mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
ToolForm: Augment tool form base class
This commit is contained in:
guerler
@@ -42,6 +42,42 @@ define(['utils/utils', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc',
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this._build();
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},
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/** Update available options */
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update: function(new_model){
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var self = this;
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this.data.matchModel(new_model, function(input_id, node) {
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var input = self.input_list[input_id];
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if (input && input.options) {
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if (!_.isEqual(input.options, node.options)) {
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// backup new options
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input.options = node.options;
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// get/update field
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var field = self.field_list[input_id];
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if (field.update) {
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var new_options = [];
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if ((['data', 'data_collection', 'drill_down']).indexOf(input.type) != -1) {
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new_options = input.options;
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} else {
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for (var i in node.options) {
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var opt = node.options[i];
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if (opt.length > 2) {
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new_options.push({
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'label': opt[0],
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'value': opt[1]
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});
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}
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}
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}
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field.update(new_options);
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field.trigger('change');
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console.debug('Updating options for ' + input_id);
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}
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}
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}
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});
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},
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/** Set form into wait mode */
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wait: function(active) {
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for (var i in this.input_list) {
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@@ -37,11 +37,9 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view',
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// link this
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var self = this;
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// configure options
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this.options = Utils.merge(options, this.optionsDefault);
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// merge form options
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var form_options = Utils.merge({
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this.options = Utils.merge(options, this.options);
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this.options = Utils.merge({
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icon : 'fa-wrench',
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title : '<b>' + options.name + '</b> ' + options.description + ' (Galaxy Tool Version ' + options.version + ')',
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operations : this._operations(),
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@@ -49,13 +47,13 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view',
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// by resetting the deferred ajax queue the number of redundant calls is reduced
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self.deferred.reset();
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self.deferred.execute(function(){
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self._updateModel($.extend(true, {}, self.form.data.create()));
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self._updateModel();
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});
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}
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}, options);
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}, this.options);
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// create form
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this.form = new Form(form_options);
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this.form = new Form(this.options);
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// create footer
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this._footer();
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@@ -65,6 +63,139 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view',
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this.$el.append(this.form.$el);
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},
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/** Builds a new model through api call and recreates the entire form
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*/
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_buildModel: function(options) {
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// link this
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var self = this;
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// construct url
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var build_url = galaxy_config.root + 'api/tools/' + options.id + '/build?';
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if (options.job_id) {
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build_url += 'job_id=' + options.job_id;
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} else {
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if (options.dataset_id) {
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build_url += 'dataset_id=' + options.dataset_id;
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} else {
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build_url += 'tool_version=' + options.version + '&';
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var loc = top.location.href;
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var pos = loc.indexOf('?');
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if (loc.indexOf('tool_id=') != -1 && pos !== -1) {
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build_url += loc.slice(pos + 1);
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}
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}
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}
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// register process
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var process_id = this.deferred.register();
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// get initial model
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Utils.request({
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type : 'GET',
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url : build_url,
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success : function(new_model) {
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// rebuild form
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self._buildForm(new_model['tool_model'] || new_model);
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// show version message
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self.form.message.update({
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status : 'success',
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message : 'Now you are using \'' + self.options.name + '\' version ' + self.options.version + '.',
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persistent : false
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});
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// process completed
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self.deferred.done(process_id);
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// log success
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console.debug('tools-form::initialize() - Initial tool model ready.');
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console.debug(new_model);
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},
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error : function(response) {
