ToolForm: Add data selector, dynamic column selector and checkboxes, extends json content for basic parameters

config/plugins/visualizations/charts/static/library/ui-table-form.js

@@ -88,7 +88,7 @@ var View = Backbone.View.extend({
                 break;
             // radiobox field
             case 'radiobutton' :
-                field = new Ui.RadioButton({
+                field = new Ui.RadioButton.View({
                     id          : 'field-' + id,
                     data        : settings_def.data,
                     value       : model.get(id),

config/plugins/visualizations/charts/static/views/types.js

@@ -35,7 +35,7 @@ return Backbone.View.extend({
         $el.append(Utils.wrap((new Ui.Label({ title : 'How many data points would you like to analyze?'})).$el));
         
         // construct chart type subset selection buttons
-        this.library = new Ui.RadioButton({
+        this.library = new Ui.RadioButton.View({
             data    : [ { label: 'Few (<500)', value: 'small' },
                         { label: 'Some (<10k)', value: 'medium' },
                         { label: 'Many (>10k)', value: 'large' }],

lib/galaxy/tools/parameters/basic.py

@@ -991,6 +991,8 @@ class SelectToolParameter( ToolParameter ):
                     # Found selected option.
                     value = option[1]
             d[ 'value' ] = value
+            
+        d[ 'display' ] = self.display
 
         return d
 
@@ -1230,6 +1232,8 @@ class ColumnListParameter( SelectToolParameter ):
     def need_late_validation( self, trans, context ):
         if super( ColumnListParameter, self ).need_late_validation( trans, context ):
             return True
+        if self.data_ref not in context:
+            return False
         # Get the selected dataset if selected
         dataset = context[ self.data_ref ]
         if dataset:
@@ -1242,6 +1246,16 @@ class ColumnListParameter( SelectToolParameter ):
         # No late validation
         return False
 
+    def to_dict( self, trans, view='collection', value_mapper=None ):
+        # call parent to_dict
+        d = super( ColumnListParameter, self ).to_dict( trans )
+
+        # add data reference
+        d[ 'data_ref' ] = self.data_ref
+        
+        # return
+        return d
+
 
 class DrillDownSelectToolParameter( SelectToolParameter ):
     """

static/scripts/mvc/tools/tools-datasets.js

@@ -0,0 +1,46 @@
+define([ 'mvc/history/history-contents' ], function( HISTORY_CONTENTS ){
+    return Backbone.Model.extend({
+        // initialize
+        initialize: function(options) {
+            // create history contents container
+            this.currHistoryContents = new HISTORY_CONTENTS.HistoryContents({});
+            
+            // identify current history id
+            this.currHistoryContents.historyId = "f597429621d6eb2b";//Galaxy.currHistoryPanel.model.id;
+            
+            // make request
+            var self = this;
+            var xhr = this.currHistoryContents.fetchAllDetails()
+                .done( function(){
+                    // log request success
+                    console.debug('tools-datasets::initialize() - Completed.');
+                    
+                    // callback
+                    options.success && options.success();
+                })
+                .fail( function(){
+                    // log request failure
+                    console.debug('tools-datasets::initialize() - Ajax request failed.');
+                });
+        },
+        
+        // filter datasets by data type
+        filterType: function(filter_type) {
+            // return matched datasets
+            return this.currHistoryContents.filter( function( content ){
+                // link details
+                var history_content_type = content.get( 'history_content_type' );
+                var data_type = content.get( 'data_type');
+                
+                // apply filter
+                return history_content_type === 'dataset';// && (data_type === filter_type || filter_type === '');
+            });
+        },
+        
+        // filter datasets by id
+        filter: function(filter_id) {
+            // return matched datasets
+            return _.first( this.currHistoryContents.filter( function( content ){ return content.get( 'id' ) === filter_id; }) );
+        }
+    });
+});

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

@@ -1,4 +1,8 @@
-define(['mvc/tools', 'mvc/ui/ui-portlet', 'mvc/ui/ui-table', 'mvc/ui/ui-misc'], function(Tools, Portlet, Table, Ui) {
+define(['mvc/ui/ui-portlet', 'mvc/ui/ui-table', 'mvc/ui/ui-misc',
+        'mvc/citation/citation-model', 'mvc/citation/citation-view',
+        'mvc/tools', 'mvc/tools/tools-template', 'mvc/tools/tools-datasets'],
+    function(Portlet, Table, Ui, CitationModel, CitationView,
+             Tools, ToolTemplate, ToolDatasets) {
 
     // create tool model
     var Model = Backbone.Model.extend({
@@ -17,14 +21,31 @@ define(['mvc/tools', 'mvc/ui/ui-portlet', 'mvc/ui/ui-table', 'mvc/ui/ui-misc'],
             // link this
             var self = this;
             
