault),this.setElement(this._template(this.options)),this.$select=this.$el.find(".select"),this.$icon_dropdown=this.$el.find(".icon-dropdown"),this.$icon_dropdown.on("click",function(){d.$select.select2&&d.$select.select2("open")});var e=null;this.$(".icon-resize").on("mousedown",function(a){var b=a.pageY,c=d.$select.height();e=e||c,$("#dd-helper").show().on("mousemove",function(a){d.$select.height(Math.max(c+(a.pageY-b),e))}).on("mouseup mouseleave",function(){$("#dd-helper").hide().off()})}),this.options.multiple&&(this.options.searchable?(this.all_button=new b.ButtonCheck({onclick:function(){var a=[];0!==d.all_button.value()&&(a=d._availableOptions()),d.value(a),d.trigger("change")}}),this.$el.prepend(this.all_button.$el)):this.$el.addClass("ui-select-multiple"),this.$select.prop("multiple",!0),this.$icon_dropdown.remove()),this.update(this.options.data),void 0!==this.options.value&&this.value(this.options.value),this.options.visible||this.hide(),this.options.wait?this.wait():this.show(),this.$select.on("change",function(){d.trigger("change")}),this.on("change",function(){d.options.onchange&&d.options.onchange(this.value())})},value:function(a){void 0!==a&&(null===a&&(a="__null__"),(this.exists(a)||this.options.multiple)&&(this.$select.val(a),this.$select.select2&&this.$select.select2("val",a)));var b=this._getValue();return this.all_button&&this.all_button.value($.isArray(b)&&b.length||0,this._size()),b},first:function(){var a=this.$select.find("option").first();return a.length>0?a.val():null},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait(),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon_dropdown.removeClass(),this.$icon_dropdown.addClass("icon-dropdown fa fa-spinner fa-spin")},unwait:function(){this.$icon_dropdown.removeClass(),this.$icon_dropdown.addClass("icon-dropdown fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},update:function(a){var b=this._getValue();this.$select.find("option").remove(),!this.options.multiple&&this.options.optional&&this.$select.append(this._templateOption({value:"__null__",label:this.options.empty_text}));for(var c in a)this.$select.append(this._templateOption(a[c]));0==this._size()?(this.disable(),this.$select.append(this._templateOption({value:"__null__",label:this.options.error_text}))):this.enable(),this.options.searchable&&(this.$select.select2("destroy"),this.$select.select2({closeOnSelect:!this.options.multiple}),this.$(".select2-container .select2-search input").off("blur")),this.value(b),null!==this._getValue()||this.options.multiple&&this.options.optional||this.value(this.first())},setOnChange:function(a){this.options.onchange=a},exists:function(a){return this.$select.find('option[value="'+a+'"]').length>0},_getValue:function(){var b=this.$select.val();return a.validate(b)?b:null},_availableOptions:function(){var a=[];return this.$select.find("option").each(function(b,c){a.push($(c).attr("value"))}),a},_size:function(){return this.$select.find("option").length},_templateOption:function(a){return'<option value="'+a.value+'">'+_.escape(a.label)+"</option>"},_template:function(a){return'<div id="'+a.id+'" class="'+a.cls+'"><select id="'+a.id+'_select" class="select"/><div class="icon-dropdown"/><div class="icon-resize"><i class="fa fa-angle-double-right fa-rotate-45"/></div></div>'}});return{View:c}});
 //# sourceMappingURL=../../../maps/mvc/ui/ui-select-default.js.map