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// process completed
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self.deferred.done(process_id);
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// log error
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console.debug('tools-form::initialize() - Initial tool model request failed.');
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console.debug(response);
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// show error
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var error_message = response.error || 'Uncaught error.';
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self.form.modal.show({
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title : 'Tool cannot be executed',
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body : error_message,
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buttons : {
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'Close' : function() {
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self.form.modal.hide();
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}
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}
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});
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}
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});
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},
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/** Request a new model for an already created tool form and updates the form inputs
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*/
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_updateModel: function() {
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// model url for request
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var model_url = this.options.update_url;
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// link this
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var self = this;
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// create the request dictionary
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var form = this.form;
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// create the request dictionary
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var current_state = {
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tool_id : this.options.id,
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tool_version : this.options.version,
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inputs : $.extend(true, {}, self.form.data.create())
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}
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// set wait mode
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form.wait(true);
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// register process
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var process_id = this.deferred.register();
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// log tool state
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console.debug('tools-form-base::_updateModel() - Sending current state (see below).');
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console.debug(current_state);
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// post job
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Utils.request({
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type : 'POST',
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url : model_url,
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data : current_state,
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success : function(new_model) {
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// update form with new model
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self.form.update(new_model['tool_model'] || new_model);
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// custom update
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self.options.update && self.options.update(new_model);
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// unset wait mode
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form.wait(false);
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// log success
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console.debug('tools-form-base::_updateModel() - Received new model (see below).');
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console.debug(new_model);
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// process completed
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self.deferred.done(process_id);
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},
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error : function(response) {
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// process completed
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self.deferred.done(process_id);
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// log error
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console.debug('tools-form-base::_updateModel() - Refresh request failed.');
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console.debug(response);
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}
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});
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},
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// create tool operation menu
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_operations: function() {
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// link this
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@@ -87,12 +218,13 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view',
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icon : 'fa-cube',
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onclick : function() {
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// here we update the tool version (some tools encode the version also in the id)
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options.id = options.id.replace(options.version, this.version);
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options.version = this.version;
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// rebuild the model and form
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var id = options.id.replace(options.version, this.version);
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var version = this.version;
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// queue model request
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self.deferred.reset();
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self.deferred.execute(function(){self._buildModel()});
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self.deferred.execute(function() {
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self._buildModel({id: id, version: version})
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});
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}
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});
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}
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@@ -18,17 +18,24 @@ define(['utils/utils', 'mvc/tools/tools-form-base'],
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this.post_job_actions = this.node.post_job_actions || {};
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// initialize parameters
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this.options = options;
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options = Utils.merge(options, {
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// set labels
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text_enable : 'Set in Advance',
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text_disable : 'Set at Runtime',
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// set labels
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this.options.text_enable = 'Set in Advance';
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this.options.text_disable = 'Set at Runtime';
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// configure workflow style
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is_dynamic : false,
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narrow : true,
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initial_errors : true,
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cls : 'ui-portlet-narrow',
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// configure workflow style
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this.options.is_dynamic = false;
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this.options.narrow = true;
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this.options.initial_errors = true;
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this.options.cls_portlet = 'ui-portlet-narrow';
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// configure model update
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update_url : galaxy_config.root + 'api/workflows/build_module',
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update : function(data) {