+            // link options
+            this.options = options;
+            
             // load tool model
             this.model = new Model({
                 id : options.id
             });
             
+            // initialize datasets
+            this.datasets = new ToolDatasets({
+                success: function() {
+                    self._initializeToolForm();
+                }
+            });
+        },
+        
+        // initialize tool form
+        _initializeToolForm: function() {
             // fetch model and render form
+            var self = this;
             this.model.fetch({
                 success: function() {
+                    // inputs
+                    self.inputs = self.model.get('inputs');
+            
                     // create portlet
                     self.portlet = new Portlet.View({
                         icon : 'fa-wrench',
@@ -41,15 +62,35 @@ define(['mvc/tools', 'mvc/ui/ui-portlet', 'mvc/ui/ui-table', 'mvc/ui/ui-misc'],
                         }
                     });
                     
-                    // table
+                    // create table
                     self.table = new Table.View();
                     
-                    // add message
+                    // create message
                     self.message = new Ui.Message();
                     self.portlet.append(self.message.$el);
                     
-                    // append portlet
+                    // append form
                     $(self.main_el).append(self.portlet.$el);
+                    
+                    // append help
+                    if (self.options.help != '') {
+                        $(self.main_el).append(ToolTemplate.help(self.options.help));
+                    }
+                    
+                    // append citations
+                    if (self.options.citations) {
+                        // append html
+                        $(self.main_el).append(ToolTemplate.citations());
+            
+                        // fetch citations
+                        var citations = new CitationModel.ToolCitationCollection();
+                        citations.tool_id = self.options.id;
+                        var citation_list_view = new CitationView.CitationListView({ collection: citations } );
+                        citation_list_view.render();
+                        citations.fetch();
+                    }
+                    
+                    // configure portlet and form table
                     self.setElement(self.portlet.content());
                     self.portlet.append(self.table.$el);
                     self.render();
@@ -59,9 +100,6 @@ define(['mvc/tools', 'mvc/ui/ui-portlet', 'mvc/ui/ui-table', 'mvc/ui/ui-misc'],
         
         // update
         render: function() {
-            // inputs
-            var settings = this.model.get('inputs');
-        
             // reset table
             this.table.delAll();
             
@@ -72,8 +110,8 @@ define(['mvc/tools', 'mvc/ui/ui-portlet', 'mvc/ui/ui-table', 'mvc/ui/ui-misc'],
             var data = new Backbone.Model();
             
             // load settings elements into table
-            for (var id in settings) {
-                this._add(settings[id], data);
+            for (var id in this.inputs) {
+                this._add(this.inputs[id], data);
             }
             
             // trigger change
@@ -83,53 +121,55 @@ define(['mvc/tools', 'mvc/ui/ui-portlet', 'mvc/ui/ui-table', 'mvc/ui/ui-misc'],
         },
         
         // add table row
-        _add: function(settings_def, data) {
+        _add: function(inputs_def, data) {
             // link this
             var self = this;
             
             // get id
-            var id = settings_def.name;
-            
-            // log
-            console.debug(settings_def);
+            var id = inputs_def.name;
             
             // field wrapper
             var field = null;
-            
+            console.log(inputs_def);
             // create select field
-            var type = settings_def.type;
+            var type = inputs_def.type;
             switch(type) {
                 // text input field
                 case 'text' :
-                    field = this.field_text(settings_def, data);
+                    field = this.field_text(inputs_def, data);
                     break;
                     
                 // select field
                 case 'select' :
-                    field = this.field_select(settings_def, data);
+                    field = this.field_select(inputs_def, data);
                     break;
                     
                 // radiobox field
                 case 'radiobutton' :
-                    field = this.field_radio(settings_def, data);
+                    field = this.field_radio(inputs_def, data);
                     break;
                 
                 // dataset
                 case 'data':
-                    field = this.field_select(settings_def, data);
+                    field = this.field_data(inputs_def, data);
                     break;
                 
-                // slider input field
+                // dataset column
+                case 'data_column':
+                    field = this.field_column(inputs_def, data);
+                    break;
+                
+                // text area field
                 case 'textarea' :
-                    field = this.field_textarea(settings_def, data);
+                    field = this.field_textarea(inputs_def, data);
                     break;
 
                 // default
                 default:
                     field = new Ui.Input({
                         id          : 'field-' + id,
-                        placeholder : settings_def.placeholder,
-                        type        : settings_def.type,
+                        placeholder : inputs_def.placeholder,
+                        type        : inputs_def.type,
                         onchange    : function() {
                             data.set(id, field.value());
                         }
@@ -138,7 +178,7 @@ define(['mvc/tools', 'mvc/ui/ui-portlet', 'mvc/ui/ui-table', 'mvc/ui/ui-misc'],
             