static/scripts/mvc/workflow/workflow-node.js

@@ -1,2 +1,2 @@
-define(["mvc/workflow/workflow-view-node"],function(a){var b=Backbone.Model.extend({initialize:function(a,b){this.app=a,this.element=b.element,this.input_terminals={},this.output_terminals={},this.tool_errors={},this.workflow_outputs=[]},getWorkflowOutput:function(a){return _.findWhere(this.workflow_outputs,{output_name:a})},isWorkflowOutput:function(a){return void 0!=this.getWorkflowOutput(a)},removeWorkflowOutput:function(a){for(;this.isWorkflowOutput(a);)this.workflow_outputs.splice(this.getWorkflowOutput(a),1)},addWorkflowOutput:function(a){this.isWorkflowOutput(a)||this.workflow_outputs.push({output_name:a})},connectedOutputTerminals:function(){return this._connectedTerminals(this.output_terminals)},_connectedTerminals:function(a){var b=[];return $.each(a,function(a,c){c.connectors.length>0&&b.push(c)}),b},hasConnectedOutputTerminals:function(){var a=this.output_terminals;for(var b in a)if(a[b].connectors.length>0)return!0;return!1},connectedMappedInputTerminals:function(){return this._connectedMappedTerminals(this.input_terminals)},hasConnectedMappedInputTerminals:function(){var a=this.input_terminals;for(var b in a){var c=a[b];if(c.connectors.length>0&&c.isMappedOver())return!0}return!1},_connectedMappedTerminals:function(a){var b=[];return $.each(a,function(a,c){var d=c.mapOver();d.isCollection&&c.connectors.length>0&&b.push(c)}),b},mappedInputTerminals:function(){return this._mappedTerminals(this.input_terminals)},_mappedTerminals:function(a){var b=[];return $.each(a,function(a,c){var d=c.mapOver();d.isCollection&&b.push(c)}),b},hasMappedOverInputTerminals:function(){var a=!1;return _.each(this.input_terminals,function(b){var c=b.mapOver();c.isCollection&&(a=!0)}),a},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()}),$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()}),$.each(this.output_terminals,function(a,b){b.destroy()}),this.app.workflow.remove_node(this),$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);!function(b){b.removeChild(a),b.appendChild(a)}(a.parentNode),$(a).removeClass("toolForm-active")},init_field_data:function(b){b.type&&(this.type=b.type),this.name=b.name,this.form_html=b.form_html,this.tool_state=b.tool_state,this.tool_errors=b.tool_errors,this.tooltip=b.tooltip?b.tooltip:"",this.annotation=b.annotation,this.post_job_actions=b.post_job_actions?b.post_job_actions:{},this.label=b.label,this.uuid=b.uuid,this.workflow_outputs=b.workflow_outputs?b.workflow_outputs:[];var c=this,d=new a({el:this.element[0],node:c});c.nodeView=d,$.each(b.data_inputs,function(a,b){d.addDataInput(b)}),b.data_inputs.length>0&&b.data_outputs.length>0&&d.addRule(),$.each(b.data_outputs,function(a,b){d.addDataOutput(b)}),d.render(),this.app.workflow.node_changed(this,!0)},update_field_data:function(a){var b=this;if(nodeView=b.nodeView,this.tool_state=a.tool_state,this.form_html=a.form_html,this.tool_errors=a.tool_errors,this.annotation=a.annotation,"post_job_actions"in a){var c=$.parseJSON(a.post_job_actions);this.post_job_actions=c?c:{}}b.nodeView.renderToolErrors();var d=nodeView.$("div.inputs"),e=nodeView.newInputsDiv(),f={};_.each(a.data_inputs,function(a){var c=b.nodeView.addDataInput(a,e);f[a.name]=c}),_.each(_.difference(_.values(nodeView.terminalViews),_.values(f)),function(a){a.el.terminal.destroy()}),nodeView.terminalViews=f,1==a.data_outputs.length&&"collection_type"in a.data_outputs[0]&&nodeView.updateDataOutput(a.data_outputs[0]),d.replaceWith(e),this.markChanged(),this.redraw()},error:function(a){var b=$(this.element).find(".toolFormBody");b.find("div").remove();var c="<div style='color: red; text-style: italic;'>"+a+"</div>";this.form_html=c,b.html(c),this.app.workflow.node_changed(this)},markChanged:function(){this.app.workflow.node_changed(this)}});return b});
+define(["mvc/workflow/workflow-view-node"],function(a){var b=Backbone.Model.extend({initialize:function(a,b){this.app=a,this.element=b.element,this.input_terminals={},this.output_terminals={},this.tool_errors={},this.workflow_outputs=[]},getWorkflowOutput:function(a){return _.findWhere(this.workflow_outputs,{output_name:a})},isWorkflowOutput:function(a){return void 0!=this.getWorkflowOutput(a)},removeWorkflowOutput:function(a){for(;this.isWorkflowOutput(a);)this.workflow_outputs.splice(this.getWorkflowOutput(a),1)},addWorkflowOutput:function(a){this.isWorkflowOutput(a)||this.workflow_outputs.push({output_name:a})},connectedOutputTerminals:function(){return this._connectedTerminals(this.output_terminals)},_connectedTerminals:function(a){var b=[];return $.each(a,function(a,c){c.connectors.length>0&&b.push(c)}),b},hasConnectedOutputTerminals:function(){var a=this.output_terminals;for(var b in a)if(a[b].connectors.length>0)return!0;return!1},connectedMappedInputTerminals:function(){return this._connectedMappedTerminals(this.input_terminals)},hasConnectedMappedInputTerminals:function(){var a=this.input_terminals;for(var b in a){var c=a[b];if(c.connectors.length>0&&c.isMappedOver())return!0}return!1},_connectedMappedTerminals:function(a){var b=[];return $.each(a,function(a,c){var d=c.mapOver();d.isCollection&&c.connectors.length>0&&b.push(c)}),b},mappedInputTerminals:function(){return this._mappedTerminals(this.input_terminals)},_mappedTerminals:function(a){var b=[];return $.each(a,function(a,c){var d=c.mapOver();d.isCollection&&b.push(c)}),b},hasMappedOverInputTerminals:function(){var a=!1;return _.each(this.input_terminals,function(b){var c=b.mapOver();c.isCollection&&(a=!0)}),a},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()}),$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()}),$.each(this.output_terminals,function(a,b){b.destroy()}),this.app.workflow.remove_node(this),$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);!function(b){b.removeChild(a),b.appendChild(a)}(a.parentNode),$(a).removeClass("toolForm-active")},setLabel:function(a){this.app.workflow.updateNodeLabel(this.label,a),this.label=a||null},init_field_data:function(b){b.type&&(this.type=b.type),this.name=b.name,this.form_html=b.form_html,this.tool_state=b.tool_state,this.tool_errors=b.tool_errors,this.tooltip=b.tooltip?b.tooltip:"",this.annotation=b.annotation,this.post_job_actions=b.post_job_actions?b.post_job_actions:{},this.setLabel(b.label),this.uuid=b.uuid,this.workflow_outputs=b.workflow_outputs?b.workflow_outputs:[];var c=this,d=new a({el:this.element[0],node:c});c.nodeView=d,$.each(b.data_inputs,function(a,b){d.addDataInput(b)}),b.data_inputs.length>0&&b.data_outputs.length>0&&d.addRule(),$.each(b.data_outputs,function(a,b){d.addDataOutput(b)}),d.render(),this.app.workflow.node_changed(this,!0)},update_field_data:function(a){var b=this;if(nodeView=b.nodeView,this.tool_state=a.tool_state,this.form_html=a.form_html,this.tool_errors=a.tool_errors,this.annotation=a.annotation,this.setLabel(a.label),"post_job_actions"in a){var c=$.parseJSON(a.post_job_actions);this.post_job_actions=c?c:{}}b.nodeView.renderToolErrors();var d=nodeView.$("div.inputs"),e=nodeView.newInputsDiv(),f={};_.each(a.data_inputs,function(a){var c=b.nodeView.addDataInput(a,e);f[a.name]=c}),_.each(_.difference(_.values(nodeView.terminalViews),_.values(f)),function(a){a.el.terminal.destroy()}),nodeView.terminalViews=f,b.nodeView.render(),1==a.data_outputs.length&&"collection_type"in a.data_outputs[0]&&nodeView.updateDataOutput(a.data_outputs[0]),d.replaceWith(e),this.markChanged(),this.redraw()},error:function(a){var b=$(this.element).find(".toolFormBody");b.find("div").remove();var c="<div style='color: red; text-style: italic;'>"+a+"</div>";this.form_html=c,b.html(c),this.app.workflow.node_changed(this)},markChanged:function(){this.app.workflow.node_changed(this)}});return b});
 //# sourceMappingURL=../../../maps/mvc/workflow/workflow-node.js.map