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self.node.update_field_data(data);
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self.form.errors(data && data.tool_model)
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}
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});
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// declare fields as optional
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Utils.deepeach(options.inputs, function(item) {
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@@ -257,73 +264,6 @@ define(['utils/utils', 'mvc/tools/tools-form-base'],
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// return final configuration
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return input_config;
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},
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/** Builds a new model through api call and recreates the entire form
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*/
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_buildModel: function() {
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Galaxy.modal.show({
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title : 'Coming soon...',
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body : 'This feature has not been implemented yet.',
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buttons : {
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'Close' : function() {
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Galaxy.modal.hide();
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}
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}
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});
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},
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/** Request a new model for an already created tool form and updates the form inputs
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*/
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_updateModel: function(current_state) {
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// link self
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var self = this;
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// create the request dictionary
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current_state = {
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tool_id : this.options.id,
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tool_version : this.options.version,
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inputs : current_state
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}
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// log tool state
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console.debug('tools-form-workflow::_refreshForm() - Refreshing states.');
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console.debug(current_state);
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// register process
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var process_id = this.deferred.register();
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// build model url for request
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var model_url = galaxy_config.root + 'api/workflows/build_module';
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// post job
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Utils.request({
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type : 'POST',
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url : model_url,
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data : current_state,
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success : function(data) {
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// update node in workflow module
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self.node.update_field_data(data);
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// highlight errors
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self.form.errors(data && data.tool_model);
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// process completed
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self.deferred.done(process_id);
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// log success
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console.debug('tools-form::_refreshForm() - States refreshed.');
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console.debug(data);
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},
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error : function(response) {
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// process completed
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self.deferred.done(process_id);
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// log error
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console.debug('tools-form::_refreshForm() - Refresh request failed.');
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console.debug(response);
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}
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});
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}
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});
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@@ -8,180 +8,24 @@ define(['utils/utils', 'mvc/ui/ui-misc', 'mvc/tools/tools-form-base', 'mvc/tools
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var View = ToolFormBase.extend({
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// initialize
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initialize: function(options) {
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// create options dictionary
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var self = this;
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options.buttons = {
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execute : new Ui.Button({
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icon : 'fa-check',
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tooltip : 'Execute: ' + options.name,
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title : 'Execute',
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cls : 'btn btn-primary',
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floating : 'clear',
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onclick : function() {
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ToolJobs.submit(self.form, options);
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}
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})
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};
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options = Utils.merge(options, {
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update_url : galaxy_config.root + 'api/tools/' + options.id + '/build',
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buttons : {
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execute : new Ui.Button({
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icon : 'fa-check',
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tooltip : 'Execute: ' + options.name,
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title : 'Execute',
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cls : 'btn btn-primary',
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floating : 'clear',
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onclick : function() {
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ToolJobs.submit(self.form, options);
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}
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})
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}
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});
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ToolFormBase.prototype.initialize.call(this, options);
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},
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/** Builds a new model through api call and recreates the entire form
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*/
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_buildModel: function() {
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// link this
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var self = this;
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// construct url
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var model_url = galaxy_config.root + 'api/tools/' + this.options.id + '/build?';
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if (this.options.job_id) {
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model_url += 'job_id=' + this.options.job_id;
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} else {
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if (this.options.dataset_id) {
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model_url += 'dataset_id=' + this.options.dataset_id;
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} else {
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model_url += 'tool_version=' + this.options.version + '&';
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var loc = top.location.href;