             // set value
             if (!data.get(id)) {
-                data.set(id, settings_def.value);
+                data.set(id, inputs_def.value);
             }
             field.value(data.get(id));
             
@@ -148,31 +188,26 @@ define(['mvc/tools', 'mvc/ui/ui-portlet', 'mvc/ui/ui-table', 'mvc/ui/ui-misc'],
             // combine field and info
             var $input = $('<div/>');
             $input.append(field.$el);
-            if (settings_def.info) {
-                $input.append('<div class="ui-table-form-info">' + settings_def.info + '</div>');
+            if (inputs_def.info) {
+                $input.append('<div class="ui-table-form-info">' + inputs_def.info + '</div>');
             }
             
             // add row to table
-            if (this.options.style == 'bold') {
-                this.table.add(new Ui.Label({title: settings_def.title, cls: 'form-label'}).$el);
-                this.table.add($input);
-            } else {
-                this.table.add('<span class="ui-table-form-title">' + settings_def.label + '</span>', '25%');
-                this.table.add($input);
-            }
-        
+            this.table.add('<span class="ui-table-form-title">' + inputs_def.label + '</span>', '25%');
+            this.table.add($input);
+            
             // add to table
             this.table.append(id);
             
             // show/hide
-            if (settings_def.hide) {
+            if (inputs_def.hide) {
                 this.table.get(id).hide();
             }
         },
         
         // text input field
-        field_text : function(settings_def, data) {
-            var id = settings_def.name;
+        field_text : function(inputs_def, data) {
+            var id = inputs_def.name;
             return new Ui.Input({
                 id          : 'field-' + id,
                 value       : data.get(id),
@@ -183,8 +218,8 @@ define(['mvc/tools', 'mvc/ui/ui-portlet', 'mvc/ui/ui-table', 'mvc/ui/ui-misc'],
         },
         
         // text area
-        field_textarea : function(settings_def, data) {
-            var id = settings_def.name;
+        field_textarea : function(inputs_def, data) {
+            var id = inputs_def.name;
             return new Ui.Textarea({
                 id          : 'field-' + id,
                 onchange    : function() {
@@ -193,12 +228,89 @@ define(['mvc/tools', 'mvc/ui/ui-portlet', 'mvc/ui/ui-table', 'mvc/ui/ui-misc'],
             });
         },
         
-        // select field
-        field_select : function (settings_def, data) {
+        // data input field
+        field_data : function(inputs_def, data) {
+            // link this
+            var self = this;
+            
+            // get element id
+            var id = inputs_def.name;
+            
+            // get datasets
+            var datasets = this.datasets.filterType();
+            
             // configure options fields
             var options = [];
-            for (var i in settings_def.options) {
-                var option = settings_def.options[i];
+            for (var i in datasets) {
+                options.push({
+                    label: datasets[i].get('name'),
+                    value: datasets[i].get('id')
+                });
+            }
+            
+            // find referenced columns
+            var column_list = _.where(this.inputs, {
+                data_ref    : id,
+                type        : 'data_column'
+            });
+            
+            // select field
+            return new Ui.Select.View({
+                id          : 'field-' + id,
+                data        : options,
+                value       : options[0].value,
+                onchange    : function(value) {
+                    // update value
+                    data.set(id, value);
+                    
+                    // find selected dataset
+                    var dataset = self.datasets.filter(value);
+        
+                    // check dataset
+                    if (dataset && column_list.length > 0) {
+                        // log selection
+                        console.debug('tool-form::field_data() - Selected dataset ' + value + '.');
+                    
+                        // get meta data
+                        var meta = dataset.get('metadata_column_types');
+                    
+                        // check meta data
+                        if (!meta) {
+                            console.debug('tool-form::field_data() - FAILED: Could not find metadata for dataset ' + value + '.');
+                        }
+                        
+                        // load column options
+                        var columns = [];
+                        for (var key in meta) {
+                            // add to selection
+                            columns.push({
+                                'label' : 'Column: ' + (parseInt(key) + 1) + ' [' + meta[key] + ']',
+                                'value' : key
+                            });
+                        }
+                
+                        // update referenced columns
+                        for (var i in column_list) {
+                            var column_field = self.list[column_list[i].name]
+                            if (column_field) {
+                                column_field.update(columns);
+                                column_field.value(column_field.first());
+                            }
+                        }
+                    } else {
+                        // log failure
+                        console.debug('tool-form::field_data() - FAILED: Could not find dataset ' + value + '.');
+                    }
+                }
+            });
+        },
+        
+        // select field
+        field_column : function (inputs_def, data) {
+            // configure options fields
+            var options = [];
+            for (var i in inputs_def.options) {
+                var option = inputs_def.options[i];
                 options.push({
                     label: option[0],
                     value: option[1]
@@ -206,56 +318,56 @@ define(['mvc/tools', 'mvc/ui/ui-portlet', 'mvc/ui/ui-table', 'mvc/ui/ui-misc'],
             }
             