static/scripts/mvc/workflow/workflow-view-node.js

@@ -1,2 +1,2 @@
-define(["mvc/workflow/workflow-view-terminals","mvc/workflow/workflow-view-data"],function(a,b){return Backbone.View.extend({initialize:function(a){this.node=a.node,this.output_width=Math.max(150,this.$el.width()),this.tool_body=this.$el.find(".toolFormBody"),this.tool_body.find("div").remove(),this.newInputsDiv().appendTo(this.tool_body),this.terminalViews={},this.outputTerminlViews={}},render:function(){this.renderToolErrors(),this.$el.css("width",Math.min(250,Math.max(this.$el.width(),this.output_width)))},renderToolErrors:function(){this.node.tool_errors?this.$el.addClass("tool-node-error"):this.$el.removeClass("tool-node-error")},newInputsDiv:function(){return $("<div class='inputs'></div>")},updateMaxWidth:function(a){this.output_width=Math.max(this.output_width,a)},addRule:function(){this.tool_body.append($("<div class='rule'></div>"))},addDataInput:function(c,d){var e=!0;d||(d=this.$(".inputs"),e=!1);var f=this.terminalViews[c.name],g="dataset_collection"==c.input_type?a.InputCollectionTerminalView:a.InputTerminalView;if(!f||f instanceof g||(f.el.terminal.destroy(),f=null),f){var h=f.el.terminal;h.update(c),h.destroyInvalidConnections()}else f=new g({node:this.node,input:c});this.terminalViews[c.name]=f;var i=f.el,j=new b.DataInputView({terminalElement:i,input:c,nodeView:this,skipResize:e}),k=j.$el;return d.append(k.prepend(f.terminalElements())),f},addDataOutput:function(c){var d=c.collection?a.OutputCollectionTerminalView:a.OutputTerminalView,e=new d({node:this.node,output:c}),f=new b.DataOutputView({output:c,terminalElement:e.el,nodeView:this});this.tool_body.append(f.$el.append(e.terminalElements()))},updateDataOutput:function(a){var b=this.node.output_terminals[a.name];b.update(a)}})});
+define(["mvc/workflow/workflow-view-terminals","mvc/workflow/workflow-view-data"],function(a,b){return Backbone.View.extend({initialize:function(a){this.node=a.node,this.output_width=Math.max(150,this.$el.width()),this.tool_body=this.$el.find(".toolFormBody"),this.tool_body.find("div").remove(),this.newInputsDiv().appendTo(this.tool_body),this.terminalViews={},this.outputTerminlViews={}},render:function(){var a,b=this.node.label;a=b?b:this.node.name,this.$el.find(".nodeTitle").text(a),this.renderToolErrors(),this.$el.css("width",Math.min(250,Math.max(this.$el.width(),this.output_width)))},renderToolErrors:function(){this.node.tool_errors?this.$el.addClass("tool-node-error"):this.$el.removeClass("tool-node-error")},newInputsDiv:function(){return $("<div class='inputs'></div>")},updateMaxWidth:function(a){this.output_width=Math.max(this.output_width,a)},addRule:function(){this.tool_body.append($("<div class='rule'></div>"))},addDataInput:function(c,d){var e=!0;d||(d=this.$(".inputs"),e=!1);var f=this.terminalViews[c.name],g="dataset_collection"==c.input_type?a.InputCollectionTerminalView:a.InputTerminalView;if(!f||f instanceof g||(f.el.terminal.destroy(),f=null),f){var h=f.el.terminal;h.update(c),h.destroyInvalidConnections()}else f=new g({node:this.node,input:c});this.terminalViews[c.name]=f;var i=f.el,j=new b.DataInputView({terminalElement:i,input:c,nodeView:this,skipResize:e}),k=j.$el;return d.append(k.prepend(f.terminalElements())),f},addDataOutput:function(c){var d=c.collection?a.OutputCollectionTerminalView:a.OutputTerminalView,e=new d({node:this.node,output:c}),f=new b.DataOutputView({output:c,terminalElement:e.el,nodeView:this});this.tool_body.append(f.$el.append(e.terminalElements()))},updateDataOutput:function(a){var b=this.node.output_terminals[a.name];b.update(a)}})});
 //# sourceMappingURL=../../../maps/mvc/workflow/workflow-view-node.js.map

