mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-16 15:45:04 +08:00
Parameters: Fix initial value for drill downs, Workflow/ToolForm: Move module building to api
This commit is contained in:
Aysam Guerler
@@ -275,10 +275,16 @@ define(['utils/utils', 'mvc/tools/tools-form-base'],
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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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// create the request dictionary
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// link self
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var self = this;
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var current_state = this.tree.finalize();
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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 : this.tree.finalize()
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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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@@ -287,11 +293,11 @@ define(['utils/utils', 'mvc/tools/tools-form-base'],
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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 + 'workflow/editor_form_post?tool_id=' + this.options.id + '&__is_dynamic__=False';
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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 : 'GET',
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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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@@ -10,13 +10,13 @@ return Backbone.Model.extend({
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initialize: function(app) {
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this.app = app;
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},
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/** Convert dictionary representation into tool api specific flat dictionary format.
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*/
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finalize: function(patch) {
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// link this
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var self = this;
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// dictionary with api specific identifiers
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this.map_dict = {};
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@@ -24,24 +24,24 @@ return Backbone.Model.extend({
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if (!this.app.section) {
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return {};
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}
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// ensure that dictionary with patching functions exists
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patch = patch || {};
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// dictionary formatted for job submission or tool form update
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var result_dict = {};
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// prepare full dictionary
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var dict = {};
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// fill dictionary from dom
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this._iterate(this.app.section.$el, dict);
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// add identifier and value to job definition
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function add(job_input_id, input_id, input_value) {
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// add entry to result dictionary
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result_dict[job_input_id] = input_value;
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// backup id mapping
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self.map_dict[job_input_id] = input_id;
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};
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@@ -53,21 +53,21 @@ return Backbone.Model.extend({
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if (node.input) {
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// get node
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var input = node.input;
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// create identifier
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var job_input_id = identifier;
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if (identifier != '') {
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job_input_id += '|';
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}
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job_input_id += input.name;
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// process input type
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switch (input.type) {
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// handle repeats
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case 'repeat':
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// section identifier
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var section_label = 'section-';
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// collect repeat block identifiers
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var block_indices = [];
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var block_prefix = null;
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@@ -81,10 +81,10 @@ return Backbone.Model.extend({
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}
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}
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}
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// sort repeat blocks
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block_indices.sort(function(a,b) { return a - b; });
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// add to response dictionary in created order
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var index = 0;
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for (var i in block_indices) {
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@@ -98,10 +98,10 @@ return Backbone.Model.extend({
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if (patch[input.test_param.type]) {
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value = patch[input.test_param.type](value);
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}
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// add conditional value
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add (job_input_id + '|' + input.test_param.name, input.id, value);
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// identify selected case
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var selectedCase = self.matchCase(input, value);
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if (selectedCase != -1) {
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@@ -116,22 +116,17 @@ return Backbone.Model.extend({
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// get field
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var field = self.app.field_list[input.id];
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if (field && field.value) {
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// get and patch field value
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// validate field value
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var value = field.value();
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if (patch[input.type]) {
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value = patch[input.type](value);
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}
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// validate field value
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if (field.skip) {
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continue;
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}
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// validate field value
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if (field.validate && !field.validate()) {
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value = null;
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}
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// get and patch field value
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if (patch[input.type]) {
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value = patch[input.type](value);
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}
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// ignore certain values
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if (input.ignore === undefined || (value !== null && input.ignore != value)) {
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// add value to submission
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@@ -149,20 +144,20 @@ return Backbone.Model.extend({
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}
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}
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}
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// start conversion
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convert('', dict);
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// return result
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return result_dict;
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},
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/** Match job definition identifier to input element identifier
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*/
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match: function (job_input_id) {
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return this.map_dict && this.map_dict[job_input_id];
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},
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/** Match conditional values to selected cases
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*/
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matchCase: function(input, value) {
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@@ -174,27 +169,27 @@ return Backbone.Model.extend({
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value = input.test_param.falsevalue || 'false';
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}
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}
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// find selected case
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for (var i in input.cases) {
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if (input.cases[i].value == value) {
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return i;
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}
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}
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// selected case not found
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return -1;
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},
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/** Matches identifier from api model to input elements
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*/
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matchModel: function(model, callback) {
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// final result dictionary
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var result = {};
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// link this
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var self = this;
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// search throughout response
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function search (id, head) {
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for (var i in head) {
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@@ -224,23 +219,23 @@ return Backbone.Model.extend({
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}
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}
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}
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// match all ids and return messages
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search('', model.inputs);
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// return matched results
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return result;
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},
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/** Matches identifier from api response to input elements
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*/
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matchResponse: function(response) {
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// final result dictionary
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var result = {};
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// link this
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var self = this;
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// search throughout response
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function search (id, head) {
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if (typeof head === 'string') {
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@@ -262,14 +257,14 @@ return Backbone.Model.extend({
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}
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}
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}
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// match all ids and return messages
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search('', response);
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// return matched results
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return result;
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},
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/** Iterate through the tool form dom and map it to the dictionary.