             // select field
-            var id = settings_def.name;
+            var id = inputs_def.name;
             return new Ui.Select.View({
                 id          : 'field-' + id,
                 data        : options,
                 value       : data.get(id),
                 onchange    : function(value) {
-                    // set new value
                     data.set(id, value);
-                    
-                    // find selected dictionary
-                    var dict = _.findWhere(options, {value: value});
-                    if (dict && dict.operations) {
-                        var operations = dict.operations;
-                        for (var i in operations.show) {
-                            var target = operations.show[i];
-                            self.table.get(target).show();
-                        }
-                        for (var i in operations.hide) {
-                            var target = operations.hide[i];
-                            self.table.get(target).hide();
-                        }
-                    }
+                }
+            });
+        },
+
+        // select field
+        field_select : function (inputs_def, data) {
+            // configure options fields
+            var options = [];
+            for (var i in inputs_def.options) {
+                var option = inputs_def.options[i];
+                options.push({
+                    label: option[0],
+                    value: option[1]
+                });
+            }
+            
+            // identify display type
+            var SelectClass = Ui.Select;
+            if (inputs_def.display == 'checkboxes') {
+                SelectClass = Ui.Checkbox;
+            }
+            
+            // select field
+            var id = inputs_def.name;
+            return new SelectClass.View({
+                id          : 'field-' + id,
+                data        : options,
+                value       : data.get(id),
+                onchange    : function(value) {
+                    data.set(id, value);
                 }
             });
         },
         
         // radio field
-        field_radio : function(settings_def, data) {
-            var id = settings_def.name;
+        field_radio : function(inputs_def, data) {
+            var id = inputs_def.name;
             return new Ui.RadioButton({
                 id          : 'field-' + id,
-                data        : settings_def.data,
+                data        : inputs_def.data,
                 value       : data.get(id),
                 onchange    : function(value) {
-                    // set new value
                     data.set(id, value);
-                    
-                    // find selected dictionary
-                    var dict = _.findWhere(settings_def.data, {value: value});
-                    if (dict && dict.operations) {
-                        var operations = dict.operations;
-                        for (var i in operations.show) {
-                            var target = operations.show[i];
-                            self.table.get(target).show();
-                        }
-                        for (var i in operations.hide) {
-                            var target = operations.hide[i];
-                            self.table.get(target).hide();
-                        }
-                    }
                 }
             });
         }

static/scripts/mvc/tools/tools-template.js

@@ -0,0 +1,19 @@
+// dependencies
+define([], function() {
+
+// tool form templates
+return {
+    help: function(content) {
+        return  '<div class="toolHelp">' +
+                    '<div class="toolHelpBody">' +
+                        content +
+                    '</div>' +
+                '</div>';
+    },
+    
+    citations: function() {
+        return  '<div id="citations"></div>';
+    }
+};
+
+});

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

@@ -0,0 +1,91 @@
+// dependencies
+define(['utils/utils'], function(Utils) {
+
+// plugin
+var View = Backbone.View.extend({
+    // options
+    optionsDefault: {
+        value           : '',
+        visible         : true,
+        cls             : '',
+        data            : [],
+        id              : Utils.uuid()
+    },
+    
+    // initialize
+    initialize : function(options) {
+        // configure options
+        this.options = Utils.merge(options, this.optionsDefault);
+            
+        // create new element
+        this.setElement(this._template(this.options));
+        
+        // hide input field
+        if (!this.options.visible) {
+            this.$el.hide();
+        }
+        
+        // set initial value
+        if (this.options.value) {
+            this.value(this.options.value);
+        }
+        
+        // current value
+        this.current = this.options.value;
+        
+        // onchange event handler. fires on user activity.
+        var self = this;
+        this.$el.find('input').on('change', function() {        
+            self.value(self._getValue());
+        });
+    },
+    
+    // value
+    value : function (new_val) {
+        // get current value
+        var before = this.current;
+        
+        // set new value
+        if (new_val !== undefined) {
+            this.$el.find('label').removeClass('active');
+            this.$el.find('[value="' + new_val + '"]').closest('label').addClass('active');
+            this.current = new_val;
+        }
+
+        // check value
+        var after = this.current;
+        if (after != before && this.options.onchange) {
+            this.options.onchange(this.current);
+        }
+
+        // get and return value
+        return this.current;
+    },
+    
+    // get value
+    _getValue: function() {
+        var selected = this.$el.find(':checked');
+        var value = null;
+        if (selected.length > 0) {
+            value = selected.val();
+        }
+        return value;
+    },
+    
+    // element
+    _template: function(options) {
+        var tmpl =  '<div class="ui-checkbox">';
+        for (key in options.data) {
+            var pair = options.data[key];
+            tmpl +=     '<input type="checkbox" name="' + options.id + '" value="' + pair.value + '" selected>' + pair.label + '<br>';
+        }
+        tmpl +=     '</div>';
+        return tmpl;
+    }
+});
+
+return {
+    View : View
+};
+
+});