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var pos = loc.indexOf('?');
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if (loc.indexOf('tool_id=') != -1 && pos !== -1) {
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model_url += loc.slice(pos + 1);
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}
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}
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}
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// register process
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var process_id = this.deferred.register();
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// get initial model
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Utils.request({
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type : 'GET',
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url : model_url,
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success : function(response) {
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// build new tool form
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self._buildForm(response);
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// notification
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self.form.message.update({
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status : 'success',
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message : 'Now you are using \'' + self.options.name + '\' version ' + self.options.version + '.',
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persistent : false
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});
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// process completed
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self.deferred.done(process_id);
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// log success
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console.debug('tools-form::initialize() - Initial tool model ready.');
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console.debug(response);
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},
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error : function(response) {
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// process completed
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self.deferred.done(process_id);
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// log error
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console.debug('tools-form::initialize() - Initial tool model request failed.');
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console.debug(response);
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// show error
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var error_message = response.error || 'Uncaught error.';
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self.form.modal.show({
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title : 'Tool cannot be executed',
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body : error_message,
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buttons : {
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'Close' : function() {
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self.form.modal.hide();
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}
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}
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});
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}
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});
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},
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/** Request a new model for an already created tool form and updates the form inputs
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*/
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_updateModel: function(current_state) {
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// link this
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var self = this;
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// create the request dictionary
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var form = this.form;
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// create the request dictionary
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var current_state = {
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tool_id : this.options.id,
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tool_version : this.options.version,
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inputs : current_state
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}
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// set wait mode
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form.wait(true);
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// register process
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var process_id = this.deferred.register();
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// log tool state
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console.debug('tools-form::_refreshForm() - Sending current state (see below).');
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console.debug(current_state);
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// build model url for request
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var model_url = galaxy_config.root + 'api/tools/' + this.options.id + '/build';
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// post job
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Utils.request({
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type : 'POST',
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url : model_url,
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data : current_state,
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success : function(new_model) {
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// update form
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form.data.matchModel(new_model, function(input_id, node) {
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var input = form.input_list[input_id];
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if (input && input.options) {
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if (!_.isEqual(input.options, node.options)) {
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// backup new options
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input.options = node.options;
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// get/update field
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var field = form.field_list[input_id];
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if (field.update) {
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var new_options = [];
|
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if ((['data', 'data_collection', 'drill_down']).indexOf(input.type) != -1) {
|
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new_options = input.options;
|
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} else {
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for (var i in node.options) {
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var opt = node.options[i];
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if (opt.length > 2) {
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new_options.push({
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||||
'label': opt[0],
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'value': opt[1]
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});
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}
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}
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}
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field.update(new_options);
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field.trigger('change');
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console.debug('Updating options for ' + input_id);
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}
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}
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}
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});
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||||
// unset wait mode
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||||
form.wait(false);
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// log success
|
||||
console.debug('tools-form::_refreshForm() - Received new model (see below).');
|
||||
console.debug(new_model);
|
||||
|
||||
// process completed
|
||||
self.deferred.done(process_id);
|
||||
},
|
||||
error : function(response) {
|
||||
// process completed
|
||||
self.deferred.done(process_id);
|
||||
|
||||
// log error
|
||||
console.debug('tools-form::_refreshForm() - Refresh request failed.');
|
||||
console.debug(response);
|
||||
}
|
||||
});
|
||||
}
|
||||
});
|
||||
|
||||
|
||||
@@ -42,6 +42,42 @@ define(['utils/utils', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc',
|
||||
this._build();
|
||||
},
|
||||
|
||||
/** Update available options */
|
||||
update: function(new_model){
|
||||
var self = this;
|
||||
this.data.matchModel(new_model, function(input_id, node) {
|