static/scripts/polyfills.js

@@ -1,2 +1,2 @@
-!function(){"use strict";window.console=window.console||{log:function(){},debug:function(){},info:function(){},warn:function(){},error:function(){},assert:function(){}},Object.assign=Object.assign||_.extend;for(var a=0,b=["ms","moz","webkit","o"],c=0;c<b.length&&!window.requestAnimationFrame;++c)window.requestAnimationFrame=window[b[c]+"RequestAnimationFrame"],window.cancelRequestAnimationFrame=window[b[c]+"CancelRequestAnimationFrame"];window.requestAnimationFrame||(window.requestAnimationFrame=function(b){var c=(new Date).getTime(),d=Math.max(0,16-(c-a)),e=window.setTimeout(function(){b(c+d)},d);return a=c+d,e}),window.cancelAnimationFrame||(window.cancelAnimationFrame=function(a){clearTimeout(a)});var d=[{name:"canvas",compatible:function(){return window.CanvasRenderingContext2D}},{name:"sessionStorage",compatible:function(){try{return Number.isInteger(sessionStorage.length)}catch(a){}return!1}}];if(d=d.filter(function(a){return!a.compatible()}).map(function(a){return a.name}),d.length){var e=document.querySelectorAll('link[rel="index"]').item(0);e&&(window.location.href=e.href+"static/incompatible-browser.html"),console.log("incompatible browser:\n"+d.join("\n"))}}();
+!function(){"use strict";window.console=window.console||{log:function(){},debug:function(){},info:function(){},warn:function(){},error:function(){},assert:function(){}},Object.assign=Object.assign||_.extend;for(var a=0,b=["ms","moz","webkit","o"],c=0;c<b.length&&!window.requestAnimationFrame;++c)window.requestAnimationFrame=window[b[c]+"RequestAnimationFrame"],window.cancelRequestAnimationFrame=window[b[c]+"CancelRequestAnimationFrame"];window.requestAnimationFrame||(window.requestAnimationFrame=function(b){var c=(new Date).getTime(),d=Math.max(0,16-(c-a)),e=window.setTimeout(function(){b(c+d)},d);return a=c+d,e}),window.cancelAnimationFrame||(window.cancelAnimationFrame=function(a){clearTimeout(a)});var d=[{name:"canvas",compatible:function(){return window.CanvasRenderingContext2D}},{name:"sessionStorage",compatible:function(){try{return window.sessionStorage.length>=0}catch(a){}return!1}}],e=d.filter(function(a){return!a.compatible()}).map(function(a){return a.name});if(e.length){var f=document.querySelectorAll('link[rel="index"]').item(0);f&&(window.location=f.href+"static/incompatible-browser.html"),console.log("incompatible browser:\n"+e.join("\n"))}}();
 //# sourceMappingURL=../maps/polyfills.js.map

templates/webapps/galaxy/history/options.mako

@@ -1,32 +0,0 @@
-<% _=n_ %>
-<%inherit file="/base.mako"/>
-<%def name="title()">History options</%def>
-    
-<h2>${_('History Options')}</h2>
-
-%if not user:
-<div class="infomessage">
-    <div>${_('You must be ')}<a target="galaxy_main" href="${h.url_for( controller='user', action='login' )}">${_('logged in')}</a>${_(' to store or switch histories.')}</div>
-</div>
-%endif
-
-<ul>
-    %if user:
-        <li><a href="${h.url_for( controller='history', action='list')}" target="galaxy_main">Previously</a> stored histories</li>
-        %if len( history.active_datasets ) > 0:
-            <li><a href="${h.url_for( controller='root', action='history_new' )}">Create</a> a new empty history</li>
-            <li><a href="${h.url_for( controller='workflow', action='build_from_current_history' )}">Construct workflow</a> from current history</li>
-            <li><a href="${h.url_for( controller='history', action='copy', id=trans.security.encode_id( history.id ) )}">Copy</a> current history</li>
-        %endif
-        <li><a href="${h.url_for( controller='history', action='share' )}" target="galaxy_main">Share</a> current history</div>
-        <li><a href="${h.url_for( controller='root', action='history_set_default_permissions' )}">Change default permissions</a> for current history</li>
-    %endif
-    %if len( history.activatable_datasets ) > 0:
-        <li><a href="${h.url_for( controller='root', action='history', show_deleted=True)}" target="galaxy_history">Show deleted</a> datasets in current history</li>
-    %endif
-    <li><a href="${h.url_for( controller='history', action='rename', id=trans.security.encode_id( history.id ) )}" target="galaxy_main">Rename</a> current history (stored as "${history.name}")</li>
-    <li><a href="${h.url_for( controller='history', action='delete_current' )}" confirm="Are you sure you want to delete the current history?">Delete</a> current history</div>
-    %if user and user.histories_shared_by_others:
-        <li><a href="${h.url_for( controller='history', action='list_shared')}" target="galaxy_main">Histories</a> shared with you by others</li>
-    %endif
-</ul>