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

@@ -1,6 +1,6 @@
 // dependencies
-define(['utils/utils', 'mvc/ui/ui-select-default', 'mvc/ui/ui-button-menu', 'mvc/ui/ui-modal'],
-        function(Utils, Select, ButtonMenu, Modal) {
+define(['utils/utils', 'mvc/ui/ui-select-default', 'mvc/ui/ui-checkbox', 'mvc/ui/ui-radiobutton', 'mvc/ui/ui-button-menu', 'mvc/ui/ui-modal'],
+        function(Utils, Select, Checkbox, RadioButton, ButtonMenu, Modal) {
 
 /**
  *  This class contains backbone wrappers for basic ui elements such as Images, Labels, Buttons, Input fields etc.
@@ -409,90 +409,6 @@ var Textarea = Backbone.View.extend({
     }
 });
 
-// plugin
-var RadioButton = Backbone.View.extend({
-    // options
-    optionsDefault: {
-        value           : '',
-        visible         : true,
-        cls             : '',
-        data            : [],
-        id              : Utils.uuid()
-    },
-    
-    // initialize
-    initialize : function(options) {
-        // configure options
-        this.options = Utils.merge(options, this.optionsDefault);
-            
-        // create new element
-        this.setElement(this._template(this.options));
-        
-        // hide input field
-        if (!this.options.visible) {
-            this.$el.hide();
-        }
-        
-        // set initial value
-        if (this.options.value) {
-            this.value(this.options.value);
-        }
-        
-        // current value
-        this.current = this.options.value;
-        
-        // onchange event handler. fires on user activity.
-        var self = this;
-        this.$el.find('input').on('change', function() {        
-            self.value(self._getValue());
-        });
-    },
-    
-    // value
-    value : function (new_val) {
-        // get current value
-        var before = this.current;
-        
-        // set new value
-        if (new_val !== undefined) {
-            this.$el.find('label').removeClass('active');
-            this.$el.find('[value="' + new_val + '"]').closest('label').addClass('active');
-            this.current = new_val;
-        }
-
-        // check value
-        var after = this.current;
-        if (after != before && this.options.onchange) {
-            this.options.onchange(this.current);
-        }
-
-        // get and return value
-        return this.current;
-    },
-    
-    // get value
-    _getValue: function() {
-        var selected = this.$el.find(':checked');
-        var value = null;
-        if (selected.length > 0) {
-            value = selected.val();
-        }
-        return value;
-    },
-    
-    // element
-    _template: function(options) {
-        var tmpl =  '<div class="btn-group ui-radiobutton" data-toggle="buttons">';
-        for (key in options.data) {
-            var pair = options.data[key];
-            tmpl +=     '<label class="btn btn-default">' +
-                            '<input type="radio" name="' + options.id + '" value="' + pair.value + '" selected>' + pair.label +
-                        '</label>';
-        }
-        tmpl +=     '</div>';
-        return tmpl;
-    }
-});
 
 // return
 return {
@@ -507,6 +423,7 @@ return {
     Message     : Message,
     Modal       : Modal,
     RadioButton : RadioButton,
+    Checkbox    : Checkbox,
     Searchbox   : Searchbox,
     Select      : Select,
     Textarea    : Textarea

