February 2015 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 05 Feb '15

05 Feb '15

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2248c4d82151/ Changeset: 2248c4d82151 Branch: stable User: jmchilton Date: 2015-02-05 17:14:01+00:00 Summary: Workflow scheduling delay fix. There were problems if all three of these conditions were met - 1) workflow from GUI, 2) workflow evaluation delayed, and 3) a delayed step was connected to a input dataset. This fixes these workflows. Affected #: 3 files diff -r 097bbb3b7d3246faaa5188a1fc2a79b01630025c -r 2248c4d82151c928a7615f9335b55aa0c55c9446 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -3202,6 +3202,27 @@ def update( self ): self.update_time = galaxy.model.orm.now.now() + def add_input( self, content, step_id ): + if content.history_content_type == "dataset": + request_to_content = WorkflowRequestToInputDatasetAssociation() + request_to_content.dataset = content + request_to_content.workflow_step_id = step_id + self.input_datasets.append( request_to_content ) + else: + request_to_content = WorkflowRequestToInputDatasetCollectionAssociation() + request_to_content.dataset_collection = content + request_to_content.workflow_step_id = step_id + self.input_dataset_collections.append( request_to_content ) + + def has_input_for_step( self, step_id ): + for content in self.input_datasets: + if content.workflow_step_id == step_id: + return True + for content in self.input_dataset_collections: + if content.workflow_step_id == step_id: + return True + return False + class WorkflowInvocationStep( object, Dictifiable ): dict_collection_visible_keys = ( 'id', 'update_time', 'job_id', 'workflow_step_id', 'action' ) diff -r 097bbb3b7d3246faaa5188a1fc2a79b01630025c -r 2248c4d82151c928a7615f9335b55aa0c55c9446 lib/galaxy/workflow/modules.py --- a/lib/galaxy/workflow/modules.py +++ b/lib/galaxy/workflow/modules.py @@ -320,6 +320,11 @@ step_outputs[ 'input_ds_copy' ] = new_hdca else: raise Exception("Unknown history content encountered") + # If coming from UI - we haven't registered invocation inputs yet, + # so do that now so dependent steps can be recalculated. In the future + # everything should come in from the API and this can be eliminated. + if not invocation.has_input_for_step( step.id ): + invocation.add_input( step_outputs.values()[ 0 ], step.id ) progress.set_outputs_for_input( step, step_outputs ) return job diff -r 097bbb3b7d3246faaa5188a1fc2a79b01630025c -r 2248c4d82151c928a7615f9335b55aa0c55c9446 lib/galaxy/workflow/run_request.py --- a/lib/galaxy/workflow/run_request.py +++ b/lib/galaxy/workflow/run_request.py @@ -284,18 +284,8 @@ value=value, type=param_types.REPLACEMENT_PARAMETERS, ) - for step_id, content in run_config.inputs.iteritems(): - if content.history_content_type == "dataset": - request_to_content = model.WorkflowRequestToInputDatasetAssociation() - request_to_content.dataset = content - request_to_content.workflow_step_id = step_id - workflow_invocation.input_datasets.append( request_to_content ) - else: - request_to_content = model.WorkflowRequestToInputDatasetCollectionAssociation() - request_to_content.dataset_collection = content - request_to_content.workflow_step_id = step_id - workflow_invocation.input_dataset_collections.append( request_to_content ) + workflow_invocation.add_input( content, step_id ) for step in workflow.steps: state = step.state https://bitbucket.org/galaxy/galaxy-central/commits/e07163fe8bdb/ Changeset: e07163fe8bdb Branch: stable User: jmchilton Date: 2015-02-05 17:14:01+00:00 Summary: Fix scheduling_manager.py for unknown attribute reference. Not sure if this was a poor rebasing or a copy and paste error. Affected #: 1 file diff -r 2248c4d82151c928a7615f9335b55aa0c55c9446 -r e07163fe8bdbc3e85f48b308ed293c46578b3294 lib/galaxy/workflow/scheduling_manager.py --- a/lib/galaxy/workflow/scheduling_manager.py +++ b/lib/galaxy/workflow/scheduling_manager.py @@ -116,7 +116,6 @@ for plugin_element in plugins_element.getchildren(): plugin_type = plugin_element.tag plugin_kwds = dict( plugin_element.items() ) - plugin_kwds.update( self.extra_kwargs ) workflow_scheduler_id = plugin_kwds.get( 'id', None ) self.__init_plugin( plugin_type, workflow_scheduler_id, **plugin_kwds ) https://bitbucket.org/galaxy/galaxy-central/commits/644deef1a578/ Changeset: 644deef1a578 Branch: stable User: jmchilton Date: 2015-02-05 18:33:59+00:00 Summary: Bugfix for bugfix d3b1f6b. d3b1f6b fix the GUI (in an obsecure use) but broke fairly typical uses of the API. Affected #: 1 file diff -r e07163fe8bdbc3e85f48b308ed293c46578b3294 -r 644deef1a5789b788552a6db7f3d6fe07d81c79d lib/galaxy/workflow/modules.py --- a/lib/galaxy/workflow/modules.py +++ b/lib/galaxy/workflow/modules.py @@ -324,7 +324,9 @@ # so do that now so dependent steps can be recalculated. In the future # everything should come in from the API and this can be eliminated. if not invocation.has_input_for_step( step.id ): - invocation.add_input( step_outputs.values()[ 0 ], step.id ) + content = step_outputs.values()[ 0 ] + if content: + invocation.add_input( content, step.id ) progress.set_outputs_for_input( step, step_outputs ) return job Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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[galaxyproject/usegalaxy-playbook] f0c67a: make toolform fancy again; update mutable configs
by GitHub 05 Feb '15

05 Feb '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f0c67a17684293e648e79eb1dae8c8116aed4e22 https://github.com/galaxyproject/usegalaxy-playbook/commit/f0c67a17684293e6… Author: martenson <cech.marten(a)gmail.com> Date: 2015-02-05 (Thu, 05 Feb 2015) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml M stage/group_vars/galaxyservers.yml Log Message: ----------- make toolform fancy again; update mutable configs

1 0

commit/galaxy-central: guerler: ToolForm: Update version selection, use underscores for internal parameters
by commits-noreply＠bitbucket.org 05 Feb '15