templates/webapps/galaxy/workflow/editor_generic_form.mako

@@ -1,12 +1,31 @@
 <form name="${form.name}" action="${h.url_for( controller='workflow', action='editor_form_post' )}" method="post">
-    <div class="toolForm">
-        <div class="toolFormTitle">${form.title}</div>
-        <div class="toolFormBody">
+    <%
+    from xml.sax.saxutils import escape
+    label = module.label
+    if label is not None:
+        title = label
+    else:
+        title = form.title
+    %>
+    <div class="ui-portlet-narrow">
+        <div class="portlet-header">
+          <div class="portlet-title">
+            <span class="portlet-title-text"><b>${title}</b></span>
+          </div>
+        </div>
+        <div class="portlet-content">
+          <div class="content">
+            <div class="ui-margin-top"></div>
+            <div>
             <input type="hidden" name="type" value="${module.type}" />
+            <input type="hidden" name="label" value="${escape(label or '')}" />
+            <table class="ui-table-plain">
+              <thead></thead>
+              <tbody>
             %if form.inputs:
               %for input in form.inputs:
                   <%
-                  cls = "form-row"
+                  cls = "section-row"
                   if input.error:
                       cls += " form-row-error"
                   extra_attributes = ""
@@ -16,38 +35,37 @@
                   if input.type:
                     type_attribute = "type=\"input.type\""
                   %>
-                  <div class="${cls}">
-                    <label>
+                  <tr class="${cls}"><td><div class="ui-table-form-element">
+                    <div class="ui-table-form-title">
                         ${input.label}:
-                    </label>
-                    <div style="float: left; width: 250px; margin-right: 10px;">
-
+                    </div>
+                    <div class="ui-table-form-field" style="display: block;">
                         <input ${type_attribute} name="${input.name | h}" value="${input.value | h}" size="30" ${extra_attributes}>
                         %if hasattr( input, "body_html" ):
                               ${input.body_html()}
                             </input>
                         %endif
-                    </div>
-                    %if input.error:
-                    <div style="float: left; color: red; font-weight: bold; padding-top: 1px; padding-bottom: 3px;">
-                        <div style="width: 300px;"><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}">&nbsp;<span style="vertical-align: middle;">${input.error}</span></div>
-                    </div>
-                    %endif
+                      %if input.error:
+                      <div style="float: left; color: red; font-weight: bold; padding-top: 1px; padding-bottom: 3px;">
+                          <div style="width: 300px;"><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}">&nbsp;<span style="vertical-align: middle;">${input.error}</span></div>
+                      </div>
+                      %endif
   
-                    %if input.help:
-                    <div class="toolParamHelp" style="clear: both;">
-                        ${input.help}
-                    </div>
-                    %endif
+                      %if input.help:
+                      <div class="ui-table-form-info">
+                          ${input.help}
+                      </div>
+                      %endif
+                    </div><!-- ui-table-form-field -->
   
-                    <div style="clear: both"></div>
-  
-                  </div>
+                  </div></td></tr>
               %endfor
             %else:
               <div class="form-row"><i>No options</i></div>
             %endif
+              </tbody>
             </table>
-        </div>
+          </div> <!-- content -->
+        </div><!-- portlet-content -->
     </div>
 </form>

test/api/test_tools.py

@@ -245,8 +245,6 @@ class ToolsTestCase( api.ApiTestCase ):
             'r2_0|text': "",
         }
         response = self._run( "validation_repeat", history_id, inputs )
-        import time
-        time.sleep(10)
         self._assert_status_code_is( response, 400 )
 
     @skip_without_tool( "multi_select" )

test/api/test_workflows.py

@@ -128,7 +128,7 @@ class BaseWorkflowsApiTestCase( api.ApiTestCase, ImporterGalaxyInterface ):
             assert source_type != "path"
             jobs_descriptions = yaml.load( has_workflow )
 
-        test_data = jobs_descriptions["test_data"]
+        test_data = jobs_descriptions.get("test_data", {})
 
         label_map = {}
         inputs = {}
@@ -174,7 +174,8 @@ class BaseWorkflowsApiTestCase( api.ApiTestCase, ImporterGalaxyInterface ):
         )
         workflow_request[ "inputs" ] = dumps( label_map )
         workflow_request[ "inputs_by" ] = 'name'
-        self.dataset_populator.wait_for_history( history_id, assert_ok=True )
+        if inputs:
+            self.dataset_populator.wait_for_history( history_id, assert_ok=True )
         url = "workflows/%s/usage" % ( workflow_id )
         invocation_response = self._post( url, data=workflow_request )
         self._assert_status_code_is( invocation_response, 200 )
@@ -1039,13 +1040,33 @@ steps:
         self.__assert_lines_hid_line_count_is( history_id, 3, 3 )
 
     @skip_without_tool( "validation_default" )
-    def test_parameter_substitution_validation( self ):
+    def test_parameter_substitution_sanitization( self ):
         substitions = dict( input1="\" ; echo \"moo" )
         run_workflow_response, history_id = self._run_validation_workflow_with_substitions( substitions )
 
         self.dataset_populator.wait_for_history( history_id, assert_ok=True )
         self.assertEquals("__dq__ X echo __dq__moo\n", self.dataset_populator.get_history_dataset_content( history_id, hid=1 ) )
 