||||
var input = self.input_list[input_id];
|
||||
if (input && input.options) {
|
||||
if (!_.isEqual(input.options, node.options)) {
|
||||
// backup new options
|
||||
input.options = node.options;
|
||||
|
||||
// get/update field
|
||||
var field = self.field_list[input_id];
|
||||
if (field.update) {
|
||||
var new_options = [];
|
||||
if ((['data', 'data_collection', 'drill_down']).indexOf(input.type) != -1) {
|
||||
new_options = input.options;
|
||||
} else {
|
||||
for (var i in node.options) {
|
||||
var opt = node.options[i];
|
||||
if (opt.length > 2) {
|
||||
new_options.push({
|
||||
'label': opt[0],
|
||||
'value': opt[1]
|
||||
});
|
||||
}
|
||||
}
|
||||
}
|
||||
field.update(new_options);
|
||||
field.trigger('change');
|
||||
console.debug('Updating options for ' + input_id);
|
||||
}
|
||||
}
|
||||
}
|
||||
});
|
||||
},
|
||||
|
||||
/** Set form into wait mode */
|
||||
wait: function(active) {
|
||||
for (var i in this.input_list) {
|
||||
|
||||
@@ -37,11 +37,9 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view',
|
||||
// link this
|
||||
var self = this;
|
||||
|
||||
// configure options
|
||||
this.options = Utils.merge(options, this.optionsDefault);
|
||||
|
||||
// merge form options
|
||||
var form_options = Utils.merge({
|
||||
this.options = Utils.merge(options, this.options);
|
||||
this.options = Utils.merge({
|
||||
icon : 'fa-wrench',
|
||||
title : '<b>' + options.name + '</b> ' + options.description + ' (Galaxy Tool Version ' + options.version + ')',
|
||||
operations : this._operations(),
|
||||
@@ -49,13 +47,13 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view',
|
||||
// by resetting the deferred ajax queue the number of redundant calls is reduced
|
||||
self.deferred.reset();
|
||||
self.deferred.execute(function(){
|
||||
self._updateModel($.extend(true, {}, self.form.data.create()));
|
||||
self._updateModel();
|
||||
});
|
||||
}
|
||||
}, options);
|
||||
}, this.options);
|
||||
|
||||
// create form
|
||||
this.form = new Form(form_options);
|
||||
this.form = new Form(this.options);
|
||||
|
||||
// create footer
|
||||
this._footer();
|
||||
@@ -65,6 +63,139 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view',
|
||||
this.$el.append(this.form.$el);
|
||||
},
|
||||
|
||||
/** Builds a new model through api call and recreates the entire form
|
||||
*/
|
||||
_buildModel: function(options) {
|
||||
// link this
|
||||
var self = this;
|
||||
|
||||
// construct url
|
||||
var build_url = galaxy_config.root + 'api/tools/' + options.id + '/build?';
|
||||
if (options.job_id) {
|
||||
build_url += 'job_id=' + options.job_id;
|
||||
} else {
|
||||
if (options.dataset_id) {
|
||||
build_url += 'dataset_id=' + options.dataset_id;
|
||||
} else {
|
||||
build_url += 'tool_version=' + options.version + '&';
|
||||
var loc = top.location.href;
|
||||
var pos = loc.indexOf('?');
|
||||
if (loc.indexOf('tool_id=') != -1 && pos !== -1) {
|
||||
build_url += loc.slice(pos + 1);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// register process
|
||||
var process_id = this.deferred.register();
|
||||
|
||||
// get initial model
|
||||
Utils.request({
|
||||
type : 'GET',
|
||||
url : build_url,
|
||||
success : function(new_model) {
|
||||
// rebuild form
|
||||
self._buildForm(new_model['tool_model'] || new_model);
|
||||
|
||||
// show version message
|
||||
self.form.message.update({
|
||||
status : 'success',
|
||||
message : 'Now you are using \'' + self.options.name + '\' version ' + self.options.version + '.',
|
||||
persistent : false
|
||||
});
|
||||
|
||||
// process completed
|
||||
self.deferred.done(process_id);
|
||||
|
||||
// log success
|
||||
console.debug('tools-form::initialize() - Initial tool model ready.');
|
||||
console.debug(new_model);
|
||||
},
|
||||
error : function(response) {
|
||||
// process completed
|
||||
self.deferred.done(process_id);
|
||||
|
||||
// log error
|
||||
console.debug('tools-form::initialize() - Initial tool model request failed.');
|
||||
console.debug(response);
|
||||
|
||||
// show error
|
||||
var error_message = response.error || 'Uncaught error.';
|
||||
self.form.modal.show({
|
||||
title : 'Tool cannot be executed',
|
||||
body : error_message,
|
||||
buttons : {
|
||||
'Close' : function() {
|
||||
self.form.modal.hide();
|
||||
}
|
||||
}
|
||||
});
|
||||
}
|
||||
});
|
||||
},
|
||||
|
||||
/** Request a new model for an already created tool form and updates the form inputs
|
||||
*/
|
||||
_updateModel: function() {
|
||||
// model url for request
|
||||
var model_url = this.options.update_url;
|
||||
|
||||
// link this
|
||||
var self = this;
|
||||
|
||||
// create the request dictionary
|
||||
var form = this.form;
|
||||
|
||||
// create the request dictionary
|
||||
var current_state = {
|
||||
tool_id : this.options.id,
|
||||
tool_version : this.options.version,
|
||||
inputs : $.extend(true, {}, self.form.data.create())
|
||||
}
|
||||
|
||||
// set wait mode
|
||||
form.wait(true);
|
||||
|
||||
// register process
|
||||
var process_id = this.deferred.register();
|
||||
|
||||
// log tool state
|
||||
console.debug('tools-form-base::_updateModel() - Sending current state (see below).');
|
||||
console.debug(current_state);
|
||||
|
||||
// post job
|
||||
Utils.request({
|
||||
type : 'POST',
|
||||
url : model_url,
|
||||
data : current_state,
|
||||
success : function(new_model) {
|
||||
// update form with new model
|
||||
self.form.update(new_model['tool_model'] || new_model);
|
||||
|
||||
// custom update
|
||||
self.options.update && self.options.update(new_model);
|
||||
|
||||
// unset wait mode
|
||||
form.wait(false);
|
||||
|
||||
// log success
|
||||
console.debug('tools-form-base::_updateModel() - Received new model (see below).');
|
||||
console.debug(new_model);
|
||||
|
||||
// process completed
|
||||
self.deferred.done(process_id);
|
||||
},
|
||||
error : function(response) {
|
||||
// process completed
|
||||
self.deferred.done(process_id);
|
||||
|
||||
// log error
|
||||
console.debug('tools-form-base::_updateModel() - Refresh request failed.');
|
||||
console.debug(response);
|
||||
}
|
||||
});
|
||||
},
|
||||
|
||||
// create tool operation menu
|
||||
_operations: function() {
|
||||
// link this
|
||||
@@ -87,12 +218,13 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view',
|
||||
icon : 'fa-cube',
|
||||
onclick : function() {
|
||||
// here we update the tool version (some tools encode the version also in the id)
|
||||
options.id = options.id.replace(options.version, this.version);
|
||||
options.version = this.version;
|
||||
|
||||
// rebuild the model and form
|
||||
var id = options.id.replace(options.version, this.version);
|
||||
var version = this.version;
|
||||
// queue model request
|
||||
self.deferred.reset();
|
||||
self.deferred.execute(function(){self._buildModel()});
|
||||
self.deferred.execute(function() {
|
||||
self._buildModel({id: id, version: version})
|
||||
});
|
||||
}
|
||||
});
|
||||
}
|
||||
|
||||
@@ -18,17 +18,24 @@ define(['utils/utils', 'mvc/tools/tools-form-base'],
|
||||
this.post_job_actions = this.node.post_job_actions || {};
|
||||
|
||||
// initialize parameters
|
||||
this.options = options;
|
||||
options = Utils.merge(options, {
|
||||
// set labels
|
||||
text_enable : 'Set in Advance',
|
||||
text_disable : 'Set at Runtime',
|
||||
|
||||
// set labels
|
||||
this.options.text_enable = 'Set in Advance';
|
||||
this.options.text_disable = 'Set at Runtime';
|
||||
// configure workflow style
|
||||
is_dynamic : false,
|
||||
narrow : true,
|
||||
initial_errors : true,
|
||||
cls : 'ui-portlet-narrow',
|
||||
|
||||
// configure workflow style
|
||||
this.options.is_dynamic = false;
|
||||
this.options.narrow = true;
|
||||
this.options.initial_errors = true;
|
||||
this.options.cls_portlet = 'ui-portlet-narrow';
|
||||
// configure model update
|
||||
update_url : galaxy_config.root + 'api/workflows/build_module',
|
||||
update : function(data) {
|
||||
self.node.update_field_data(data);
|
||||
self.form.errors(data && data.tool_model)
|
||||
}
|
||||
});
|
||||
|
||||
// declare fields as optional
|
||||
Utils.deepeach(options.inputs, function(item) {
|
||||
@@ -257,73 +264,6 @@ define(['utils/utils', 'mvc/tools/tools-form-base'],
|
||||
|
||||
// return final configuration
|
||||
return input_config;
|
||||
},
|
||||
|
||||
/** Builds a new model through api call and recreates the entire form
|
||||
*/
|
||||
_buildModel: function() {
|
||||
Galaxy.modal.show({
|
||||
title : 'Coming soon...',
|
||||
body : 'This feature has not been implemented yet.',
|
||||
buttons : {
|
||||
'Close' : function() {
|
||||
Galaxy.modal.hide();
|
||||
}
|
||||
}
|
||||
});
|
||||
},
|
||||
|
||||
/** Request a new model for an already created tool form and updates the form inputs
|
||||
*/
|
||||
_updateModel: function(current_state) {
|
||||
// link self
|
||||
var self = this;
|
||||
|
||||
// create the request dictionary
|
||||
current_state = {
|
||||
tool_id : this.options.id,
|
||||
tool_version : this.options.version,
|
||||
inputs : current_state
|
||||
}
|
||||
|
||||
// log tool state
|
||||
console.debug('tools-form-workflow::_refreshForm() - Refreshing states.');
|
||||
