Merge branch 'guerler-workflow_form_000' into dev

client/galaxy/scripts/galaxy.workflow_editor.canvas.js

@@ -1078,19 +1078,23 @@ $.extend( Workflow.prototype, {
             this.activate_node(node);
         }
     },
-    clear_active_node : function() {
+    clear_active_node : function(callback) {
         if ( this.active_node ) {
             this.active_node.make_inactive();
             this.active_node = null;
         }
-        parent.show_form_for_tool( "<div>No node selected</div>" );
+        if (parent.__NEWTOOLFORM__) {
+            parent.show_tool_form( "<div>No node selected</div>", {id: 'no-node'}, callback );
+        } else {
+            parent.show_form_for_tool( "<div>No node selected</div>" );
+        }
     },
     activate_node : function( node ) {
         if ( this.active_node != node ) {
             this.check_changes_in_active_form();
             this.clear_active_node();
             if (parent.__NEWTOOLFORM__) {
-                parent.show_form_for_tool( node.form_html, node );
+                parent.show_tool_form( node.form_html, node );
             } else {
                 parent.show_form_for_tool( node.form_html + node.tooltip, node );
             }
@@ -1104,7 +1108,7 @@ $.extend( Workflow.prototype, {
             // Reactive with new form_html
             this.check_changes_in_active_form(); //Force changes to be saved even on new connection (previously dumped)
             if (parent.__NEWTOOLFORM__) {
-                parent.show_form_for_tool( node.form_html, node );
+                parent.show_tool_form( node.form_html, node );
             } else {
                 parent.show_form_for_tool( node.form_html + node.tooltip, node );
             }

client/galaxy/scripts/galaxy.workflows.js

@@ -83,6 +83,14 @@ $( function() {
 
     // Initialize workflow state
     reset();
+
+    // get available datatypes for post job action options
+    datatypes = JSON.parse($.ajax({
+        type    : 'GET',
+        url     : galaxy_config.root + 'api/datatypes',
+        async   : false
+    }).responseText);
+
     // Load the datatype info
     $.ajax( {
         url: get_datatypes_url,
@@ -204,10 +212,10 @@ $( function() {
     }
 
     function edit_workflow_attributes() {
-        workflow.clear_active_node();
-        $('.right-content').hide();
-        $('#edit-attributes').show();
-
+        workflow.clear_active_node(function() {
+            $('.right-content').hide();
+            $('#edit-attributes').show();
+        });
     }
 
     // On load, set the size to the pref stored in local storage if it exists
@@ -447,6 +455,47 @@ function show_workflow_parameters(){
     }
 }
 
+function show_tool_form( text, node, callback ) {
+    require(['utils/utils', 'mvc/tools/tools-form-workflow'], function(Utils, ToolsForm){
+        // initialize tags and identifiers
+        var cls = 'right-content';
+        var id  = cls + '-' + node.id;
+
+        // grab panel container
+        var $container = $('#' + cls);
+
+        // remove previous notifications
+        var $current = $container.find('#' + id);
+        if ($current.length > 0 && $current.find('.section-row').length == 0) {
+            $current.remove();
+        }
+
+        // check if tool form already exists
+        if ($container.find('#' + id).length == 0) {
+            var $el = $('<div id="' + id + '" class="' + cls + '"/>');
+            if (Utils.isJSON(text)) {
+                var options = JSON.parse(text);
+                options.datatypes = datatypes;
+                $el.append((new ToolsForm.View(options)).$el);
+            } else {
+                $el.append(text);
+            }
+            $container.append($el);
+        }
+
+        // hide everything
+        $('.' + cls).hide();
+
+        // show current form
+        $container.find('#' + id).show();
+        $container.show();
+        $container.scrollTop();
+
+        // temporary fix for async require callback
+        callback && callback();
+    });
+}
+
 function show_form_for_tool( text, node ) {
     $('.right-content').hide();
     $("#right-content").show().html( text );

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

@@ -17,7 +17,7 @@ return Backbone.Model.extend({
             var id = $(this).attr('id');
             var field = self.app.field_list[id];
             if (field) {
-                sum += id + ':' + JSON.stringify(field.value && field.value()) + ';';
+                sum += id + ':' + JSON.stringify(field.value && field.value()) + ':' + field.collapsed + ';';
             }
         });
         return sum;
@@ -113,6 +113,11 @@ return Backbone.Model.extend({
 
                                 // ignore certain values
                                 if (input.ignore === undefined || input.ignore != value) {
+                                    // replace value by collapsible value
+                                    if (field.collapsed && input.collapsible_value) {
+                                        value = input.collapsible_value;
+                                    }
+
                                     // add value to submission
                                     add (job_input_id, input.id, value);
 

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

@@ -10,8 +10,8 @@ define([], function() {
             // set text labels and icons for optional button
             this.text_enable    = app.options.text_enable || 'Enable';
             this.text_disable   = app.options.text_disable || 'Disable';
-            this.cls_enable     = app.options.cls_enable || 'fa fa-plus-square';
-            this.cls_disable    = app.options.cls_disable || 'fa fa-minus-square';
+            this.cls_enable     = app.options.cls_enable || 'fa fa-caret-square-o-down';
+            this.cls_disable    = app.options.cls_disable || 'fa fa-caret-square-o-up';
 
             // link field
             this.field = options.field;
@@ -31,13 +31,8 @@ define([], function() {
             this.$field.prepend(this.field.$el);
 
             // decide wether to expand or collapse optional fields
-            this.field.skip = false;
-            var v = this.field.value && this.field.value();
-            this.field.skip = Boolean(options.collapsible &&
-                                        (v === this.default_value ||
-                                         String(v) === String(this.default_value) ||
-                                         Number(v) === Number(this.default_value) ||
-                                         JSON.stringify(v) === JSON.stringify(this.default_value)));
+            this.field.collapsed =  options.collapsible && options.value &&
+                                    JSON.stringify(options.value) == JSON.stringify(options.collapsible_value);
 
             // refresh view
             this._refresh();
@@ -46,7 +41,7 @@ define([], function() {
             var self = this;
             this.$optional.on('click', function() {
                 // flip flag
-                self.field.skip = !self.field.skip;
+                self.field.collapsed = !self.field.collapsed;
 
                 // refresh view
                 self._refresh();
@@ -78,16 +73,15 @@ define([], function() {
             this.$optional_icon.removeClass().addClass('icon');
 
             // identify state
-            if (!this.field.skip) {
+            if (!this.field.collapsed) {
                 // enable input field
                 this.$field.fadeIn('fast');
                 this._tooltip(this.text_disable, this.cls_disable);
-            
+                this.app.trigger('change');
             } else {
                 // disable input field
                 this.$field.hide();
                 this._tooltip(this.text_enable, this.cls_enable);
-                // reset field value
                 this.field.value && this.field.value(this.default_value);
             }
         },

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

@@ -316,11 +316,13 @@ define(['utils/utils',
 
             // create input field wrapper
             var input_element = new InputElement(this.app, {
-                label           : input_def.label || input_def.name,
-                default_value   : input_def.default_value,
-                collapsible     : input_def.collapsible,
-                help            : input_def.help,
-                field           : field
+                label               : input_def.label || input_def.name,
+                value               : input_def.value,
+                default_value       : input_def.default_value,
+                collapsible         : input_def.collapsible,
+                collapsible_value   : input_def.collapsible_value,
+                help                : input_def.help,
+                field               : field
             });
 
             // add to element list

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

@@ -24,10 +24,6 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view',
             // set element
             this.setElement('<div/>');
 
-            // append to body
-            this.container = options.container || 'body';
-            $(this.container).append(this.$el);
-
             // create form
             this._buildForm(options);
         },

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

@@ -7,6 +7,9 @@ define(['utils/utils', 'mvc/tools/tools-form-base'],
     // create form view
     var View = ToolFormBase.extend({
         initialize: function(options) {
+            // link this
+            var self = this;
+
             // link with node representation in workflow module
             this.node = workflow.active_node;
             if (!this.node) {
@@ -37,35 +40,39 @@ define(['utils/utils', 'mvc/tools/tools-form-base'],
                 }
             });
 