+    @skip_without_tool( "validation_repeat" )
+    def test_parameter_substitution_validation_value_errors_0( self ):
+        history_id = self.dataset_populator.new_history()
+        workflow_id = self._upload_yaml_workflow("""
+class: GalaxyWorkflow
+steps:
+ - tool_id: validation_repeat
+   state:
+     r2:
+      - text: "abd"
+""")
+        workflow_request = dict(
+            history="hist_id=%s" % history_id,
+            parameters=dumps( dict( validation_repeat={"r2_0|text": ""} ) )
+        )
+        url = "workflows/%s/invocations" % workflow_id
+        invocation_response = self._post( url, data=workflow_request )
+        # Take a valid stat and make it invalid, assert workflow won't run.
+        self._assert_status_code_is( invocation_response, 400 )
+
     @skip_without_tool( "validation_default" )
     def test_parameter_substitution_validation_value_errors_1( self ):
         substitions = dict( select_param="\" ; echo \"moo" )

test/api/workflows_format_2/converter.py

@@ -91,7 +91,7 @@ def _python_to_workflow(as_python, conversion_context):
         as_python["steps"] = steps_as_dict
         steps = steps_as_dict
 
-    for i, step in steps.iteritems():
+    for step in steps.itervalues():
         step_type = step.get("type", None)
         if "run" in step:
             if step_type is not None:
@@ -113,7 +113,7 @@ def _python_to_workflow(as_python, conversion_context):
             run_to_step_function(conversion_context, step, run_action)
             del step["run"]
 
-    for i, step in steps.iteritems():
+    for step in steps.itervalues():
         step_type = step.get("type", "tool")
         step_type = STEP_TYPE_ALIASES.get(step_type, step_type)
         if step_type not in STEP_TYPES:
@@ -148,14 +148,14 @@ def convert_inputs_to_steps(inputs, steps):
         if "label" not in input_def and "id" not in input_def:
             raise Exception("Input must define a label.")
 
-        raw_label = __rip_value(input_def, "label")
-        raw_id = __rip_value(input_def, "id")
+        raw_label = input_def.pop("label", None)
+        raw_id = input_def.pop("id", None)
         label = raw_label or raw_id
 
         if not label:
             raise Exception("Input label must not be empty.")
 
-        input_type = __rip_value(input_def, "type", "data")
+        input_type = input_def.pop("type", "data")
         if input_type in ["File", "data", "data_input"]:
             step_type = "data_input"
         elif input_type in ["collection", "data_collection", "data_collection_input"]:
@@ -380,15 +380,6 @@ def __join_prefix(prefix, key):
     return new_key
 
 
-def __rip_value(input_def, key, default=None):
-    if key in input_def:
-        value = input_def[key]
-        del input_def[key]
-    else:
-        value = default
-    return value
-
-
 def __init_connect_dict(step):
     if "connect" not in step:
         step["connect"] = {}

test/base/interactor.py

@@ -280,6 +280,8 @@ class GalaxyInteractorApi( object ):
         return wait
 
     def __job_ready( self, job_id, history_id ):
+        if job_id is None:
+            raise ValueError("__job_ready passed empty job_id")
         job_json = self._get( "jobs/%s" % job_id ).json()
         state = job_json[ 'state' ]
         try:
@@ -290,6 +292,8 @@ class GalaxyInteractorApi( object ):
             raise
 
     def __history_ready( self, history_id ):
+        if history_id is None:
+            raise ValueError("__history_ready passed empty history_id")
         history_json = self._get( "histories/%s" % history_id ).json()
         state = history_json[ 'state' ]
         try:
@@ -300,6 +304,8 @@ class GalaxyInteractorApi( object ):
             raise
 
     def _summarize_history_errors( self, history_id ):
+        if history_id is None:
+            raise ValueError("_summarize_history_errors passed empty history_id")
         print "History with id %s in error - summary of datasets in error below." % history_id
         try:
             history_contents = self.__contents( history_id )

test/casperjs/api-anon-history-permission-tests.js

@@ -67,10 +67,12 @@ spaceghost.test.begin( 'Test permissions for accessible, published, and inaccess
         this.test.comment( 'show should work for history: ' + history.name );
         this.test.assert( this.api.histories.show( history.id ).id === history.id,
             'show worked' );
-        this.test.comment( 'copying should fail for history (multiple histories not allowed): ' + history.name );
-        this.api.assertRaises( function(){
-            this.api.histories.create({ history_id : history.id });
-        }, 403, 'API authentication required for this request', 'update authentication required' );
+
+        this.test.comment( 'copying should work for history (replacing the original history): ' + history.name );
+        var copiedHistory = this.api.histories.create({ history_id : history.id });
+        var historiesIndex = this.api.histories.index();
+        this.test.assert( historiesIndex.length === 1, 'only one history after copy' );
+        this.test.assert( historiesIndex[0].id === copiedHistory.id, 'original history with copy' );
 