05 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/494418e72cf0/ Changeset: 494418e72cf0 User: guerler Date: 2015-02-05 18:34:51+00:00 Summary: ToolForm: Update version selection, use underscores for internal parameters Affected #: 12 files diff -r ff2b00fcbd70e3d7ce10b0444412cc68d2ede46f -r 494418e72cf0007e909c7f4b9134cd2b82df49e2 client/galaxy/scripts/mvc/tools/tools-form-base.js --- a/client/galaxy/scripts/mvc/tools/tools-form-base.js +++ b/client/galaxy/scripts/mvc/tools/tools-form-base.js @@ -15,12 +15,10 @@ this.optionsDefault = { // uses dynamic fields instead of text fields is_dynamic : true, - // shows form in compact view mode - compact : false, + // shows form in narrow view mode + narrow : false, // shows errors on start - initial_errors : false, - // use default value for disabled fields - use_defaults : false + initial_errors : false }; // configure options @@ -58,9 +56,66 @@ $(this.container).append(this.$el); // build this form - this._buildForm(); + this.build(this.options); }, + /** Main tool form build function. This function is called once a new model is available. + */ + build: function(options) { + // link this + var self = this; + + // reset events + this.off('refresh'); + this.off('reset'); + + // reset field list, which contains the input field elements + this.field_list = {}; + + // reset sequential input definition list, which contains the input definitions as provided from the api + this.input_list = {}; + + // reset input element list, which contains the dom elements of each input element (includes also the input field) + this.element_list = {}; + + // creates a tree/json data structure from the input form + this.tree = new ToolTree(this); + + // request history content and build form + this.content = new ToolContent(this); + + // update model data + self.options.inputs = options && options.inputs; + + // create ui elements + this._renderForm(options); + + // rebuild the underlying data structure + this.tree.finalize(); + + // show errors on startup + if (options.initial_errors) { + this._errors(options); + } + + // add refresh listener + this.on('refresh', function() { + // by using/resetting the deferred ajax queue the number of redundant calls is reduced + self.deferred.reset(); + self.deferred.execute(function(){self._updateModel()}); + }); + + // add reset listener + this.on('reset', function() { + for (var i in this.element_list) { + this.element_list[i].reset(); + } + }); + + // refresh + this.trigger('refresh'); + }, + /** Shows the final message (usually upon successful job submission) */ reciept: function($el) { @@ -105,63 +160,6 @@ } } }, - - /** Main tool form build function. This function is called once a new model is available. - */ - _buildForm: function() { - // link this - var self = this; - - // reset events - this.off('refresh'); - this.off('reset'); - - // reset field list, which contains the input field elements - this.field_list = {}; - - // reset sequential input definition list, which contains the input definitions as provided from the api - this.input_list = {}; - - // reset input element list, which contains the dom elements of each input element (includes also the input field) - this.element_list = {}; - - // creates a tree/json data structure from the input form - this.tree = new ToolTree(this); - - // request history content and build form - this.content = new ToolContent(this); - - // link model options - var options = this.options; - - // create ui elements - this._renderForm(options); - - // rebuild the underlying data structure - this.tree.finalize(); - - // show errors on startup - if (options.initial_errors) { - this._errors(options); - } - - // add refresh listener - this.on('refresh', function() { - // by using/resetting the deferred ajax queue the number of redundant calls is reduced - self.deferred.reset(); - self.deferred.execute(function(){self._updateModel()}); - }); - - // add reset listener - this.on('reset', function() { - for (var i in this.element_list) { - this.element_list[i].reset(); - } - }); - - // refresh - this.trigger('refresh'); - }, /** Renders the UI elements required for the form */ @@ -175,7 +173,7 @@ // button for version selection var requirements_button = new Ui.ButtonIcon({ icon : 'fa-info-circle', - title : (!options.compact && 'Requirements') || null, + title : (!options.narrow && 'Requirements') || null, tooltip : 'Display tool requirements', onclick : function() { if (!this.visible) { @@ -200,7 +198,7 @@ // button for version selection var versions_button = new Ui.ButtonMenu({ icon : 'fa-cubes', - title : (!options.compact && 'Versions') || null, + title : (!options.narrow && 'Versions') || null, tooltip : 'Select another tool version' }); if (options.versions && options.versions.length > 1) { @@ -213,8 +211,8 @@ 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; + self.options.id = self.options.id.replace(self.options.version, this.version); + self.options.version = this.version; // rebuild the model and form self.deferred.reset(); @@ -230,7 +228,7 @@ // button menu var menu_button = new Ui.ButtonMenu({ icon : 'fa-caret-down', - title : (!options.compact && 'Options') || null, + title : (!options.narrow && 'Options') || null, tooltip : 'View available options' }); @@ -306,7 +304,7 @@ }); // remove padding - if (options.compact) { + if (options.narrow) { this.portlet.$content.css('padding', '0px'); } diff -r ff2b00fcbd70e3d7ce10b0444412cc68d2ede46f -r 494418e72cf0007e909c7f4b9134cd2b82df49e2 client/galaxy/scripts/mvc/tools/tools-form-workflow.js --- a/client/galaxy/scripts/mvc/tools/tools-form-workflow.js +++ b/client/galaxy/scripts/mvc/tools/tools-form-workflow.js @@ -21,9 +21,13 @@ this.options = options; // set labels - this.options.text_enable = 'In Advance'; - this.options.text_disable = 'At Runtime'; - this.options.use_defaults = true; + this.options.text_enable = 'In Advance'; + this.options.text_disable = 'At Runtime'; + + // configure workflow style + this.options.is_dynamic = false; + this.options.narrow = true; + this.options.initial_errors = true; // declare fields as optional Utils.deepeach(options.inputs, function(item) { diff -r ff2b00fcbd70e3d7ce10b0444412cc68d2ede46f -r 494418e72cf0007e909c7f4b9134cd2b82df49e2 client/galaxy/scripts/mvc/tools/tools-form.js --- a/client/galaxy/scripts/mvc/tools/tools-form.js +++ b/client/galaxy/scripts/mvc/tools/tools-form.js @@ -24,7 +24,7 @@ } ToolFormBase.prototype.initialize.call(this, options); }, - + /** Builds a new model through api call and recreates the entire form */ _buildModel: function() { @@ -47,31 +47,28 @@ } } } - + // register process var process_id = this.deferred.register(); - + // get initial model Utils.request({ type : 'GET', url : model_url, success : function(response) { - // link model data update options - self.options = response; - - // build form - self._buildForm(); - + // build new tool form + self.build(response); + // notification self.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); @@ -79,11 +76,11 @@ 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.modal.show({ @@ -98,7 +95,7 @@ } }); }, - + /** Request a new model for an already created tool form and updates the form inputs */ _updateModel: function() { @@ -112,11 +109,11 @@ return null; } }); - + // log tool state console.debug('tools-form::_refreshForm() - Refreshing states.'); console.debug(current_state); - + // activates/disables spinner for dynamic fields to indicate that they are currently being updated function wait(active) { for (var i in self.input_list) { @@ -131,10 +128,10 @@ } } } - + // set wait mode wait(true); - + // register process var process_id = this.deferred.register(); @@ -179,13 +176,13 @@ } } }); - + // unset wait mode wait(false); - + // process completed self.deferred.done(process_id); - + // log success console.debug('tools-form::_refreshForm() - States refreshed.'); console.debug(new_model); @@ -193,7 +190,7 @@ error : function(response) { // process completed self.deferred.done(process_id); - + // log error console.debug('tools-form::_refreshForm() - Refresh request failed.'); console.debug(response); diff -r ff2b00fcbd70e3d7ce10b0444412cc68d2ede46f -r 494418e72cf0007e909c7f4b9134cd2b82df49e2 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2254,8 +2254,8 @@ """ Recursively creates a tool dictionary containing repeats, dynamic options and updated states. """ - job_id = kwd.get('job_id', None) - dataset_id = kwd.get('dataset_id', None) + job_id = kwd.get('__job_id__', None) + dataset_id = kwd.get('__dataset_id__', None) is_dynamic = string_as_bool(kwd.get('__is_dynamic__', True)) # load job details if provided diff -r ff2b00fcbd70e3d7ce10b0444412cc68d2ede46f -r 494418e72cf0007e909c7f4b9134cd2b82df49e2 static/scripts/mvc/tools/tools-form-base.js --- a/static/scripts/mvc/tools/tools-form-base.js +++ b/static/scripts/mvc/tools/tools-form-base.js @@ -15,12 +15,10 @@ this.optionsDefault = { // uses dynamic fields instead of text fields is_dynamic : true, - // shows form in compact view mode - compact : false, + // shows form in narrow view mode + narrow : false, // shows errors on start - initial_errors : false, - // use default value for disabled fields - use_defaults : false + initial_errors : false }; // configure options @@ -58,9 +56,66 @@ $(this.container).append(this.$el); // build this form - this._buildForm(); + this.build(this.options); }, + /** Main tool form build function. This function is called once a new model is available. + */ + build: function(options) { + // link this + var self = this; + + // reset events + this.off('refresh'); + this.off('reset'); + + // reset field list, which contains the input field elements + this.field_list = {}; + + // reset sequential input definition list, which contains the input definitions as provided from the api + this.input_list = {}; + + // reset input element list, which contains the dom elements of each input element (includes also the input field) + this.element_list = {}; + + // creates a tree/json data structure from the input form + this.tree = new ToolTree(this); + + // request history content and build form + this.content = new ToolContent(this); + + // update model data + self.options.inputs = options && options.inputs; + + // create ui elements + this._renderForm(options); + + // rebuild the underlying data structure + this.tree.finalize(); + + // show errors on startup + if (options.initial_errors) { + this._errors(options); + } + + // add refresh listener + this.on('refresh', function() { + // by using/resetting the deferred ajax queue the number of redundant calls is reduced + self.deferred.reset(); + self.deferred.execute(function(){self._updateModel()}); + }); + + // add reset listener + this.on('reset', function() { + for (var i in this.element_list) { + this.element_list[i].reset(); + } + }); + + // refresh + this.trigger('refresh'); + }, + /** Shows the final message (usually upon successful job submission) */ reciept: function($el) { @@ -105,63 +160,6 @@ } } }, - - /** Main tool form build function. This function is called once a new model is available. - */ - _buildForm: function() { - // link this - var self = this; - - // reset events - this.off('refresh'); - this.off('reset'); - - // reset field list, which contains the input field elements - this.field_list = {}; - - // reset sequential input definition list, which contains the input definitions as provided from the api - this.input_list = {}; - - // reset input element list, which contains the dom elements of each input element (includes also the input field) - this.element_list = {}; - - // creates a tree/json data structure from the input form - this.tree = new ToolTree(this); - - // request history content and build form - this.content = new ToolContent(this); - - // link model options - var options = this.options; - - // create ui elements - this._renderForm(options); - - // rebuild the underlying data structure - this.tree.finalize(); - - // show errors on startup - if (options.initial_errors) { - this._errors(options); - } - - // add refresh listener - this.on('refresh', function() { - // by using/resetting the deferred ajax queue the number of redundant calls is reduced - self.deferred.reset(); - self.deferred.execute(function(){self._updateModel()}); - }); - - // add reset listener - this.on('reset', function() { - for (var i in this.element_list) { - this.element_list[i].reset(); - } - }); - - // refresh - this.trigger('refresh'); - }, /** Renders the UI elements required for the form */ @@ -175,7 +173,7 @@ // button for version selection var requirements_button = new Ui.ButtonIcon({ icon : 'fa-info-circle', - title : (!options.compact && 'Requirements') || null, + title : (!options.narrow && 'Requirements') || null, tooltip : 'Display tool requirements', onclick : function() { if (!this.visible) { @@ -200,7 +198,7 @@ // button for version selection var versions_button = new Ui.ButtonMenu({ icon : 'fa-cubes', - title : (!options.compact && 'Versions') || null, + title : (!options.narrow && 'Versions') || null, tooltip : 'Select another tool version' }); if (options.versions && options.versions.length > 1) { @@ -213,8 +211,8 @@ 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; + self.options.id = self.options.id.replace(self.options.version, this.version); + self.options.version = this.version; // rebuild the model and form self.deferred.reset(); @@ -230,7 +228,7 @@ // button menu var menu_button = new Ui.ButtonMenu({ icon : 'fa-caret-down', - title : (!options.compact && 'Options') || null, + title : (!options.narrow && 'Options') || null, tooltip : 'View available options' }); @@ -306,7 +304,7 @@ }); // remove padding - if (options.compact) { + if (options.narrow) { this.portlet.$content.css('padding', '0px'); } diff -r ff2b00fcbd70e3d7ce10b0444412cc68d2ede46f -r 494418e72cf0007e909c7f4b9134cd2b82df49e2 static/scripts/mvc/tools/tools-form-workflow.js --- a/static/scripts/mvc/tools/tools-form-workflow.js +++ b/static/scripts/mvc/tools/tools-form-workflow.js @@ -21,9 +21,13 @@ this.options = options; // set labels - this.options.text_enable = 'In Advance'; - this.options.text_disable = 'At Runtime'; - this.options.use_defaults = true; + this.options.text_enable = 'In Advance'; + this.options.text_disable = 'At Runtime'; + + // configure workflow style + this.options.is_dynamic = false; + this.options.narrow = true; + this.options.initial_errors = true; // declare fields as optional Utils.deepeach(options.inputs, function(item) { diff -r ff2b00fcbd70e3d7ce10b0444412cc68d2ede46f -r 494418e72cf0007e909c7f4b9134cd2b82df49e2 static/scripts/mvc/tools/tools-form.js --- a/static/scripts/mvc/tools/tools-form.js +++ b/static/scripts/mvc/tools/tools-form.js @@ -24,7 +24,7 @@ } ToolFormBase.prototype.initialize.call(this, options); }, - + /** Builds a new model through api call and recreates the entire form */ _buildModel: function() { @@ -47,31 +47,28 @@ } } } - + // register process var process_id = this.deferred.register(); - + // get initial model Utils.request({ type : 'GET', url : model_url, success : function(response) { - // link model data update options - self.options = response; - - // build form - self._buildForm(); - + // build new tool form + self.build(response); + // notification self.