-            // declare conditional fields as not optional
+            // mark values which can be determined at runtime
             Utils.deepeach(options.inputs, function(item) {
                 if (item.type) {
-                    if (item.type == 'conditional') {
-                        item.test_param.collapsible = false;
-                    } else {
-                        if ((['data', 'data_collection']).indexOf(item.type) == -1) {
-                            item.collapsible = true;
-                        }
+                    if ((['data', 'data_collection']).indexOf(item.type) == -1) {
+                        item.collapsible = true;
+                        item.collapsible_value = {'__class__': 'RuntimeValue'};
                     }
                 }
             });
 
-            // load extension
-            var self = this;
-            Utils.get({
-                url     : galaxy_config.root + 'api/datatypes',
-                cache   : true,
-                success : function(datatypes) {
-                    self.datatypes = datatypes;
-                    self._makeSections(options.inputs);
-                    ToolFormBase.prototype.initialize.call(self, options);
+            // declare conditional and data input fields as not collapsible
+            Utils.deepeach(options.inputs, function(item) {
+                if (item.type) {
+                    if (item.type == 'conditional') {
+                        item.test_param.collapsible = false;
+                    }
                 }
             });
+
+            // configure custom sections
+            this._makeSections(options);
+
+            // create final tool form
+            ToolFormBase.prototype.initialize.call(this, options);
         },
 
         /** Builds all sub sections
         */
-        _makeSections: function(inputs){
+        _makeSections: function(options){
+            // initialize local variables
+            var inputs = options.inputs;
+            var datatypes = options.datatypes;
+
             // for annotation
             inputs[Utils.uid()] = {
                 label   : 'Annotation / Notes',
@@ -104,20 +111,20 @@ define(['utils/utils', 'mvc/tools/tools-form-base'],
 
                 // add output specific actions
                 for (var i in this.node.output_terminals) {
-                    inputs[Utils.uid()] = this._makeSection(i);
+                    inputs[Utils.uid()] = this._makeSection(i, datatypes);
                 }
             }
         },
 
         /** Builds sub section with step actions/annotation
         */
-        _makeSection: function(output_id){
+        _makeSection: function(output_id, datatypes){
             // format datatypes
             var extensions = [];
-            for (key in this.datatypes) {
+            for (key in datatypes) {
                 extensions.push({
-                    0 : this.datatypes[key],
-                    1 : this.datatypes[key]
+                    0 : datatypes[key],
+                    1 : datatypes[key]
                 });
             }
 

client/galaxy/scripts/mvc/ui/ui-slider.js

@@ -63,6 +63,7 @@ var View = Backbone.View.extend({
         var pressed = [];
         this.$text.on('keyup', function(e) {
             pressed[e.which] = false;
+            self.options.onchange && self.options.onchange($(this).val());
         });
         this.$text.on('keydown', function (e) {
             var v = e.which;
@@ -99,9 +100,7 @@ var View = Backbone.View.extend({
             this.$text.val(new_val);
 
             // trigger on change event
-            if (this.options.onchange) {
-                this.options.onchange(new_val);
-            }
+            this.options.onchange && this.options.onchange(new_val);
         }
 
         // return current value

client/galaxy/scripts/utils/utils.js

@@ -18,6 +18,16 @@ function deepeach(dict, callback) {
     }
 }
 
+/**
+ * Check if a string is a json string
+ * @param{String}   text - Content to be validated
+ */
+function isJSON(text) {
+    return /^[\],:{}\s]*$/.test(text.replace(/\\["\\\/bfnrtu]/g, '@').
+        replace(/"[^"\\\n\r]*"|true|false|null|-?\d+(?:\.\d*)?(?:[eE][+\-]?\d+)?/g, ']').
+        replace(/(?:^|:|,)(?:\s*\[)+/g, ''));
+};
+
 /**
  * Sanitize/escape a string
  * @param{String}   content - Content to be sanitized
@@ -254,7 +264,8 @@ return {
     sanitize: sanitize,
     textify: textify,
     validate: validate,
-    deepeach: deepeach
+    deepeach: deepeach,
+    isJSON: isJSON
 };
 
 });

config/galaxy.ini.sample

@@ -837,7 +837,7 @@ use_interactive = True
 #toolform_upgrade = True
 
 # Use new tool form in workflow editor
-#workflow_toolform_upgrade = False
+#workflow_toolform_upgrade = True
 
 # Enable Galaxy to communicate directly with a sequencer
 #enable_sequencer_communication = False

lib/galaxy/tools/__init__.py

@@ -2362,6 +2362,8 @@ class Tool( object, Dictifiable ):
                     return 'false'
             elif isinstance(v, basestring) or isnumber:
                 return v
+            elif isinstance(v, dict) and hasattr(v, '__class__'):
+                return v
             else:
                 return None
 
@@ -2389,10 +2391,16 @@ class Tool( object, Dictifiable ):
             dict[key] = value
 
         # check the current state of a value and update it if necessary
-        def check_state(trans, input, default_value, context):
-            value = default_value
+        def check_state(trans, input, value, context):
             error = 'State validation failed.'
 
+            # do not check unvalidated values
+            if isinstance(value, galaxy.tools.parameters.basic.RuntimeValue):
+                return [ { '__class__' : 'RuntimeValue' }, None ]
+            elif isinstance( value, dict ):
+                if value.get('__class__') == 'RuntimeValue':
+                    return [ value, None ]
+
             # skip dynamic fields if deactivated
             if is_workflow and input.is_dynamic:
                 return [value, None]
@@ -2400,10 +2408,10 @@ class Tool( object, Dictifiable ):
             # validate value content
             try:
                 # resolves the inconsistent definition of boolean parameters (see base.py) without modifying shared code
-                if input.type == 'boolean' and isinstance(default_value, basestring):
-                    value, error = [string_as_bool(default_value), None]
+                if input.type == 'boolean' and isinstance(value, basestring):
+                    value, error = [string_as_bool(value), None]
                 else:
-                    value, error = check_param(trans, input, default_value, context, history=history)
+                    value, error = check_param(trans, input, value, context, history=history)
             except Exception, err:
                 log.error('Checking parameter %s failed. %s', input.name, str(err))
                 pass

lib/galaxy/tools/parameters/basic.py

@@ -158,7 +158,10 @@ class ToolParameter( object, Dictifiable ):
 
     def value_to_basic( self, value, app ):
         if isinstance( value, RuntimeValue ):
-            return { "__class__": "RuntimeValue" }
+            return { '__class__': 'RuntimeValue' }
+        elif isinstance( value, dict ):
+            if value.get('__class__') == 'RuntimeValue':
+                return value
         return self.to_string( value, app )
 
     def value_from_basic( self, value, app, ignore_errors=False ):
@@ -631,7 +634,7 @@ class FTPFileToolParameter( ToolParameter ):
             value = [ value ]
         lst = []
         for val in value:
-            if val is None:
+            if val in [ None, '' ]:
                 lst = []
                 break
             if isinstance( val, dict ):

static/maps/mvc/form/form-data.js.map

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static/maps/mvc/form/form-input.js.map

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static/maps/mvc/form/form-section.js.map

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static/maps/mvc/tools/tools-form-workflow.js.map

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static/maps/mvc/ui/ui-slider.js.map

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static/maps/utils/utils.js.map

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static/scripts/mvc/form/form-data.js