         // read functions for history contents
         this.test.comment( 'index of history contents should work for history: ' + history.name );
@@ -99,7 +101,7 @@ spaceghost.test.begin( 'Test permissions for accessible, published, and inaccess
         this.test.comment( 'copying should fail for history (implicit multiple histories): ' + history.name );
         this.api.assertRaises( function(){
             this.api.histories.create({ history_id : history.id });
-        }, 403, 'API authentication required for this request', 'copy failed with error' );
+        }, 403, 'History is not accessible by user', 'copy failed with error' );
 
         // read functions for history contents
         this.test.comment( 'index and show of history contents should fail for history: ' + history.name );

test/casperjs/api-anon-history-tests.js

@@ -23,6 +23,9 @@ spaceghost.test.begin( 'Test API functions for histories with an anonymous user'
         this.test.assert( historyShow.id === index[0].id, 'Is the first history' );
         this.test.assert( this.hasKeys( historyShow, [ 'id', 'name', 'user_id' ] ) );
 
+        this.test.comment( 'Calling create should work for an anonymous user' );
+        this.test.assert( this.api.histories.index().length === 1, 'Now has two histories' );
+
 
         // ------------------------------------------------------------------------------------------- anon forbidden
         //TODO: why not return the current history?
@@ -30,11 +33,6 @@ spaceghost.test.begin( 'Test API functions for histories with an anonymous user'
         var recent = this.api.histories.show( 'most_recently_used' );
         this.test.assert( recent.id === historyShow.id, 'most_recently_used returned current' );
 
-        this.test.comment( 'Calling create should fail for an anonymous user' );
-        this.api.assertRaises( function(){
-            this.api.histories.create({ name: 'new' });
-        }, 403, 'API authentication required for this request', 'create failed with error' );
-
         this.test.comment( 'Calling delete should fail for an anonymous user' );
         this.api.assertRaises( function(){
             this.api.histories.delete_( historyShow.id );

test/docker/base/Dockerfile

@@ -59,22 +59,22 @@ RUN mkdir /etc/galaxy && cd /tmp/ansible && mkdir roles && \
     apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
 RUN cd $GALAXY_ROOT && \
-    echo "Prepopuating postgres database" && \
+    echo "Prepopulating postgres database" && \
     su -c '/usr/lib/postgresql/9.3/bin/pg_ctl -o "-F" start -D /opt/galaxy/db' postgres && \
     sleep 3 && \
     GALAXY_CONFIG_DATABASE_CONNECTION="postgresql://root@localhost:5930/galaxy" sh create_db.sh && \
-    echo "Prepopuating sqlite database" && \
+    echo "Prepopulating sqlite database" && \
     GALAXY_CONFIG_DATABASE_CONNECTION="sqlite:////opt/galaxy/galaxy.sqlite" sh create_db.sh && \
     sh /opt/galaxy/start_mysql.sh && \
-    echo "Prepopuating mysql database" && \
+    echo "Prepopulating mysql database" && \
     GALAXY_CONFIG_DATABASE_CONNECTION="mysql://galaxy:galaxy@localhost/galaxy?unix_socket=/var/run/mysqld/mysqld.sock" sh create_db.sh && \
     echo "Prepopulating toolshed postgres database" && \
     su -c '/usr/lib/postgresql/9.3/bin/pg_ctl -o "-F" start -D /opt/galaxy/db' postgres && \
     GALAXY_CONFIG_DATABASE_CONNECTION="postgresql://root@localhost:5930/toolshed" sh create_db.sh tool_shed && \
-    echo "Prepopuating toolshed sqlite database" && \
+    echo "Prepopulating toolshed sqlite database" && \
     GALAXY_CONFIG_DATABASE_CONNECTION="sqlite:////opt/galaxy/toolshed.sqlite" sh create_db.sh tool_shed && \
     sh /opt/galaxy/start_mysql.sh && \
-    echo "Prepopuating toolshed mysql database" && \
+    echo "Prepopulating toolshed mysql database" && \
     GALAXY_CONFIG_DATABASE_CONNECTION="mysql://galaxy:galaxy@localhost/toolshed?unix_socket=/var/run/mysqld/mysqld.sock" sh create_db.sh tool_shed
 
 # bcftools for Galaxy.

test/docker/base/run_test_wrapper.sh

@@ -8,7 +8,7 @@ then
     sleep 3
     GALAXY_TEST_INSTALL_DB_MERGED="true"
     GALAXY_TEST_DBURI="postgres://root@localhost:5930/galaxy?client_encoding=utf8"
-    TOOL_SHED_TEST_DBURI="postgres://root@localhost:5930/toolshed"
+    TOOL_SHED_TEST_DBURI="postgres://root@localhost:5930/toolshed?client_encoding=utf8"
 elif [ "$GALAXY_TEST_DATABASE_TYPE" = "mysql" ];
 then
     sh /opt/galaxy/start_mysql.sh