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); @@ -79,11 +76,11 @@ 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.modal.show({ @@ -98,7 +95,7 @@ } }); }, - + /** Request a new model for an already created tool form and updates the form inputs */ _updateModel: function() { @@ -112,11 +109,11 @@ return null; } }); - + // log tool state console.debug('tools-form::_refreshForm() - Refreshing states.'); console.debug(current_state); - + // activates/disables spinner for dynamic fields to indicate that they are currently being updated function wait(active) { for (var i in self.input_list) { @@ -131,10 +128,10 @@ } } } - + // set wait mode wait(true); - + // register process var process_id = this.deferred.register(); @@ -179,13 +176,13 @@ } } }); - + // unset wait mode wait(false); - + // process completed self.deferred.done(process_id); - + // log success console.debug('tools-form::_refreshForm() - States refreshed.'); console.debug(new_model); @@ -193,7 +190,7 @@ error : function(response) { // process completed self.deferred.done(process_id); - + // log error console.debug('tools-form::_refreshForm() - Refresh request failed.'); console.debug(response); diff -r ff2b00fcbd70e3d7ce10b0444412cc68d2ede46f -r 494418e72cf0007e909c7f4b9134cd2b82df49e2 static/scripts/packed/mvc/tools/tools-form-base.js --- a/static/scripts/packed/mvc/tools/tools-form-base.js +++ b/static/scripts/packed/mvc/tools/tools-form-base.js @@ -1,1 +1,1 @@ -define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree"],function(g,h,f,k,i,a,d,c,e,j,b){return Backbone.View.extend({initialize:function(l){this.optionsDefault={is_dynamic:true,compact:false,initial_errors:false,use_defaults:false};this.options=g.merge(l,this.optionsDefault);console.debug(this.options);var m=parent.Galaxy;if(m&&m.modal){this.modal=m.modal}else{this.modal=new k.Modal.View()}if(m&&m.currUser){this.is_admin=m.currUser.get("is_admin")}else{this.is_admin=false}this.container=this.options.container||"body";this.deferred=new h();this.setElement("<div/>");$(this.container).append(this.$el);this._buildForm()},reciept:function(l){$(this.container).empty();$(this.container).append(l)},highlight:function(m,n,l){var o=this.element_list[m];if(o){o.error(n||"Please verify this parameter.");if(!l){$(this.container).animate({scrollTop:o.$el.offset().top-20},500)}}},_errors:function(n){this.trigger("reset");if(n&&n.errors){var o=this.tree.matchResponse(n.errors);for(var m in this.element_list){var l=this.element_list[m];if(o[m]){this.highlight(m,o[m],true)}}}},_buildForm:function(){var l=this;this.off("refresh");this.off("reset");this.field_list={};this.input_list={};this.element_list={};this.tree=new b(this);this.content=new e(this);var m=this.options;this._renderForm(m);this.tree.finalize();if(m.initial_errors){this._errors(m)}this.on("refresh",function(){l.deferred.reset();l.deferred.execute(function(){l._updateModel()})});this.on("reset",function(){for(var n in this.element_list){this.element_list[n].reset()}});this.trigger("refresh")},_renderForm:function(u){var t=this;this.message=new k.Message();var q=new k.ButtonIcon({icon:"fa-info-circle",title:(!u.compact&&"Requirements")||null,tooltip:"Display tool requirements",onclick:function(){if(!this.visible){this.visible=true;t.message.update({persistent:true,message:c.requirements(u),status:"info"})}else{this.visible=false;t.message.update({message:""})}}});if(!u.requirements||u.requirements.length==0){q.$el.hide()}var m=new k.ButtonMenu({icon:"fa-cubes",title:(!u.compact&&"Versions")||null,tooltip:"Select another tool version"});if(u.versions&&u.versions.length>1){for(var o in u.versions){var r=u.versions[o];if(r!=u.version){m.addMenu({title:"Switch to "+r,version:r,icon:"fa-cube",onclick:function(){u.id=u.id.replace(u.version,this.version);u.version=this.version;t.deferred.reset();t.deferred.execute(function(){t._buildModel()})}})}}}else{m.$el.hide()}var p=new k.ButtonMenu({icon:"fa-caret-down",title:(!u.compact&&"Options")||null,tooltip:"View available options"});if(u.biostar_url){p.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(u.biostar_url+"/p/new/post/")}});p.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(u.biostar_url+"/t/"+u.id+"/")}})}p.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="+u.id)}});if(this.is_admin){p.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+u.id+"/download"}})}this.section=new j.View(t,{inputs:u.inputs});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new f.View({icon:"fa-wrench",title:"<b>"+u.name+"</b> "+u.description+" (Galaxy Tool Version "+u.version+")",cls:"ui-portlet-slim",operations:{requirements:q,menu:p,versions:m},buttons:this.buttons});if(u.compact){this.portlet.$content.css("padding","0px")}this.portlet.append(this.message.$el,true);this.portlet.append(this.section.$el);this.$el.empty();this.$el.append(this.portlet.$el);if(u.help!=""){this.$el.append(c.help(u.help))}if(u.citations){var s=$("<div/>");var l=new i.ToolCitationCollection();l.tool_id=u.id;var n=new a.CitationListView({el:s,collection:l});n.render();l.fetch();this.$el.append(s)}if(u.message){this.message.update({persistent:true,status:"warning",message:u.message})}}})}); \ No newline at end of file +define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree"],function(g,h,f,k,i,a,d,c,e,j,b){return Backbone.View.extend({initialize:function(l){this.optionsDefault={is_dynamic:true,narrow:false,initial_errors:false};this.options=g.merge(l,this.optionsDefault);console.debug(this.options);var m=parent.Galaxy;if(m&&m.modal){this.modal=m.modal}else{this.modal=new k.Modal.View()}if(m&&m.currUser){this.is_admin=m.currUser.get("is_admin")}else{this.is_admin=false}this.container=this.options.container||"body";this.deferred=new h();this.setElement("<div/>");$(this.container).append(this.$el);this.build(this.options)},build:function(m){var l=this;this.off("refresh");this.off("reset");this.field_list={};this.input_list={};this.element_list={};this.tree=new b(this);this.content=new e(this);l.options.inputs=m&&m.inputs;this._renderForm(m);this.tree.finalize();if(m.initial_errors){this._errors(m)}this.on("refresh",function(){l.deferred.reset();l.deferred.execute(function(){l._updateModel()})});this.on("reset",function(){for(var n in this.element_list){this.element_list[n].reset()}});this.trigger("refresh")},reciept:function(l){$(this.container).empty();$(this.container).append(l)},highlight:function(m,n,l){var o=this.element_list[m];if(o){o.error(n||"Please verify this parameter.");if(!l){$(this.container).animate({scrollTop:o.$el.offset().top-20},500)}}},_errors:function(n){this.trigger("reset");if(n&&n.errors){var o=this.tree.matchResponse(n.errors);for(var m in this.element_list){var l=this.element_list[m];if(o[m]){this.highlight(m,o[m],true)}}}},_renderForm:function(u){var t=this;this.message=new k.Message();var q=new k.ButtonIcon({icon:"fa-info-circle",title:(!u.narrow&&"Requirements")||null,tooltip:"Display tool requirements",onclick:function(){if(!this.visible){this.visible=true;t.message.update({persistent:true,message:c.requirements(u),status:"info"})}else{this.visible=false;t.message.update({message:""})}}});if(!u.requirements||u.requirements.length==0){q.$el.hide()}var m=new k.ButtonMenu({icon:"fa-cubes",title:(!u.narrow&&"Versions")||null,tooltip:"Select another tool version"});if(u.versions&&u.versions.length>1){for(var o in u.versions){var r=u.versions[o];if(r!=u.version){m.addMenu({title:"Switch to "+r,version:r,icon:"fa-cube",onclick:function(){t.options.id=t.options.id.replace(t.options.version,this.version);t.options.version=this.version;t.deferred.reset();t.deferred.execute(function(){t._buildModel()})}})}}}else{m.$el.hide()}var p=new k.ButtonMenu({icon:"fa-caret-down",title:(!u.narrow&&"Options")||null,tooltip:"View available options"});if(u.biostar_url){p.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(u.biostar_url+"/p/new/post/")}});p.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(u.biostar_url+"/t/"+u.id+"/")}})}p.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+u.id)}});if(this.is_admin){p.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+u.id+"/download"}})}this.section=new j.View(t,{inputs:u.inputs});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new f.View({icon:"fa-wrench",title:"<b>"+u.name+"</b> "+u.description+" (Galaxy Tool Version "+u.version+")",cls:"ui-portlet-slim",operations:{requirements:q,menu:p,versions:m},buttons:this.buttons});if(u.narrow){this.portlet.$content.css("padding","0px")}this.portlet.append(this.message.$el,true);this.portlet.append(this.section.$el);this.$el.empty();this.$el.append(this.portlet.$el);if(u.help!=""){this.$el.append(c.help(u.help))}if(u.citations){var s=$("<div/>");var l=new i.ToolCitationCollection();l.tool_id=u.id;var n=new a.CitationListView({el:s,collection:l});n.render();l.fetch();this.$el.append(s)}if(u.message){this.message.update({persistent:true,status:"warning",message:u.message})}}})}); \ No newline at end of file diff -r ff2b00fcbd70e3d7ce10b0444412cc68d2ede46f -r 494418e72cf0007e909c7f4b9134cd2b82df49e2 static/scripts/packed/mvc/tools/tools-form-workflow.js --- a/static/scripts/packed/mvc/tools/tools-form-workflow.js +++ b/static/scripts/packed/mvc/tools/tools-form-workflow.js @@ -1,1 +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.use_defaults=true;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}}); \ No newline at end of file +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;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}}); \ No newline at end of file diff -r ff2b00fcbd70e3d7ce10b0444412cc68d2ede46f -r 494418e72cf0007e909c7f4b9134cd2b82df49e2 static/scripts/packed/mvc/tools/tools-form.js --- a/static/scripts/packed/mvc/tools/tools-form.js +++ b/static/scripts/packed/mvc/tools/tools-form.js @@ -1,1 +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;this.job_handler=new a(this);this.buttons={execute:new e.Button({icon:"fa-check",tooltip:"Execute: "+g.name,title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){f.job_handler.submit()}})};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.options=k;f._buildForm();f.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.modal.show({title:"Tool cannot be executed",body:l,buttons:{Close:function(){f.modal.hide()}}})}})},_updateModel:function(){var f=this;var g=this.tree.finalize({data:function(k){if(k.values.length>0&&k.values[0]&&k.values[0].src==="hda"){return f.content.get({id:k.values[0].id,src:"hda"}).id_uncoded}return null}});console.debug("tools-form::_refreshForm() - Refreshing states.");console.debug(g);function j(n){for(var l in f.input_list){var m=f.field_list[l];var k=f.input_list[l];if(k.is_dynamic&&m.wait&&m.unwait){if(n){m.wait()}else{m.unwait()}}}}j(true);var i=this.deferred.register();var h=galaxy_config.root+"api/tools/"+this.options.id+"/build?tool_version="+this.options.version;c.request({type:"GET",url:h,data:g,success:function(k){f.tree.matchModel(k,function(m,q){var l=f.input_list[m];if(l&&l.options){if(!_.isEqual(l.options,q.options)){l.options=q.options;var r=f.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)}}}});j(false);f.deferred.done(i);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(k)},error:function(k){f.deferred.done(i);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(k)}})}});return{View:d}}); \ No newline at end of file +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;this.job_handler=new a(this);this.buttons={execute:new e.Button({icon:"fa-check",tooltip:"Execute: "+g.name,title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){f.job_handler.submit()}})};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.build(k);f.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.modal.show({title:"Tool cannot be executed",body:l,buttons:{Close:function(){f.modal.hide()}}})}})},_updateModel:function(){var f=this;var g=this.tree.finalize({data:function(k){if(k.values.length>0&&k.values[0]&&k.values[0].src==="hda"){return f.content.get({id:k.values[0].id,src:"hda"}).id_uncoded}return null}});console.debug("tools-form::_refreshForm() - Refreshing states.");console.debug(g);function j(n){for(var l in f.input_list){var m=f.field_list[l];var k=f.input_list[l];if(k.is_dynamic&&m.wait&&m.unwait){if(n){m.wait()}else{m.unwait()}}}}j(true);var i=this.deferred.register();var h=galaxy_config.root+"api/tools/"+this.options.id+"/build?tool_version="+this.options.version;c.request({type:"GET",url:h,data:g,success:function(k){f.tree.matchModel(k,function(m,q){var l=f.input_list[m];if(l&&l.options){if(!_.isEqual(l.options,q.options)){l.options=q.options;var r=f.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)}}}});j(false);f.deferred.done(i);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(k)},error:function(k){f.deferred.done(i);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(k)}})}});return{View:d}}); \ No newline at end of file diff -r ff2b00fcbd70e3d7ce10b0444412cc68d2ede46f -r 494418e72cf0007e909c7f4b9134cd2b82df49e2 templates/webapps/galaxy/tool_form.mako --- a/templates/webapps/galaxy/tool_form.mako +++ b/templates/webapps/galaxy/tool_form.mako @@ -9,8 +9,7 @@ ## 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. params = dict(trans.request.params) - if 'id' in params: - params['dataset_id'] = params['id'] + params['__dataset_id__'] = params.get('id', None) self.form_config = tool.to_json(trans, **params) self.form_config.update({ 'id' : tool.id, diff -r ff2b00fcbd70e3d7ce10b0444412cc68d2ede46f -r 494418e72cf0007e909c7f4b9134cd2b82df49e2 templates/webapps/galaxy/workflow/editor_tool_form.mako --- a/templates/webapps/galaxy/workflow/editor_tool_form.mako +++ b/templates/webapps/galaxy/workflow/editor_tool_form.mako @@ -15,9 +15,6 @@ 'id' : tool.id, 'job_id' : trans.security.encode_id( job.id ) if job else None, 'history_id' : trans.security.encode_id( trans.history.id ), - 'is_dynamic' : False, - 'compact' : True, - 'initial_errors' : True, 'container' : '#right-content' }) %> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: Bugfix for bugfix d3b1f6b.
by commits-noreply＠bitbucket.org 05 Feb '15