@@ -1,2 +1,2 @@
-define(["utils/utils"],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},checksum:function(){var a="",b=this;return this.app.section.$el.find(".section-row").each(function(){var c=$(this).attr("id"),d=b.app.field_list[c];d&&(a+=c+":"+JSON.stringify(d.value&&d.value())+";")}),a},create:function(){function a(a,b,d){c.map_dict[a]=b,e[a]=d}function b(d,e){for(var f in e){var g=e[f];if(g.input){var h=g.input,i=d;switch(""!=d&&(i+="|"),i+=h.name,h.type){case"repeat":var j="section-",k=[],l=null;for(var m in g){var n=m.indexOf(j);-1!=n&&(n+=j.length,k.push(parseInt(m.substr(n))),l||(l=m.substr(0,n)))}k.sort(function(a,b){return a-b});var f=0;for(var o in k)b(i+"_"+f++,g[l+k[o]]);break;case"conditional":var p=c.app.field_list[h.id].value();a(i+"|"+h.test_param.name,h.id,p);var q=c.matchCase(h,p);-1!=q&&b(i,e[h.id+"-section-"+q]);break;case"section":b(!h.flat&&i||"",g);break;default:var r=c.app.field_list[h.id];if(r&&r.value){var p=r.value();if((void 0===h.ignore||h.ignore!=p)&&(a(i,h.id,p),h.payload))for(var s in h.payload)a(s,h.id,h.payload[s])}}}}}var c=this,d={};this._iterate(this.app.section.$el,d);var e={};return this.map_dict={},b("",d),e},match:function(a){return this.map_dict&&this.map_dict[a]},matchCase:function(a,b){"boolean"==a.test_param.type&&(b="true"==b?a.test_param.truevalue||"true":a.test_param.falsevalue||"false");for(var c in a.cases)if(a.cases[c].value==b)return c;return-1},matchModel:function(a,b){function c(a,d){for(var f in d){var g=d[f],h=g.name;switch(""!=a&&(h=a+"|"+h),g.type){case"repeat":for(var i in g.cache)c(h+"_"+i,g.cache[i]);break;case"conditional":var j=g.test_param&&g.test_param.value,k=e.matchCase(g,j);-1!=k&&c(h,g.cases[k].inputs);break;case"section":c(h,g.inputs);break;default:var l=e.map_dict[h];l&&b(l,g)}}}var d={},e=this;return c("",a.inputs),d},matchResponse:function(a){function b(a,e){if("string"==typeof e){var f=d.map_dict[a];f&&(c[f]=e)}else for(var g in e){var h=g;if(""!==a){var i="|";e instanceof Array&&(i="_"),h=a+i+h}b(h,e[g])}}var c={},d=this;return b("",a),c},_iterate:function(a,b){var c=this,d=$(a).children();d.each(function(){var a=this,d=$(a).attr("id");if($(a).hasClass("section-row")){b[d]={};var e=c.app.input_list[d];e&&(b[d]={input:e}),c._iterate(a,b[d])}else c._iterate(a,b)})}})});
+define(["utils/utils"],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},checksum:function(){var a="",b=this;return this.app.section.$el.find(".section-row").each(function(){var c=$(this).attr("id"),d=b.app.field_list[c];d&&(a+=c+":"+JSON.stringify(d.value&&d.value())+":"+d.collapsed+";")}),a},create:function(){function a(a,b,d){c.map_dict[a]=b,e[a]=d}function b(d,e){for(var f in e){var g=e[f];if(g.input){var h=g.input,i=d;switch(""!=d&&(i+="|"),i+=h.name,h.type){case"repeat":var j="section-",k=[],l=null;for(var m in g){var n=m.indexOf(j);-1!=n&&(n+=j.length,k.push(parseInt(m.substr(n))),l||(l=m.substr(0,n)))}k.sort(function(a,b){return a-b});var f=0;for(var o in k)b(i+"_"+f++,g[l+k[o]]);break;case"conditional":var p=c.app.field_list[h.id].value();a(i+"|"+h.test_param.name,h.id,p);var q=c.matchCase(h,p);-1!=q&&b(i,e[h.id+"-section-"+q]);break;case"section":b(!h.flat&&i||"",g);break;default:var r=c.app.field_list[h.id];if(r&&r.value){var p=r.value();if((void 0===h.ignore||h.ignore!=p)&&(r.collapsed&&h.collapsible_value&&(p=h.collapsible_value),a(i,h.id,p),h.payload))for(var s in h.payload)a(s,h.id,h.payload[s])}}}}}var c=this,d={};this._iterate(this.app.section.$el,d);var e={};return this.map_dict={},b("",d),e},match:function(a){return this.map_dict&&this.map_dict[a]},matchCase:function(a,b){"boolean"==a.test_param.type&&(b="true"==b?a.test_param.truevalue||"true":a.test_param.falsevalue||"false");for(var c in a.cases)if(a.cases[c].value==b)return c;return-1},matchModel:function(a,b){function c(a,d){for(var f in d){var g=d[f],h=g.name;switch(""!=a&&(h=a+"|"+h),g.type){case"repeat":for(var i in g.cache)c(h+"_"+i,g.cache[i]);break;case"conditional":var j=g.test_param&&g.test_param.value,k=e.matchCase(g,j);-1!=k&&c(h,g.cases[k].inputs);break;case"section":c(h,g.inputs);break;default:var l=e.map_dict[h];l&&b(l,g)}}}var d={},e=this;return c("",a.inputs),d},matchResponse:function(a){function b(a,e){if("string"==typeof e){var f=d.map_dict[a];f&&(c[f]=e)}else for(var g in e){var h=g;if(""!==a){var i="|";e instanceof Array&&(i="_"),h=a+i+h}b(h,e[g])}}var c={},d=this;return b("",a),c},_iterate:function(a,b){var c=this,d=$(a).children();d.each(function(){var a=this,d=$(a).attr("id");if($(a).hasClass("section-row")){b[d]={};var e=c.app.input_list[d];e&&(b[d]={input:e}),c._iterate(a,b[d])}else c._iterate(a,b)})}})});
 //# sourceMappingURL=../../../maps/mvc/form/form-data.js.map