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*/
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_iterate: function(parent, dict) {
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@@ -279,15 +274,15 @@ return Backbone.Model.extend({
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children.each(function() {
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// get child element
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var child = this;
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// get id
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var id = $(child).attr('id');
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// create new branch
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if ($(child).hasClass('section-row')) {
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// create sub dictionary
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dict[id] = {};
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// add input element if it exists
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var input = self.app.input_list[id];
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if (input) {
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@@ -295,7 +290,7 @@ return Backbone.Model.extend({
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input : input
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}
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}
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// fill sub dictionary
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self._iterate(child, dict[id]);
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} else {
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@@ -2250,13 +2250,12 @@ class Tool( object, Dictifiable ):
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return tool_dict
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def to_json (self, trans, **kwd):
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def to_json (self, trans, kwd={}, is_dynamic=True):
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"""
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Recursively creates a tool dictionary containing repeats, dynamic options and updated states.
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"""
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job_id = kwd.get('__job_id__', None)
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dataset_id = kwd.get('__dataset_id__', None)
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is_dynamic = string_as_bool(kwd.get('__is_dynamic__', True))
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# load job details if provided
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job = None
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@@ -1618,6 +1618,8 @@ class DrillDownSelectToolParameter( SelectToolParameter ):
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return UnvalidatedValue( None )
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initial_values = []
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recurse_options( initial_values, self.get_options( trans=trans, other_values=context ) )
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if len( initial_values ) == 0:
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initial_values = None
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return initial_values
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def value_to_display_text( self, value, app ):
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@@ -76,14 +76,10 @@ class ToolsController( BaseAPIController, UsesVisualizationMixin ):
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GET /api/tools/{tool_id}/build
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Returns a tool model including dynamic parameters and updated values, repeats block etc.
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"""
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tool_id = urllib.unquote_plus( id )
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tool_version = kwd.get( 'tool_version', None )
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tool = self.app.toolbox.get_tool( tool_id, tool_version )
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if not tool:
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trans.response.status = 500
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return { 'error': 'Could not find tool with id \'%s\'' % tool_id }
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return tool.to_json(trans, **kwd)
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tool = self._get_tool( id, tool_version=tool_version, user=trans.user )
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return tool.to_json(trans, kwd)
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@_future_expose_api
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@web.require_admin
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def reload( self, trans, tool_id, **kwd ):
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@@ -6,6 +6,8 @@ from __future__ import absolute_import
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import uuid
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import logging
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import copy
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import urllib
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from sqlalchemy import desc, or_, and_
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from galaxy import exceptions, util
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from galaxy.model.item_attrs import UsesAnnotations
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@@ -17,6 +19,7 @@ from galaxy.web.base.controller import SharableMixin
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from galaxy.workflow.extract import extract_workflow
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from galaxy.workflow.run import invoke, queue_invoke
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from galaxy.workflow.run_request import build_workflow_run_config
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from galaxy.workflow.modules import module_factory
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log = logging.getLogger(__name__)
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@@ -305,6 +308,52 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
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raise exceptions.RequestParameterInvalidException( message )
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return self.workflow_contents_manager.workflow_to_dict( trans, stored_workflow, style="instance" )
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@expose_api
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def build_module( self, trans, payload={}):
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"""
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POST /api/workflows/build_module
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Builds module details including a tool model for the workflow editor.