05 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ff2b00fcbd70/ Changeset: ff2b00fcbd70 User: jmchilton Date: 2015-02-05 18:32:56+00:00 Summary: Bugfix for bugfix d3b1f6b. d3b1f6b fix the GUI (in an obsecure use) but broke fairly typical uses of the API. Affected #: 1 file diff -r b6349ba5cda26cdea678c4842136e50363c0629f -r ff2b00fcbd70e3d7ce10b0444412cc68d2ede46f lib/galaxy/workflow/modules.py --- a/lib/galaxy/workflow/modules.py +++ b/lib/galaxy/workflow/modules.py @@ -330,7 +330,9 @@ # so do that now so dependent steps can be recalculated. In the future # everything should come in from the API and this can be eliminated. if not invocation.has_input_for_step( step.id ): - invocation.add_input( step_outputs.values()[ 0 ], step.id ) + content = step_outputs.values()[ 0 ] + if content: + invocation.add_input( content, step.id ) progress.set_outputs_for_input( step, step_outputs ) return job Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 4 new changesets
by commits-noreply＠bitbucket.org 05 Feb '15

05 Feb '15

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/73e9ca698df3/ Changeset: 73e9ca698df3 User: jmchilton Date: 2015-02-05 17:27:46+00:00 Summary: Fix workflow schedulers to fallback onto sample like other config files. Affected #: 1 file diff -r 2f436edb5288bf750382ae1ccddd95ed611db6a1 -r 73e9ca698df3f0da3fe145878938cdf60978d17c lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -143,7 +143,6 @@ self.collect_outputs_from = [ x.strip() for x in kwargs.get( 'collect_outputs_from', 'new_file_path,job_working_directory' ).lower().split(',') ] self.template_path = resolve_path( kwargs.get( "template_path", "templates" ), self.root ) self.template_cache = resolve_path( kwargs.get( "template_cache_path", "database/compiled_templates" ), self.root ) - self.workflow_schedulers_config_file = resolve_path( kwargs.get( 'workflow_schedulers_config_file', 'config/workflow_schedulers_conf.xml' ), self.root ) self.local_job_queue_workers = int( kwargs.get( "local_job_queue_workers", "5" ) ) self.cluster_job_queue_workers = int( kwargs.get( "cluster_job_queue_workers", "3" ) ) self.job_queue_cleanup_interval = int( kwargs.get("job_queue_cleanup_interval", "5") ) @@ -459,6 +458,7 @@ shed_data_manager_config_file=[ 'shed_data_manager_conf.xml', 'config/shed_data_manager_conf.xml' ], shed_tool_data_table_config=[ 'shed_tool_data_table_conf.xml', 'config/shed_tool_data_table_conf.xml' ], tool_sheds_config_file=[ 'config/tool_sheds_conf.xml', 'tool_sheds_conf.xml', 'config/tool_sheds_conf.xml.sample' ], + workflow_schedulers_config_file=['config/workflow_schedulers_conf.xml', 'config/workflow_schedulers_conf.xml.sample'], ) listify_defaults = dict( https://bitbucket.org/galaxy/galaxy-central/commits/d3b1f6b04d4b/ Changeset: d3b1f6b04d4b User: jmchilton Date: 2015-02-05 17:27:46+00:00 Summary: Workflow scheduling delay fix. There were problems if all three of these conditions were met - 1) workflow from GUI, 2) workflow evaluation delayed, and 3) a delayed step was connected to a input dataset. This fixes these workflows. Affected #: 3 files diff -r 73e9ca698df3f0da3fe145878938cdf60978d17c -r d3b1f6b04d4b4fb9db667afdfb2beb78db5226a0 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -3253,6 +3253,27 @@ def update( self ): self.update_time = galaxy.model.orm.now.now() + def add_input( self, content, step_id ): + if content.history_content_type == "dataset": + request_to_content = WorkflowRequestToInputDatasetAssociation() + request_to_content.dataset = content + request_to_content.workflow_step_id = step_id + self.input_datasets.append( request_to_content ) + else: + request_to_content = WorkflowRequestToInputDatasetCollectionAssociation() + request_to_content.dataset_collection = content + request_to_content.workflow_step_id = step_id + self.input_dataset_collections.append( request_to_content ) + + def has_input_for_step( self, step_id ): + for content in self.input_datasets: + if content.workflow_step_id == step_id: + return True + for content in self.input_dataset_collections: + if content.workflow_step_id == step_id: + return True + return False + class WorkflowInvocationStep( object, Dictifiable ): dict_collection_visible_keys = ( 'id', 'update_time', 'job_id', 'workflow_step_id', 'action' ) diff -r 73e9ca698df3f0da3fe145878938cdf60978d17c -r d3b1f6b04d4b4fb9db667afdfb2beb78db5226a0 lib/galaxy/workflow/modules.py --- a/lib/galaxy/workflow/modules.py +++ b/lib/galaxy/workflow/modules.py @@ -326,6 +326,11 @@ step_outputs[ 'input_ds_copy' ] = new_hdca else: raise Exception("Unknown history content encountered") + # If coming from UI - we haven't registered invocation inputs yet, + # so do that now so dependent steps can be recalculated. In the future + # everything should come in from the API and this can be eliminated. + if not invocation.has_input_for_step( step.id ): + invocation.add_input( step_outputs.values()[ 0 ], step.id ) progress.set_outputs_for_input( step, step_outputs ) return job diff -r 73e9ca698df3f0da3fe145878938cdf60978d17c -r d3b1f6b04d4b4fb9db667afdfb2beb78db5226a0 lib/galaxy/workflow/run_request.py --- a/lib/galaxy/workflow/run_request.py +++ b/lib/galaxy/workflow/run_request.py @@ -297,18 +297,8 @@ value=value, type=param_types.REPLACEMENT_PARAMETERS, ) - for step_id, content in run_config.inputs.iteritems(): - if content.history_content_type == "dataset": - request_to_content = model.WorkflowRequestToInputDatasetAssociation() - request_to_content.dataset = content - request_to_content.workflow_step_id = step_id - workflow_invocation.input_datasets.append( request_to_content ) - else: - request_to_content = model.WorkflowRequestToInputDatasetCollectionAssociation() - request_to_content.dataset_collection = content - request_to_content.workflow_step_id = step_id - workflow_invocation.input_dataset_collections.append( request_to_content ) + workflow_invocation.add_input( content, step_id ) for step in workflow.steps: state = step.state https://bitbucket.org/galaxy/galaxy-central/commits/ff56bdbf7b3e/ Changeset: ff56bdbf7b3e User: jmchilton Date: 2015-02-05 17:27:46+00:00 Summary: Fix scheduling_manager.py for unknown attribute reference. Not sure if this was a poor rebasing or a copy and paste error. Affected #: 1 file diff -r d3b1f6b04d4b4fb9db667afdfb2beb78db5226a0 -r ff56bdbf7b3e1a7a19eaab24be8d2ac6b8aa970c lib/galaxy/workflow/scheduling_manager.py --- a/lib/galaxy/workflow/scheduling_manager.py +++ b/lib/galaxy/workflow/scheduling_manager.py @@ -116,7 +116,6 @@ for plugin_element in plugins_element.getchildren(): plugin_type = plugin_element.tag plugin_kwds = dict( plugin_element.items() ) - plugin_kwds.update( self.extra_kwargs ) workflow_scheduler_id = plugin_kwds.get( 'id', None ) self.__init_plugin( plugin_type, workflow_scheduler_id, **plugin_kwds ) https://bitbucket.org/galaxy/galaxy-central/commits/b6349ba5cda2/ Changeset: b6349ba5cda2 User: jmchilton Date: 2015-02-05 17:27:46+00:00 Summary: Improved error message if things don't match up when recovering workflows. Ideally this shouldn't really happen - but this should help if it does. Affected #: 1 file diff -r ff56bdbf7b3e1a7a19eaab24be8d2ac6b8aa970c -r b6349ba5cda26cdea678c4842136e50363c0629f lib/galaxy/workflow/run.py --- a/lib/galaxy/workflow/run.py +++ b/lib/galaxy/workflow/run.py @@ -251,7 +251,13 @@ step_outputs = self.outputs[ connection.output_step.id ] if step_outputs is STEP_OUTPUT_DELAYED: raise modules.DelayedWorkflowEvaluation() - replacement = step_outputs[ connection.output_name ] + output_name = connection.output_name + try: + replacement = step_outputs[ output_name ] + except KeyError: + template = "Workflow evaluation problem - failed to find output_name %s in step_outputs %s" + message = template % ( output_name, step_outputs ) + raise Exception( message ) if isinstance( replacement, model.HistoryDatasetCollectionAssociation ): if not replacement.collection.populated: if not replacement.collection.waiting_for_elements: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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[galaxyproject/usegalaxy-playbook] c55a48: disable new toolform by Aysam's request
by GitHub 05 Feb '15