static/scripts/mvc/form/form-input.js

@@ -1,2 +1,2 @@
-define([],function(){return Backbone.View.extend({initialize:function(a,b){this.app=a,this.text_enable=a.options.text_enable||"Enable",this.text_disable=a.options.text_disable||"Disable",this.cls_enable=a.options.cls_enable||"fa fa-plus-square",this.cls_disable=a.options.cls_disable||"fa fa-minus-square",this.field=b.field,this.default_value=b.default_value,this.setElement(this._template(b)),this.$field=this.$el.find(".ui-table-form-field"),this.$optional=this.$el.find(".ui-table-form-optional"),this.$optional_icon=this.$el.find(".ui-table-form-optional").find(".icon"),this.$error_text=this.$el.find(".ui-table-form-error-text"),this.$error=this.$el.find(".ui-table-form-error"),this.$field.prepend(this.field.$el),this.field.skip=!1;var c=this.field.value&&this.field.value();this.field.skip=Boolean(b.collapsible&&(c===this.default_value||String(c)===String(this.default_value)||Number(c)===Number(this.default_value)||JSON.stringify(c)===JSON.stringify(this.default_value))),this._refresh();var d=this;this.$optional.on("click",function(){d.field.skip=!d.field.skip,d._refresh(),d.app.trigger("change")})},error:function(a){this.$error_text.html(a),this.$error.show(),this.$el.addClass("ui-error")},reset:function(){this.$error.hide(),this.$el.removeClass("ui-error")},_refresh:function(){this.$optional_icon.removeClass().addClass("icon"),this.field.skip?(this.$field.hide(),this._tooltip(this.text_enable,this.cls_enable),this.field.value&&this.field.value(this.default_value)):(this.$field.fadeIn("fast"),this._tooltip(this.text_disable,this.cls_disable))},_tooltip:function(a,b){this.$optional.length&&this.$optional_icon.addClass(b).tooltip({placement:"bottom"}).attr("data-original-title",a).tooltip("fixTitle").tooltip("hide")},_template:function(a){var b='<div class="ui-table-form-element"><div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"/></div><div class="ui-table-form-title">';return b+=a.collapsible?'<div class="ui-table-form-optional"><i class="icon"/>'+a.label+"</div>":a.label,b+='</div><div class="ui-table-form-field">',b+='<div class="ui-table-form-info">',a.help&&(b+=a.help),b+="</div>",b+="</div></div>"}})});
+define([],function(){return Backbone.View.extend({initialize:function(a,b){this.app=a,this.text_enable=a.options.text_enable||"Enable",this.text_disable=a.options.text_disable||"Disable",this.cls_enable=a.options.cls_enable||"fa fa-caret-square-o-down",this.cls_disable=a.options.cls_disable||"fa fa-caret-square-o-up",this.field=b.field,this.default_value=b.default_value,this.setElement(this._template(b)),this.$field=this.$el.find(".ui-table-form-field"),this.$optional=this.$el.find(".ui-table-form-optional"),this.$optional_icon=this.$el.find(".ui-table-form-optional").find(".icon"),this.$error_text=this.$el.find(".ui-table-form-error-text"),this.$error=this.$el.find(".ui-table-form-error"),this.$field.prepend(this.field.$el),this.field.collapsed=b.collapsible&&b.value&&JSON.stringify(b.value)==JSON.stringify(b.collapsible_value),this._refresh();var c=this;this.$optional.on("click",function(){c.field.collapsed=!c.field.collapsed,c._refresh(),c.app.trigger("change")})},error:function(a){this.$error_text.html(a),this.$error.show(),this.$el.addClass("ui-error")},reset:function(){this.$error.hide(),this.$el.removeClass("ui-error")},_refresh:function(){this.$optional_icon.removeClass().addClass("icon"),this.field.collapsed?(this.$field.hide(),this._tooltip(this.text_enable,this.cls_enable),this.field.value&&this.field.value(this.default_value)):(this.$field.fadeIn("fast"),this._tooltip(this.text_disable,this.cls_disable),this.app.trigger("change"))},_tooltip:function(a,b){this.$optional.length&&this.$optional_icon.addClass(b).tooltip({placement:"bottom"}).attr("data-original-title",a).tooltip("fixTitle").tooltip("hide")},_template:function(a){var b='<div class="ui-table-form-element"><div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"/></div><div class="ui-table-form-title">';return b+=a.collapsible?'<div class="ui-table-form-optional"><i class="icon"/>'+a.label+"</div>":a.label,b+='</div><div class="ui-table-form-field">',b+='<div class="ui-table-form-info">',a.help&&(b+=a.help),b+="</div>",b+="</div></div>"}})});
 //# sourceMappingURL=../../../maps/mvc/form/form-input.js.map

static/scripts/mvc/form/form-section.js

@@ -1,2 +1,2 @@
-define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/ui/ui-portlet","mvc/form/form-repeat","mvc/form/form-input","mvc/form/form-parameters"],function(a,b,c,d,e,f,g){var h=Backbone.View.extend({initialize:function(a,c){this.app=a,this.inputs=c.inputs,c.cls="ui-table-plain",c.cls_tr="section-row",this.table=new b.View(c),this.parameters=new g(a,c),this.setElement(this.table.$el),this.render()},render:function(){this.table.delAll();for(var a in this.inputs)this.add(this.inputs[a])},add:function(b){var c=jQuery.extend(!0,{},b);c.id=b.id=a.uid(),this.app.input_list[c.id]=c;var d=c.type;switch(d){case"conditional":this._addConditional(c);break;case"repeat":this._addRepeat(c);break;case"section":this._addSection(c);break;default:this._addRow(c)}},_addConditional:function(a){var b=this;a.test_param.id=a.id;var c=this._addRow(a.test_param);c.options.onchange=function(c){var d=b.app.data.matchCase(a,c);for(var e in a.cases){var f=a.cases[e],g=a.id+"-section-"+e,h=b.table.get(g),i=!1;for(var j in f.inputs)if(!f.inputs[j].hidden){i=!0;break}e==d&&i?h.fadeIn("fast"):h.hide()}b.app.trigger("change")};for(var d in a.cases){var e=a.id+"-section-"+d,f=new h(this.app,{inputs:a.cases[d].inputs});f.$el.addClass("ui-table-section"),this.table.add(f.$el),this.table.append(e)}c.trigger("change")},_addRepeat:function(a){function b(b){var e=a.id+"-section-"+d++,f=new h(c.app,{inputs:b});g.add({id:e,$el:f.$el,ondel:function(){g.del(e),c.app.trigger("change")}})}for(var c=this,d=0,g=new e.View({title:a.title,title_new:a.title,min:a.min,max:a.max,onnew:function(){b(a.inputs),c.app.trigger("change")}}),i=a.min,j=_.size(a.cache),k=0;k<Math.max(j,i);k++){var l=null;l=j>k?a.cache[k]:a.inputs,b(l)}var m=new f(this.app,{label:a.title,help:a.help,field:g});this.table.add(m.$el),this.table.append(a.id)},_addSection:function(a){var b=this,e=new h(b.app,{inputs:a.inputs}),f=new c.ButtonIcon({icon:"fa-eye-slash",tooltip:"Show/hide section",cls:"ui-button-icon-plain"}),g=new d.View({title:a.title,cls:"ui-portlet-section",operations:{button_visible:f}});g.append(e.$el),g.append($("<div/>").addClass("ui-table-form-info").html(a.help));var i=!1;g.$content.hide(),g.$header.css("cursor","pointer"),g.$header.on("click",function(){i?(i=!1,g.$content.hide(),f.setIcon("fa-eye-slash")):(i=!0,g.$content.fadeIn("fast"),f.setIcon("fa-eye"))}),this.app.on("expand",function(a){g.$el.find("#"+a).length>0&&!i&&g.$header.trigger("click")}),a.expanded&&g.$header.trigger("click"),this.table.add(g.$el),this.table.append(a.id)},_addRow:function(a){var b=a.id,c=this.parameters.create(a);this.app.field_list[b]=c;var d=new f(this.app,{label:a.label||a.name,default_value:a.default_value,collapsible:a.collapsible,help:a.help,field:c});return this.app.element_list[b]=d,this.table.add(d.$el),this.table.append(b),a.hidden&&this.table.get(b).hide(),c}});return{View:h}});
+define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/ui/ui-portlet","mvc/form/form-repeat","mvc/form/form-input","mvc/form/form-parameters"],function(a,b,c,d,e,f,g){var h=Backbone.View.extend({initialize:function(a,c){this.app=a,this.inputs=c.inputs,c.cls="ui-table-plain",c.cls_tr="section-row",this.table=new b.View(c),this.parameters=new g(a,c),this.setElement(this.table.$el),this.render()},render:function(){this.table.delAll();for(var a in this.inputs)this.add(this.inputs[a])},add:function(b){var c=jQuery.extend(!0,{},b);c.id=b.id=a.uid(),this.app.input_list[c.id]=c;var d=c.type;switch(d){case"conditional":this._addConditional(c);break;case"repeat":this._addRepeat(c);break;case"section":this._addSection(c);break;default:this._addRow(c)}},_addConditional:function(a){var b=this;a.test_param.id=a.id;var c=this._addRow(a.test_param);c.options.onchange=function(c){var d=b.app.data.matchCase(a,c);for(var e in a.cases){var f=a.cases[e],g=a.id+"-section-"+e,h=b.table.get(g),i=!1;for(var j in f.inputs)if(!f.inputs[j].hidden){i=!0;break}e==d&&i?h.fadeIn("fast"):h.hide()}b.app.trigger("change")};for(var d in a.cases){var e=a.id+"-section-"+d,f=new h(this.app,{inputs:a.cases[d].inputs});f.$el.addClass("ui-table-section"),this.table.add(f.$el),this.table.append(e)}c.trigger("change")},_addRepeat:function(a){function b(b){var e=a.id+"-section-"+d++,f=new h(c.app,{inputs:b});g.add({id:e,$el:f.$el,ondel:function(){g.del(e),c.app.trigger("change")}})}for(var c=this,d=0,g=new e.View({title:a.title,title_new:a.title,min:a.min,max:a.max,onnew:function(){b(a.inputs),c.app.trigger("change")}}),i=a.min,j=_.size(a.cache),k=0;k<Math.max(j,i);k++){var l=null;l=j>k?a.cache[k]:a.inputs,b(l)}var m=new f(this.app,{label:a.title,help:a.help,field:g});this.table.add(m.$el),this.table.append(a.id)},_addSection:function(a){var b=this,e=new h(b.app,{inputs:a.inputs}),f=new c.ButtonIcon({icon:"fa-eye-slash",tooltip:"Show/hide section",cls:"ui-button-icon-plain"}),g=new d.View({title:a.title,cls:"ui-portlet-section",operations:{button_visible:f}});g.append(e.$el),g.append($("<div/>").addClass("ui-table-form-info").html(a.help));var i=!1;g.$content.hide(),g.$header.css("cursor","pointer"),g.$header.on("click",function(){i?(i=!1,g.$content.hide(),f.setIcon("fa-eye-slash")):(i=!0,g.$content.fadeIn("fast"),f.setIcon("fa-eye"))}),this.app.on("expand",function(a){g.$el.find("#"+a).length>0&&!i&&g.$header.trigger("click")}),a.expanded&&g.$header.trigger("click"),this.table.add(g.$el),this.table.append(a.id)},_addRow:function(a){var b=a.id,c=this.parameters.create(a);this.app.field_list[b]=c;var d=new f(this.app,{label:a.label||a.name,value:a.value,default_value:a.default_value,collapsible:a.collapsible,collapsible_value:a.collapsible_value,help:a.help,field:c});return this.app.element_list[b]=d,this.table.add(d.$el),this.table.append(b),a.hidden&&this.table.get(b).hide(),c}});return{View:h}});
 //# sourceMappingURL=../../../maps/mvc/form/form-section.js.map