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

@@ -0,0 +1,93 @@
+// dependencies
+define(['utils/utils'], function(Utils) {
+
+// plugin
+var View = Backbone.View.extend({
+    // options
+    optionsDefault: {
+        value           : '',
+        visible         : true,
+        cls             : '',
+        data            : [],
+        id              : Utils.uuid()
+    },
+    
+    // initialize
+    initialize : function(options) {
+        // configure options
+        this.options = Utils.merge(options, this.optionsDefault);
+            
+        // create new element
+        this.setElement(this._template(this.options));
+        
+        // hide input field
+        if (!this.options.visible) {
+            this.$el.hide();
+        }
+        
+        // set initial value
+        if (this.options.value) {
+            this.value(this.options.value);
+        }
+        
+        // current value
+        this.current = this.options.value;
+        
+        // onchange event handler. fires on user activity.
+        var self = this;
+        this.$el.find('input').on('change', function() {        
+            self.value(self._getValue());
+        });
+    },
+    
+    // value
+    value : function (new_val) {
+        // get current value
+        var before = this.current;
+        
+        // set new value
+        if (new_val !== undefined) {
+            this.$el.find('label').removeClass('active');
+            this.$el.find('[value="' + new_val + '"]').closest('label').addClass('active');
+            this.current = new_val;
+        }
+
+        // check value
+        var after = this.current;
+        if (after != before && this.options.onchange) {
+            this.options.onchange(this.current);
+        }
+
+        // get and return value
+        return this.current;
+    },
+    
+    // get value
+    _getValue: function() {
+        var selected = this.$el.find(':checked');
+        var value = null;
+        if (selected.length > 0) {
+            value = selected.val();
+        }
+        return value;
+    },
+    
+    // element
+    _template: function(options) {
+        var tmpl =  '<div class="btn-group ui-radiobutton" data-toggle="buttons">';
+        for (key in options.data) {
+            var pair = options.data[key];
+            tmpl +=     '<label class="btn btn-default">' +
+                            '<input type="radio" name="' + options.id + '" value="' + pair.value + '" selected>' + pair.label +
+                        '</label>';
+        }
+        tmpl +=     '</div>';
+        return tmpl;
+    }
+});
+
+return {
+    View : View
+};
+
+});

static/scripts/packed/mvc/tools/tools-datasets.js

@@ -0,0 +1 @@
+define(["mvc/history/history-contents"],function(a){return Backbone.Model.extend({initialize:function(c){this.currHistoryContents=new a.HistoryContents({});this.currHistoryContents.historyId="f597429621d6eb2b";var b=this;var d=this.currHistoryContents.fetchAllDetails().done(function(){console.debug("tools-datasets::initialize() - Completed.");c.success&&c.success()}).fail(function(){console.debug("tools-datasets::initialize() - Ajax request failed.")})},filterType:function(b){return this.currHistoryContents.filter(function(c){var d=c.get("history_content_type");var e=c.get("data_type");return d==="dataset"})},filter:function(b){return _.first(this.currHistoryContents.filter(function(c){return c.get("id")===b}))}})});