05 Feb '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c55a48d5a1f2b839e19bcd5bd8fec116fd9fc087 https://github.com/galaxyproject/usegalaxy-playbook/commit/c55a48d5a1f2b839… Author: martenson <cech.marten(a)gmail.com> Date: 2015-02-05 (Thu, 05 Feb 2015) Changed paths: M stage/group_vars/galaxyservers.yml Log Message: ----------- disable new toolform by Aysam's request

1 0

commit/galaxy-central: guerler: Workflow: Fix text and boolean parameter handling, simplify module update
by commits-noreply＠bitbucket.org 05 Feb '15

05 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2f436edb5288/ Changeset: 2f436edb5288 User: guerler Date: 2015-02-05 15:08:45+00:00 Summary: Workflow: Fix text and boolean parameter handling, simplify module update Affected #: 3 files diff -r 6133a80c7a08b88f1e7d2e83456acdc329b88b47 -r 2f436edb5288bf750382ae1ccddd95ed611db6a1 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -263,8 +263,15 @@ else: return form_builder.TextField( self.name, self.size, value ) + def to_string( self, value, app ): + """Convert a value to a string representation suitable for persisting""" + if value is None: + return '' + else: + return str( value ) + def to_html_value( self, value, app ): - if not value: + if value is None: return '' else: return self.to_string( value, app ) @@ -335,13 +342,6 @@ return "" raise ValueError( "An integer is required" ) - def to_string( self, value, app ): - """Convert a value to a string representation suitable for persisting""" - if value is None: - return "" - else: - return str( value ) - def to_python( self, value, app ): try: return int( value ) @@ -414,13 +414,6 @@ return "" raise ValueError( "A real number is required" ) - def to_string( self, value, app ): - """Convert a value to a string representation suitable for persisting""" - if value is None: - return "" - else: - return str( value ) - def to_python( self, value, app ): try: return float( value ) @@ -480,7 +473,7 @@ return [ 'true' ] def to_python( self, value, app ): - return ( value == 'True' ) + return ( value in [ 'True', 'true' ]) def get_initial_value( self, trans, context, history=None ): return self.checked diff -r 6133a80c7a08b88f1e7d2e83456acdc329b88b47 -r 2f436edb5288bf750382ae1ccddd95ed611db6a1 lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -619,17 +619,25 @@ } ) # create tool model and default tool state (if missing) - tool_model = None if type == 'tool' and not tool_state: tool_model = module.tool.to_json(trans, **incoming) module.state.inputs = copy.deepcopy(tool_model['state_inputs']) + return { + 'tool_model': tool_model, + 'tool_state': module.get_state(), + 'data_inputs': module.get_data_inputs(), + 'data_outputs': module.get_data_outputs(), + 'tool_errors': module.get_errors(), + 'form_html': module.get_config_form(), + 'annotation': annotation, + 'post_job_actions': module.get_post_job_actions(incoming) + } # update module state module.update_state( incoming ) if type == 'tool': return { - 'tool_model': tool_model, 'tool_state': module.get_state(), 'data_inputs': module.get_data_inputs(), 'data_outputs': module.get_data_outputs(), diff -r 6133a80c7a08b88f1e7d2e83456acdc329b88b47 -r 2f436edb5288bf750382ae1ccddd95ed611db6a1 lib/galaxy/workflow/modules.py --- a/lib/galaxy/workflow/modules.py +++ b/lib/galaxy/workflow/modules.py @@ -684,8 +684,11 @@ input_dicts.append( { "name": name, "description": "runtime parameter for tool %s" % self.get_name() } ) return input_dicts - def get_post_job_actions( self ): - return self.post_job_actions + def get_post_job_actions( self, incoming=None): + if incoming is None: + return self.post_job_actions + else: + return ActionBox.handle_incoming(incoming) def get_config_form( self ): self.add_dummy_datasets() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: pep8, cleanup in galaxy/buildapp
by commits-noreply＠bitbucket.org 05 Feb '15