static/scripts/mvc/tools/tools-form-base.js

@@ -1,2 +1,2 @@
-define(["utils/utils","utils/deferred","mvc/ui/ui-misc","mvc/form/form-view","mvc/tools/tools-template","mvc/citation/citation-model","mvc/citation/citation-view"],function(a,b,c,d,e,f,g){return Backbone.View.extend({initialize:function(a){var c=parent.Galaxy;this.is_admin=c&&c.currUser?c.currUser.get("is_admin"):!1,this.deferred=new b,this.setElement("<div/>"),this.container=a.container||"body",$(this.container).append(this.$el),this._buildForm(a)},_buildForm:function(b){var c=this;this.options=a.merge(b,this.options),this.options=a.merge({icon:"fa-wrench",title:"<b>"+b.name+"</b> "+b.description+" (Galaxy Tool Version "+b.version+")",operations:this._operations(),onchange:function(){c.deferred.reset(),c.deferred.execute(function(){c._updateModel()})}},this.options),this.form=new d(this.options),this._footer(),this.$el.empty(),this.$el.append(this.form.$el)},_buildModel:function(b){var c=this;this.options.id=b.id,this.options.version=b.version;var d=galaxy_config.root+"api/tools/"+b.id+"/build?";if(b.job_id)d+="job_id="+b.job_id;else if(b.dataset_id)d+="dataset_id="+b.dataset_id;else{d+="tool_version="+b.version+"&";var e=top.location.href,f=e.indexOf("?");-1!=e.indexOf("tool_id=")&&-1!==f&&(d+=e.slice(f+1))}var g=this.deferred.register();a.request({type:"GET",url:d,success:function(a){c._buildForm(a.tool_model||a),c.form.message.update({status:"success",message:"Now you are using '"+c.options.name+"' version "+c.options.version+".",persistent:!1}),c.deferred.done(g),console.debug("tools-form::initialize() - Initial tool model ready."),console.debug(a)},error:function(a){c.deferred.done(g),console.debug("tools-form::initialize() - Initial tool model request failed."),console.debug(a);var b=a.error||"Uncaught error.";c.form.modal.show({title:"Tool cannot be executed",body:b,buttons:{Close:function(){c.form.modal.hide()}}})}})},_updateModel:function(){var b=this.options.update_url||galaxy_config.root+"api/tools/"+this.options.id+"/build",c=this,d=this.form,e={tool_id:this.options.id,tool_version:this.options.version,inputs:$.extend(!0,{},c.form.data.create())};d.wait(!0);var f=this.deferred.register();console.debug("tools-form-base::_updateModel() - Sending current state (see below)."),console.debug(e),a.request({type:"POST",url:b,data:e,success:function(a){c.form.update(a.tool_model||a),c.options.update&&c.options.update(a),d.wait(!1),console.debug("tools-form-base::_updateModel() - Received new model (see below)."),console.debug(a),c.deferred.done(f)},error:function(a){c.deferred.done(f),console.debug("tools-form-base::_updateModel() - Refresh request failed."),console.debug(a)}})},_operations:function(){var a=this,b=this.options,d=new c.ButtonMenu({icon:"fa-cubes",title:!b.narrow&&"Versions"||null,tooltip:"Select another tool version"});if(b.versions&&b.versions.length>1)for(var f in b.versions){var g=b.versions[f];g!=b.version&&d.addMenu({title:"Switch to "+g,version:g,icon:"fa-cube",onclick:function(){var c=b.id.replace(b.version,this.version),d=this.version;a.deferred.reset(),a.deferred.execute(function(){a._buildModel({id:c,version:d})})}})}else d.$el.hide();var h=new c.ButtonMenu({icon:"fa-caret-down",title:!b.narrow&&"Options"||null,tooltip:"View available options"});return b.biostar_url&&(h.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/p/new/post/")}}),h.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/local/search/page/?q="+b.name)}})),h.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+b.id)}}),this.is_admin&&h.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+b.id+"/download"}}),b.requirements&&b.requirements.length>0&&h.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){this.visible?(this.visible=!1,a.form.message.update({message:""})):(this.visible=!0,a.form.message.update({persistent:!0,message:e.requirements(b),status:"info"}))}}),b.sharable_url&&h.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(b.sharable_url)}}),{menu:h,versions:d}},_footer:function(){var a=this.options;if(""!=a.help&&this.form.$el.append(e.help(a)),a.citations){var b=$("<div/>"),c=new f.ToolCitationCollection;c.tool_id=a.id;var d=new g.CitationListView({el:b,collection:c});d.render(),c.fetch(),this.form.$el.append(b)}}})});
+define(["utils/utils","utils/deferred","mvc/ui/ui-misc","mvc/form/form-view","mvc/tools/tools-template","mvc/citation/citation-model","mvc/citation/citation-view"],function(a,b,c,d,e,f,g){return Backbone.View.extend({initialize:function(a){var c=parent.Galaxy;this.is_admin=c&&c.currUser?c.currUser.get("is_admin"):!1,this.deferred=new b,this.setElement("<div/>"),this._buildForm(a)},_buildForm:function(b){var c=this;this.options=a.merge(b,this.options),this.options=a.merge({icon:"fa-wrench",title:"<b>"+b.name+"</b> "+b.description+" (Galaxy Tool Version "+b.version+")",operations:this._operations(),onchange:function(){c.deferred.reset(),c.deferred.execute(function(){c._updateModel()})}},this.options),this.form=new d(this.options),this._footer(),this.$el.empty(),this.$el.append(this.form.$el)},_buildModel:function(b){var c=this;this.options.id=b.id,this.options.version=b.version;var d=galaxy_config.root+"api/tools/"+b.id+"/build?";if(b.job_id)d+="job_id="+b.job_id;else if(b.dataset_id)d+="dataset_id="+b.dataset_id;else{d+="tool_version="+b.version+"&";var e=top.location.href,f=e.indexOf("?");-1!=e.indexOf("tool_id=")&&-1!==f&&(d+=e.slice(f+1))}var g=this.deferred.register();a.request({type:"GET",url:d,success:function(a){c._buildForm(a.tool_model||a),c.form.message.update({status:"success",message:"Now you are using '"+c.options.name+"' version "+c.options.version+".",persistent:!1}),c.deferred.done(g),console.debug("tools-form::initialize() - Initial tool model ready."),console.debug(a)},error:function(a){c.deferred.done(g),console.debug("tools-form::initialize() - Initial tool model request failed."),console.debug(a);var b=a.error||"Uncaught error.";c.form.modal.show({title:"Tool cannot be executed",body:b,buttons:{Close:function(){c.form.modal.hide()}}})}})},_updateModel:function(){var b=this.options.update_url||galaxy_config.root+"api/tools/"+this.options.id+"/build",c=this,d=this.form,e={tool_id:this.options.id,tool_version:this.options.version,inputs:$.extend(!0,{},c.form.data.create())};d.wait(!0);var f=this.deferred.register();console.debug("tools-form-base::_updateModel() - Sending current state (see below)."),console.debug(e),a.request({type:"POST",url:b,data:e,success:function(a){c.form.update(a.tool_model||a),c.options.update&&c.options.update(a),d.wait(!1),console.debug("tools-form-base::_updateModel() - Received new model (see below)."),console.debug(a),c.deferred.done(f)},error:function(a){c.deferred.done(f),console.debug("tools-form-base::_updateModel() - Refresh request failed."),console.debug(a)}})},_operations:function(){var a=this,b=this.options,d=new c.ButtonMenu({icon:"fa-cubes",title:!b.narrow&&"Versions"||null,tooltip:"Select another tool version"});if(b.versions&&b.versions.length>1)for(var f in b.versions){var g=b.versions[f];g!=b.version&&d.addMenu({title:"Switch to "+g,version:g,icon:"fa-cube",onclick:function(){var c=b.id.replace(b.version,this.version),d=this.version;a.deferred.reset(),a.deferred.execute(function(){a._buildModel({id:c,version:d})})}})}else d.$el.hide();var h=new c.ButtonMenu({icon:"fa-caret-down",title:!b.narrow&&"Options"||null,tooltip:"View available options"});return b.biostar_url&&(h.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/p/new/post/")}}),h.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/local/search/page/?q="+b.name)}})),h.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+b.id)}}),this.is_admin&&h.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+b.id+"/download"}}),b.requirements&&b.requirements.length>0&&h.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){this.visible?(this.visible=!1,a.form.message.update({message:""})):(this.visible=!0,a.form.message.update({persistent:!0,message:e.requirements(b),status:"info"}))}}),b.sharable_url&&h.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(b.sharable_url)}}),{menu:h,versions:d}},_footer:function(){var a=this.options;if(""!=a.help&&this.form.$el.append(e.help(a)),a.citations){var b=$("<div/>"),c=new f.ToolCitationCollection;c.tool_id=a.id;var d=new g.CitationListView({el:b,collection:c});d.render(),c.fetch(),this.form.$el.append(b)}}})});
 //# sourceMappingURL=../../../maps/mvc/tools/tools-form-base.js.map