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

@@ -1 +1 @@
-define(["mvc/tools","mvc/ui/ui-portlet","mvc/ui/ui-table","mvc/ui/ui-misc"],function(b,c,a,f){var e=Backbone.Model.extend({initialize:function(g){this.url=galaxy_config.root+"api/tools/"+g.id+"?io_details=true"}});var d=Backbone.View.extend({main_el:"body",initialize:function(h){var g=this;this.model=new e({id:h.id});this.model.fetch({success:function(){g.portlet=new c.View({icon:"fa-wrench",title:"<b>"+g.model.get("name")+"</b> "+g.model.get("description"),buttons:{execute:new f.ButtonIcon({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",floating:"clear",onclick:function(){}})}});g.table=new a.View();g.message=new f.Message();g.portlet.append(g.message.$el);$(g.main_el).append(g.portlet.$el);g.setElement(g.portlet.content());g.portlet.append(g.table.$el);g.render()}})},render:function(){var g=this.model.get("inputs");this.table.delAll();this.list=[];var h=new Backbone.Model();for(var i in g){this._add(g[i],h)}for(var i in this.list){this.list[i].trigger("change")}},_add:function(g,j){var h=this;var m=g.name;console.debug(g);var k=null;var i=g.type;switch(i){case"text":k=this.field_text(g,j);break;case"select":k=this.field_select(g,j);break;case"radiobutton":k=this.field_radio(g,j);break;case"data":k=this.field_select(g,j);break;case"textarea":k=this.field_textarea(g,j);break;default:k=new f.Input({id:"field-"+m,placeholder:g.placeholder,type:g.type,onchange:function(){j.set(m,k.value())}})}if(!j.get(m)){j.set(m,g.value)}k.value(j.get(m));this.list[m]=k;var l=$("<div/>");l.append(k.$el);if(g.info){l.append('<div class="ui-table-form-info">'+g.info+"</div>")}if(this.options.style=="bold"){this.table.add(new f.Label({title:g.title,cls:"form-label"}).$el);this.table.add(l)}else{this.table.add('<span class="ui-table-form-title">'+g.label+"</span>","25%");this.table.add(l)}this.table.append(m);if(g.hide){this.table.get(m).hide()}},field_text:function(g,h){var i=g.name;return new f.Input({id:"field-"+i,value:h.get(i),onchange:function(j){h.set(i,j)}})},field_textarea:function(g,h){var i=g.name;return new f.Textarea({id:"field-"+i,onchange:function(){h.set(i,field.value())}})},field_select:function(g,l){var h=[];for(var j in g.options){var k=g.options[j];h.push({label:k[0],value:k[1]})}var m=g.name;return new f.Select.View({id:"field-"+m,data:h,value:l.get(m),onchange:function(p){l.set(m,p);var r=_.findWhere(h,{value:p});if(r&&r.operations){var n=r.operations;for(var o in n.show){var q=n.show[o];self.table.get(q).show()}for(var o in n.hide){var q=n.hide[o];self.table.get(q).hide()}}}})},field_radio:function(g,h){var i=g.name;return new f.RadioButton({id:"field-"+i,data:g.data,value:h.get(i),onchange:function(l){h.set(i,l);var n=_.findWhere(g.data,{value:l});if(n&&n.operations){var j=n.operations;for(var k in j.show){var m=j.show[k];self.table.get(m).show()}for(var k in j.hide){var m=j.hide[k];self.table.get(m).hide()}}}})}});return{View:d}});
+define(["mvc/ui/ui-portlet","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-datasets"],function(f,i,j,h,a,e,c,g){var d=Backbone.Model.extend({initialize:function(k){this.url=galaxy_config.root+"api/tools/"+k.id+"?io_details=true"}});var b=Backbone.View.extend({main_el:"body",initialize:function(l){var k=this;this.options=l;this.model=new d({id:l.id});this.datasets=new g({success:function(){k._initializeToolForm()}})},_initializeToolForm:function(){var k=this;this.model.fetch({success:function(){k.inputs=k.model.get("inputs");k.portlet=new f.View({icon:"fa-wrench",title:"<b>"+k.model.get("name")+"</b> "+k.model.get("description"),buttons:{execute:new j.ButtonIcon({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",floating:"clear",onclick:function(){}})}});k.table=new i.View();k.message=new j.Message();k.portlet.append(k.message.$el);$(k.main_el).append(k.portlet.$el);if(k.options.help!=""){$(k.main_el).append(c.help(k.options.help))}if(k.options.citations){$(k.main_el).append(c.citations());var l=new h.ToolCitationCollection();l.tool_id=k.options.id;var m=new a.CitationListView({collection:l});m.render();l.fetch()}k.setElement(k.portlet.content());k.portlet.append(k.table.$el);k.render()}})},render:function(){this.table.delAll();this.list=[];var k=new Backbone.Model();for(var l in this.inputs){this._add(this.inputs[l],k)}for(var l in this.list){this.list[l].trigger("change")}},_add:function(l,n){var k=this;var q=l.name;var o=null;console.log(l);var m=l.type;switch(m){case"text":o=this.field_text(l,n);break;case"select":o=this.field_select(l,n);break;case"radiobutton":o=this.field_radio(l,n);break;case"data":o=this.field_data(l,n);break;case"data_column":o=this.field_column(l,n);break;case"textarea":o=this.field_textarea(l,n);break;default:o=new j.Input({id:"field-"+q,placeholder:l.placeholder,type:l.type,onchange:function(){n.set(q,o.value())}})}if(!n.get(q)){n.set(q,l.value)}o.value(n.get(q));this.list[q]=o;var p=$("<div/>");p.append(o.$el);if(l.info){p.append('<div class="ui-table-form-info">'+l.info+"</div>")}this.table.add('<span class="ui-table-form-title">'+l.label+"</span>","25%");this.table.add(p);this.table.append(q);if(l.hide){this.table.get(q).hide()}},field_text:function(k,l){var m=k.name;return new j.Input({id:"field-"+m,value:l.get(m),onchange:function(n){l.set(m,n)}})},field_textarea:function(k,l){var m=k.name;return new j.Textarea({id:"field-"+m,onchange:function(){l.set(m,field.value())}})},field_data:function(n,q){var l=this;var r=n.name;var p=this.datasets.filterType();var m=[];for(var o in p){m.push({label:p[o].get("name"),value:p[o].get("id")})}var k=_.where(this.inputs,{data_ref:r,type:"data_column"});return new j.Select.View({id:"field-"+r,data:m,value:m[0].value,onchange:function(w){q.set(r,w);var y=l.datasets.filter(w);if(y&&k.length>0){console.debug("tool-form::field_data() - Selected dataset "+w+".");var x=y.get("metadata_column_types");if(!x){console.debug("tool-form::field_data() - FAILED: Could not find metadata for dataset "+w+".")}var v=[];for(var u in x){v.push({label:"Column: "+(parseInt(u)+1)+" ["+x[u]+"]",value:u})}for(var t in k){var s=l.list[k[t].name];if(s){s.update(v);s.value(s.first())}}}else{console.debug("tool-form::field_data() - FAILED: Could not find dataset "+w+".")}}})},field_column:function(l,o){var k=[];for(var m in l.options){var n=l.options[m];k.push({label:n[0],value:n[1]})}var p=l.name;return new j.Select.View({id:"field-"+p,data:k,value:o.get(p),onchange:function(q){o.set(p,q)}})},field_select:function(l,p){var k=[];for(var m in l.options){var n=l.options[m];k.push({label:n[0],value:n[1]})}var o=j.Select;if(l.display=="checkboxes"){o=j.Checkbox}var q=l.name;return new o.View({id:"field-"+q,data:k,value:p.get(q),onchange:function(r){p.set(q,r)}})},field_radio:function(k,l){var m=k.name;return new j.RadioButton({id:"field-"+m,data:k.data,value:l.get(m),onchange:function(n){l.set(m,n)}})}});return{View:b}});