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"""
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tool_id = payload.get( 'tool_id', None )
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tool_version = payload.get( 'tool_version', None )
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tool_inputs = payload.get( 'inputs', None )
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annotation = payload.get( 'annotation', '' )
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# load tool
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tool = self._get_tool( tool_id, tool_version=tool_version, user=trans.user )
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# initialize module
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trans.workflow_building_mode = True
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module = module_factory.from_dict( trans, {
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'type' : 'tool',
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'tool_id' : tool.id,
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'tool_state' : None
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} )
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# create tool model and default tool state (if missing)
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tool_model = module.tool.to_json(trans, tool_inputs, is_dynamic=False)
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module.state.inputs = copy.deepcopy(tool_model['state_inputs'])
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return {
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'tool_model' : tool_model,
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'tool_state' : module.get_state(),
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'data_inputs' : module.get_data_inputs(),
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'data_outputs' : module.get_data_outputs(),
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'tool_errors' : module.get_errors(),
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'form_html' : module.get_config_form(),
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'annotation' : annotation,
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'post_job_actions' : module.get_post_job_actions(tool_inputs)
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}
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#
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# -- Helper methods --
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#
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def _get_tool( self, id, tool_version=None, user=None ):
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id = urllib.unquote_plus( id )
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tool = self.app.toolbox.get_tool( id, tool_version )
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if not tool or not tool.allow_user_access( user ):
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raise exceptions.ObjectNotFound("Could not find tool with id '%s'" % id)
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return tool
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def __api_import_new_workflow( self, trans, payload, **kwd ):
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data = payload['workflow']
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@@ -217,6 +217,7 @@ def populate_api_routes( webapp, app ):
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webapp.mapper.resource_with_deleted( 'user', 'users', path_prefix='/api' )
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webapp.mapper.resource( 'genome', 'genomes', path_prefix='/api' )
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webapp.mapper.resource( 'visualization', 'visualizations', path_prefix='/api' )
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webapp.mapper.connect( '/api/workflows/build_module', action='build_module', controller="workflows" )
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webapp.mapper.resource( 'workflow', 'workflows', path_prefix='/api' )
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webapp.mapper.resource_with_deleted( 'history', 'histories', path_prefix='/api' )
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webapp.mapper.connect( '/api/histories/{history_id}/citations', action='citations', controller="histories" )
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@@ -609,7 +609,6 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
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This is used for the form shown in the right pane when a node
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is selected.
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"""
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tool_state = incoming.pop('tool_state', None)
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trans.workflow_building_mode = True
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module = module_factory.from_dict( trans, {
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@@ -617,22 +616,7 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
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'tool_id': tool_id,
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'tool_state': tool_state
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} )
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# create tool model and default tool state (if missing)
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if type == 'tool' and not tool_state:
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tool_model = module.tool.to_json(trans, **incoming)
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module.state.inputs = copy.deepcopy(tool_model['state_inputs'])
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return {
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'tool_model': tool_model,
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'tool_state': module.get_state(),
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'data_inputs': module.get_data_inputs(),
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'data_outputs': module.get_data_outputs(),
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'tool_errors': module.get_errors(),
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'form_html': module.get_config_form(),
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'annotation': annotation,
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'post_job_actions': module.get_post_job_actions(incoming)
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}
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# update module state
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module.update_state( incoming )
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@@ -669,7 +653,8 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
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module = module_factory.new( trans, type, **kwargs )
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tool_model = None
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if type == 'tool':
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tool_model = module.tool.to_json(trans)
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tool_model = module.tool.to_json(trans, is_dynamic=False)
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module.state.inputs = copy.deepcopy(tool_model['state_inputs'])
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return {
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'type': module.type,
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'name': module.get_name(),
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@@ -275,10 +275,16 @@ define(['utils/utils', 'mvc/tools/tools-form-base'],
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/** Request a new model for an already created tool form and updates the form inputs
|
||||
*/
|
||||
_updateModel: function() {
|
||||
// create the request dictionary
|
||||
// link self
|
||||
var self = this;
|
||||
var current_state = this.tree.finalize();
|
||||
|
||||
|
||||
// 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 : this.tree.finalize()
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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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@@ -287,11 +293,11 @@ define(['utils/utils', 'mvc/tools/tools-form-base'],
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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 + 'workflow/editor_form_post?tool_id=' + this.options.id + '&__is_dynamic__=False';
|
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var model_url = galaxy_config.root + 'api/workflows/build_module';
|
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// post job
|
||||
Utils.request({
|
||||
type : 'GET',
|
||||
type : 'POST',
|
||||
url : model_url,
|
||||
data : current_state,
|
||||
success : function(data) {
|
||||
|
||||
@@ -10,13 +10,13 @@ return Backbone.Model.extend({
|
||||
initialize: function(app) {
|
||||
this.app = app;
|
||||
},
|
||||
|
||||
|
||||
/** Convert dictionary representation into tool api specific flat dictionary format.