console.debug(current_state);
|
||||
|
||||
// register process
|
||||
var process_id = this.deferred.register();
|
||||
|
||||
// build model url for request
|
||||
var model_url = galaxy_config.root + 'api/workflows/build_module';
|
||||
|
||||
// post job
|
||||
Utils.request({
|
||||
type : 'POST',
|
||||
url : model_url,
|
||||
data : current_state,
|
||||
success : function(data) {
|
||||
// update node in workflow module
|
||||
self.node.update_field_data(data);
|
||||
|
||||
// highlight errors
|
||||
self.form.errors(data && data.tool_model);
|
||||
|
||||
// process completed
|
||||
self.deferred.done(process_id);
|
||||
|
||||
// log success
|
||||
console.debug('tools-form::_refreshForm() - States refreshed.');
|
||||
console.debug(data);
|
||||
},
|
||||
error : function(response) {
|
||||
// process completed
|
||||
self.deferred.done(process_id);
|
||||
|
||||
// log error
|
||||
console.debug('tools-form::_refreshForm() - Refresh request failed.');
|
||||
console.debug(response);
|
||||
}
|
||||
});
|
||||
}
|
||||
});
|
||||
|
||||
|
||||
@@ -8,180 +8,24 @@ define(['utils/utils', 'mvc/ui/ui-misc', 'mvc/tools/tools-form-base', 'mvc/tools
|
||||
var View = ToolFormBase.extend({
|
||||
// initialize
|
||||
initialize: function(options) {
|
||||
// create options dictionary
|
||||
var self = this;
|
||||
options.buttons = {
|
||||
execute : new Ui.Button({
|
||||
icon : 'fa-check',
|
||||
tooltip : 'Execute: ' + options.name,
|
||||
title : 'Execute',
|
||||
cls : 'btn btn-primary',
|
||||
floating : 'clear',
|
||||
onclick : function() {
|
||||
ToolJobs.submit(self.form, options);
|
||||
}
|
||||
})
|
||||
};
|
||||
options = Utils.merge(options, {
|
||||
update_url : galaxy_config.root + 'api/tools/' + options.id + '/build',
|
||||
buttons : {
|
||||
execute : new Ui.Button({
|
||||
icon : 'fa-check',
|
||||
tooltip : 'Execute: ' + options.name,
|
||||
title : 'Execute',
|
||||
cls : 'btn btn-primary',
|
||||
floating : 'clear',
|
||||
onclick : function() {
|
||||
ToolJobs.submit(self.form, options);
|
||||
}
|
||||
})
|
||||
}
|
||||
});
|
||||
ToolFormBase.prototype.initialize.call(this, options);
|
||||
},
|
||||
|
||||
/** Builds a new model through api call and recreates the entire form
|
||||
*/
|
||||
_buildModel: function() {
|
||||
// link this
|
||||
var self = this;
|
||||
|
||||
// construct url
|
||||
var model_url = galaxy_config.root + 'api/tools/' + this.options.id + '/build?';
|
||||
if (this.options.job_id) {
|
||||
model_url += 'job_id=' + this.options.job_id;
|
||||
} else {
|
||||
if (this.options.dataset_id) {
|
||||
model_url += 'dataset_id=' + this.options.dataset_id;
|
||||
} else {
|
||||
model_url += 'tool_version=' + this.options.version + '&';
|
||||
var loc = top.location.href;
|
||||
var pos = loc.indexOf('?');
|
||||
if (loc.indexOf('tool_id=') != -1 && pos !== -1) {
|
||||
model_url += loc.slice(pos + 1);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// register process
|
||||
var process_id = this.deferred.register();
|
||||
|
||||
// get initial model
|
||||
Utils.request({
|
||||
type : 'GET',
|
||||
url : model_url,
|
||||
success : function(response) {
|
||||
// build new tool form
|
||||
self._buildForm(response);
|
||||
|
||||
// notification
|
||||
self.form.message.update({
|
||||
status : 'success',
|
||||
message : 'Now you are using \'' + self.options.name + '\' version ' + self.options.version + '.',
|
||||
persistent : false
|
||||
});
|
||||
|
||||
// process completed
|
||||
self.deferred.done(process_id);
|
||||
|
||||
// log success
|
||||
console.debug('tools-form::initialize() - Initial tool model ready.');
|
||||
console.debug(response);
|
||||
},
|
||||
error : function(response) {
|
||||
// process completed
|
||||
self.deferred.done(process_id);
|
||||
|
||||
// log error
|
||||
console.debug('tools-form::initialize() - Initial tool model request failed.');
|
||||
console.debug(response);
|
||||
|
||||
// show error
|
||||
var error_message = response.error || 'Uncaught error.';
|
||||
self.form.modal.show({
|
||||
title : 'Tool cannot be executed',
|
||||
body : error_message,
|
||||
buttons : {
|
||||
'Close' : function() {
|
||||
self.form.modal.hide();
|
||||
}
|
||||
}
|
||||
});
|
||||
}
|
||||
});
|
||||
},
|
||||
|
||||
/** Request a new model for an already created tool form and updates the form inputs
|
||||
*/
|
||||
_updateModel: function(current_state) {
|
||||
// link this
|
||||
var self = this;
|
||||
|
||||
// create the request dictionary
|
||||
var form = this.form;
|
||||
|
||||
// create the request dictionary
|
||||
var current_state = {
|
||||
tool_id : this.options.id,
|
||||
tool_version : this.options.version,
|
||||
inputs : current_state
|
||||
}
|
||||
|
||||
// set wait mode
|
||||
form.wait(true);
|
||||
|
||||
// register process
|
||||
var process_id = this.deferred.register();
|
||||
|
||||
// log tool state
|
||||
console.debug('tools-form::_refreshForm() - Sending current state (see below).');
|
||||
console.debug(current_state);
|
||||
|
||||
// build model url for request
|
||||
var model_url = galaxy_config.root + 'api/tools/' + this.options.id + '/build';
|
||||
|
||||
// post job
|
||||
Utils.request({
|
||||
type : 'POST',
|
||||
url : model_url,
|
||||
data : current_state,
|
||||
success : function(new_model) {
|
||||
// update form
|
||||
form.data.matchModel(new_model, function(input_id, node) {
|
||||
var input = form.input_list[input_id];
|
||||
if (input && input.options) {
|
||||
if (!_.isEqual(input.options, node.options)) {
|
||||
// backup new options
|
||||
input.options = node.options;
|
||||
|
||||
// get/update field
|
||||
var field = form.field_list[input_id];
|
||||
if (field.update) {
|
||||
var new_options = [];
|
||||
if ((['data', 'data_collection', 'drill_down']).indexOf(input.type) != -1) {
|
||||
new_options = input.options;
|
||||
} else {
|
||||
for (var i in node.options) {
|
||||
var opt = node.options[i];
|
||||
if (opt.length > 2) {
|
||||
new_options.push({
|
||||
'label': opt[0],
|
||||
'value': opt[1]
|
||||
});
|
||||
}
|
||||
}
|
||||
}
|
||||
field.update(new_options);
|
||||
field.trigger('change');
|
||||
console.debug('Updating options for ' + input_id);
|
||||
}
|
||||
}
|
||||
}
|
||||
});
|
||||
|
||||
// unset wait mode
|
||||
form.wait(false);
|
||||
|
||||
// log success
|
||||
console.debug('tools-form::_refreshForm() - Received new model (see below).');
|
||||
console.debug(new_model);
|
||||
|
||||
// process completed
|
||||
self.deferred.done(process_id);
|
||||
},
|
||||
error : function(response) {
|
||||
// process completed
|
||||
self.deferred.done(process_id);
|
||||
|
||||
// log error
|
||||
console.debug('tools-form::_refreshForm() - Refresh request failed.');
|
||||
console.debug(response);
|
||||
}
|
||||
});
|
||||
}
|
||||
});
|
||||
|
||||
|
||||
@@ -1 +1 @@
|
||||
define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/form/form-section","mvc/form/form-data"],function(c,b,e,a,d){return Backbone.View.extend({initialize:function(f){this.optionsDefault={is_dynamic:true,narrow:false,initial_errors:false,cls:"ui-portlet-limited"};this.options=c.merge(f,this.optionsDefault);console.debug(this.options);var g=parent.Galaxy;if(g&&g.modal){this.modal=g.modal}else{this.modal=new e.Modal.View()}this.setElement("<div/>");this._build()},wait:function(j){for(var g in this.input_list){var h=this.field_list[g];var f=this.input_list[g];if(f.is_dynamic&&h.wait&&h.unwait){if(j){h.wait()}else{h.unwait()}}}},reciept:function(f){this.$el.empty();this.$el.append(f)},highlight:function(g,h,f){var i=this.element_list[g];if(i){i.error(h||"Please verify this parameter.");if(!f){$("html, body").animate({scrollTop:i.$el.offset().top-20},500)}}},errors:function(h){this.trigger("reset");if(h&&h.errors){var i=this.data.matchResponse(h.errors);for(var g in this.element_list){var f=this.element_list[g];if(i[g]){this.highlight(g,i[g],true)}}}},_build:function(){var f=this;this.off("change");this.off("reset");this.field_list={};this.input_list={};this.element_list={};this.data=new d(this);this._renderForm();this.data.create();if(this.options.initial_errors){this.errors(this.options)}var g=this.data.checksum();this.on("change",function(){var h=f.data.checksum();if(h!=g){g=h;f.options.onchange&&f.options.onchange()}});this.on("reset",function(){for(var h in this.element_list){this.element_list[h].reset()}})},_renderForm:function(){this.message=new e.Message();this.section=new a.View(this,{inputs:this.options.inputs});this.portlet=new b.View({icon:"fa-wrench",title:this.options.title,cls:this.options.cls,operations:this.options.operations,buttons:this.options.buttons});this.portlet.append(this.message.$el.addClass("ui-margin-top"));this.portlet.append(this.section.$el);this.$el.empty();this.$el.append(this.portlet.$el);if(this.options.message){this.message.update({persistent:true,status:"warning",message:this.options.message})}console.debug("tools-form-base::initialize() - Completed.")}})});
|
||||