static/scripts/mvc/tools/tools-form-workflow.js

@@ -1,2 +1,2 @@
-define(["utils/utils","mvc/tools/tools-form-base"],function(a,b){var c=b.extend({initialize:function(c){if(this.node=workflow.active_node,!this.node)return void console.debug("FAILED - tools-form-workflow:initialize() - Node not found in workflow.");this.post_job_actions=this.node.post_job_actions||{},c=a.merge(c,{text_enable:"Set in Advance",text_disable:"Set at Runtime",is_workflow:!0,narrow:!0,initial_errors:!0,cls:"ui-portlet-narrow",update_url:galaxy_config.root+"api/workflows/build_module",update:function(a){d.node.update_field_data(a),d.form.errors(a&&a.tool_model)}}),a.deepeach(c.inputs,function(a){a.type&&("conditional"==a.type?a.test_param.collapsible=!1:-1==["data","data_collection"].indexOf(a.type)&&(a.collapsible=!0))});var d=this;a.get({url:galaxy_config.root+"api/datatypes",cache:!0,success:function(a){d.datatypes=a,d._makeSections(c.inputs),b.prototype.initialize.call(d,c)}})},_makeSections:function(b){b[a.uid()]={label:"Annotation / Notes",name:"annotation",type:"text",area:!0,help:"Add an annotation or note for this step. It will be shown with the workflow.",value:this.node.annotation};var c=this.node.output_terminals&&Object.keys(this.node.output_terminals)[0];if(c){b[a.uid()]={name:"pja__"+c+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(this.post_job_actions["EmailAction"+c])),ignore:"false",help:"An email notification will be send when the job has completed.",payload:{host:window.location.host}},b[a.uid()]={name:"pja__"+c+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(this.post_job_actions["DeleteIntermediatesAction"+c])),ignore:"false",help:"Delete intermediate outputs if they are not used as input for another job."};for(var d in this.node.output_terminals)b[a.uid()]=this._makeSection(d)}},_makeSection:function(a){function b(c,d){d=d||[],d.push(c);for(var f in c.inputs){var g=c.inputs[f];if(g.action){if(g.name="pja__"+a+"__"+g.action,g.argument&&(g.name+="__"+g.argument),g.payload)for(var h in g.payload){var i=g.payload[h];g.payload[g.name+"__"+h]=i,delete i}var j=e.post_job_actions[g.action+a];if(j){for(var k in d)d[k].expanded=!0;g.value=g.argument?j.action_arguments&&j.action_arguments[g.argument]||g.value:"true"}}g.inputs&&b(g,d.slice(0))}}var c=[];for(key in this.datatypes)c.push({0:this.datatypes[key],1:this.datatypes[key]});c.sort(function(a,b){return a.label>b.label?1:a.label<b.label?-1:0}),c.unshift({0:"Sequences",1:"Sequences"}),c.unshift({0:"Roadmaps",1:"Roadmaps"}),c.unshift({0:"Leave unchanged",1:"__empty__"});var d={title:"Add Actions: '"+a+"'",type:"section",flat:!0,inputs:[{action:"RenameDatasetAction",argument:"newname",label:"Rename dataset",type:"text",value:"",ignore:"",help:'This action will rename the result dataset. Click <a href="https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/Variables">here</a> for more information.'},{action:"ChangeDatatypeAction",argument:"newtype",label:"Change datatype",type:"select",ignore:"__empty__",value:"__empty__",options:c,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",argument:"tags",label:"Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{title:"Assign columns",type:"section",flat:!0,inputs:[{action:"ColumnSetAction",argument:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]},e=this;return b(d),d}});return{View:c}});
+define(["utils/utils","mvc/tools/tools-form-base"],function(a,b){var c=b.extend({initialize:function(c){var d=this;return this.node=workflow.active_node,this.node?(this.post_job_actions=this.node.post_job_actions||{},c=a.merge(c,{text_enable:"Set in Advance",text_disable:"Set at Runtime",is_workflow:!0,narrow:!0,initial_errors:!0,cls:"ui-portlet-narrow",update_url:galaxy_config.root+"api/workflows/build_module",update:function(a){d.node.update_field_data(a),d.form.errors(a&&a.tool_model)}}),a.deepeach(c.inputs,function(a){a.type&&-1==["data","data_collection"].indexOf(a.type)&&(a.collapsible=!0,a.collapsible_value={__class__:"RuntimeValue"})}),a.deepeach(c.inputs,function(a){a.type&&"conditional"==a.type&&(a.test_param.collapsible=!1)}),this._makeSections(c),void b.prototype.initialize.call(this,c)):void console.debug("FAILED - tools-form-workflow:initialize() - Node not found in workflow.")},_makeSections:function(b){var c=b.inputs,d=b.datatypes;c[a.uid()]={label:"Annotation / Notes",name:"annotation",type:"text",area:!0,help:"Add an annotation or note for this step. It will be shown with the workflow.",value:this.node.annotation};var e=this.node.output_terminals&&Object.keys(this.node.output_terminals)[0];if(e){c[a.uid()]={name:"pja__"+e+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(this.post_job_actions["EmailAction"+e])),ignore:"false",help:"An email notification will be send when the job has completed.",payload:{host:window.location.host}},c[a.uid()]={name:"pja__"+e+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(this.post_job_actions["DeleteIntermediatesAction"+e])),ignore:"false",help:"Delete intermediate outputs if they are not used as input for another job."};for(var f in this.node.output_terminals)c[a.uid()]=this._makeSection(f,d)}},_makeSection:function(a,b){function c(b,d){d=d||[],d.push(b);for(var e in b.inputs){var g=b.inputs[e];if(g.action){if(g.name="pja__"+a+"__"+g.action,g.argument&&(g.name+="__"+g.argument),g.payload)for(var h in g.payload){var i=g.payload[h];g.payload[g.name+"__"+h]=i,delete i}var j=f.post_job_actions[g.action+a];if(j){for(var k in d)d[k].expanded=!0;g.value=g.argument?j.action_arguments&&j.action_arguments[g.argument]||g.value:"true"}}g.inputs&&c(g,d.slice(0))}}var d=[];for(key in b)d.push({0:b[key],1:b[key]});d.sort(function(a,b){return a.label>b.label?1:a.label<b.label?-1:0}),d.unshift({0:"Sequences",1:"Sequences"}),d.unshift({0:"Roadmaps",1:"Roadmaps"}),d.unshift({0:"Leave unchanged",1:"__empty__"});var e={title:"Add Actions: '"+a+"'",type:"section",flat:!0,inputs:[{action:"RenameDatasetAction",argument:"newname",label:"Rename dataset",type:"text",value:"",ignore:"",help:'This action will rename the result dataset. Click <a href="https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/Variables">here</a> for more information.'},{action:"ChangeDatatypeAction",argument:"newtype",label:"Change datatype",type:"select",ignore:"__empty__",value:"__empty__",options:d,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",argument:"tags",label:"Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{title:"Assign columns",type:"section",flat:!0,inputs:[{action:"ColumnSetAction",argument:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]},f=this;return c(e),e}});return{View:c}});
 //# sourceMappingURL=../../../maps/mvc/tools/tools-form-workflow.js.map