|
||||
*/
|
||||
finalize: function(patch) {
|
||||
// link this
|
||||
var self = this;
|
||||
|
||||
|
||||
// dictionary with api specific identifiers
|
||||
this.map_dict = {};
|
||||
|
||||
@@ -24,24 +24,24 @@ return Backbone.Model.extend({
|
||||
if (!this.app.section) {
|
||||
return {};
|
||||
}
|
||||
|
||||
|
||||
// ensure that dictionary with patching functions exists
|
||||
patch = patch || {};
|
||||
|
||||
|
||||
// dictionary formatted for job submission or tool form update
|
||||
var result_dict = {};
|
||||
|
||||
// prepare full dictionary
|
||||
var dict = {};
|
||||
|
||||
|
||||
// fill dictionary from dom
|
||||
this._iterate(this.app.section.$el, dict);
|
||||
|
||||
|
||||
// add identifier and value to job definition
|
||||
function add(job_input_id, input_id, input_value) {
|
||||
// add entry to result dictionary
|
||||
result_dict[job_input_id] = input_value;
|
||||
|
||||
|
||||
// backup id mapping
|
||||
self.map_dict[job_input_id] = input_id;
|
||||
};
|
||||
@@ -53,21 +53,21 @@ return Backbone.Model.extend({
|
||||
if (node.input) {
|
||||
// get node
|
||||
var input = node.input;
|
||||
|
||||
|
||||
// create identifier
|
||||
var job_input_id = identifier;
|
||||
if (identifier != '') {
|
||||
job_input_id += '|';
|
||||
}
|
||||
job_input_id += input.name;
|
||||
|
||||
|
||||
// process input type
|
||||
switch (input.type) {
|
||||
// handle repeats
|
||||
case 'repeat':
|
||||
// section identifier
|
||||
var section_label = 'section-';
|
||||
|
||||
|
||||
// collect repeat block identifiers
|
||||
var block_indices = [];
|
||||
var block_prefix = null;
|
||||
@@ -81,10 +81,10 @@ return Backbone.Model.extend({
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
// sort repeat blocks
|
||||
block_indices.sort(function(a,b) { return a - b; });
|
||||
|
||||
|
||||
// add to response dictionary in created order
|
||||
var index = 0;
|
||||
for (var i in block_indices) {
|
||||
@@ -98,10 +98,10 @@ return Backbone.Model.extend({
|
||||
if (patch[input.test_param.type]) {
|
||||
value = patch[input.test_param.type](value);
|
||||
}
|
||||
|
||||
|
||||
// add conditional value
|
||||
add (job_input_id + '|' + input.test_param.name, input.id, value);
|
||||
|
||||
|
||||
// identify selected case
|
||||
var selectedCase = self.matchCase(input, value);
|
||||
if (selectedCase != -1) {
|
||||
@@ -116,22 +116,17 @@ return Backbone.Model.extend({
|
||||
// get field
|
||||
var field = self.app.field_list[input.id];
|
||||
if (field && field.value) {
|
||||
// get and patch field value
|
||||
// validate field value
|
||||
var value = field.value();
|
||||
if (patch[input.type]) {
|
||||
value = patch[input.type](value);
|
||||
}
|
||||
|
||||
// validate field value
|