static/scripts/packed/mvc/tools/tools-template.js

@@ -0,0 +1 @@
+define([],function(){return{help:function(a){return'<div class="toolHelp"><div class="toolHelpBody">'+a+"</div></div>"},citations:function(){return'<div id="citations"></div>'}}});

static/scripts/packed/mvc/ui/ui-checkbox.js

@@ -0,0 +1 @@
+define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{value:"",visible:true,cls:"",data:[],id:a.uuid()},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));if(!this.options.visible){this.$el.hide()}if(this.options.value){this.value(this.options.value)}this.current=this.options.value;var c=this;this.$el.find("input").on("change",function(){c.value(c._getValue())})},value:function(c){var d=this.current;if(c!==undefined){this.$el.find("label").removeClass("active");this.$el.find('[value="'+c+'"]').closest("label").addClass("active");this.current=c}var e=this.current;if(e!=d&&this.options.onchange){this.options.onchange(this.current)}return this.current},_getValue:function(){var c=this.$el.find(":checked");var d=null;if(c.length>0){d=c.val()}return d},_template:function(d){var c='<div class="ui-checkbox">';for(key in d.data){var e=d.data[key];c+='<input type="checkbox" name="'+d.id+'" value="'+e.value+'" selected>'+e.label+"<br>"}c+="</div>";return c}});return{View:b}});

static/scripts/packed/mvc/ui/ui-radiobutton.js

@@ -0,0 +1 @@
+define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{value:"",visible:true,cls:"",data:[],id:a.uuid()},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));if(!this.options.visible){this.$el.hide()}if(this.options.value){this.value(this.options.value)}this.current=this.options.value;var c=this;this.$el.find("input").on("change",function(){c.value(c._getValue())})},value:function(c){var d=this.current;if(c!==undefined){this.$el.find("label").removeClass("active");this.$el.find('[value="'+c+'"]').closest("label").addClass("active");this.current=c}var e=this.current;if(e!=d&&this.options.onchange){this.options.onchange(this.current)}return this.current},_getValue:function(){var c=this.$el.find(":checked");var d=null;if(c.length>0){d=c.val()}return d},_template:function(d){var c='<div class="btn-group ui-radiobutton" data-toggle="buttons">';for(key in d.data){var e=d.data[key];c+='<label class="btn btn-default"><input type="radio" name="'+d.id+'" value="'+e.value+'" selected>'+e.label+"</label>"}c+="</div>";return c}});return{View:b}});

templates/webapps/galaxy/tool_form.api.mako

@@ -1,10 +1,47 @@
 <%inherit file="/base.mako"/>
+
+<%
+    # load tool help
+    tool_help = ''
+    if tool.help:
+        if tool.has_multiple_pages:
+            tool_help = tool.help_by_page[tool_state.page]
+        else:
+            tool_help = tool.help
+
+        # Help is Mako template, so render using current static path.
+        tool_help = tool_help.render( static_path=h.url_for( '/static' ), host_url=h.url_for('/', qualified=True) )
+
+        # Convert to unicode to display non-ascii characters.
+        if type( tool_help ) is not unicode:
+            tool_help = unicode( tool_help, 'utf-8')
+    endif
+
+    # check if citations exist
+    tool_citations = False
+    if tool.citations:
+        tool_citations = True
+
+    # form configuration
+    self.form_config = {
+        'id'        : tool.id,
+        'help'      : tool_help,
+        'citations' : tool_citations
+    }
+%>
+${h.js( "libs/bibtex" )}
 <script>
     require(['mvc/tools/tools-form'], function(ToolsForm){
         $(function(){
-            var form = new ToolsForm.View({
-                id : '${tool.id}'
-            });
+            var form = new ToolsForm.View(${ h.to_json_string(self.form_config) });
         });
     });
 </script>
+
+%if tool.tool_shed_repository:
+    <% tool_url = tool.tool_shed_repository.get_sharable_url( tool.app ) %>
+    %if tool_url:
+        <br/>
+        ${ render_msg( 'This tool was installed from a ToolShed, you may be able to find additional information by following this link: <a href="%s" target="_blank">%s</a>' % ( tool_url, tool_url ), 'info' ) }
+    %endif
+%endif