05 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6133a80c7a08/ Changeset: 6133a80c7a08 User: dannon Date: 2015-02-05 14:45:15+00:00 Summary: pep8, cleanup in galaxy/buildapp Affected #: 1 file diff -r cca00d61df85a6ecd1be49265f0c92e7482b91f9 -r 6133a80c7a08b88f1e7d2e83456acdc329b88b47 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -6,8 +6,6 @@ import os import os.path import atexit -import warnings -import glob from paste import httpexceptions import pkg_resources @@ -28,6 +26,7 @@ class GalaxyWebApplication( galaxy.web.framework.webapp.WebApplication ): pass + def app_factory( global_conf, **kwargs ): """ Return a wsgi application serving the root object @@ -41,7 +40,7 @@ else: try: from galaxy.app import UniverseApplication - app = UniverseApplication( global_conf = global_conf, **kwargs ) + app = UniverseApplication( global_conf=global_conf, **kwargs ) except: import traceback traceback.print_exc() @@ -65,8 +64,8 @@ webapp.add_route( '/datasets/:dataset_id/display/{filename:.+?}', controller='dataset', action='display', dataset_id=None, filename=None) webapp.add_route( '/datasets/:dataset_id/:action/:filename', controller='dataset', action='index', dataset_id=None, filename=None) webapp.add_route( '/display_application/:dataset_id/:app_name/:link_name/:user_id/:app_action/:action_param', - controller='dataset', action='display_application', dataset_id=None, user_id=None, - app_name = None, link_name = None, app_action = None, action_param = None ) + controller='dataset', action='display_application', dataset_id=None, user_id=None, + app_name=None, link_name=None, app_action=None, action_param=None ) webapp.add_route( '/u/:username/d/:slug/:filename', controller='dataset', action='display_by_username_and_slug', filename=None ) webapp.add_route( '/u/:username/p/:slug', controller='page', action='display_by_username_and_slug' ) webapp.add_route( '/u/:username/h/:slug', controller='history', action='display_by_username_and_slug' ) @@ -103,7 +102,6 @@ log.error("Static middleware is enabled in your configuration but this is a uwsgi process. Refusing to wrap in static middleware.") else: webapp = wrap_in_static( webapp, global_conf, plugin_frameworks=[ app.visualizations_registry ], **kwargs ) - #webapp = wrap_in_static( webapp, global_conf, plugin_frameworks=None, **kwargs ) if asbool(kwargs.get('pack_scripts', False)): log.warn( "The 'pack_scripts' option is deprecated" ) pack_scripts() @@ -112,7 +110,6 @@ galaxy.model.mapping.metadata.engine.connection_provider._pool.dispose() except: pass - # Close any pooled database connections before forking try: galaxy.model.tool_shed_install.mapping.metadata.engine.connection_provider._pool.dispose() except: @@ -137,32 +134,32 @@ controller='history_contents', path_prefix='/api/histories/:history_id/contents', parent_resources=dict( member_name='history', collection_name='histories' ), - ) + ) # Legacy access to HDA details via histories/:history_id/contents/:hda_id webapp.mapper.resource( 'content', - 'contents', - controller='history_contents', - name_prefix='history_', - path_prefix='/api/histories/:history_id', - parent_resources=dict( member_name='history', collection_name='histories' ) ) - webapp.mapper.connect("history_contents_display", - "/api/histories/:history_id/contents/:history_content_id/display", - controller="datasets", - action="display", - conditions=dict(method=["GET"])) + 'contents', + controller='history_contents', + name_prefix='history_', + path_prefix='/api/histories/:history_id', + parent_resources=dict( member_name='history', collection_name='histories' ) ) + webapp.mapper.connect( "history_contents_display", + "/api/histories/:history_id/contents/:history_content_id/display", + controller="datasets", + action="display", + conditions=dict(method=["GET"])) webapp.mapper.resource( 'user', - 'users', - controller='group_users', - name_prefix='group_', - path_prefix='/api/groups/:group_id', - parent_resources=dict( member_name='group', collection_name='groups' ) ) + 'users', + controller='group_users', + name_prefix='group_', + path_prefix='/api/groups/:group_id', + parent_resources=dict( member_name='group', collection_name='groups' ) ) webapp.mapper.resource( 'role', - 'roles', - controller='group_roles', - name_prefix='group_', - path_prefix='/api/groups/:group_id', - parent_resources=dict( member_name='group', collection_name='groups' ) ) + 'roles', + controller='group_roles', + name_prefix='group_', + path_prefix='/api/groups/:group_id', + parent_resources=dict( member_name='group', collection_name='groups' ) ) _add_item_tags_controller( webapp, name_prefix="history_content_", path_prefix='/api/histories/:history_id/contents/:history_content_id' ) @@ -173,17 +170,17 @@ name_prefix="workflow_", path_prefix='/api/workflows/:workflow_id' ) _add_item_annotation_controller( webapp, - name_prefix="history_content_", - path_prefix='/api/histories/:history_id/contents/:history_content_id' ) + name_prefix="history_content_", + path_prefix='/api/histories/:history_id/contents/:history_content_id' ) _add_item_annotation_controller( webapp, - name_prefix="history_", - path_prefix='/api/histories/:history_id' ) + name_prefix="history_", + path_prefix='/api/histories/:history_id' ) _add_item_annotation_controller( webapp, - name_prefix="workflow_", - path_prefix='/api/workflows/:workflow_id' ) + name_prefix="workflow_", + path_prefix='/api/workflows/:workflow_id' ) _add_item_provenance_controller( webapp, - name_prefix="history_content_", - path_prefix='/api/histories/:history_id/contents/:history_content_id' ) + name_prefix="history_content_", + path_prefix='/api/histories/:history_id/contents/:history_content_id' ) webapp.mapper.resource( 'dataset', 'datasets', path_prefix='/api' ) webapp.mapper.resource( 'tool_data', 'tool_data', path_prefix='/api' ) @@ -216,27 +213,28 @@ webapp.mapper.resource( 'datatype', 'datatypes', path_prefix='/api', - collection={ 'sniffers': 'GET', 'mapping' : 'GET', 'converters': 'GET' }, + collection={ 'sniffers': 'GET', 'mapping': 'GET', 'converters': 'GET' }, parent_resources=dict( member_name='datatype', collection_name='datatypes' ) ) - #webapp.mapper.connect( 'run_workflow', '/api/workflow/{workflow_id}/library/{library_id}', controller='workflows', action='run', workflow_id=None, library_id=None, conditions=dict(method=["GET"]) ) webapp.mapper.resource( 'search', 'search', path_prefix='/api' ) webapp.mapper.resource( 'page', 'pages', path_prefix="/api") webapp.mapper.resource( 'revision', 'revisions', - path_prefix='/api/pages/:page_id', - controller='page_revisions', - parent_resources=dict( member_name='page', collection_name='pages' ) ) + path_prefix='/api/pages/:page_id', + controller='page_revisions', + parent_resources=dict( member_name='page', collection_name='pages' ) ) - webapp.mapper.connect( "history_archive_export", "/api/histories/{id}/exports", - controller="histories", action="archive_export", conditions=dict( method=[ "PUT" ] ) ) - webapp.mapper.connect( "history_archive_download", "/api/histories/{id}/exports/{jeha_id}", - controller="histories", action="archive_download", conditions=dict( method=[ "GET" ] ) ) + webapp.mapper.connect( "history_archive_export", + "/api/histories/{id}/exports", controller="histories", + action="archive_export", conditions=dict( method=[ "PUT" ] ) ) + webapp.mapper.connect( "history_archive_download", + "/api/histories/{id}/exports/{jeha_id}", controller="histories", + action="archive_download", conditions=dict( method=[ "GET" ] ) ) webapp.mapper.connect( "create_api_key", "/api/users/:user_id/api_key", - controller="users", action="api_key", user_id=None, conditions=dict( method=["POST"] ) ) + controller="users", action="api_key", user_id=None, + conditions=dict( method=["POST"] ) ) # visualizations registry generic template renderer - webapp.add_route( '/visualization/show/:visualization_name', - controller='visualization', action='render', visualization_name=None ) + webapp.add_route( '/visualization/show/:visualization_name', controller='visualization', action='render', visualization_name=None ) # Deprecated in favor of POST /api/workflows with 'workflow' in payload. webapp.mapper.connect( 'import_workflow_deprecated', '/api/workflows/upload', controller='workflows', action='import_new_workflow_deprecated', conditions=dict( method=['POST'] ) ) @@ -446,8 +444,8 @@ parent_resources=dict( member_name="job", collection_name="jobs" ) ) _add_item_extended_metadata_controller( webapp, - name_prefix="history_dataset_", - path_prefix='/api/histories/:history_id/contents/:history_content_id' ) + name_prefix="history_dataset_", + path_prefix='/api/histories/:history_id/contents/:history_content_id' ) # ==================== # ===== TOOLSHED ===== @@ -463,46 +461,46 @@ # Galaxy API for tool shed features. webapp.mapper.resource( 'tool_shed_repository', 'tool_shed_repositories', - member={ 'repair_repository_revision' : 'POST', - 'exported_workflows' : 'GET', - 'import_workflow' : 'POST', - 'import_workflows' : 'POST' }, - collection={ 'get_latest_installable_revision' : 'POST', - 'reset_metadata_on_installed_repositories' : 'POST' }, + member={ 'repair_repository_revision': 'POST', + 'exported_workflows': 'GET', + 'import_workflow': 'POST', + 'import_workflows': 'POST' }, + collection={ 'get_latest_installable_revision': 'POST', + 'reset_metadata_on_installed_repositories': 'POST' }, controller='tool_shed_repositories', name_prefix='tool_shed_repository_', path_prefix='/api', - new={ 'install_repository_revision' : 'POST' }, + new={ 'install_repository_revision': 'POST' }, parent_resources=dict( member_name='tool_shed_repository', collection_name='tool_shed_repositories' ) ) - # ==== Trace/Metrics Logger # Connect logger from app if app.trace_logger: webapp.trace_logger = app.trace_logger # metrics logging API - #webapp.mapper.connect( "index", "/api/metrics", + # webapp.mapper.connect( "index", "/api/metrics", # controller="metrics", action="index", conditions=dict( method=["GET"] ) ) - #webapp.mapper.connect( "show", "/api/metrics/{id}", + # webapp.mapper.connect( "show", "/api/metrics/{id}", # controller="metrics", action="show", conditions=dict( method=["GET"] ) ) - webapp.mapper.connect( "create", "/api/metrics", - controller="metrics", action="create", conditions=dict( method=["POST"] ) ) + webapp.mapper.connect( "create", "/api/metrics", controller="metrics", + action="create", conditions=dict( method=["POST"] ) ) def pack_scripts(): from glob import glob from subprocess import call cmd = "java -jar scripts/yuicompressor.jar --type js static/scripts/%(fname)s -o static/scripts/packed/%(fname)s" - raw_js= [os.path.basename(g) for g in glob( "static/scripts/*.js" )] + raw_js = [os.path.basename(g) for g in glob( "static/scripts/*.js" )] for fname in raw_js: if os.path.exists('static/scripts/packed/%s' % fname): if os.path.getmtime('static/scripts/packed/%s' % fname) > os.path.getmtime('static/scripts/%s' % fname): - continue # Skip, packed is newer than source. + continue # Skip, packed is newer than source. d = dict( fname=fname ) log.info("%(fname)s --> packed/%(fname)s" % d) call( cmd % d, shell=True ) + def _add_item_tags_controller( webapp, name_prefix, path_prefix, **kwd ): # Not just using map.resources because actions should be based on name not id controller = "%stags" % name_prefix @@ -511,24 +509,24 @@ map = webapp.mapper # Allow view items' tags. map.connect(name, path, - controller=controller, action="index", - conditions=dict(method=["GET"])) + controller=controller, action="index", + conditions=dict(method=["GET"])) # Allow remove tag from item map.connect("%s_delete" % name, "%s/tags/:tag_name" % path_prefix, - controller=controller, action="delete", - conditions=dict(method=["DELETE"])) + controller=controller, action="delete", + conditions=dict(method=["DELETE"])) # Allow create a new tag with from name map.connect("%s_create" % name, "%s/tags/:tag_name" % path_prefix, - controller=controller, action="create", - conditions=dict(method=["POST"])) + controller=controller, action="create", + conditions=dict(method=["POST"])) # Allow update tag value map.connect("%s_update" % name, "%s/tags/:tag_name" % path_prefix, - controller=controller, action="update", - conditions=dict(method=["PUT"])) + controller=controller, action="update", + conditions=dict(method=["PUT"])) # Allow show tag by name map.connect("%s_show" % name, "%s/tags/:tag_name" % path_prefix, - controller=controller, action="show", - conditions=dict(method=["GET"])) + controller=controller, action="show", + conditions=dict(method=["GET"])) def _add_item_extended_metadata_controller( webapp, name_prefix, path_prefix, **kwd ): @@ -536,11 +534,13 @@ name = "%sextended_metadata" % name_prefix webapp.mapper.resource(name, "extended_metadata", path_prefix=path_prefix, controller=controller) + def _add_item_annotation_controller( webapp, name_prefix, path_prefix, **kwd ): controller = "%sannotations" % name_prefix name = "%sannotation" % name_prefix webapp.mapper.resource(name, "annotation", path_prefix=path_prefix, controller=controller) + def _add_item_provenance_controller( webapp, name_prefix, path_prefix, **kwd ): controller = "%sprovenance" % name_prefix name = "%sprovenance" % name_prefix @@ -566,11 +566,11 @@ # upstream server if asbool(conf.get( 'use_remote_user', False )): from galaxy.web.framework.middleware.remoteuser import RemoteUser - app = RemoteUser( app, maildomain = conf.get( 'remote_user_maildomain', None ), - display_servers = util.listify( conf.get( 'display_servers', '' ) ), - admin_users = conf.get( 'admin_users', '' ).split( ',' ), - remote_user_header = conf.get( 'remote_user_header', 'HTTP_REMOTE_USER' ), - remote_user_secret_header = conf.get('remote_user_secret', None) ) + app = RemoteUser( app, maildomain=conf.get( 'remote_user_maildomain', None ), + display_servers=util.listify( conf.get( 'display_servers', '' ) ), + admin_users=conf.get( 'admin_users', '' ).split( ',' ), + remote_user_header=conf.get( 'remote_user_header', 'HTTP_REMOTE_USER' ), + remote_user_secret_header=conf.get('remote_user_secret', None) ) # The recursive middleware allows for including requests in other # requests or forwarding of requests, all on the server side. if asbool(conf.get('use_recursive', True)): @@ -626,6 +626,7 @@ log.debug( "Enabling 'Request ID' middleware" ) return app + def wrap_in_static( app, global_conf, plugin_frameworks=None, **local_conf ): from galaxy.web.framework.middleware.static import CacheableStaticURLParser as Static urlmap, cache_time = galaxy.web.framework.webapp.build_url_map( app, global_conf, local_conf ) @@ -642,6 +643,7 @@ # URL mapper becomes the root webapp return urlmap + def build_template_error_formatters(): """ Build a list of template error formatters for WebError. When an error @@ -651,6 +653,7 @@ formatters = [] # Formatter for mako import mako.exceptions + def mako_html_data( exc_value ): if isinstance( exc_value, ( mako.exceptions.CompileException, mako.exceptions.SyntaxException ) ): return mako.exceptions.html_error_template().render( full=False, css=False ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dannon: Prevent uwsgi from ever loading static middleware -- it can serve static files directly with appropriate routes in its config (see wiki).
by commits-noreply＠bitbucket.org 05 Feb '15