test/qunit/tests/workflow_editor_tests.js

@@ -2,6 +2,7 @@
 define([
     "sinon-qunit",
     "test-app",
+    'utils/utils',
     "mvc/workflow/workflow-view",
     "mvc/workflow/workflow-node",
     "mvc/workflow/workflow-view-node",
@@ -11,6 +12,7 @@ define([
 ], function(
     sinon,
     testApp,
+    Utils,
     App,
     Node,
     NodeView,
@@ -296,8 +298,8 @@ define([
         setup: function() {
             this.input_terminal = { destroy: sinon.spy(), redraw: sinon.spy() };
             this.output_terminal = { destroy: sinon.spy(), redraw: sinon.spy() };
-            this.element = $("<div><div class='toolFormBody'></div></div>");
             this.app = create_app();
+            this.element = this.app.$newNodeElement( "tool", "newnode" );
             this.node = new Node( this.app, { element: this.element } );
             this.node.input_terminals.i1 = this.input_terminal;
             this.node.output_terminals.o1 = this.output_terminal;
@@ -311,22 +313,24 @@ define([
             f();
             ok( node_changed_spy.calledWith( node ) );
         },
-        init_field_data_simple: function() {
-            var data = {
+        init_field_data_simple: function(option_overrides) {
+            var data = Utils.merge(option_overrides, {
                 data_inputs: [ {name: "input1", extensions: [ "data" ] } ],
                 data_outputs: [ {name: "output1", extensions: [ "data" ] } ],
-            };
+                label: null,
+            });
             this.node.init_field_data( data );
         },
-        update_field_data_with_new_input: function() {
-            var new_data = {
+        update_field_data_with_new_input: function(option_overrides) {
+            var new_data = Utils.merge(option_overrides, {
                 data_inputs: [
                     { name: "input1", extensions: [ "data" ] },
                     { name: "extra_0|input1", extensions: [ "data" ] },
                 ],
                 data_outputs: [ {name: "output1", extensions: [ "data" ] } ],
-                post_job_actions: "{}"
-            };
+                post_job_actions: "{}",
+                label: "New Label"
+            });
             this.node.update_field_data( new_data );
         }
     } );
@@ -368,6 +372,7 @@ define([
                 tooltip: "tool tooltip",
                 annotation: "tool annotation",
                 workflow_outputs: [ {"output_name": "out1"} ],
+                label: "Cat that data.",
             };
             node.init_field_data( data );
             equal( node.type, "tool" );
@@ -376,6 +381,7 @@ define([
             equal( node.tool_state, "ok" );
             equal( node.tooltip, "tool tooltip" );
             equal( node.annotation, "tool annotation" );
+            equal( node.label, "Cat that data." );
             deepEqual( node.post_job_actions, {} );
             deepEqual( node.workflow_outputs, [  {"output_name": "out1"} ] );
         } );
@@ -394,9 +400,26 @@ define([
             equal( test.$( ".input-terminal" ).length, 1 );
             equal( test.$( ".rule" ).length, 1 );
             equal( test.$( ".toolFormBody" ).children().length, 3 );
+            equal( test.$( ".nodeTitle" ).text(), "newnode" );
+            ok( test.$( ".toolFormTitle" ).find("i").hasClass("fa-wrench") );
         } );
     } );
 
+    test( "node title behavior", function() {
+        var test = this;
+        this.expect_workflow_node_changed( function( ) {
+            // Node created with name newnode
+            equal( test.$( ".nodeTitle" ).text(), "newnode" );
+            // init_field_data_simple doesn't change label, so it should
+            // remain original name.
+            test.init_field_data_simple();
+            equal( test.$( ".nodeTitle" ).text(), "newnode" );
+            // Despite awkward name, update does change the label...
+            test.update_field_data_with_new_input();
+            equal( test.$( ".nodeTitle" ).text(), "New Label" );
+        });
+    });
+
     test( "update_field_data updated data inputs and outputs", function() {
         var test = this;
         this.expect_workflow_node_changed( function( ) {

test/tool_shed/functional/test_1460_data_managers.py

@@ -60,7 +60,7 @@ class TestDataManagers( ShedTwillTestCase ):
                                                     owner=common.test_user_1_name,
                                                     category_id=self.security.encode_id( category.id ),
                                                     strings_displayed=[] )
-        # Upload the edited tool dependency definition to the package_lapack_3_4_1440 repository.
+        # Upload the data manager files to the repository.
         self.upload_file( repository,
                           filename=data_manager_tar_file,
                           filepath=None,

test/unit/managers/test_UserManager.py

@@ -182,7 +182,7 @@ class UserSerializerTestCase( BaseTestCase ):
         self.assertIsInstance( serialized[ 'nice_total_disk_usage' ], basestring )
         self.assertIsInstance( serialized[ 'quota_percent' ], ( type( None ), float ) )
         self.assertIsInstance( serialized[ 'tags_used' ], list )
-        self.assertIsInstance( serialized[ 'requests' ], list )
+        self.assertIsInstance( serialized[ 'has_requests' ], bool )
 
         self.log( 'serialized should jsonify well' )
         self.assertIsJsonifyable( serialized )

test/unit/workflows/test_modules.py

@@ -19,7 +19,7 @@ def test_valid_new_tool_has_no_errors():
     trans = MockTrans()
     mock_tool = mock.Mock()
     trans.app.toolbox.tools[ "cat1" ] = mock_tool
-    tool_module = modules.module_factory.new( trans, "tool", tool_id="cat1" )
+    tool_module = modules.module_factory.new( trans, "tool", content_id="cat1" )
     assert not tool_module.get_errors()
 
 
@@ -194,7 +194,7 @@ def test_cannot_create_tool_modules_for_missing_tools():
     trans = MockTrans()
     exception = False
     try:
-        modules.module_factory.new( trans, "tool", tool_id="cat1" )
+        modules.module_factory.new( trans, "tool", content_id="cat1" )
     except Exception:
         exception = True
     assert exception