static/scripts/mvc/ui/ui-slider.js

@@ -1,2 +1,2 @@
-define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:a.uid(),min:null,max:null,step:null,precise:!1,split:1e4},initialize:function(b){var c=this;this.options=a.merge(b,this.optionsDefault),this.setElement(this._template(this.options)),this.useslider=null!==this.options.max&&null!==this.options.min&&this.options.max>this.options.min,null===this.options.step&&(this.options.step=1,this.options.precise&&this.useslider&&(this.options.step=(this.options.max-this.options.min)/this.options.split)),this.useslider?(this.$slider=this.$el.find("#slider"),this.$slider.slider(this.options),this.$slider.on("slide",function(a,b){c.value(b.value)})):this.$el.find(".ui-form-slider-text").css("width","100%"),this.$text=this.$el.find("#text"),void 0!==this.options.value&&this.value(this.options.value),this.$text.on("change",function(){c.value($(this).val())});var d=[];this.$text.on("keyup",function(a){d[a.which]=!1}),this.$text.on("keydown",function(a){var b=a.which;d[b]=!0,8==b||9==b||13==b||37==b||39==b||b>=48&&57>=b||190==b&&-1==$(this).val().indexOf(".")&&c.options.precise||189==b&&-1==$(this).val().indexOf("-")||d[91]||d[17]||event.preventDefault()})},value:function(a){return void 0!==a&&(null!==a&&""!==a&&(isNaN(a)&&(a=0),null!==this.options.max&&(a=Math.min(a,this.options.max)),null!==this.options.min&&(a=Math.max(a,this.options.min))),this.$slider&&this.$slider.slider("value",a),this.$text.val(a),this.options.onchange&&this.options.onchange(a)),this.$text.val()},_template:function(a){return'<div id="'+a.id+'" class="ui-form-slider"><input id="text" type="text" class="ui-form-slider-text"/><div id="slider" class="ui-form-slider-element"/></div>'}});return{View:b}});
+define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:a.uid(),min:null,max:null,step:null,precise:!1,split:1e4},initialize:function(b){var c=this;this.options=a.merge(b,this.optionsDefault),this.setElement(this._template(this.options)),this.useslider=null!==this.options.max&&null!==this.options.min&&this.options.max>this.options.min,null===this.options.step&&(this.options.step=1,this.options.precise&&this.useslider&&(this.options.step=(this.options.max-this.options.min)/this.options.split)),this.useslider?(this.$slider=this.$el.find("#slider"),this.$slider.slider(this.options),this.$slider.on("slide",function(a,b){c.value(b.value)})):this.$el.find(".ui-form-slider-text").css("width","100%"),this.$text=this.$el.find("#text"),void 0!==this.options.value&&this.value(this.options.value),this.$text.on("change",function(){c.value($(this).val())});var d=[];this.$text.on("keyup",function(a){d[a.which]=!1,c.options.onchange&&c.options.onchange($(this).val())}),this.$text.on("keydown",function(a){var b=a.which;d[b]=!0,8==b||9==b||13==b||37==b||39==b||b>=48&&57>=b||190==b&&-1==$(this).val().indexOf(".")&&c.options.precise||189==b&&-1==$(this).val().indexOf("-")||d[91]||d[17]||event.preventDefault()})},value:function(a){return void 0!==a&&(null!==a&&""!==a&&(isNaN(a)&&(a=0),null!==this.options.max&&(a=Math.min(a,this.options.max)),null!==this.options.min&&(a=Math.max(a,this.options.min))),this.$slider&&this.$slider.slider("value",a),this.$text.val(a),this.options.onchange&&this.options.onchange(a)),this.$text.val()},_template:function(a){return'<div id="'+a.id+'" class="ui-form-slider"><input id="text" type="text" class="ui-form-slider-text"/><div id="slider" class="ui-form-slider-element"/></div>'}});return{View:b}});
 //# sourceMappingURL=../../../maps/mvc/ui/ui-slider.js.map