05 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cca00d61df85/ Changeset: cca00d61df85 User: dannon Date: 2015-02-05 14:35:36+00:00 Summary: Prevent uwsgi from ever loading static middleware -- it can serve static files directly with appropriate routes in its config (see wiki). Affected #: 1 file diff -r 1989401bb9009e76fbaaafdeeffa68c0f12959ab -r cca00d61df85a6ecd1be49265f0c92e7482b91f9 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -86,9 +86,24 @@ # Wrap the webapp in some useful middleware if kwargs.get( 'middleware', True ): webapp = wrap_in_middleware( webapp, global_conf, **kwargs ) - if asbool( kwargs.get( 'static_enabled', True ) ): - webapp = wrap_in_static( webapp, global_conf, plugin_frameworks=[ app.visualizations_registry ], **kwargs ) - #webapp = wrap_in_static( webapp, global_conf, plugin_frameworks=None, **kwargs ) + # TEST FOR UWSGI -- TODO save this somewhere so we only have to do it once. + is_uwsgi = False + try: + # The uwsgi module is automatically injected by the parent uwsgi + # process and only exists that way. If anything works, this is a + # uwsgi-managed process. + import uwsgi + is_uwsgi = uwsgi.numproc + is_uwsgi = True + except ImportError: + # This is not a uwsgi process, or something went horribly wrong. + pass + if asbool( kwargs.get( 'static_enabled', True) ): + if is_uwsgi: + log.error("Static middleware is enabled in your configuration but this is a uwsgi process. Refusing to wrap in static middleware.") + else: + webapp = wrap_in_static( webapp, global_conf, plugin_frameworks=[ app.visualizations_registry ], **kwargs ) + #webapp = wrap_in_static( webapp, global_conf, plugin_frameworks=None, **kwargs ) if asbool(kwargs.get('pack_scripts', False)): log.warn( "The 'pack_scripts' option is deprecated" ) pack_scripts() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dannon: Fixed typo'd require for lunr.
by commits-noreply＠bitbucket.org 05 Feb '15