||||
if (field.skip) {
|
||||
continue;
|
||||
}
|
||||
|
||||
// validate field value
|
||||
if (field.validate && !field.validate()) {
|
||||
value = null;
|
||||
}
|
||||
|
||||
// get and patch field value
|
||||
if (patch[input.type]) {
|
||||
value = patch[input.type](value);
|
||||
}
|
||||
|
||||
// ignore certain values
|
||||
if (input.ignore === undefined || (value !== null && input.ignore != value)) {
|
||||
// add value to submission
|
||||
@@ -149,20 +144,20 @@ return Backbone.Model.extend({
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
// start conversion
|
||||
convert('', dict);
|
||||
|
||||
|
||||
// return result
|
||||
return result_dict;
|
||||
},
|
||||
|
||||
|
||||
/** Match job definition identifier to input element identifier
|
||||
*/
|
||||
match: function (job_input_id) {
|
||||
return this.map_dict && this.map_dict[job_input_id];
|
||||
},
|
||||
|
||||
|
||||
/** Match conditional values to selected cases
|
||||
*/
|
||||
matchCase: function(input, value) {
|
||||
@@ -174,27 +169,27 @@ return Backbone.Model.extend({
|
||||
value = input.test_param.falsevalue || 'false';
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
// find selected case
|
||||
for (var i in input.cases) {
|
||||
if (input.cases[i].value == value) {
|
||||
return i;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
// selected case not found
|
||||
return -1;
|
||||
},
|
||||
|
||||
|
||||
/** Matches identifier from api model to input elements
|
||||
*/
|
||||
matchModel: function(model, callback) {
|
||||
// final result dictionary
|
||||
var result = {};
|
||||
|
||||
|
||||
// link this
|
||||
var self = this;
|
||||
|
||||
|
||||
// search throughout response
|
||||
function search (id, head) {
|
||||
for (var i in head) {
|
||||
@@ -224,23 +219,23 @@ return Backbone.Model.extend({
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
// match all ids and return messages
|
||||
search('', model.inputs);
|
||||
|
||||
// return matched results
|
||||
return result;
|
||||
},
|
||||
|
||||
|
||||
/** Matches identifier from api response to input elements
|
||||
*/
|
||||
matchResponse: function(response) {
|
||||
// final result dictionary
|
||||
var result = {};
|
||||
|
||||
|
||||
// link this
|
||||
var self = this;
|
||||
|
||||
|
||||
// search throughout response
|
||||
function search (id, head) {
|
||||
if (typeof head === 'string') {
|
||||
@@ -262,14 +257,14 @@ return Backbone.Model.extend({
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
// match all ids and return messages
|
||||
search('', response);
|
||||
|
||||
|
||||
// return matched results
|
||||
return result;
|
||||
},
|
||||
|
||||
|
||||
/** Iterate through the tool form dom and map it to the dictionary.