define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/form/form-section","mvc/form/form-data"],function(c,b,e,a,d){return Backbone.View.extend({initialize:function(f){this.optionsDefault={is_dynamic:true,narrow:false,initial_errors:false,cls:"ui-portlet-limited"};this.options=c.merge(f,this.optionsDefault);console.debug(this.options);var g=parent.Galaxy;if(g&&g.modal){this.modal=g.modal}else{this.modal=new e.Modal.View()}this.setElement("<div/>");this._build()},update:function(f){var g=this;this.data.matchModel(f,function(j,n){var h=g.input_list[j];if(h&&h.options){if(!_.isEqual(h.options,n.options)){h.options=n.options;var o=g.field_list[j];if(o.update){var m=[];if((["data","data_collection","drill_down"]).indexOf(h.type)!=-1){m=h.options}else{for(var l in n.options){var k=n.options[l];if(k.length>2){m.push({label:k[0],value:k[1]})}}}o.update(m);o.trigger("change");console.debug("Updating options for "+j)}}}})},wait:function(j){for(var g in this.input_list){var h=this.field_list[g];var f=this.input_list[g];if(f.is_dynamic&&h.wait&&h.unwait){if(j){h.wait()}else{h.unwait()}}}},reciept:function(f){this.$el.empty();this.$el.append(f)},highlight:function(g,h,f){var i=this.element_list[g];if(i){i.error(h||"Please verify this parameter.");if(!f){$("html, body").animate({scrollTop:i.$el.offset().top-20},500)}}},errors:function(h){this.trigger("reset");if(h&&h.errors){var i=this.data.matchResponse(h.errors);for(var g in this.element_list){var f=this.element_list[g];if(i[g]){this.highlight(g,i[g],true)}}}},_build:function(){var f=this;this.off("change");this.off("reset");this.field_list={};this.input_list={};this.element_list={};this.data=new d(this);this._renderForm();this.data.create();if(this.options.initial_errors){this.errors(this.options)}var g=this.data.checksum();this.on("change",function(){var h=f.data.checksum();if(h!=g){g=h;f.options.onchange&&f.options.onchange()}});this.on("reset",function(){for(var h in this.element_list){this.element_list[h].reset()}})},_renderForm:function(){this.message=new e.Message();this.section=new a.View(this,{inputs:this.options.inputs});this.portlet=new b.View({icon:"fa-wrench",title:this.options.title,cls:this.options.cls,operations:this.options.operations,buttons:this.options.buttons});this.portlet.append(this.message.$el.addClass("ui-margin-top"));this.portlet.append(this.section.$el);this.$el.empty();this.$el.append(this.portlet.$el);if(this.options.message){this.message.update({persistent:true,status:"warning",message:this.options.message})}console.debug("tools-form-base::initialize() - Completed.")}})});
|
||||
@@ -1 +1 @@
|
||||
define(["utils/utils","utils/deferred","mvc/ui/ui-misc","mvc/form/form-view","mvc/tools/tools-template","mvc/citation/citation-model","mvc/citation/citation-view"],function(f,d,g,c,a,e,b){return Backbone.View.extend({initialize:function(h){var i=parent.Galaxy;if(i&&i.currUser){this.is_admin=i.currUser.get("is_admin")}else{this.is_admin=false}this.deferred=new d();this.setElement("<div/>");this.container=h.container||"body";$(this.container).append(this.$el);this._buildForm(h)},_buildForm:function(i){var h=this;this.options=f.merge(i,this.optionsDefault);var j=f.merge({icon:"fa-wrench",title:"<b>"+i.name+"</b> "+i.description+" (Galaxy Tool Version "+i.version+")",operations:this._operations(),onchange:function(k){h.deferred.reset();h.deferred.execute(function(){h._updateModel($.extend(true,{},h.form.data.create()))})}},i);this.form=new c(j);this._footer();this.$el.empty();this.$el.append(this.form.$el)},_operations:function(){var j=this;var k=this.options;var n=new g.ButtonMenu({icon:"fa-cubes",title:(!k.narrow&&"Versions")||null,tooltip:"Select another tool version"});if(k.versions&&k.versions.length>1){for(var m in k.versions){var h=k.versions[m];if(h!=k.version){n.addMenu({title:"Switch to "+h,version:h,icon:"fa-cube",onclick:function(){k.id=k.id.replace(k.version,this.version);k.version=this.version;j.deferred.reset();j.deferred.execute(function(){j._buildModel()})}})}}}else{n.$el.hide()}var l=new g.ButtonMenu({icon:"fa-caret-down",title:(!k.narrow&&"Options")||null,tooltip:"View available options"});if(k.biostar_url){l.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(k.biostar_url+"/p/new/post/")}});l.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(k.biostar_url+"/local/search/page/?q="+k.name)}})}l.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="+k.id)}});if(this.is_admin){l.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+k.id+"/download"}})}if(k.requirements&&k.requirements.length>0){l.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){if(!this.visible){this.visible=true;j.form.message.update({persistent:true,message:a.requirements(k),status:"info"})}else{this.visible=false;j.form.message.update({message:""})}}})}if(k.sharable_url){l.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(k.sharable_url)}})}return{menu:l,versions:n}},_footer:function(){var i=this.options;if(i.help!=""){this.form.$el.append(a.help(i))}if(i.citations){var k=$("<div/>");var h=new e.ToolCitationCollection();h.tool_id=i.id;var j=new b.CitationListView({el:k,collection:h});j.render();h.fetch();this.form.$el.append(k)}}})});
|
||||
define(["utils/utils","utils/deferred","mvc/ui/ui-misc","mvc/form/form-view","mvc/tools/tools-template","mvc/citation/citation-model","mvc/citation/citation-view"],function(f,d,g,c,a,e,b){return Backbone.View.extend({initialize:function(h){var i=parent.Galaxy;if(i&&i.currUser){this.is_admin=i.currUser.get("is_admin")}else{this.is_admin=false}this.deferred=new d();this.setElement("<div/>");this.container=h.container||"body";$(this.container).append(this.$el);this._buildForm(h)},_buildForm:function(i){var h=this;this.options=f.merge(i,this.options);this.options=f.merge({icon:"fa-wrench",title:"<b>"+i.name+"</b> "+i.description+" (Galaxy Tool Version "+i.version+")",operations:this._operations(),onchange:function(j){h.deferred.reset();h.deferred.execute(function(){h._updateModel()})}},this.options);this.form=new c(this.options);this._footer();this.$el.empty();this.$el.append(this.form.$el)},_buildModel:function(j){var i=this;var h=galaxy_config.root+"api/tools/"+j.id+"/build?";if(j.job_id){h+="job_id="+j.job_id}else{if(j.dataset_id){h+="dataset_id="+j.dataset_id}else{h+="tool_version="+j.version+"&";var l=top.location.href;var m=l.indexOf("?");if(l.indexOf("tool_id=")!=-1&&m!==-1){h+=l.slice(m+1)}}}var k=this.deferred.register();f.request({type:"GET",url:h,success:function(n){i._buildForm(n.tool_model||n);i.form.message.update({status:"success",message:"Now you are using '"+i.options.name+"' version "+i.options.version+".",persistent:false});i.deferred.done(k);console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(n)},error:function(n){i.deferred.done(k);console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(n);var o=n.error||"Uncaught error.";i.form.modal.show({title:"Tool cannot be executed",body:o,buttons:{Close:function(){i.form.modal.hide()}}})}})},_updateModel:function(){var j=this.options.update_url;var h=this;var k=this.form;var i={tool_id:this.options.id,tool_version:this.options.version,inputs:$.extend(true,{},h.form.data.create())};k.wait(true);var l=this.deferred.register();console.debug("tools-form-base::_updateModel() - Sending current state (see below).");console.debug(i);f.request({type:"POST",url:j,data:i,success:function(m){h.form.update(m.tool_model||m);h.options.update&&h.options.update(m);k.wait(false);console.debug("tools-form-base::_updateModel() - Received new model (see below).");console.debug(m);h.deferred.done(l)},error:function(m){h.deferred.done(l);console.debug("tools-form-base::_updateModel() - Refresh request failed.");console.debug(m)}})},_operations:function(){var j=this;var k=this.options;var n=new g.ButtonMenu({icon:"fa-cubes",title:(!k.narrow&&"Versions")||null,tooltip:"Select another tool version"});if(k.versions&&k.versions.length>1){for(var m in k.versions){var h=k.versions[m];if(h!=k.version){n.addMenu({title:"Switch to "+h,version:h,icon:"fa-cube",onclick:function(){var o=k.id.replace(k.version,this.version);var i=this.version;j.deferred.reset();j.deferred.execute(function(){j._buildModel({id:o,version:i})})}})}}}else{n.$el.hide()}var l=new g.ButtonMenu({icon:"fa-caret-down",title:(!k.narrow&&"Options")||null,tooltip:"View available options"});if(k.biostar_url){l.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(k.biostar_url+"/p/new/post/")}});l.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(k.biostar_url+"/local/search/page/?q="+k.name)}})}l.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="+k.id)}});if(this.is_admin){l.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+k.id+"/download"}})}if(k.requirements&&k.requirements.length>0){l.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){if(!this.visible){this.visible=true;j.form.message.update({persistent:true,message:a.requirements(k),status:"info"})}else{this.visible=false;j.form.message.update({message:""})}}})}if(k.sharable_url){l.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(k.sharable_url)}})}return{menu:l,versions:n}},_footer:function(){var i=this.options;if(i.help!=""){this.form.$el.append(a.help(i))}if(i.citations){var k=$("<div/>");var h=new e.ToolCitationCollection();h.tool_id=i.id;var j=new b.CitationListView({el:k,collection:h});j.render();h.fetch();this.form.$el.append(k)}}})});
|
||||
@@ -1 +1 @@
|
||||