05 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1989401bb900/ Changeset: 1989401bb900 User: dannon Date: 2015-02-05 13:38:14+00:00 Summary: Fixed typo'd require for lunr. Affected #: 3 files diff -r 19079eea7d2285d701866b0df77beeff20a677e8 -r 1989401bb9009e76fbaaafdeeffa68c0f12959ab client/galaxy/scripts/mvc/tools.js --- a/client/galaxy/scripts/mvc/tools.js +++ b/client/galaxy/scripts/mvc/tools.js @@ -2,7 +2,7 @@ * Model, view, and controller objects for Galaxy tools and tool panel. */ - define( ["libs/underscore", "viz/trackster/util", "mvc/data", "libs/lunr.js" ], + define( ["libs/underscore", "viz/trackster/util", "mvc/data", "libs/lunr" ], function(_, util, data) { /** diff -r 19079eea7d2285d701866b0df77beeff20a677e8 -r 1989401bb9009e76fbaaafdeeffa68c0f12959ab static/scripts/mvc/tools.js --- a/static/scripts/mvc/tools.js +++ b/static/scripts/mvc/tools.js @@ -2,7 +2,7 @@ * Model, view, and controller objects for Galaxy tools and tool panel. */ - define( ["libs/underscore", "viz/trackster/util", "mvc/data", "libs/lunr.js" ], + define( ["libs/underscore", "viz/trackster/util", "mvc/data", "libs/lunr" ], function(_, util, data) { /** diff -r 19079eea7d2285d701866b0df77beeff20a677e8 -r 1989401bb9009e76fbaaafdeeffa68c0f12959ab static/scripts/packed/mvc/tools.js --- a/static/scripts/packed/mvc/tools.js +++ b/static/scripts/packed/mvc/tools.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/trackster/util","mvc/data","libs/lunr.js"],function(x,a,y){var g={hidden:false,show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},toggle:function(){this.set("hidden",!this.get("hidden"))},is_visible:function(){return !this.attributes.hidden}};var e=Backbone.Model.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(z){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new e(this.toJSON())},set_value:function(z){this.set("value",z||"")}});var i=Backbone.Collection.extend({model:e});var k=e.extend({});var d=e.extend({set_value:function(z){this.set("value",parseInt(z,10))},get_samples:function(){return d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}});var f=d.extend({set_value:function(z){this.set("value",parseFloat(z))}});var t=e.extend({get_samples:function(){return x.map(this.get("options"),function(z){return z[0]})}});e.subModelTypes={integer:d,"float":f,data:k,select:t};var j=Backbone.Model.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[],outputs:[]},urlRoot:galaxy_config.root+"api/tools",initialize:function(z){this.set("inputs",new i(x.map(z.inputs,function(A){var B=e.subModelTypes[A.type]||e;return new B(A)})))},toJSON:function(){var z=Backbone.Model.prototype.toJSON.call(this);z.inputs=this.get("inputs").map(function(A){return A.toJSON()});return z},remove_inputs:function(A){var z=this,B=z.get("inputs").filter(function(C){return(A.indexOf(C.get("type"))!==-1)});z.get("inputs").remove(B)},copy:function(A){var B=new j(this.toJSON());if(A){var z=new Backbone.Collection();B.get("inputs").each(function(C){if(C.get_samples()){z.push(C)}});B.set("inputs",z)}return B},apply_search_results:function(z){(x.indexOf(z,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()},set_input_value:function(z,A){this.get("inputs").find(function(B){return B.get("name")===z}).set("value",A)},set_input_values:function(A){var z=this;x.each(x.keys(A),function(B){z.set_input_value(B,A[B])})},run:function(){return this._run()},rerun:function(A,z){return this._run({action:"rerun",target_dataset_id:A.id,regions:z})},get_inputs_dict:function(){var z={};this.get("inputs").each(function(A){z[A.get("name")]=A.get("value")});return z},_run:function(B){var C=x.extend({tool_id:this.id,inputs:this.get_inputs_dict()},B);var A=$.Deferred(),z=new a.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(C),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(D){return D!=="pending"}});$.when(z.go()).then(function(D){A.resolve(new y.DatasetCollection().reset(D))});return A}});x.extend(j.prototype,g);var q=Backbone.View.extend({});var n=Backbone.Collection.extend({model:j});var v=Backbone.Model.extend(g);var l=Backbone.Model.extend({defaults:{elems:[],open:false},clear_search_results:function(){x.each(this.attributes.elems,function(z){z.show()});this.show();this.set("open",false)},apply_search_results:function(A){var B=true,z;x.each(this.attributes.elems,function(C){if(C instanceof v){z=C;z.hide()}else{if(C instanceof j){if(C.apply_search_results(A)){B=false;if(z){z.show()}}}}});if(B){this.hide()}else{this.show();this.set("open",true)}}});x.extend(l.prototype,g);var c=Backbone.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search_url:"",visible:true,query:"",results:null,clear_key:27},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var B=this.attributes.query;if(B.length<this.attributes.min_chars_for_search){this.set("results",null);return}var A=B+"*";if(this.timer){clearTimeout(this.timer)}$("#search-clear-btn").hide();$("#search-spinner").show();var z=this;this.timer=setTimeout(function(){$.get(z.attributes.search_url,{query:A},function(C){z.set("results",C);$("#search-spinner").hide();$("#search-clear-btn").show()},"json")},200)},clear_search:function(){this.set("query","");this.set("results",null)}});x.extend(c.prototype,g);var o=Backbone.Model.extend({initialize:function(z){this.attributes.tool_search=z.tool_search;this.attributes.tool_search.on("change:results",this.apply_search_results,this);this.attributes.tools=z.tools;this.attributes.layout=new Backbone.Collection(this.parse(z.layout))},parse:function(A){var z=this,B=function(E){var D=E.model_class;if(D.indexOf("Tool")===D.length-4){return z.attributes.tools.get(E.id)}else{if(D==="ToolSection"){var C=x.map(E.elems,B);E.elems=C;return new l(E)}else{if(D==="ToolSectionLabel"){return new v(E)}}}};return x.map(A,B)},clear_search_results:function(){this.get("layout").each(function(z){if(z instanceof l){z.clear_search_results()}else{z.show()}})},apply_search_results:function(){var A=this.get("tool_search").get("results");if(A===null){this.clear_search_results();return}var z=null;this.get("layout").each(function(B){if(B instanceof v){z=B;z.hide()}else{if(B instanceof j){if(B.apply_search_results(A)){if(z){z.show()}}}else{z=null;B.apply_search_results(A)}}})}});var s=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var m=s.extend({tagName:"div",render:function(){var z=$("<div/>");z.append(Handlebars.templates.tool_link(this.model.toJSON()));if(this.model.id==="upload1"){z.find("a").on("click",function(A){A.preventDefault();Galaxy.upload.show()})}this.$el.append(z);return this}});var b=s.extend({tagName:"div",className:"toolPanelLabel",render:function(){this.$el.append($("<span/>").text(this.model.attributes.text));return this}});var r=s.extend({tagName:"div",className:"toolSectionWrapper",initialize:function(){s.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(Handlebars.templates.panel_section(this.model.toJSON()));var z=this.$el.find(".toolSectionBody");x.each(this.model.attributes.elems,function(A){if(A instanceof j){var B=new m({model:A,className:"toolTitle"});B.render();z.append(B.$el)}else{if(A instanceof v){var C=new b({model:A});C.render();z.append(C.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast"))}});var p=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){this.$el.append(Handlebars.templates.tool_search(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}this.$el.find("[title]").tooltip();return this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){this.model.clear_search();this.$el.find(":input").val(this.model.attributes.search_hint_string);this.focus_and_select();return false},query_changed:function(z){if((this.model.attributes.clear_key)&&(this.model.attributes.clear_key===z.which)){this.clear();return false}this.model.set("query",this.$el.find(":input").val())}});var w=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var z=this;var A=new p({model:this.model.get("tool_search")});A.render();z.$el.append(A.$el);this.model.get("layout").each(function(C){if(C instanceof l){var B=new r({model:C});B.render();z.$el.append(B.$el)}else{if(C instanceof j){var D=new m({model:C,className:"toolTitleNoSection"});D.render();z.$el.append(D.$el)}else{if(C instanceof v){var E=new b({model:C});E.render();z.$el.append(E.$el)}}}});z.$el.find("a.tool-link").click(function(D){var C=$(this).attr("class").split(/\s+/)[0],B=z.model.get("tools").get(C);z.trigger("tool_link_click",D,B)});return this},handle_search_results:function(){var z=this.model.get("tool_search").get("results");if(z&&z.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}});var u=Backbone.View.extend({className:"toolForm",render:function(){this.$el.children().remove();this.$el.append(Handlebars.templates.tool_form(this.model.toJSON()))}});var h=Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new w({collection:this.collection});this.tool_form_view=new u()},render:function(){this.tool_panel_view.render();this.tool_panel_view.$el.css("float","left");this.$el.append(this.tool_panel_view.$el);this.tool_form_view.$el.hide();this.$el.append(this.tool_form_view.$el);var z=this;this.tool_panel_view.on("tool_link_click",function(B,A){B.preventDefault();z.show_tool(A)})},show_tool:function(A){var z=this;A.fetch().done(function(){z.tool_form_view.model=A;z.tool_form_view.render();z.tool_form_view.$el.show();$("#left").width("650px")})}});return{ToolParameter:e,IntegerToolParameter:d,SelectToolParameter:t,Tool:j,ToolCollection:n,ToolSearch:c,ToolPanel:o,ToolPanelView:w,ToolFormView:u}}); \ No newline at end of file +define(["libs/underscore","viz/trackster/util","mvc/data","libs/lunr"],function(x,a,y){var g={hidden:false,show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},toggle:function(){this.set("hidden",!this.get("hidden"))},is_visible:function(){return !this.attributes.hidden}};var e=Backbone.Model.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(z){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new e(this.toJSON())},set_value:function(z){this.set("value",z||"")}});var i=Backbone.Collection.extend({model:e});var k=e.extend({});var d=e.extend({set_value:function(z){this.set("value",parseInt(z,10))},get_samples:function(){return d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}});var f=d.extend({set_value:function(z){this.set("value",parseFloat(z))}});var t=e.extend({get_samples:function(){return x.map(this.get("options"),function(z){return z[0]})}});e.subModelTypes={integer:d,"float":f,data:k,select:t};var j=Backbone.Model.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[],outputs:[]},urlRoot:galaxy_config.root+"api/tools",initialize:function(z){this.set("inputs",new i(x.map(z.inputs,function(A){var B=e.subModelTypes[A.type]||e;return new B(A)})))},toJSON:function(){var z=Backbone.Model.prototype.toJSON.call(this);z.inputs=this.get("inputs").map(function(A){return A.toJSON()});return z},remove_inputs:function(A){var z=this,B=z.get("inputs").filter(function(C){return(A.indexOf(C.get("type"))!==-1)});z.get("inputs").remove(B)},copy:function(A){var B=new j(this.toJSON());if(A){var z=new Backbone.Collection();B.get("inputs").each(function(C){if(C.get_samples()){z.push(C)}});B.set("inputs",z)}return B},apply_search_results:function(z){(x.indexOf(z,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()},set_input_value:function(z,A){this.get("inputs").find(function(B){return B.get("name")===z}).set("value",A)},set_input_values:function(A){var z=this;x.each(x.keys(A),function(B){z.set_input_value(B,A[B])})},run:function(){return this._run()},rerun:function(A,z){return this._run({action:"rerun",target_dataset_id:A.id,regions:z})},get_inputs_dict:function(){var z={};this.get("inputs").each(function(A){z[A.get("name")]=A.get("value")});return z},_run:function(B){var C=x.extend({tool_id:this.id,inputs:this.get_inputs_dict()},B);var A=$.Deferred(),z=new a.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(C),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(D){return D!=="pending"}});$.when(z.go()).then(function(D){A.resolve(new y.DatasetCollection().reset(D))});return A}});x.extend(j.prototype,g);var q=Backbone.View.extend({});var n=Backbone.Collection.extend({model:j});var v=Backbone.Model.extend(g);var l=Backbone.Model.extend({defaults:{elems:[],open:false},clear_search_results:function(){x.each(this.attributes.elems,function(z){z.show()});this.show();this.set("open",false)},apply_search_results:function(A){var B=true,z;x.each(this.attributes.elems,function(C){if(C instanceof v){z=C;z.hide()}else{if(C instanceof j){if(C.apply_search_results(A)){B=false;if(z){z.show()}}}}});if(B){this.hide()}else{this.show();this.set("open",true)}}});x.extend(l.prototype,g);var c=Backbone.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search_url:"",visible:true,query:"",results:null,clear_key:27},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var B=this.attributes.query;if(B.length<this.attributes.min_chars_for_search){this.set("results",null);return}var A=B+"*";if(this.timer){clearTimeout(this.timer)}$("#search-clear-btn").hide();$("#search-spinner").show();var z=this;this.timer=setTimeout(function(){$.get(z.attributes.search_url,{query:A},function(C){z.set("results",C);$("#search-spinner").hide();$("#search-clear-btn").show()},"json")},200)},clear_search:function(){this.set("query","");this.set("results",null)}});x.extend(c.prototype,g);var o=Backbone.Model.extend({initialize:function(z){this.attributes.tool_search=z.tool_search;this.attributes.tool_search.on("change:results",this.apply_search_results,this);this.attributes.tools=z.tools;this.attributes.layout=new Backbone.Collection(this.parse(z.layout))},parse:function(A){var z=this,B=function(E){var D=E.model_class;if(D.indexOf("Tool")===D.length-4){return z.attributes.tools.get(E.id)}else{if(D==="ToolSection"){var C=x.map(E.elems,B);E.elems=C;return new l(E)}else{if(D==="ToolSectionLabel"){return new v(E)}}}};return x.map(A,B)},clear_search_results:function(){this.get("layout").each(function(z){if(z instanceof l){z.clear_search_results()}else{z.show()}})},apply_search_results:function(){var A=this.get("tool_search").get("results");if(A===null){this.clear_search_results();return}var z=null;this.get("layout").each(function(B){if(B instanceof v){z=B;z.hide()}else{if(B instanceof j){if(B.apply_search_results(A)){if(z){z.show()}}}else{z=null;B.apply_search_results(A)}}})}});var s=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var m=s.extend({tagName:"div",render:function(){var z=$("<div/>");z.append(Handlebars.templates.tool_link(this.model.toJSON()));if(this.model.id==="upload1"){z.find("a").on("click",function(A){A.preventDefault();Galaxy.upload.show()})}this.$el.append(z);return this}});var b=s.extend({tagName:"div",className:"toolPanelLabel",render:function(){this.$el.append($("<span/>").text(this.model.attributes.text));return this}});var r=s.extend({tagName:"div",className:"toolSectionWrapper",initialize:function(){s.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(Handlebars.templates.panel_section(this.model.toJSON()));var z=this.$el.find(".toolSectionBody");x.each(this.model.attributes.elems,function(A){if(A instanceof j){var B=new m({model:A,className:"toolTitle"});B.render();z.append(B.$el)}else{if(A instanceof v){var C=new b({model:A});C.render();z.append(C.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast"))}});var p=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){this.$el.append(Handlebars.templates.tool_search(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}this.$el.find("[title]").tooltip();return this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){this.model.clear_search();this.$el.find(":input").val(this.model.attributes.search_hint_string);this.focus_and_select();return false},query_changed:function(z){if((this.model.attributes.clear_key)&&(this.model.attributes.clear_key===z.which)){this.clear();return false}this.model.set("query",this.$el.find(":input").val())}});var w=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var z=this;var A=new p({model:this.model.get("tool_search")});A.render();z.$el.append(A.$el);this.model.get("layout").each(function(C){if(C instanceof l){var B=new r({model:C});B.render();z.$el.append(B.$el)}else{if(C instanceof j){var D=new m({model:C,className:"toolTitleNoSection"});D.render();z.$el.append(D.$el)}else{if(C instanceof v){var E=new b({model:C});E.render();z.$el.append(E.$el)}}}});z.$el.find("a.tool-link").click(function(D){var C=$(this).attr("class").split(/\s+/)[0],B=z.model.get("tools").get(C);z.trigger("tool_link_click",D,B)});return this},handle_search_results:function(){var z=this.model.get("tool_search").get("results");if(z&&z.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}});var u=Backbone.View.extend({className:"toolForm",render:function(){this.$el.children().remove();this.$el.append(Handlebars.templates.tool_form(this.model.toJSON()))}});var h=Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new w({collection:this.collection});this.tool_form_view=new u()},render:function(){this.tool_panel_view.render();this.tool_panel_view.$el.css("float","left");this.$el.append(this.tool_panel_view.$el);this.tool_form_view.$el.hide();this.$el.append(this.tool_form_view.$el);var z=this;this.tool_panel_view.on("tool_link_click",function(B,A){B.preventDefault();z.show_tool(A)})},show_tool:function(A){var z=this;A.fetch().done(function(){z.tool_form_view.model=A;z.tool_form_view.render();z.tool_form_view.$el.show();$("#left").width("650px")})}});return{ToolParameter:e,IntegerToolParameter:d,SelectToolParameter:t,Tool:j,ToolCollection:n,ToolSearch:c,ToolPanel:o,ToolPanelView:w,ToolFormView:u}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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