|
||||
*/
|
||||
_iterate: function(parent, dict) {
|
||||
@@ -279,15 +274,15 @@ return Backbone.Model.extend({
|
||||
children.each(function() {
|
||||
// get child element
|
||||
var child = this;
|
||||
|
||||
|
||||
// get id
|
||||
var id = $(child).attr('id');
|
||||
|
||||
|
||||
// create new branch
|
||||
if ($(child).hasClass('section-row')) {
|
||||
// create sub dictionary
|
||||
dict[id] = {};
|
||||
|
||||
|
||||
// add input element if it exists
|
||||
var input = self.app.input_list[id];
|
||||
if (input) {
|
||||
@@ -295,7 +290,7 @@ return Backbone.Model.extend({
|
||||
input : input
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
// fill sub dictionary
|
||||
self._iterate(child, dict[id]);
|
||||
} else {
|
||||
|
||||
@@ -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="In Advance";this.options.text_disable="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","drill_down","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:""});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:"",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(){var d=this;var e=this.tree.finalize();console.debug("tools-form-workflow::_refreshForm() - Refreshing states.");console.debug(e);var g=this.deferred.register();var f=galaxy_config.root+"workflow/editor_form_post?tool_id="+this.options.id+"&__is_dynamic__=False";b.request({type:"GET",url:f,data:e,success:function(h){d.node.update_field_data(h);d._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||{};this.options=e;this.options.text_enable="In Advance";this.options.text_disable="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","drill_down","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:""});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:"",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(){var d=this;var e={tool_id:this.options.id,tool_version:this.options.version,inputs:this.tree.finalize()};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._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}});
|
||||
@@ -1 +1 @@
|
||||
define(["utils/utils"],function(a){return Backbone.Model.extend({initialize:function(b){this.app=b},finalize:function(g){var b=this;this.map_dict={};if(!this.app.section){return{}}g=g||{};var f={};var e={};this._iterate(this.app.section.$el,e);function d(j,i,h){f[j]=h;b.map_dict[j]=i}function c(p,s){for(var n in s){var k=s[n];if(k.input){var u=k.input;var o=p;if(p!=""){o+="|"}o+=u.name;switch(u.type){case"repeat":var j="section-";var x=[];var r=null;for(var w in k){var q=w.indexOf(j);if(q!=-1){q+=j.length;x.push(parseInt(w.substr(q)));if(!r){r=w.substr(0,q)}}}x.sort(function(y,i){return y-i});var n=0;for(var l in x){c(o+"_"+n++,k[r+x[l]])}break;case"conditional":var v=b.app.field_list[u.id].value();if(g[u.test_param.type]){v=g[u.test_param.type](v)}d(o+"|"+u.test_param.name,u.id,v);var h=b.matchCase(u,v);if(h!=-1){c(o,s[u.id+"-section-"+h])}break;case"section":c("",k);break;default:var t=b.app.field_list[u.id];if(t&&t.value){var v=t.value();if(g[u.type]){v=g[u.type](v)}if(t.skip){continue}if(t.validate&&!t.validate()){v=null}if(u.ignore===undefined||(v!==null&&u.ignore!=v)){d(o,u.id,v);if(u.payload){for(var m in u.payload){d(m,u.id,u.payload[m])}}}}}}}}c("",e);return f},match:function(b){return this.map_dict&&this.map_dict[b]},matchCase:function(b,d){if(b.test_param.type=="boolean"){if(d=="true"){d=b.test_param.truevalue||"true"}else{d=b.test_param.falsevalue||"false"}}for(var c in b.cases){if(b.cases[c].value==d){return c}}return -1},matchModel:function(d,f){var b={};var c=this;function e(g,p){for(var m in p){var k=p[m];var n=k.name;if(g!=""){n=g+"|"+n}switch(k.type){case"repeat":for(var l in k.cache){e(n+"_"+l,k.cache[l])}break;case"conditional":var q=k.test_param&&k.test_param.value;var h=c.matchCase(k,q);if(h!=-1){e(n,k.cases[h].inputs)}break;default:var o=c.map_dict[n];if(o){f(o,k)}}}}e("",d.inputs);return b},matchResponse:function(d){var b={};var c=this;function e(l,j){if(typeof j==="string"){var g=c.map_dict[l];if(g){b[g]=j}}else{for(var h in j){var f=h;if(l!==""){var k="|";if(j instanceof Array){k="_"}f=l+k+f}e(f,j[h])}}}e("",d);return b},_iterate:function(d,e){var b=this;var c=$(d).children();c.each(function(){var h=this;var g=$(h).attr("id");if($(h).hasClass("section-row")){e[g]={};var f=b.app.input_list[g];if(f){e[g]={input:f}}b._iterate(h,e[g])}else{b._iterate(h,e)}})}})});