define(["utils/utils","mvc/tools/tools-form-base"],function(b,a){var c=a.extend({initialize:function(e){this.node=workflow.active_node;if(!this.node){console.debug("FAILED - tools-form-workflow:initialize() - Node not found in workflow.");return}this.post_job_actions=this.node.post_job_actions||{};this.options=e;this.options.text_enable="Set in Advance";this.options.text_disable="Set at Runtime";this.options.is_dynamic=false;this.options.narrow=true;this.options.initial_errors=true;this.options.cls_portlet="ui-portlet-narrow";b.deepeach(e.inputs,function(f){if(f.type){f.optional=(["data","data_hidden","hidden","repeat","conditional"]).indexOf(f.type)==-1}});b.deepeach(e.inputs,function(f){if(f.type){if(f.type=="conditional"){f.test_param.optional=false}}});var d=this;b.get({url:galaxy_config.root+"api/datatypes",cache:true,success:function(f){d.datatypes=f;d._makeSections(e.inputs);a.prototype.initialize.call(d,e)}})},_makeSections:function(d){d[b.uuid()]={label:"Annotation / Notes",name:"annotation",type:"text",area:true,help:"Add an annotation or note for this step. It will be shown with the workflow.",value:this.node.annotation};var f=this.node.output_terminals&&Object.keys(this.node.output_terminals)[0];if(f){d[b.uuid()]={name:"pja__"+f+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(this.post_job_actions["EmailAction"+f])),ignore:"false",help:"An email notification will be send when the job has completed.",payload:{host:window.location.host}};d[b.uuid()]={name:"pja__"+f+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(this.post_job_actions["DeleteIntermediatesAction"+f])),ignore:"false",help:"Delete intermediate outputs if they are not used as input for another job."};for(var e in this.node.output_terminals){d[b.uuid()]=this._makeSection(e)}}},_makeSection:function(h){var g=[];for(key in this.datatypes){g.push({0:this.datatypes[key],1:this.datatypes[key]})}g.sort(function(j,i){return j.label>i.label?1:j.label<i.label?-1:0});g.unshift({0:"Sequences",1:"Sequences"});g.unshift({0:"Roadmaps",1:"Roadmaps"});g.unshift({0:"Leave unchanged",1:"__empty__"});var f={label:"Add Actions: '"+h+"'",type:"section",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:g,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."},{label:"Assign columns",type:"section",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."}]};var d=this;function e(n,o){o=o||[];o.push(n);for(var m in n.inputs){var k=n.inputs[m];if(k.action){k.name="pja__"+h+"__"+k.action;if(k.argument){k.name+="__"+k.argument}if(k.payload){for(var s in k.payload){var q=k.payload[s];k.payload[k.name+"__"+s]=q;delete q}}var r=d.post_job_actions[k.action+h];if(r){for(var l in o){o[l].expand=true}if(k.argument){k.value=r.action_arguments&&r.action_arguments[k.argument]||k.value}else{k.value="true"}}}if(k.inputs){e(k,o.slice(0))}}}e(f);return f},_buildModel:function(){Galaxy.modal.show({title:"Coming soon...",body:"This feature has not been implemented yet.",buttons:{Close:function(){Galaxy.modal.hide()}}})},_updateModel:function(e){var d=this;e={tool_id:this.options.id,tool_version:this.options.version,inputs:e};console.debug("tools-form-workflow::_refreshForm() - Refreshing states.");console.debug(e);var g=this.deferred.register();var f=galaxy_config.root+"api/workflows/build_module";b.request({type:"POST",url:f,data:e,success:function(h){d.node.update_field_data(h);d.form.errors(h&&h.tool_model);d.deferred.done(g);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(h)},error:function(h){d.deferred.done(g);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(h)}})}});return{View:c}});
|
||||
define(["utils/utils","mvc/tools/tools-form-base"],function(b,a){var c=a.extend({initialize:function(e){this.node=workflow.active_node;if(!this.node){console.debug("FAILED - tools-form-workflow:initialize() - Node not found in workflow.");return}this.post_job_actions=this.node.post_job_actions||{};e=b.merge(e,{text_enable:"Set in Advance",text_disable:"Set at Runtime",is_dynamic:false,narrow:true,initial_errors:true,cls:"ui-portlet-narrow",update_url:galaxy_config.root+"api/workflows/build_module",update:function(f){d.node.update_field_data(f);d.form.errors(f&&f.tool_model)}});b.deepeach(e.inputs,function(f){if(f.type){f.optional=(["data","data_hidden","hidden","repeat","conditional"]).indexOf(f.type)==-1}});b.deepeach(e.inputs,function(f){if(f.type){if(f.type=="conditional"){f.test_param.optional=false}}});var d=this;b.get({url:galaxy_config.root+"api/datatypes",cache:true,success:function(f){d.datatypes=f;d._makeSections(e.inputs);a.prototype.initialize.call(d,e)}})},_makeSections:function(d){d[b.uuid()]={label:"Annotation / Notes",name:"annotation",type:"text",area:true,help:"Add an annotation or note for this step. It will be shown with the workflow.",value:this.node.annotation};var f=this.node.output_terminals&&Object.keys(this.node.output_terminals)[0];if(f){d[b.uuid()]={name:"pja__"+f+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(this.post_job_actions["EmailAction"+f])),ignore:"false",help:"An email notification will be send when the job has completed.",payload:{host:window.location.host}};d[b.uuid()]={name:"pja__"+f+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(this.post_job_actions["DeleteIntermediatesAction"+f])),ignore:"false",help:"Delete intermediate outputs if they are not used as input for another job."};for(var e in this.node.output_terminals){d[b.uuid()]=this._makeSection(e)}}},_makeSection:function(h){var g=[];for(key in this.datatypes){g.push({0:this.datatypes[key],1:this.datatypes[key]})}g.sort(function(j,i){return j.label>i.label?1:j.label<i.label?-1:0});g.unshift({0:"Sequences",1:"Sequences"});g.unshift({0:"Roadmaps",1:"Roadmaps"});g.unshift({0:"Leave unchanged",1:"__empty__"});var f={label:"Add Actions: '"+h+"'",type:"section",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:g,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."},{label:"Assign columns",type:"section",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."}]};var d=this;function e(n,o){o=o||[];o.push(n);for(var m in n.inputs){var k=n.inputs[m];if(k.action){k.name="pja__"+h+"__"+k.action;if(k.argument){k.name+="__"+k.argument}if(k.payload){for(var s in k.payload){var q=k.payload[s];k.payload[k.name+"__"+s]=q;delete q}}var r=d.post_job_actions[k.action+h];if(r){for(var l in o){o[l].expand=true}if(k.argument){k.value=r.action_arguments&&r.action_arguments[k.argument]||k.value}else{k.value="true"}}}if(k.inputs){e(k,o.slice(0))}}}e(f);return f}});return{View:c}});
|
||||
@@ -1 +1 @@
|
||||
define(["utils/utils","mvc/ui/ui-misc","mvc/tools/tools-form-base","mvc/tools/tools-jobs"],function(c,e,b,a){var d=b.extend({initialize:function(g){var f=this;g.buttons={execute:new e.Button({icon:"fa-check",tooltip:"Execute: "+g.name,title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){a.submit(f.form,g)}})};b.prototype.initialize.call(this,g)},_buildModel:function(){var f=this;var g=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){g+="job_id="+this.options.job_id}else{if(this.options.dataset_id){g+="dataset_id="+this.options.dataset_id}else{g+="tool_version="+this.options.version+"&";var i=top.location.href;var j=i.indexOf("?");if(i.indexOf("tool_id=")!=-1&&j!==-1){g+=i.slice(j+1)}}}var h=this.deferred.register();c.request({type:"GET",url:g,success:function(k){f._buildForm(k);f.form.message.update({status:"success",message:"Now you are using '"+f.options.name+"' version "+f.options.version+".",persistent:false});f.deferred.done(h);console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(k)},error:function(k){f.deferred.done(h);console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(k);var l=k.error||"Uncaught error.";f.form.modal.show({title:"Tool cannot be executed",body:l,buttons:{Close:function(){f.form.modal.hide()}}})}})},_updateModel:function(g){var f=this;var i=this.form;var g={tool_id:this.options.id,tool_version:this.options.version,inputs:g};i.wait(true);var j=this.deferred.register();console.debug("tools-form::_refreshForm() - Sending current state (see below).");console.debug(g);var h=galaxy_config.root+"api/tools/"+this.options.id+"/build";c.request({type:"POST",url:h,data:g,success:function(k){i.data.matchModel(k,function(m,q){var l=i.input_list[m];if(l&&l.options){if(!_.isEqual(l.options,q.options)){l.options=q.options;var r=i.field_list[m];if(r.update){var p=[];if((["data","data_collection","drill_down"]).indexOf(l.type)!=-1){p=l.options}else{for(var o in q.options){var n=q.options[o];if(n.length>2){p.push({label:n[0],value:n[1]})}}}r.update(p);r.trigger("change");console.debug("Updating options for "+m)}}}});i.wait(false);console.debug("tools-form::_refreshForm() - Received new model (see below).");console.debug(k);f.deferred.done(j)},error:function(k){f.deferred.done(j);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(k)}})}});return{View:d}});
|
||||
define(["utils/utils","mvc/ui/ui-misc","mvc/tools/tools-form-base","mvc/tools/tools-jobs"],function(c,e,b,a){var d=b.extend({initialize:function(g){var f=this;g=c.merge(g,{update_url:galaxy_config.root+"api/tools/"+g.id+"/build",buttons:{execute:new e.Button({icon:"fa-check",tooltip:"Execute: "+g.name,title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){a.submit(f.form,g)}})}});b.prototype.initialize.call(this,g)}});return{View:d}});
|
||||
Reference in New Issue
Block a user