tool-form.js

/**
    This is the regular tool form.
*/
define([ 'utils/utils', 'mvc/ui/ui-misc', 'mvc/ui/ui-modal', 'mvc/tool/tool-form-base' ],
    function( Utils, Ui, Modal, ToolFormBase ) {
    var View = ToolFormBase.extend({
        initialize: function( options ) {
            var self = this;
            options.listen_to_history = true;
            options.always_refresh = false;
            this.modal = parent.Galaxy.modal || new Modal.View();
            ToolFormBase.prototype.initialize.call( this, Utils.merge({
                customize: function( options ) {
                    // build execute button
                    options.buttons = {
                        execute: execute_btn = new Ui.Button({
                            icon     : 'fa-check',
                            tooltip  : 'Execute: ' + options.name + ' (' + options.version + ')',
                            title    : 'Execute',
                            cls      : 'ui-button btn btn-primary',
                            floating : 'clear',
                            onclick  : function() {
                                execute_btn.wait();
                                self.portlet.disable();
                                self.submit( options, function() {
                                    execute_btn.unwait();
                                    self.portlet.enable();
                                } );
                            }
                        })
                    };
                    // remap feature
                    if ( options.job_id && options.job_remap ) {
                        options.inputs[ 'rerun_remap_job_id' ] = {
                            label       : 'Resume dependencies from this job',
                            name        : 'rerun_remap_job_id',
                            type        : 'select',
                            display     : 'radio',
                            ignore      : '__ignore__',
                            value       : '__ignore__',
                            options     : [ [ 'Yes', options.job_id ], [ 'No', '__ignore__' ] ],
                            help        : 'The previous run of this tool failed and other tools were waiting for it to finish successfully. Use this option to resume those tools using the new output(s) of this tool run.'
                        }
                    }
                }
            }, options ) );
        },

        /** Submit a regular job.
         * @param{dict}     options   - Specifies tool id and version
         * @param{function} callback  - Called when request has completed
         */
        submit: function( options, callback ) {
            var self = this;
            var job_def = {
                tool_id         : options.id,
                tool_version    : options.version,
                inputs          : this.data.create()
            }
            this.trigger( 'reset' );
            if ( !self.validate( job_def ) ) {
                Galaxy.emit.debug( 'tool-form::submit()', 'Submission canceled. Validation failed.' );
                callback && callback();
                return;
            }
            if ( options.action !== Galaxy.root + 'tool_runner/index' ) {
                var $f = $( '<form/>' ).attr( { action: options.action, method: options.method, enctype: options.enctype } );
                _.each( job_def.inputs, function( value, key ) { $f.append( $( '<input/>' ).attr( { 'name': key, 'value': value } ) ) } );
                $f.hide().appendTo( 'body' ).submit().remove();
                callback && callback();
                return;
            }
            Galaxy.emit.debug( 'tool-form::submit()', 'Validation complete.', job_def );
            Utils.request({
                type    : 'POST',
                url     : Galaxy.root + 'api/tools',
                data    : job_def,
                success : function( response ) {
                    callback && callback();
                    self.$el.empty().append( self._templateSuccess( response ) );
                    parent.Galaxy && parent.Galaxy.currHistoryPanel && parent.Galaxy.currHistoryPanel.refreshContents();
                },
                error   : function( response ) {
                    callback && callback();
                    Galaxy.emit.debug( 'tool-form::submit', 'Submission failed.', response );
                    var input_found = false;
                    if ( response && response.err_data ) {
                        var error_messages = self.data.matchResponse( response.err_data );
                        for (var input_id in error_messages) {
                            self.highlight( input_id, error_messages[ input_id ]);
                            input_found = true;
                            break;
                        }
                    }
                    if ( !input_found ) {
                        self.modal.show({
                            title   : 'Job submission failed',
                            body    : ( response && response.err_msg ) || self._templateError( job_def ),
                            buttons : {
                                'Close' : function() {
                                    self.modal.hide();
                                }
                            }
                        });
                    }
                }
            });
        },

        /** Validate job dictionary.
         * @param{dict}     job_def   - Job execution dictionary
        */
        validate: function( job_def ) {
            var job_inputs  = job_def.inputs;
            var batch_n     = -1;
            var batch_src   = null;
            for ( var job_input_id in job_inputs ) {
                var input_value = job_inputs[ job_input_id ];
                var input_id    = this.data.match( job_input_id );
                var input_field = this.field_list[ input_id ];
                var input_def   = this.input_list[ input_id ];
                if ( !input_id || !input_def || !input_field ) {
                    Galaxy.emit.debug('tool-form::validate()', 'Retrieving input objects failed.');
                    continue;
                }
                if ( !input_def.optional && input_value == null ) {
                    this.highlight( input_id );
                    return false;
                }
                if ( input_value && input_value.batch ) {
                    var n = input_value.values.length;
                    var src = n > 0 && input_value.values[ 0 ] && input_value.values[ 0 ].src;
                    if ( src ) {
                        if ( batch_src === null ) {
                            batch_src = src;
                        } else if ( batch_src !== src ) {
                            this.highlight( input_id, 'Please select either dataset or dataset list fields for all batch mode fields.' );
                            return false;
                        }
                    }
                    if ( batch_n === -1 ) {
                        batch_n = n;
                    } else if ( batch_n !== n ) {
                        this.highlight( input_id, 'Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>' + n + '</b> selection(s) while a previous field contains <b>' + batch_n + '</b>.' );
                        return false;
                    }
                }
            }
            return true;
        },

        _templateSuccess: function( response ) {
            if ( response.jobs && response.jobs.length > 0 ) {
                var njobs = response.jobs.length;
                var njobs_text = njobs == 1 ? '1 job has' : njobs + ' jobs have';
                var $message = $( '<div/>' ).addClass( 'donemessagelarge' )
                                .append( $( '<p/>' ).text( njobs_text + ' been successfully added to the queue - resulting in the following datasets:' ) );
                _.each( response.outputs, function( output ) {
                    $message.append( $( '<p/>' ).addClass( 'messagerow' ).append( $( '<b/>' ).text( output.hid + ': ' + output.name ) ) );
                });
                $message.append( $( '<p/>' ).append( '<b/>' ).text( 'You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from \'running\' to \'finished\' if completed successfully or \'error\' if problems were encountered.' ) );
                return $message;
            } else {
                return this._templateError( response );
            }
        },

        _templateError: function( response ) {
            return  $( '<div/>' ).addClass( 'errormessagelarge' )
                .append( $( '<p/>' ).text( 'The server could not complete the request. Please contact the Galaxy Team if this error persists.' ) )
                .append( $( '<pre/>' ).text( JSON.stringify( response, null, 4 ) ) );
        }
    });

    return {
        View: View
    };
});