|
||||
define(["utils/utils"],function(a){return Backbone.Model.extend({initialize:function(b){this.app=b},finalize:function(g){var b=this;this.map_dict={};if(!this.app.section){return{}}g=g||{};var f={};var e={};this._iterate(this.app.section.$el,e);function d(j,i,h){f[j]=h;b.map_dict[j]=i}function c(p,s){for(var n in s){var k=s[n];if(k.input){var u=k.input;var o=p;if(p!=""){o+="|"}o+=u.name;switch(u.type){case"repeat":var j="section-";var x=[];var r=null;for(var w in k){var q=w.indexOf(j);if(q!=-1){q+=j.length;x.push(parseInt(w.substr(q)));if(!r){r=w.substr(0,q)}}}x.sort(function(y,i){return y-i});var n=0;for(var l in x){c(o+"_"+n++,k[r+x[l]])}break;case"conditional":var v=b.app.field_list[u.id].value();if(g[u.test_param.type]){v=g[u.test_param.type](v)}d(o+"|"+u.test_param.name,u.id,v);var h=b.matchCase(u,v);if(h!=-1){c(o,s[u.id+"-section-"+h])}break;case"section":c("",k);break;default:var t=b.app.field_list[u.id];if(t&&t.value){var v=t.value();if(t.validate&&!t.validate()){v=null}if(g[u.type]){v=g[u.type](v)}if(u.ignore===undefined||(v!==null&&u.ignore!=v)){d(o,u.id,v);if(u.payload){for(var m in u.payload){d(m,u.id,u.payload[m])}}}}}}}}c("",e);return f},match:function(b){return this.map_dict&&this.map_dict[b]},matchCase:function(b,d){if(b.test_param.type=="boolean"){if(d=="true"){d=b.test_param.truevalue||"true"}else{d=b.test_param.falsevalue||"false"}}for(var c in b.cases){if(b.cases[c].value==d){return c}}return -1},matchModel:function(d,f){var b={};var c=this;function e(g,p){for(var m in p){var k=p[m];var n=k.name;if(g!=""){n=g+"|"+n}switch(k.type){case"repeat":for(var l in k.cache){e(n+"_"+l,k.cache[l])}break;case"conditional":var q=k.test_param&&k.test_param.value;var h=c.matchCase(k,q);if(h!=-1){e(n,k.cases[h].inputs)}break;default:var o=c.map_dict[n];if(o){f(o,k)}}}}e("",d.inputs);return b},matchResponse:function(d){var b={};var c=this;function e(l,j){if(typeof j==="string"){var g=c.map_dict[l];if(g){b[g]=j}}else{for(var h in j){var f=h;if(l!==""){var k="|";if(j instanceof Array){k="_"}f=l+k+f}e(f,j[h])}}}e("",d);return b},_iterate:function(d,e){var b=this;var c=$(d).children();c.each(function(){var h=this;var g=$(h).attr("id");if($(h).hasClass("section-row")){e[g]={};var f=b.app.input_list[g];if(f){e[g]={input:f}}b._iterate(h,e[g])}else{b._iterate(h,e)}})}})});
|
||||
@@ -10,7 +10,7 @@ ${h.css('base', 'jquery-ui/smoothness/jquery-ui')}
|
||||
## This avoids making two separate requests since the classic form requires the mako anyway.
|
||||
params = dict(trans.request.params)
|
||||
params['__dataset_id__'] = params.get('id', None)
|
||||
self.form_config = tool.to_json(trans, **params)
|
||||
self.form_config = tool.to_json(trans, params)
|
||||
self.form_config.update({
|
||||
'id' : tool.id,
|
||||
'job_id' : trans.security.encode_id( job.id ) if job else None,
|
||||
|
||||
@@ -6,11 +6,9 @@
|
||||
## TEMPORARY: create tool dictionary in mako while both tool forms are in use.
|
||||
## This avoids making two separate requests since the classic form requires the mako anyway.
|
||||
from galaxy.tools.parameters import params_to_incoming
|
||||
incoming = {
|
||||
'__is_dynamic__' : False
|
||||
}
|
||||
incoming = {}
|
||||
params_to_incoming( incoming, tool.inputs, module.state.inputs, trans.app, to_html=False)
|
||||
self.form_config = tool.to_json(trans, **incoming)
|
||||
self.form_config = tool.to_json(trans, incoming, is_dynamic=False)
|
||||
self.form_config.update({
|
||||
'id' : tool.id,
|
||||
'job_id' : trans.security.encode_id( job.id ) if job else None,
|
||||
|
||||
Reference in New Issue
Block a user