static/scripts/utils/utils.js

@@ -1,2 +1,2 @@
-define(["libs/underscore"],function(a){function b(a,c){for(var d in a){var e=a[d];e&&"object"==typeof e&&(c(e),b(e,c))}}function c(a){return $("<div/>").text(a).html()}function d(a){if(a instanceof Array||(a=[a]),0===a.length)return!1;for(var b in a)if(["__null__","__undefined__",null,void 0].indexOf(a[b])>-1)return!1;return!0}function e(a){var a=a.toString();if(a){a=a.replace(/,/g,", ");var b=a.lastIndexOf(", ");return-1!=b&&(a=a.substr(0,b)+" or "+a.substr(b+1)),a}return""}function f(a){top.__utils__get__=top.__utils__get__||{},a.cache&&top.__utils__get__[a.url]?(a.success&&a.success(top.__utils__get__[a.url]),console.debug("utils.js::get() - Fetching from cache ["+a.url+"].")):g({url:a.url,data:a.data,success:function(b){top.__utils__get__[a.url]=b,a.success&&a.success(b)},error:function(b){a.error&&a.error(b)}})}function g(a){var b={contentType:"application/json",type:a.type||"GET",data:a.data||{},url:a.url};"GET"==b.type||"DELETE"==b.type?(b.url+=-1==b.url.indexOf("?")?"?":"&",b.url=b.url+$.param(b.data,!0),b.data=null):(b.dataType="json",b.url=b.url,b.data=JSON.stringify(b.data)),$.ajax(b).done(function(b){if("string"==typeof b)try{b=b.replace("Infinity,",'"Infinity",'),b=jQuery.parseJSON(b)}catch(c){console.debug(c)}a.success&&a.success(b)}).fail(function(b){var c=null;try{c=jQuery.parseJSON(b.responseText)}catch(d){c=b.responseText}a.error&&a.error(c,b)})}function h(a,b){var c=$('<div class="'+a+'"></div>');c.appendTo(":eq(0)");var d=c.css(b);return c.remove(),d}function i(a){$('link[href^="'+a+'"]').length||$('<link href="'+galaxy_config.root+a+'" rel="stylesheet">').appendTo("head")}function j(b,c){return b?a.defaults(b,c):c}function k(a,b){var c="";if(a>=1e11)a/=1e11,c="TB";else if(a>=1e8)a/=1e8,c="GB";else if(a>=1e5)a/=1e5,c="MB";else if(a>=100)a/=100,c="KB";else{if(!(a>0))return"<strong>-</strong>";a=10*a,c="b"}var d=Math.round(a)/10;return b?d+" "+c:"<strong>"+d+"</strong> "+c}function l(){return top.__utils__uid__=top.__utils__uid__||0,"uid-"+top.__utils__uid__++}function m(){var a=new Date,b=(a.getHours()<10?"0":"")+a.getHours(),c=(a.getMinutes()<10?"0":"")+a.getMinutes(),d=a.getDate()+"/"+(a.getMonth()+1)+"/"+a.getFullYear()+", "+b+":"+c;return d}return{cssLoadFile:i,cssGetAttribute:h,get:f,merge:j,bytesToString:k,uid:l,time:m,request:g,sanitize:c,textify:e,validate:d,deepeach:b}});
+define(["libs/underscore"],function(a){function b(a,c){for(var d in a){var e=a[d];e&&"object"==typeof e&&(c(e),b(e,c))}}function c(a){return/^[\],:{}\s]*$/.test(a.replace(/\\["\\\/bfnrtu]/g,"@").replace(/"[^"\\\n\r]*"|true|false|null|-?\d+(?:\.\d*)?(?:[eE][+\-]?\d+)?/g,"]").replace(/(?:^|:|,)(?:\s*\[)+/g,""))}function d(a){return $("<div/>").text(a).html()}function e(a){if(a instanceof Array||(a=[a]),0===a.length)return!1;for(var b in a)if(["__null__","__undefined__",null,void 0].indexOf(a[b])>-1)return!1;return!0}function f(a){var a=a.toString();if(a){a=a.replace(/,/g,", ");var b=a.lastIndexOf(", ");return-1!=b&&(a=a.substr(0,b)+" or "+a.substr(b+1)),a}return""}function g(a){top.__utils__get__=top.__utils__get__||{},a.cache&&top.__utils__get__[a.url]?(a.success&&a.success(top.__utils__get__[a.url]),console.debug("utils.js::get() - Fetching from cache ["+a.url+"].")):h({url:a.url,data:a.data,success:function(b){top.__utils__get__[a.url]=b,a.success&&a.success(b)},error:function(b){a.error&&a.error(b)}})}function h(a){var b={contentType:"application/json",type:a.type||"GET",data:a.data||{},url:a.url};"GET"==b.type||"DELETE"==b.type?(b.url+=-1==b.url.indexOf("?")?"?":"&",b.url=b.url+$.param(b.data,!0),b.data=null):(b.dataType="json",b.url=b.url,b.data=JSON.stringify(b.data)),$.ajax(b).done(function(b){if("string"==typeof b)try{b=b.replace("Infinity,",'"Infinity",'),b=jQuery.parseJSON(b)}catch(c){console.debug(c)}a.success&&a.success(b)}).fail(function(b){var c=null;try{c=jQuery.parseJSON(b.responseText)}catch(d){c=b.responseText}a.error&&a.error(c,b)})}function i(a,b){var c=$('<div class="'+a+'"></div>');c.appendTo(":eq(0)");var d=c.css(b);return c.remove(),d}function j(a){$('link[href^="'+a+'"]').length||$('<link href="'+galaxy_config.root+a+'" rel="stylesheet">').appendTo("head")}function k(b,c){return b?a.defaults(b,c):c}function l(a,b){var c="";if(a>=1e11)a/=1e11,c="TB";else if(a>=1e8)a/=1e8,c="GB";else if(a>=1e5)a/=1e5,c="MB";else if(a>=100)a/=100,c="KB";else{if(!(a>0))return"<strong>-</strong>";a=10*a,c="b"}var d=Math.round(a)/10;return b?d+" "+c:"<strong>"+d+"</strong> "+c}function m(){return top.__utils__uid__=top.__utils__uid__||0,"uid-"+top.__utils__uid__++}function n(){var a=new Date,b=(a.getHours()<10?"0":"")+a.getHours(),c=(a.getMinutes()<10?"0":"")+a.getMinutes(),d=a.getDate()+"/"+(a.getMonth()+1)+"/"+a.getFullYear()+", "+b+":"+c;return d}return{cssLoadFile:j,cssGetAttribute:i,get:g,merge:k,bytesToString:l,uid:m,time:n,request:h,sanitize:d,textify:f,validate:e,deepeach:b,isJSON:c}});
 //# sourceMappingURL=../../maps/utils/utils.js.map

templates/webapps/galaxy/tool_form.mako

@@ -22,6 +22,7 @@ ${h.css('base', 'jquery-ui/smoothness/jquery-ui')}
         require(['mvc/tools/tools-form'], function(ToolsForm){
             $(function(){
                 var form = new ToolsForm.View(${ h.dumps(self.form_config) });
+                $('body').append(form.$el);
             });
         });
     </script>

templates/webapps/galaxy/workflow/editor.mako

@@ -14,16 +14,17 @@
     <!--[if lt IE 9]>
       <script type='text/javascript' src="${h.url_for('/static/scripts/libs/IE/excanvas.js')}"></script>
     <![endif]-->
-
     ${h.js( "libs/jquery/jquery.event.drag",
             "libs/jquery/jquery.event.drop",
             "libs/jquery/jquery.event.hover",
             "libs/jquery/jquery.form",
             "libs/jquery/jstorage",
+            "libs/jquery/jquery-ui",
             "galaxy.workflow_editor.canvas",
             "libs/jquery/jquery.autocomplete",
             "galaxy.autocom_tagging",
-            "galaxy.workflows" )}
+            "galaxy.workflows",
+            "libs/bibtex" )}
 
     <!--[if lt IE 7]>
     <script type='text/javascript'>
@@ -33,7 +34,7 @@
 
     <script type='text/javascript'>
         // Switch for new tool form
-        %if util.string_as_bool(trans.app.config.get('workflow_toolform_upgrade',  False)):
+        %if util.string_as_bool(trans.app.config.get('workflow_toolform_upgrade',  True)):
         __NEWTOOLFORM__ = true;
         %endif
         
@@ -74,7 +75,7 @@
 <%def name="stylesheets()">
 
     ## Include "base.css" for styling tool menu and forms (details)
-    ${h.css( "base", "autocomplete_tagging", "tool_menu" )}
+    ${h.css( "base", "autocomplete_tagging", "tool_menu", "jquery-ui/smoothness/jquery-ui" )}
 
     ## But make sure styles for the layout take precedence
     ${parent.stylesheets()}

templates/webapps/galaxy/workflow/editor_tool_form.mako

@@ -1,7 +1,5 @@
 ## TEMPORARY SWITCH FOR THE NEW TOOL FORM
-%if util.string_as_bool(trans.app.config.get('workflow_toolform_upgrade',  False)):
-    ${h.js("libs/bibtex", "libs/jquery/jquery-ui")}
-    ${h.css('jquery-ui/smoothness/jquery-ui')}
+%if util.string_as_bool(trans.app.config.get('workflow_toolform_upgrade',  True)):
     <%
         ## TEMPORARY: create tool dictionary in mako while both tool forms are in use.
         ## This avoids making two separate requests since the classic form requires the mako anyway.
@@ -16,13 +14,7 @@
             'container'         : '#right-content'
         })
     %>
-    <script>
-        require(['mvc/tools/tools-form-workflow'], function(ToolsForm){
-           $(function(){
-                var form = new ToolsForm.View(${ h.dumps(self.form_config) });
-            });
-        });
-    </script>
+    ${ h.dumps(self.form_config) }
 %else:
     <%
     from galaxy.tools.parameters import DataToolParameter, RuntimeValue